2009 - a year of science anniversaries.

Declared International Year of Astronomy by the United

Nations, it is also the sesquicentenary (150th year) of the publication of “On the Origin of
Species” by Charles Darwin, thus ISS2009 is themed “Genes to Galaxies”. The second week
of the ISS also coincides with 40th anniversary celebrations of the Apollo 11 lunar landing, with
Man’s first steps on a world outside our own.
This book contains the lectures given at ISS2009 Genes to Galaxies, the 35th Professor Harry
Messel International Science School for high school students, held within the School of Physics
at The University of Sydney from 12 - 25 July, 2009. 145 students attended ISS2009 from 10
countries: Canada, China, India, Japan, Malaysia, New Zealand, Singapore, Thailand, the UK
and the USA, and every state and territory of Australia.

35th Professor Harry Messel International Science School

Editors
Adam Selinger, Executive Officer of the Science Foundation for Physics, the
University of Sydney
Professor Anne Green, Head of the School of Physics and Director of the
Science Foundation for Physics, the University of Sydney
Authors
Associate Professor Alaina Ammit, Associate Dean (Research & Innovation)
in the Faculty of Pharmacy at the University of Sydney
Professor Jennie Brand-Miller, Professor of Human Nutrition in the School
of Molecular and Microbial Biosciences at the University of Sydney
Dr Helen Johnston, Research Fellow in the School of Physics at the
University of Sydney
Wayne Lee, Altair Vehicle Systems Manager at NASA, USA
Professor Geraint Lewis, Professor in Astronomy and Astrophysics in School
of Physics at the University of Sydney
Associate Professor Charley Lineweaver, Senior Fellow at the Research
School of Earth Sciences at the Australian National University
Dr Naomi McClure-Griffiths, Science Leader at the CSIRO Telescope
National Facility
Professor Michel Morange, Professor in Biology at Ecole normale
supérieure, France
Professor Jill Tarter, Director of the SETI Institute, USA
Professor Malcolm Walter, Director of the Australian Centre for
Astrobiology at the University of New South Wales
Professor Peter Waterhouse, ARC Federation Fellow in School of Molecular
and Microbial Biosciences at the University of Sydney Edited by Selinger & Green
Dr Karl Kruszelnicki, Julius Sumner Miller Fellow at the University of Sydney
Published 2009 by the Science Foundation for Physics within the University The
of Sydney University
of Sydney

35th Professor Harry Messel International Science School

2009

Edited by Adam Selinger and Anne Green 12-25 July 2009

UPSXXXXX
 The lecture series of the
35th Professor Harry Messel
International Science School
12-25 July 2009
Edited by Adam Selinger and Anne Green

The Science Foundation for Physics within

the University of Sydney
“In the Pursuit of Excellence”
Editors
Mr Adam Selinger, Executive Officer
Professor Anne Green, Director
The Science Foundation for Physics within The University of Sydney, Australia
A course of lectures given at the 35th Professor Harry Messel International Science School for High
School Students organised by the Science Foundation for Physics within The University of Sydney
12–25 July 2009
There are several people to thank for the production of this book of lectures. Firstly thanks to all of
our contributors, who have given their time to the ISS and have been generous in providing a chap-
ter for each of their lectures; to Professors Bob Hewitt and Dick Hunstead and Dr John O’Byrne for
their proof-reading of the pages within, and to the design team at University Publishing Service.
The Science Foundation for Physics
School of Physics A28
The University of Sydney NSW 2006 Australia
www.physics.usyd.edu.au/foundation
© Copyright Science Foundation for Physics June 2009
All rights reserved. No part of this publication may be reproduced, stored in a retrieval system
or transmitted in any form or by any means, electronic, electrostatic, magnetic tape, mechanical,
photocopying, recording or otherwise, without permission in writing from the Science Foundation
for Physics, The University of Sydney.
Designed and printed by the University Publishing Service, the University of Sydney.
Genes to Galaxies
ISBN: 978-0-9599471-2-0
Contents
The Messel Endowment . . . . . . . . . . . . . . . . . . . 5
Supporters of ISS2009 . . . . . . . . . . . . . . . . . . . . 8
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . 9
History of the ISS . . . . . . . . . . . . . . . . . . . . . 10
Authors . . . . . . . . . . . . . . . . . . . . . . . . . 12
The search for the earliest life on Earth
Malcolm Walter . . . . . . . . . . . . . . . . . . . . . . . . . . 14
The search for life on Mars
Malcolm Walter . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Paleolithic nutrition: what did our ancestors eat?
Jennie Brand Miller, Neil Mann and Loren Cordain . . . . . . . . . . . . 28
A Walk Around the Neighbourhood:
Understanding the Nature and Structure of the Milky Way
Naomi M McClure-Griffiths . . . . . . . . . . . . . . . . . . . . . 44
Gene Silencing I A virus defence pathway and a technology.
Peter Waterhouse . . . . . . . . . . . . . . . . . . . . . . . . . 56
Dr Karl: The X-Chromosome eXplained . . . . . . . . . . . . . 66
The frontiers of current biological research
Michel Morange . . . . . . . . . . . . . . . . . . . . . . . . . 74
Why is it important to read On the Origin of Species in 2009?
Michel Morange . . . . . . . . . . . . . . . . . . . . . . . . . 84
Cosmic Evolution: The Birth, Life & Death of Galaxies
Geraint F. Lewis . . . . . . . . . . . . . . . . . . . . . . . . . . 92
Gene Silencing II Gene regulation
Peter Waterhouse . . . . . . . . . . . . . . . . . . . . . . . . . 106
SETI - Planning for Success:
Who Will Speak to Earth? What Will They Say?
Jill Tarter . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
Six Minute of Terror
Wayne Lee . . . . . . . . . . . . . . . . . . . . . . . . . . . 126
Dr Karl: Man on Moon Conspiracy . . . . . . . . . . . . . . 138
Extremophiles & Exoplanets
Jill Tarter . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
New Stars in NASA’s Constellation
Wayne Lee & Erisa K. Hines . . . . . . . . . . . . . . . . . . . . 156
Asthma and Airway Remodelling:
Targeting Mitogen-activated Protein Kinases as Future Therapeutics
Melanie Manetsch, Emma E. Ramsay and Alaina J. Ammit . . . . . . . . . 170
Cosmobiology: Our Place in the Universe
Charles H. Lineweaver . . . . . . . . . . . . . . . . . . . . . . . 182
The Private Life of a Proton
Helen Johnston . . . . . . . . . . . . . . . . . . . . . . . . . . 198
Research at the School of Physics . . . . . . . . . . . . . . . . . 216
Help us to Honour Excellence . . . . . . . . . . . . . . . . . 224
The Messel Endowment
To ensure the continuation of the Professor Harry Messel International Science School the Science
Foundation for Physics established The Messel Endowment in 1999.
From 2003 to 2006 an active capital campaign for The Messel Endowment, chaired by Mr John
Hooke CBE, raised around $2.9Million. Currently the Endowment holds over $3.1Million. The
goal is to accrue a total of $5Million through gifts and grants to ensure the ISS can be run in perpe-
tuity, whilst allowing for rising costs over the years.
The Messel Endowment is open to accept donations at any time and currently has over 200 sup-
porters. Donations of $2.00 and over are tax-deductible (to Australian residents). Pledged gifts (i.e.
donations spread over a three to five year period) are also accepted and are tax deductible.
The ISS now has over 4,000 alumni, with many going on to outstanding achievements in their
chosen fields, including science, medicine, engineering and technology. The ISS honours excellence
in our high-achieving youth. It encourages them to reach their full potential and pursue careers in
science and its related areas.
A donation to The Messel Endowment is an investment in the future of these young scientists. A
donation form can be found at the back of this book and at www.physics.usyd.edu.au/foundation.

Extra Galactic Donors $1Million and over

Department of Innovation, Industry, Science and Research
Mr Ming Tee Lee & Mulpha Australia Limited

Galactic Donors $100,000 to $999,999

Hermon Slade Foundation
Nell & Hermon Slade Trust
Science Foundation for Physics

Stellar Donors $10,000 to $99,999

ANZ Banking Group Ltd IBM Australia Limited
Mr Terrey P Arcus James Hardie Industries Pty Ltd
Mr Robert Arnott Dr Peter Jones
Australian Business Limited Macquarie Charitable Foundation Limited
Emeritus Professor Maxwell H Brennan AO Emeritus Professor Harry Messel AC CBE
& Mrs Ionie M Brennan Mr Michael Messel
Dr Gregory Clark Mr Jim O’Connor
Cochlear Limited OneSteel Limited
Emeritus Professor Richard Collins Queensland Cyber Infrastructure
& Mrs Marilyn Collins Foundation Limited
Mr Trevor Danos The James N Kirby Foundation Pty Limited
Cecil & Ida Green Foundation USA Foundation
Associate Professor Robert G Hewitt Westpac Banking Corporation
& Mrs Helen Hewitt Mr Albert YL Wong
Mr John A L Hooke CBE Mr Thomas Yim
Planetary Donors $1,000 to $9,999
Mr Fraser Allan Lahili Pty Limited
Anonymous Mr Reginald J Lamble AO
ASA ITF Foundation for the Advancement of Ms Danielle M Landy
Astronomy Dr David Malin
Dr Joseph A Beunen Mrs Kathy Manettas
Dr Kenneth Coles AM & Ms Rowena Danziger Mr Nicholas Manettas
through the Kenneth Coles Foundation Mr Peter Manettas AM
Professor Lawrence E Cram Dr Bruce McAdam & Mrs Janice McAdam
Mr David C Davidson Dr Jenny Nicholls
Emeritus Professor John Davis Dr Brian J O’Brien
Mrs Georgina Donaldson Dr Stephen D Segal
Ms Jane Dyson Mr Basil Sellers AM
Mr Steven K Eckowitz Dr Emery Severin & Mrs Sharman Severin
Dr Robert Every Southcorp Limited
Dr Robin B Fitzsimons Ms Valma G Steward
Mr David Frecker Mr John A Vipond
Professor Anne Green Mr Christopher C Vonwiller
Mr Graham H Hall Mr Raymond Walton & Mrs Margit Walton
Mr David Herrman & Mrs Hillda Herrman Mr Thomas M F Yim on behalf of Alex Yim
Mr Anthony Johnston

Asteroidal Donors Upwards to $999

Mr Arun Abey Mr Julian J Dryden
Ms Hyacinth Alfonso Mr Ian A Dyson
Ms Belinda H Allen Ms Julie K Ellinas
Dr Kevin C Allman Professor David R Fraser
Ms Jenny Allum Mrs Irene P Gibson
Mrs Chrissie Athis Mr Greg and Mrs Gabriella Howard
Mr George Athis Mr Sang Huynh
Barker College Mr Steven Kambouris
Mrs Helen Bell Dr Toni R Kesby
Emeritus Professor Louis C Birch Ms Tomoko Kikuchi
Dr David G Blair Mrs R Lambert
Sir Walter Bodmer Mr Wen W Ma
Ms Elana Bont Dr Robert H Masterman
Dr George F Brand Dr John E.W. Lambert-Smith
Mr John Bright and Ms Karen Palmer Associate Professor Donald D Millar
Mr Arthur J Buchan Mr Alan K Milston OAM
Mr Jeff Close Miss Mary Moore
Dr Claire E Cupitt Ms Alison Muir
Mr Ian G Dennis Dr Hugh S Murdoch
Ms Margaret A Desgrand Mr Robert R B Murphy
Mrs Iona S Dougherty Mr Spiro J Pandelakis

6 | Genes to Galaxies
Mr Frank Papadopoulos
& Mrs June Papadopoulos
Mr George Papadopoulos
Mr John Paterson
Mr Harry J Pemble
Mr Peter C Perry
Dr Christopher J E Phillips
Mr Enrico Piccioli
Ms Yvonne Pitsikas
Mr Geoffrey D Pople
Mr Allan F Rainbird
Mr John W L Rawson
Dr David Z Robinson
Miss Gracie Robinson
Dr P E Rolan
Professor Roger Short
Dr J. E.W. L. Smith
Mr Tim M Smyth
Mr Duncan Sutherland
The Australian Association of Phi Beta Kappa
The Outsiders Club of ISS2007
The Super Secret Club of ISS2005
Mr Gavin M Thomson
Dr Jennifer J Turner
Mr John H Valder
Ms Alex Viglienzone
Ms Jennifer H F Wanless
Dr David R V Wood
Ms Anne Woods
Mr Thomas M F Yim on behalf of Jerome Yim
Dr Xian Zhou
Fr Mervyn J F Ziesing
School of Physics
Building
Image:
Dr Phil Dooley
ISS 2009 | 7
Supporters of ISS2009
The Science Foundation for Physics warmly thanks the supporters of the
2009 ISS: Genes to Galaxies
The Messel Endowment
Department of Education and Training, NSW Government (DET)
Department of Innovation, Industry, Science and Research, Australian Government (DIISR)
The Kirby Foundation
Adolph Basser Trust
Faculty of Science, The University of Sydney
Chancellor’s Committee, The University of Sydney
The Smithsonian Institute
Mr Robert Arnott
Mr Greg Clark
Mr Trevor Danos
Mr Ron Enestrom
Associate Professor Robert Hewitt & Mrs Helen Hewitt
Mr John Hooke CBE
Associate Professor Brian James & Dr Ferg Brand through Dr Wie Xu
Dame Leonie Kramer
Mr Bruce McAdam & Mrs Janice McAdam
Mr Robert Rich
Mr Albert Wong
other individuals through the Foundation’s Annual Appeal

Australian students were selected with the support of the NSW Department of Education and
Training, and Science Teachers Associations in Victoria, Tasmania, South Australia, the Northern
Territory, the ACT and Western Australia. The following institutions assisted in the selection and
travel of the overseas students:
The Affiliated High School of Peking University, China
Rivers Collegiate, Canada
Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan
Ministry of Education, Malaysia
The Royal Society of New Zealand
Ministry of Education, Singapore
Ministry of Education, Thailand
The Association for Science Education, UK
The Royal Institution of Great Britain
The National Endowment for Science, Technology and the Arts (NESTA), UK
Department of Energy, USA
Raman Research Institute, India

8 | Genes to Galaxies
Preface
The Science Foundation for Physics within the
University of Sydney is delighted to present
the 35th Professor Harry Messel International
Science School (ISS) for high school students,
from 12-25 July 2009.
This anniversary year is the UN-designated
International Year of Astronomy and celebrates
both 400 years since Galileo first turned his
telescope to the heavens and the 150th anni-
versary of the publication of Charles Darwin’s
treatise ‘On the Origin of Species’. Therefore
the theme for ISS2009 is Genes to Galaxies,
acknowledging the immense contribution
made to science by these two great minds. The
second week of the ISS also coincides with
the 40th anniversary of the first landing on
the moon by Apollo 11 astronauts. It brings
together our themes of evolution and space
exploration, with speculation of possible intel-
ligent life beyond the Earth.
The primary aim of all the Science Schools is to
acknowledge the excellence of the scholars who
have been selected on the basis of their aca-
demic abilities, passion for science and leader-
ship qualities. A new initiative for this ISS is the
introduction of a module on Leadership and
Ethics in Science, produced with the support
of the Smithsonian Institute and introduced
during the opening lecture by the Chief Justice
of Australia, the Honourable Robert French,
himself an ISS alumnus.
The presence of some 144 gifted young people
from many countries creates an environment in
which each scholar can experience the values of
different cultures and learn new ways of doing
things. The Science Foundation stands for the
Pursuit of Excellence, and is pleased to have an
opportunity to acknowledge and reward excel-
lence in these young people.
The International Science School can only be
held because of the generous financial contri-
butions into The Messel Endowment and to
the ISS from our supporters, and because of
the time and energy donated by the lecturers.
Like the Science Foundation itself, the sup-
porters, donors and lecturers are committed
to promoting science education at the very
highest level of excellence. On behalf of the
Foundation, I express my grateful thanks to all
these benefactors.
To our scholars this year, I wish you a most
enriching fortnight here at the University of
Sydney and trust that you, like those before
you, will enjoy a remarkable and memorable
experience, make many life-long friends and
feel empowered to pursue your passion for
science.
With very warm wishes
Professor Anne Green
Sydney, June 2009
ISS 2009 | 9
History of the ISS
The Professor Harry Messel International
Science School has a long and distinguished
history. The 144 students attending ISS2009:
Genes to Galaxies are the 35th group to gather
at the University of Sydney for the Science
School – in all, well over 4000 have attended a
Science School since they began in 1958.
Initially the Schools were annual events, and
the first four Schools, held between 1958 and
1961, were for teachers. In 1962 Professor
Harry Messel, the founder of the ISS, changed
the focus to honour excellence in senior high
school students and to encourage them to con-
sider careers in science.
A Truly International
Science School
One student from New Zealand attended the
very first Science School in 1962, and overseas
students have been a feature of the ISS ever
since. In 1967, ten students travelled from
the USA to attend the School; the following
year they were joined by five from the United
Kingdom and five from Japan.
South-East Asia joined the ISS in 1985 when
students attended from Singapore, Malaysia,
Thailand and the Philippines – however, that
was the only time the Philippines has partici-
pated. China has sent five students to every ISS
since 1999, except for 2003 when the SARS
epidemic restricted travel in the region and
they reluctantly withdrew. In 2007 we were un-
fortunate not to be joined by Malaysia but we
did welcome India for the first time.
This year we are very pleased that for the
first time we will be joined by students from
Canada, in fact from the home town of Harry
Messel, the originator of this program. Thus
ISS2009 has students attending from ten
countries in total: Canada, China, India, Japan,
Malaysia, New Zealand, Singapore, Thailand,
the UK and the USA, and of course, every state
and territory of Australia.
10 | Genes to Galaxies
The Great Lecturers
One of the features of the International Science
Schools is the lecture series. Past ISS lectur-
ers include James Watson, who won a Nobel
Prize for discovering the structure of DNA,
and Jerome Friedman, also a Nobel laureate
for work on particle physics. Sir Hermann
Bondi (physicist and astronomer at Cambridge
University), Margaret Burbidge (astronomer
and champion for women in science), Carl
Sagan (famous astronomer and science broad-
caster) and Lord Robert May (President of the
Royal Society in the UK) have all given talks at
the ISS.
And of course, who could forget the brilliant
science demonstrations of Professor Julius
“Why is it so?” Sumner Miller, which were
such a popular feature of the ISS that they
spawned a television show! These days, Dr Karl
Kruszelnicki (the University’s Julius Sumner
Miller Fellow) entertains and enthuses the ISS
Scholars with his famous Great Moments in
Science.
Between 1960 and 1979 the ISS lectures were
shown on television – in fact, many people re-
call waking up early on Sundays to make sure
they didn’t miss the telecast! One member of
the School of Physics here at the University of
Sydney is adamant that the lectures shown on
TV were a key part of her decision to become
an astronomer.
Today, the ISS is no longer a feature of the
television schedule, but we have moved on to
embrace new technology. In 2003 part of the
lecture series was broadcast on the internet as
a trial run, and in 2007 the entire series was
made available as both video webcast and au-
dio podcast. In 2009 this book of lectures will
be made available on-line, together with pod-
casts of the lectures, thus available to anyone
with internet access on Earth, and beyond.
Science School 1958-2007
For High School Teachers

Year Teachers Theme

Selected Lectures in Modern Physics and the
1958 123
Astronomer’s Universe
Lecture notes on an introductory course in modern
1959 123
physics and nuclear power and radioisotopes
1960 123 From Nucleus to Universe
1961 123 Space and the Atom
TOTAL 492

International Science Schools For High School Students

Year Boys Girls Total Theme

1962 108 45 153 A Journey through Space and the Atom
1963 104 51 155 The Universe of Time and Space
1964 106 53 159 Light and Life in the Universe
1965 114 42 156 Time (and Relativity)
1966 104 52 156 Atoms to Andromeda
1967 101 57 158 Apollo and the Universe
1968 109 20 129 Man in Inner and Outer Space
1969 118 21 139 Nuclear Energy Today and Tomorrow
1970 99 33 132 Pioneering in Outer Space
1971 87 35 122 Molecules to Man
1972 95 28 123 Brain Mechanisms and the Control of Behaviour
1973 93 29 122 Focus on the Stars
1974 90 33 123 Solar Energy
1975 76 43 119 Our Earth
1977 54 50 104 Australian Animals and their Environment
1979 63 52 115 Energy for Survival
1981 50 65 115 Biological Manipulation of Life
1983 67 51 118 Science Update 1983
1985 71 59 130 The Study of Populations
1987 70 56 126 Highlights in Science
1989 69 58 127 Today’s Science Tomorrow’s Technology
1991 61 70 131 Living with the Environment
1993 60 72 132 Carbon: Element of Energy and Life
1995 55 80 135 Breakthrough! Creativity & Progress in Science
1997 72 65 137 Light
1999 73 66 139 Millennium Science
2001 70 71 141 Impact Science
2003 54 85 139 From Zero to Infinity
2005 73 66 139 Waves of the Future
2007 68 65 133 Ecoscience
TOTALS 2434 1573 4007

ISS 2009 | 11
Authors

Associate Professor Alaina Ammit is Associate

Dean (Research & Innovation) at the Faculty of
Pharmacy, University of Sydney. She has earned an
international reputation for her work elucidating
pro-inflammatory signalling pathways in asthma and
airway remodelling.

Professor Jennie Brand-Miller holds a Personal

Chair in Human Nutrition in the Human Nutrition Unit,
School of Molecular and Microbial Biosciences at the
University of Sydney. She is internationally recognised
for her work on carbohydrates and diabetes, particularly
the glycemic index of foods.

Dr Helen Johnston obtained her PhD at the California

Institute of Technology. Subsequently she obtained post-
doctoral appointments in The Netherlands, at the Anglo-
Australian Observatory and at the University of Sydney.
Her research interests are the study of neutron stars and
black holes in binary star systems, and the
supermassive black holes at the centres of radio galaxies.

Mr Wayne Lee is Altair Vehicle Systems Manager

at NASA. Previously Wayne enjoyed great success as
the mission planner for Mars operations at NASA’s Jet
Propulsion Laboratory in Pasadena, California. During
the mission, Wayne worked with all the elements of the
flight team to coordinate trajectories, science plans and
spacecraft operations into the overall mission itinerary.

Professor Geraint Lewis was born in Old South

Wales, and studied Physics at London University and
Cambridge. Since completing his PhD he has worked
in the State University of New York, Victoria University
in Canada, and the University of Washington in Seattle.
He then became a Research Astronomer at the Anglo-
Australian Observatory before joining The University of
Sydney in 2002 to continue his studies of cosmology.

12 | Genes to Galaxies
Associate Professor Charles H. Lineweaver is
the coordinator of the Australian National University’s
Planetary Science Institute and holds a joint appoint-
ment as an Associate Professor in the Research School of
Astronomy and Astrophysics and the Research School of
Earth Sciences.

Dr Naomi McClure-Griffiths is a Senior Post-Doctoral

Fellow at the CSIRO Australia Telescope National Facility.
Her research has dramatically reshaped our knowledge of
of the structure and evolution of our galactic home – the
Milky Way.

Professor Michel Morange was trained in biochemis-

try and molecular biology at the Pasteur Institute in Paris.
He then turned to cell biology, and entered into François
Jacob’s lab in the same Institute. With Olivier Bensaude, he
created in 1991, at the Ecole normale supérieure in Paris,
a group whose project was to characterise the regulation of
heat shock gene expression.

Professor Jill Tarter holds the Bernard M. Oliver Chair

for SETI (Search for Extraterrestrial Intelligence) and
is Director of the Center for SETI Research at the SETI
Institute in Mountain View, California. Jill is popularly
known for being portrayed by Jodie Foster in the film
Contact.

Professor Malcolm Walter is Professor of Astrobiology

at the University of NSW and Director of the Australian
Centre for Astrobiology based there. He has worked for 45
years on the geological evidence of early life on Earth, and
more recently on the search for life on Mars. He has also
worked as an oil exploration consultant and a consultant
to museums.

Professor Peter Waterhouse is internationally recog-

nised for his groundbreaking research on plant viruses. He
led the way in uncovering the mechanism, roles and ap-
plications of post-transcriptional gene silencing in plants,
also termed RNA interference (RNAi).

Authors | 13
The search for
the earliest life
on Earth
Malcolm Walter
T he record of life on Earth takes
two forms: fossils and other evi-
dence in the geological record,
and what is encoded in the ge-
nomes of living organisms.

The rock record – limitations

What we can learn from rocks diminishes back
through time. The further we go back in time,
the fewer the rocks preserved. That is because
of natural recycling processes: rocks weather,
turn to sediment that is washed into seas and
lakes, get buried by more sediment, and get
“subducted” and melted during “tectonism”
(continental drift). The result is there are no
known well-preserved rocks older than 3.5
billion years (Ga) old. The Earth is 4.56 Ga old
(Figure 1). So we don’t know much about the
first billion years of Earth history. Life arose
during that time. We know that because we
have fossils 3.5 Ga old from Western Australia.
Even at 3.5 Ga there are only two known
regions of rock preserved, the Pilbara region
of Western Australia, and the Barberton
Mountainland of South Africa.
 Figure 1:
Geological time
displayed as a
clock, in billions of
years. Major events
in the evolution of
life are indicated.
Reproduced from
Des Marais, D.J.
(2000) When Did
Photosynthesis emerge
on Earth? Science 289:
1703-1705 with the
permission of David
DesMarais

From about 3 Ga onwards we have lots of rocks The universal tree also suggests that the most
to examine for evidence of life, so we can be primitive organisms with living close relatives
more confident about our interpretations. were hyperthermophiles, that is, they lived at
high temperatures, more than 80˚C. So in the
Events in the history of life are dated mostly
ancient rock record we should be looking for
using the fact that some isotopes of elements
the deposits of former hot springs to see what
are unstable and break down at known rates to
lived in them. We know how to find such
form other isotopes and elements. The usual
deposits – they are often ores of gold, silver,
method of dating very ancient rocks uses ura-
copper, lead and zinc.
nium and lead isotopes bound in crystals of
zircon, zirconium silicate.

Universal tree of life

There is a second way to uncover the earliest
history of life. That history is encoded in the
genes of living organisms. Using the subtle
differences in the chemistry of the genetic mol-
ecules DNA and RNA “molecular biologists”
have been able to work out the relationships of
all current life on Earth. The result is a chart of
relationships, one of the greatest achievements
of science in the last 100 years.
Life clusters into three great “superkingdoms”
or “domains”, the Bacteria, Archaea and
Eucarya (Figure 2). From this we can see that
most life on Earth is microscopic. This is con-
sistent with the geological record that shows us
that until about 600 Ma almost all fossils are
of microbes. Figure 2: The Universal Tree of Life, a
chart of the relationships of all extant life.
Source: Wikimedia Commons

16 | Genes to Galaxies
Earth - The first billion years
Like the other planets, the Earth formed from
a great cloud of dust and gas. Under the influ-
ence of gravity the cloud clumped into rocky
and icy lumps that grew bigger and bigger. The
volatile molecules were driven to the cooler
further parts of the solar system as the Sun be-
gan to generate heat, forming the “gas giants”,
Jupiter, Saturn, Uranus and Neptune, the com-
ets, and other objects such as Pluto. The small
rocky planets, composed of less volatile mate-
rial, Mercury, Venus, Earth and Mars, formed
close to the Sun. By 4.56 Ga they were about
their present size. However, for the next billion
years the growth process, “accretion”, contin-
ued and was very violent. Soon after 4.56 Ga
an object the size of Mars smashed into the
Earth with such energy as to melt and vapor-
ise the surface of the planet, throwing a vast
amount of material into orbit, which cooled to
form the Moon. Frequent impacts from giant
asteroids continued until about 3.9 Ga. Some
of these would have vaporised the developing
oceans, generating a “steam atmosphere”. Life
might have started in this violent period but
have been extinguished. We do not know.
Imagine an Earth with thousands of volcanos,
no continents but perhaps numerous islands
that would later clump together to become
continents, and a hot ocean. Somewhere life
got started and managed to survive, proliferate
and take over to generate the surface environ-
ment we now depend on for our existence.
Faint evidence of the presence of life is found
in highly altered 3.9 Ga rocks from Greenland.
There are no conventional fossils, just sugges-
tive patterns of carbon isotopes.
A snapshot at 3.5 Ga
We know from studying the rocks of the
Pilbara region and the Barberton Mountainland
that life was well established by 3.5 Ga. Despite
occasional controversies, the evidence can be
described as compelling because multiple lines
of evidence reinforce and support each other.
Figure 3: Shark Bay stromatolites in the
shallow subtidal environment.
Malcolm Walter
1. Stromatolites. These are macroscopic sedi-
mentary structures resulting from the activities
of “mats” of microbes living on the seafloor
and in lakes. They still form in some modern
environments such as Shark Bay in Western
Australia (Figure 3), so we are able to observe
how they form and use this information to help
interpret the ancient forms.
In 3.43 Ga rocks in the Pilbara region, a wide
range of different forms of stromatolites (Figure
4) formed all the way from a rocky coastline to
offshore in several tens of metres of water. In
3.5 Ga rocks there are stromatolites at the vents
of former hot springs.
2. Microfossils. These are fossilised microbes
(Figure 5). Despite the fact that microbes have
no hard parts they are sometimes fossilised
when they become embedded in precipitated
silica which then hardens to form a rock called
chert. They can be found by using an optical
microscope to examine slices of chert so thin
that light can pass through them.
3. Carbon isotopes. Carbon has two stable
isotopes, 12C and 13C. Some biochemical proc-
esses such as photosynthesis preferentially use
compounds of “light” carbon, 12C. This results
in the cellular matter being enriched in 12C,
leaving the water in which the organisms grew
enriched in 13C. If calcium carbonate then
precipitates out of the water to form limestone,
and the microbes die and are fossilised in the
The search for the earliest life on Earth | 17

Figure 5: Filamentous microfossil 3.5
billion years old from near Marble
Bar in the Pilbara region of Western
Australia. The drawing on the right is a
reconstruction.
Photographs courtesy of J. William Schopf and
reproduced with permission.
18 | Genes to Galaxies
Figure 4:
Stromatolites 3.43
billion years old
west of Marble
Bar in the Pilbara
region of Western
Australia.
Malcolm Walter
limestone, the carbon isotope pattern is pre-
served. This pattern is found throughout Earth
history back to 3.5 Ga and possibly to 3.8 Ga.
Complex life at 3.0 Ga?
Recently, large and relatively complex micro-
fossils have been found in 3.0 Ga rocks in the
Pilbara (Figure 6). These include spheroids up
to 80µm wide, some with internal small sphe-
roids, and discoidal structures with flanges, like
classical pictures of “flying saucers”. It is not
known what sort of organisms these were, but
their large size and relative complexity hint that
they might be eukaryotes.
All the hard evolution
over by 2.5 Ga
There are many well preserved rock succes-
sions at 2.5-2.8 Ga and abundant evidence of
life. All life was still microscopic, as far as we
know. All three domains are represented in the
geological record. Some continents had formed
and stromatolites were abundant in lakes and
shallow seas. Though the evidence is not un-
equivocal it is likely that the main stromatolite-
builders were cyanobacteria; this is deduced
from the morphology of the stromatolites and
some poorly preserved microfossils. The pres-
ence of cyanobacteria at this time is strongly
indicated by another type of evidence: “bi-
omarkers”. These are hydrocarbon molecules
that can be found in especially well preserved

Figure 6: Spindle-shaped microfossil at
least 3.0 billion years old from the Pilbara
region of Western Australia. About 40 µm
in maximum dimension.
Photograph courtesy of Kenichiro Sugitani and
reproduced with permission.
sediments. Oil contains abundant biomarkers.
After organisms die, decay and are buried in
sediment some chemical components of their
cells survive. Some of these organic compounds
are characteristic of particular types of organ-
isms, so when found in rocks they are markers
for the former presence of these organisms.
Compounds characteristic of cyanobacteria,
and others characteristic of eukaryotes have
been found in 2.7-2.8 Ga rocks in the Pilbara
region and in South Africa. There is some
controversy about this work as it is difficult to
prove that these molecules are not later con-
taminants, but most of the evidence indicates
that they are as old as the rocks in which they
are found.
So we know that by 2.5 Ga, and probably
much earlier, all three domains of life were
flourishing on Earth. That means that most
of the biochemical processes that characterise
modern life had evolved by that time. All sub-
sequent evolution has utilised those basic proc-
esses first established by microbes.
How did life start?
There is a simple answer to that question:
no-one knows. However, there are ways to ap-
proach the problem, and a great deal has been
learned in the last 50 years. A famous experi-
ment was conducted in 1952 by Stanley Miller
(then a university student in Chicago) and his
supervisor Harold Urey. They filled a glass flask
with a mixture of gases considered to represent
the composition of the atmosphere on the early
Earth – methane, ammonia, hydrogen, carbon
monoxide and water. To represent lightning
they created electrical sparks through the mix-
ture of gases. The result was a brown liquid
that when analysed was found to contain ami-
no acids. These are the building blocks of pro-
tein molecules that are essential components
of the cells of all living organisms. So they had
demonstrated one possible step in the origin
of life. Since then it has been discovered that
there are many other ways that quite complex
carbon compounds (“organic compounds”) can
form by natural chemical processes. This even
happens in gas clouds in the universe (about
100 different carbon compounds have been
identified in such clouds), and so would have
been part of the cloud that condensed to form
the solar system.
It is a long way from organic compounds to life
and much is yet to be learned. For example,
no-one has yet been able to synthesise a pro-
tein molecule, let alone the genetic molecules
RNA and DNA. But there are comprehensive
hypotheses about how life might have started
and many of the necessary steps have been
shown to be feasible. Perhaps viruses played a
role before there were cells. A potentially very
informative approach is to determine what
essential components of cells are found in the
most primitive forms of life known, and ex-
trapolate back to predict what the earliest cells
were probably like.
The search for the earliest life on Earth | 19
The search for
life on Mars
Malcolm Walter
I t has long been thought that there
might be life on Mars. A century ago
some astronomers thought that they
could see canals on Mars and imagined
a dying civilisation on a drying planet strug-
gling to survive. In the 1950’s astronomers
noticed that patches of colour on Mars change
with the seasons and thought that this might
be due to seasonal changes in vegetation. In
the 1960’s and 70’s some enthusiasts saw in
the first fuzzy pictures from Mars pyramids
and a giant face.
All were deceived. Modern high resolution
images show that there are no canals, pyra-
mids or faces. And the colour changes result
from seasonal dust storms.

Why focus on Mars?

Over the last decade more than 350 “extra-
solar” planets have been discovered and our
own solar system has been explored in ever
increasing detail. There could be life on many
planets and moons, though none has yet been
found, but Mars is special. That is because we

Figure 1: An image of Mars showing the
northern polar cap. The white patches are
water-ice clouds.
Image courtesy of NASA/nasaimages.org
have discovered that early in its history it was
warm and wet, like the Earth, although now it
is a frozen desert (Fig. 1).
All life on Earth requires liquid water, and so
the assumption is made that that will also be
true of life elsewhere. Similarly, all life on Earth
is constructed from compounds of carbon, and
this too is assumed to be true of life elsewhere.
This is just a normal conservative scientific ap-
proach, of making predictions on the basis of
current knowledge. It does not rule out other
possibilities, but indicates where the focus
should lie.
The Ages of features on Mars
As yet no samples have been collected on Mars
and returned for analysis, so we have no direct
dates for the features we observe. However,
there is an indirect way of determining ap-
proximate ages. Like all the rocky planets Mars
accreted from the infall of asteroids, meteorites,
comets and dust. The rate of infall, “bombard-
ment”, was very high early in the life of the
solar system and diminished to the current very
low rate about 3.9 billion years ago. We know a
22 | Genes to Galaxies
little about rates of bombardment because sam-
ples of the Moon collected during the Apollo
missions have been dated here on Earth, and
those dates can be directly related to the crater-
ing of the Moon. It is assumed that the rates
would have been similar on Mars.
So for Mars we can count the number of craters
in a particular region and on that basis deter-
mine the approximate age of the landscape.
This is how we know that the “warm and wet”
period was more than three billion years ago.
Water on Mars
It has been known since the NASA Mariner
missions in the 1960s that something liquid
flowed on the surface of Mars early in its his-
tory. That is demonstrated by an abundance
of now-dry river valleys (Fig. 2). Liquid water
now is not stable on the surface of Mars be-
cause of very low temperatures combined with
low atmospheric pressures (Fig. 3). As a result,
water ice sublimes directly to vapour without
passing through a liquid phase. Even at the
current very low temperatures there is still an
active “hydrological cycle”. One of the Viking
landers in 1976 observed water frost on rocks
and the Phoenix lander in 2008 observed snow
falling.
A range of observations have demonstrated that
the polar caps of Mars are a mixture of carbon
dioxide ice and water ice. Recent studies using
Figure 2: Dry river valleys and meteorite
craters, imaged by Mariner 9. The imaged
area is several hundred kilometres wide.
Image courtesy of NASA/nasaimages.org

gamma ray spectroscopy and ground penetrat-
ing radar observations from satellites have
shown that water ice is very widespread on the
planet, but most is covered by sediment. There
is evidence of glaciers.
So there is no shortage of water. There will
be liquid water at depth in the crust of Mars
because the interior of the planet is hot. That
Figure 4: The largest known volcano in
the solar system, Olympus Mons on Mars.
It is 500 km in diameter and 27 km high. I
Image courtesy of NASA/nasaimages.org
Figure 3: A phase
diagram comparing
the surface
environments on
Earth and Mars,
showing why pure
liquid water can not
exist on the surface
on Mars.
Image courtesy of
NASA/nasaimages.org
is known because there are volcanoes that
have been active in the last few million years.
Olympus Mons is an example (Fig. 4).
At the equator in Summer, water could be
liquid within a hundred metres of the ground
surface. There is evidence that even now occa-
sionally water comes to the surface, perhaps af-
ter an earthquake or a meteorite strike. NASA’s
orbiter Mars Global Surveyor discovered large
numbers of small gullies on the walls of me-
teorite craters (Frontis piece). The gullies are
fresh and have not been eroded by the wind,
and new ones appeared over the lifetime of
the mission (Fig. 5). Although it is not known
with certainty, the most plausible explanation
is that the gullies were eroded by brief outflows
of liquid water from underground aquifers.
More recently, possible droplets of water were
photographed on the legs of the Phoenix lander
in 2008 (Fig. 6).
Meteorites from Mars
In 1996 NASA held a press conference in
Washington DC to announce the possible
discovery of life on Mars. Naturally enough
this generated a huge amount of attention
worldwide.
The discovery involved meteorite ALH84001
(Fig. 7). This meteorite was discovered in the
The search for life on Mars | 23
 Figure 5: Recently
formed gullies
on the rim of an
impact crater. These
are considered
to be evidence
that occasionally
liquid water from
underground
aquifers reaches the
surface and flows
for long enough to
erode these features.
Image courtesy of NASA/
nasaimages.org

Allen Hills in Antarctica in 1984 and was the
first to be catalogued that year, hence the name.
Amongst the thousands of meteorites that
have been found, 34 are known to have come
from Mars. We know that because they have a
distinctive chemical and mineralogical compo-
sition different from any other rocks found on
the Earth or the Moon, and different from all
other meteorites. Trapped within tiny bubbles
in one of these meteorites are gases that match
the composition of the atmosphere of Mars.
It happened like this: an asteroid hit Mars and
blasted surface rocks off at such a high velocity
that they could escape the gravity of Mars. The
force of the blast melted parts of the rocks and
as they flew up through the atmosphere gases
were trapped in the melt. The rocks cooled in
space, permanently trapping the gases.
Back on Earth, in a laboratory in Houston, the
rock was broken open and examined with an
electron microscope. Structures resembling
fossil microbes were found on the broken
surfaces (Fig. 8). That discovery led to more
detailed analyses to determine whether the
meteorite contained any other evidence of life.
Organic compounds called polycyclic aromatic

Figure 6: The globules shown boxed on a leg of the Phoenix lander in 2008 are
interpreted by some scientists as water that can remain liquid because it is extremely
salty.
Image courtesy of NASA/nasaimages.org

24 | Genes to Galaxies

hydrocarbons (“PAH’s”) were found, along with
distinctive patterns of carbon isotopes. This
and other evidence formed the basis for the
claim that the meteorite contained evidence of
the former presence of life on Mars.
Since 1996 many scientists have studied
ALH84001 using a wide range of sophisticated
techniques. The conclusion is that all of the
observed features can be explained by non-
biological chemical processes, and none is
evidence for life. This is typical of how science
works: hypotheses are offered and then many
are refuted.
Methane in the Martian
atmosphere
Telescopes on Earth can be used to analyse the
atmosphere of Mars because different gases
have characteristic infrared spectra. In 2003,
patches of atmosphere rich in methane were
discovered. Three large patches, or “plumes”,
are now known. This is significant because
methane is unstable on Mars and would break
down rapidly. So there must be active sources
spewing the methane out of the crust. This also
happens on Earth where there are two types of
sources: volcanoes and microbes.
Figure 7:
Meteorite
ALH84001
which was once
considered to
contain evidence of
life on Mars.
Image courtesy of
NASA/nasaimages.org
This demonstrates that Mars is still an active
planet. It is not possible at present to determine
whether the methane is biological or geological
in origin. On Earth that distinction is made by
measuring the carbon isotopic composition of
the methane. Biological processes strongly se-
lect the lighter isotope, 12C, whereas geological
processes do not. It is not yet possible to meas-
ure the isotopic composition on Mars but there
are plans to do so on a forthcoming mission.
Exploration to date
There have been more than 40 attempted mis-
sions to Mars, the first in 1960. In the early
years there were many failures but the success
rate now is very high. Only two successful mis-
sions have had the specific goal of searching for
life, NASA’s Viking 1 & 2 in 1976. Both were
stationary landers with onboard laboratories
to analyse for organic compounds and to test
for gases produced by living organisms. One
experiment gave ambiguous results but it is
now accepted that no life was detected. In
retrospect that result is not surprising. It is now
known that the surface of Mars is highly oxi-
dising, so any organic compounds that might
have been present would have been destroyed.
In addition, Mars lacks both a substantial
The search for life on Mars | 25
Figure 8: An electron micrograph of a broken surface on meteorite ALH84001. The
numerous spheroidal structures are 20-50 nanometres wide. These and the worm-like
structure were at first interpreted as fossil microbes.
Image courtesy of NASA/nasaimages.org

magnetosphere and an ozone shield, so both
cosmic and ultraviolet radiation reach the sur-
face and would kill any organisms present.
So is there life on Mars?
We have learned over the last 50 years that
the conditions essential for life as we know it
existed widely on Mars early in its history, and
still exist in subterranean environments and
occasionally on the surface. But so far the only
hint that there is life is the presence of methane
in the atmosphere.
Within 20 years we will have much more in-
formation from robotic vehicles and we may be
able to gather enough information to suggest
the presence of life. A final demonstration may
require the return of samples, and such a mis-
sion is being planned for 2020. That mission
will be both enormously complex and enor-
mously expensive.
I think it is very likely that there was microbial
life on Mars and probably still is. But I think
we will have to wait until astronauts go to Mars
later this century to finally determine whether
or not there is or was life there.
And the obvious question is, why bother? The
answer is that the question of whether we are
alone in the universe is one of the most pro-
found questions we face. If there are microbes
on Mars, and if we can demonstrate that they
had a separate origin from life on Earth, then
we will be able to predict that life is abundant
throughout the universe. Somewhere out there
will be other industrial societies, probably far
more advanced than ours.

26 | Genes to Galaxies
The search for life on Mars | 27
Paleolithic
nutrition:what
did our ancestors
eat?
Janette Brand Miller
Neil Mann
Loren Cordain
P aleolithic nutrition is the study of
diets consumed by our early ‘stone
age’ ancestors, members of our spe-
cies who lived from around 750,000
years ago up until 10,000 years ago (Figure 1).
During this period, hominids relied on stone
technology to sustain their scavenging, hunting
and gathering lifestyle (Figure 2). Paleolithic
diets are a subject of interest for various reasons.
Apart from the intrinsic value of knowing more
about our past, many health experts have sug-
gested that the ‘native diet’ during human evolu-
tion is the healthiest diet, the one that meets
all our nutritional needs and to which we are
genetically adapted. Just as veterinarians try to
give zoo animals a diet closest to that which they
consumed in the wild, many nutritionists believe
that the diet eaten for the greater part of one mil-
lion years of human evolution is the ideal diet.
Conversely, they believe that modern illnesses
such as type 2 diabetes and coronary heart dis-
ease are a consequence of eating a diet to which
we are not genetically adapted (Figure 3). The
last 10,000 years ago (a mere ‘tick’ on the evolu-
tionary clock) have brought near inconceivable
changes to diet and physical activity.
 Paleolithic Nutrition First stone tools appear in the fossil
record ~2.4 MYA

 Why were they

made? What were
they used for?
 Butchering of
scavenged animals
 Flakes for slicing
 Core for chopping

Prof. Jennie Brand-Miller Human Nutrition Unit

Figure 1 Figure 2

African Climate
Discordance Hypothesis
20 MYA and 7 MYA
 The discordance
between modern diets
and paleolithic diets
contributes to many
diet related health
problems of modern
man

Declining rainfall…. Contraction of rainforest

Figure 3 Figure 4

Native Diet of Our Closest

Transition from Ape to Human
Living Relative
 94% plant foods  Bipedalism
 chiefly ripe fruit  Opposable thumb
 6% animal foods - small  Reduction in body
vertebrates & insects hair
 A large metabolically  Increase in brain size
active gut is needed to & complexity
process large amounts  Decrease in gut size
of less energetically & metabolic activity
dense, fibrous plant
foods

Figure 5 Figure 6

30 | Genes to Galaxies
Climate dictates food sources
For most of geological time, the world’s climate
was warmer and more homogeneous than it
is today (Figure 4). Our pre-human ancestors
who lived in Africa >7 million years ago en-
joyed a warm, moist environment and gathered
ripe fruits, leaves and berries from the tropical
forests (Figure 4 and 5). But gradually the plan-
et cooled. About 2.5 million years ago, a severe
Ice Age sent global temperatures plummeting
and prompted the conversion of moist African
woodland into much drier open savanna. As
the grasslands expanded, the tree cover shrank
and one or more species of forest dwelling
chimpanzee evolved into bipedal hominids
(Figure 6). Homo habilis who lived 2 million
years BP supplemented a largely vegetarian diet
with meat left over from predators’ kills (i.e.
they scavenged). But Homo erectus who lived
1.5 million years BP is known to have actively
hunted. Many scientists believe that hunting
was the pressure that selected for the larger and
larger brain of our species, Homo sapiens sapiens
(the phrase “man the hunter” originated with
this idea)(Figure 7 and 8).
As one Ice Age followed another, hunting and
fishing became a dominant way of life in both
warm and cold environments. During Ice Ages,
large amounts of water become locked into
the polar ice caps, making the whole planet
drier because less water falls as rain and snow.
Plant growth slows, rainforests shrink and
grasslands dominate the landscape. Herbivores
came into their own and grazing animals
multiplied in their millions. From 50,000
years ago, we know that Neanderthals were
cold-climate hunters of large game. Indeed,
over winter they subsisted primarily on game.
One large mammoth kill would have nourished
a family group of 50 individuals for at least
3 months. Similarly, Cro-Magnon man who
replaced the Neanderthals about 35,000 years
ago, lived through the coldest of the Ice Ages
on a high meat diet. The Hall of Bulls in the
famous Lascaux Caves in southern France is a
testament to the importance of animals to the
people who lived 17,000 years ago (Figure 9).
Similarly, we know that the ancestors of the
Aborigines who inhabited Australia 40-50,000
years ago led a hunting and shellfish gathering
Paleolithic nutrition: what did our ancestors eat? | 31
existence. Even during the warm inter-glacials,
parts of the world remained cold (e.g. Arctic
and sub-arctic regions) and continued to have
little vegetation. The human inhabitants of
those regions maintained a hunting/fishing
existence right up to recent times. Indeed, the
Inuit and other native Canadians are a modern
day example of a group whose historic diet was
high in animal food and low in plant matter.
During the early and mid 20th century, anthro-
pologists studied the planet’s few remaining
hunter-gatherer societies. To their surprise,
they found them generally free of the signs
and symptoms of the so-called diseases of
civilization. Although their nutritional patterns
probably would not have been identical to
hominids living during the Paleolithic period,
they represent the best ‘window’ we have into
the range and quantity of wild and unculti-
vated foods making up humanity’s ‘native’ diet.
Consequently, the characterization and descrip-
tion of hunter-gatherer diets has important
implications in designing therapeutic diets that
reduce the risk for chronic diseases in modern,
western cultures.
These ethnographic and anthropological stud-
ies tell us that there was no single, uniform
diet which typified the nutritional patterns
of all pre-agricultural humans. Humans were
masters of flexibility, with the ability to live in a
rain forest or near the polar ice caps. Yet, based
upon limited information, many anthropolo-
gists incorrectly concluded that the universal
pattern of subsistence was one in which plant
foods contributed the majority of food energy.
However, more recent and comprehensive
ethnographic compilations (Cordain et al,
2000a) as well as quantitative dietary analyses
in foraging populations, have been unable to
confirm the conclusions of these earlier studies.
In fact, the later studies demonstrated that ani-
mal foods, rather than plant foods, comprised
the majority of energy in the typical hunter-
gatherer diet.
Unfortunately, in the context of western diets,
increasing meat consumption (particularly
red and processed meat) is linked to a greater
risk of cardiovascular disease. In countries like
the USA, meats contribute much of the fat,
 Inclusion of more animal food in the Evidence of Complex Big Game
diet allowed brain to enlarge Hunting in Homo Sapiens
  How?  Anatomically modern
  Humans expend 20-25% of H. sapiens appear
RMR to fuel the brain whereas (~100,000 yrs ago)
chimps require 8%
 A spear point was
  Two possibilities:
found lodged in the
(1) increases in total metabolic
vertebra of a giant
rate
buffalo at Klasies River
(2) reduction in size &
Cave, South Africa
metabolic rate of another
organ Aiello LC Wheeler. The expensive tissue

(60-120,000 yrs ago)
hypothesisCurr Anthropol 1995 36:199-221.

Figure 7 Figure 8

Hall of Bulls -Lascaux Cave,

France (17,000 yrs ago) Plant Foods
 How important
(quantitatively) were
gathered foods in the diets
of pre-agricultural humans?
 Only quantitative evidence
comes from observations of
early ethnographers who
studied world’s ‘remnant’
hunter-gatherers

Figure 9 Figure 10

Dependence on gathered plant foods Dependence on hunted animal foods

Frequency Distribution of Subsistence Dependence (n = 229) Frequency Distribution of Subsistence Dependence (n = 229)

50 45 100
45 42 On average, plant 90
89 On average,
40 35 35 foods contributed 80
hunted animal
35 25-35% of energy foods contributed
Frequency
Frequency

30 70
30
60
26-35% of energy
25 23 Only 13% obtained
20 more than half their 50 47

energy from plant 40 36

15 11
foods 30
10 6 21
5 2 20
0 11
0 10
8
5
9
Mode = (26-35%)
3
0-5 6-15 16-25 26-35 36-45 46-55 56-65 66-75 76-85 86-100
0
0 Median = (26-35%)
0-5 6-15 16-25 26-35 36-45 46-55 56-65 66-75 76-85 86-100

% Dependence % Dependence

Figure 11 Figure 12

32 | Genes to Galaxies
and more importantly, about one third of the
saturated fat, the kind mostly clearly linked
to adverse outcomes. Thus, a high meat diet,
regardless of its fat quantity and type, is gener-
ally perceived to be unhealthy and to promote
cardiovascular and other chronic diseases.
Yet Australian red meat derived from grazing
animals is generally lean, low in saturated fat
and contains significant amounts of healthy
long chain omega-3 fats. Our research provides
evidence that the animal foods that dominated
hunter-gatherer diets were also low in saturated
fat and high in good fats. This nutritional pat-
tern would not have promoted atherosclerosis
(hardening of the arteries) or chronic disease.
Confusion over pre-
agricultural diets
Early theories on the natural, or native hu-
man diet assumed that Paleolithic people were
skilled hunters of big game whose diets were
primarily carnivorous in nature. However, by
early 1970s, this “Man the Hunter” explana-
tion was being contested by Richard Lee and
other anthropologists on the basis of evidence
suggesting that contemporary hunter-gatherer
peoples consumed more gathered plants than
hunted animal food (Lee, 1968) (Figure 10).
For example, Lee’s studies of the African !Kung
people demonstrated that gathered plant foods
comprised 67% of their average daily energy
intake while hunted animal foods encompassed
the remaining third. Lee further compiled data
from 58 hunter-gatherer societies who were
listed in the Ethnographic Atlas (Murdock,
1967), showing that hunted animal food made
up only 35 per cent of food intake, irrespective
of latitude.
Over the next 30 or so years, Richard Lee’s
analysis was widely misinterpreted to mean
that gathered plant foods typically provided
the major food energy in worldwide hunter-
gatherer diets, while hunted animal foods made
up the balance. But this general perception
is incorrect because fished animal foods must
be summed with hunted animal foods in the
analysis of the ethnographic data to more cor-
rectly evaluate dietary plant to animal energy
ratios (i.e. the percentage of energy contributed
Paleolithic nutrition: what did our ancestors eat? | 33
by plants versus animal foods). Our analysis
(Figures 11-14) of Gray’s Ethnographic Atlas
data (Gray, 1999) showed that the dominant
foods in most hunter-gatherer diets were de-
rived from animal food sources. We found that
nearly 3 in 4 of the world’s hunter gatherer
populations obtained at least half of their food
energy from hunted and fished animal foods,
whereas fewer than 1 in 7 obtained more than
half their calories from gathered plant foods.
Not a single hunter-gatherer society was com-
pletely vegetarian. The statistical mean among
all 229 hunter-gatherer societies in Gray’s atlas
indicated that 68% of calories came from ani-
mal foods and 32% from gathered plant foods
(Figure 15).
Quantitative studies of
hunter gatherer diets
The major limitation of ethnographic data is
that much of the information is subjective in
nature. Murdock’s scoring for the five basic
subsistence economies in the Ethnographic Atlas
were approximations, rather than precisely
measured food intake data. Fortunately, more
exact, quantitative dietary studies were car-
ried out on a small number of hunter-gatherer
societies. Table 1 lists these studies and shows
the plant to animal subsistence ratios. The
mean score for animal food subsistence is 65%,
while that for plant food subsistence is 35%.
These values are similar to our analysis of the
entire (n = 229) sample of hunter-gatherer
societies (Figure 15). If we exclude the two
polar hunter-gatherer populations (who have
no choice but to eat animal food because of
the inaccessibility of plant foods) from Table 1,
the mean score for animal subsistence is ~60%
and that for plant food subsistence is ~40%.
Consequently, there is remarkably close agree-
ment between the quantitative data in Table 1
and the ethnographic data.
Other evidence for meat eating
Isotope studies of fossil bones can tell us more
information about the type of foods that our
ancestors ate. Isotopic analysis of the skeletons
of Neanderthals (Richards et al, 2000a) and
Paleolithic humans (Richards et al, 2000b)
 Dependence on fished animal foods Total dependence on animal foods
Frequency Distribution of Subsistence Dependence (n = 229) (hunted + fished)
On average, all
40
37
38 50 46 animal foods
36 On average, fishing 45
35 34 45 42 (hunted and fished)
contributed 26-35%

Frequency
30 40 contributed >66%
Frequency

30
of energy 35
35 of energy
25
30
23
21
30
20 25 23

15
20
15
10
Mode = (46-55%) 10 6
5 5
5
Median = (26-35%) 5 2 Mode = (66-75%)
0 0
0
0
0 Median = (86-100%)
0-5 6-15 16-25 26-35 36-45 46-55 56-65 66-75 76-85 86-100 0-5 6-15 16-25 26-35 36-45 46-55 56-65 66-75 76-85 86-100

% Dependence % Dependence

Figure 13 Figure 14

Plant:Animal Ratios Foods not present in pre-

Hunter Gatherer Modern Diets agricultural diets
Breads, Cereals, Rice and Pasta Dairy Products Added Salt

32 % 38 %
Plant Animal
Food 62 %
68 % Plant Food
Animal Food
Food Refined Vegetable Oils Refined Sugars
Alcohol
(except honey)

Mean values, National Food Consumption

229 Hunter Gatherer Survey 1987-88
Societies

Figure 15 Figure 16

Dietary Macronutrients Recommended Dietary

Hunter Gatherer vs Modern Values Macronutrient Intake
ETOH-
Protein 3% Protein
15% 15%
Protein Fat Fat Fat
19-35 % 28-47 % 34% 30% or less

CHO CHO
CHO 49% 55% or more
22-40 %

Hunter Gatherer Societies Present USA Values American Heart Association

n=133 (58.1%) NHANES III Recommended Diet

Figure 17 Figure 18

34 | Genes to Galaxies
Table 1: Quantitatively determined proportions of plant and animal food in hunter-
gatherer diets.

Population Location Latitude % animal food % plant food

Aborigines Australia 12S 77 23
Ache Paraguay 25S 78 22
Anbarra Australia 12S 75 25
Efe Africa 2N 44 56
Eskimo Greenland 69N 96 4
Gwi Africa 23S 26 74
Hadza Africa 3S 48 52
Hiwi Venezuela 6N 75 25
!Kung Africa 20S 33 67
!Kung Africa 20S 68 32
Nukak Columbia 2N 41 59
Nunamiut Alaska 68N 99 1
Onge Andaman 12N 79 21

suggests that the dominance of animal foods are essential cellular lipids that are found only
in the human diet was not simply a recent in animal foods. The implication is that by eat-
phenomenon limited to contemporary hunter- ing abundant pre-formed sources of these fatty
gatherers, but rather one with a long history. acids, our bodies gradually lost the ability to
These studies provide objective evidence that synthesise them ‘in house’.
the diets of hominids living in Europe during
Finally, our species (again like cats) has a
the Paleolithic were indistinguishable from that
limited capacity to synthesize the amino
of carnivores such as arctic foxes and wolves.
acid taurine from its precursor amino acids.
Indeed, hominids may have experienced genet-
Vegetarian diets are known to result in lower
ic adaptations to animal-based diets early on in
blood concentrations of taurine. This implies
their evolution, analogous to those of obligate
that the need to synthesize taurine may have
carnivores such as cats (felines).
been unnecessary because dietary sources of
Carnivorous diets reduce the evolutionary pre-formed taurine had relaxed the selective
selective pressures that act to maintain ana- pressure to maintain the metabolic machinery.
tomical and physiological features needed to
There are additional signs that we were grow-
process and metabolize large amounts of plant
ing dependent on animal food sources. One of
matter. Like cats, humans have experienced
our essential micronutrients is Vitamin B12 and
a reduction in gut size and metabolic activity,
found only in animal foods. Similarly, the rich-
along with a concurrent expansion of brain
est sources of iron, iodine, folic acid and vita-
size (Figure 7). This occurred at the very same
min A are animal foods. The most common nu-
time that more and more energetically dense
trient deficiencies today are associated with low
animal food was incorporated. The brain is a
meat consumption. Iron deficiency anaemia
very energy-demanding organ, responsible for
is prevalent in both rich and poor countries,
about one quarter of our basal metabolic rate.
while iodine deficiency affects up to 2 billion
Further, similar to obligate carnivores, humans
people world wide, resulting in goitre, cretin-
have a limited ability to manufacture the long
ism and enough mental retardation to reduce
chain, highly polyunsaturated fatty acids that
a population’s average IQ. (Incidentally, iodine
characterize our complex brain and nervous
deficiency is rising sharply in Australia because
system. Long chain polyunsaturated fatty acids
dairy manufacturers no longer use iodophors as

Paleolithic nutrition: what did our ancestors eat? | 35


The USDA Food Pyramid
Fats Oils & Sweets
use sparingly
Meat, Poultry, Fish, Dry Beans,
Milk, Yogurt & Cheese
Eggs & Nuts
2-3 Servings
2-3 Servings
Vegetables
3-5 Servings Fruit
2-4 Servings
Bread, Cereal, Rice
& Pasta
6-11 Servings
Figure 19
cleansing agents in dairy factories). Folic acid
deficiency causes a birth defect in which the
brain and spinal cord do not develop normally,
a condition known as ‘neural tube defect’.
Although dark green leafy vegetables are a good
source of folic acid, the very richest source is
animal liver, a commodity regularly consumed
by our hunter-gatherer ancestors. Finally, hu-
mans have a finite capacity to convert the yel-
low/orange coloured carotenoids in plant foods
into vitamin A. Today, vitamin A deficiency
blindness is the most common cause of vision
loss in the world and again, the richest sources
of vitamin A are liver and animal flesh. So
gradually, but surely, we evolved a metabolism
that depended on at least moderate intake of
animal foods.
Hunter-gatherer
foraging strategies
Our analyses of both the ethnographic data and
the quantitative dietary data (Table 1) show
that animal foods were our preferred energy
source, even when plant food sources were
available year round such as in the tropics.
Only when it was difficult to procure animal
food sources, or when energy-dense, easily
procured plant foods were available (eg the
mongongo nut for the South African !Kung
people), did plant foods prevail as a major en-
ergy component in hunter-gatherer diets.
36 | Genes to Galaxies
Human Evolutionary Food Pyramid
Figure 20
Foraging humans are similar to other animals
in natural settings in that they attempt to
maximize the energy ‘capture’ rate, i.e. the
ratio between the energy obtained from a food
source compared to the energy expenditure
needed to acquire it while hunting, fishing
or gathering (this is known as the Optimal
Foraging Theory). Table 2 shows the energy
return rates for a variety of plant and animal
foods that were known components of hunter-
gatherer diets. Clearly, animal foods yield the
highest energy return rates, and larger animals
generally produce greater energy returns than
smaller animals. Although the potential food
mass would be similar between a single deer
weighing 45 kg and 1,600 mice weighing 30 g
each, foraging humans would have to expend
significantly more energy capturing the 1,600
mice than a single deer. Hence, the killing of
larger animals increases the energy capture/
energy expenditure ratio not only because it
reduces energy expenditure, but because it in-
creases the total energy captured.
Due to the relative constancy of the protein
content of an animal’s muscle mass, the energy
density of an edible carcass is almost entirely
dependent upon its body fat content. Varying
amounts of body fat determine the protein to
fat energy ratio in an edible carcass. Because
smaller animal species have proportionately
less body fat than larger species, their carcasses
contain more protein as a percentage of their
available food energy. Hunter-gatherers tended
Table 2: Energy return rates upon encounter from foraged foods.

Food Food Type Return rate (kcal/hr)

Collared peccary Animal 65,000
Antelope, deer, bighorn
Animal 16,000 – 32,000
sheep
Jack rabbits Animal 13,500 – 15,400
Cottontail rabbits, gophers Animal 9,000 – 10,800
Paca Animal 7,000
Coati Animal 7,000
Squirrel (large) Animal 5,400 – 6,300
Roots Plant 1,200 – 6,300
Fruits Plant 900 – 6,000
Armadillo Animal 5,900
Snake Animal 5,900
Bird Animal 4,800
Seeds Plant 500 – 4,300
Lizard (large) Animal 4,200
Squirrel (small) Animal 2,800 – 3,600
Honey Plant 3,300
Ducks Animal 2,000 – 2,700
Insect larvae Animal 1,500 – 2,400
Fish Animal 2,100
Palm heart Plant 1,500
Acorns Plant 1,500
Pine nuts Plant 800 – 1,400+
Mongongo nuts Plant 1,300
Grass seeds Plant 100 – 1,300

to shun very small animals or fat-depleted ani-
mals because of their excessive protein content.
Historical accounts documented the adverse
health effects that occurred when people were
forced to rely solely on fat-depleted, wild ani-
mals (Speth & Spielmann, 1983). Excessive
protein consumption without additional sourc-
es of fat or carbohydrate caused a condition de-
scribed as “rabbit starvation” in early American
explorers. They suffered nausea, diarrhea and
even death if very lean small animals were the
only source of food. Clinically, this syndrome
is probably caused by the finite ability of the
liver to up-regulate the rate-limiting enzymes
that synthesise urea, culminating in very high
levels of ammonium ions and acidic amino
acids in the blood. For the foraging human, the
avoidance of excessive dietary protein was an
important factor in shaping their food procure-
ment strategies. Lean meat, therefore, could
not be eaten in unlimited quantities, but rather
had to be accompanied by sufficient fat, or by
carbohydrate derived from plant food sources.
This simple physiological fact could explain
our innate drive to consume fatty and sweet
foods.
Modern vs traditional
food choices
Before the development of agriculture and
animal husbandry, dietary choices would have
been limited to minimally processed, wild plant
and animal foods. With the initial domestica-
tion of plants and animals, the original nutrient
characteristics of foods changed, subtly at first

Paleolithic nutrition: what did our ancestors eat? | 37

but more rapidly with advancing technology
after the Industrial Revolution. Food processing
procedures were developed which had pro-
found physiological implications.
Today we eat many types of food that were
absent from the diet of Paleolithic people.
Dairy products, cereals, refined sugars, refined
vegetable oils, and alcohol make up over 70%
of the total daily energy consumed by people in
developed nations (Figure 16). But these types
of foods would have contributed little or none
of the energy in the typical pre-agricultural hu-
man diet. Additionally, mixtures of foods that
make up much of our present diet (eg, cookies,
cake, breakfast cereals, bagels, rolls, muffins,
crackers, chips, snack foods, pizza, soft drinks,
candy, ice cream, condiments, and salad dress-
ings) were absent.
Dairy foods Humans, like all mammals, would
have consumed the milk of their own species
during infancy. However, after weaning, the
consumption of milk and milk products of
other mammals would have been minimal.
Sheep, goats and cows were not domesticated
until ~10,000 years ago and direct evidence of
dairying dates to only ~6000 years ago. Most of
the world’s population still does not consume
milk beyond infancy. It should not be surpris-
ing therefore to learn that more than 80% of
humans do not have the capacity to hydrolyse
lactose, the carbohydrate in milk, after early
childhood. However, European Caucasians and
their descendents in America and Australia,
who have been exposed to dairying for several
thousand years, can generally digest lactose
well throughout life.
Cereals Wild cereal grains are usually small,
difficult to harvest, and virtually indigestible
without processing (grinding) and cooking. For
this reason, Paleolithic people ate little of them.
Grinding tools in the fossil record represents a
reliable indication of when and where cultures
began to include cereal grains in their diet.
Ground stone mortars, bowls, and cup holes
first appeared from 40,000 years ago to 12,000
years ago. Domestication of emmer and einkorn
wheat heralded the beginnings of early agricul-
ture in southeastern Turkey about 10,000 years
ago. There was therefore little or no previous
38 | Genes to Galaxies
evolutionary experience for cereal grain con-
sumption throughout human evolution. Again,
it should not be surprising to learn that many
people are allergic to the gluten protein found
in wheat, rye and barley. Known as celiac
disease, it causes the body’s immune system to
attack itself and affects more than one in every
133 people.
Today, most cereals consumed in the west-
ern diet are highly processed refined grains.
Preceding the Industrial Revolution, all cereals
were ground with the use of stone milling tools,
and unless the flour was sieved, it contained
the entire contents of the cereal grain, includ-
ing the germ, bran, and endosperm. With
the invention of mechanized steel roller mills
and automated sifting devices in the latter
part of the 19th century, the nutritional and
physiological characteristics of milled grain
changed, becoming virtually pure starch from
just the seed endosperm. As a consequence,
the foods made from fine flours, such as bread,
are quickly digested and absorbed, and raise
blood sugars rapidly when consumed. Many
recent studies suggest that carbohydrates that
are digested and absorbed quickly (known as
high glycemic index foods), increase the risk
of chronic diseases such as type 2 diabetes and
cardiovascular disease (Barclay et al. 2008).
Alcohol In contrast to dairy products, cereal
grains, refined sugars, and refined oils, alcohol
consumption represents a relatively minor frac-
tion (1 or 2%) of the total energy consumed in
western diets. The earliest evidence for wine
drinking from domesticated vines comes from a
pottery jar dated ~7000 years BP from northern
Iran. The fermentation process that produces
wine takes place naturally and, without doubt,
must have occurred countless times before hu-
mans learned to control the process. As grapes
reach their peak of ripeness in the fall, they
may swell in size and burst, thereby allowing
the sugars in the juice to be exposed to yeasts
growing on the skins and to produce carbon
dioxide and ethanol. Because of seasonal fluc-
tuations in fruit availability and the limited
liquid storage capacity of hunter-gatherers, it is
likely that fermented fruit drinks, such as wine,
would have made an insignificant contribution
to total energy in Paleolithic diets.
Salt The total quantity of salt included in the
typical diet of westernized nations amounts
to nearly 10 g/day. About 75% is derived from
salt added to processed foods by manufactur-
ers; 15% comes from discretionary sources (ie,
cooking and table salt use), and the remainder
occurs naturally in basic foodstuffs. The system-
atic mining, manufacture, and transportation
of salt have their origin in the last 10,000 years.
The earliest salt use is thought to have taken
place in China about 6000 BC. Paleolithic
hunter-gatherers living in coastal areas probably
dipped food in seawater or used dried salt in a
manner similar to nearly all Polynesian socie-
ties at the time of European contact. But most
recently studied inland hunter-gatherers add no
or little salt to their food.
Diet and chronic disease
in hunter-gatherers
Dietary fat
In our analysis of hunter-gatherer diets
(Cordain et al, 2000), we found that most
groups exceeded the dietary recommendation
to eat 30% or less of energy as fat (Figures 17
and 18). In fact, over half of them consumed
amounts not too dissimilar to current western
and Mediterranean dietary intakes. Despite
this, the available evidence suggests that hunt-
er-gatherers were generally free of the signs and
symptoms of cardiovascular disease. Research
shows that indigenous populations that derive
the majority of their diet from animal products
have surprisingly low levels of cholesterol and
other fats in the blood. Moreover, death certifi-
cates, autopsies and clinical studies indicate a
low incidence of coronary heart disease among
the Inuit and other polar populations, consum-
ing high intakes of animal foods. However, in
western diets, higher animal food consumption
is frequently associated with increased mortal-
ity from chronic disease. The low incidence
of cardiovascular disease among indigenous
populations subsisting largely on animal foods
represents a paradox.
There is now strong evidence that the absolute
amount of dietary fat is less important in re-
ducing the risk for cardiovascular disease than
the type of fat. Fatty acids that increase blood
Paleolithic nutrition: what did our ancestors eat? | 39
cholesterol levels include lauric acid (C12:0),
myristic acid (C14:0), palmitic acid (C16:0),
and some trans fatty acids (Grundy, 1997),
whereas monounsaturated (MUFA) and poly-
unsaturated (PUFA) fatty acids reduce choles-
terol levels. Stearic acid (C18:0), the major fatty
acid in chocolate and lean red meat is neutral.
Omega-3 long chain PUFA, found in fish and
seafood in general and Australian grass fed beef
and lamb, have wide ranging protective capaci-
ties including the ability to reduce blood lipids.
Consequently, it is possible to consume high
fat diets that do not produce an adverse blood
lipid profile or cardiovascular disease.
In their classic study of Greenland Eskimos
who had a near absence of cardiovascular dis-
ease, Bang and Dyerberg (1980) contrasted the
dietary and blood lipid profiles of the Eskimos
to Danes (Table 3). Despite a much greater ani-
mal food intake than the Danes, the Eskimos
maintained a more healthful blood lipid profile.
The reduced cholesterol levels in the Eskimos
are likely accounted for by the higher dietary
intake of ‘good’ fats. The protein intake of the
Eskimos was more than twice as high as the
Danes, and this pattern (elevated protein at the
expense of carbohydrate) is characteristic of
hunter-gatherers (Cordain et al, 2000a).
Dietary protein
Our analyses of contemporary hunter-gatherer
diets show that the average protein intake was
as high as 35% energy (Figure 16). This is
more than twice the level consumed by cur-
rent western populations (~15% energy). High
protein intake in western diets is perceived
to be linked to high calcium excretion in the
urine and faster progression of kidney disease.
Yet, paradoxically, high protein diets have
been shown to improve metabolic control in
type 2 diabetes patients. In her classic study of
Australian Aborigines temporarily reverting to
a hunter-gatherer lifestyle, Kerin O’Dea showed
that animal foods contributed ~65% of the total
energy, producing an overall macro-nutrient
distribution of 54% protein, 33% carbohydrate
and 13% fat energy. Following a 7-week period
living as hunter-gatherers in their traditional
country in north-western Australia, 10 diabetic,
overweight Aborigines experienced either a
Table 3: Dietary and blood lipid characteristics of Greenland Eskimos and Danes.
Variable
Dietary intake:
Protein (% energy)
Fat (% energy)
Carbohydrate (% energy)
Saturated fat (% total fat)
Monounsaturated fat (% total fat)
Polyunsaturated fat (% total fat)
n-6 PUFA (g)
n-3 PUFA (g)
Blood lipid values
Total cholesterol (mmol/liter)
Triglycerides (mmol/liter)
great improvement or complete normalization
of all of the major metabolic abnormalities
characteristic of diabetes (O’Dea, 1984).
The fossil record indicates pre-agricultural hu-
mans generally maintained greater bone mass
than modern humans and hence greater bone
strength and resistance to fractures (Bridges,
1995; Ruff et al, 1993). Greater bone strength
has been attributed to the greater activity pat-
terns of pre-agricultural humans, which in turn
would have increased bone loading. It is also
quite likely that the high fruit and vegetable
consumption in hunter-gatherer diets would
have buffered the high acid load and subse-
quent high calcium excretion brought about
by a high protein diet. In western diets, meats,
cheeses and cereal grains yield high potential
renal acid loads and hence may promote oste-
oporosis (thinning of the bones) by producing
a net metabolic acidosis. In contrast, fruits and
vegetables yield a net alkaline renal load, and
high fruit and vegetable diets have been shown
to decrease urinary calcium excretion rates.
Consequently, in hunter gatherer populations
consuming high protein diets, a concomitant
consumption of high levels of fruits and vegeta-
bles may have countered the effects of a high
protein diet.
40 | Genes to Galaxies
Eskimos Danes
26.0 11.0
37.0 42.0
37.0 47.0
22.8 52.7
57.3 34.6
19.2 12.7
5.4 10.0
13.7 2.8
5.33 + 0.78 6.24 + 1.00
0.61 + 0.44 1.32 + 0.53
Dietary carbohydrate
Our studies also demonstrate that the carbo-
hydrate content of hunter-gatherer diets would
have ranged from 22 to 40% of total energy
(Figure 16). The values within this range are
considerably lower than average values in west-
ern diets or recommended levels (50-60% or
more of total energy). Although current advice
to reduce risk of cardiovascular disease is to
replace saturated fats with carbohydrate (Figure
17), there is mounting evidence to indicate
that low fat, high carbohydrate diets may elicit
undesirable changes in blood fats, including
reductions in the good cholesterol (HDL) and
triglycerides. Because of these untoward blood
lipid changes, substitution of MUFA for satu-
rated fats has been suggested as a more effec-
tive strategy than substitution of carbohydrate
for saturated fats in order to lower the risk of
cardiovascular disease.
Hunter gatherer diets would not only have
contained less carbohydrate than that typically
found in western diets, but there are impor-
tant qualitative differences in the types of
carbohydrates. Western diets are characterized
by carbohydrate foods with a high glycemic
index (e.g. potatoes, bread, processed cereal
products) whereas the wild plant foods which
would have been consumed by hunter-gather-
ers generally maintain a high fiber content, are
slowly digested and produce low glycemic and
insulin responses. Observational studies sug-
gest that foods with a high glycemic load and
low fiber content increase the risk for type 2
diabetes (Barclay et al, 2008).
Other environmental factors
It is likely that hunter-gatherers consumed very
high intakes of antioxidants and phytonutrients
and undertook more intense physical exercise
or work patterns (Cordain et al, 1998). These
characteristics would have provided pre-agri-
cultural people with further protection from
chronic diseases such as diabetes. Biochemical
studies of hunter-gatherers have shown high
plasma concentrations of folate and vitamin
B12. Adequate intake of these two vitamins
along with vitamin B6 reduce homocysteine, an
important risk factor for cardiovascular disease.
Hunter-gatherers rarely if ever added salt to
their foods, and studies of salt-free Yanomamo
Indians have shown these indigenous people
to maintain low blood pressures that do not
increase with age. Finally, except for certain
American Indian societies (starting about 5,000
years ago), regular smoking of tobacco was un-
known in hunter-gatherers. Any or all of these
dietary and environmental elements would
have operated together with the macronutrient
characteristics of hunter-gather diets to reduce
signs and symptoms of the chronic diseases
that plague western societies.
Conclusions
The diet of our ancestors was characterized
by higher intake of meat and lower intake
of plant foods than is generally recognized.
Modern human beings display physiological
features which suggest an increasingly carnivo-
rous diet during human evolution. Our large
brains increased in size at the expense of the
gastronintestinal tract and dictated high intake
of nutrient-rich foods. The high reliance on
animal foods may not have elicited an adverse
blood lipid profile because of the benefits of
high dietary protein and low level of dietary
carbohydrate. Although fat intake would have
been similar to or higher than that found in
western diets, there were important qualitative
differences. The high levels of MUFA and PUFA
Paleolithic nutrition: what did our ancestors eat? | 41
and omega-3 fatty acids, would have served
to inhibit the development of cardiovascular
disease. Other dietary characteristics including
high intakes of antioxidants, fibre, vitamins and
phytochemicals along with a low salt intake
may have operated synergistically with lifestyle
characteristics (more exercise, less stress and
no smoking) to further deter the development
of disease. The modern healthy food pyramid
with its foundation based on cereals rich in car-
bohydrate supplemented with small amounts
of animal foods (Figure 19) differs greatly from
the human evolutionary pyramid (Figure 20).
Yet it is still possible to consume a healthy
diet based on evolutionary principles in which
the quality of fat, protein and carbohydrate
are more critical that their quantity or energy
distribution. Indeed, the insights gained from
Paleolithic nutrition are likely to influence fu-
ture dietary guidelines around the world.
Although concerted attempts were made to acknowledge the
source of all images, in some cases this could not be ascertained.
Please contact the author if an infringement has taken place.
Further reading
Barclay A, Petocz P, McMillan-Price J, Flood
VM, Prvan T, Mitchell P, Brand-Miller JC.
Glycemic index, glycemic load and chronic
disease risk – a meta-analysis of observational
studies. Am J Clin Nutr 2008; 87: 627-37.
Cordain L, Watkins BA & Mann NJ (2001):
Fatty acid composition and energy density of
foods available to African hominids: evolution-
ary implications for human brain development.
World Rev. Nutr. Diet. 90, 000-000.
Cordain L, Brand Miller J, Eaton SB, Mann N,
Holt SHA & Speth JD (2000a): Plant-animal
subsistence ratios and macronutrient energy
estimations in worldwide hunter-gatherer diets.
Am. J. Clin. Nutr. 71, 682-692.
Cordain L, Brand Miller J, Eaton SB & Mann
N (2000b): Macronutrient estimations in
hunter-gatherer diets. Am. J. Clin. Nutr. 72,
1589-1590.
Cordain L, Gotshall RW, Eaton SB & Eaton SB
(1998): Physical activity, energy expenditure
and fitness: an evolutionary perspective. Int. J.
Sports Med. 19, 328-335.
Dahlberg F (1981): Introduction. In: Woman Australian Aborigines after temporary reversion
the Gatherer, ed. F Dahlberg, pp 1-33. New to traditional lifestyle. Diabetes 33, 596-603.
Haven: Yale University Press.
Richards MP & Hedges RM (2000b): Focus:
Eaton SB & Konner M (1985): Paleolithic Gough’s Cave and Sun Hole Cave human
nutrition. A consideration of its nature and cur- stable isotope values indicate a high animal
rent implications. N. Engl. J. Med. 312, 283- protein diet in the British Upper Palaeolithic. J.
289. Archaeol. Sci. 27, 1-3.
Eaton SB, Konner M & Shostak M (1988a): Sinclair HM (1953): The diet of Canadian
Stone agers in the fast lane: chronic degenera- Indians and Eskimos. Proc. Nutr. Soc. 12, 69-
tive diseases in evolutionary perspective. Am. J. 82.
Med. 84,739-749.
Speth JD (1989): Early hominid hunting and
Eaton SB, Shostak M & Konner M (1988b): scavenging: the role of meat as an energy
The Paleolithic Prescription. New York: Harper source. J. Hum. Evol. 18, 329-343.
Row.
Speth JD & Spielmann KA (1983): Energy
Kaplan H & Hill K (1992): Human subsistence source, proein metabolism, and hunter-gatherer
behavior. In: Evolution, Ecology and Human subsistence strategies. J. Anthropol Archaeol. 2,
Behavior, eds, EA Smith & B Winterhalder, pp 1-31.
167-202. Chicago: Aldine.
Kaplan H, Hill K, Lancaster J & Hurtado AM
(2000): A theory of human life history evolu-
tion: diet, intelligence, and longevity. Evol.
Anthropol. 9, 156-185.
Lee RB (1968): What hunters do for a living, or
how to make out on scarce resources. In: Man
the Hunter, eds. RB Lee & I DeVore, pp 30-48.
Chicago: Aldine.
Lee RB (1979): The !Kung San: Men, Women,
and Work in a Foraging Society. Cambridge:
Cambridge University Press.
Mann, N (2000). Dietary lean red meat and hu-
man evolution. Eur J Nutr 39: 71-79.
McArthur M (1960): Food consumption and
dietary levels of groups of aborigines living on
naturally occurring foods. In: Records of the
American-Australian Scientific Expedition to
Arnhem Land, ed. CP Mountford, pp 90-135.
Melbourne: Melbourne University Press.
Meehan B (1982): Shell Bed to Shell Midden.
Canberra: Australian Institute of Aboriginal
Studies.
Murdock GP (1967): Ethnographic atlas: a
summary. Ethnology 6,109-236.
O’Dea K (1984): Marked improvement in
carbohydrate and lipid metabolism in diabetic

42 | Genes to Galaxies
Paleolithic nutrition: what did our ancestors eat? | 43
A Walk Around the Neighbourhood:

Understanding
the Nature and
Structure of
the Milky Way
N. M. McClure-Griffiths
W e live in a hefty spiral-
patterned galaxy called
the Milky Way. Though
we can all see the Galaxy
on a nightly basis, we know surprisingly little
about our home. Some very important ques-
tions about the shape and structure of the
Milky Way remain unanswered: Exactly how
big is the galaxy? Where is the Sun in relation
to the Galactic Centre? If we could look at the
Milky Way from above what would it look like
and how many spiral arms would it have? How
does the Milky Way evolve and how do we in-
teract with our neighbours? I will take us on a
walk around the Milky Way revealing what we
do know about the structure of the galaxy and
how it lives its life. I will finish with some of
the things we hope to learn in the next decade
as new telescopes become available and help us
solve the mysteries of our home.
One of the first things you might do upon
moving into a new house is take a walk
around the neighbourhood. What’s around
the corner? Where’s the nearest shop? How far
to the school? Even though we’ve been living
in our home galaxy, the Milky Way, since the
beginning of time we don’t really know much
about the neighbourhood. We can’t go out
and explore the neighbourhood because the
neighbourhood is far too big. Just going to the
star next door would take about 30,000 years.
Instead, most of what we know about the
Milky Way neighbourhood comes from astron-
omy and its mostly ground-based telescopes. In
this chapter I will try to give you a brief tour of
the Milky Way, hopefully answering questions
about what the Milky Way looks like, how it
lives its life, and how it interacts with some of
its nearest neighbours.
The Milky Way as a galaxy
Stars are grouped throughout the universe
in islands called galaxies. Galaxies take on a
variety of different shapes, but many look like
large pinwheels. The closest galaxy is the one
in which we live, the Milky Way. Most of us are
probably familiar with the Milky Way as a great
band of white-ish stars stretching from horizon
to horizon. On a dark night, particularly in
the Southern Hemisphere, the Milky Way is
the most striking feature in the sky. Figure 1
is a wonderful example of how the Milky Way
looks in the night sky both in the Northern
and Southern Hemispheres. Our name for this
band of stars comes from the Latin name for
it: “via lactea”, meaning milky road or milky
way. We often refer to the Milky Way by its
Greek derived name “The Galaxy”, which also
means “milky”.
Studying the Milky Way is simultaneously
made easy by its close proximity and difficult
because we are deeply embedded within the
Galaxy. Even with years of study we are still
struggling to understand the basic properties
and structure of the Galaxy. We do know that
the Milky Way is a rather hefty galaxy, made up
of something like 200 to 300 billion stars and
weighing in at about 600 billion times the mass
of the Sun or a little over 1 x 1042 kg. Mass
estimates for the Milky Way are based on meas-
uring the rotational speed of the Galaxy as far
out as possible and using basic laws of gravity
(Kepler’s Laws) to estimate the mass enclosed
in the orbit.

Figure 1: Images of the Milky Way in the night sky taken from both the Northern and
Southern Hemispheres. The Milky Way stretches from horizon to horizon as a band of
“milky” white stars and the occasional dust cloud that blocks out the starlight from
behind the clouds. Also visible here are the Large and Small Magellanic Clouds as light
purple spots near the centre of the right-hand image. These are some of our nearest
galaxy neighbours.
Image credit: Axel Mellinger / http://home.arcor-online.de/axel.mellinger/

46 | Genes to Galaxies

Taking measure of the Milky Way diameter is
in many ways even more tricky. Most of what
we know about the structure of the Galaxy
more than a few thousand light-years1 from the
Sun comes from measurements made of radio
and infrared radiation, which pierce through
the fog of the Galaxy’s interstellar gas and dust.
Because the Milky Way is viewed as a relatively
thin band of stars on the sky we have long
known that it must be a disk-like structure. In
fact, the Milky Way has dimensions somewhat
like a compact disc. The stars lie in a disk of
diameter about 100,000 light-years (LY) with a
thickness of only about 1000 LY. Surrounding
the disk is a spherical ball of mostly gas and a
few stars called the halo. This halo is important
to the evolution of the Milky Way as a whole
and we’ll come back to it later.
The Sun lies about 26,000 LY from the centre
of the Galaxy, but this number has been the
1 A light-year is the distance light travels in one year or
9.5 x 1012 km.
Figure 2: Artist’s
impression of the
Milky Way as it
might appear if
we could fly out
of it and look
back down. The
model used here
is assembled from
many pieces of
information about
the spiral structure
and bar structure
of the Galaxy. The
position of the Sun
is marked and most
of the spiral arms
are named.
NASA/JPL-Caltech/R.
Hurt (SSC-Caltech)
source of great uncertainty for the entire history
of Milky Way studies. The most recent meas-
urement, painstakingly made with one of the
world’s largest optical telescopes, Keck, give a
value of 26000 LY with an error range of 2000
LY (Ghez et al 2008). Other reliable measure-
ments suggest values as low as 24,700 LY or as
high as 27,600 LY. Most other properties of the
Galaxy’s structure, including the full extent of
the disk and its height depend on the Galactic
Centre distance so it is crucial to measure it as
accurately as possible.
We also know that the Milky Way is shaped
like a pinwheel in what is known as a barred
spiral-type galaxy. Each one of the arms of the
pinwheel is made up of very bright, massive
stars. While the space between spiral arms
also has many stars, these are generally smaller
and less bright. The result, if we could see
the Milky Way from above, might look like
the artist’s impression shown in Figure 2. The
number and position of these arms has been
A Walk Around the Neighbourhood | 47
very difficult to determine and the model as-
sembled in Figure 2 is our best guess from the
data available to us. The problem of determin-
ing what the Milky Way spiral structure has
been likened to the problem of trying to see the
forest through the trees. We can easily see the
trees, but we can’t walk around the forest and
map it out so it is very difficult to assess what
the forest, as a whole, would look like.
Some aspects of the spiral model of the Milky
Way are very new. For example, it was only
in 2005 through results coming out of the
Spitzer Space Telescope that we realised just
how prominent the bar of the Milky Way is.
Measurements of old stars traced in the infrared
by Spitzer revealed that the bar extends about
14,000 light-years on both sides of the centre
of the Galaxy at an angle of about 45 degrees
to the line between the Sun and the Centre of
the Galaxy (Benjamin et al. 2005). Other new
features are the most distant spiral arm, shown
in Figure 2 to the bottom right. This spiral arm
was discovered entirely as a gaseous spiral arm
in 2004 by researchers using radio telescopes
here in Australia (McClure-Griffiths et al.
2004). The arm spirals outwards from about
60,000 light-years from the Galactic centre
to 80,000 light-years, putting it beyond the
known extent of the disk of stars in the Milky
Way. If we could see the arm in visible light
on the sky we would see it traced through 70
degrees of angle on the sky.
The components of the
Milky Way: stars, gas,
dust, magnetic fields
The Milky Way that we see in the night sky is
dominated by stars. However, there is much
more to the Milky Way than the stars. Stars
make up the bulk of the mass of the Galaxy,
but gas and dust between the stars play im-
portant roles in the evolution of the Galaxy,
including the formation of new stars. About 5%
of the mass of the Galaxy is in the form of the
gas and dust between the stars, the interstellar
medium (ISM). Of that, almost 9 out of every
10 particles (atoms or molecules) are hydrogen.
Hydrogen is the lightest element there is, so
if we were to count by mass, about 40% of
48 | Genes to Galaxies
the mass of the ISM is atomic hydrogen. The
rest of the ISM is made up of progressively
heavier elements and even molecules like
Carbon Monoxide, Ammonia, Formaldehyde,
etc. In the densest areas of the ISM, complex
molecules, referred to as dust, exist. It is this
dust that forms the dark patches along the
Milky Way that we view in the night sky. These
complex molecules block the light from stars
behind them and make dark constellations.
The ISM is a varied place. The gas has densities
varying from 0.001 atoms per cubic centimetre
up through “dense” regions with 1 million
atoms or molecules per cubic centimetre. And
while these so-called “dense” regions have a lot
of matter for interstellar gas, they are still much
less dense than most things on Earth. Air at sea
level, for example, has a density of about 1019
molecules per cubic centimetre. That’s thirteen
orders of magnitude more dense than a dense
area of interstellar space! Even the best vacuum
that we can produce on Earth results in about
1010 molecules per cubic centimetre. Not only
does the density vary, but the temperature also
varies to keep roughly in step with the density
so that there is equal pressure in most parts
of interstellar space. The relationship between
pressure, P, the density, n, and the temperature,
T, is given by the familiar gas law: P=nkT,
and k is Boltzmann’s constant. For example, in
regions where the density is about 1 atom per
cubic centimetre the temperature is about 5000
degrees and in areas where the density is 0.001
atoms per cubic centimetre the temperature is
nearly one million degrees.
The ISM isn’t static, either. The gas within the
galaxy is constantly in motion. All of the gas
in the Galaxy rotates about the centre of the
Galaxy. This rotation is caused by tight orbits
around the mass contained within the orbit.
Near the Sun the rotational speed is 220 km/s
or 792,000 km/hr! On top of that there are
small-scale motions that move gas about with
velocities of up to 1000 km/s.
While the stars act like the rock of the earth,
the gas acts like the atmosphere for the Galaxy.
It is through the gas that information about
temperature and pressure – Galactic weather
systems – are conveyed from one place to
another. So how do these weather systems
develop? We’ll discuss that in the next section
when thinking about how the Milky Way lives
its life.
How Does the Milky
Way Live its Life?
The formation and evolution of galaxies like
the Milky Way is a topic of current study. How
do the bits and pieces of cold gas left floating
around the Universe come together to form a
galaxy? What influences how galaxies live their
lives? Although we don’t have clear answers
about how the Milky Way formed, there has
been enormous progress in the past few years
on studying how the Milky Way lives its life. It
is the interstellar gas that largely controls the li-
fecycle of the Milky Way. After all, it is from the
gas that stars form and it is to the gas that the
stars return when they die. We know that most
stars are formed in clouds of molecular gas,
which are the densest areas of interstellar space.
It is only in these dense areas that enough mat-
ter can accumulate in a small enough area for
gravity to pull it together in a tight ball so that
nuclear fusion can ignite the gas as a star. The
topic of how exactly stars form is an interest-
ing one and one that dominates a great deal of
astrophysical research, but we’ll leave that topic
for another day. Right now, we’ll focus just on
how gas cools and condenses to form molecu-
lar clouds, what disrupts gas in the Milky Way
and whether that gas flows in or out of the
Galaxy.
Disrupting Interstellar Gas
The basic cycle of life and death in the inter-
stellar medium is shown in Figure 3. Most of
interstellar space is filled with diffuse (density
of 1 atom per cubic centimetre), warm (tem-
peratures of ~5000 K) atomic hydrogen. This
gas is disrupted by a variety of forces and inter-
stellar processes.
The first process we discuss disrupts the gas
on scales of tens to thousands of light-years.

Figure 3: Cartoon diagram of the evolution of gas in the interstellar medium. This
diagram shows how gas moves through its various stages, such as diffuse interstellar
medium to molecular clouds and on to stars and what processes effect how the gas
makes these transitions. Blue arrows represent processes where gas must cool and red
arrows represent processes that can heat the gas.
J Dawson (Naygoya University/CSIRO)

A Walk Around the Neighbourhood | 49

This takes the form of energetic outflows as-
sociated with massive stars. Massive stars are
usually classified as stars more than about
eight times the mass of the Sun. Massive stars
have a particularly powerful effect on diffuse
gas both through their stellar winds and also
the supernova explosions that mark the end of
their lives. All stars blow a wind of protons and
electrons off their surface, pushed outwards by
the enormous pressure of radiation from the
star. For stars like the Sun this wind is reason-
ably benign, and the Earth’s magnetic field
is enough to mostly shield the surface of the
Earth from its effects. Massive stars, though,
are quite a lot more powerful! These stars have
stellar winds that move one-millionth the mass
of the Sun per year outwards at velocities of
Figure 4: Stellar wind bubble blown
around the massive star complex RCW
79 as imaged by the Spitzer Space
Telescope’s GLIMPSE project. The bright
red rim is made mostly of interstellar dust
that glows in the infrared. The object has
a diameter of about 70 light-years and was
probably formed over the course of about
1 million years.
NASA/JPL-Caltech/E Churchwell (University of
Wisconsin-Madison)
50 | Genes to Galaxies
up to 1000 km/s. Massive stars live relatively
short lives, only lasting 100 million to 1 mil-
lion years depending on their mass, but over
the course of their lives they will blow out 1038
Mega-Joules (MJ), or 1037 kWh, of energy. To
put that in perspective, an atomic bomb blast
carries 108 - 1011 MJ of energy and the average
Australian household consumes about 85 MJ
each year. The extraordinary energy output of
stellar winds has a huge impact on the diffuse
interstellar gas, by heating, ionising and dis-
placing it. Stellar winds around a small number
of stars effectively blow bubbles into the
interstellar gas, creating so-called “stellar wind
bubbles”. Figure 4 shows a stellar wind bubble
around the star complex, RCW 79, which is
about 70 light-years in diameter and filled with
hot gas from the stars that blew the bubble.
The bright rim of the bubble is made mostly of
dust that glows in the infrared after being ex-
cited by the ultraviolet radiation coming off the
stars in the centre (Churchwell et al 2006).
After a lifetime of blowing powerful stellar
winds, massive stars end their lives in spec-
tacular supernova explosions. These explo-
sions take only a matter of minutes but during
that time the star expels the majority of its
mass, leaving behind a neutron packed core
or sometimes a black hole. The expelled mat-
ter flies outwards from the star at velocities
up to 10,000 km/s carrying another 1038 MJ
of energy into the diffuse interstellar gas. The
gas immediately surrounding the supernova
is heated to millions of degrees and ionised
before it starts moving outwards like a gigantic
snowplow sweeping up all of the gas in front of
it in a wall of rapidly moving and condensing
gas. These supernova driven snowplows can
push for ten thousand years or more. Because
massive stars tend to live in groups together
the interstellar medium can feel the effects of
several hundred massive stars whose stellar
winds and supernovae have evacuated regions
up to a thousand light-years across, called
superbubbles or supershells. An example of a
gigantic supershell is shown in Figure 5. This
image shows diffuse atomic hydrogen gas in
the interstellar medium where the dark region
in the centre is the largely evacuated supershell
spanning almost 2000 light-years (McClure-
Griffiths et al 2003).

Through the actions of stellar winds and
supernova explosions massive stars are good
recyclers. Most of their mass is expelled back
into the interstellar medium where it can be
recycled into new stars. Nothing in space is a
perfect recycler, though. A small fraction of the
mass of the stars remains irretrievably locked
up in the form of neutron stars and black holes.
This locked-up mass has important implica-
tions for the lifecycle of the Galaxy so we’ll
come back to it later.
Condensing Interstellar Gas
In order to complete the recycling of expelled
interstellar matter into stars the ordinary dif-
fuse matter needs to become dense molecular
clouds. We know that stars are formed in mo-
lecular clouds. So in order for stars to form it is
critical that the diffuse matter that fills most of
interstellar space must first condense to form
molecules and large molecular cloud com-
plexes. On the largest scales, gas is condensed
by the spiral pattern of the Galaxy that moves
Figure 5: Gigantic supershell GSH
277+00+36 imaged shown in diffuse
atomic hydrogen emission. The bright
areas are where gas has been swept up by
hundreds of stellar winds and supernovae
leaving a largely evacuated cavity (dark
black) in the centre. The cavity has a
diameter of nearly 2000 light-years.
N McClure-Griffiths, CSIRO/ATNF
like a wave through the disk. In the same way
that waves move through the ocean, very large
waves move in a spiral pattern through the disk
of the Galaxy. These waves are responsible for
the pinwheel or spiral pattern that we infer for
the Milky Way and see in many other galaxies.
At the crests of the spiral waves the ordinar-
ily diffuse gas is compressed to form the giant
molecular cloud complexes and eventually the
very bright, massive stars that are characteristic
of spiral arms in galaxies. These spiral waves
operate on the scale of the Galaxy – that is
many thousands of light-years.
Bubbles and superbubbles like those described
above are also important in sweeping together
enough gas to form molecular clouds. The
powerful snowplow action of an expanding
superbubble can increase the density of the
interstellar gas from the one particle per cubic
centimetre to at least several thousand particles
per cubic centimetre and that may be enough
for gravity to take over and pull together even
more matter to make a dense molecular cloud.
Recent observations suggest that this process is
indeed happening in both of the objects shown
in Figures 4 & 5. New stars have already
formed out of the molecular material swept up
along the edges of the bubble shown in Figure
4 (Churchwell et al 2005) and along the walls
of the object in Figure 5 there are small molec-
ular clouds. We assume that it is only a matter
of time before these form stars.
Gas moving into and out of the Galaxy
Another key part of the Milky Way lifecycle
is how gas moves into and out of the Galaxy.
The Milky Way is not a closed box – there is a
constant outflow of material and this is more
than compensated for by a constant influx.
The question of how gas escapes the disk of
A Walk Around the Neighbourhood | 51
the Galaxy has been a long-standing topic of
research. Basic calculations show that given
how much gas lies in the Galactic halo above
the disk, if there weren’t significant outflow to
push up against the halo it would collapse onto
the disk under its own weight. And yet, there is
no evidence that the halo in the Milky Way – or
in any other galaxy – is collapsing. So what is
holding the halo up? One source of outflow for
the Milky Way is the very superbubbles that we
discussed above. Superbubbles around many
massive stars can grow very large indeed. In
fact they can grow so large that their diameters
exceed the thickness of the Galaxy. Once a
supershell becomes ~2000 light-years across it
finds itself expanding into a much less dense
medium and its expansion effectively runs
away. The situation is very similar to an atomic
bomb explosion; as long as the explosion is
expanding outwards close to the surface of the Figure 6: A mushroom-shaped cloud
Earth the explosion pathway is roughly spheri- of hydrogen poking ~1000 lighyears out
cal. However, as the explosion continues to of our galaxy may have been formed by
expand upward in the Earth’s atmosphere it en- exploding stars.
counters less and less material to push against Jayanne English et al/U Manitoba/CGPS
and is able to push faster in that direction. This
leads to the ‘mushroom clouds’ that we associ-
ate with atomic blasts. An expanding super- source of heating and distributes gas enriched
bubble extending into the Galaxy’s atmosphere by supernovae around the Galaxy. Calculations
displays the same sort of behaviour, sometimes show that we need dozens of chimneys to
forming a ‘mushroom cloud’ or at the very least support the Milky Way halo. In recent years
breaking open with channels leading away there have been a number of searches for these
from the Galactic disk to the halo. chimney-like objects but the number of known
chimneys can still be counted on one hand. So
Examples of both types of objects are visible in either another process must help provide sup-
the Milky Way. Figure 6 shows a classic mush- port for the halo or our observations are miss-
room cloud object of atomic hydrogen gas from ing many chimneys.
the Northern Milky Way, which may have been
formed through stellar winds and supernovae You might worry that if gas is flowing out of
in the disk (English et al. 2. The object shown the disk of the Galaxy like air out of a leaking
in Figure 5 and discussed above is the other tyre that the Milky Way would eventually run
type of large superbubble where the ‘mush- out of gas. In fact, the situation is even worse
room cap’ is not visible but the object definitely than that. Not only is gas leaking out of the
breaks into multiple (one at the top and two disk but also matter is continually locked into
below) dark channels that lead up to the halo a non-gaseous state in the neutron stars, black
of the Galaxy. This latter type of object is often holes and white dwarfs that mark the end of
called a “chimney” because the hot gas filling stars’ lives. So, if gas is leaking out of the disk
the interior of the superbubble can vent out the and more gas is locked away in an irretrievable
chimneys created by the breaking superbub- state how does the Milky Way continue to have
ble. This flow of hot gas is absolutely essential gas enough to form stars? The answer to that
for supporting the halo against collapse under question is something that drives a great deal of
its own weight. The vented gas also supplies a modern Milky Way research. We can perform

52 | Genes to Galaxies
some very simple calculations that show that
the rate at which new stars are formed in the
Milky Way should have exhausted all of the
interstellar gas and star formation should have
ceased long ago. And yet, we know that this is
not true as we observe gas in the present-day
Galaxy and continuing star formation. This
gas supply problem is not solved but there are
some indications that there is a slow trickle of
gas from extragalactic space and the Galactic
halo itself that makes it way on to the disk to
feed our gas hungry Galaxy.
The gas flowing into the Galaxy takes several
forms. One form are so-called “high velocity
clouds”, which litter the Galaxy’s halo and get
their name because they are moving quickly
with respect to the Galaxy. These clouds of cool
hydrogen were discovered in the 1960’s and it
was immediately realised that they might be a
potential source of gas influx. Despite that, it
has taken many years to find clear examples
of high velocity clouds interacting with the
Milky Way. One of the nicest recent examples is
shown in Figure 7, which is of a large cloud of
cold hydrogen called Smith’s Cloud that is on
a collision course with the Milky Way. Smith’s
Cloud is 11,000 light-years long and 2,500
light-years wide. At present it is only 8,000
light-years from the Milky Way disk and mov-
ing towards the disk at more than 240 km/s,
aimed to strike the Milky Way’s disk at an
angle of about 45 degrees. The cloud contains
enough hydrogen to make a million stars like
the Sun; so it is clear that objects like these
have a role to play in keeping the Galaxy well
fed (Lockman et al. 2008).
You may be wondering where hydrogen
clouds like Smith’s Cloud come from. For
clouds as massive as this there are two main
hypotheses: first, that they are left over from
the formation of the Milky Way and second,
that they have been pulled off nearby galaxies
that interact with the Milky Way (see Wakker
& van Woerden 1997). The first hypothesis
works with the idea that the Milky Way came
together from many smaller building blocks,
put together something like Lego. The building
blocks are gravitationally attracted to a central
mass and as they fall in they start spinning,
which gives our Galaxy its rotation. Invariably
Figure 7:
Hydrogen gas in
the high velocity
cloud, Smith’s
Cloud. The
comet-like shape
indicates the
cloud’s direction
of motion, which is
inclined at about
45 degrees to the
disk of the Milky
Way. The cloud is
travelling at more
than 240 km/s and
will collide with the
Galaxy in about 40
million years.
Courtesy: Bill Saxton/
NRAO/AUI/NSF
A Walk Around the Neighbourhood | 53

not all of the building blocks come together at
once and some are left to trickle into the Milky
Way over time. Some high velocity clouds are
almost certainly of this origin.
The second origin for high velocity clouds is
that large chunks of gas are stripped off other
galaxies as they pass near the Milky Way. This
is also known to occur. One excellent example
is the Magellanic Stream, shown in Figure 8
on an image of the Southern sky in hydrogen
gas. The Magellanic Stream is the long verti-
cal stripe of gas running from blue through to
orange down the centre of the image. This gas
is stripped off the Large and Small Magellanic
Clouds, which are small galaxies neighbouring
(about 150,000 light-years away) the Milky
Way. Each galaxy has a mass of 1/10 (or less)
the mass of the Milky Way so as they pass near
the Milky Way our Galaxy steals material from
them, which streams behind their direction of
motion like the tail of a comet. This stripped
material slowly makes its way onto the disk of
the Galaxy to feed its star formation habit.
Another form of gas influx is from matter con-
densed directly from the halo. As we discussed
above, chimneys can expel hot gas from the
disk up into the Galaxy’s halo. Most of this gas
doesn’t escape the Galaxy’s gravitational field so
it remains in the halo floating around for mil-
lions of years. Over time the gas may cool and
54 | Genes to Galaxies
Figure 8: Atomic hydrogen gas in the
Southern sky showing the Magellanic
Stream as the almost vertical band in
blue through orange at the centre of
the image. The Magellanic Stream trails
behind the Large and Small Magellanic
Clouds presumably pulled off these
low mass neighbouring galaxies by
the intense gravitational force of the
Milky Way.
N McClure-Griffiths, CSIRO/ATNF
as it does, gradually condense much like rain-
drops, before it falls back onto the Galactic disk
(Shapiro & Field 1976). The direct evidence
for this activity is very difficult to come by, but
nonetheless we assume that it must be happen-
ing at least to some degree in the Milky Way.
All of these methods: gas leftover from the for-
mation of the Milky Way, gas stripped off near-
by galaxies, and cooling halo gas can provide
some gas influx for the Milky Way. However, if
we add up all of the cool gas we observe in the
halo of the Milky Way we find that there still is
not enough to fully feed the star formation of
the Milky Way over its history (Putman 2006).
Clearly either the influx rate was much higher
in the past, which is unlikely, or we are miss-
ing some gas. Current research is underway to
discover the “missing” gas.
What are the big remaining
mysteries and prospects
for future discovery?
The structure and nature of the Milky Way
are far from completely understood. There are
a number of big mysteries that remain about
the Galaxy’s structure and how it operates. For
example, we still don’t have a very good idea
about how many spiral arms there in the Milky
Way and exactly where they are. The map
presented in Figure 2 is our current best guess, References:
but most Milky Way researchers would argue
that a lot of work needs to be done to con- Benjamin et al. First GLIMPSE Results on
vince ourselves that this is a valid guess. Even the Stellar Structure of the Galaxy. The
relatively simple things like the distance to Astrophysical Journal (2005) vol. 630 pp. L149
the centre of the Galaxy are still being refined Churchwell et al. The Bubbling Galactic Disk.
with recent changes of up to 10%. More dif- The Astrophysical Journal (2006) vol. 649 pp.
ficult questions like, where exactly is the edge 759
of the Milky Way disk are very much up in
English et al. The Galactic Worm GW 123.4-
the air. On the topic of the nature of the Milky
1.5: A Mushroom-shaped H I Cloud. The
Way there are many things that we still don’t
Astrophysical Journal Letters (2000) vol. 533
understand. Some of these we have identified
pp. L25-L28
here, such as: how do molecular clouds form
from diffuse atomic gas? Where are all of the Ghez et al. Measuring Distance and Properties
chimneys that are needed to hold up the halo? of the Milky Way’s Central Supermassive Black
Where is the missing mass of the Galactic halo Hole with Stellar Orbits. The Astrophysical
that is needed to continue to fuel star forma- Journal (2008) vol. 689, pp.1044-1062
tion in the Milky Way? And lying at the heart
Lockman et al. The Smith Cloud: A High-
of many questions about the life of the Milky
Velocity Cloud Colliding with the Milky Way.
Way is the role of magnetic fields, which we
The Astrophysical Journal (2008) vol. 679 pp.
have not discussed at all here. The Milky Way
L21
is threaded with a magnetic field, much like the
Earth is threaded with a magnetic field. We be- McClure-Griffiths et al. A Distant Extended
lieve that the magnetic fields of the Milky Way Spiral Arm in the Fourth Quadrant of the
control how gas moves around, how molecular Milky Way. The Astrophysical Journal Letters
clouds form, even how stars form, but we (2004) vol. 607 pp. L127
know very little about this elusive component.
McClure-Griffiths et al. Loops, Drips, and Walls
The future is bright for a better understanding in the Galactic Chimney GSH 277+00+36. The
of the Milky Way. The next fifteen years will see Astrophysical Journal (2003) vol. 594 pp. 833
a variety of new telescopes, each one very well
Putman. Potential Condensed Fuel for the
suited to answering some of the big questions
Milky Way. The Astrophysical Journal (2006)
about the Milky Way. In just a few years time
vol. 645 pp. 1164-1168
we will see the Atacama Large Millimetre Array
start operating in Chile, adding answers to the Shapiro et al. Consequences of a New Hot
key questions of how molecular clouds form Component of the Interstellar Medium.
and how stars from these clouds. In Australia Astrophysical Journal (1976) vol. 205 pp. 762
we hope to host Square Kilometre Array by Wakker et al. High-Velocity Clouds. Annual
2020, which will be able to get at those elusive Review of Astronomy and Astrophysics (1997)
magnetic fields amongst many other things. vol. 35 pp. 217-266
Space based telescopes will measure distances
to tens of thousands of stars giving us a much
better idea of the Milky Way spiral structure.
And finally Extremely Large optical telescopes
will be built in the next decade with the hope
of being able to explore in other galaxies the
processes that we can see in the Milky Way.
The next fifteen years will hopefully bring
about a revolution in our understanding of the
Milky Way!

A Walk Around the Neighbourhood | 55

Gene Silencing I

A virus
defence
pathway
and a
technology
Peter Waterhouse
T he development and use of vac-
cines against viruses such as
polio, smallpox, and measles
have to be among the great ac-
complishments of medical science. The history
of how it all started from Edward Jenner’s dis-
covery (that milkmaids and dairymen infected
with the mild cowpox virus were protected
against smallpox) is widely known. However, it
is not so generally appreciated that plants can
also be protected from a severe virus by prior
infection with a mild strain of a closely related
virus. This “cross protection” in plants was
recognized as early as the 1920s, but plants do
not possess an antibody-based immune system,
so the mechanism underlying this defence
remained a mystery for many decades. A few
years prior to the turn of the millennium, our
understanding began to dawn and after a flurry
of research the existence of an unsuspected,
but immensely powerful, mechanism, in both
plants and animals, has been revealed. This
mechanism can be triggered and directed to not
only provide protection against viruses but also
to silence any gene, and has led to a technology
called RNA interference (RNAi) which is being
used for applications ranging from improved
agricultural traits to fighting cancer.
In this first of my two chapters, I will describe
how the gene silencing pathway was discov-
ered, and how it works, and then give some
examples of how it has been exploited. In
the second chapter, I will describe how this
mechanism turned out to be a sophisticated
multidimensional pathway which not only
protects cells against viruses but also tightly
controls the regulation of genes required for
normal development in almost all forms of
multi-cellular life.
Genes and Transgenes
Genes are encoded in the nucleotide sequences
of double stranded (ds) DNA molecules, which
are folded up to form chromosomes in the nu-
cleus of eukaryotic cells. Each gene is made up
of three adjacent sections: the “promoter”, the
“coding region”, and the “ terminator”, (Figure
1). The promoter sequence defines where an
enzyme (called a polymerase) binds to the DNA
and starts to copy the sequence of one strand of
the DNA into molecules of single stranded (ss)
RNA. This copying proceeds across the coding
region and stops when it reaches the termina-
tor sequence. The RNA production is in the
nucleus but once made, each RNA molecule
(called messenger RNA) is transported to the
main compartment of the cell (the cytoplasm)
where it is used as the template for another
enzyme complex (the ribosome) to decipher
Figure 1: Layout of a gene and the central dogma
58 | Genes to Galaxies
the sequence for the production of a protein of
the inferred amino-acid sequence. This DNA to
RNA to Protein is called the central dogma. As
I hope will become clear, it is also important to
note that the DNA is in a double stranded form
(with the two strands binding together like a
zipped-up zip), but the messenger RNA is sin-
gle stranded (like one side of an unzipped zip).
And the zipping rule of dsDNA is very simple,
for two strands to bind together they must have
“complementary” sequences. Each nucleotide
can be one of four types called (in abbreviated
form) A, C, G or T, and A will only bind to T
and C will only bind to G. So, for example,
if a short strand of DNA has the nucleotide
sequence =>ACGTAT it will only zip up nicely
with a strand having the sequence TGCATA<=
(the arrows are to show that strands have polar-
ity and when two strands zip up they actually
point in opposite directions).
The other take-home message I want to convey
is that our understanding of how a gene is
composed of three sections allows us to make
transgenes. As you will see in the next section,
we make a transgene that is inserted into a
plant so that it makes the coat protein of a virus
but not the whole virus. We do this simply by
taking a dsDNA copy of a plant gene, replacing
the coding region of the plant gene with the
coding region of the virus coat protein gene,
and then inserting this [plant promoter- virus
coat protein coding region – plant terminator]
piece of dsDNA into a chromosome of a plant
(Figure 2).
 Making a Plant Transgene
Promoter
Plant gene
Virus gene coding region*
Plant transgene
*The gene has been converted to dsDNA from the ssRNA version in the virus.
Figure 2: Making a plant transgene
Virus Protection.
Viruses can cause serious losses to almost all
of our food crops and plant breeders have
spent considerable effort to find and incorpo-
rate natural virus-resistance genes into them.
Nevertheless, for many virus/crop combina-
tions there are no known natural resistance
genes or there are single resistance genes which
are under threat of being overcome by evolving
virus strains. However, in the early 1980’s re-
searchers started determining the nucleotide se-
quences of plant viruses and this led the way to
the production of pathogen-derived resistance
genes. Most plant viruses have genomes made
of single stranded RNA which encode at least
Plant Viruses
Fig 3
Healthy and
Virus-Infected
Potato
Figure 3: Plant viruses
Gene Silencing I: A virus defence pathway and a technology | 59
Coding Region Terminator
+
three genes: a replicase gene – to replicate the
genomic RNA, a movement protein gene – to
help the virus genome spread from cell to cell,
and a coat protein gene to wrap up the genome
into a protective particle for movement, often
by an insect vector, from plant to plant. (Figure
3). In 1986, a team of pioneering virologists
showed that when a transgene made from
the coat protein gene of tobacco mosaic virus
(TMV) was inserted into the chromosomes
of a plant, the “transformed” plant became
TMV resistant. This stimulated plant virolo-
gists, including my group at CSIRO, to make
transgenes from many different viruses and put
them into lots of different crop plants – and
Aphids
- vectors of
plant viruses
Virus particles
Basic Virus Genome
with some success. The curious thing was that,
with the exception of TMV, only a small pro-
portion of plants containing these transgenes
had virus resistance and the ones that produced
the highest levels of transgene protein tended
to be the ones that had no protection. Also,
completely counter to expectation, the plants
in which the transgene seemed to be producing
little or no protein were the ones with the virus
resistance. So what was going on?
It is not the protein that does it!
When a transgene was made by placing the
coding region for the virus gene in a back-to-
front orientation between the promoter and the
terminator and then transformed into plants,
surprisingly, some of them were resistant to the
virus. This transgene could not be producing
the virus protein. It would be like trying to
read a sentence of English from right to left -
we call this an antisense gene. This showed us
that it was not the protein, itself, but something
else about the transgene that was conferring the
resistance. When we looked at the plants that
showed resistance and those that didn’t, the
striking feature was that those with resistance
had multiple adjacent copies of the transgene
(and there were always two adjacent copies in
opposite orientations); those with no protection
had only one or a few copies (Figure 4A). One
possible explanation was that the terminators
were not working with 100% efficiency in
Figure 4: Integration of virus transgene
60 | Genes to Galaxies
these adjacent and opposite transgene copies,
so the promoter of one sometimes directed the
synthesis of RNA molecules that continued into
the coding region of the adjacent gene, and
vice versa. In this situation the plant would
be making two opposite strands of RNA that
could bind together in a similar way to dsDNA.
(Figure 4B).
The double stranded
RNA experiment
From our earlier experiments, we had plants
with a single copy of a virus transgene (let’s call
this a sense transgene) and plants with a single
copy of the antisense version of the transgene.
None of these plants showed any resistance to
the virus. We postulated that if the formation
of virus-derived dsRNA from the transgenes
was the key to generating virus resistance we
could test this by a simple crossing experiment.
We took pollen from a “sense” transgene plant
and crossed it onto emasculated flowers of an
“antisense” transgene plant, collected the seed
that was set, germinated them, then inoculated
the seedlings with the virus - and got a beauti-
ful result. One quarter of the plants showed
resistance to the virus and three quarters were
susceptible. And when we analysed the ge-
netic make-up of the plants, the quarter with
resistance had inherited both the sense and
antisense transgenes, whereas the susceptible
plants had inherited either the sense transgene,
or the antisense transgene, or neither (Figure
5). This convinced us that dsRNA was the trig-
ger that was somehow protecting the plants
against the virus.

How does it work? part 1

As mentioned in the first section of this
chapter, a healthy cell contains lots of dsDNA
and ssRNA, but it does not contain dsRNA.
The only time a cell contains dsRNA is when
it is infected with a replicating RNA virus.
Therefore, the model we proposed was that a
virus defence pathway already exists in plants
and is triggered by dsRNA; it operates by using
the sequence of the dsRNA to direct enzymes
to destroy ssRNA molecules of the same or
complimentary sequence (Figure 6). So, what
we had been doing by using transgenes to ex-
press a piece of the virus genome as dsRNA was
to forewarn the cell of the virus’s sequence so
that it was primed and ready to destroy it even
before infection. This has obvious parallels with
the vaccination strategy we use to protect our-
selves from viruses such as polio and measles.
Figure 6: The intrinsic virus defence
mechanism in plants
Can we use this pathway
to silence genes?
There are lots of interesting and useful things
that can be done if one can silence specific
genes in a plant or animal, as we will see later.
Therefore, we wondered if we could use this
viral defence to specifically silence some of a
plant’s own genes. On the basis of our dsRNA
induction model, all we need to do to silence a
specific gene is make the cell perceive that the
messenger RNA of that gene is from a virus,
and we can do this by expressing transgenic

Figure 5: Sense x antisense experiment

Gene Silencing I: A virus defence pathway and a technology | 61

dsRNA containing the same sequence as the
target messenger RNA. The defence mechanism
will then be directed to destroy the messenger
RNA before it can be deciphered into the pro-
tein it encodes.
Hairpin RNAs
Making a plant with both a sense and an anti-
sense transgene, either by the crossing strategy
already described or by transforming a plant
simultaneously with two transgenes, is hard
work. Also, when two complementary RNA
molecules are made from two different genes
the two molecules have to find each other in
the cell before they can zip up to form dsRNA.
We thought of a solution: make a transgene
that makes an RNA which looks like a hair-
pin. This is a single strand of RNA, coded for
by one transgene, but the last section of the
molecule is complementary to the first sec-
tion so it folds back and zips up into a hairpin
shape (Figure 7). One of our first tests, in
whole plants, was to try to silence the chalcone
synthase gene in our favourite model plant -
Arabidopsis. This plant produces dark brown
seeds and the enzyme that makes this brown
pigment is chalcone synthase. So, we took a
section of the coding region of the chalcone
synthase gene, made it into a hairpin (hp) RNA
transgene and transformed Arabidopsis with it.
Figure 7: One of the first hpRNA
transgenes silencing a plant gene
62 | Genes to Galaxies
This gave us an unequivocal result, the plants
produced bright yellow seed (Figure 7). When
we got this result, we knew we were really on
to something. Technology with widespread ap-
plications – and this technology of introducing
a dsRNA or hpRNA into plant or animal cells
for the silencing of genes has become known as
RNA interference or RNAi.
How does it work? part 2
While we were finding out that dsRNA can
direct silencing in plants, Andy Fire and Craig
Mello, in the United States, were making simi-
lar discoveries in nematodes. In fact, they were
to win the Nobel Prize in 2007 for their discov-
ery. And it turns out that this pathway exists in
almost all eukaryotic multicellular organisms
ranging from mosses to mammals. By looking
at how the gene silencing pathway could be
disrupted by different mutants in plants, insects
and nematodes has led to a deep understanding
of the enzymes and processes involved, with
perhaps the best understanding coming from
work using Drosophila (the fruit fly).
All of these eukaryotes share two key proteins
(Dicer and Argonaute - some call this latter
one, Slicer) which, with a number of acces-
sory proteins, make the silencing process work
(Figure 8). Dicer recognises dsRNA and cuts it
up into fragments, about 21 nucleotides long,
and transfers each fragment to an Argonaute
molecule. The Argonaute protein cuts and
discards one of the strands but retains the other
to use as a guide. Using the retained strand, the
Argonaute examines all of the ssRNA molecules
in the cell and if an RNA is found that has a
Target RNA
Figure 8: The RNA interference
mechanism
stretch of 21 nucleotides that is exactly comple-
mentary to the guide sequence, the Argonaute
acts like a pair of scissors and cuts the “target”
RNA in the middle of the recognised sequence.
Because the dsRNA being introduced into the
cell is usually several hundred nucleotides
long, it is Diced up into many different 21nt
fragments, and each one is loaded into a dif-
ferent Argonaute molecule. This means that a
single target ssRNA molecule may be cleaved in
several different places by the loaded Argonaute
population. Chopping the target RNA into
pieces prevents it from being translated into
protein, thus silencing the gene.
A few examples
RNAi has been used or has shown potential for
many purposes including human therapeutics
(Table 1) and functional genomics. The entire
nucleotide sequences of the genomes of a
number of species (including human, fruit fly,
nematode, and Arabidopsis) have been deter-
mined. From these sequences we can predict
the coding regions of all of the genes within
each genome. However for a significant propor-
tion of these genes, we have little or no idea
about their functions. So, large scale projects
are currently underway using RNAi to silence
each of these genes, one by one, in nematodes
and in Arabidopsis so that the changes in form
or behaviour that result from silencing the
genes can give clues about their roles.
Table 1
Fig 9
Therapeutic potential of RNAi
in Humans
Neurological
Obesity
disorder
Various forms of High blood
Cancer Cholesterol
Spinal muscular
Depression
atrophy
Growth hormone
HIV
deficiency
Diabetes Hepatitis B
Malaria Hepatitis C
Gene Silencing I: A virus defence pathway and a technology | 63
There have been some amazing applications of
RNAi in plants, such as coffee plants that pro-
duce decaffeinated beans and opium poppies
that produce desirable pharmaceutical com-
pounds, and I would like to finish this chapter
with three further examples that hopefully give
an idea of how useful and versatile the technol-
ogy can be.
One of the important aspects of crop produc-
tion is flowering time. For instance, if a cereal
crop flowers too early, it may have not yet
made sufficient energy stores to fuel its maxi-
mum grain production. Similarly, if it flowers
too late in the season there may be insufficient
time to produce a good yield. So, being able to
control flowering time in plants could be a very
useful tool in horticulture and agriculture. In
Arabidopsis, there is a gene called FLC which
represses flowering and we have used RNAi to
switch it off and bring on flowering (Figure 9).
This clearly shows that the technology has the
potential to regulate flowering time in crops.
An application of RNAi in plants that is much
closer to agricultural use is the silencing of
genes involved with seed-oil production. Some
seed-oils are much better for human health
than others, and some oils are more stable at
high temperatures than others. It all depends
on the fatty acid composition of the oil. For
example palm oil is very high in palmitic acid
which makes it stable at high temperatures but
also unhealthy for human consumption, as it
raises LDL cholesterol levels. Olive oil, on the
Custom-made changes using RNAi
Fig 9
Custom-made changes using RNAi
Virus Immunity
Virus Immunity
Flowering Time
Flowering Time
Pharmaceuticals
Pharmaceuticals
Bluerose
Blue rose Healthy
Healthy
Oils
Oils
Healthy
HealthyOils
Oils
Figure 9: Custom-made changes using
RNAi
other hand, is high in linoleic acid which is and antisense RNA.Proc Natl Acad Sci U S A.
much healthier for human consumption, but it 1998; 95: 13959-64.
is not stable at high temperatures and therefore
Zamore PD, Tuschl T, Sharp PA, Bartel
not good for frying. Almost everyone knows
DP.RNAi: double-stranded RNA directs the
about growing cotton plants for their fibre, but
ATP-dependent cleavage of mRNA at 21 to 23
it is less well known that the seeds contain high
nucleotide intervals.Cell. 2000; 101: 25-33.
levels of oil. Unfortunately, the oil composition
is similar to palm oil. The best oil for heat sta- Wesley SV, Helliwell CA, Smith NA, Wang MB,
bility and with no negative effects on cholester- Rouse DT, Liu Q, Gooding PS, Singh SP, Abbott
ol levels is one which is high in oleic acid. We D, Stoutjesdijk PA, Robinson SP, Gleave AP,
have used RNAi to silence the gene in cotton Green AG, Waterhouse PM. Construct design
which codes for the enzyme that converts oleic for efficient, effective and high-throughput
acid into a different fatty acid. This has altered gene silencing in plants. Plant J. 2001, 27: 581-
the seed-oil from being around 10% to an 90.
impressive 75% oleic acid. If these plants were
Liu Q, Singh SP, Green AG. High-stearic and
used in agriculture it would produce two crops,
High-oleic cottonseed oils produced by hairpin
fibre and seed-oil, for the price of one. The last
RNA-mediated post-transcriptional gene silenc-
example is very close to being a commercial
ing.Plant Physiol. 2002; 129: 1732-43.
reality. It will not feed our stomachs but it may
soothe our souls. A biotech company with its Allen RS, Millgate AG, Chitty JA, Thisleton
origins in Melbourne has produced a blue rose J, Miller JA, Fist AJ, Gerlach WL, Larkin PJ.
– a colour that has not been achieved during RNAi-mediated replacement of morphine with
centuries of rose breeding. The first step was to the nonnarcotic alkaloid reticuline in opium
introduce a transgene into roses that produced poppy. Nature Biotechnol. 2004; 22: 1559-66
the blue pigment from a different plant species. Katsumoto Y, Fukuchi-Mizutani M, Fukui Y,
Unfortunately, the rose kept on making a red Brugliera F, Holton TA, Karan M, Nakamura N,
pigment, resulting in a purple flower. However, Yonekura-Sakakibara K, Togami J, Pigeaire A,
by adding an RNAi transgene to silence the red Tao GQ, Nehra NS, Lu CY, Dyson BK, Tsuda
pigment gene, the world now has a beautiful S, Ashikari T, Kusumi T, Mason JG, Tanaka Y.
blue rose. Engineering of the rose flavonoid biosynthetic
pathway successfully generated blue-hued
Further Reading flowers accumulating delphinidin. Plant Cell
Abel PP, Nelson RS, De B, Hoffmann N, Rogers Physiol. 2007; 48: 1589-600.
SG, Fraley RT, Beachy RN.Delay of disease de-
velopment in transgenic plants that express the
tobacco mosaic virus coat protein gene.Science.
1986; 232:738-43.
Hamilton AJ, Baulcombe DC.A species of small
antisense RNA in posttranscriptional gene si-
lencing in plants.Science. 1999; 286: 950-2.
Fire A, Xu S, Montgomery MK, Kostas SA,
Driver SE, Mello CC.Potent and specific ge-
netic interference by double-stranded RNA
in Caenorhabditis elegans.Nature. 1998; 391:
806-11.
Waterhouse PM, Graham MW, Wang MB.Virus
resistance and gene silencing in plants can be
induced by simultaneous expression of sense

64 | Genes to Galaxies
Gene Silencing I: A virus defence pathway and a technology | 65
 Reproduced with kind permission HarperCollins Publishers Australia
(c) Karl S. Kruszelnicki Pty Ltd 2009
www.abc.net.au/science/k2

The
X-Chromosome
eXplained
Back in the Olden Days, before research into cloning and stem cells,
most people didn’t know much about genetics or DNA. However,
they had a vague impression that there was something called the ‘X-
chromosome’, so named because it looked like the letter ‘X’. Well,
this is not the case, but as an aside, the X-chromosome did help
give the world Communism.

Shape of DNA
Every cell in your body (except for the red blood cells) carries DNA.
(Red blood cells are so dedicated to their job of carrying oxygen
efficiently, that everything irrelevant has been stripped off including
the DNA. Red blood cells are not made by other red blood cells —
they are made by stem cells in the bone marrow in the long flat
bones of your body.)
The human DNA is a very skinny and very long molecule. The
DNA in each molecule is a few billionths of a metre wide, but if you
stretched it all out it would be a few metres long. It looks like a
ladder with two side rails and about three billion rungs joining the
side rails to each other.

74 Please EXPLAIN

66 | Genes to Galaxies
The X-Chromosome eXplained 75

The X-Chromosome eXplained | 67

 This ladder is twisted into a right-handed spiral as part of an
efficient way of folding something a few metres long into a space
smaller than one-millionth of a metre wide. The twisted ladder is
about 2.3 nm (nanometres or billionths of a metre) wide. The
scientific name for this molecular structure is a ‘double helix’.
The ‘rungs’ are 0.34 nm apart. There are four different types of
rungs, called A, T, C and G. The ladder is twisted and one complete
‘turn’ of the spiral is 3.4 nm, so 10 rungs will fit into one turn. The
scientific name for the rungs is ‘nucleotides’ or ‘base pairs’.

Genetic Code
One of the great scientific discoveries of the 20th
century was that the rungs were actually a ‘code’ to make
amino acids. The famous ‘Genetic Code’ is amazingly
simple and yet incredibly deep. If you put enough amino
acids together, you have a protein. If you put enough
proteins together, you have a living creature (OK, you
need a few other things as well).
Three rungs (nucleotides/base pairs) in a row have
enough information to tell the ‘machinery’ in the cell to
make an amino acid. Look at the first rung. There are four
possibilities: A, T, C or G (the four different types of
rung). There are the same four possibilities for the
second rung, and for the third rung. So the total number
of different combinations is 4 x 4 x 4 = 64 (running from
AAA to TCG to GGG).
However there are only about 20 common amino acids
in life on Earth. So there is some redundancy, i.e. several
combinations of A, T, C and G will give the same amino
acid. For example, the combinations CGC, CGA, CGG, AGA
and AGG will all tell the ‘machinery’ in the cell to make
the amino acid arginine. However, at the other extreme,
two of the amino acids have only a single combination
each, e.g. methionine and tryptophan.

76 Please EXPLAIN

68 | Genes to Galaxies
 Job of DNA
Our DNA is, among other things, an architect’s blueprint that will
make and then maintain a human being.
Most of the time, the DNA exists as a myriad of long slender
filaments, floating all tangled up in the nucleus of the cell but not at
all neatly condensed. This gives them a huge surface area, which
makes it easy for the ‘machinery’ in the cell to ‘read’ the DNA to
make proteins. These proteins could be insulin from your pancreas,
enzymes from the cells in your gut to dissolve your food or muscle
in your muscle cells to move your arms, legs and eyelids.

Chromosomes
Whenever a cell is about to split into two more cells, the DNA will
condense for a brief time into little clumps. A skinny strand of DNA
gets wound into a coil, and this coil gets wound again, and so on
— a process called ‘DNA supercoiling’. As part of this process,
proteins are wrapped by the coiling DNA and also wrap around the
DNA. These clumps that appear when a cell divides are the famous
chromosomes. They have a central point and four arms, making
them look a little like the letter ‘X’.
By the way, the number of chromosomes varies with the species
— just eight in the fruit fly, 46 in human beings and hares, 48 in
gorillas and chimpanzees, 104 in goldfish and a massive 380 in
butterflies.
Chromosomes were first seen in cells by the Swiss botanist Karl
Wilhelm von Nageli in 1842. Chromosomes are really hard to see,
but if you soak the cells with the right dyes you can then see these
coloured bodies — hence the name ‘chromo’ meaning ‘colour’ and
‘some’ meaning ‘body’.
The original technique to visualise chromosomes was to ‘poison’
the cell with a drug called colchicine, which locks the cell in at a
certain stage of division. The scientists then stained the cell with
dyes to make the chromosomes obvious, took a photograph (via a
microscope) of the chromosomes, developed the photograph, cut
out the chromosomes with scissors, arranged them in pairs and

The X-Chromosome eXplained 77

The X-Chromosome eXplained | 69

 stuck them down with sticky tape. Nowadays, it’s done with fancy,
digital computer magic.

Shapes of Chromosomes
Chromosomes come in two main shapes.
The so-called Linear Shape is the ‘classic’ X-shape.
But it doesn’t really look like an ‘X’. Instead of four
separate arms all coming from a single point, there are
usually two sets of parallel legs. Usually, there are two
shorter arms (called ‘p’ from the French word petit
meaning ‘small’) and two longer arms (called ‘q’, because
‘q’ is the next letter in the alphabet after ‘p’). Like the Y-
chromosome, this is another case of a name being
chosen because it’s the next letter in the alphabet.
The other chromosome shape is the circle. This is
often found in smaller creatures, such as bacteria.

Mystery of Chromosomes
It took a long time to learn about our chromosomes. In fact, until
1955, we thought that human beings had 48 chromosomes — the
real number is 46.
They were a huge mystery until very recently, the most
mysterious of them all being the 45th chromosome. Part of the
mystery surrounding this particular chromosome was its involvement
in diseases carried by females. Although these diseases, which
included haemophilia and red–green colour blindness, didn’t affect
females, they affected males — very strange.
For a long time, this mystery remained unsolved. In algebra, the
symbol ‘X’ stands for the unknown quantity, as in the X-Factor — and
this is how the X-chromosome was given its name. (If it was named
after its shape, then all the chromosomes would be called ‘X’.)

78 Please EXPLAIN

70 | Genes to Galaxies
 And the Y-chromosome? Well, it was pretty mysterious too. ‘Y’
is the next letter in the alphabet after ‘X’, which is how the
Y-chromosome got its name. It’s as simple as ABC.

Communism
So what’s the link with Communism? Admittedly, it is a little tenuous
but it is related to the X-chromosome.
It seems that Queen Victoria had a spontaneous mutation in her
X-chromosome that could cause the bleeding disease, haemophilia.
This led (via some very convoluted logic) to Communism.

The X-Chromosome eXplained 79

The X-Chromosome eXplained | 71

 Queen Victoria had nine children. Her third child, Alice, who
carried this mutation in her X-chromosome, married Louis IV, Grand
Duke of Hesse, in Germany and passed the haemophilia mutation
to her daughter, Alix. Alix, who took the name Alexandra when she
was baptised into the Russian Orthodox Church, married Nicholas
Romanov, who became Czar Nicholas II of Russia. She passed the
haemophilia mutation to her fifth child, and first son, Alexei. He
suffered from debilitating haemophilia from an early age, not very
favourable for someone destined to be the future Czar.

Unfortunate Czar Nicholas II

Czar Nicholas II had his fair share of worries — most of them
unrelated to his wife’s chromosomes.
He had not been properly trained to be the Czar of Russia. For
example, when approached by a respectful delegation of peasants
and workers who asked for some reasonable constitutional reforms
to improve their wretched lives, he made long-lasting enemies by
angrily rejecting them. If he had been diplomatically trained, he
could so easily have responded carefully, making the peasants his
lifelong allies.
On 28 June 1914, the Austrian Archduke Franz Ferdinand was
assassinated in Sarajevo by a member of a gang called the Serbian
Black Hand. In retaliation, Austria declared war on Serbia. Czar
Nicholas II, an ally of Serbia, mobilised his army against Austria.
Because Germany was an ally of Austria, he was now at war with
two countries. Helping start World War I doesn’t look so good on
your CV.
Incredibly, things got even worse. His army lost many battles,
four million Russians dying in the first year of battle alone. So he
took over command of the army and lost even more battles. The
difference now was that as Commander in Chief, he was personally
responsible.
General unrest led to an outbreak of revolution in the capital,
St Petersburg. But because Nicholas was away from the capital, he
was unable to control it. And it didn’t help that his wife Alexandra

80 Please EXPLAIN

72 | Genes to Galaxies
was a German — not a very popular nationality in Russia at the time
of World War I.
All this led to enormous unrest and, ultimately, to the Bolshevik
uprising.
Part of the Czar’s inability to attend properly to his duties of
office may have been his preoccupation with the terrible
haemophilia of their only son, Alexei. Therefore, he failed in his regal
duty to govern Russia properly. And that’s how the X-chromosome
played a mysterious part in giving the world Communism …

References
Angier, Natalie, ‘For motherly X chromosome, gender is only the beginning’,
The New York Times, 1 May 2007.
Steven, Richard F., ‘The History of haemophilia in the royal families of Europe’,
British Journal of Haematology, April 1999, pp 25–32.

The X-Chromosome eXplained 81

The X-Chromosome eXplained | 73

The frontiers
of current
biological
research
Michel Morange
What are the frontiers?
In this lecture, I will try to define the current
frontiers of knowledge in biology. There are dif-
ferent ways to have view of them. The frontiers
of knowledge can be conceived of as the place
where scientists are actively digging, the ques-
tions they are presently asking. If one compares
scientific progress to the displacement of a cell
like a macrophage, sliding on a substrate of
knowledge, extending its pseudopods towards
new unexplored territories, the frontier of
knowledge can be seen as this tiny territory be-
tween the most advanced pseudopods and the
terra incognita in front of them.
But the frontiers of knowledge can also be seen
as the limits of knowledge, as the obstacles that
have to be overcome, as the gaps that have to
be filled. If you ask biologists, they will give
you a list of unanswered questions, a series of
current descriptions that are considered insuffi-
cient. The limits of knowledge also dramatically
emerge when biological knowledge is used for
practical issues, as in fighting diseases. Progress
is being made in the fight against cancer, but
at too slow a pace. Neurodegenerative diseases
are increasingly well described, but no one
therapeutic strategy has yet proved compelling.
Here, the frontiers of knowledge coincide with
the limits of our action. The way to overcome
these limits is presently unknown.
As François Jacob said “Yet, while it is part of
our nature to produce a future, the system is
geared in such a way that our predictions have
to remain dubious. We cannot think of our-
selves without a following instant, but we can-
not know what this instant will be like. What
we can guess today will not be realized. Change
is bound to occur anyway, but the future will
be different from what we believe. This is espe-
cially true in science. The search for knowledge
is an endless process and one can never tell
how it is going to turn out. Unpredictability is
in the nature of the scientific enterprise. If what
is to be found is really new, then it is by defini-
tion unknown in advance. There is no way of
telling where a particular line of research will
lead” (Jacob 1982).
So, the frontiers of knowledge are different
from the future of biology, and it would be
unreasonable to hope to say what biology will
be tomorrow. All we can do is to give a picture
of present trends in research. Some trends cor-
respond to efforts made to overcome the limits
of knowledge, but others are simply the conse-
quence of the progress made in one technology,
in one new experimental approach.
I will organize this lecture in three parts. In the
first, I will show you that molecular descrip-
tions still have a strong explanatory power, and
that these descriptions will continue to have
an important place in the future of biologi-
cal research. In the second, I will argue that
they must be complemented, and extended.
The rather static descriptions given so far will
become more and more dynamic, and a global
picture will replace the present piecemeal de-
scriptions. Finally, a strong trend in biological
research, already clearly visible, is the progres-
sive encounter between two branches of bio-
logical research which hitherto have remained
far apart: functional biology, i.e., biochemistry,
molecular and cell biology, and physiology,
all disciplines in which scientists describe the
76 | Genes to Galaxies
mechanisms at work within organisms, and
evolutionary biology, in which researchers seek
to provide scenarios for the evolution of organ-
isms. This current trend fleshes out the hitherto
abstract scenarios of evolutionary biologists,
and provides explanations for the emergence
of complex macromolecular nanomachines.
I am convinced that the exchange of models
between the two branches of biology will con-
siderably enrich biological knowledge.
I Molecular descriptions conserve
their explanatory power
It is frequently said today that biology must
abandon the reductionist approach which had
been dominant during the era of molecular
biology, when the secret of life was looked
for in the characterization of isolated macro-
molecules. A global vision should replace the
previous reductionist one. Molecular biology
is dead, and the period when it dominated the
landscape of biological disciplines should be
seen as a sad period in the history of biology.
Such statements are at odds with the present
situation of biology (Morange 2008). The
“paradigm” of molecular biology consisted in
looking for the explanation of functions in the
structural descriptions of macromolecules.
The structure of DNA was emblematic of the
way structure explains the function of macro-
molecules. The structure of DNA immediately
showed how this molecule was able to bear
genetic information. It explained how it was
able to generate two identical copies of itself,
by separation of the two strands, and synthesis
of the complementary strand. It also showed,
as Jim Watson and Francis Crick immediately
understood, how the sequence of nucleotides
might be the code by which genes had their
effects within organisms. The same heuristic
value of the structural description is also clearly
visible in the case of proteins and enzymes.
The structures explain how the molecules are
able to fulfil their functions. For enzymes, the
description of the amino acids in the active site
explains how these enzymes are able to catalyze
specific chemical reactions. Other functions of
proteins, such as the capacity to be a receptor
for a signal or a channel for ions, can also been
explained by a precise structural description of
these proteins and of the way they behave as
nanomachines. We will consider one of many
possible examples. The potassium channel,
located in the cell membrane, is involved in
the production of the nerve influx, i.e., the
way nerve cells communicate with other nerve
cells, and activate target cells such as muscle
cells. It was demonstrated more than fifty
years ago that the nerve influx results from the
occurrence of transient transmembrane cur-
rents, due to the passage of ions across the cell
membrane. It was later shown that the passage
of ions was permitted by the existence of pro-
tein channels. The structure of these channels
has been characterized, and it has been fully
explained how the channels are able to fulfil
their three functions: to open transiently when
the transmembrane voltage is altered by the
propagation of the nerve influx, to close after a
short time, and to be specific for one particular
ion (Jiang et al. 2003). To provide this explana-
tion, the static structure revealed by X-ray dif-
fraction studies is used to provide a scenario of
the internal movements of the macromolecule,
how its different parts move one relative to the
other. This dynamic description explains how
these proteins are able to work as superb na-
nomachines to fulfil their functions.
The heuristic power of structural determina-
tion, its capacity to provide satisfactory expla-
nations of the behaviour of macromolecules,
is not decreasing: the opposite is true. The
huge progress made in these methods, the
development of new methods providing a more
dynamic description of the internal movements
of these nanomachines, and the possibility of
using the information gathered to design new
therapeutic agents make it highly improbable
that the role of structural information in the
explanations of biologists will diminish. The
description at higher levels of organization will
probably expand (see later), but these new lev-
els will not replace the molecular level. What
was learned from the description of macromol-
ecules will remain at the core of our knowledge
of organisms. The macromolecular level is not
one among many other levels: it is the level at
which information is encoded in the genome.
This gives it a preeminent role.
The frontiers of current biological research | 77
The founders of molecular biology, such as
Francis Crick and Jacques Monod, said that
they had discovered the secret of life. Clearly,
many questions remain unsolved in biology,
and much exciting work awaits future biolo-
gists! The development of an organ as complex
as the brain is clearly not understood. And the
way to fight many diseases is unknown. But
Crick and Monod were not wrong. Some fun-
damental principles explaining the characteris-
tics of present-day organisms have been under-
stood – the existence of genetic information, of
a genetic code. The advances in understanding
organisms have been so dramatic that it is now
reasonable to conceive of synthesizing a living,
totally artificial organism, as some synthetic
biologists now do.
II Molecular explanations must be
complemented, and extended
There are different ways to complement the
current molecular description of organisms.
The first is to follow the same path as during
the last decades. Recently, totally new phe-
nomena have been discovered. They do not
abolish the previous observations, but they add
a layer of complexity. Whereas the regulation of
gene expression was attributed to proteins, the
so-called transcription factors, microRNAs are
increasingly seen to play a part in gene regula-
tion. Similarly, regulation of gene expression
by the control of proteins surrounding DNA,
the histones and more generally the chroma-
tin, appears more and more important. These
epigenetic marks can be transmitted through
cell division, and in some cases as in plants,
through generations. They can be modified by
the environment, and they give organisms a
capacity to stably adapt to new environments
by modifications that do not alter genetic in-
formation. In addition, the numerous studies
done on the different molecular networks in
cells – gene regulatory and signalling networks
– unveil interactions and regulations never
seen before.
Even more significant are the technological
developments that complement the structural
determination, and make it more precise and
more dynamic. The first consists in studying
isolated macromolecules, by using tricks per-
mitting their micromanipulation. The result is
a better and more physical description of the
way they act as nanomachines. The second
consists in observing individual molecules di-
rectly in cells. This has been made possible by
the development of molecular tools – the use
of fluorescent proteins which can be coupled
with the molecules under study – and a paral-
lel dramatic progress in the sensitivity of the
physical devices allowing the detection of these
weak signals.
New phenomena have been discovered, or at
least revealed, by the use of these new tech-
nologies, and they raise important and still
unresolved questions. It was anticipated, due
to the low numbers of molecules in cells, and
the slow rate of some of the most important
reactions, such as the initiation of transcription,
that many processes in cells would not be regu-
lar, but vary in a random way. The existence of
these stochastic variations, called “noise”, was
rapidly demonstrated (Raser and O’Shea 2004).
For instance, transcription of the same gene
can differ from one cell to another, as well as
between the two copies of the same gene.
The discovery of this phenomenon, thanks to
the development of the new technologies that
I described previously, raises at least two im-
portant questions. The first concerns the way
organisms are able to cope with these stochastic
variations. Is the architecture of the molecular
networks specially designed to buffer these
stochastic variations? The latter can generate a
diversity of phenotypes unrelated to the diver-
sity of genotypes. Is this phenotypic plasticity
exploited by organisms to adapt to changing
environments? These questions have received
preliminary answers, but much remains
to be learnt about these newly discovered
phenomena.
There is a marked tendency in present biologi-
cal research to collect information on individu-
al molecules in order to predict the behaviour
of the complex systems of which these macro-
molecules are a part. Traditional descriptions
in molecular and cell biology were qualitative.
Components of the networks, and relations
between these components, were represented
78 | Genes to Galaxies
on a simple diagram, and the global behaviour
of the system was interpreted with the help
of this diagram. But the complexity of these
networks, with the existence of multiple posi-
tive and negative feedback loops, has become
such that interpretations become more and
more problematic, and the predictions incor-
rect. These limits were clearly revealed by the
knockout experiments initiated by biologists at
the beginning of the 1990s. One gene, whose
individual function was believed to be well
known, was selectively inactivated, and the ef-
fects on the organism of this inactivation were
highly different from those expected. Similarly,
in cancer, the networks involved in the control
of cell division have been fully described, but
this description remains insufficient to predict
– and sometimes even to explain – the effects
observed following the modifications of one or
other of the components of these networks that
occur during the formation of tumours.
Biologists are convinced that these limits will
be overcome by the use of formal, mathemati-
cal models reproducing the behaviour of these
complex networks. The task is gigantic, due
to the huge number of different components,
the heterogeneity of the medium in which
they work, and the still poor knowledge of
their in vivo concentrations. Whatever these
difficulties, models have an increasing place
in the work of biologists. They play roles that
they traditionally had in physics, but that are
new in biological research. They can help
biologists to construct new regulatory circuits
and functional modules. This is the case in
synthetic biology, when new functional devices
are introduced into recipient (bacterial) organ-
isms. Formal models can also help biologists
to check whether they have correctly described
a system, the macromolecular components in-
volved, and the relations between them. If the
behaviour of the system is stable, and correctly
reproduces the in vivo behaviour, the answer
will be positive. Otherwise, the results afforded
by the model will help biologists to look for
these missing components and relations. The
model can also be used to test a simple hypoth-
esis, to see whether it is consistent with current
knowledge. It can avoid useless (wet) experi-
ments and force experimenters to make their
hypotheses more precise. These changes in the
way of doing research, what is called episte-
mology, are probably more important than the
increase in knowledge or the development of
new technologies in the design of what will be
biology in the mid and late 21st century.
III The encounter
between functional and
evolutionary biology
In a famous article published in 1961, the great
evolutionist Ernst Mayr noticed that there were
two highly different categories of biologists:
those interested in the way cells and organisms
function, in the elucidation of the complex
mechanisms behind this perfect functioning,
and those more interested in the raison d’être
of these complex functions and the adapta-
tion they provide to organisms harbouring
them. The first category includes physiologists,
molecular and cell biologists, biochemists; the
second, evolutionists, but also ecologists and
zoologists. Geneticists are at the boundary
between the two groups: they can be molecular
geneticists or population geneticists. Ernst
Mayr underlined the differences between the
two approaches, and their complementarity
(Mayr 1961). But this complementarity was
one of principle, not of facts. Functional biolo-
gists worked as if the complex structures they
studied had no history, were not the product
of evolution; and evolutionary biologists paid
no attention to the mechanisms behind adapta-
tion, considering that organisms had multiple
possibilities to adapt, and that the description
of the mechanisms by which they specifically
adapted would add nothing to our understand-
ing of the evolutionary process. The gap be-
tween the two forms of biology was the niche
in which the supporters of Intelligent Design
found their arguments: they stated that there
are no natural explanations for the emergence
of these splendid functional devices in organ-
isms: they may only have been designed by a
superior intelligence.
During the last century there were some at-
tempts to fill the gap between the two forms
of biology. But these efforts did not lead to the
development of research programmes. One
The frontiers of current biological research | 79
reason, but not the only one, was the difficulty
of the task, and the lack of an appropriate
methodology. Another reason was mutual
ignorance, resulting from the different univer-
sity training of functional and evolutionary
biologists.
The situation is rapidly changing, for differ-
ent and converging reasons. The first is the
progress of transdisciplinarity within biology.
The trigger was the development of genom-
ics and post-genomics, which required the
skills of computer scientists, mathematicians,
physicists, and engineers. This new group of
“biologists” had not been trained to find the
separation between the two branches of biol-
ogy “natural”. When they started to work in
biology, they rapidly moved from functional
to evolutionary questions, without having the
feeling of committing a transgression.
This is particularly evident in systems biol-
ogy, where researchers seek to describe the
organization of macromolecules in complex
networks in cells and organisms, and the be-
haviour of these networks. Leaders in the field,
such as Uri Alon and Stanislas Leibler, rapidly
moved from a description of these systems to
questions about their origin, and the adaptive
value they provide. Some of the scenarios imag-
ined for their origin and/or adaptive value were
sometimes naive, or supported by inadequate
observations (Keller 2005). These researchers
clearly demonstrated the value, but also the
difficulty, of bringing together the two forms of
biology.
The second reason for the encounter between
these two branches of biology is also a natu-
ral consequence of the development of gene
sequencing programmes. A sequence is not
informative per se. One of the only ways to
extract information from a sequence is to com-
pare it with other sequences. This comparison
can be used to discover the function of hitherto
unknown genes, and the question is therefore
limited to functional biology. But, in general,
comparison of sequences, or of the organiza-
tion of genes in the genome, immediately leads
to questions about the evolution of the systems
under comparison. These questions can be
limited to a description of what happened, for
instance a characterization of the genes that
were duplicated or deleted during the evolu-
tion of one or other species, but questions soon
arise regarding the selective pressures that have
moulded evolutionary history.
The discovery of the genes controlling develop-
ment, the “master genes” such as the homeotic
genes, and of their conservation during evolu-
tion, has attracted the attention of evolution-
ists. More and more studies in a new discipline
dubbed “Evo-Devo” aim to relate modifications
in structure and/or expression of these devel-
opmental genes to the evolutionary transitions
revealed by the work of palaeontologists.
Molecular mechanisms for these transitions are
proposed, as well as evolutionary scenarios for
their emergence.
In the previous case, the efforts to fill the gap
between functional and evolutionary biology
were made by evolutionists. But the opposite
can be true, and more and more evolutionary
questions spontaneously emerge from the work
of molecular and cell biologists. One reason
is that the molecular descriptions have been
pushed so far that molecular explanations re-
veal their limits. The specific characteristics of
a functional device, for instance a multi-molec-
ular system, can only be found in the complex
evolutionary process which has generated it.
Consider, for instance, a superb nanomachine
like a chaperonin, in charge of the correct fold-
ing of proteins in cells - the process by which
the long polypeptide chains attain their native
structures. Why are only some proteins of the
cell the targets of the chaperonin? The explana-
tions in terms of differences in the physico-
chemical characteristics of the target proteins
are not wrong, but they must be complemented
by other explanations putting the complex rela-
tions between proteins and their chaperonins
in an evolutionary perspective, and by trying
to explicate the selective pressures exerted on
these complex systems (Kerner et al. 2005).
The recent possibility of studying evolution in
vitro, to put “the Beagle in a bottle” as beauti-
fully said in an article in Nature (Buckling et al.
2009), was a major event in moving functional
and evolutionary biology closer one together.
The possibility of studying evolution in the
laboratory is not new. Pioneering work was
done, for instance, on the fruit fly Drosophila.
But these early studies rapidly reached their
limits in the number of organisms included, the
number of generations that could be studied,
and in the practical possibility of relating the
transformations observed to the genetic and
molecular mechanisms underlying them. Such
limits were overcome by the adoption of bac-
teria (or viruses) as model systems, and also by
the in vitro study of the evolution of macromol-
ecules, RNAs and proteins. The path followed
by evolution, the constraints on the system,
the trade-off between antagonistic changes are
no longer “abstract words”, but can be identi-
fied with precise molecular events. And the
same strategies can now be applied to naturally
evolving more complex organisms, such as
the rapidly evolving cichlid fishes in the East-
African great lakes (Kocher 2004).
Synthetic biology adds a new dimension to
these efforts. It will be possible in the future
to test molecular functional devices that have
not been selected by evolution. In this way, it
will be possible to discriminate in the ensemble
of possibilities to which life has not yet had
access those that are forbidden and those that
have not yet been exploited by organisms, or
to which access was made more difficult by the
choices initially made.
Needless to say, this work reduces the gap
between functional and evolutionary biology.
More and more work is being done in this di-
rection and represents a strong trend in biology.
One discipline, epidemiology, was a precur-
sor in the encounter between the two forms
of biology. To explain the emergence of an
epidemic or a pandemic requires a descrip-
tion of the nature of the pathogenic agent,
but also the characteristics of the disease and
of its transmission in the human population.
The capacity of a pathogen to evolve and its
complex relations with its hosts have been pro-
gressively described. The studies have become
more and more precise. The genomes of most
pathogens being small, a full description of
them and of their evolution in parallel with the
development of an epidemic has been possible,
as in the case of HIV and AIDS. The resistance

80 | Genes to Galaxies
of pathogens to treatments, such as antibiot-
ics, has been fully explored: the mechanisms
involved have been described in the smallest
detail, as has the propagation of resistance.
The study of diseases like cancer is also benefit-
ting from these combined efforts of functional
and evolutionary biologists. Instead of being
considered as the simple result of the addition
of somatic mutations, the formation of tumours
and metastases is now seen as a long evolution-
ary process in which cancer cells progressively
adapt to new niches within the organism.
More generally, the study of diseases is giving
increasing scope to evolutionary considera-
tions. To explain pathology affecting human
beings, one must take into account the recent
evolutionary history that has generated modern
humans, and the ecological niche in which this
evolutionary history took place.
By comparing the models and results of both
branches of biology, scientists will be able to
elaborate a less naive vision of what happened
during evolution. Such a naive vision is obvious
in the case of the evolutionary origin of modern
humans, perhaps because so much is at stake!
For the moment, one has the choice between
the naive models of evolutionists trying to
describe how our ancestors left the branches
of the trees and stood up in the savanna, and
those of geneticists and molecular biologists
outlining the crucial change in one gene, the
“language gene” (Vargha-Khadem et al. 2005)
or the “jaw gene” (Stedman et al. 2004).
Human evolution was far more complex,
more tortuous, and so much remains to be
discovered!
Conclusion
The closer relations progressively established
between functional and evolutionary biology
will deeply affect the way biology is studied.
Consider, for instance, the importance of
model organisms in 20th century biology: the
fruit fly (Drosophila), bacteria (Escherichia coli
and its bacteriophages), the nematode, mice.
Most efforts by biologists were focused on these
systems. They were not useless, they permitted
the characterization of the most fundamental
mechanisms operating in organisms. The new
The frontiers of current biological research | 81
biology will probably be more open to diver-
sity, to a plurality of models, to what happens
in nature and not in the test tube or in the
laboratory.
Fundamental progress was made during the
20th century in the description of macromo-
lecular mechanisms. The complex evolutionary
history of these mechanisms, and the diversity
it generated, have yet to be described. This
shift in interest is clearly visible when one
considers the question of life. As I mentioned
previously, the founders of molecular biology
were convinced that they had discovered the
secret of life. And they were not wrong! But
what remains to be described is the complex
process which generated life and its different
forms. From a question of principles, the ques-
tion of life has been transformed into a histori-
cal question. To reproduce extant forms of life
artificially is an objective which is no longer
beyond the reach of synthetic biologists. But
to understand how life emerged is a different
question, which is far from being solved. How
the complex systems in organisms progressively
emerged, and how they were gradually coupled
during the long prehistory of life will require
the work of many biologists. I hope that many
of you who attend these lectures will partici-
pate in this exciting adventure!
Bibliography:
Angus Buckling, R. Craig Maclean, Michael A.
Brockhurst and Nick Colegrave (2009) “The
Beagle in a bottle”; Nature 457: 824-829
François Jacob (1982) The possible and the
actual (Seattle: University of Washington Press)
Youxing Jiang et al. (2003) “X-ray structure of
a voltage-dependent K+ channel”; Nature 423:
33-41
Evelyn Fox Keller (2005) “Revisiting ‘scale free’
networks”; BioEssays 27: 1060-1068
Michael J. Kerner et al. (2005) “Proteome-wide
analysis of chaperonin-dependent protein fold-
ing in Escherichia coli”; Cell 122: 209-220
Thomas D. Kocher (2004) “Adaptive evolu-
tion and explosive speciation: the cichlid fish
model”; Nature Reviews/Genetics 5: 288-298
Ernst Mayr (1961) “Cause and effect in biol-
ogy”; Science 134: 1501-1506
Michel Morange (2008) “The death of molecu-
lar biology?”; Hist. Phil. Life Sci. 30: 31-42
Jonathan M. Raser and Erin K. O’Shea (2004)
“Control of stochasticity in eukaryotic gene
expression”; Science 304: 1811-1814
Hansell H. Stedman et al. (2004) “Myosin gene
mutation correlates with anatomical changes in
the human lineage”; Nature 428: 415-418
Faraneh Vargha-Khadem, David G. Gadian,
Andrew Copp and Mortimer Mishkin (2005)
“FOXP2 and the neuroanatomy of speech and
language”; Nature Reviews/Neuroscience 6: 131-
138

82 | Genes to Galaxies
The frontiers of current biological research | 83
Why is it important to read

On the Origin
of Species in
2009?
Michel Morange
I n the previous lecture, I showed how
the theory of evolution has an increas-
ingly important role in present-day
biology. Not only is evolutionary biol-
ogy an important subdiscipline of biology, but
evolutionary questioning is progressively being
introduced into the different parts of functional
biology. What was the origin of these complex
molecular devices? Can we reconstitute the
processes by which they were progressively
elaborated during evolution?
My aim now will be different. It is to return
to the main author of the theory of evolution,
Charles Darwin. I will try to convince you
that in 2009 it is still important to read On the
Origin of Species by Means of Natural Selection, or
the Preservation of Favoured Races in the Struggle
for Life (hereafter OS; Darwin 1859), more im-
portant than reading all the commentaries that
have been written on Darwin. It is important,
despite the fact that the theory of evolution is
no longer what it was for Darwin. Reading OS
remains crucial because it is a lesson in honest
and excellent science.
I will successively remind you of some of
the major facts concerning Darwin, but also
how the theory of evolution has dramatically
changed since his time. Then, I will turn my
attention to OS, and give you a reader’s guide.
I will argue that Darwin, and Darwin’s work,
remain highly important for us today.
I Some important characteristics
of Darwin’s work, and the
transformations of the
evolutionary theory
As you all know, the work of Darwin is spread
through various books. After he returned from
his trip around the world on the HMS Beagle,
Darwin progressively elaborated his theory of
evolution by means of natural selection. His
project was to publish a huge treatise, compris-
ing all the data that he had collected in favour
of his theory. This changed dramatically when
he received in 1858 a manuscript from Alfred
Russel Wallace proposing a theory very similar
to his own. He decided to publish rapidly one
book, OS, a kind of summary of the treatise he
had been planning. The remaining material was
presented in three other books: The Variations
of Animals and Plants under Domestication,
which contained his model of heredity known
as the theory of pangenesis (1868), The Descent
of Man and Selection in Relation to Sex (1871),
and The Expression of the Emotions in Man and
Animals (1872). These four books represent
the core of Darwin’s theory. But Darwin also
wrote many monographs on highly different
subjects: on the reproduction of orchids, on
the role of worms in the formation of soils, on
insectivorous plants, on barnacles, etc. Darwin
was a true naturalist, interested by the facts of
Nature. This is clearly apparent when one reads
the notebooks that he published after his long
journey on the Beagle.
Despite this diversity of interests, microorgan-
isms, bacteria, are totally absent from OS. The
book was published too early, at a time when
microbiology was progressively emerging
through the work of Louis Pasteur and Robert
Koch. This is a pity when one knows the strong
experimental support that microorganisms
bring today to the theory of evolution.
86 | Genes to Galaxies
Darwin also lacked any explanation for two
important facts constituting the basis of his
theory. He had no mechanistic explanation for
the spontaneous variations that he observed
in organisms, what he called “the plasticity of
organisms”. This lack of explanation forced
him to ascribe to the direct action of the exter-
nal environment a role not attributed to it by
modern-day evolutionists. In a similar way, he
had no explanation for the capacity of these
variations to be transmitted to the offspring of
affected organisms. He proposed his theory of
pangenesis in his second book. This attempt
generated the production of other models,
and progresses towards a satisfactory theory of
heredity, an objective reached with the redis-
covery of Mendel’s Laws in 1900. But his own
model was clearly wrong, giving as it did a
large role to the heredity of acquired character-
istics, and contradicting the then young cellular
theory.
These weaknesses and omissions in the work of
Darwin were corrected by his successors, and
I will briefly recall some of the major advances
that have progressively shaped the modern
theory of evolution.
In the 1880s, the German naturalist August
Weismann provided strong theoretical and
experimental arguments against the existence
of the heredity of acquired characteristics. In
the 1920s, there was a progressive emergence
of population genetics, i.e., quantitative models
of inheritance of the allelic forms of genes.
They gave a precise, quantitative description of
fitness. These models demonstrated that varia-
tions, leading to a small increase in fitness, are
nevertheless capable of invading the population
under study in a limited number of genera-
tions. The encounter between genetics and the
Darwinian theory of evolution, initiated by the
rise of population genetics, was completed in
the 1930s with the wide movement of unifica-
tion called the Evolutionary Synthesis. Three
contributions to this synthesis are emblematic:
Theodosius Dobzhansky demonstrated that the
observations made by geneticists on Drosophila
in their laboratories explained the variations
observed in nature in wild populations. Ernst
Mayr provided strong arguments in favour of
the formation of new species by geographic
isolation – the so-called allopatric model.
George Simpson showed that palaeontologists’
observations on fossils were not incompatible
with the models elaborated by population
geneticists. Evolutionary Synthesis remains the
framework in which evolutionary biologists
work today.
This does not mean, however, that evolutionary
biology has not been enriched by many new
contributions since the 1930s. After the Second
World War, the interpretation of evolutionary
facts in terms of strategies, strategies of organ-
isms and, later, strategies of genes, appeared
and has progressively assumed increasing im-
portance, not only in explaining evolutionary
facts, but also a heuristic tool, permitting biolo-
gists to imagine evolutionary scenarios. The
development of molecular biology also had a
huge impact on evolutionary theory. Molecular
data provided decisive arguments in favour of
a common origin for all organisms on Earth.
Comparison of protein and gene sequences be-
came the dominant tool to elaborate phyloge-
netic trees. Molecular data were used to correct
previous phylogenetic trees – such as the rela-
tions between humans and our cousins, gorillas
and chimpanzees. Molecular biology also ex-
plained the origin of the variations that under-
pin evolution, and showed their diversity: from
the point mutation of a nucleotide, leading to
the replacement of one amino acid by another
in a polypeptide chain, to more drastic events
such as insertions and deletions, gene duplica-
tion, and even duplication and translocation of
part of or a whole chromosome.
Molecular data also showed that most of these
variations are neutral, and escape the filter
of natural election, as first proposed by the
Japanese evolutionary biologist Motoo Kimura
(Kimura 1983). More recently, the discovery
of developmental genes – such as the home-
otic genes – led to the formation of a new
discipline, Evo-Devo: the evolution of organ-
isms is related to the variations in structure or
regulation of the family of genes involved in
the control of development. Evo-Devo is one
of these lines of research where the separation
between functional and evolutionary biology is
progressively erased. Other discoveries, such as
microorganisms’ capacity to control their rate
Why is it important to read On the Origin of Species in 2009? | 87
of mutation in conditions of stress, have also
contributed to the elaboration of this complex
ensemble of theories, models and mechanisms
that constitutes the modern theory of evolu-
tion. Epigenetic variations are also progres-
sively being allocated a role in this complex
ensemble.
The present state of evolutionary theory dif-
fers considerably from the theory elaborated
by Darwin, and first published 150 years ago,
even if the concept of natural selection still has
an important place in present-day explanations.
I will provide two examples to illustrate these
huge differences. Darwin accepted the exist-
ence of an inheritance of acquired characteris-
tics, whereas the modern theory of evolution
totally rejects. Darwin did not experimentally
test his theory, whereas experimental evolution,
“evolution in a bottle”, is playing an increasing-
ly important part in the work of evolutionists.
The historical contribution of Darwin was de-
cisive. But, for the reasons mentioned before,
it is probably a mistake to call this complex
ensemble of models and theories on evolution
“Darwinism”. First, because it is an anomaly
in the landscape of scientific disciplines. The
contributions of Newton and Einstein to phys-
ics were as important as those of Darwin to
biology. Yet Newton and Einstein have not
given their names to the theories and models
that emerged from their work. To identify a
theory and a man (or a woman) is the rule for
ideologies – like Marxism – not for scientific
theories. More seriously, to identify the modern
theory of evolution with the name and work
of Darwin leads to totally biased debates and
questions. Was Darwin right or wrong? Is
the theory of Darwin still valid today? These
questions have no sense. Darwin was both
right and wrong, and only a part of his theory
is valid today. It is a common rule in science:
scientific knowledge permanently evolves, and
the contributions of scientists, even the most
important ones, are bricks in the ever-evolving
edifice of science.
In contrast, the right question is rarely asked:
is this complex ensemble of theories, models
and practices, which is called “the theory of
evolution”, likely to be found to be wrong in
the more or less distant future? The answer is
obviously “no”. First, there is no other ensem-
ble of theories and models likely to replace
the present theory of evolution. The work of
evolutionists does not consist in trying to falsify
the theory of evolution, but rather in determin-
ing which scenarios are able to explain this and
that evolutionary variation, the relative role
of adaptation (selection), the constraints and
neutral variations in one or other evolutionary
transformation. Maybe new evolutionary mech-
anisms – including, for instance, epigenetic
modifications – will be described, and their
place in set of explanations available to evolu-
tionary biologists discussed. More and more
“molecular flesh” will be added to the skeletons
of proposed scenarios. But the present theory
of evolution provides a good framework in
which to try to explain the evolutionary facts.
This does not mean that evolutionary facts
are already fully explained. Far from it. Much
remains to be explained. Explanations are
still preliminary, too abstract. A selection has
to be made between different scenarios, and
the molecular mechanisms underlying these
scenarios have to be described. Nonetheless,
researchers clearly have a theoretical frame-
work well adapted to explaining the evolution
of organisms.
II My personal feelings when
reading On the Origin of Species
The above considerations do not diminish
Darwin’s major contribution or the interest in
reading OS in 2009. Not to find in it eternal
truths, but to see how scientific knowledge is
progressively acquired. Considering the huge
number of publications devoted to Darwin, his
personal contribution and his time, it would
be more time-consuming, and less fruitful, to
read this abundant literature than to open OS.
The reader must not expect an easy read: OS is
hard-going, sometimes boring with its apparent
repetitions, and its lack of an obvious organi-
zation. For instance, instead of immediately
presenting his theory, Darwin starts his book
with an apparent long digression on the varia-
tions observed in animals under domestication.
This first impression is incorrect. OS is a highly
organized book, but not simply so as to present
88 | Genes to Galaxies
the theory of evolution by natural selection, but
rather to answer objections that might be, or
had already been, raised. One must not forget
that the first versions of the theory were elabo-
rated twenty years before the publication of
OS, that Darwin had already discussed it with
some of the most famous scientists of his time,
and that he himself was highly conscious of the
difficulties his theory had to face.
Another difficulty when reading OS is that it
appears that Darwin has not yet made up his
mind on some important issues regarding his
theory, such as the inheritance of habits, and
more generally the inheritance of acquired
characteristics. At some places in the text,
Darwin gives the former an important role,
whereas at others, he gives natural selection the
dominant if not exclusive role.
Another characteristic of the way Darwin pro-
ceeds which, when discovered, makes the read-
ing of OS more evident is his extensive use of
the specialized studies he has done on pigeons,
barnacles, orchids, etc. They are treated as
model systems in which different facets of the
theory can be tested, at least in thought experi-
ments. This recurrent use of the same examples
explains the apparent repetitive character of the
book.
When these obstacles have been overcome,
the richness of the book grips the reader. The
developments on Man and sexual selection,
which were fully explored in the later books,
are already clearly depicted in OS. Facts emerg-
ing from the study of human beings are used to
support the theory, as are those from the study
of other organisms. For the careful reader, it
is absolutely obvious that Man fully belongs
to Nature, and that his evolution has obeyed
the same rules as those followed by other
organisms. The importance of sexual selec-
tion, besides natural selection, is also clearly
mentioned.
What is most striking is that OS prefigures
many of the developments of the theory of
evolution which occupied research throughout
the 20th century, and the attendant debates. By
this I do not mean that Darwin was a precur-
sor, that he anticipated the work of 20th century
biologists. Rather, by exploring the difficulties
that his theory encountered, Darwin guessed this is no longer the case today, when experi-
some of the directions where it would be mental evolution is assuming an increasing
possible to overcome them. I will just give a role in the work of biologists. Nevertheless, the
few of many examples. Darwin insists on the weakness of any historical explanation persists.
important role of unselected variations in the
A second difficulty of the Darwin’s theory stems
evolution of organisms, a clear anticipation of
from the complexity of the events under study.
the neutralist theory developed by the Japanese
The action of natural selection is the result of a
researcher Motoo Kimura in the 20th century.
complex interaction between all the organisms
Darwin suggests also that the rate of variations
present in a given ecosystem – if we adopt a
can be modulated by the environment. Such a
present-day expression – not, as is commonly
possibility was demonstrated at the end of the
said, the result of the direct interaction of an
20th century in microorganisms, and its sig-
organism with its environment. The full de-
nificance actively discussed. Nonetheless, one
scription of this complex interaction is highly
has to admit that it was impossible for Darwin
difficult for the naturalist, if not impossible.
to see the true significance of this possibility,
The same is true if one considers extinctions,
at a time when nothing was known about the
the extreme possible consequence of the
mechanisms generating these variations, and
“struggle for life”. Once again, it is impossible,
when it was even conceived as possible that
according to Darwin, to understand why a
the environment directly moulded organisms.
given species has disappeared in the past. This
Darwin also perceived the possibility that a var-
emphasis on the complexity of the relations
iation could be beneficial not to its owner, but
between organisms, and between organisms
also to the other members of the same species.
and their environment, is a characteristic of
But he was not able to develop the conceptual
Darwin’s thought. It has deep resonances with
tools – kin selection, group selection – that
the present-day use of the theory of complexity
would be necessary to justify such a possibility.
to unravel the functioning of organisms and
The book is also important because it exhibits ecosystems. The bad side of this emphasis is
the difficulties of Darwin’s theory. The first that the explanatory and predictive power of
originates in the fact that Darwin proposed Darwin’s theory is reduced to the point where it
a radically new principle of explanation, at vanishes altogether!
odds with those used in other disciplines.
Another challenge to the theory concerns the
Consider physics: scientists try to explain the
explanation of discontinuities in the evolution-
phenomena they observe by the existence of
ary process, the most obvious of which is the
laws, or of mechanisms. The theory of evolu-
formation of new species. Darwin’s theory is
tion by variation and natural selection is not a
based on the existence of a continuous spec-
law, and even if it is frequently described as a
trum of variations. For Darwin, naturally oc-
mechanism, it has nothing in common with the
curring variations are of small amplitude. The
mechanisms considered by physicists. Not only
transformation of organisms is a continuous
is the theory unusual, but its validity is limited
process. Nevertheless, evolution of organisms
to the domain of organisms, a scandal for many
is characterized by huge evolutionary leaps,
physicists! Since organisms are a part of the
discontinuities, one of which is the formation
natural world, how is it possible that they obey
of new species. How can discontinuity origi-
specific laws? These unusual characteristics of
nate from a continuous process? How can a
Darwinian theory partially explain the opposi-
new species emerge? This is a highly difficult
tion that it has encountered, and the reluctance
and recurrent question. The problem of specia-
with which it has been accepted.
tion occupied the minds of many evolutionary
This theory is also difficult per se. First, because biologists during the 20th century, and is still
it is a theory accounting for historical facts. doing so at the beginning of the 21st century.
Direct experiments to test the theory were not
There are two additional difficulties with
realized at the time of Darwin, and the theory
Darwin’s theory. The first concerns the notion
could only provide scenarios. As we have seen,

Why is it important to read On the Origin of Species in 2009? | 89

of progress. Is the evolution of organisms syn- said – but simply reflects the fact that these
onymous with progress? Darwin was deeply alternative theories and models were the best
influenced by the French physiologist Henri placed at that time to explain some of the
Milne Edwards, and considered that, in human observations that had been made. For Darwin,
societies as in organisms, evolution leads to a it would have been dogmatic to favour one ex-
diversification of the functions of the different planatory model to the exclusion of all others.
parts, a process of specialization, which can be
Reading OS is also important for two additional
considered as progress. But he was also con-
reasons. The first is that it demonstrates the
vinced that evolution had no sense, no direc-
plethora of observations and facts that Darwin
tion, that it depended on the complex interac-
recorded on both animals and plants. Such
tions of organisms in a permanently changing
an encyclopaedic culture was already excep-
environment. How was it possible to reconcile
tional among naturalists of Darwin’s time, and
these two opposing views? Darwin did not, and
Darwin has been criticized for “dissipating” his
ambiguity on the existence (or not) of progress
efforts. We must remember this characteristic
in the organic world pervades the pages of OS.
of Darwin’s science. The work of Darwin is
In some parts of the book, Darwin uses the
praised by all contemporary biologists. But do
words “superior” and “inferior” to designate dif-
they realize that such work would be impos-
ferent animals and plants without any restric-
sible in the present-day context, when spe-
tions, whereas in other parts of the book he
cialization and fragmentation of disciplines are
states that it is impossible to provide any valid
dominant within biology (and other sciences)?
criterion to justify the assertion that one organ-
ism is superior or inferior to another. Another, rarely mentioned, characteristic of the
work of Darwin is the role that humans played
This balance between two different opinions
in the discovery of the theory of natural selec-
is a recurrent characteristic of OS (and of all
tion. Most of the examples used by Darwin
the other works of Darwin). In some parts of
originate in human practices: the action of
the book, Darwin considers, for instance, that
artificial selection, but also the changes which
there are no differences between what one calls
were the consequences of the colonization of
“varieties” and “species”, and in others Darwin
new territories by Western Europeans, and the
states that the difference is obvious, or looks for
reciprocal acclimatization of plants and animals
criteria to distinguish them. These hesitations
which resulted from this process. Darwin even
must not be considered as weaknesses of OS.
used the experience he accumulated in his
They are testimonies to the difficulties Darwin
private garden. It is evident that OS, which
encountered in exploring the radically new
concerns the evolution of organisms in Nature,
questions raised by his theory. They are the
would not have been possible without the
signs of ongoing intellectual efforts to find sat-
observations made on the transformation of
isfactory answers to highly difficult questions.
Nature by human actions. This shows that sci-
OS is a report of a “work in progress”. These
ence is not the passive observation of Nature,
hesitations also show the honesty of Darwin,
but rather the result of the active transforma-
who never sweeps the difficulties encountered
tion of it by human beings.
by his theory under the carpet.
In addition, Darwin does not exclude that Conclusion
alternative theories and models might have
an explanatory value. He favours the power Reading OS in 2009 is important. Not because
of natural selection, but leaves the inheritance the book represents the state of the art on the
of acquired characteristics a role in the overall mechanisms of evolution. Our knowledge has
process of evolution. Likewise, he underlines advanced immeasurably since Darwin’s day! It
the role of variations of small amplitude, but is important, because it shows how scientific
does not exclude the existence of variations of knowledge is progressively acquired, through
large amplitude, and of leaps in evolution. This hesitation and error. It shows what scientific
is not a sign of cautiousness – as is frequently activity must be: an open enterprise, with a

90 | Genes to Galaxies
spirit of honesty, an emphasis on particular ex- Bibliography:
planatory schemes without rejection of others,
if there are no reasons to exclude them. Charles Darwin (1859) On the Origin of Species
by Means of Natural Selection, or the Preservation
It would be a mistake in this anniversary of Favoured Races in the Struggle for Life
year to praise Darwin, and his work, without (London: Murray)
mentioning its limits, hesitations, and errors.
Darwin made a decisive breakthrough in bio- Charles Darwin (1868) The Variations of
logical thinking. This breakthrough was so de- Animals and Plants under Domestication
cisive that he was alone, ahead of his contem- (London: Murray)
poraries, trying to fit his theory with the ob- Charles Darwin (1871) The Descent of Man and
servations made by naturalists over centuries. Selection in Relation to Sex (London: Murray)
The amplitude and the difficulty of this task
Charles Darwin (1872) The Expression of the
are most evident in what concerns the place of
Emotions in Man and Animals (London: Murray)
human beings in Nature. Darwin devoted two
of his major books to show how closely hu- Motoo Kimura (1983) The Neutral Theory of
mans are related to other organisms, that they Molecular Evolution (Cambridge: Cambridge
share with them many different behavioural, University Press)
anatomical and physiological characteristics.
The natural consequence was that Darwin was
convinced that the mechanism of evolution
by natural selection operated in the forma-
tion of human beings, and is still operating in
and among human populations. Nevertheless,
Darwin hesitated. With fewer racial prejudices
than most of his contemporaries, scandalized
by slavery, he emphasized the importance of
altruistic behaviours among humans. How to
reconcile these opposing views on the wide-
spread action of natural selection and on the
specific characteristics of human societies?
Darwin did not, and he refused to eliminate the
action of natural election from human societies.
How would it have been possible to do that
for the naturalist who included human history
in the natural history of organisms? Darwin
did not consider the disappearance of some
primitive human populations “unnatural”, or
the control of human reproduction useless. To
acknowledge this duality in Darwin’s writings
is simply to admit the difficulty of finding the
right place for radically new theories. Darwin
was not a saint, but a great scientist and an
honest man.

Why is it important to read On the Origin of Species in 2009? | 91

Cosmic Evolution:

The Birth, Life

& Death of
Galaxies
Geraint F. Lewis
The Sky at Night
In this International Year of Astronomy, we
celebrate the 400th anniversary of Galileo turn-
ing his telescope to the skies. What he saw
revolutionized our understanding of our place
in the heavens, and set us along the road of
astronomical discoveries that continues today.
Following Galileo, generations of astronomers
scanned the sky and slowly the nature of our
Universe was revealed. At first it was thought
that the Universe was a simple place, and that
the Sun was but one of an infinite number of
stars that filled an infinite heavens. Even to the
naked eye, it is apparent that this could not be
the truth as that stars are not simply scattered
over the sky, but tend to lie in a band known as
the Milky Way.
Intensive detective work at the end of the
1800s and early 1900s uncovered the true
nature of the Milky Way, showing that the Sun
lives with many others (roughly 250 billion)
in an “island Universe”. Rather than being a
shapeless ‘blob’, the Galaxy possesses beauti-
ful structure, with the majority of stars lie in

a disk, with pronounced spiral arms, orbiting
a central ball of stars known as the Galactic
Bulge. The scale of the Galaxy1 is staggering (in
human terms), and the disk is 100,000 light
years2, with the Sun located roughly 28,000
light years away from the Galactic Centre, bur-
ied deep in the disk which is ‘only’ 3000 light
years thick (Figure 1).
Using the Doppler shifting of light, astronomers
were eventually able to determine the veloci-
ties of stars and gas within the Galaxy, directly
measuring the rotation of the disk. We can use
Newton’s famous laws of motion and gravity to
calculate the expected Galactic motions, assum-
ing that the only mass present is what we can
see. The results were, to say the least, shocking,
1 Our galaxy is usually known as the Milky Way or simply
the Galaxy.
2 A light year, as the name suggests, is the distance that
light covers in a year. As light travels at 300,000 km/s,
this corresponds to roughly 9460000000000 km, or
9.46x1015m in scientific notation).
94 | Genes to Galaxies
Figure 1: The structure of the Milky Way
viewed from above (top) and the side
(bottom), showing the galactic disk, with
spiral arms, orbiting the central bulge.
ESA
with all the stars in the disk moving around the
centre of the Galaxy at a little over 200km/s, far
faster than our naïve expectations. Astronomers
were led to the conclusion that there must be
more mass out there than we can see, much,
much more. In fact, the vast majority of the
mass (~95%) must be this “dark matter”, which
emits no light but whose gravitational influence
holds our Galaxy together; exactly what this
dark matter is remains a major outstanding
problem in astronomy.
The Universe of Galaxies
As astronomers were unravelling the structure
of our own Galaxy, their observations revealed
it was not alone in the cosmos, but is just one
of billions within the observable Universe.
Surprisingly, right next-door to us, at the cos-
mologically small distance of two million light
years, is the Andromeda Galaxy, almost a twin
of our own, being similar in size and possessing
its own beautiful spiral disk and bulge of stars
(Figure 2).
Observations of our local patch of the Universe
also reveal the Milky Way and the Andromeda
Galaxy are not alone but are accompanied by
a host of much smaller ‘dwarf’ galaxies, con-
taining between a few million and few billion
stars. Unlike the larger galaxies, these dwarfs
do not possess the grand spiral disk structure,
but are usually amorphous blobs, roughly the
same shape as a rugby ball, or even possess no
real structure at all. Two of the closest of these
dwarfs are actually visible to the naked eye as
the Large and Small Magellanic Clouds that
can be seen in the night skies of the Southern
Hemisphere. In fact, there are almost fifty of
these dwarf galaxies accompanying the Milky
Way and Andromeda in a family known as the
Local Group.
Looking into the deeper Universe, we see
that not all large galaxies are spiral, and most
are actually larger versions of the spheroidal
 Figure 2: A montage of galaxies, with our
nearest neighbour, the Andromeda Galaxy
appearing at upper-left, a large elliptical
at the upper-right, and several dwarf
galaxies in the lower panels. While the
elliptical and the dwarfs appear to similar,
they are hugely different in size. To see the
huge diversity of galaxies, visit Galaxy Zoo
(www.galaxyzoo.org).
Adam Block/ NOAO/AURA/NSF; Canada-France-
Hawaii Telescope & Coelum; NASA, ESA and
C. Conselice

few other large galaxies, and many more dwarf

galaxies, but the giants are found in the cen-
tres of huge agglomerations of large galaxies,
numbering hundreds or thousands, known as
galaxy clusters.
So, galaxies do not live alone, and are found
to reside in groups and clusters, although
these galactic families are not strewn randomly
throughout the Universe. Cutting-edge instru-
mentation, like the 2dF spectrograph at the
Anglo-Australian Telescope in Coonabarabran,
blobs we see in the vicinity of our own Galaxy.
has allowed astronomers to measure the
These ‘elliptical’ galaxies possess a huge range
distances to a large number of galaxies and
of sizes; while the dwarfs are a million times
produce a map of the Universe, showing that
smaller than the Milky Way, the largest, the
galaxies are spread through the Universe on
giant ellipticals, are a hundred times more mas-
a sponge-like structure, clusters joined by
sive (Figure 2). Just like the Milky Way and
filaments of galaxies and groups, with huge,
Andromeda, most galaxies live in groups with a

Figure 3: The
results of the 2dF
Galaxy Redshift
Survey, which
measured the
distances to more
than 200,000
galaxies out to
a distance of
roughly two billion
light years. We
sit at the centre
of this picture,
and it is clear
that the galaxies
are laid out on a
Image courtesy of the 2dFGRS Team
fine structure of
clusters, filaments
and voids.

Cosmic Evolution: The Birth, Life & Death of Galaxies | 95

almost empty voids, some being more than 300
million light years across (Figure 3).
Clearly, the Universe is not a higgled-piggledy
mess of stars and matter, but contains rich
structure of well-defined objects, the galaxies,
laid out in rich patterns of knots, the clusters
and groups, and voids. Immediately, we are
faced with a difficult question; astronomers
have determined that the Universe began al-
most 14 billion years, in the cataclysmic event
known as the Big Bang. Soon after its birth,
there were no stars or galaxies, only a smoothly
distributed gas and dark matter, so where
did all the rich structure we observe today
come from?
Out of the Dark Ages
Understanding exactly what kicked off the
Big Bang still remains one of the biggest out-
standing questions in astronomy, but we do
know that during the very initial stages of the
Universe, a rapid burst of accelerated expan-
sion, known as ‘inflation’, fill the Universe
with a smooth distribution of radiation, dark
matter and hot gas. Vitally for the evolution of
galaxies, inflation blew up tiny, microscopic
energy fluctuations (due to the weird action of
quantum mechanics on the smallest scales) that
resulted in tiny differences in density scattered
through the Universe, seeding it with the birth
sites of galaxies.
Once inflation ends, the Universal expansion
settles down to a more sedate rate. However,
the very slight density differences imprinted by
the rapid expansion begin to play their impor-
tant role, and the dark matter and gas begins to
move under the action of gravity, flowing into
the denser regions. Just after the Big Bang, the
gas is extremely hot and is a sea of electrons
and nuclei (a plasma), but the expansion of
the Universe allows the gas to cool and form
normal atoms of hydrogen and helium. The
radiation released in the Big Bang also cools to
longer and longer wavelengths and, if we could
visit the first half a billion years of the Universe,
before the first stars would have formed, it
would be completely dark with no sources of
light; astronomers have labelled this period of
the Universe’s history as ‘the Dark Ages’.
96 | Genes to Galaxies
The Universe continues to expand, and the gas
continues to cool, and it begins to pool into the
denser regions, eventually reaching the densi-
ties needed for it to fragment and collapse into
the first generation of stars. These stars, com-
prised of only hydrogen and helium, are mas-
sive and burn brightly, lighting up the Universe
for the first time. But this early stage of the life
of the Universe looks very different to today,
with small pockets of bright stars lighting up
the densest knots of dark matter, and there is
nothing that we could identify as a ‘modern-
day’ galaxy. So what happens next?
While the bright, first generation of stars are
visually the most significant things in the early
Universe, the irresistible pull of gravity has
continued its work, with the denser regions
pulling in more and more dark matter and,
associated with it, the first generations of stars.
These stars evolve quickly and explode as
violent supernovae, throwing their gas, now
enriched with the heavier elements generated
in their cores as part of the process of nuclear
fusion, into interstellar space. This gas forms
the fuel for subsequent generations of stars,
and eventually, after several generations, will
form stars like our own Sun.
The Power of Gravity
Even with the birth of the first stars, the
Universe is still a relatively simple place, with
pockets of stars scattered through space, so
how are astronomers to understand the com-
plex flows of matter that would lead to the for-
mation of a galaxy like the Milky Way? This is a
tricky question as the motions of matter under
the pull of gravity can be very complicated and
is effectively unsolvable with paper and pencil3.
Faced with this, astronomers have turned to
a new approach to tackle the problem of the
3 Those familiar with the application of Newton’s laws
of gravity and motion to the movement of planets will
know that we can write out the mathematical form
of an orbit (an ellipse with the Sun at one focus).
This two-body problem (the Sun and the planet) is
easy to solve, but adding one more mass makes the
problem intractable and we can’t simply write out the
orbit of three-bodies without make lots of simplifying
assumptions. Given this, it’s easy to understand why it
is difficult to work out the orbits of trillions and trillions
of bits of mass in an expanding Universe.

Figure 4: Three ‘snapshots’ of the
numerical evolution of a cosmological
volume, starting from the early Universe
(top) to the present day (bottom); the
box size is roughly one billion light years
across. As the Universe evolves, more
structure becomes apparent as matter
flows into the denser regions.
Nicholas Martin & Rodrigo Ibata (Observatoire de
Strasburg)
evolution of matter in an expanding Universe;
basically they build their own Universes
within a computer, sit back and let gravity do
its magic.
What is required to build this ‘numerical simu-
lation’ of the Universe? In principle it’s quite
simple (but, of course, in practice it’s not).
Cosmic Evolution: The Birth, Life & Death of Galaxies | 97
Take a box that represents a large chunk of the
Universe, say 300 million light years on a size.
Fill this box with particles that represent the
distribution of matter in the Universe, with
more particle in regions which are more dense,
and less in the voids, and arrange the particles
to represent the almost smooth distribution of
mass in the early Universe. Then all we have to
do is to turn on the laws of physics, including
gravity and the universal expansion, and let
it evolve. Typically, state-of-the-art simulated
Universes require billions of particles and can
run for months on supercomputers.
The results of these numerical simulations
are no less than spectacular (Figure 4)! In
the initial stages, we can see the matter in the
Universe smoothly distributed throughout
the Cosmos, and as the Universe expands,
the density of matter steadily falls. However,
something interesting starts to happen and we
can see clumps and bumps appear in the mat-
ter distribution; it must be remembered that
these simulations represent a huge volume of
the Universe today and each of these lumps
contain masses which are billions times the
mass of the Sun. The expansion continues
and we can clearly see mass flowing into the
denser regions, with the knots increasing in
size. Intriguingly, a pattern emerges and the
clumps of matter are not isolated but are con-
nected through filaments and sheets, with these
bounding huge areas of low density.
In these pictures, the matter distribution we
see represents the dark matter evolution, but as
it is the dominant component of matter in the
Universe (making up 90% of all matter) it is
this component that dictates the motion. As gas
and stars will follow the dark matter, where we
have high concentrations of dark mark matter
we should expect high densities of stars and
gas, so the tightest knots in the simulations
represent the sites of galaxies, and where these
are grouped together, at the intersection of
the filaments and sheets, represent clusters of
galaxies.
Examining the final stages of the Cosmic evolu-
tion, we can compare the distribution of galax-
ies in our synthetic Universe to that on the sky
(Figure 3) and we see and the results are pretty

Figure 5: A computer simulation of the
formation of the Local Group of Galaxies.
The upper-left panel shows an early
stage of the Universe, when matter was
quite smoothly distributed and shows
no structure, but as the Universe ages
and we move down the picture, we can
see structure begin to form. By the final
panel, representing the present day,
there are several large lumps which are
the large galaxies like our own Milky Way,
as well as a myriad of smaller galaxies
buzzing around.
Institute for Theoretical Physics · University of Zürich
impressive; our synthetic Universe possesses
clusters and groups of galaxies, distributed
along a spongy surface, interspaced with huge
voids, precisely what we see in the actual dis-
tribution of galaxies seen in large scale surveys.
This is quite amazing!
Remember that to make our synthetic Universe,
we simply set up our initial matter distribution
(with very slight bumps and wiggles which
were due to the inflation of quantum fluctua-
tions in the very early stages of the Universe),
and allowed the action of gravity to evolve it
over billions of years.
98 | Genes to Galaxies
Violent Upbringings
Seeing how well our synthetic Universe repre-
sents our observed Universe gives us a warm
and fuzzy feeling, but what does it tell us about
the growth of an individual galaxy like our
own Milky Way? Instead of looking at a huge
volume of the Universe, we can focus our nu-
merical simulations on the growth of a volume
similar to our own Local Group, and within
that we can watch the individual galaxies grow
(Figure 5).
Initially, the situation looks similar to our large
cosmological volume, with dense knots form-
ing within an overall smooth background, but
this entire region represents just one small
region of slightly higher density within the
evolving Universe. Quickly, a large-scale dense
region forms due to the flow of matter, and it
is this that will become the modern-day Local
Group. The region is now filled with a myriad
of dense knots of matter, buzzing around in
the gravitational field like angry flies, but it’s
also apparent that the number of small flies is
dropping as some larger concentrations of mass
emerge. Just what is happening?
Looking a little closer, it can be seen initially
that a couple of small lumps, of roughly the
same size, crash together, and this smashing
merges the two into a single, larger lump. This
resultant larger lump now has a stronger gravi-
tational field, and its tidal influence reaches
further, capturing and disrupting more small
lumps. Over a period of time, these lumps
(which become the sites of modern-day galax-
ies) dominate their local environment, and by
the final stage of this scenario is much of the
mass has flowed into several large features, rep-
resenting large galaxies like the Milky Way and
Andromeda, as well as a sea of smaller clumps
of dark matter and stars, the dwarf galaxies like
the Magellanic Clouds.
While the overall picture appears to be quite
rosy, there are a few issues that have dogged
astronomers over the last decade, the main be-
ing the missing dwarf galaxy problem. With a
glance of the last frame of Figure 5, we can see
that there are many hundreds of dwarf galaxies
orbiting the large galaxies, and so we should
expect to see many of these in the vicinity
Figure 6: The black and white portions of this image are photographic images of
the central bulge of the Milky Way; if you go out on a clear night in the Southern
Hemisphere, you can see that this covers a huge area of sky. The brown smudge is the
Sagittarius Dwarf galaxy, which is actually on the far side of the Galaxy and crashing into
the disk. The dwarf is invisible to the naked eye and can be only imaged by identifying its
stars as being separate from those in the Milky Way. Rose Wyse/John Hopkins University

of the Milky Way. Over the last few decades,
we have surveyed the sky to unprecedented
depths, and the conclusion is that the expected
population of dwarf galaxies is just not there,
with only one tenth the number predicted
by the numerical simulations. This puzzle is
not fully resolved, but many think that these
dwarfs are actually out there, but in their form-
ative stage, early bursts of star formation blew
all the gas out and after the first generation of
stars, there was no remaining material to form
the next generation. With no stars, this leaves
the dwarfs as invisible, dark matter lumps,
buzzing around but unseen; whether this is the
case or not still waits to be solved.
If we examine the growth of a galaxy like our
own Milky Way in detail, we can understand
how it has cannibalised smaller systems during
its growth. Initially, when all the knots of mat-
ter are the same size, the collisions between
any two are quite violent, and the lumps crash
together to form larger lumps. However, once
the proto-galaxy has become established, be-
coming the local dominant mass, the situation
changes. As small masses get too close, the tidal
gravitational force on them increases, with stars
and dark matter being stripped from their outer
edges. The closer they get, the more material is
ripped off, until their orbit brings them as close
as possible before taking them away to larger
distances. Soon, it is on its way in again, and
again the process of tidal stripping begins anew,
with more material being ripped off. The proc-
ess continues for several orbits until the little
galaxy has completely boiled away.

Cosmic Evolution: The Birth, Life & Death of Galaxies | 99

What happens to the stars and dark matter that
is ripped from the cannibalised galaxy? As it
begins its demise, this matter moves along in
the orbit of the dwarf, both infront and behind,
and forming extensive tidal tails that can even-
tually wrap the entire galaxy. As time goes on,
these tails eventually dissipate, and the stars
and dark matter in the dwarf are completely
mixed with that of the growing galaxy, and
any memory of the cannibalised dwarf is com-
pletely erased.
Middle Age Spread
In the early life of our Milky Way, it must have
consumed many small dwarf galaxies over a
relatively short period, to establish itself with
the Local Group. Initially, the dark matter,
stars and, importantly, gas will be present in a
roughly spherical blob, and once enough mate-
rial has been accreted, the gas will cool and col-
lapse to form the spiral disk that characterizes
the Milky Way4. It is tempting to think that the
growth of the Galaxy is now over and all we
have to do is to sit back, relax and watch the
stars age.
Returning to our simulated Universe we can see
that this is not the case. While the Milky Way
had a voracious appetite when it was young,
it should not have given up the consumption
of little dwarfs, and hence be still growing,
even today. Is there any evidence of this when
we take a long, hard look at our Galaxy? For
a long time, the answer was thought to be no,
and that the Milky Way basically looked like
a sedately aging, large spiral galaxy, with no
evidence of ongoing cannibalism; it looked like
our home galaxy was as large as it was going to
get, but things were about to change.
Over the last few decades, astronomers have
turned a battery of new, sensitive instruments
towards the sky, surveying large regions to
unprecedented depths. Coupled with this
has been the development of “multi-fibre
4 The process of turning an embryonic galaxy into either
a spiral or elliptical is thought to depend on how much
angular momentum (or spin) it has; those with spin
give spirals, those without result in ellipticals. The
amount of spin can be determined by the tugs from the
environment that the young galaxy finds itself in, or due
to the violence of the collisions it has undergone.
100 | Genes to Galaxies
spectrographs” that allow us to analyse the light
from several hundred stars at the same time,
providing not only important chemical infor-
mation, but also stellar velocities through the
Doppler shift. One of the first targets of study
was our own Galactic bulge, with astronomers
hoping to use the velocities of stars to give us
a detailed picture of the overall distribution of
matter in the central regions. This work was
the subject of the PhD studies of Rodrigo Ibata,
then at the University of Cambridge, and he
used the 3.9m Anglo-Australian Telescope to
obtain a large sample of stars over the bulge.
At first, things appeared quite straight-forward,
with the velocities of stars moving as we
would expect, buzzing around the centre of
the Galaxy, although as he obtained velocities
for stars in the southern regions of the bulge,
something quite unexpected happened;
Rodrigo picked up another bunch of stars
moving independently of those in the Galactic
Bulge. Initially thinking little of it, Rodrigo
continued to examine his data, finding this
second population of stars was spread over a
large region of the sky. Given the number of
stars that he had detected, he was led to the
conclusion that this second population must
represent a small dwarf galaxy moving through
the halo of the Milky Way, colliding with the
spiral disk on the other side of the bulge to the
sun. Scrutinizing old, large-scale photographic
images of the region, a large, but very sparse
population of stars, now named the Sagittarius
Dwarf, was identified as the source of the ad-
ditional stars; this interloper had been hiding
in plain sight, but, being so diffuse, no one had
noticed it previously. (Figure 6)
The discovery of the Sagittarius Dwarf galaxy
resulted in a flurry of activity, with its ragged
appearance confirming that it was slowly be-
ing dismembered by the stronger gravitational
field of the Milky Way; in a few more orbits
(each lasting roughly 750 million years) the
Sagittarius Dwarf will have completely dis-
solved, its stars and dark matter completely
mingled with those of our own Galaxy. But if
this is the case, then we should expect there
to be the long tidal streams of stars, represent-
ing material torn from the dwarf during its
demise, to lie across the sky, although given
Figure 7: An artists representation of
the Sagittarius Tidal Stream, the debris
torn off the Sagittarius Dwarf as it is
dismembered by the gravitational field
of the Milky Way. The stream completely
wraps the galaxy.
David Martinez (MPIA) & Gabriel Perez (IAC)
the faintness of the dwarf, we would expect
the stream to also be extremely faint. In the
ensuing years, dedicated detective work sought
to isolate stars that could lie in the Sagittarius
Stream, with a handful of bright ‘Carbon stars’5
possibly lighting up the stream’s location.
During the same period, the 2-Micron All Sky
Survey (2MASS6) was mapping out a huge
area of the sky in the infrared, identifying
bright stars within the halo of our Galaxy. By
zeroing in on the expected brightness of stars
associated with any debris from the Sagittarius
Dwarf, the expected tidal stream was revealed
in all its glory, spectacularly wrapping around
the Galaxy, from one pole to the other and back
again. These results clearly show that the Milky
Way is busy digesting the Sagittarius dwarf,
5 Giant Carbon Stars are old stars that have evolved into
their Red Giant phase. Their atmospheres are cool and
rich in carbon, allowing carbon monoxide to form. The
presence of this molecule eats huge chunks out of the
spectrum of light emitted by the star, making them easy
to identify.
6 http://www.ipac.caltech.edu/2mass
Cosmic Evolution: The Birth, Life & Death of Galaxies | 101
Figure 8: A computer simulation of the
demise of the Canis Major dwarf galaxy.
Unlike, the Sagittarius dwarf, this galaxy
lies in the plane of the Galactic disk and its
tidal streamers are completely threaded
through the stellar populations of the
Milky Way.
Nicolas Martin & Rodrigo Ibata, Observatoire de
Strasbourg, 2003
growing by 100 million new stars in the proc-
ess. (Figure 7)
The discovery of the Sagittarius tidal stream
confirmed that our overall picture for the
formation and evolution of galaxies is correct,
with an early burst of feasting now replaced
with a slow and steady munching on snacks
that stray too close. But is the Sagittarius Dwarf
all that the Milky Way is currently consum-
ing? Our computer models say no, leading
to a further search for evidence of galactic
cannibalism in our own backyard. A detailed
examination of the 2MASS view of our own
Galactic Halo doesn’t seem to show anything
else as prominent as Sagittarius, but the picture
changed as astronomers started to look closer
to the disk of the Milky Way. Traditionally
this area is difficult to study due to the huge
number of stars, as well as gas and dust, that
obscure the view. However, a team of astrono-
mers, led by Nicholas Martin at Strasbourg
Observatory, used the huge catalogue of stars
produced by 2MASS to do just this, and found,
in the constellation of Canis Major, nestled
just under the disk, a small dwarf galaxy. This
was extremely surprising as this little galaxy
would be suffering greater gravitational stress
than Sagittarius, and would also be being torn
apart. The astronomers concluded that a huge
ring of stars, known as the Monoceros Ring and
circling the disk of our Milky Way, could be the
tidal debris torn from the Canis Major dwarf
galaxy.
The edge of our Galactic Disk, which can be
warped and flared, is a messy place, and the
interpretation of Canis Major as being a distinct
dwarf galaxy is not universally accepted. If it
is, however, then its future is slightly differ-
ent to that of the Sagittarius Dwarf galaxy; its
ultimate demise is not in question, but unlike
Sagittarius, which is dumping its stars into
our Galactic Halo, Canis Major’s debris will be
mixed with the stars in the disk of our own
Milky Way. We are left, therefore, with one
remaining question: was our own Sun born
within the disk of the Milky Way, the child of
previous generations of stars that lived their
entire lives and died within the Galaxy, or are
the Sun or its parent immigrants, brought in
during the accretion of a now destroyed dwarf
galaxy? As we develop newer instruments that
will allow us to take the census of the velocities
102 | Genes to Galaxies
and chemical fingerprints of huge populations
of stars, we may be able to answer this intrigu-
ing question.
We Are Not Alone
The story is not over, and like the late-night
telemarketer we have to face the fact that “and
there’s more!” While 2MASS was surveying
the sky in the infrared, the Sloan Digital Sky
Survey (SDSS7) was undertaking a similar
project in the optical. Like 2MASS, astronomers
scoured the images looking for new types of
galaxies and structures within the Milky Way,
especially the telltale signs of ongoing feast-
ing, like the Sagittarius and Monoceros tidal
streams. Again, the results were surprising,
with one of the regions studied intensely being
named the “Field of Streams” because of what it
revealed. (Figure 9)
The Field of Streams covers a huge swathe of
sky, with the disk of the Milky Way running
along the right-hand side. Clearly visible in
the picture are the Monoceros Stream, shown
in blue at the right, and also the Sagittarius
Stream which runs from right to left across
the image; intriguingly the stream appears to
7 http://www.sdss.org
Figure 9: The
Field of Streams,
a small part of the
Sloan Digital Sky
Survey. In this field,
which covers a
quarter of the area
of the night sky,
the Sagittarius and
Monoceros Stream
are clearly visible,
as is a previously
unknown stream,
named the Orphan
Stream.
Vasily Belokurov, SDSS-
II Collaboration
split into two, showing that it wraps the Milky
Way not once, but twice! Quite unexpectedly,
however, running from the top to the bottom of
the image was a completely unknown stream,
named the Orphan Stream, the tidal debris
from another disrupting dwarf. While this field
remains the most spectacular, our ongoing
large-scale survey of our Galaxy continued to
reveal more and more evidence for ongoing,
and ancient, accretion of our little cosmic
companions, the dwarf galaxies within the
Local Group, and showing that the Milky Way’s
growth appears to be far from over.
Our Bright, but Scary Future
It may seem that our Milky Way’s future is pret-
ty clear, gently chomping on any little dwarf
galaxy that strays too close, and slowly grow-
ing old while retaining its stately spiral disk.
The picture is not so rosy when we remember
that the Milky Way is not the only large galaxy
in the nearby Universe, but shares the Local
Group with the Andromeda Galaxy, a spiral gal-
axy similar to our own. Every hour the distance
between these two giants decreases by half a
Cosmic Evolution: The Birth, Life & Death of Galaxies | 103
million kilometres; in roughly three billion
years, these galaxies are destined to collide.
There is some uncertainty in the details of the
collision8, but the event is inevitable; we have
to ask, therefore, what will happen in such a
collision? Again, computers come to the rescue
and we can smash together the Milky Way and
Andromeda, over and over again, to under-
stand the details of the collision. John Dubinski
at the University of Toronto in Canada has un-
dertaken a very detailed study of our upcoming
galactic collision and collected together a series
of beautiful images and animations to illustrate
what will happen (Figure 10)9.
As the galaxies approach one another, noth-
ing really happens and both retain their spiral
8 While we know how fast Andromeda is approaching
us, it is very difficult to calculate how fast it is moving
across the sky. If this ‘peculiar’ velocity is zero, then
we will suffer a head-on collision, with the collision
becoming more glancing as its value is increased. We
estimate the value to be less than around 100 km/s and
so we expect the collision to be almost head-on, and
hence quite violent.
9 http://www.galaxydynamics.org/
Figure 10: A
computer simulation
of the future collision
between Andromeda
and the Milky Way
galaxies. At first,
as the galaxies
approach, little
happens, but once
the gravitational
pulls increase
sufficiently, the disks
of these two galaxies
are destroyed. The
final remnant, which
resembles a train
wreck, will settle
down to give a
featureless elliptical
galaxy.
Copyright © 2008 John
Dubinski

Figure 11: A Hubble Space Telescope
image of the Antenna Galaxy, actually a
pair of colliding spirals. The hot blue stars
were born in the collision and will burn
brightly for a short time before exploding
as supernovae. This is probably the future
of our own Milky Way and the Andromeda
galaxy.
NASA/STSci
disk structure. However, as the gravitational
tidal pulls of one on another steadily increase,
the spiral disks start to warp and distort.
Eventually the pulls become too strong and the
disks are ripped apart and flung from the galax-
ies, spreading out to form extensive tidal arms.
The collision continues and some of the stars
and gas are lost into extragalactic space. The
remaining material begins to sink back together
as the galactic bulges finally merge into a single
body of stars.
Interestingly, during such galactic collisions,
the probability of two individual stars colliding
is tiny, as they are very small compared to their
typical separation, and they sail harmlessly
past one another. However, the disks of large
spirals, like our own Milky Way, also contain
a substantial quantity of cold gas, known as
molecular clouds, which slam into each other
104 | Genes to Galaxies
during the collisions. This results in the clouds
fragmenting and collapsing in a vigorous burst
of star formation, with the collision lit up by
strings of hot, blue stars; at this point, our col-
liding galaxies will resemble the well-studied
‘Antenna galaxy’ (Figure 11).
These hot, blue stars live fast and die young,
and in a few tens of millions of years will be
gone, but what will be left of Andromeda and
the Milky Way? Some of the stars (including
possibly the Sun which has roughly five billion
years of life left) will have been ejected into
intergalactic space, left to lonely wander the
Cosmos. The rest will eventually settle down
into a single galaxy, but unlike the two grand
spirals that existed before the merger, this
remnant (sometimes known as ‘Milkomeda’) is
a giant featureless blob of stars, and the colli-
sion has created an elliptical galaxy. If our Sun
remains within this new galaxy, any creature
staring up at the future sky will see a very dif-
ferent view to ours today, with no Milky Way
stretching around the sky, only a uniform sea of
stars in all directions.
Return to the Dark Ages
As we have seen, in a few billon years from
now, the Milky Way and Andromeda will be
destroyed, merged into a single large elliptical
galaxy. However, the evolution of this galaxy is
not completely over, as dwarf galaxies remain-
ing within the Local Group will still be future
food if they stray too close and get dismem-
bered by the gravitational field of the large gal-
axy. It is now time to think of what the distant
future hold for the Milkomeda?
We know that the Local Group is streaming
through intergalactic space, caught in the gravi-
tational field of the nearest cluster of galaxies,
in the constellation of Virgo, and it appears that
our destiny is to eventually fall into and merge
with this cluster, like so many dwarf galaxies
have with the Milky Way. However, things are
not so simple, as we need to think not only
about our motion through the Cosmos, but
also that the Universe is expanding. One of the
most significant cosmological results of the last
decade has been the realisation that the rate of
expansion is not slowing down, the prevailing
thought through the twentieth century, but
is actually accelerating due to the presence
of mysterious ‘dark energy’ that pervades the
Cosmos. This acceleration will have a signifi-
cant influence on our remaining evolution,
driving all galaxies and clusters to greater and
greater distances, until Virgo is too far away to
influence us. In the very distant future, a hun-
dred billion years from now, all galaxies will be
receding from the Milkomeda so fast that they
will become unobservable, and the night sky
beyond the local stars will be pitch black.
The accelerated expansion leave the Milkomeda
apparently alone in the Universe, and when
all of the local dwarfs have been consumed
there is little to do except for the stars to age
gracefully, slowly burning their hydrogen into
heavier elements. Every so often, any remain-
ing massive stars may explode in a supernova,
throwing their gas back between the stars and
providing raw material for the building more
stars, but more and more matter gets locked up
in small, red dwarfs that, rather than exploding
when they exhaust their nuclear fuel, simply
switch off and cool down, slowly radiating
away their energy.
Unfortunately, the very, very distant future of
our Universe appears to be quite grim, and
after a hundred trillion years, all star-formation
has ceased and the Milkomeda is filled with
the remnants of star formation; black holes and
white dwarfs from more massive stars, and the
dead and dying red dwarfs. Eventually, it is
thought that the basic constituents of matter,
the particles that make up the nuclei of atoms,
will begin to decay, turning the stellar remnants
into nothing but radiation and elementary par-
ticles. At the same time, black holes also decay
through a process known as Hawking radia-
tion, and the Milkomedea slowly evaporates
until, after a trillion, trillion, trillion, trillion
years, it will have dissolved into effectively
nothingness; the Universe will have arrived at a
new, never ending Dark Age.
Cosmic Evolution: The Birth, Life & Death of Galaxies | 105
The End?
The distant future of the Universe appears to
be a dark and lonely space, with essentially
nothing but the emptiness of space to keep
you company. Is this truly the fate of all the
stars and galaxies we see today? Some think
not! There is a chink in our scientific armour
and that is the fact that science is not a single,
all encompassing theory that can be applied
to all reaches of the Universe. In physics, we
rely on two very powerful, but incompatible,
theories; Einstein’s theory of General Relativity
which describes the action of gravity and the
large scale Universe, and Quantum Mechanics,
which explains the seemingly wacky proper-
ties of subatomic particles. We have known
for a long time that in regimes where both of
these are important, including the birth of the
Universe, they step on each other’s toes, and
confusion reigns. This is why we cannot under-
stand the very beginning of the Big Bang.
Scientists are, however, making inroads, with
ideas such as string theory and loop quantum
gravity beginning to meld gravity and quantum
mechanics. This has led to some interesting
ideas, with some, such as Neil Turok and Paul
Steinhardt, suggesting that the Universe is a
‘brane’, one of many floating in a higher dimen-
sional sea. They suggest that once our Universe
is large enough and old enough, it may collide
with another, leading to a new Big Bang and a
rebirth of our entire Universe and the cycle of
star birth, life and death will start again; surely
the Universe is the ultimate in recycling!
Until we have that final theory, the unification
of gravity and quantum mechanics, such ideas
are more fancy that rigorous science, and the
true ultimate fate of the Universe remains a
mystery. Hopefully, one day in the not too dis-
tant future, a smart, young scientist will see the
trail that leads to the solution of this mystery,
unveiling the darkest secrets of the Universe
and answering our most sought after questions.
While I am certain this person will not be the
author of this article, I do hope that it will be
someone who has read it.
Gene Silencing II

Gene
regulation
Peter Waterhouse
I n my first chapter, I described how the
existence of a virus protection mecha-
nism in plants was discovered, how it
operates, and how the mechanism has
been exploited in biotechnology applications.
In this second chapter, I continue the story
about this RNA degradation mechanism - of
which has some even more unexpected twists
to come.

Plant and Animal Dicer

Bioinformatics
The term “bioinformatics” has slightly differ-
ent meanings to different people, but to me
it means the computer-mediated analysis of
nucleotide and amino acid sequences in genes
and genomes, and this is becoming an increas-
ingly important tool in biological research.
One aspect of bioinformatics is to look at the
amino acid (aa) sequences of proteins that are
known to have related biological functions
and to see if there are stretches of aa sequences
that are conserved within them. These regions
are called domains. One can then look at the
aa sequences of biologically uncharacterised
 proteins to see if they contain any known do-
mains, and if they do, to use them to make pre-
dictions about the possible biological functions
of the proteins under scrutiny. This is exactly
the approach we took to search for plant and
animal Dicer genes. Some elegant biochemical
work by researchers in the USA, using a puri-
fied protein from Drosophila identified it to be
responsible for cutting up dsRNA into ~21nt
dsRNA fragments and to be the Dicer protein
mediating RNAi. When the sequence of this
protein was examined, it was found to contain
a number of domains (Figure 1A). These were:
two different helicase domains, two RNAseIII
domains, one dsRNA binding domain, one
PAZ domain and one DUF283 domain. The
presence of the helicase, RNAseIII and dsRNA
binding domains was totally understandable:
a helicase is an enzyme that unwinds dsRNA
g1A– or dsDNA, RNAseIII
Domains found isinananenzyme
Animalthat cuts
Dicer Protein
RNA, and a dsRNA binding domain (not
surprisingly)
Fig 1isAfound in proteins
– Domains that
found in an bind
Animal
to Dicer Protein
dsRNA. These are properties quite likely to be
possessed by an enzyme that is going to bind,
unwind (to allow access), and cut dsRNA. The
PAZ domain gets its name from a stretch of aa
sequence found to be shared by three proteins
called : Piwi, Argonaute and Zwille. DUF283
is the wonderfully named domain of unknown
function number 283. Armed with these
domains we searched plant, fungal and other
animal genomes for genes that encoded single
proteins containing all of these domains. We
found (Figure 1B) only one such Dicer gene in
each mammalian genome, two such genes in
insects, but found plants to have taken it to the
extreme and have at least four of these genes
(in Arabidopsis), and up to six (in rice) .
Why does a plant
need four Dicers?
Mice and men can survive quite happily with
one Dicer, so why have plants got so many?

Helicase N Helicase C DUF283 PAZ RNaseIII RNaseIII dsRNAB

Helicase N Helicase C DUF283 PAZ RNaseIII RNaseIII dsRNAB

Figure 1A: Domains found in an Animal Dicer Protein

Fig 1 B - Evolution of Dicer Genes
ig 1 B - Evolution of Dicer Genes

Figure 1B: Evolution of Dicer Genes

108 | Genes to Galaxies

When we compared the sequences of the
Dicer-like (DCL) genes in plants we found that
although rice has six, it has four different types
(two are duplicated), which match the four
different genes in Arabidopsis. So, if we call the
Arabidopsis DCL genes 1, 2, 3 and 4, then rice
contains one DCL1, two DCL2s, two DCL3s
and one DCL4. To see what functions these
genes might have, we obtained Arabidopsis
plants which are singly mutant for each of
these genes. We were expecting these mutant
plants to look fairly normal but to be more
susceptible to virus infection. We also thought
that having four DCLs may simply be a way of
Figure 2 Dicer mutants in Arabidopsis
DCL1 Wild DCL2 DCL3 DCL4
mutant type mutant mutant mutant
Figure 2: Dicer mutants in Arabidopsis
Figure 3 Arabidopsis plants with mutant DCL genes
Wildtype DCL2 mutant
DCL4 mutant DCL2&4 mutant DCL2,3 &4 mutant
Figure 3: Arabidopsis plants with mutant
DCL genes
Figure 4: DCL2, DCL3 and DCL4 in viral defence
boosting a plant’s defence capacity. Mammals
have an immune system to combat viruses and
may therefore not need this increased multiple
Dicer-mediated capacity. Uninfected Arabidopsis
plants that are mutant for DCL2, DCL3 or
DCL4 all look much like wild-type plants
(Figure 2), but plants that are mutant for DCL1
are very peculiar – dwarfed and twisted – and I
will come back to what DCL1 is doing later in
the chapter. So we challenged the DCL2, DCL3
and DCL4 mutant plants with a virus and
looked to see if they developed extreme virus
symptoms and whether the virus RNA genome
was being chopped up into ~21nt fragments.
We, also, stacked the mutations so that we had
double and triple mutants. The triple DCL2/
DCL3/DCL4 mutant plant looked very similar
to wild type - when not infected by a virus
(Figure 3), but when infected had much higher
levels of virus and more severe symptoms than
the wild-type plants, or indeed the single or
double mutants. This confirmed our hypothesis
that these three Dicers were providing defence
against viruses. The double mutants also gave
us a nice insight into the processing of the
dsRNAs. The DCL2/DCL3 mutant produced
virus dsRNA fragments of 21nts, the DCL3/
DCL4 mutant produced 22nt virus fragments,
and the DCL2/DCL4 mutant gave 24nt virus
fragments. This shows that each of the three
DCLs is chopping up the virus dsRNA and that
the DCL4 enzyme produces 21nt fragments,
the DCL2 enzyme produces 22nt fragments
and DCL3 produces 24nt fragments (Figure
4). When we transformed plants with hpRNA
transgenes, their RNAs were also processed
by DCL2, DCL3 and DCL4 into 22nt, 24nt
Gene Silencing II: Gene regulation | 109
 and 21nt fragments, showing that RNAi, as
proposed in the first chapter, is operating by
the virus defence mechanism. Interestingly, we
could detect almost no small dsRNA-derived
fragments in the DCL2/DCL3/DCL4 triple mu-
tant, suggesting that DCL1 is doing something
other than virus protection.
Virus-encoded silencing
suppressors
If plants have a virus defence mechanism that
destroys the replicating and single stranded
forms of their RNA genome, as suggested
above, how is it that virtually every species of
plant is known to be susceptible to infection by
at least one – and commonly by many – differ-
ent viruses? I previously described plant viruses
as having a basic set of three genes encoding
a replicase, a movement protein, and a coat
protein. However, I did not describe the func-
tion of one other type of viral gene. When we
were first determining the sequences of virus
genomes, it was relatively easy to identify the
replicase, movement and coat protein genes
but there was often a gene in the viral genome
with a function that was difficult to predict. It
turns out that these genes are silencing sup-
pressor genes (Figure 5). The protein from such
a gene suppresses the plant’s RNAi mechanism
and by doing so protects the virus from being
destroyed. This is a classic example of the war
that is waged between a pathogen and its host.
The virus infects the plant, the plant responds
by evolving a defence mechanism, the virus
Figure 5 - Luteovirus particle and RNA genome From the domains contained in the DCL1
F-box-like
silencing
suppressor
article and RNA genome
Replicase
F-box-like
silencing
suppressor
Replicase Movement Coat
Figure 5: Luteovirus particle and its RNA
genome
110 | Genes to Galaxies
counters this by evolving a way of inactivating
the plant’s defence mechanism. Different types
of plant viruses have different silencing sup-
pressor genes. Some bind to the small RNAs
made by the DCLs preventing them from be-
ing loaded into Argonautes, others inactivate
DCLs - preventing them from dicing the viral
dsRNAs. But my favourite group of viruses, the
luteoviruses, have an even more elegant way
of inactivating the RNAi mechanism. Plants
have an intrinsic system that degrades their
own proteins ensuring that each protein has a
specific working life. This operates by a system
called the proteosome which degrades proteins
when they have been labelled with a tag, and
this tag is placed onto proteins by a mecha-
nism that is guided by “F-box” proteins. The
first protein that a luteovirus produces when
it infects a plant cell is a silencing suppressor
protein that mimics a plant F-box protein.
This protein guides the tagging of Argonaute
proteins. So, by making one small protein the
virus guides the plant’s protein turn-over sys-
tem against a key component of the plant’s viral
defence system!
What is DCL1 doing?
Returning to the mutant DCL experiment, the
plants that were mutant for DCL1 showed a
really weird phenotype, even when they were
not infected by a virus. Also, we found in the
virus-infected DCL2/DCL3/DCL4 triple mutant
that the virus was not diced into small RNAs.
Taken all together this suggested DCL1 was
doing something other than virus defence.
protein, one would predict that it would have a
similar enzymatic activity to DCL2, DCL3 and
DCL4 - and it does. We thought we had been
really clever when we designed single stranded
hairpin (hp) RNAs as a way of guiding RNAi
against
our targetCoat
Movement genes. In fact, nature was
hundreds of millions of years ahead of us. It
turns out that almost all multi-cellular organ-
isms (plant and animal) produce their own
hpRNAs that are processed by DCL1 to pro-
duce 21nt RNAs, which are used by Argonaute
to guide the regulation of endogenous messen-
ger RNAs, and that DCL1 is essential for nor-
mal development. For normal development to
occur certain genes must be switched off, espe-
cially at the time of developmental transitions,
such as developing from a juvenile to an adult
form of a nematode or insect, or from vegeta-
tive to floral growth in plants. This switching
off is performed by the small RNAs produced
by DCL1 from special hpRNAs produced by
the plant at the right time and in the right tis-
sue. DCL1 differs from DCLs 2,3 and 4 in that
it specifically cuts out only one 21nt small RNA
from its hpRNA precursor (Figure 6), and this
is called a micro (mi)RNA. In Arabidopsis there
are at least 187 different miRNAs and there are
many more than this in animals (see Table 1).
Figure 7 - DCL1 and Argonaute (AGO1) mutant plants
Table 1
If DCL1 is not produced, the miRNAs cannot
be cut out of their precursor hpRNA molecules
and cannot be used by Argonaute to regulate
the target genes. This explains why our DCL1
mutant plant has such a weird phenotype – it
is a plant with incorrect developmental regu-
lation. Also, if we look at plants mutant for
Argonaute, they too look bizarre (Figure 7).
This is not surprising because the regulation
system cannot operate without both of these
proteins. In fact, both the DCL1 mutant and
Argonaute mutant shown in the photographs
are not completely inactive mutants but rather
a mutation that produces a truncated version of
Wildtype DCL1 mutant AGO1 mutant

Number of differ-
Species
ent microRNAs
Arabidopsis 187
Nematode 156
Drosophila 152
Mouse 547
Human 706

Figure 7: DCL1 and Argonaute (AGO1)

Figure 6 mutant plants
DCL-mediated production of small RNAs and actions of guided Argonautes

AG04 DNA
Epigenetic
changes
24nt

ds-RNA DCL3
DCL1

DCL2 DCL4
21nt
miRNA
AG01
22nt 21nt
AG01 AG01
mRNA cleavage

Developmental regulation RNA cleavage RNA cleavage

Viral & transposon defence

and development

Figure 6: DCL-mediated production of small RNAs and actions of guided Argonautes

Gene Silencing II: Gene regulation | 111

the DCL1 protein (missing the last 1/20th piece Indeed, plants and animals altered by artificial
of the protein) and a mutation that has only miRNAs are now beginning to be produced.
one amino acid different from the wild-type
Argonaute protein. Indeed, a totally inactive Further Reading
DCL1 or Argonaute gene in multi-cellular or-
ganisms is almost always lethal. Bernstein E, Caudy AA, Hammond SM,
Hannon GJ. Role for a bidentate ribonuclease
in the initiation step of RNA interference.
Future Research and Technology Nature. 2001, 409:295-6.
In an earlier section, I described how DCL3
Ding SW, Voinnet O. Antiviral immunity di-
chops up viral dsRNA into 24nt small RNAs as
rected by small RNAs. Cell. 2007, 130: 3-26.
part of an RNA virus defence pathway. It has
recently been found that DCL3’s major role is Margis R, Fusaro AF, Smith NA, Curtin SJ,
not so much in the control of RNA viruses, but Watson JM, Finnegan EJ, Waterhouse PM.
more in the control of DNA viruses. DCL3 still The evolution and diversification of Dicers in
cuts up dsRNA that is somehow produced from plants. FEBS Lett. 2006, 58: 2442-50.
the DNA virus, but the 24nt RNAs that are pro-
Mallory AC, Vaucheret H. Functions of micro-
duced are not loaded into the Argonaute that I
RNAs and related small RNAs in plants. Nat
have been discussing (AGO1), but rather into a
Genet. 2006, 38:850.
related protein called Argonaute 4. This protein
does not cleave single stranded RNA like its Fusaro AF, Matthew L, Smith NA, Curtin SJ,
cousin, but rather directs the compression of Dedic-Hagan J, Ellacott GA, Watson JM, Wang
dsDNA with sequences that are complementary MB, Brosnan C, Carroll BJ, Waterhouse PM.
to the 24nt RNA fragments. This prevents the RNA interference-inducing hairpin RNAs in
genes in the viral dsDNA from being copied plants act through the viral defence pathway.
into messenger RNA. Significantly, this also EMBO Rep. 2006, 11: 168-75.
happens for the protection of plants from trans- Pfeffer, P. Dunoyer, F. Heim, K. E. Richards,
posons – which are like retroviruses – which G. Jonard, and V. Ziegler-Graff . P0 of Beet
are in very large numbers in a normal plant Western Yellows Virus Is a Suppressor of
genome and if not repressed by DCL3 would Posttranscriptional Gene Silencing Journal of
move around causing all kinds of mutations. It Virology, 2002, 76: 6815-6824.
is also just beginning to emerge that this form
of RNA-directed DNA compression is a very
important process, not only for plants in their
control of viruses and transposons, but also
in both plants and animals in terms of normal
gene regulation – for example – in the inactiva-
tion of one of the X chromosomes (an essential
process) of human females. This control of
gene expression by DNA compression is called
epigenetics and this is a research field that, I
think, will be at the forefront of medical and
molecular plant and animal research over the
next decade.
Another area which will probably become a
major new technology is the use of artificial
miRNAs. We understand how to make trans-
genes that encode hpRNA templates which
DCL1 will process into miRNAs. Therefore,
we can use them to silence genes in much the
same way as RNAi but with more precision.

112 | Genes to Galaxies

Gene Silencing II: Gene regulation | 113
SETI - Planning for Success: Who Will
Speak to Earth?

What Will
They Say?
Jill Tarter
P
lanning for the successful detection
of a signal from extraterrestrial intelli-
gence covers the territory from making
sure there is champagne on ice at the
observatory to trying to figure out how to hold
a global conference where all cultural, histori-
cal, religious, political, and creative traditions,
that are embodied by humans on planet Earth,
can be represented in a discussion of whether
and how we might reply. Science fiction and
the motion picture industry have provided lots
of scenarios depicting the aftermath of signal
detection, many are unrealistic, many are not
very satisfactory, almost all reflect the political
tensions around the globe at the time they were
created. What should we, the scientists who
are attempting to detect a signal, set out as our
protocol for behavior? At the SETI Institute,
we’ve spent some time thinking about these
questions; both before 1993 when we were
funded by NASA (a federal agency), and after,
as we raise private and corporate contributions
to continue the search efforts.
The protocol fluctuates over time, as we have
more experience with false-positive detections,
as our search efforts evolve, as humans around
the world becomes more aware of our explora-
tory research, and as technology flattens the
world and offers both solutions and challenges
to global communication. This chapter will
give an overview of current plans, and future
projects, all of which are based upon the con-
viction that information about the detection of
a signal and any information encoded within
a signal are the property of all humankind.
Furthermore, it is important to state up front
that in those places in this chapter where
opinions are presented, usually in the absence
of data, the opinionated statements strongly
reflect the biases and views of the author, a
scientist who continues to be impressed by the
tyranny of light speed – it’s currently impos-
sible for us to get ‘There’ and it may be hard for
‘Them’ to get here.
Introduction: The
Arecibo Message
In 1974, the large radio telescope in Arecibo,
Puerto Rico was upgraded with both a new
surface of perforated aluminum panels and a
new radar transmitter working at a frequency
of 2380 MHz. To mark the completion of
the upgrade project, Frank Drake, then the
Director of the Observatory, decided to hold a
commissioning ceremony during which the ra-
dar transmitter was used to transmit a message
to space. The Arecibo telescope does not point
very far away from the zenith direction, and the
ceremony and transmission were timed to coin-
cide with the arrival of the Governor of Puerto
Rico. This meant that the direction towards
which the message was transmitted was a large
globular cluster of stars called M13 that hap-
pened to be overhead at the appropriate mo-
ment, even though those stars were more than
25,000 light years away, and any inhabitants of
that region would not receive the message until
the year 26,974 AD! The message consisted of
1679 bits (1’s or 0’s represented by the switch-
ing between two closely spaced frequencies)
and was repeated twice, lasting only a few min-
utes. More about the content of that message
later, for now it is the act of sending a message
that is of interest. Perhaps Prof. Drake chose
such a distant target because he anticipated the
116 | Genes to Galaxies
possibility of negative reaction to the message
transmission. And there was a lot of reaction.
The most prominent critic of the Arecibo mes-
sage transmission was the British Astronomer
Royal, Sir Martin Ryle, who wrote to Drake and
the newspapers complaining that it was “very
hazardous to reveal our existence and location
to the Galaxy; for all we know, any creatures
out there might be malevolent - or hungry.”
This criticism ignores the fact that it is already
too late to conceal our presence; the Earth has
been ‘leaking’ signals into space for nearly a
century, via our broadcast radio and TV signals.
However, Prof. Ryle’s comments do mark the
inception of a discourse on the merits of active
transmission vs. passive SETI listening. In turn,
this discourse raises the questions: if we ever
decide that it is appropriate to transmit, either
ab initio or as a reply to a message received in
the future, then who should speak for Earth
and what should they say? These are big ques-
tions, and of the type not routinely discussed
in the course of doing scientific research – but
they come to the forefront very quickly when
the science is SETI. Is Ryle right, was Drake
putting the Earth (and you and me) in great
peril by transmitting the Arecibo message?
All Intelligent Civilizations
Are Not Equal
Should active transmission be a part of SETI?
SETI research is currently being carried out in
several locations worldwide, occasionally even
in Australia. I work at the largest of these re-
search facilities, the SETI Institute, a non-profit
corporation in Mountain View, California.
We have grown steadily since we opened our
doors in 1984, and now typically have about
150 people working at the Institute, but only a
handful work with me in the Center for SETI
Research. The rest of my colleagues pursue
astrobiology in the Carl Sagan Center for the
Study of Life in the Universe, or education and
public outreach in our E/PO Center.
In 1997, the SETI Institute convened a series
of workshops that, among other things, seri-
ously discussed the appropriate guidelines for
interstellar discourse. The results of those dis-
cussions are part of a book, titled SETI 2020.
The workshops attempted to set out a roadmap
for the activities to be pursued by the Center
for SETI Research at the SETI Institute over
the next two decades. One of the participants,
Prof. Paul Horowitz from Harvard University,
summed up the reality of our terrestrial situa-
tion as follows: 21st century humans have an
asymmetric relationship with the universe; we
are a very young technology (~100 years) in a
very old galaxy (~ 10 billion years) – any tech-
nology that we can detect is going to be much
older than we are, and we should follow their
lead. That asymmetry led the workshop partici-
pants to these detailed conclusions :
• If or when we achieve contact with another
civilization, it will certainly be more techno-
logically advanced than we are. Contact with
a less technologically advanced civilization
is not now a possibility. In fact, any civiliza-
tions we contact are statistically likely to be
far more advanced. When the evolution of
planets and their attendant technologies re-
quire billions of years, it is unlikely that two
technological civilizations will be synchro-
nized to better than a million years.
• If it happens at all, there always has to be a
first contact between two technological civi-
lizations. Statistically, it is extremely unlikely
that our first contact with an ETI civiliza-
tion will also be its first contact with an ETI
civilization. Thus the advanced technology
we detect will have experienced this type
of encounter many times before. It already
may have established a galactic protocol for
information interchange, to which ab initio
transmissions by Earth will have no chance
of adhering. Thus we justify our asym-
metrical listen only strategy by recognizing
our asymmetrical position amongst galactic
civilizations. We are among the youngest!
• Transmitting is a more expensive strategy
than receiving. Within the next two decades,
the parameter space explored for signals can
be extended by the compounded growth
rate of many technologies. Transmissions
could benefit from these same exponential
improvements in technology, but with the
limited resources likely to be available
during this same period, we could not
SETI - Planning for Success: Who Will Speak to Earth? What Will They Say? | 117
add significantly to the high power of our
leakage radiation. As that leakage abates or
becomes more noise-like this argument loses
its force. Transmission will not be rewarded
for decades, perhaps centuries, because of
the great distances and round-trip travel
times for signals. Our resources are con-
strained, and it is thus prudent to pursue a
passive program of exploration that might
provide a positive result within years.
So far, this has all been a set of relatively
straight forward scientific arguments. The
SETI Institute has had no difficulty adopting
these points of view, and they guide the ap-
proach that we take in our SETI observing
programs today – listen only. But the partici-
pants included one more bullet that moves
beyond strictly scientific argument, and
that’s where things get interesting.
• Transmission is a diplomatic act, an activity
that should be undertaken on behalf of all
humans. We lack the cultural maturity to
accomplish such a cohesive action. Some
Working Group participants felt strongly
that this active strategy should not be
embarked upon unilaterally, without con-
sultation and consent. While most of the
participants believed that transmitting now
would be merely harmless and wasteful, a
few members felt that transmissions should
not be carried out without international
consultation and approval by appropriate
international administrative bodies.
Well, I guess that NASA never read the SETI
2020 report. On February 4, 2008, to celebrate
the 50th anniversary of the founding of NASA,
and the 40th anniversary of the day the song
was written, NASA used a Deep Space Network
transmitter to send the Beatles’ song “Across
the Universe” in the direction of the North Star,
Polaris. Again this message only lasted a few
minutes, but did NASA Administrator Michael
Griffin join with Frank Drake in putting our
planet in permanent peril? Not really, these
short duration stunts have literally no prob-
ability of being intercepted. Did Administrator
Griffin undertake this transmission on behalf of
all humans? I don’t remember being consulted,
were you? And that’s the more serious question.
The SETI 2020 workshop participants sug-
gested that ‘international consultation and ap-
proval’ should be sought prior to undertaking
a transmitting strategy, and they assumed that
such approval would come from ‘appropriate
international administrative bodies’. In much
earlier scientific discussions conducted under
the auspices of the International Academy of
Astronautics and the International Institute of
Space Law, scientists, diplomats, and lawyers
interested in SETI had drawn up an informal
protocol with the impressive title “Declarations
of Principles Concerning Activities Following
the Detection of Extraterrestrial Intelligence
” which also presumed a measure of interna-
tional approval. In that protocol, the text of
Article 8 stated “No response to a signal or
other evidence of extraterrestrial intelligence
should be sent until appropriate international
consultations have taken place. The procedures
for such consultations will be the subject of
a separate agreement, declaration or arrange-
ment.” Most scientific teams conducting
SETI observations adopted this protocol as
their own policy. In 2000 the United Nations
Committee on the Peaceful Uses of Outer Space
was informed of this protocol, and documents
were formally filed away, perhaps for action at
some future time. Today, we still have no global
form of governance, there are no appropriate
international administrative bodies that can
speak for all humans. Nevertheless, in ways
not imagined even a decade ago, all humans
may soon be able to speak for themselves using
social-networking technologies that are rapidly
becoming global in what appears to be a viral,
and unstoppable spread. Before too long, it
will be possible to have a global conversation
with all cultures, traditions, ideologies, and
points of view participating. And note that it
will be YOUR generation that is having this
conversation, not MINE. I can raise the issues
in this chapter and encourage you to prepare
to answer them, but it is you and the rest of
the younger global inhabitants that will need to
feel your way forward towards an outcome that
represents all humans. It will take a while, and
I think that technology will continue to assist
the process in unforeseen ways (Twitter and its
descendants might do this), but you probably
have time to be deliberate.
118 | Genes to Galaxies
Although it could happen tomorrow, detection
of a signal that raises the question of a reply
will probably require a lot more searching than
we’ve done to date. And no, I don’t think that
they will arrive in shiny spaceships any time
soon (and there’s no solid evidence that they’ve
done so in the past either!) But you might be
interested to know that at this very moment,
messages are deliberately being broadcast into
space by dozens of entrepreneurs, who have
acquired access to decommissioned telecomm
transmitters around the globe. What messages
are they sending? The transmissions are the
personal wisdom, philosophies, hopes, fears,
and fantasies of those individuals that the vari-
ous marketing web sites have persuaded to part
with some cold hard cash. I’m not kidding;
search the internet for yourself. But I wouldn’t
waste your money. There is little chance that
your message to the cosmos will be received.
Those transmitted signals are relatively weak,
and they are far too ephemeral to represent a
realistic active-SETI transmission program. It
is the short-lived nature of these and previous
transmission activities that convinces me that
a realistic, active-SETI program is far in the
future, even if a global conversation should
conclude that it’s a good idea.
Humans, at this stage of our evolution, aren’t
very good at conceiving and fulfilling five-year
plans, and our success with 100 or 500-year
plans is pretty pathetic! If we Earthlings plan
to conduct a systematic, active-SETI program,
it will be necessary to keep at it for many
thousand years, or more. That’s because a
transmission program that lasts n years will
generate signals that travel through space, at a
rate of one light-year (~ 9.5 trillion kilometers)
per year, growing weaker as they propagate
and spread out, until they reach a potential
recipient who is d light years away. The signals
will be detectable by that recipient for only n
years. That means that during the evolutionary
history of the potential recipient, they must
be looking at Earth, with the right receiv-
ing tools, during the n-year window that the
signals present themselves. Unless n is a very
big number, the chances that the recipients are
looking Earthward when our signal arrives will
be very small (see Figure 1).
Figure 1: Diagram of a signal beamed towards a distant receiver, lasting only n years.
Therefore, I think that active-SETI programs
will have to wait until humans “grow up”
enough to be able to conceive and execute very
long term projects.
Are other scientists dealing with these kinds of
questions? A close parallel in terms of moral,
ethical, and risk-appraisal discussions are the
very active debates now taking place within
the small portion of the scientific community
involved in Planetary Protection. Among the
astrobiologists at the SETI Institute, there are
some researchers who worry about the poten-
tial for forward and backward contamination
of life on Earth due to the planned robotic and
human explorations of other bodies in our own
Solar System. Although we now contemplate
the possibility of microbial life in the briny
oceans beneath the frozen ice surfaces of the gi-
ant moons of Jupiter (Europa, Ganymede, and
Callisto), and perhaps even Saturn’s tiny moon
Enceladus, the focus of concern over con-
tamination is primarily Mars. Might microbes
brought back from Mars threaten life on Earth,
or might terrestrial organisms brought to Mars
by human and robotic explorers contaminate
that planet and threaten any native Martian life
forms? If life exists in liquid aquifers beneath
the frigid desert surface of Mars, might it pose a
danger to life on Earth?
Do humans have the right to ‘terraform’ Mars
in order to make that planet more habitable for
us? One way to improve the chances for sur-
vival of the human race, and protect it against a
SETI - Planning for Success: Who Will Speak to Earth? What Will They Say? | 119
future, civilization-ending impact from a giant
asteroid might be to spread humans to at least
one other planet. We’re looking hard at Mars
as that destination. Just because we can do so,
should we do so? In truth, we’ve already made
similar decisions for planet Earth. We are rou-
tinely destroying rain forests and other habitats
in order to benefit some groups of humans
economically, at the expense of an uncounted
number of species of life that we have yet to
discover in those wild habitats. If we eliminate
unique and undiscovered forms of life on this
planet, then there should be no reason not
to do the same on Mars. Or if we decide to
preserve Martian life forms because they are
precious, then shouldn’t we preserve precious,
as yet unknown, life forms on Earth? These are
not questions that any of my colleagues and I
debated when we were in graduate school, but
scientific exploration is taking us in new direc-
tions, and as a result we need to expand the
boundaries of what it means to do science.
How Do You Speak To An Alien?
Let’s return to the 1974 Arecibo message. A
nice explanation of the components of the
Arecibo message appears on the Wikipedia web
site http://en.wikipedia.org/wiki/Arecibo_mes-
sage. As previously mentioned, the message
consisted of 1679 bits, and the transmission
was repeated twice. The repetition is impor-
tant, because it lets the recipient know that
they got it all. The number of bits is important
because it helps to decode the message. 1679
is the product of two prime numbers 23 x 73.
Our concept of numbers and mathematics
encourages us to think that any extraterrestrial
technology will have a way of counting, and
that numbers will be prime in their numbering
system as well as in ours. On this planet we
have now documented an isolated Amazonian
community whose language and thought
patterns do not include this sort of detailed
numerology, there are no words for the quan-
tity of objects or specific numbers. But these
people have not constructed transmitters or
receivers for interstellar communication. Our
bias is that mathematics will be universal for
any technological civilization, but we should
try to remember that it is in fact a bias. Our
stereoscopic, binocular vision system provides
us with depth perception, and the evolution
of our brain and our training allow us to in-
terpret two-dimensional representations, or
abstractions of information. This may not be a
universal capability of all technological civiliza-
tions either, but we find it hard to imagine any
other way of perceiving detailed information,
and so the Arecibo message incorporates this
bias as well. What can you do with the product
of 23 and 73? You could take a linear string of
1679 bits and rearrange it into 73 columns and
23 rows, or 73 rows and 23 columns to make
a two-dimensional picture, using two different
colors for the two different binary bits. In the
case of the Arecibo message, the choice of 23
Figure 2: 1974 Arecibo message arranged
in 2-dimensions, and decoded.
120 | Genes to Galaxies
columns (see Figure 2) yields a definite pat-
tern, even if not an obvious message, whereas a
73-column display looks pretty random.
So what did the Arecibo message say? In ad-
dition to assuming that we have mathemat-
ics in common with the recipients trying to
decipher this message, the message also made
use of the fact that anyone receiving the mes-
sage would have had to detect it with a radio
telescope and would realize that the message
had been transmitted at a particular radio
frequency, or wavelength (wavelength = c/
frequency = 12.6 cm, where c is the speed of
light). The wavelength therefore is a shared
unit of measurement, a common ruler. So the
message starts out (if your custom is to read
from top to bottom) with a counting lesson,
showing the graphical, binary representation
of the numbers 1 to 10. These numbers are
then used to give the atomic numbers of the
biogenic elements H, C, N, O, P – the stuff our
DNA is made from! Next comes the formulas
for the base pairs of Adenine, Thymine (A-T),
and Cytosine, Guanine (C-G) along with the
dioxyribose-phosphate backbone of DNA, and
a representation of its double helix structure,
and an estimation of the number of nucleotides
in the human genome (not yet sequenced
when this message was sent). The population
of humans on Earth (only 4 billion in 1974),
a human stick figure with a measurement bar
indicating the human is 14 wavelengths tall.
A cartoon of our solar system, with the third
planet from the Sun offset towards the human,
indicates where the message came from. Finally
(or first if your custom is to read bottom up)
the spherical Arecibo telescope and the trans-
mitted message rays are depicted with a blatant
brag that it is 2430 wavelengths in diameter. A
pithy message, perhaps not easily understood;
also perhaps not what you might have chosen
to tell others about us. We’ve made a few more
attempts, not with transmitted signals, but with
greeting cards carried by spacecraft.
In 1972 and 1973, NASA launched the Pioneer
10 and 11 spacecraft to explore Jupiter and
Saturn. But they didn’t stop there; these space-
craft had sufficient energy to allow them to
leave the solar system and travel towards the
stars (slowly – it will be millions of years before
Figure 3: Plaque attached to Pioneer 10 and 11.
either vehicle approaches a star). Once it was
understood that these objects would travel into
interstellar space, Carl Sagan convinced NASA
to include a plaque on each to send a message
to any distant technologies that might happen
to discover them (see http://en.wikipedia.org/
wiki/Pioneer_plaque). These plaques include
a handy ruler, though this time it isn’t based
on the frequency of a radio transmission, but
rather the frequency of the fundamental spin-
flip transmission of the hydrogen atom (1420
MHz or a wavelength of 21 cm) which is the
most abundant and simplest element in the
universe. Figure 2 has a diagram of the space-
craft with humans beside it for scale and their
height given in wavelengths. The human male
has his hand raised in greeting (or perhaps
it means something else to those who might
eventually find it). The solar system is shown
with an indication of the spacecraft’s trajectory.
The 14-legged spider is actually a map that says
where and when in the galaxy this craft was
launched. The key to deciphering the map is
SETI - Planning for Success: Who Will Speak to Earth? What Will They Say? | 121
to realize that radio astronomical pulsars each
have unique periods for their pulses, and that
with age pulsars spin down and their pulse
rates slow. The directions from the map center
show the radial directions away from Earth
in which the pulsars lie, the length of the line
represents their distance, and the binary code
along each line gives the precise pulse period
(in time units of 1/frequency = 7 x 10-10 sec)
at the epoch of spacecraft launch. There is a
15th leg, without a binary period, and that
shows the distance and direction from Earth to
the Galactic center. In the early 1970’s much of
the public and media seemed more concerned
with the naked bodies on this plaque than with
the content of the message!
In 1977 NASA reused this pulsar map, and
the hydrogen line as part of the covers for
a two golden records containing the sights
and sounds of Earth that were attached to
the Voyager 1 and 2 spacecraft (the offend-
ing naked humans occur only in the encoded
information on the record itself, see http://
en.wikipedia.org/wiki/Voyager_Golden_
Record). The Voyagers also left the solar system
after completing a grand tour of the outer
planets, and since they are traveling faster than
Pioneer 10 and 11, they are now the most
distant objects made by humans, and their tra-
jectories will take them to the vicinity of nearby
stars in less than 100,000 years. Since a record
afforded much more opportunity for includ-
ing information about us, a committee chaired
by Carl Sagan was created to decide upon the
content. The record contains greetings from
the children of Earth in 55 different languages,
as well as a message of peace from the then
President of the United States, Jimmy Carter.
90 minutes of music, believed by the commit-
tee to be a fair representation of the musical
history and traditions of Earth, are included
for the discovers’ listening pleasure (should
they have ears or other appropriate acoustical
sensors), as are dozens of natural and human-
created sounds of the planet. 115 drawings and
photographs are encoded as analog signals on
the record (the record cover explains how to
recreate the images), and these can be viewed
at http://voyager.jpl.nasa.gov/spacecraft/scenee-
arth.html. In true form, the committee created
an edited, approved, and highly biased view of
Figure 4: Successful detection of the carrier signal from the Voyager 1 spacecraft at a
distance of 106 AU
122 | Genes to Galaxies
life on Earth; it is hugely biased towards hu-
mans, with little regard for the enormously im-
portant and diverse microbial community with
which we share our world, or the other ani-
mals, but then it is the humans who built the
spacecraft. The image set contains no poverty,
hunger, disease, war, pollution, deforestation,
overcrowding, or any other indication of a less
than perfect world. We can expect that if the
Voyagers are ever found by another technologi-
cal civilization, and the contents of the record
are ever deciphered, they will probably realize
that we were putting our best foot forward.
Quite apart from the technical difficulties, and
the truth in advertising issues, the images that
are included tell us humans a great deal, but
they require a shared contextual background
for interpretation. We take that context for
granted, indeed it is very difficult to ignore or
unlearn what it is we’ve evolved to interpret.
Perhaps young children have the best capacity
for ignoring what they ‘know’ and seeing these
images as others, who are not us, might do. As
an example take one particular image of sprint-
ers in the Olympics, rather than seeing the im-
age as depicting great athletic prowess, a child
might ignore the notion of distance perspective
and see instead two species; the big and the
Figure 5: Detection of Voyager 1 signal with software detection algorithm.
small. The big species is strange because it is
not quite bilaterally symmetric; each individual
has only 1 ½ lower limbs, and it isn’t always
the same side that is missing half a limb. And
of course most children can delight in the fact
that this home planet has invented anti-gravity,
because none of the big species is touching the
ground! As the committee members confessed,
this exercise was as much an effort intended for
humans as for extraterrestrials. Billions of years
from now, when the Sun has evolved into a red
giant and the Earth has been consumed within
its atmosphere, the Voyagers will preserve this
flattering encapsulation of the aspirations of
those who built these craft.
At the SETI Institute, we have another relation-
ship with Voyager 1 – we use it as our fiducial
or standard candle on the sky. Because it is so
far away, the carrier signal that it emits to en-
able NASA to track its motion, and downlink
its data, arrives at the Earth as a very faint sig-
nal moving on the sky at nearly the same rate
as the distant stars. In fact that’s what we might
expect a signal from ET to look like, and we’ve
built very sensitive signal detection equipment
to detect such emissions. As we have been
commissioning the Allen Telescope Array over
the past year, we’ve pointed our 42 dishes at
SETI - Planning for Success: Who Will Speak to Earth? What Will They Say? | 123
this spacecraft repeatedly to insure that our
beamformers and control and detection soft-
ware are all working like they should. Figure
4 presents a ‘waterfall plot’ showing a small
piece of the spectrum surrounding the Voyager
1 signal as a function of time. Each point on
this plot represents a 1 second observation with
spectral channels that are each 1 Hz wide. The
Green lines are intended to focus your eye in
the right place. This signal is hard to detect
with the naked eye, but Figure 5 illustrates
that it is easily detected with the SETI special
purpose signal detection software – assuming
everything is working properly. Some day we
hope to detect such a signal from someone
else’s technology.
Earth Speaks
In 2009, the SETI Institute participated in the
Kids Science Challenge contest [http://www.
kidsciencechallenge.com/], in which young
students were challenged to help us figure
out ways to make our search for ET better.
The winner, Kamau Hamilton a 6th grade
student from New York City, suggested that
extraterrestrials might not speak English, so
that we should plan on communicating with
the sounds of Earth. He was too young to have
known about the Voyager golden record, but he
independently came up with the same idea. We
invited Kamau to record sounds of Earth that
hadn’t existed in 1977, and we used his visit
to the SETI Institute to launch a web-based
project we’ve been thinking about for a long
time. This is a first tiny step towards holding
a global conversation to answer the questions:
who will speak for Earth and what should they
say? My colleague, Douglas Vakoch a social
scientist, has been wondering whether there
are any cultural universals (ideas, practices,
memes) that can be found in every human
group around the globe, now and perhaps
throughout time – things that really belong in
a message to ET if we want to define who we
are. Earth Speaks [http://earthspeaks.seti.org/]
is a web site on which we’ve posted Kamau’s
sounds of Earth. Now people around the world
are encouraged to contribute their own sounds,
peculiar to their locality, and their ideas of what
we should say or would like to say in a mes-
sage to an extraterrestrial to this web site. We
don’t have any plans to actually transmit these
messages, rather the content of these submis-
sions are being categorized and tagged with
key words and with region of origin as part of a
research project to uncover cultural universals.
The posts have been fun to read, one of my
early favorites ended with “… Also, don’t kid-
nap us and poke us. We hate that.”
Now that you have finished this article, you
can help us plan for success. Please go to the
Earth Speaks website and let us know what you
think should be contained in a message from
humans to extraterrestrial intelligence.

124 | Genes to Galaxies

SETI - Planning for Success: Who Will Speak to Earth? What Will They Say? | 125
Six Minutes
of Terror
Wayne Lee

The research described in this paper was carried out at the Jet Propulsion Laboratory,
California Institute of Technology, under a contract with the National Aeronautics and
Space Administration.
Copyright 2009 California Institute of Technology.
Government sponsorship acknowledged.
U ntil that night, I had thought
that moments frozen in time
where your life flashes in
front of you only occurred
in the movies. I glanced down at my watch.
In California, it was 8:40 p.m. on January
3, 2004, and it seemed as if we had hit the
ground over an hour ago. In reality, our rover
Spirit had landed on Mars only five minutes
ago, but its radio beacon was nowhere to be
heard. We had no idea whether Spirit was safe-
ly on the ground, but unable to communicate
for reasons unknown, or whether the rover’s
tiny electronic heartbeat had been terminated
by an untimely demise.
I looked down at my display console in
the mission control center at the NASA Jet
Propulsion Laboratory. My boss, Rob Manning,
was sitting next to me. He called up a window
with a plot of Spirit’s signal strength as a func-
tion of time. I was frantically pointing to the
flat line indicating a zero signal at the current
time. Manning, an eternal optimist, and a virtu-
al legend within the NASA robotic space flight
community by virtue of having pulled off the
only previous Mars landing in recent history,
calmly pointed to a blip on the graph repre-
senting a point in time somewhere in the past.
Unfortunately, we had no idea whether the blip
indicating a positive radio signal was before or
after the expected landing time. If it were after,
then we would have had positive evidence that
Sprit had at least survived the initial impact.
The problem was that in our haste to get the
mission control display software ready for
landing day, we had forgotten to program the
computer to stamp the tick marks on the graph
with the time of signal receipt. There was no
way to tell for certain.
I looked around the mission control room and
saw seemingly optimistic faces, but they were
somehow unable to mask uncomfortable body
language present only when one has a knot
in the pit of their stomach. The supremely ar-
rogant side of me wanted to tell everybody to
have a little faith that Sprit was still alive. The
other side of me was experiencing the so-called
“life flashback” phenomena. I was mentally
reviewing every decision we had made over the
previous 40 months of designing, building, and
testing the landing system for the rover and be-
ginning to second-guess a fair number of them.
One of my first thoughts was to question
whether we should have even attempted
something this ambitious on such a short time
scale. Unfortunately, we did not have much
of a choice. The world of Mars exploration
NASA/nasaimages.org
128 | Genes to Galaxies
40 months prior was clouded with uncer-
tainty about the future. Spectacular success
from the Independence Day landing of Mars
Pathfinder in 1997 was followed by the em-
barrassing crash of the Mars Polar Lander
shortly before its scheduled touchdown in
December 1999. Subsequently, NASA manage-
ment in Washington put all future Mars shots
on hold due to a loss of confidence in the
once-proud program.
In early 2000, a small group of respected en-
gineers, including Manning and future Spirit
mission operations manager Mark Adler,
concocted a seemingly innocuous proposal to
achieve redemption. Their theory was seem-
ingly simple and foolproof. Why not re-fly the
same landing system that led to the wildly suc-
cessful Mars Pathfinder landing back in 1997?
Unlike the ill-fated Polar Lander, Pathfinder
was a proven landing system. “We even have
spare parts left over,” they argued.
The catch was that the payload Pathfinder put
on the surface, a small pyramidal-shaped base
station barely knee-height in size, and a six-
wheeled rover the size of a small laser printer,
was scientifically uninspiring with respect to a
second flight. Back in 1997, the goal was sim-
ply to demonstrate that NASA was still capable
of landing something on Mars despite having
not done so since the Viking missions back in
1976. However, the unwritten laws governing
efficient use of exploration funds mandated
that the next mission following Pathfinder
not only land safely, but deliver more ad-
vanced science.
“No problem,” countered Manning and Adler.
What if the small base station and tiny rover
was replaced with a single, larger rover capa-
ble of roaming a kilometer from the landing
site over a period of 90 days? For a science
payload, Manning and Adler proposed to tap
into the ingenuity of professor Steve Squyres
from Cornell University. Squyres was a well-
respected geologist who was in the midst of de-
veloping a sophisticated set of tools for a future
mission to return Martian rocks to Earth using
robotic vehicles. These instruments would
allow the rover to both remotely sense the
chemical composition of rocks and drill into
their interiors for a microscopic examination.
Overall, the concept sounded great, but I have
to admit that I believed there was no chance
that the mission would be approved.
I was quite surprised in August 2000 when
senior NASA management not only announced
approval for the mission, but also decided
to fund two rovers with each one flying on a
separate launch. The reasoning was simple.
In theory, the odds for achieving at least one
successful landing would dramatically increase
if we sent two rovers. In practice, this strategy
resulted in a tremendous amount of pressure
on the flight team to go “two for two” because
the natural tendency of the media would focus
attention on the failed mission rather than the
successful one. As an added measure of pres-
sure, NASA management asked for a launch in
June 2003. Spacecraft normally take 48 months
or more to design and build. We were given
only 33. The chance for redemption was not
going to come easily.
The mission was officially dubbed the “Mars
Exploration Rovers,” or MER for short. Just
prior to launch, NASA would christen the two
as Spirit and Opportunity. However, for the
first three years of the effort, we knew them as
an impersonal MER-A and MER-B, respectively.
While most of the project’s engineers went off
to figure out how to design a sophisticated six-
wheeled rover the size of a small ride-on lawn
mower, I was given the assignment of leading
what was initially a small group of engineers
challenged with figuring out how to land the
vehicles in one piece.
Strangely enough, a good way to visualize
the enormous challenge we faced in landing
the rovers on Mars is to think about a rocket
launch. These events are quite spectacular
to watch due to the sheer amount of energy
released. In fact, in order to send Spirit and
Opportunity to Mars, enough energy was
released by the two Delta 2 launch vehicles to
propel the vehicle to a speed over 30 times fast-
er than a speeding bullet at the time of rocket
burnout. At that speed, one could fly from
Sydney to Los Angeles in about 15 minutes.
By the time the two rovers reached Mars about
seven months later, they were still moving at a
respectable speed of nearly 22,000 kilometers
per hour. Put simply, that is a speed in excess
of 25 times the speed of sound on Mars, or
what aerodynamicists refer to as Mach 25. The
challenge was in removing all of that remaining
energy from the system in under six minutes.
Each Delta 2 rocket utilized a stack of fuel
35 meters high in order to propel Spirit and
Opportunity to Mars. It would have been
practically impossible for our tiny rovers to
carry an equivalent amount of rocket fuel for
NASA/nasaimages.org
Six Minutes of Terror | 129
deceleration at Mars. Instead, we relied on at-
mospheric drag to slow the vehicles. However,
this seemingly clever solution was not without
its drawbacks. When an object moves through
an atmosphere at hypersonic speeds, the colli-
sion with the air molecules slows the vehicle,
but at the expense of generating an enormous
amount of heat. Our computer simulations
indicated that the rovers would be subject to
heating of about 60 watts per square centim-
eter. Although this amount may not sound
impressive, imagine holding onto 25 incan-
descent light bulbs in the palm of your hand.
If the rovers had been directly subjected to the
heat from atmospheric entry, they would have
been incinerated.
The key to survival was to encapsulate the
vehicles in a protective shell. Each rover was
designed so that its six wheels and wing-like
solar panels could fold up to allow the entire
assembly to fit in a pyramidal shaped volume.
Once folded, the vehicle was placed on the bot-
tom face of a metal tetrahedron split open with
the other three edges folded down. The edges
were then folded back up to encapsulate the
rover with the tetrahedron. Next, the encapsu-
lated assembly was placed inside a composite
backshell structure shaped like a blunt cone
with an open bottom. A saucer-shaped heat-
shield was then attached to bottom, open face
of the backshell to seal the tetrahedron inside.
This entire system was designed to fly into the
Martian atmosphere seemingly backward with
the blunt end facing forward.
Starting with Mercury, followed by Gemini,
and ending with Apollo, three generations of
astronaut ferrying spacecraft utilized this blunt-
body capsule shape to successfully reenter the
Earth’s atmosphere. We put the same idea to
use at Mars. Harvey Allen, who was one of the
foremost American aerodynamic geniuses of
the 1950s, pioneered the theory that this seem-
ingly unintuitive shape from an aerodynamic
perspective would both provide a tremendous
amount of drag, while limiting the amount
of heat generated by the deceleration proc-
ess. Nevertheless, at the point of maximum
deceleration about two minutes after entry
into the Martian atmosphere, our analysis
indicated that the outer skin of the heatshield
NASA/nasaimages.org

130 | Genes to Galaxies

would be exposed to a temperature of nearly
1500 degrees C.
As implied by the name, the job of the saucer-
shaped heatshield was to take the brunt of the
heating from flying through the atmosphere at
hypersonic speeds. The skeleton was construct-
ed from carbon composite, but coated with a
special cork-like material dubbed SLA-561V.
Within this code-name, the “A” stands for
“ablator” which is a type of material that chars
at low to moderate heat rates, and then dissoci-
ates and flakes off at higher levels of heating.
This process protects an entry capsule in two
ways. First, the heating energy goes into char-
ring the heatshield rather than the tetrahedron
or rover within. Additional heat is subsequently
carried away from the capsule within the dis-
sociated material.
One of the initial problems we faced was in
determining an adequate amount of SLA-561V
with which to coat the heatshield. If we con-
structed the ablator layer too thin, we would
risk the danger of burn through. Unfortunately,
we faced a lot of pressure from management to
reduce the mass of the heatshield because the
estimates for rover mass were coming in heaver
than expected. We knew that the computer
programs that sized the requisite thickness for
the SLA-561V always erred on a thicker answer
due to the uncertainty in estimating both the
external heating environment and the response
of the ablator material to heat. The question
was, “by how much?”
After months of debate, we convinced our heat-
shield experts to agree to reduce the thickness
from the originally recommended 1.9 centim-
eters down to 1.4 in an effort to shave about 20
kilograms from the system. The next step was
to prove that such a thickness was adequate
to prevent the capsule from overheating. Our
solution involved using a remarkable facility at
the NASA Ames Research Center in California
called the arc jet. This machine is about 20 me-
ters long and with a 60 MegaWatts rating, con-
sumes enough electricity to light a small city.
Essentially, the arc jet shoots a super-hot stream
of gas into a small test chamber at the end of
the machine. We verified our design assump-
tions by placing small samples of SLA-561V,
MASS Digital Image for Cornell/NASA
cut to the desired thickness, in the chamber
and then measuring its performance.
Besides keeping the capsule cool, we faced
another key challenge in ensuring survival dur-
ing the fiery deceleration through the Martian
atmosphere. Somehow, we needed to ensure
that the capsule maintained enough aerody-
namic stability to keep the blunt heatshield end
facing forward at all times. Our aerodynamics
team at the NASA Langley Research Center
in Virginia initially utilized a technique called
computational fluid dynamics, or CFD for
short, to make the initial predictions. CFD is a
technique where the area around the capsule
is divided into tiny squares that form a grid.
Then, a powerful supercomputer computes the
flow of air around the capsule by numerically
solving the equations of fluid motion within
each part of the grid.
Numerical techniques such as CFD are ex-
tremely powerful tools, but limitations exist.
The Langley engineers warned us that the
computer solutions provided somewhat reason-
able estimates for the capsule’s aerodynamics
at speeds greater than Mach 10, but less so at
Mach 5 and below. In order to verify the ac-
curacy of the CFD, they proposed that we con-
duct a test at a ballistic range facility. This sort
of test would involve the use of a naval-war-
ship-like cannon to shoot a small, palm-sized,
tungsten model of the capsule down a 200-me-
ter interior corridor. Laser activated cameras
spaced at even intervals down the range would
be used to photograph the model during flight.
By looking at the orientation of the capsule
Six Minutes of Terror | 131
within the photos, the Langley engineers would
then be able to infer its aerodynamic properties
and match them to the CFD results.
We selected the ballistic range at the Eglin Air
NASA/nasaimages.org
Force Base in Florida as the location to conduct
the test. The Air Force was happy to oblige us,
and they invited us to come down in the Fall
of 2001. In an unfortunate twist of fate, we
selected September 11th as our test date. I will
always remember the moment that morning
when Prasun Desai, our lead flight dynamics
engineer from Langley, came running into the
hotel lobby to tell me that a “small plane” had
just crashed into the World Trade Center. We
had no idea of the magnitude of the tragedy
that would unfold that day, and we had a dead-
line to meet, so we decided to continue onto
Eglin to conduct the test.
In retrospect, running the test that morning
was a poor decision. We did not realize the
magnitude of the large boom set off when the
cannon shot the capsule down the range at
Mach 5. The explosion shook the building,
which was a normal effect, but also managed to
rattle the nerves of base personnel who subse-
quently called the commander’s office to ask if
the facility was under attack. Not surprisingly,
the Air Force shut us down for the day. Over
the next few months, we learned the bitter real-
ity of working for the space program. We had
a launch date to meet in less than two years,
and a schedule slip was practically impossible
because launches are possible only every 26
132 | Genes to Galaxies
months when Earth and Mars are perfectly
aligned. It was extremely difficult to continue
to work and not be emotionally distracted
by the events of the world. But, there was
no choice.
Fortunately, the Air Force invited us back to
Eglin a month later to complete the ballistic
range testing. By then, we had begun to turn
our attention to the next issue in our long
queue of problems to address. Specifically, the
Martian atmosphere is so thin that insufficient
air exists to fully decelerate the capsule. In fact,
even if the rovers survived the fiery decelera-
tion from Mach 25, they would still impact the
ground with a velocity greater than the speed
of sound without further intervention. The
solution involved deploying a large parachute
close to the ground to further increase the drag
on the capsule.
Designing a parachute suitable for use on a
Mars landing presented somewhat different
challenges than crafting one for skydiving on
Earth. One primary issue was ensuring a suffi-
ciently strong chute. No matter how low to the
ground we chose to open the chute in order to
minimize deployment speed and therefore force
seen by the fabric, there was no way to avoid
the violence of a supersonic deployment. Our
initial calculations indicated that we required
a chute with a diameter of about 9 meters and
capable of withstanding the possibility of over
11 metric tons of force at a predicted inflation
speed up to 1,600 kilometers per hour. Due to
space limitations, we were forced to limit the
mass of the chute to about 20 kilograms, and
fit the entire fabric assembly in a volume barely
bigger than a small, bathroom-sized trash can.
In order to put a large chute in such a small
space, our engineers were forced to utilize a
super-thin blend of nylon and polyester for its
construction.
By late spring of 2002, the team was ready
to test the chute to determine whether the
fragile design would withstand the forces of
deployment. Unfortunately, we did not have
the means to conduct a realistic flight test at
supersonic speeds. Instead, our plan was to
take a flight prototype chute to the Orchard
Proving Grounds in Idaho, anchor it with a
2,700-kilogram weight, and then drop it out
of a helicopter. The large weight was designed
to subject the chute to the requisite force at
the time of inflation. When the appointed test
time arrived, we held our collective breaths,
and then watched in shock as the chute fabric
ripped to shreds. The entire test article, an-
chored by the huge weight, hit the ground at
high speeds, and the team spent the remainder
of the morning digging the contraption out
of the ground. To make matters worse, post-
test analysis indicated that the anchor weight
was too light to generate the force expected
during parachute deployment in the Martian
atmosphere!
We were now faced with two problems. First,
the team needed to find the weakness in the
design of the fabric and the stitching. Then,
we also needed to determine a method to ad-
equately test the chute. Our solution involved
going back to the Ames Research Center to
utilize the world’s largest wind tunnel. NASA
engineers refer to this place as the “80 x 120”
in reference to the cross-sectional dimensions
of its test chamber in feet. I remember walking
into the tunnel for the first time and feeling my
jaw drop when I realized that the interior was
almost as large as the Staples Center Arena that
is the home to the Los Angeles Lakers, and that
the six fans that pumped air through the tunnel
compared in height to a two-story house.
MASS Digital Image for Cornell/NASA
In theory, our two-step wind tunnel test strat-
egy seemed foolproof. During the first step,
we would inflate a prototype test chute using
a low-speed wind flow, and then walk under
the inflated canopy to look for suspected stress
points. After applying extra stitching to rein-
force those weak points, we would then put the
chute back into the tunnel and turn the wind
flow up to hurricane-like speeds of 80 knots to
generate the same magnitude of forces expected
in the thin Martian atmosphere at supersonic
speeds. Unfortunately, our streak of bad luck
continued as we encountered yet a third prob-
lem. During the first test in the tunnel, the
chute canopy did not inflate. It simply opened
and collapsed in a motion similar to a jellyfish
propelling itself through water. We now had to
prove that this effect, nicknamed “squidding,”
would not occur on Mars.
Nobody would have guessed at the time that
we would spend the next eight months in a
mad dash of trial and error to determine how
to debug the inflation problem, strengthen the
weak points in the canopy, retest the proto-
types to prove to everybody’s satisfaction that
all was well, and then finally manufacture the
actual chutes that would find their way onto
the two capsules bound for Mars. Normally,
manufactured components would have been
delivered to the rover’s assembly room at the
Jet Propulsion Laboratory in California. The
tightness of the schedule forced us to deliver
the flight chutes for integration almost directly
to the launch pad at the Kennedy Space Center
in Florida. As an added measure of franticness,
we executed the final verification test of the up-
dated design prototype in June 2003, the same
month as the launch.
Despite the long hours put into the design of
this enormous chute, our calculations showed
that the size was still too small to fully deceler-
ate the capsule to a safe landing. In fact, we
determined that after the flight-computer-
commanded chute deployment at an altitude of
about 8 kilometers and speed of 1,600 kilom-
eters per hour, the capsule would decelerate to
a terminal velocity of about 270 kilometers per
hour in less than a minute. The laws of phys-
ics, conspiring with the thinness of the Martian
atmosphere, guaranteed that the capsule would
Six Minutes of Terror | 133
decelerate no further than terminal velocity
even if we waited the entirety of the remaining
90 seconds prior to ground impact. In stark
contrast, a person falling out of an airplane on
Earth without a parachute reaches a terminal
velocity of only 195 kilometers per hour.
So, after four minutes of fiery flight to decel-
erate from 22,000 kilometer per hour, and
another two minutes on the parachute to slow
down from 1,600 kph, we would still need at
least one other way to remove the final 270
kph from the system to achieve a safe land-
ing. In reality, our design employed two more
deceleration devices. The first of the two was a
relatively simple set of three, downward-point-
ing rocket motors mounted to the inside wall
of the backshell. These “retros,” as we called
them, contained just enough propellant to
theoretically slow the capsule to zero velocity.
However, getting the vehicle in a configuration
to fire the rockets was a complicated matter.
Since the rockets were mounted inside the
capsule for protection from the heat of entry
into the Mars atmosphere, we first needed to
jettison the heatshield to expose the exhaust
nozzles to the exterior environment. Then, the
tetrahedron containing the rover would be me-
chanically lowered on a tether-like bridle into a
position suspended 20 meters below the back-
shell. This complicated sequence was designed
to complete in 40 seconds and ensured that
MASS Digital Image for Cornell/NASA
134 | Genes to Galaxies
the rover stayed well out of the way of the hot
exhaust gasses expelled from the retros during
firing. We were reminded of this important fact
during rocket testing when a technician left a
small metallic object near the test stand. The
exhaust cut through the metal easier than a hot
knife through butter.
Unfortunately, thousands of computer simula-
tions told us that enough uncertain variables
existed that zero velocity after retro firing
would never be achieved. For example, the
landing radar measuring altitude and velocity
to allow the flight computer to ignite the rock-
ets at the precise time had a 1% error potential,
the amount of thrust imparted by the retros
was temperature dependent and could vary by
2%, and an onboard camera system used to
detect and correct wind-induced lateral motion
by firing tiny horizontal-pointed rockets had an
error potential of 25 kilometer per hour. With
all of these sources of performance uncertainty,
we calculated that the tetrahedron-encapsulat-
ed rover could still hit the ground at a speed of
up to 90 kilometers per hour on a bad day.
As crazy as it sounds, we elected to allow the
tetrahedron to slam into the ground and cush-
ion the impact, as opposed to actively attempt-
ing to reduce the residual post-retro-firing
velocity to zero. The second of the two final
deceleration devices, a set of protective airbags
encapsulating the tetrahedron, served as the
key to this extreme strategy. Our space-fairing
airbags operated on a conceptual principle
loosely similar to automobile airbags, and were
demonstrated as feasible for use at Mars during
the Pathfinder landing in 1997. However, a big
difference between Mars and car airbags is that
ours were constructed from the bullet-proof
vest material Kevlar in order to resist rock
strikes on the Martian surface.
When we started working on the landing sys-
tem design back in the fall of 2000, our initial
plan naively involved using the Pathfinder
airbag blueprints to fabricate new bags with
the old design. One of our first priorities in-
volved determining whether the old design was
capable of cushioning the impact of a heavier
vehicle. During Pathfinder, the total mass
of equipment that hit the ground, including

NASA/nasaimages.org
spacecraft, tetrahedron, and airbags, weighed
in at less than 400 kilograms. For Spirit and
Opportunity, this figure was expected to in-
crease by an additional 150 kilograms. In order
to verify performance with this extra mass, we
raided the National Air and Space Museum in
Washington to retrieve the Pathfinder flight
spare airbags out of a display, and then pressed
them back into service as a test article.
We attempted to conduct our first airbag test
the week before Christmas of 2000 in the large
vacuum chamber at the NASA Plumbrook
Station in Sandusky, Ohio. This chamber tow-
ers nearly 100 meters high and looks almost
like the containment dome of a nuclear reac-
tor when viewed from the outside. Our test
strategy involved the use of bungee cords to
propel the airbags from the top of the chamber
onto jagged Hawaiian volcanic rocks at the bot-
tom. The rocks were an integral part of the test
because most of our potential Martian landing
sites were littered with small rocks. There was
no question as to whether the airbags would
encounter rocks at the time of landing. The
question was, “how many rocks would the
vehicle strike?”
During the first test, it was extremely sobering
to see the airbags hit the rocks at the bottom of
the chamber, pop, and then instantly deflate.
In hindsight, this failure was the first warning
that the airbag development process would
be extremely challenging. At the time, we
somehow refused to acknowledge reality and
attributed the failure to the fact that the airbag
material was weakened by prolonged exposure
to ultraviolet light emitted from the powerful
spotlights in the Pathfinder spacecraft assembly
room. That foolish theory was disproved when
the test team showed up in Ohio early the next
year with a set of freshly manufactured airbags.
New bags yielded the same results as they
subsequently ripped upon striking the rocks in
the chamber.
Now, we were in a real quandary. Airbags, by
their very nature of being constructed out of
fabric rather than metal, are extremely dif-
ficult to analyze using computer simulations,
especially when it comes to proving that they
will be resilient to tearing when striking rocks
at high speeds. We quickly realized that the
only way to gauge whether a design concept
would work was to take a prototype into the
test chamber. Unfortunately, testing was a long,
tedious affair. Each test cycle consumed nearly
two days and required hoisting the bags to the
top of the chamber, waiting almost eight hours
for the vacuum pumps to reduce the air pres-
sure to Mars levels, retrieving the bags from the
chamber after the drop, and then sewing up the
ripped fabric in preparation for the next test.
After each test, the airbag design team would
enter the chamber to inspect the damage
induced by the rocks and ascertain the ro-
bustness of the current design concept. Each
rock was of a unique size and shape, and was
covered with a unique color of chalk dust.
By looking at the color residue on rips in the
airbag, we were able to determine the culprit
rocks causing the damage. Our nemesis was
a small, 30-centimeter tall rock powered with
black chalk. Although seeming innocuous in
size, this rock contained a sharp, tooth-like
projection at the top that ripped through many
design concepts. I often fell asleep at night
worrying about the “black rock.”
Each test failure compounded the time pres-
sure on the team to arrive at a working solu-
tion prior to launch. A test airbag could only
be patched up for eight drops before the toll
of abuse rendered it useless. And, if a design
concept failed, the process of redesign and
manufacturing a new test prototype consumed
nearly four months. In total we executed over
Six Minutes of Terror | 135

50 test drops between 2001 and 2003 to arrive
at a viable concept. That final design consisted
of eight layers of Kevlar in vulnerable areas to
keep rocks from penetrating the inner bladder
of inflation gas. And, in a desperate schedule
situation similar to the parachute, the actual
flight airbags bound for Mars were delivered di-
rectly to the Kennedy Space Center rather than
to the spacecraft assembly facility in California.
With the myriad of technical challenges to
overcome on both the landing system and
rover side of the design, Spirit and Opportunity
barely made it to the pad in time for their lift-
offs in June and July 2003, respectively. After
our hardware left the Earth, I had mistakenly
thought that we were looking at seven easy and
quiet months in transit to Mars. In retrospect,
I should have realized that our experiences
over the past 33 months were an indicator
that nothing came easily on this mission. In
fact, the time between launch and landing
amounted to some of the busiest moments dur-
ing the mission.
One of the first things we discovered after
launch was that our predictions of the vehicle
dynamics during retrorocket firing failed to ac-
count for all the force disturbances in the sys-
tem. So, we went out into the California desert
over the summer of 2003 to perform full-scale
test firings in order to gather data that allowed
us to reprogram the flight computer to com-
pensate. Then, a few days prior to Christmas,
a huge dust storm developed on Mars. This
storm effectively thinned the Mars atmosphere
136 | Genes to Galaxies
NASA/nasaimages.org
and put the vehicle at risk of deploying the
parachute too close to the surface. After a lot
of debate with uncertain facts, we made the
decision to reprogram the flight computer
again. This time, we asked it to deploy the
chute earlier, and while at a faster velocity, to
compensate for the thin atmosphere. The down
side was an increase in risk to ripping the chute
due to excessive forces during inflation.
Yet another serious problem surfaced with one
week to go prior to landing. Jason Willis, one
of our lead avionics engineers, discovered a
serious flaw in the electronics responsible for
triggering pyrotechnic initiated events such
as parachute deployment, heatshield jettison,
airbag inflation, and retrorocket ignition.
Normally, the flight computer arms these pyro-
technics for firing only seconds prior to use for
safety reasons. Test results from our high fidel-
ity electronics testbed indicated a subtle timing
bug in the circuit that caused the arming com-
mand to be ineffective. The only viable solution
was to order the flight computer to remove the
safety inhibits and enter the atmosphere with
all the pyros dangerously armed.
And, just when I thought we were finally ready
despite the risky solutions we were forced to
implement, I received a phone call from lead
flight dynamics engineer Prasun Desai the night
before Spirit’s landing. Right when I was sit-
ting down to watch a football game to unwind,
Desai informed me that the team had just
found a programming error in the sophisticated
simulations we had been using to prove to
ourselves that the onboard software would be
able to fly the vehicle through the atmosphere.
Although this revelation was not exactly the
same as saying that the software was not going
to work, it was nevertheless not a reassuring
phone call. He promised me that they would
work through the night to fix the simulation.
Less than 24 hours later, I discovered first hand
why our Mars Exploration Program manager
had dubbed landing the “six minutes of terror.”
At precisely 8:29 in the evening on January
3rd, 2004, the capsule containing the Spirit
rover plunged into the top of the Martian
atmosphere moving at 25 times the speed of
sound. During that first minute of atmospheric
flight, very little deceleration occurred due to
the extreme thinness of the upper Martin at-
mosphere. I remember looking at the altimeter
on my display console in mission control and
watching the altitude tick off alarmingly quick
at a rate of one mile every second – 70 miles,
69, 68, 67, 66.
“We’re dropping like a falling rock,” I mut-
tered to myself. In reality, I probably used
another word other than “falling” that began
with the same letter. Fortunately, my headset
microphone was off, and the comment did not
get broadcast over the loop and onto national
television. For the previous three years, we had
studied the simulations results, and we knew
just how fast the vehicle would fall on Mars.
However, studying graphs and numbers falls
woefully short in terms of preparing for the
shocking reality of watching it happen in real
time. One way or another, Spirit would reach
the ground in six minutes, and the outcome
of exhausting and stressful work depended on
the autopilot, 40 months of sound engineer-
ing judgment, and the hands of fate. There
was nothing we could do other than watch
and pray.
During most of the fiery plunge through the
Martian atmosphere, a tiny radio beacon from
Spirit chirped out simple electronic beeps
to let us know that she was still alive. When
the signal terminated near the time of ex-
pected ground impact, we were left wondering
whether a distant cousin of our “black rock”
had sliced open the airbags, or whether the
winds were too high, or whether the radar
had provided a bad retrorocket firing solution,
or heaven forbid, we had simply overlooked
a careless mistake somewhere in the system.
While Manning and I stared at my computer
console looking for an answer we knew we
would not find, our communications engineer,
Polly Estabrook, was on the phone talking
nonstop with the ground crews of our radio
tracking stations around the globe.
After 15 minutes of awkward silence in the
control center, Estabook startled me with an
excited, “they see it, they see it!” That procla-
mation was followed by instant mad celebra-
tion inside mission control worthy of a winning
goal scored in the final minutes of a World Cup
final. I have to admit that I was probably the
only one in the room who missed the celebra-
tion, at least initially. My responsibility was to
call out “safe touchdown” once we established
proof, and the skeptic in me wanted more
evidence from Estabrook other than an excited
proclamation. I never gave the call, but it hard-
ly mattered. A little faith had already delivered
the answer the others were awaiting.
Just prior to the successful landing of the
Opportunity rover three weeks later, Desai
assured me that the simulation was working
this time around and asked if I had any plans
for the evening before landing. “Don’t know,”
I replied, “but I’m getting too old for this
stuff, so I’m turning off my cell phone in case
anybody calls.”
Six Minutes of Terror | 137
 Reproduced with kind permission HarperCollins Publishers Australia
(c) Karl S. Kruszelnicki Pty Ltd 2009
www.abc.net.au/science/k2

Man on Moon Conspiracy

On 15 February 2001, the American Fox TV Network broadcast a
program called Conspiracy Theory: Did We Land on the Moon?
Mitch Pileggi, an X-Files actor, hosted this hour-long show, which
claimed that NASA had faked the entire Apollo moon project by
filming it in a movie studio. This myth has a small following —
according to both a 1995 Time Poll and a 1999 Gallup Poll, about
6% of Americans ‘doubt’ that 12 astronauts walked on the Moon.
The conspiracy theorists cite all kinds of evidence.
For example, they point out that in all the photographs that
supposedly show the astronauts on the airless surface of the
Moon, you cannot see the stars in the black sky. The explanation
is simple. Even today’s best quality film cannot simultaneously
show both a very bright object (white spacesuit in sunlight) and a
very faint object (star). Story Mugrave, an astronaut who has flown
in a space shuttle six times, said that whenever he was outside
the shuttle in the bright sunlight, he couldn’t see the stars either.
But when the shuttle was in the shadow of the Earth and his eyes
had time to adapt to the darker environment, he could then see
the stars. (By the way, all the Moon missions happened during the
Moon’s day — which lasts about 14 Earth days — so that the
astronauts could see what they were doing.) And anyhow, when did
you last see stars in the sky in daytime?
The hoax believers also point out that in the photos, the
shadows of the astronauts and the various pieces of scientific

102 GREAT MYTHCONCEPTIONS

138 | Genes to Galaxies

apparatus on the Moon’s surface are not quite parallel. They
should be parallel, these doubters claim, if lit by only a single,
distant light source such as the Sun. This is true — but only if you
are working with both a level surface and a three-dimensional
field. When you try to show the three-dimensional reality of a
bumpy surface in a flat two-dimensional photograph, the shadows
fall in slightly different directions.
The conspiracy theorists also claim that the ripple in the
American flag, as seen in the still photos, is proof that the landing
was faked in a movie studio, because only moving air can make a
flag ripple. This is nonsense — for a few reasons. First, there is no
wind in a movie studio — unless the wind machine is switched on.
Second, if there were enough wind in a movie studio to ripple the
flag, it would have also moved the dust at their feet. But third, and
most importantly, the ripple was a well-documented accident. The
workshops at the Manned Spacecraft Center in Houston, Texas,
attached the nylon American flag to vertical and horizontal bars.

Man on Moon Conspiracy 103

Man on Moon Conspiracy | 139

 These bars were telescopic, to save space before they were used.
Neil Armstrong and Buzz Aldrin had trouble with the horizontal
telescopic rod, and were unable to pull it all the way out. This gave
the flag a ripple. Because the flag ‘looked’ realistic, later Apollo
crews intentionally left the horizontal rod partially retracted.
In fact, the wobbling flag helps prove that the astronauts were
on the Moon. The flag is wobbling because it has just been set
up. And it continues to wobble for a short while in a very unusual
fashion. This is because the gravity on the Moon is one-sixth the
gravity on Earth, and because there is no air on the Moon to
quickly stifle the movement of the flag.
But the incontrovertible proof that human beings did go to the
Moon is the existence of a total of 382 kg of Moon rocks, which
have been examined by thousands of independent geologists
around the world. These rocks have been compared to a few
dozen Moon rocks that landed in Antarctica, after being blasted
off the Moon by meteor impacts, and to some Moon rocks
recovered by unmanned Russian spacecraft. All of these Moon
rocks share the same characteristics.
Moon rocks are very odd. First, they have a very low water
content. Second, they are riddled with strange little holes, because
they have been hit by cosmic rays on the airless surface of the
Moon for millions of years. The Moon rocks are very different from
Earth rocks, and could not be faked by any current technology. To
manufacture fake Moon rocks, you would have to squash them
using about 1000 atmospheres of pressure, while keeping them at
about 1100°C for a few years. Then, while keeping them under
pressure, you would have to cool them slowly for a few more years.
There is another proof. Since 1969, new geological dating
methods have been invented, and applied to the Moon rocks —
and all the dating methods give the same dates for the Moon
rocks. If there was a conspiracy, NASA scientists in 1969 would
have to have worked out what new dating methods would be
invented over the next 30 years, and fake their rocks accordingly.
After looking at all the evidence, I prefer to follow the words of
the 1937 Nobel Prize winner in Medicine, Albert Szent-Gyorgyi: ‘The

104 GREAT MYTHCONCEPTIONS

140 | Genes to Galaxies

Apollo flights demand that the word “impossible” be struck from
the scientific dictionary. They are the greatest encouragement for
the human spirit.’

More Objections

There are dozens of problems with this ‘faked moon landing’

conspiracy theory, but I will deal with just a few. (If you want to read
more, check out Phil Plait’s ‘Bad Astronomy’ home page at
www.badastronomy.com).
One problem — how do you fool the entire worldwide network of
400 000 scientists, engineers, clerks, lawyers, accountants, technicians
and librarians, who helped to make this monumental project happen?
Another problem — the pictures. NASA broadcast the lunar
landings live, and made them available to the TV networks of the
world at no charge. Most of these pictures are fairly fuzzy, because
the technology wasn’t very good in those days. But they also released
1359 ultra-high-quality 70 mm film frames, 17 very high-quality pairs
of 35 mm lunar surface stereoscopic photographs, and 58 134 high-
quality16 mm film frames. Is this the act of an organisation trying to
cover up a big conspiracy?

Real Conspiracy
Theory

Why are there no photographs of Neil Armstrong walking on the

Moon? On the first Moon mission, Michael Collins stayed in orbit
around the Moon, while Neil Armstrong and Buzz Aldrin explored the
surface of the Moon.

Man on Moon Conspiracy 105

Man on Moon Conspiracy | 141

 Here is a neat, and totally unprovable, conspiracy (which I heard
from a physicist, who knew another physicist, who had met Wernher
von Braun, the famous rocket scientist — so it must be true!).
Apparently, Buzz Aldrin was supposed to be the first man to walk
on the Moon. But at the last minute, Neil Armstrong pulled rank — he
was the commander of Apollo 11, after all — and decided that he
would be the first person to walk on the Moon.
So (according to this conspiracy theory) Buzz Aldrin got his
revenge by refusing to take any photos of Neil Armstrong. The only
photos of Neil Armstrong on the Moon are tiny reflections of him
(taken by himself ) in the golden faceplate of Buzz Aldrin’s spacesuit
helmet.

References
‘Apollo Moon Landing — A resource for understanding
the hoax claims: did man really walk on the moon?’,
National Space Centre, UK: www.spacecentre.co.uk.
Matthews, Robert & Allen, Marcus, ‘Hot debate: did America
go to the moon?’, Focus, February 2003, pp. 73–76.

106 GREAT MYTHCONCEPTIONS

142 | Genes to Galaxies

Man on Moon Conspiracy | 143
Extremophiles
& Exoplanets:
Expanding the Potentially Habitable
Real Estate in the Galaxy

Jill Tarter
W
e discovered the very first plan-
etary worlds in orbit around
a body other than the Sun in
19911. They were small bod-
ies (0.02, 4.3 and 3.9 times as massive as the
Earth) and presented a puzzle because they or-
bit a neutron star (the remnant core of a more
massive star that had previously exploded as a
supernova) and it was not clear whether these
bodies survived the explosion or reformed from
the stellar debris. They still present a puzzle,
but today we know of more than 350 other
planetary bodies in orbit around hundreds of
garden-variety stars in the prime of their life
cycle. Many of these planets are more massive
than Jupiter, and some orbit closer to their host
stars than Mercury around the Sun. To date we
have not found another planetary system that
is an exact analog of the Earth (and the other
planets of our solar system) orbiting a solar-
type star, but we think that is because we have
not yet had the right observing instruments.
Those are on the way! In the next few years,
we should know whether other Earth-mass
planets are plentiful or scarce.
At the same time that we have been develop-
ing the capabilities to detect distant Earths, we
have also been finding that life on Earth occurs
in places that earlier scientists would have
considered too hostile to support life. Scientists
were wrong, or at least didn’t give microbes
the respect they deserve. We now know that
extremophiles can exist (and sometimes thrive)
in the most astounding places: at the bottom of
the ocean around hydrothermal vents, in ice,
in pure salt, in boiling acid, and irradiated by
massive doses of UV and X-rays. There do ap-
pear to be places on Earth that are too dry for
even these (mostly microbial) extremophiles, or
perhaps our sensors aren’t yet sensitive enough
to find them.
Since life-as-we-know-it is so extraordinarily
hardy, might it exist today (or in the past) on
any of the exoplanets that are being found?.A
group of scientists known as astrobiologists are
trying to answer that question. This lecture will
discuss what appears to be possible in the near
future, as well as the questions that will likely
remain unanswered until new technologies
enable new explorations in the more distant
future. It might even turn out that our first in-
dication of another inhabited world will be the
signals deliberately generated by its inhabitants
– that’s right, SETI, the search for extraterres-
trial intelligence.
Exoplanets
In his book Plurality of Worlds, Steven J. Dick2
has chronicled the millennia of discourse about
other inhabited worlds, based upon deeply
held religious or philosophical belief systems.
The popularity of the idea of extraterrestrial
life has waxed and waned and, at its nadir, put
its proponents at mortal risk. Scientists at the
beginning of the 21st century have a marvelous
opportunity to shed light on this old ques-
tion of habitable worlds through observation,
experimentation, and interpretation, without
recourse to belief systems and without risking
their lives. A good place to keep track of the
newest planet discoveries is the interactive cata-
log of the Extrasolar Planet Encyclopedia web
site http://exoplanet.eu/catalog.php. At a glance
you will be able to see how many new planets
have been announced in the time between
146 | Genes to Galaxies
when I submitted this manuscript, and when
you are reading it. Today the tally is 353 plan-
ets orbiting 294 bodies (including those puz-
zling pulsar planets).
Exoplanets are primarily detected by indirect
techniques: astrometry, radial velocity studies,
transits, and gravitational micro-lensing. The
first two of these detection methods measure
the reflex motion of the star due to the mutual
gravitational attraction between planet and
star; the third measures the minute diminution
of brightness that occurs periodically when a
favorably aligned planet passes between its star
and our telescope, blocking some of the star’s
light; the final method measures the brighten-
ing of a distant star when another (unseen)
star and its orbiting planet align perfectly and
the gravitational masses of the star and planet
bend the light from the distant star causing it
to appear brighter. Only very recently have we
actually seen images of objects we believe to
be planets in orbits around stellar hosts. The
Hubble Space Telescope was used with a cora-
nographic mask to block out the light from the
star Fomalhaut (think of holding up your hand
to block out the light from a distant street light
while you look for something faint in the area
surrounding your hand). In 2004 observations
showed a small (single-pixel) bright object
located in a large disk of dust, far from the star
(115 astronomical units from the star, or 115
times as far from the star as the Earth is from
the Sun). This object was confirmed as a planet
Fomalhaut b when an HST 2006 observation
showed that it had moved slightly along a
believable orbital track. A series of rapid im-
ages of the star HR 8799 using a groundbased
telescopes allowed observers to remove the
effects of atmospheric distortion and to im-
age 3 giant-planet point-sources orbiting at
distances of 24, 38, and 68 AU, far from the
star. The smallest mass planet to date (exclud-
ing those puzzling pular planets) orbits the
very low mass star Gliese 581, and has a mass
of 1.9 Earth masses. The reflex motions of the
star that are induced by the planetary orbit are
greater and easier to observe if the star mass is
small. What we haven’t found is a planet like
the Earth orbiting its star at just the right dis-
tance so that its surface temperature might be
conducive to permitting liquid water. This just-
so region around any star is called the habitable
zone. For the Sun, it stretches from just outside
Venus’s orbit to the orbit of Mars; for more
massive stars the habitable zone is further from
the star, and it is closer in for lower mass stars.
We think that such terrestrial analogs exist, but
we have not had the capability to detect them
until now, with the launch of spacecraft capa-
ble of making precise measurements of stellar
brightness to search for transits. The Kepler
spacecraft is expected to detect a handful of
Earth-sized planets within the next few years.
If it doesn’t, we will have to revise our thinking
about the way stars and protoplanetary disks of
gas and dust actually form planets.
Most of the planets discovered are giants, and
many have been surprising, and many are in
orbits that are highly inclined to the equatorial
plane of the star, unlike those of our own solar
system. ‘Hot Jupiters’ in short period orbits
very close to their host stars, and an abundance
of high eccentricity (non-circular) orbits were
surprising discoveries, though we are begin-
ning to have reasonable explanations based on
interactions with viscous protoplanetary disks
and a version of cosmic billiards. Initially it
was assumed that the presence of hot Jupiters
would doom any terrestrial planets within the
habitable zone, but recent studies by Raymond
et al3 argue that it is possible to have wet, ter-
restrial planets, even though a Jupiter-mass
planet has migrated through their orbital radii
on its way towards the star. The near-term
future, with a suite of new instruments, holds
promise for the detection of other Earths, large
moons of gas-giant planets, and other poten-
tially habitable cosmic real estate. The next
obvious question is: will they be inhabited?.
Extremophiles and Weird Life
Astrobiology is the science that deals with the
origin, evolution, distribution, and future of life
in the universe. It has been successful in bring-
ing together scientific specialists from many
different disciplines to tackle these big-picture
questions. Many of my colleagues at the SETI
Institute are astrobiologists studying organisms
living in extreme conditions (by human stand-
ards) in an attempt to better understand the
origin of life on Earth and the potential habit-
able real estate for life beyond Earth. In the
past few decades we have expanded the range
of conditions recognized as suitable for life. Life
is no longer confined between the boiling and
freezing points of water. Hyperthermophiles
live at high temperatures (and sometimes also
high pressures), the current record holder be-
ing archean microbial Strain 121 that thrives
at 121 ºC metabolizing iron, but it can sur-
vive up to 130 ºC4. At the other extreme,
the psychrophilic bacterium Psychromonas
ingrahamii survives and reproduces (very
slowly) at -12 ºC in the ice off Point Barrow,
Alaska5. Macroscopic ice worms occupy and
move through the Alaskan glaciers as well as
the methane ice seeps on the floor of the Gulf
of Mexico using natural antifreeze to protect
their cellular structures.6 Sunlight, once ar-
gued to be the source of energy for all life, is
completely absent miles beneath the surface
of the ocean, around the deep hydrothermal
vents, where a rich and diverse community
of organisms thrives in the dark, at enormous
pressures. Small blind shrimp there have devel-
oped IR-sensing eye spots to navigate the vent
environs or to travel from one vent to another
using their thermal signatures7. Some chemical
process (or processes) within the vents also
produces minute quantities of visible light
that are harvested by green sulfur bacteria for
photosynthesis even though many hours go by
between photons8. Humans increasingly pro-
tect themselves from exposure to UV radiation
as the protective layer of atmospheric ozone
thins, since our DNA lacks sufficient repair
mechanisms to survive intense radiation envi-
ronments. Yet organisms inhabiting the highest
freshwater lakes on Earth, in the caldera of the
Lincancabur volcano overlooking the Atacama
desert, have adapted to the huge UV load that
their altitude and evaporating environment
present9. Colleagues from the SETI Institute
free-dive in these lakes each austral spring to
catalog these organisms and study the DNA
repair mechanisms they have elaborated. If life
once occupied Mars, similar mechanisms might
have been employed by organisms seeking to
survive the dual stresses of increased radiation
and desiccation due to loss of planetary atmos-
phere. Even more spectacular, Deinococcus
Extremophiles & Exoplanets | 1473
radiodurans can withstand millions of rads
of hard radiation because its DNA repair
mechanisms are so effective. This skill probably
evolved, not because it encountered naturally
high radiation environments, but because des-
iccation causes the same sorts of breaks in DNA
linkage; a sufficiently robust repair mechanism
can endow survival independent of the damage
source10. As a result, this microbe is the focus
of many bioremediation programs to deal with
radioactive materials, and is being sought in
the Atacama to demarcate areas just too dry for
life. Neutral pH was once thought essential for
life, but acidophiles are plentiful; cyanobacte-
ria and fish can survive at pH ~4, but the red
alga Cyanidium caldarium and the green alga
Dunaliella acidophila can live at pH below 111.
In the ground waters of industrial slag heaps,
extremely alkaline-tolerant microbes have
been found thriving at a pH of 12.812. While
salt has been used historically to preserve food
from decay due to bacterial action, halophilic
archean microbes have been found living
within pure NaCl crystals13. Astronomers may
find it extremely unpleasant to live beyond the
‘just right’ bounds of our current terrestrial
environment, but clearly life has a greater toler-
ance and no lack of innovative ways of making
a living. Within the past few years, we have
begun to accept the concept of the ‘deep hot
biosphere’, and to acknowledge that perhaps
ten times as much biomass is resident in the
crust beneath our feet, as compared to the
surface biomass with which we have long been
familiar14. All these biological adaptations must
inform our searches for life elsewhere in the
universe.
Mindful of the adaptability of life to extreme
environments, we should reconsider our
own solar system (where we may have some
hope of systematic in-situ sampling) and we
should expand our inspection to any bodies
capable of providing raw materials and energy
sources that might be exploited by biology of
any sort. Thus, in addition to the terrestrial
planets Venus, Mars, and Earth (which were
all biologically connected during an earlier
epoch of planet building and bombardment),
we should consider the large icy satellites of
Jupiter and Saturn, namely Europa, Ganymede,
148 | Genes to Galaxies
Callisto, and Enceladus where liquid, briny,
water oceans are thought to exist beneath their
icy outer crusts. Titan might be a world hosting
biology on its surface without liquid water as a
solvent, although the presence of a subsurface
water ice slush is now fairly certain. Perhaps
results from the ESA’s Venus Express mission
will shed light on whether the chemical dis-
equilibria previously noted in the Venusean
atmosphere require explanations involving
Grinspoon’s revival of the Sagan and Salpeter
‘sinkers, floaters, hunters and scavengers’15.
For the foreseeable future NASA will continue
a ‘follow the water’ strategy, returning to Mars
with robots and humans to look for signs of ex-
tinct life from a wetter, warmer epoch or even
for subsurface extant life. The seasonal and
inhomogeneous appearance of trace amounts of
methane in the tenuous Martian atmosphere16
might be explained by the presence of metha-
nogens in subsurface liquid aquifers, or by the
more prosaic, geological transformation of oli-
vine rock, but that too requires flowing water.
Subsequent missions may venture to Europa
to verify the existence of a massive water ocean
and to examine the tantalizing discolorations
near the surface cracks that could be the end
products of organic molecule irradiation17,
and then, later still, return to make a sterile
penetration of the ice and search for life in the
water below.
The resilience and diversity of extremophiles
have now also focused attention on life-as-
we-don’t-yet-know-it. Life on Earth (even
extremophiles) seems completely connected;
life-as-we-know-it appears to have had a single
common ancestor. But what about life-as-we-
don't-yet-know-it?.Might it exist on Earth
today in extreme environments, and remain
undetected because of our instrumental biases
towards carbon-based organisms?.Might it ex-
ist on other bodies in our solar system, and in
the planetary systems of other stars, perfectly
suited to those local environmental conditions?.
What are the limits of organic life in planetary
systems? Its a heady question that, if answered,
may reveal just how crowded our Earth and the
cosmos could be with alien biology. In 2007,
the National Academy of Sciences released
a report on “The Limits of Organic Life in
Planetary Systems”18, that is life with an alter-
nate biochemistry, what they called ‘weird life’.
How would we recognize life based on different
biosolvents, different nucleotides, different
metabolic pathways?.What instruments should
we develop to aid human and robotic explorers
undertaking a search for other forms of life?.
It seems impossible to avoid one particular trap
of being 21st century humans. In seeking life,
or its technological by-products, we cannot
search for what we cannot conceive, and it is
also impossible to guarantee that we will cor-
rectly interpret what we find. This conundrum
has been shared by all past explorers. Those
who were successful pushed ahead, with the
tools at their disposal, or tools they invented.
As my colleague Seth Shostak is fond of saying
“Columbus didn’t wait for a 747 to cross the
Atlantic”; neither should astrobiologists.
Biosignatures and
Technosignatures (SETI)
Moving out beyond the solar system, the focus
will be on exoplanets, but here it will not be
possible to consider in-situ sample collections,
at least not for a long time; remote observations
will have to suffice. The first task will be the de-
tection and subsequent imaging of a terrestrial-
mass planet within the stellar habitable zone.
Just how exactly like the Earth does another
environment have to be in order to host life?.
Ward and Brownlee19 have argued that an exact
duplicate of the terrestrial environment, its
history, large moon, and giant-planet shields
are required for anything bigger than microbial
life. However, Darling20 reviews the arguments
and concludes that other astronomers might
exist on many worlds. In fact the evidence is
consistent with life, including intelligent life,
existing on many worlds or exclusively only on
Earth; there is as yet no evidence. We have an
example of “one”, we cannot know from tracing
the detailed history of that single example what
the branching ratio might be for the experiment
of life; how many other ways might things have
gone but didn’t, at what rate, with what end
result?.The number “two” will be all-important
in answering this question, as in the second
example of an independent origin of life
The next step will be to attempt to conduct a
chemical assay of the atmosphere of any terres-
trial planet imaged in orbit around nearby stars.
Transiting hot Jupiters have already permitted
the first analysis of chemical constituents of
exoplanet atmospheres. Observations of HD
209458b reveal sodium, hydrogen, oxygen and
carbon in an extended atmosphere and/or es-
caping from the planet21. The Terrestrial Planet
Finder (TPF) (previously studied by NASA
and now on indefinite hold) and the Darwin
constellation under development by ESA may
eventually launch during the first half of the
21st century, perhaps combined as an interna-
tional mission. Telescopes on these spacecraft
are intended to suppress the light from a central
star, using either an occulting coronagraph at
visible wavelengths or interferometric nulling in
the infrared (IR), thereby spatially resolving and
directly detecting reflected starlight from any
terrestrial exoplanets orbiting within the stellar
habitable zone; enormous precision is required
to separate the very faint reflected light from
the planet from the very much brighter star
close by 22. Once an image has been formed,
very long observations will attempt to collect
sufficient light to reveal absorption lines in the
exoplanet spectrum due to trace atmospheric
constituents that might be clues to the presence
of biology on the planetary surface.
As difficult a technical challenge as implement-
ing these spacecraft will be, perhaps an even
greater challenge will be deciding what spectral
signature(s) does or does not constitute a reli-
able biomarker. Using the present Earth as an
example, chemical disequilibrium is one very
promising sign. The coexistence of the very
reactive molecular oxygen and methane gases
in our own modern atmosphere is the direct
result of photosynthetic cyanobacteria and
plants as well as the fermenting bacteria within
termites, ruminants, and rice paddies23. But the
paleoearth would have presented a very differ-
ent picture during the billions of years when
life was present, but had not yet participated
in the elevation of atmospheric oxygen (O2)
levels; for that world, we must ask about the
undeniable biosignatures of methanogens?.
Additionally, one must ask if there are any abi-
otic processes that can yield the same result?.
Extremophiles & Exoplanets | 1493
For exoplanets, the harsh realities of the remote
observational circumstances are further chal-
lenges; it does not now seem feasible to simul-
taneously observe the visible bands of oxygen
and the thermal IR signature of methane in a
single instrument. The broad absorption feature
of ozone (at λ 9.3 μm) in the atmosphere of an
exoplanet is currently the favored biosignature
for complex life-as-we-know-it, if the host star
is sun-like24. When the primary is an M dwarf,
other molecules such as nitrous oxide (N2O),
and methyl chloride (CH3Cl) may be detectable
along with ozone 25. While there are abiotic
sources of oxygen, and therefore ozone, an on-
going biological source appears to be required
for substantial atmospheric ozone concentra-
tions on a geologically active planet. Any future
announcements of atmospheric ozone detection
from an exoplanet and a potential linkage to
biota are likely to be accompanied by a long
list of caveats, which the media will ignore.
However, spectral absorption features alone are
unlikely to distinguish between a future detec-
tion of alien microbes or mathematicians. To
find the latter we need to search for technosig-
natures, we need to do SETI.
“Are we alone?” is really a loaded question. The
detection of life on another world (extant or ex-
tinct) is a real possibility within the lifetimes of
the students participating in this International
Science School. That is a thrilling possibil-
ity. Detection of irrefutable biosignatures will
provide the pivotal ‘number two’ in the record
of life in the universe, but at a very deep level,
humans want to know whether other intel-
ligent creatures also view the cosmos and
wonder how they came to be. Like the term
‘life’, there is really no acceptable definition of
‘intelligence’. Nevertheless we may be able to
remotely deduce its existence over interstellar
distances. If we can find technosignatures –
evidence of some technology that modifies its
environment in ways that are detectable – then
we will be permitted to infer the existence, at
least at some time, of intelligent technologists.
As with biosignatures, it is not possible to
enumerate all the potential technosignatures
of technology-as-we-don’t-yet-know-it, but
we can define systematic search strategies for
equivalents of some 21st century terrestrial
150 | Genes to Galaxies
technologies. The science fiction author Arthur
Clarke has suggested that “any sufficiently
advanced technology will be indistinguishable
from magic”; if they occur at all, detections of
advanced technologies will probably occur as
the accidental result of our detailed studies of
the natural universe.
SETI is that subspecialty of astrobiology that
currently conducts systematic explorations for
other technology-as-we-know-it; primarily it
searches for electromagnetic radiation – radio
or optical signals. SETI predates the current
field of astrobiology, beginning life as a valid
field of exploratory science in 1959 with the
publication of the first paper on this subject in
a refereed journal26. This first paper advocated
a search for radio signals, but the suggestion
of searching for pulsed optical laser signals
followed shortly thereafter in 196127. SETI
provides another plausible avenue for discover-
ing habitable worlds by attempting to detect
the actions of technological inhabitants. More
than a hundred SETI searches can be found
in the literature28. To see the search strategies
that have been used, look at the http://archive.
seti.org/searcharchive/. The list begins with
Project Ozma in 196029, the first search for
radio signals from nearby sun-like stars. While
these searches may seem like a large effort, the
sum total of all these investigations has covered
only a minute fraction of the search-parameter
space. Imagine looking at a single glass of water
scooped from the ocean, and examining it to
see whether there are any fish in the ocean.
That’s a pretty good analogy to how much of
the cosmos we’ve been able to search so far –
one glass from an entire ocean.
Signals might be generated for the benefit of the
transmitting technology or to deliberately at-
tract the attention of another civilization. While
it may be possible for us to detect unintentional
leakage radiation from another technology,
deliberate signals, transmitted to be detectable,
are the most likely to be found. Furthermore,
any detectable signals will have originated from
a technology far older than our own. If tech-
nology tends to be a long-lived phenomenon
among galactic civilizations, then statistics favor
the detection of signals from a technology dur-
ing its old age. If technology, in general, is a
short-lived phenomenon, then it will be unde- to be unable to produce. Today we search for
tectable because the chance that two short-lived narrowband radio signals – a single channel on
technological civilizations would not only be the radio dial. Natural radio emission occurs
close to one another, but also overlap in time at many frequencies, but technology can com-
during the 10 billion year history of the Milky press a lot of power into a single frequency. The
Way is vanishingly small. For this reason, Philip computerized signal detection algorithms in use
Morrison has called SETI the archeology of the can detect narrowband signals that are continu-
future. The finite speed of light guarantees that ously on, or that pulse on and off, and they can
any detected signal will tell us about the trans- be constant in frequency or change frequency
mitter’s past, but the detection of any signal during the observation due to accelerations
tells us that it is possible for us to have a long between transmitter and receiver. Natural,
technological future30. This is one of the things background radio noise from Galactic synchro-
that makes SETI important to me, and why I tron emission rises rapidly at frequencies below
feel that I have the best job in the world. 1 GHz (1 billion Hz), while the noise from at-
mospheric water vapor and oxygen contributes
Although we’ve been doing SETI for almost 50
above 10 GHz; radio SETI searches have a goal
years now, most of the time, most SETI searches
of systematically exploring the naturally quiet
are off the air. Historically the searches have
Terrestrial Microwave Window from 1-10 GHz.
been conducted on telescopes constructed for
Since the signals may be as narrow as 1 Hz,
conducting other scientific observing programs,
it means we need to search through 9 billion
so there has been little telescope time available
channels on the radio dial! An example of such
for SETI (the piggy-back SETI@home project
a signal appears in the chapter on planning for
is a notable counter example to this). Today
SETI success. While nature is quiet at these
the situation is changing as new instruments
frequencies, our cell phones, satellites, garage
intended for dedicated SETI use are commis-
door openers and microwave ovens generate
sioned and beginning to look at the sky. This is
lots of signals that cause interference. Radio
an exciting time because our tools may finally
telescopes are located far from population
be getting to be commensurate with the magni-
centers, and astronomers must use a great deal
tude of our task.
of computational effort to work around this
Deliberate signals, intended to be detected, interference.
might be engineered in one of two ways; they
At optical frequencies, signals exhibiting ex-
could appear to be ‘almost astrophysical’, or
treme time compression (short, broadband laser
they could appear to be ‘obviously technologi-
pulses) are searched for with photon counters
cal’. The distinct benefit of the former scheme
having nanosecond rise times, a regime with no
is that such signals are very likely to be cap-
known sources of astrophysical background31.
tured as a young technology (like us) begins to
Because interstellar dust begins to absorb opti-
deploy multiple sensors to study the universe
cal pulses over distances beyond ~1000 light
around it. Eventually some graduate student
years, it is desirable to extend the optical SETI
searching through observational databases
search into the infrared so that more of the
might discover something peculiar about one
galaxy becomes accessible. This will happen
of the entries, and thus discover that the signal
when, and if, the requisite fast photon counters
is actually engineered. Our rapidly improv-
become available and affordable in the IR.
ing astronomical observing capability and our
Other modulation schemes employed by cur-
curiosity about the cosmos should insure that
rent terrestrial communications technologies
we eventually discover any such ‘almost astro-
can produce signals whose statistical properties
physical’ signals. On the other hand, the detec-
differ from the Gaussian noise of astrophysi-
tion of ‘obviously technological’ signals will
cal emitters, but they are harder to recognize
require construction of specific instrumentation
than the simple artifacts now being sought. As
not available from astronomical observing
Moore’s Law delivers more affordable comput-
programs, because the characteristics of the ET
ing, SETI programs are beginning to search for
signals are precisely those that we expect nature
more complex signals.

Extremophiles & Exoplanets | 1513

At any frequency, there are two basic search
strategies that can be implemented; move
quickly across the sky (or a portion thereof) to
cover as much of the spatial dimension of the
cosmos as possible, or select individual direc-
tions deemed to have a higher a priori prob-
ability of harboring a technological civilization
and make targeted observations in those direc-
tions for longer periods of time. The former
strategy minimizes the assumptions about the
source of the signal, but in general, the surveys
will achieve poorer sensitivity as the result of
the smaller telescopes and shorter dwell times
typical of this strategy. By developing a list
of plausible targets, it is possible to achieve
significantly better sensitivity through integra-
tion and signal processing gain for a wider
range of signal types. However, if the target list
is constructed under the wrong assumptions,
detection probabilities are lowered rather than
improved. In both cases it is desirable, but
seldom affordable, to accomplish the task of
signal detection and recognition in real-time,
or near-real-time, so that immediate follow up
of candidate signals is enabled before they can
vary with time, and opportunities for distin-
guishing between terrestrial and extraterrestrial
technologies can be exploited.
Dan Werthimer and a group at UC Berkeley’s
Space Science Lab has operated a series of
increasingly capable SERENDIP detectors op-
erating at radio observatories in a commensal
(or piggy-back) mode to achieve maximum
access to the sky for conducting random, SETI
sky surveys. The SETI observers don’t control
the telescope pointing, but they eventually end
up surveying most of the available sky from
any site. Recently, SERENDIP V began tak-
ing data at Arecibo, the world’s largest radio
telescope, working with the multi-beam ALFA
receiver to search seven directions on the sky
simultaneously and analyse 300 MHz of the
spectrum in the vicinity of the 21 cm Hydrogen
line. A few % of the data collected by ALFA
and SERENDIP V, at the precisely 1420 MHz
(21 cm), is analyzed on the pioneering SETI@
home global distributed computing platform
(http://setiathome.ssl.berkeley.edu/). If you are
interested, you can download a screen saver
that works as a background program on your
own computer to search for SETI signals in
152 | Genes to Galaxies
a small piece of recorded data automatically
shipped to you from UC Berkeley, and you can
join more than 3 million people who are help-
ing the search. A commensal SETI search at the
Parkes Observatory in NSW, based on earlier
SERENDIP technologies, is now being reno-
vated, and may provide another opportunity for
more local participation in SETI.
In Northern California, the SETI Institute and
the University of California Berkeley Radio
Astronomy Lab have partnered to build the
Allen Telescope Array (ATA) at the Hat Creek
Radio Observatory for the purpose of simul-
taneously surveying the radio sky for signals
of astrophysical and technological origin32.
Ultimately the array will consist of 350 anten-
nas, each 6.1m in diameter, extending over
a maximum baseline of 900 m. Currently it
is operating as the ATA-42, with the first 42
dishes spread over 300 m. The ATA provides
simultaneous access to any frequency between
500 MHz and 11.2 GHz, a system temperature
~ 50K, four separately tunable intermediate
frequency channels feeding a suite of signal
processing backends. The backend instrumen-
tation can produce wide-angle radio images
of the sky with ~20000 resolution pixels and
1024 spectral channels per pixel, and at the
same time, study 3 point sources of interest
within its large field of view using phased up
beams at two different frequencies.  This new
approach to commensally sharing the sky al-
lows SETI and traditional radio astronomical
science to both utilize the telescope nearly
full time. Unlike, the SERENDIP systems at
Arecibo, the SETI signal detection takes place
in near-real-time. The ~250,000 stars in our
current catalog of ‘habstars’ provides a few stel-
lar targets in every array field of view at lower
frequencies and enables efficient commensal
observing. Another catalog of about 3500 target
directions is enabling a survey of 20 square
degrees surrounding the Galactic center, within
which are located some 10 billion distant stars.
Whereas the targeted searches of nearby ‘hab-
cat’ stars would detect transmitters as strong as
the current radar signals we generate to study
our ionosphere, at the distance of the Galactic
center this survey would detect a transmitter
with a power equivalent to 20,000 Arecibo
planetary radars.
The ATA is the first attempt to manufacture the University of Western Sydney34 an OSETI
a radio telescope by taking advantage of cost program has been in operation for several years
discounts from economies of scale, consumer conducting a targeted search of nearby stars.
off-the-shelf components (primarily from the
Looking towards the future, when the ATA is
telcom industry), and inexpensive commercial
fully built out, ASKAP becomes operational,
manufacturing technologies. Like ASKAP, now
and then eventually the Square Kilometre Array
being built in Western Australia, it is one of the
comes on, we are hoping that some of the
pathfinders for the Square Kilometre Array, a
students reading this chapter will be inspired
project to build an international observatory
to take over from us. At the SETI Institute, we
with 100 times the collecting area of the full
plan for success and actively try to educate the
350-dish ATA. The ATA is very much a Moore’s
next generation of scientists. We have devel-
Law telescope. Whereas all the data from 500
oped a year-long integrated science curriculum
MHz to 11.2 GHz is brought to the central
for ninth graders, called Voyages Through Time,
processing center as analog signals, only a small
and two of its modules have been adapted for
portion of that data is currently digitized and
use in science classes in NSW.
sent to the astronomical and SETI processors.
In the future, as digitizers and processors get In addition to Phillip Morrison’s hopeful
cheaper, the array will improve its capability by characterization of SETI as the archeology of
investigating more and more of the spectrum the future, I think that SETI is extraordinarily
simultaneously. The ATA will continue to allow important because it provides an opportunity to
us to increase the speed with which we explore change the perspective of every person on this
the cosmos. planet. The successful detection of a signal, or
even the serious discussion of that possibility,
Moore’s Law improvements have helped optical
would have the effect of holding up a mirror
SETI (OSETI) programs every bit as much as
to the Earth. In this mirror we, all of us, would
they have enabled the ATA. At Harvard, Paul
be forced to see ourselves as Earthlings, all the
Horowitz and his students are using a new,
same when compared to the detected extrater-
dedicated, OSETI telescope for a survey of the
restrials. SETI can help to trivialize the differ-
60% of the northern sky visible from the Oak
ences among humans that we find so divisive
Ridge Observatory in Massachusetts33. The tel-
today. This is why, when I got to make a wish
escope is housed in a building enthusiastically
to change the world as part of my TED prize
constructed with student labor. The 72-inch pri-
(http://www.tedprize.org/jill-tarter/) earlier
mary and 3-inch secondary mirrors have been
this year, I said “I wish that you would em-
manufactured inexpensively by fusing glass
power Earthlings everywhere to become active
over a spherical form and then polishing, be-
participants in the ultimate search for cosmic
cause the system does not require image quality
company.”
optics. The detection system is based on eight
pairs of 64-pixel Hamamatsu fast photodiodes, SETI might succeed in my lifetime, in your
and custom electronics for real-time detec- lifetimes, or never. There is no satisfactory way
tion. This new telescope searches for powerful to make an estimate. The wisest summary still
transmitters from a large collection of stars by remains the last sentence in the original 1959
conducting meridian transit scans of the sky in Nature journal article: “ The probability of
1.6°x 0.2° strips (with a dwell time, due to the success is difficult to estimate, but if we never
Earth’s rotation, of about one minute). The sky search the chance of success is zero”. So I invite
visible from that site can be scanned in approxi- you to stay tuned because some of us are de-
mately 150 clear nights. The survey sensitivity termined to keep searching, and we could use
should be adequate to detect laser pulses from your help!
the analog of a current Helios-class laser being
transmitted through a 10 m telescope up to a
distance of 1000 light years. Closer to home,
at the Campbelltown Rotary Observatory at

Extremophiles & Exoplanets | 1533

References
1. Wolszczan, A., & Frail, D. A. “A Planetary
System around the Millisecond Pulsar PSR
1257+12” 1992, Nature, 355, 145.
2. Dick, S.J. (1984) Plurality of Worlds:
The Extraterrestrial Life Debate from
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New Stars
in NASA’s
Constellation
Wayne Lee
Erisa K. Hines

The research described in this paper was conducted within the Constellation
program at the National Aeronautics and Space Administration.
Copyright 2009 California Institute of Technology.
Government sponsorship acknowledged.
Image courtesy NASA/John Frassanito & Associates
I magine waking up after eight hours and
floating down off your bunk onto the
floor. You bounce down the hallway
to the food station where you make a
hot cup of instant coffee and hydrate your pre-
packaged breakfast before quickly showering
and checking in with mission control. Passing
by a small window in the corridor, you pause
for a moment and take in the magnificent
desolation surrounding the outpost. Lucky for
you, your lunar base location also provides
for a spectacular view of Earthrise out of a
small window. You have been anxiously await-
ing today because you are headed out on an
enclosed, pressurized dune buggy to monitor
the cargo offloading of a resupply lander that
arrived a day ago. It brought not just logistics
(food, water, supplies), but also a new and im-
proved in-situ resource tool that should make
helium-3 harvesting three times faster than
what the outpost can process out of the lunar
rocks and soil today.
Sound like science fiction? Exciting? By 2024
the United States, along with the help of
international partners, plans to establish a
permanent outpost on the moon where we proper operational functionality before setting
master how to function and survive in a new course to intercept the moon.
and harsh environment far from home. The
Three days later, the crew is prepped and ready
Constellation Program, NASA’s implementation
to transfer into Altair, the vehicle that lands on
of the bold policy for American space explora-
the surface, while Orion stays in orbit for the
tion in the 21st century, is currently developing
duration of their stay on the moon. In conjunc-
and testing new technologies to enable multiple
tion with many “go’s” from mission control,
astronauts to live and work on the moon, or
the vehicles separate, and Altair positions itself
places even further away such as Mars. The
to align with the desired landing site. A high-
moon has no breathable atmosphere, tempera-
thrust engine burn slows the 45,000-kilogram
tures that range from +100 to -173 °C on a
vehicle down from orbital velocity to a compa-
daily basis, and gravity only 1/6 that of Earth’s.
rably slow 1 meter per second at touchdown in
Though we have sent humans to the moon
approximately 14 minutes. The initial missions
before, we did so for a very limited amount of
are expected to last for seven days on the sur-
time and with limited capability to explore. By
face, allowing the crew to explore scientifically
increasing requirements such as the number
interesting and challenging locations on the
of astronauts we want to send simultaneously,
moon such as ice, geographic formations, and
the locations we want to visit, the amount of
unique mineralogical terrain. Future missions
time we want to stay, and the goals we want to
are more focused on assembling and utilizing
accomplish, there are many details and exciting
the outpost. Once established, mission dura-
technology challenges waiting to be solved in
tions may last for up to 210 days at a time.
the next decade before we launch.
The Exploration Systems Architecture Study
How do we get there? performed by NASA identified ten preferred
Constellation’s purpose is to execute a challeng-
ing space-faring plan that includes developing
and operating spacecraft for transportation to
and from the moon, and resources to sustain a
semi-permanent human presence on the lunar
surface. Two primary spacecraft, Orion and
Altair, serve as the backbone of the program’s
transportation architecture. Orion, a dual-pur-
pose vehicle for missions to the International
Space Station (ISS) as well as lunar orbit, is
responsible for the safe launch and return of
the crew to Earth. Altair’s primary purpose is
to take the crew down to the moon’s surface, as
well as any cargo that needs to be transported,
and then safely launch the crew back into low
lunar orbit (LLO) to mate with Orion for the
journey home. Each spacecraft utilizes a dif-
ferent launch vehicle to boost it into space: the
Ares I for Orion and the Ares V for Altair.
Orion and Altair are designed to launch within
90 minutes of each other from the same launch
pads currently in use by the Space Shuttle
at the Kennedy Space Center in Florida. The Figure 1: Shackleton Crater taken by
two vehicles plan to mate in low Earth orbit the European Space Agency’s SMART-1
(LEO) where the crew checks out both to verify spacecraft in January of 2006.
ESA/Space-X (Space Exploration Institute)

158 | Genes to Galaxies

 

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Figure 2: ALTAIR Process. ESA/Space-X (Space Exploration Institute)
locations of interest on the moon based on ei-
ther scientific rationale such as geomorphology,
or for exploration to seek out elements avail-
able for resource utilization. The Aitken Basin
at the lunar south pole is one of these locations.
It is the largest and oldest basin known on the
moon, and the primary conceptual destina-
tion for an outpost. Shackleton Crater (Figure
1) is a point of interest internal to the Basin.
Its center is completely shadowed year round
resulting in temperatures near -170 °C, while
its raised edges see almost perpetual sunlight,
a noteworthy feature due to the feasibility of
using solar cells for power generation. At 19
kilometers across, relatively small for a lunar
crater, it is one of many difficult places to land,
but is an exciting destination due to the po-
tential presence of ice in the crater that could
provide life-sustaining resources for an outpost.
Orion
Orion, currently being developed by Lockheed
Martin for NASA, has the responsibility for not
only transporting four astronauts to the moon
and home again, but also taking over the Space
Shuttle’s role of ferrying six crew members
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to the ISS. Because of the relative difficulty
in executing a lunar mission, Orion is being
developed in two phases known as “Block 1”
and “Block 2.” This two-phase development
scheme allows the design to quickly reach ini-
tial operating capability for Shuttle replacement
by 2015, but incorporate the more technically
challenging upgrades for lunar missions a few
years later. The major difference impacting
vehicle design for the lunar upgrade is the du-
ration for which the system must remain func-
tional. The short-duration lunar stays where
astronauts operate in a science-gathering mode
last for seven days on the surface, resulting in a
total Orion mission duration of approximately
16 days. For the long-duration mission where
astronauts spend up to 210 days at a lunar
outpost, Orion must remain in orbit around the
moon that much longer before returning the
crew home. (Figure 2).
For a crewed lunar mission, the astronauts
launch from Earth to LEO in the Orion vehicle.
(Figure 3). Once in LEO, the crew performs
a precision docking maneuver to mate Orion
with Altair prior to heading for the moon. In
today’s concept, the crew has access to Altair
New Stars in NASA’s Constellation | 159
via a docking tunnel, but inhabits Orion until
reaching low lunar orbit (LLO). Once in LLO,
the crew places Orion into a quiescent state
and enters Altair for the descent to the lunar
surface. Orion continues orbiting the moon,
passing over the landing location of Altair ap-
proximately every two hours, for the duration
of the lunar surface stay. During this time,
Orion generally serves as a communication
relay for Altair if the Earth is out of view from
the surface, and also performs regular rocket
burns to maintain a stable orbit. Once the
crew’s stay reaches duration, they ascend into
orbit with Altair, rendezvous, re-dock with and
enter Orion, and then jettison the Altair ascent
vehicle before returning home.
For the reentry, descent and landing phase
of the mission, one of the most critical and
intense phases even compared to the landing
on the moon, Orion utilizes one of the largest
thermal protection systems (heatshield) ever
designed at five meters in diameter. Much of
the heatshield material ablates away due to
extremely high temperatures of 2,600 °C dur-
ing the time Orion decelerates through the at-
mosphere from an initial entry speed of nearly
11 kilometers per second. Unlike the Shuttle,
Orion does not utilize wings and therefore
does not perform runway landings. Instead,
a sequence of two drogue parachutes triggers
the deployment of three giant main chutes to
slow the spacecraft to a cushy splashdown of 7
meters per second in the ocean.
Orion’s command module resembles the Apollo
command module in that the shape is a blunt-
body cone capable of withstanding the ex-
tremely high heating experienced during Earth
reentry. It is the habitable portion of the Orion
vehicle. The service module provides capabili-
ties necessary during the mission, such as the
engine used to return from LLO to Earth and
consumables like water, and is jettisoned prior
to reentry. The vehicle configuration at launch
also incorporates a launch abort rocket system
to rapidly whisk the capsule away from the
launch vehicle in the unlikely event of a rocket
mishap on the launch pad or during ascent.
For electrical power, Orion relies on two radial
solar arrays that each span five meters across.
Therefore, Orion’s orientation with respect to
the sun at any given time is extremely criti-
cal for the health of the vehicle. Exposure to
micrometeoroids, orbital debris, and radiation
increases with longer mission durations, sub-
sequently increasing the robustness required of
the array design.
Orion’s internal space, known as “habitable vol-
ume,” is extremely limited due to limitations on
the weight and dimensions the Ares 1 design
is capable of launching. The spacecraft interior
contains 2.5 times the space of the Apollo cap-
sule, but for twice as many astronauts. With a

Figure 3: Orion vehicle in low earth orbit with solar arrays deployed.
NASA/John Frassanito & Associates

160 | Genes to Galaxies

Figure 4: Orion and Altair in a mated configuration on the way to the moon prior to lunar
orbit insertion. NASA/John Frassanito & Associates
volume of 11 cubic meters, each crewmember
has limited personal space to eat and drink,
let alone take a shower. (Imagine a room three
meters long and two meters square, about the
size of a large sport utility vehicle.) The Space
Shuttle might seem luxurious comparatively
where the astronauts currently enjoy a private
bathroom, as opposed to Orion’s solution of
using a small curtain to separate the toilet
area from the rest of the crew. Tomorrow’s
astronauts must be prepared for close quarters,
albeit for only a few days!
Altair
Altair, also known simply as the “lunar lander,”
provides the capability to take four astronauts
and any necessary payload from LLO down
to almost any location on the moon’s surface.
Unfortunately, Altair has limited capacity for
payloads due to the space required to house
the crew and other life support logistics such
as breathing systems, water, and space suits. In
order to build an outpost on the moon requir-
ing living and working quarters, as well as large
mobility robots, it is necessary to have a way
to carry much heavier payloads than normally
possible in the presence of crew. Therefore,
Altair is being designed with three possible
configuration variants:
1. short-duration crewed variant – a seven-day
exploratory mission where Altair provides all
life support logistics necessary
2. long-duration outpost variant – an extended
mission of up to 210 days where Altair pro-
vides the way down to the surface and back
into orbit, and an outpost is expected to sus-
tain the crew for the duration
3. cargo-only variant – crew quarters and life
support are stripped out to maximize the
amount of cargo (over 14 metric tons) that
can be delivered
For a crewed mission, Altair launches from
Earth on an Ares V, mates with the Orion in
LEO, and then undergoes a functional check-
out by the crew to verify proper operations of
critical systems such as life support, power, and
guidance. Following the three-day journey to
the moon, Altair is responsible for providing
the propulsion for it and Orion on at least three
major rocket burns resulting in close to 4,200
meters per second of total velocity change or
“delta V.” The first burn takes the Orion and
Altair vehicles out of the trans-lunar trajectory
and places them in an orbit around the moon
at approximately 100 kilometers in altitude.
At this point, the crew transfers out of their
cramped Orion home into a more cramped
Altair home to prepare for their final hours
before landing. Prior to descent, a short burn
New Stars in NASA’s Constellation | 161
to adjust the orbit plane may be necessary to to prevent loss due to boil off. After landing on
fine-tune the targeting to the landing site, and the moon, residual propellants feed a fuel cell,
final system checks are completed before com- Altair’s primary power source. That need for
mitting to the final powered descent burn. power, and possibly water as a fuel cell reaction
by-product, is expected to last up to 210 days.
Over 60% of Altair’s mass consists of propellant
to carry out the mission. If managing the cryogenic propellants for an
extended period of time presents technical
The current Altair design is equipped with a
challenges, one might wonder why we use
large cryogenic liquid oxygen and hydrogen
them. For a quick transit to the moon, cryo-
(LOX/LH2) main descent propulsion system,
genics provide an extremely high specific im-
and a smaller hypergolic reaction control
pulse. The consequence is that the propellant
system that burns monomethyl hydrazine and
is extremely efficient in terms of energy release
nitrogen textroxide (MMH/NTO) propellant.
potential per unit mass. Other types, includ-
These small thrusters provide thrust for minor
ing choices with easier thermal management
attitude corrections to Altair and Orion when
requirements, would be less mass efficient and
mated, as well as small, planned burns that are
therefore result in the need to carry more pro-
inefficient for the main engine.
pellant to perform the same job. Such a mass
The significant difficulty of using cryogenic increase would potentially result in a vehicle
propellant for the main engine lies in the prohibitively heavy to fly.
mission duration and the propellant’s low
For a cargo mission, Altair launches from Earth
saturation temperature for the designated tank
and transits directly to the moon without dock-
pressure. Current launch systems utilizing
ing with an Orion capsule. By not requiring
cryogenic fuels typically perform a single burn
time in orbit to transfer crew and supplies, a
almost immediately after lift-off that is complet-
cargo Altair can execute a simpler orbit initia-
ed in less than 20 minutes. In contrast, Altair’s
tion sequence to position itself for a direct
trip to the moon takes a minimum of 4 days
landing and avoid orbiting the moon alto-
from the time of lift-off, and extreme challenges
gether. In order to accomplish this autonomous
exist in keeping the propellant sufficiently cold
landing, Altair relies on intelligent sensors and/

Figure 5: Altair accompanied by three crewmembers in an artist’s conception of what a

sortie mission might look like on the l`unar surface.
Image courtesy NASA/John Frassanito & Associates

162 | Genes to Galaxies

or pre-placed beacons in order to touch down
on the lunar surface, while avoiding major
rocks, craters, and other hazardous obstacles
placed in its path. This capability becomes
extremely critical when trying to land multiple
Altairs within a kilometer or less of one another
during the outpost construction campaign.
The Apollo landings all took place during
lunar “noon” and in the equatorial region. The
lighting allowed them to see rocks and craters
during descent more easily than if they had
encountered long shadows caused by landing
at a time with the sun near the moon’s hori-
zon. Apollo missions also landed in relatively
smooth terrain known as “Mare.” These loca-
tions allowed the astronauts to aim for rela-
tively large landing zones with low probabilities
of steep craters or large rocks. Due to the
Constellation goal of exploring a more diverse
set of regions on the moon, Altair will face situ-
ations that may put it in darkly lit, or rough re-
gions known as hummocky uplands, with cra-
ters as wide as 295 kilometers (crater “Bailly”)
and as deep as 8.8 kilometers (Newton).
There are several potential technologies that
Altair and the crew might employ for safe land-
ing. One specific solution might be in design
conflict with another, so determining the right
combination of those solutions is challenging.
A stronger structure may withstand impact
from hazards or higher loads at landing, but
can add prohibitive amounts of mass. A softer
landing, or one that allows the vehicle to
maneuver away from hazards in real-time, typi-
cally results in carrying more fuel and requiring
tightly constrained control of the vehicle. Better
sensors result in easier detection of hazards,
but rely on more costly computer processing
hardware and algorithm development. There
are many different sensor options currently
under consideration that could aid Altair and
its crew in knowing its position relative to
landmarks, helping it to line up with maps of
the surface generated by orbiting satellites, or

Figure 6: Exploded view of the Ares I

vehicle with Orion in its position at launch.
Image courtesy NASA/John Frassanito & Associates

New Stars in NASA’s Constellation | 163

identifying and avoiding hazards in real-time
once within a few kilometers of the surface.
NASA’s Lunar Reconnaissance Orbiter
(LRO) and India’s first mission to the moon,
Chandrayaan-1, are among two of the robotic
lunar orbiter missions that are providing topo-
logical data to assist the Constellation program
in choosing landing sites for Altair. The qual-
ity of the data and amount of coverage help
determine the robustness of Altair’s landing
capability required to safely touch down at the
selected sites. Chandrayaan-1 will also focus on
performing high resolution mineralogical and
chemical imaging in shadowed polar regions
as well as searching for surface or sub-surface
water-ice. This data will inform scientists as to
the highly desired landing locations based on
scientific merit versus vehicle capability to land
in challenging terrain.
Once on the surface, Altair either provides life
support and habitat functions as mentioned
previously, or sits dormant during the crew’s
stay at the outpost. At the conclusion of the
surface mission, Altair’s ascent vehicle, the
same module utilized by the crew during
descent, will blast off and head for low lunar
orbit. The bottom portion of the vehicle, con-
sisting of the descent engine, empty fuel tanks,
and landing gear, serves as a launch pad for the
ascent vehicle and is left behind on the lunar
surface. For this part of the mission, Altair
Figure 7: The Ares V approximately 6 seconds after ignition as it lifts from the launch
pad at Cape Kennedy. Image courtesy NASA/John Frassanito & Associates
164 | Genes to Galaxies
utilizes an engine and propulsion system de-
signed specifically for the ascent to lunar orbit
and rendezvous with Orion. After rendezvous
and docking, the crew then transfers back into
Orion through the hatch and prepares for re-
turn to Earth. Prior to the trip home, the crew
commands Orion to jettison Altair and places
it on a trajectory to minimize interference with
future missions.
Ares I and Ares V
Because a combined launch of both vehicles is
mass prohibitive for a single rocket, and Altair
weighs almost twice as much as Orion, each
spacecraft warrants its own launch vehicle.
Both Orion’s and Altair’s boosters draw from
existing technologies where feasible, but new
capabilities are also being developed. Orion
utilizes a design called the Ares I. This rocket,
currently under development at the Marshall
Space Flight Center in Huntsville, Alabama, is
a thin, 99-meter tall vehicle capable of lifting
25 metric tons to LEO. The Ares I first stage
is a single, five-segment, reusable solid rocket
booster derived from the Space Shuttle pro-
gram’s reusable solid rocket motor. It separates
133 seconds after launch and is recovered from
the Atlantic Ocean and reused. The upper stage
employs a liquid fueled engine derived from
the original Saturn V’s J-2, and burns for 495
seconds to take Orion to an altitude of 134
kilometers. After separation from the upper
stage, Orion boosts itself into a circular orbit
while the upper stage reenters the atmosphere
and plunges into the Indian Ocean.
In contrast to Orion, Altair utilizes the giant
Ares V booster. Prior to the Constellation effort,
the largest and most powerful rocket ever built
was the Saturn V for the Apollo Program. The
three-stage Saturn, an engineering marvel of
the 1960’s, stood 111 meters high and utilized
five F-1 engines to produce greater than 33
million Newtons of thrust for the first stage. It
boasted a LEO payload capability of 344 metric
tons. The Ares V is a two-stage liquid-fueled
rocket that stands two meters shorter than the
Saturn V, but is still taller than the length of a
soccer field. This rocket is capable of boosting
414 metric tons to LEO. It relies on two reus-
able solid rocket boosters, similar in design
to the Ares I first stage, which strap onto the
sides to assist a first stage powered by six RS-
68B engines. The second stage, referred to as
the Earth Departure Stage (EDS), performs the
trans-lunar insertion burn for the mated Orion-
Altair vehicle. This maneuver transitions the
spacecraft from an Earth orbit to a path that
will intersect the Moon.
In looking ahead at a Mars capability, the Ares
V is being designed such that additional solid
rocket boosters can be adjoined providing ad-
ditional lift capacity for heavier spacecraft.

Surface Systems
The technologies to sustain life on the moon
and beyond are in the earliest stages of devel-
opment, but already have some very exciting
prototypes under test in exotic locales such as
the Mojave Desert and Antarctica. One element
of living on the moon is mobility, both for
people and objects such as science experiments
and living quarters. The moon, while much
smaller than the Earth, is still a large place to

Figure 8: An exploded view of the Ares

V with Altair in its launch position. The
Earth Departure Stage (EDS) can be seen
below Altair.
Image courtesy NASA/John Frassanito & Associates

New Stars in NASA’s Constellation | 165

 Figure 9: An
evening test run
of the NASA-
prototyped
“chariot” concept
in the Arizona
desert.
Image courtesy NASA
Desert RATS team

Figure 10: The

enclosed rover
concept being
tested in the
Arizona desert.
The rover shares
the shared chassis
of the “chariot”
concept.
Image courtesy NASA
Desert RATS team

explore. The Apollo astronauts walked around
in spacesuits, and used their “open air” lunar
rover to explore up to a few kilometers from
the landing site. Constellation astronauts can
also perform walking excursions near the land-
ing location, but a small enclosed rover is being
designed to provide a shirt-sleeve environment
for two crew to live for days at a time while
driving 20 to 30 kilometers away from the
habitat location. Today’s rover concept is a six-
legged vehicle with 12 wheels. The prototype
was recently taken out to the Arizona desert
where engineers tested it to understand its
maneuverability, obstacle avoidance capability,
and ease of controllability.
Similar to the enclosed rover, the design of the
habitats and workspaces is challenging due the

166 | Genes to Galaxies

constraint of landing them on a limited-size
vehicle such as Altair. They require packaging
that occupies as little space and mass as possi-
ble. Engineers are currently working on designs
that collapse around a central, rigid core and
inflate or expand once on the surface. Multiple
modules can be connected together through
common airlock doors, including a hatch to
pull up and park the enclosed rover when not
in use. The scalability of designs is a key factor
due to the flexibility of designing either one
module to meet all needs, or the luxury of uti-
lizing several specific modules. Radiation and
micrometeoroid hazard robustness also affect
habitat design, providing an opportunity for
material specialists to develop unique, light-
weight methods to provide protection.
These large modules dictate the need for the
ability to unload large, heavy objects down
from the top of Altair’s deck, a height equiva-
lent to a three-story ledge. Once removed from
the deck, astronauts will need to transport the
modules over rocks, craters, and other pieces
of unloaded hardware before reaching the final
destination. ATHLETE, the All-Terrain Hex-
Legged Extra-Terrestrial Explorer, is another
lunar surface concept being designed to do just
that. It utilizes jointed, six-degree-of-freedom
limbs to help it crawl on and off of the Altair,
maneuver next to an Altair to help with repairs
or resource retrieval, or align two habitats for
proper connection to increase living and work
space. Both remote control and autonomous
operations are currently being tested to allow
a crewmember to operate it while remaining
within the relatively safe confines of an estab-
lished outpost, or perform other work while
the ATHLETE accomplishes its tasks.
Human suit design is also a large part of the
Constellation effort. Engineers are working to
design astronaut surface suits less bulky than
the Apollo units, while more adept at provid-
ing a healthy, safe environment, and capable
of reporting diagnostics of the crew member’s
health. Certain aspects of the suit may assist an
astronaut in performing strenuous tasks such as
lifting heavy objects, or facilitating exercise by
providing muscular resistance. Another team
is looking at the types of ancillary telemetry to
collect, and efficient display techniques such
as using a heads-up display when an astronaut
is out working. For example, if a crewmember
is out exploring and their rover encounters a
problem, the presence of an internal guidance
and map capability could help them get home.
In addition to the habitat, suit, and mobility
technologies, there exist other surface capabili-
ties under development to facilitate communi-
cations, to extract natural resources found on
the moon, and to increase the autonomy de-
sired of robots. It is also important that aspects
of the spacecraft design employ the concept of
reusability because of the difficulty in landing
material on the moon. For example, potential
components include power sources, water
and fuel processing and storage hardware, and
avionics boxes suitable for both Altair and
reuse at the outpost after the conclusion of the
Altair mission.
In addition to all of the scientific and engineer-
ing discovery, it is desired that as many of us
here on Earth share in the experiences of the
astronauts on the moon. In order to accomplish
this goal, NASA plans to beam back high-
definition video so that we can be involved
with the work of the astronauts, and explore
alongside them!
What’s so exciting
about the moon?
In 1969, when our first Apollo mission landed
two astronauts on the moon, it was an engi-
neering feat of a lifetime. After the upset of
losing the race to the Soviet Union for the
first satellite in orbit, and the first human to
orbit and return to Earth, the United States
placed humans on another celestial body.
Unfortunately, the scientific enlightenment
and excitement of exploring a heavenly locale
that was all but an impossible dream for many
millennia of human history, was cut short after
only six short missions.
Our reasons for going to the moon in 1969
were very different from what they are today.
There is no longer a “space race,” no Cold War,
no need to be the first to accomplish putting
a human on the moon. However, what has
not changed is our desire to continue learning
New Stars in NASA’s Constellation | 167
about and exploring the universe that waits
outside of our comfortable, earthly bubble.
Many nations have spent substantial time, ef-
fort, and resources exploring our solar system,
including Venus, Mars, and the moons of
Saturn and Jupiter. We have telescopes that see
far beyond what many of us ever thought ex-
isted. Searching for Earth-like planets or gravi-
tational waves beyond our solar system provide
an understanding of our universe’s origins.
We continue to be excited and intrigued by
tales told via Star Trek and 2001: A Space
Odyssey, which says something about our
capacity and yearning for exploration. In ad-
dition, the Moon provides a unique place to
study our universe’s origins due to the lack
of changes compared to Earth and the other
planets. The lunar surface has been much less
affected than the Earth by forces of erosion
such as plate tectonics, volcanism, and wind
and water. Consequently, much of the original
formation is more intact than any other known
body we can currently study.
Learning how to survive and be productive on
the moon, a short 363,000 kilometers away,
places us one step closer to traveling to more
distant bodies such as Mars. We can experi-
ment with different concepts of transport, logis-
tics, construction, in-situ resource utilization,
and different communication schemes that may
require inhabitants to operate independent
from Earth for a period of time, or advance our
technology solutions that simply enable us to
survive in a non-earthlike environment. For
example, we have learned a significant amount
about how microgravity affects humans physi-
ologically. Mars gravity is slightly stronger than
the moon’s at 3/8 that of the Earth. By under-
standing the effects of 1/6-Earth lunar gravity
on humans over extended periods of time, we
can better prepare the proper training, exercise
regimens, and diet to mitigate the effects of
Mars gravity.
168 | Genes to Galaxies
Conclusion
Sending robotic missions to far away places is
significant to learning a great deal about the
basics of a planet or comet, but in order to
perform more in-depth science that requires
real-time decision making and adaptation, we
need the capability to explore first hand. To
accomplish this imperative, we must invest
in and establish our knowledge of how to live
and operate safely in harsh environments. The
moon provides an excellent opportunity by
being relatively close to home, but still posing
challenging problems in all aspects of the mis-
sion. Can you imagine producing your own
oxygen for breathing, out of soil? How can we
create or bring resources that are reusable or
recyclable into something useful again? What
kind of telescope is best for placement in a
shadowed crater such that it can accomplish
radio astronomy without interference from
the Earth?
While the Constellation program has estab-
lished a plan to fulfill the American space
policy of going to the moon and beyond, it has
not done so in a vacuum. The effort required
for developing and sustaining the capability to
function in a permanent way beyond our Earth
home is promoting numerous international
partnerships between both old space-faring
foes such as the United States and Russia, and
newcomers just getting started. Those such as
Japan and the European Union are increasing
contributors to our knowledge and under-
standing of the universe. This exploration effort
also draws on many different groups of people
as we consider how to build a thriving com-
munity that ultimately needs teachers, doctors,
engineers, scientists and other citizens. Also
thanks to the efforts of independent enter-
prises, almost anyone will have the opportunity
to personally participate in exploration of the
moon during this lifetime.
NASA’s effort to renew and establish a capability
for human exploration on the moon is an excit-
ing frontier for many reasons. Constellation’s
success depends on national and international
support, as well as the success of its many
projects such as Orion and Altair to fulfill their
missions. And, back to the moon we go, but
not just for the moon’s sake; for the sake of the
moon, Mars, and beyond.

References and Good Resources

National Aeronautics and Space Administration
(NASA). The Vision for Space Exploration. NP-
2004-01-334-HQ. NASA. Washington D.C.
National Academy of Sciences. The Scientific
Context for Exploration of the Moon. National
Academies Press. 2007. Washington D. C.
Latest Constellation News including test vid-
eos, pictures and information: http://www.nasa.
gov/mission_pages/constellation/main/index.
html
Testing surface in-situ technologies in Hawaii:
http://www.nasa.gov/directorates/esmd/home/
hawaii_lunar_tests.html
Information about Shackleton Crater:
http://www.esa.int/esaMI/SMART-1/
SEMP7QOFHTE_0.html
Saturn V Information: http://www.daviddarling.
info/encyclopedia/S/Saturn_rocket.html
Moon Crater Resource: http://museumvictoria.
com.au/DiscoveryCentre/Infosheets/Planets/
The-Moon/

New Stars in NASA’s Constellation | 169

Asthma
and Airway
Remodelling:
Targeting Mitogen-activated Protein
Kinases as Future Therapeutics

Melanie Manetsch
Emma E. Ramsay
Alaina J. Ammit
A sthma is a chronic disorder of
the airways affecting millions of
people worldwide. Airways are
remodelled, or thickened, result-
ing in airway obstruction and a decline in lung
function. Airway remodelling is considered
to be a consequence of long-term inflamma-
tion. As the current drugs for treating airway
remodelling have side effects, we urgently
need to target the inflammatory pathways that
control the development of the remodelled
phenotype in the airway. A wealth of studies
has implicated the mitogen-activated protein
kinase (MAPK) family of phosphoproteins as
critical signalling molecules that drive pro-
inflammatory pathways. Thus, inhibition of
MAPKs has emerged as an attractive strategy
for reversing inflammation and remodelling
in asthma. This chapter will focus on target-
ing MAPKs as future therapeutics. We will
briefly outline the use of small molecule MAPK
inhibitors, and then explore the potential of
harnessing the power of an endogenous MAPK
deactivator – MAPK phosphatase 1 (MKP-1) –
in inhibiting MAPK-mediated pro-remodelling
functions. Our recent studies demonstrate that
MKP-1 deactivates MAPK signalling in airway
smooth muscle cells; a pivotal airway cell in
asthma and airway remodelling. Thus, this
chapter will focus on the role of MAPKs in the
development of the pro-remodelling phenotype
in asthma and highlight the promise of novel
anti-inflammatory strategies designed to reverse
the development of the airway remodelling
phenotype by regulating the anti-inflammatory
protein – MKP-1.
What is asthma?
If you have asthma, you experience episodes
of wheezing, chest tightness and shortness of
breath in response to a variety of “triggers”.
This occurs because the airways in your lungs
narrow, making it more difficult for air to get
through. Over 2.2 million Australians have
asthma. This includes 1 in 4 children, 1 in 7
teenagers and 1 in 10 adults (Source: National
Asthma Campaign). Because “when you can’t
breathe, nothing else matters” (American Lung
Association), asthma is an important and de-
bilitating disease that we need to understand
more about so that we can beat it!
What causes asthma?
Asthma is a complex disease with both ge-
netic and environmental causes. Why do we
get asthma? The causes are many and varied.
Allergy may play a big role. According to the
National Asthma Campaign, 8 in 10 Australians
with asthma have positive allergy test results.
Allergy occurs when your immune system
reacts to substances (known as allergens) in the
environment that do not bother most people.
These allergens can be found in house dust
mites, pets, pollen, moulds and foods and
can “trigger” asthma. You may be born with
a genetic tendency to develop allergic dis-
eases (called “atopy”); or allergy may develop
throughout life. There are still a large number
of unanswered questions about the develop-
ment of allergic disease but currently much
intense research is being performed all around
the world to understand more about the links
between allergic disease and asthma.
172 | Genes to Galaxies
What is the cellular
basis of asthma?
Asthma is characterized by inflammation
and airway hyper-responsiveness. An acute
asthma attack can be brought on by exposure
to triggers. Exposure to triggers induces air-
way inflammation characterized by mast cell
degranulation and an influx of lymphocytes
and eosinophils. These cells secrete various
agents capable of perpetuating inflammation
and provoking airway smooth muscle contrac-
tion (bronchospasm). Accordingly, the majority
of therapeutic agents used for asthma seek to
minimize the development or consequences
of airway inflammation (corticosteroids) or
directly promote airway smooth muscle relaxa-
tion (β2-agonists).
What is airway remodelling?
Asthma is a treatable health condition and we
have a number of effective drug treatments
to tackle acute asthmatic attacks. With good
asthma management, asthmatics can lead nor-
mal, active lives. But, there are still a number of
unanswered questions. We now know that the
airways of asthmatics can become “thickened”
or remodelled over time. This occurs when the
inflammation that is part of an acute asthmatic
attack is not treated or controlled effectively.
The consequence of uncontrolled asthma is
that permanent changes in the airways can
occur and unfortunately, these cannot be
completely reversed with current treatments.
As development of remodelled airways is cor-
related with deterioration of lung function,
we urgently require therapies that reduce
and reverse structural changes in remodelled
airways. Although corticosteroids can inhibit
some aspects of remodelling, side effects ex-
ist and thus, corticosteroid-sparing strategies
to prevent airway remodelling require further
investigation.
Airway smooth muscle plays an integral role in
acute asthma and airway remodelling
In the Respiratory Research Group at the
University of Sydney we have focussed on the
role of the airway smooth muscle in asthma
and airway remodelling. Airway smooth mus-
cle is no longer viewed simply as a bystander
structural cell passively maintaining the airway
wall integrity and responsible for bronchoc-
onstriction; it has now emerged that airway
smooth muscle plays a critical active role in the
pathogenesis of asthma and airway remodel-
ling. When an acute asthma attack is triggered,
airway smooth muscle is bathed in a wide
variety of inflammatory mediators released by
mast cells upon degranulation and by-products
of gene expression from lymphocytes and
eosinophils. The airway smooth muscle then
undergoes a number of important cellular
reactions in response to these stimuli. Cells un-
dergo calcium–mediated contraction and un-
dergo bronchoconstriction that is typical of an
asthmatic attack. Additionally, a number of im-
portant pro-remodelling genes are activated in
airway smooth muscle cells. The protein prod-
ucts of this gene expression result in increased
cell growth and increased production of pro-
fibrotic proteins. It is this increase in airway
smooth muscle mass (due to both increased
airway smooth muscle cells numbers and also
an increase in the amount of fibrotic proteins
in and around the airway smooth muscle cells)
that is considered to contribute strongly to
the “thickening” of the airway wall. Because
increased airway wall thickening results in
reduced airway calibre (4), airway remodelling
is a significant contributor to the exaggerated
airway narrowing observed in asthmatics. It is
generally considered that airway remodelling is
a consequence of long-term inflammation, and
although numerous cell types contribute to air-
way remodelling, the increase in airway smooth
muscle mass has the largest impact on airway
narrowing in asthma (5). Thus, airway smooth
muscle plays an integral role in acute asthma
and chronic airway remodelling and under-
standing the underlying signalling pathways
will allow us to design future drug strategies
for reversing inflammation and remodelling in
asthma.
MAPKs - signalling pathways
that drive development
of airway remodelling
Our recent work has highlighted the impor-
tance of the mitogen-activated protein kinase
(MAPK) super family of signalling molecules
in the pro-remodelling functions of airway
smooth muscle cells. There are three members
of the MAPK superfamily: (1) p38 MAPK; (2)
c-Jun N-terminal kinase (JNK); (3) extracellular
signal-regulated kinase (ERK, also known as
p44/p42 or ERK1/ERK2). These enzymes are
involved in the intracellular signal transduction
pathways mediated by a variety of stimuli (in-
cluding cytokines, chemokines, growth factors,
neurotransmitters and environmental stresses,
such as allergens, respiratory viruses and
airborne pollutants). To become activated by
these various signals, the MAPKs pass through
ATP-dependent phosphorylation cascades
that consist of three protein kinases connected
in series. Activation of MAPKs requires dual
phosphorylation at the threonine (Thr) and
tyrosine (Tyr) residues of the Thr-X-Tyr sites in
the activation loop (where X is glutamic acid in
the case of ERKs, proline in JNKs, and glycine
in p38 MAPK). Many important substrates
for MAPKs are transcription factors and after
activation the MAPKs migrate to the nucleus
of the cell and there they phosphorylate di-
verse transcription factors on specific sites and
therefore control gene expression. In this way,
MAPKs work at the key positions of many
intracellular signalling pathways and regulate
various cellular processes, from gene expres-
sion of pro-fibrotic proteins and inflammatory
cytokines, to regulation of proliferative path-
ways by increasing levels of cell cycle proteins
to induce cell growth. A wealth of studies has
implicated the MAPK family of phosphopro-
teins as critical signalling molecules that drive
pro-inflammatory pathways. Thus, inhibition
of MAPKs has emerged as an attractive strategy
for reversing inflammation and remodelling in
asthma. Thus, MAPKs have emerged as critical
pathways that drive development of airway re-
modelling to significantly contribute to asthma
pathophysiology (6, 7)
The Respiratory Research Group at the
University of Sydney has been at the forefront
of discovery of the MAPK pathways respon-
sible for critical pro-remodelling functions in
airway smooth muscle cells, such as: increased
synthetic function, production of cytokines
(8-10) and pro-fibrotic proteins (11-13); and
increased cell growth ((13-16)). We now wish
Asthma and Airway Remodelling | 173
to use our knowledge to aid the future design
of drugs that help tackle the development of
airway remodelling in asthma.
Mitogen-activated protein
kinases (MAPKs) as future
therapeutic targets
As recent research underscores the importance
of the MAPK signalling pathways in key airway
smooth muscle functions that underlie the
development of the remodelled phenotype,
these pathways may be targeted as therapeutic
strategies in the future. As the current drugs
for treating inflammation (corticosteroids)
have side effects, we urgently need to target the
inflammatory pathways that control the devel-
opment of the remodelling phenotype in the
airway, as this knowledge may yield corticos-
teroid-sparing strategies in the future. In this
chapter we focus on two approaches: firstly, use
of small molecule inhibitors to inhibit MAPK
pathways; and secondly, harnessing the power
of endogenous MAPK deactivators, such as
MAPK phosphatase 1 (MKP-1).
174 | Genes to Galaxies
MAPK inhibitors
Recent research has begun to elucidate sig-
nalling pathways responsible for key airway
smooth muscle functions that underlie the
development of the remodelled phenotype
(reviewed in (17)). Of the MAPK super family,
most research in the airway smooth muscle
cell arena has focused on the role of the p38
MAPK- and ERK-mediated pathways. Although
an oversimplification, p38 MAPK pathways
are considered responsible for synthetic func-
tion and the secretion of cytokines, while
ERK-mediated pathways dominate in airway
smooth muscle proliferation (reviewed by (18,
19)). JNK has only been investigated somewhat
more recently and has been shown to regulate
cytokine gene expression and protein secretion
(20). Thus, as the importance of the MAPK
pathways in airway smooth muscle cell biol-
ogy and inflammatory airway diseases such as
asthma and airway remodelling are emerging,
these pathways may be targeted as therapeutic
strategies in the future.
p38 MAPK: p38 MAPK is activated by an ATP-
dependent dual phosphorylation at Thr180
and Tyr182 residues. Many laboratories around
the world have designed and synthesized small
molecules that block the ATP binding site of
p38 MAPK, yielding a large number of poten-
tial p38 MAPK inhibitors (reviewed in (21,
22)). The prototypical p38 MAPK inhibitor
is SB203580, one of the first generation p38
inhibitors and widely used as pharmacological
tool to study p38 MAPK pathways. We (9, 10,
23) and others (24, 25) have used SB203580
in vitro to highlight the key role played by
p38 MAPK in secretion of pro-inflammatory
cytokines from airway smooth muscle cells (9,
10). The importance of p38 MAPK inhibition
as a pharmacotherapeutic approach in asthma
has been further underscored by demonstra-
tion of reduced pulmonary inflammation and
airway hyperreactivity in a mouse model of
asthma (26). In vivo, the use of SB203580 as
an anti-inflammatory drug has been obstructed
by its liver toxicity, as the pyridinyl imidazoles
were found to inhibit hepatic cytochrome P450
enzymes (27). Promising anti-inflammatory
actions have been observed in an in vivo model
with the p38 MAPK inhibitors SD-282 (28)
and further investigations into non-toxic p38
MAPK inhibitors are currently under intense
investigation worldwide.
ERK: Dual threonine and tyrosine phosphor-
ylations activate both ERKs, at Thr202/Tyr204
for ERK1 and Thr185/Tyr187 for ERK2. MAPK
pathways are activated by dual phosphoryla-
tion by respective upstream activators. For
ERK, the upstream kinase is mitogen-activated
protein kinase, known as MEK. There are a
number of MEK inhibitors such as U0126 and
PD98059. These have been used extensively in
vitro in airway smooth muscle cells to delineate
pro-proliferative pathways. We (15, 29) and
others (30, 31) have demonstrated that ERK-
dependent pathways control growth.
JNK: The JNK phosphorylation sites are
Thr183 and Tyr185. Relatively less is known
about the role of JNK in airway smooth muscle
pro-remodelling functions in vitro, although
airway smooth muscle hyperplasia and inflam-
matory cytokine release in mice chronically
exposed to allergens is inhibited by the admin-
istration of SP600125, a JNK inhibitor (32).
MKP-1: what is it?
Cellular function is profoundly affected by both
strength and duration of MAPK activation,
which must be strictly controlled to modulate
functional outcome. This crucial negative
feedback control is achieved by the balanced
interplay between MAPK activation by diverse
environmental and chemical stimuli and the
negative feedback mechanism mediated by pro-
tein phosphatases such as MAPK phosphatases
(MKPs) (33, 34). Several MKPs have been
classified (34) and in general they all regulate
MAPK activity in a negative feedback mecha-
nism by dephosphorylating the threonine and
the tyrosine residues in the activation loop
“Thr-X-Tyr-motif” of these signalling enzymes.
Since these phosphatases dephosphorylate both
Asthma and Airway Remodelling | 175
the threonine and the tyrosine residues they
are also called dual-specificity phosphatases
(DUSPs). Although all MKPs have highly
conserved structural elements they vary in
subcellular localization, substrate specificity,
tissue distribution and also in their inducibility
by various stimuli. The characteristic structural
elements of MKPs are within all MKPs homo-
logue dual-specificity phosphatase (DUSP)
domain in the C-terminal half which leads to
the dual dephosphorylation on the threonine
and tyrosine residues of MAPKs, and a MAPK-
binding domain situated in the N-terminal half.
This domain is very important for the quality of
the interaction between MKPs and MAPKs and
therefore plays a crucial role in the regulation
of the enzymatic specificity (35, 36).
MKP-1, the prototypical member of the MKP
family, is an immediate early gene located in
the nuclear compartment and that means that
its transcription is induced instantly after expo-
sure to diverse stimuli such as growth factors,
heat shock and stress. Many of these stimuli
are the same as those that also activate MAPKs
(36-39). MKP-1 is the first-discovered MKP
and controls the MAPK signalling pathway by
inactivating these enzymes through dephos-
phorylation (40-42). MAPKs are activated by
pro-inflammatory mediators and diverse stress
stimuli and therefore play a very important
role in the innate and inflammatory immune
response (43). The inhibitory effect of MKP-1
on MAPK activation and therefore the modula-
tion of pro-inflammatory processes indicate the
importance of MKP-1 in this cellular pathway.
Therefore the attenuation of MAPK signalling
by MKP-1 could be a promising target to re-
duce the inflammatory responses mediated by
MAPK activation.
Current anti-asthma
therapies and MKP-1: what
do we know so far?
Inhaled corticosteroids are first-line anti-in-
flammatory therapy in asthma. However, there
is increasing evidence that the combination
of an anti-inflammatory corticosteroid with
long-acting bronchodilator β2-agonists results
in superior therapeutic benefit, when compared
176 | Genes to Galaxies
with each component administered alone (re-
viewed in (44)). ”Understanding the molecular
basis of this fundamental clinical observation
is a Holy Grail of current respiratory diseases
research as it could permit the rational exploi-
tation of this effect with the development of
new ‘optimized’ corticosteroid/β2-agonists com-
bination therapies” (44). It is this question that
we have begun to address. We have focused
our investigations on the endogenous MAPK
deactivator – MKP-1 – as MKP-1 acts as a criti-
cal negative regulator of the myriad pro-inflam-
matory pathways activated by MAPKs. We (10)
and others (45) have recently discovered that
the anti-inflammatory action of corticosteroids
in ASM cells occurs via upregulation of MKP-1.
Moreover, the corticosteroid-inducible gene
MKP-1 is enhanced by long-acting β2-agonists
(46), and the enhanced expression of MKP-1
may explain the beneficial effects of β2-agonists/
corticosteroid combination therapies in the
repression of inflammatory gene expression in
asthma (44). Thus, further investigations into
the molecular basis of MKP-1 regulation are
urgently required as this new knowledge may
lead to elucidation of “optimized” corticoster-
oid-sparing therapies.
How is MKP-1 regulated?
MKP-1 is a 367 amino acid protein expressed
by an immediate-early gene (37). Stimuli
which activate MAPKs also induce MKP-1
protein that then acts back on MAPKs as an
important negative feedback controller to limit
the strength and duration of MAPK-mediated
cellular signalling (reviewed in (47)). However,
the increase in MKP-1 protein levels is tran-
sient, as MKP-1 protein (expressed as a result
of increased transcription and/or mRNA stabil-
ity) then undergoes rapid degradation by the
proteasomal machinery. Investigations into
how MKP-1 is regulated will allow us to fully
explore the potential of harnessing the power
of an endogenous MAPK deactivator – MKP-
1 – to inhibit MAPK-mediated pro-remodelling
functions.
It is known that the activity of MKP-1 can be
regulated at different levels. There are several
approaches to regulate the expression of MKP-
1 not only on the transcriptional level but also
 `

Time after stimulation

(min) (h)
0 5 10 30 1 2 4 24
- MG132 MKP-1
+ MG132 MKP-1

Figure C. MKP-1 is proteasomally degraded in airway smooth muscle cells.

Airway smooth muscle cells were pretreated with and without the proteasome
inhibitor MG132 (10 µM), before stimulation with 10 ng/ml platelet derived
growth factor-BB. Western blotting for MKP-1 was performed.

on the post-transcriptional and on the post-
translational level. Shortly after exposure to
the diverse stimuli (such as stress and growth
factors) the transcription of MKP-1 is induced
and mRNA levels are highly increased. The
mechanism by which the transcriptional induc-
tion is mediated is currently not completely
understood but since MKP-1 can be induced
by various stimuli the transcriptional induc-
tion and regulation seems to be a promising
target for the modulation of the inflammatory
response (42). The post-transcriptional regula-
tion of MKP-1 stability is another mechanism
to alter the enzymatic activity of this phos-
phatase. It has been shown that the MKP-1
stability can be increased through phosphoryla-
tion by ERK1/2 and that leads to an accumula-
tion of MKP-1 in the cell and therefore may
enhance the activity of MKP-1 (42, 48). To
what extent the enhanced expression of MKP-1
has positive or maybe also negative outcomes is
not completely known. The modulation of the
interactions between MKP-1 and its substrates
is a subject of the post-translational regulation
of MKP-1 activity. The substrate specificity de-
pends on diverse structural elements of MKP-1
and the modulation of this interaction could
also be a mechanism to enhance the phos-
phatase activity and hence the inactivation of
the MAPK pathway and therefore the efficacy of
the anti-inflammatory reaction in the immune
response. If it is possible to inhibit or attenuate
the proteosomal degradation of MKP-1, that
would provide another promising opportunity
to regulate the MKP-1 activity. We are currently
working on achieving a greater understanding
of the multiple levels of regulation of MKP-1
regulation so that we can increase MKP-1 and
reduce MAPK-mediated signalling.
Our current work: how
is MKP-1 degraded?
Thus, because MKP-1 serves a crucial negative
feedback role in regulating pro-remodelling
signal transduction, discovering mechanisms to
regulate the protein level or enzymatic activity
of this endogenous MAPK-deactivator may be
exploited as a novel anti-inflammatory strategy
in asthma and airway remodelling. Thus, in
order to achieve our aim of increasing MKP-1
to reduce MAPK-mediated signalling, we need
a greater understanding of the three levels of
MKP-1 regulation: (i) transcriptional; (ii) post-
transcriptional; and (iii) translational. We are
currently examining how MKP-1 is regulated
at the translational level, that is, how MKP-1 is
degraded by the proteasome – the garbage bin
of the cell. As mentioned earlier, stimuli which
activate MAPKs also induce MKP-1 protein.
However, the increase in MKP-1 protein levels
is transient, as MKP-1 then undergoes rapid
degradation by the proteasomal machinery.
If we can understand how and why MKP-1
is degraded, we could design molecules that
could specifically block MKP-1 degradation
and thus allow MKP-1 protein levels to remain
high. We are currently a long way from our
goal but our preliminary evidence obtained in
airway smooth muscle cells shows that stimula-
tion increases MKP-1 protein levels (peaking
at ~ 2 hours) but the protein degrades over
time. We have used a non-specific proteasome
inhibitor – MG132 – and confirmed that we
can inhibit proteasomal degradation and keep

Asthma and Airway Remodelling | 177

MKP-1 levels high. We now need to investigate
whether we can do this just for MKP-1 protein.
Future directions and significance
Asthma is a widespread chronic health prob-
lem. Airway remodelling underlies asthma, but
unfortunately, the pharmacotherapy currently
available for combating remodelling has had
limited success. We need to understand how
to control airway remodelling to be able to im-
prove treatments for asthma. With our work we
will increase our knowledge of the mechanistic
basis of asthma focusing on the role of the
MAPK pro-remodelling signalling pathways.
In this chapter we have highlighted the use of
small molecule MAPK inhibitors in vitro and in
vivo and explored the potential of harnessing
the power of an endogenous MAPK deactivator
– MKP-1 – in inhibiting MAPK-mediated pro-
remodelling functions. It is our hope that the
elucidation of novel molecular strategies and
drug candidates targeting the pro-remodelling
MAPK signalling pathway will serve as a future
pharmacotherapeutic approach to treating and
preventing airway remodelling.
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Asthma and Airway Remodelling | 181

Cosmobiology:
Our Place in
the Universe
Charles H. Lineweaver
H ere we sit on a ball of silicate
with beating hearts, opposable
thumbs and curious minds.
How did we get here? How
did the evolution of non-living things, such as
galaxies, stars and planets, create the ingredi-
ents and the conditions for the emergence of
life? Which aspects of this evolution are unique
to the Earth and which are common in the
universe? Are we alone? These cosmobiological
questions are sharpened and partially answered
by the overview presented here.

How in the universe

did we get here?
In the fictional story “Hitchhikers Guide to the
Galaxy”, the Improbability Drive called into
existence a sperm whale several miles above the
surface of an alien planet (Adams, 1999). As it
falls through the atmosphere:
“this poor innocent creature had very little
time to come to terms with its identity as a
whale before it then had to come to terms
with not being a whale anymore… Ah….!
Figure 1: How did we get here? This deep
image of a tiny fraction of the sky (~ 10 -7)
shows ~ 10 4 of the ~10 11 galaxies in the
observable universe. The square insert is
a detail from one of the galaxies, showing
an aerobic bipedal encephalated mammal
on a moon, breathing oxygen imported
from the blue planet in the background.
We find ourselves on that blue planet 13.7
billion years after the Big Bang, falling
at ~400 kilometers per second through
an almost empty and possibly infinite
universe. How in the universe did we get
to be in such an unlikely situation? Images:
NASA Hubble Ultra Deep Field and NASA
68-H-1401 and AS11-40-5903.
NASA/STScI
What’s happening? It thought. Er, excuse me,
who am I? Hello? Why am I here? What’s my
purpose in life? What do I mean by who am
I? Calm down, get a grip now…And wow!
Hey! What’s this thing suddenly coming to-
ward me very fast? Very, very fast. So big and
flat and round, it needs a big wide-sounding
name like…ow…ound…round…ground!
That’s it! That’s a good name – ground! I
wonder if it will be friends with me? And the
rest, after a sudden wet thud, was silence.”
Like this discombobulated sperm whale, many
of us are trying to come to terms with our
identities as life forms, before not being life
forms anymore. We are hopeful that a scientific
understanding of how we fit into the universe
can help combobulate us.
Our scientific discombobulation begins with
the origin of the universe. Our best ideas about
184 | Genes to Galaxies
Figure 2: On the largest scales we will
always be lost. This image represents
the possible multiverse. Each bubble is a
separate universe that was born from its
mother universe and which, in turn can
give birth to baby universes. Our universe
may have been born as some random
fluctuation of a patch of space-time
foam in our mother universe that went
through a process called inflation. In this
diagram, our three dimensional universe
is flattened into two dimensions and is
represented by the surface of one of the
small blue bubbles. In the square box,
each black smudge represents a galaxy.
The entire box full of galaxies shows only
a small portion of our universe. The pink
circle inside the box shows the extent of
our observable universe, which is only
an infinitesimally small part of the entire
universe (i.e., of our blue bubble). We are
in the centre of our observable universe.
Figure 1 shows us the galaxies between us
and the edge of our observable universe
along one line of sight. Figure 3 is an
image of the surface of our observable
universe (the pink circle) 13.7 billion years
ago when our entire universe was filled
with a hot plasma rather than galaxies.
Unlike the finite surface of the blue bubble
shown here, our universe may be spatially
infinite.
Reproduced with kind permission from Sky and
Telescope “The Self-Reproducing Universe” by
Eugene F. Mallove, Copyright @ September 1988 by
Sky Publishing Corporation.
the very earliest moments of the Big Bang come
from a combination of cosmology and quantum
mechanics called quantum cosmology. In quan-
tum cosmology, there is no place for unique,
one-off events — rather there are ensembles
and probability distributions. Thus, quantum
cosmology suggests that the event that we
call the origin of our universe is not a unique
event. It is one of many. Quantum cosmology
suggests that our universe is just one of a pos-
sibly infinite number of other universes, which
together we call the multiverse (Figure 2). We
don’t know how the universes in the multiverse
are connected to each other or whether we can
ever find evidence for their existence in our
universe. Some cosmologists speculate that
these disconnected universes have different
laws of physics or possibly the same laws but
with different constants, i.e. different values for
“c”, the speed of light or for “G”, the strength
of gravity. One thing seems clear though,
despite our increasing understanding of our
surroundings, our observations or our universe
and others will always be limited. Thus, on the
very largest scales we are and always will be
lost, like that sperm whale falling through the
atmosphere of an alien planet.
How did our universe begin?
The expansion and cooling of the universe is
the basis of modern cosmology and a prerequi-
site for life. In the beginning, at the Big Bang,
13.7 billion years ago, the universe was very
hot. There was no life and there were no struc-
tures in the universe. The matter, subatomic
particles, atoms and molecules that we now
take for granted did not exist. As the hot Big
Bang cooled, matter came into existence, prob-
ably about 10-33 seconds after the Big Bang. We
aren’t sure how this happened, but according to
inflationary models, the most dramatic events
occurred in the first fractions of a second after
the Big Bang, during a period at the end of
inflation called “reheating”. Vacuum potential
energy of a scalar field became the tangible and
clumpable energy and matter that we are more
familiar with. Poorly understood symmetry
violations (Sahkarov 1967) led to an excess
of matter over anti-matter and a universe

Figure 3: The best photo ever taken of the Big Bang. The photons detected to make
this map travelled for 13.7 billion years and are the oldest photons we can detect. They
were emitted from the surface of last scattering at the edge of our observable universe
when the universe was about 380,000 years old and had a temperature of ~3000 K. As
the universe expanded, these 3000 K photons became redshifted and cooled to the 3K
photons we now observe. The pattern of hot (red) and cool (dark blue) spots has been
used to obtain the most accurate estimates of the contents, age and size of the universe.
Image: NASA/WMAP Science Team.

Cosmobiology: Our Place in the Universe | 185

Figure 4: As the universe expands and cools, structures freeze out of the
undifferentiated vacuum energy and quark-gluon plasma, like snowflakes from a cooling
cloud. Structures that freeze out include, first matter at very high energies, then protons
and neutrons, then nuclei, atoms and molecules. The thick diagonal line labeled “CMB”
is the temperature of the cosmic microwave background, which is the temperature of the
universe. The universe became transparent when it cooled down to about 3000 K and
atoms (mostly hydrogen) formed out of the cooling plasma of electrons and protons (see
the horizontal line labeled “atoms”). Figure 3 is an image of the CMB at that time. See
Lineweaver and Schwartzman (2004) for details.

dominated by matter. Then at 10-3 seconds
after the Big Bang, matter – in the form of a
quark-gluon plasma – cooled and condensed
into protons and neutrons. Within three
minutes these particles had condensed into
light nuclei during a period called “Big Bang
nucleosynthesis”. As the universe continued to
cool, atoms formed for the first time about half
a million years after the Big Bang. The universe
was a thermal heat bath of photons and atoms
in chemical equilibrium. Figure 3 is a full-sky
map of the cosmic microwave background
radiation. It shows the thermal heat bath of
the universe 380,000 years after the Big Bang.
There were no stars or galaxies. Life is not pos-
sible in such an environment. In thermal and
chemical equilibrium, no free energy is avail-
able, and free energy, not just energy, is what
life requires (Lineweaver & Egan 2008).
During the 13.7 billion years since the Big
Bang, the universe expanded, the heat bath
cooled and life (at least on Earth) emerged. Life
did not emerge simply because the universe
cooled down to have the right temperature
for H2O to be a liquid. Life needed a source of
free energy unavailable from an environment
in chemical and thermal equilibrium. The ori-
gin of all sources of free energy can be traced
back to the initial low gravitational entropy of
the unclumped matter in the universe (e.g.,
Lineweaver & Egan 2008). The gravitational
collapse of this matter produced galaxies, stars
and planets and is the source of all dissipative
structures and activities, (including life) in the
universe. Notice in the upper right of Figure 4
the small interval of logarithmic time during
which free energy from stars has been available
to power life in the universe. The first stars
formed about 200 million years after the Big

186 | Genes to Galaxies

Figure 5: Any life forms in the universe depend on sources of free energy in the
universe. These sources come in three kinds: gravitational (left), nuclear (middle) and
chemical (right). Left panel: dissipation in an accretion disk leads to angular momentum
exchange between two small masses (two light greyballs). The mass that loses angular
momentum falls in. The one that gains momentum is expelled. Accretion disks are
dissipative structures which, like more traditional life forms, must be fed – must have a
source of free energy – to maintain their structure. Middle panel: the binding energy
per nucleon due to the strong nuclear force provides the gradient that makes fusion
and fission drive nuclei towards iron. Right panel: the energy that heterotrophic life (like
ourselves) extracts from organic compounds, or that chemotrophic life extracts from
inorganic compounds, can be understood as electrons sinking deeper into electrostatic
potential wells. In every redox pair, the electron starts out high in the electron donor
(light grey ball) and ends up (black ball) lower in the potential of the electron acceptor
(cf. Nealson and Conrad 1999, their Figure. 3). These three sources of free energy are not
independent of each other. For example, gravitational collapse (left) enables solar fusion
(middle) which powers life on Earth (right). Image from Lineweaver and Egan (2008).

Bang ( ~ 1016 seconds) when hydrogen cooled
down to 50 – 100 K. Before this time there
were no stars and therefore no free energy to
drive life. There was also no oxygen to make
H2O until several million years after the first
generation of massive stars.
Life as we know it is based on molecules;
clumps of atoms that froze out of the cooling
universe when the temperature of the universe
fell below molecular binding energies (Figure
4). Thus, the expansion and cooling of the
universe has been the most basic prerequisite
for the origin of molecules and molecular life.
But life cannot be made out of the cooling
hydrogen and helium produced in the Big
Bang. Many generations of massive stars had
to form and die before the ashes of nuclear
fusion accumulated to contain enough oxygen,
carbon, nitrogen, sulfur and phosphorus to
produce watery environments and allow the
chemical evolution of carbon molecules into
hydrocarbons, carbohydrates and life.
Four elements make up more than 99% of
the atoms in terrestrial life: hydrogen, oxygen,
carbon and nitrogen or HOCN. Add seven
more elements to this mix (S, P, Cl, Na, Mg, K
and Ca) and we have more than 99.99% of the
atoms in terrestrial life. Of all these ingredients,
only hydrogen was made in the Big Bang, the
rest were produced in the hot fusing cauldrons
of massive stars. Their ubiquity ensures that
the ingredients for life are present throughout
the cosmos.

Cosmobiology: Our Place in the Universe | 187

There are many reasons to believe that terrestri-
al planets, broadly defined, in habitable zones
are ubiquitous in the Universe (Lineweaver
et al 2003). For example, planets are formed
in accretion disks and accretion disks are
necessary ingredients in our best models of
star formation. The latest observations and
simulations are consistent with the possibility
that rocky planets orbit the majority of stars.
Even if we accept that terrestrial planets are
common, in order for life to emerge and evolve
into something interesting, millions or even
billions of years in a clement stable aqueous
environment may be required. Supernovae are
the required suppliers of O, C, N, S and P but
if they explode nearby they can also extinguish
life. Thus, there may be a Galactic Habitable
Zone close enough to the debris of supernovae
to enjoy a complex chemistry but far enough
away from supernovae to enjoy a clement envi-
ronment for the billions(?) of years required for
the biological evolution of interesting organ-
isms (Lineweaver et al 2004).
Two ways to approach
the origin of life
Figure 6 shows the formation of the Earth and
the origin of life on Earth within the context of
the history of the universe. There are two main
ways to approach the origin of life on Earth.
One way is to start at the initial conditions of
the Big Bang at the bottom of Figure. 6 and
work your way up, forward in time, through a
series of evolutionary processes described by
cosmology, astrophysics and chemistry includ-
ing the expansion and cooling of the universe.
This is described in the previous page. This
chronological approach produces a rather
straightforward and deterministic descrip-
tion of how the universe evolved and became
conducive for life. This deterministic approach
can explain how the ingredients of life – the
elements and molecular building blocks were
produced. The building blocks (or monomers)
are important for understanding the origin of
life because life seems to work on the Lego
principle. Monomers are strung together to
form polymers out of which all terrestrial life is
made: amino acids are strung together to form
proteins, nucleotides to form RNA, fatty acids
188 | Genes to Galaxies
to form lipids and monosaccharides to form
carbohydrates.
However, we don’t know the specific condi-
tions of the proto-biochemistry such as the
specific auto-catalytic molecular reactions that
allowed the correlated polymerization of these
monomers. We don’t know the environments
and pathways of molecular evolution that
led to the origin of life. In the chronological
cascade from the Big Bang to the origin of life,
we are still very ignorant about the transition
from the building blocks of life to the things
we now recognize as “life”. Our uncertainty is
represented by the brown roots of the tree of
life shown in Figure 6. Half a dozen good ideas
are still slugging it out to explain this transition
– it’s a work in progress.
The other way to approach the origin of life is
to start with the living organisms at the top of
Figure 6, at the ends of all the branches and
work your way down, backwards in time to the
last universal common ancestor (LUCA) of all
extant life forms. Then make some informed
guesses about the origin of life on Earth, based
on the characteristics of LUCA – What did
it look like? How did it make a living? This
procedure is similar to the way linguists use
the common properties of a family of languages
to make informed guesses about the extinct
ancestor language which diverged to produce
the family. Figures 3, 4, and 5 illustrate some
of the processes of the bottom up approach,
while Figures 7 and 8 are related to the top
down approach.
From an aqueous environment on a rocky
planet, life emerged on Earth about 4 billion
years ago and branched into the three domains:
Eubacteria, Archaea and Eukarya shown at the
top of Figures. 6, 7 and 8. All life forms on this
planet that have protein factories called ribos-
omes can be classified into one of these three
domains. These three domains are the basic
branches of the terrestrial tree of life. Figure 7
sketches the basic branches and sub-branches
of life on Earth. Most of the kinds of life that
you might be most familiar with (animals,
plants and fungi) are just three short twigs on
the tree labeled respectively “Homo”, “Zea” and
“Coprinus” (Figure. 7).

Figure 6: The history of the universe
since the big bang. The hot big bang
(bottom) produced hydrogen and helium
(labeled “H” and “He”). Clouds of H
and He gravitationally collapsed to form
stars of various masses. The massive
blue stars exploded after a few million
years and spewed into interstellar space
the ashes from the nuclei that had fused
in their cores. After ~ 9 billion years of
such reprocessing and accumulation,
our Sun formed 4.56 billion years ago
from a gravitationally collapsing cloud
of molecular hydrogen contaminated
with oxygen, carbon, nitrogen and other
heavy elements. The Earth formed from
this contamination as the accretion disk
around the young Sun fragmented from
lack of feeding.
Cosmobiology: Our Place in the Universe | 189
We do not know if such a tree of life exists on
other terrestrial planets. However, we can use
this tree to make better guesses about what
forms of life we should expect elsewhere. For
example, life forms at the root of this tree are
the common ancestor of all life on Earth. They
are simpler and less quirky than the life forms
they evolved into and therefore these simpler
organisms may be more representative of what
we should expect to find at the base of alien
trees of life, i.e., as far as predicting aliens goes,
the smart money is on hyperthermophilic bac-
teria, not vertebrates.
Consider two cosmobiological facts: (1) ter-
restrial biogenesis occurred rapidly, i.e., life
formed on Earth more than 3.5 billion years
ago, probably as soon as it could have after the
heavy bombardment subsided; (2) terrestrial
planets are not made of anything unique–life
and planet Earth are made of the most com-
mon elements available in the Universe. These
facts suggest that life may be common on ter-
restrial planets throughout the Universe. See
Lineweaver & Davis (2002) for details.
Combining our knowledge of the cooling of the
universe, of the formation of stars and planets,
of the composition of those planets and the
earliest forms of life on Earth, is one example
of how cosmobiology brings together the study
of life forms and cosmic processes to help us
understand how we fit into the universe and
how we compare to other life forms that may
inhabit the Universe.
If we consider viruses to be alive then Figure. 7
does not show all life. If viruses or bits of RNA
played an important role in the origin of life,
then in neglecting viruses we have thrown the
baby out with the bath water. For the begin-
ning of a viral phylogeny, see Ward (2007).
The debate about what life is, and how to rec-
ognize it, is at the heart of the question: What
is our place in the universe? This is the Holy
Grail of cosmobiology. To make progress, we
need to explore the martian subsurface and
analyze the atmospheres of the nearest 100
or 1000 terrestrial planets. NASA is prepar-
ing to build the Terrestrial Planet Finder and
ESA is preparing Darwin. Both are putting
their money on using interferometric infrared
Figure 7: Phylogenic tree of terrestrial life based on the 16s subunit of ribosomal RNA.
An estimate of the position of the last universal common ancestor (LUCA) of all life is at
the center of the tree, labeled “Root”. The deepest and shortest branches of this tree
are all hyperthermophilic: organisms that can survive above 90° C. Therefore, LUCA at
the root of the tree was probably hyperthermophilic. Life started as a hyperthermophilic
eubacteria or archaea and branched out (see Wong 2008 but also Boussau et al 2008).
Maximal growth temperatures have been used to assign colours to the branches and
thus to construct this biological thermometer on billion year time scales. The distance
from the root to the end of each branch corresponds to the same amount of time –
roughly 3.5 or 4.0 billion years. Because the ticking of the 16s molecular clock is not
exactly uniform, the distances from the root to the ends of the branches are not the same
length. Among the Eucarya in the lower left are the three twigs of complex multicellular
life: Coprinus (representing fungi), Homo (humans, representing animals) and Zea (corn,
representing plants). The common ancestor of fungi, animals and plants lived ~1.5
billion years ago (Hedges et al 2004). The last 200 million years of vertebrate evolution
corresponds to the last ~2 mm of the twig labeled “Homo”. Diagram from Lineweaver
and Schwartzman (2004) based on Pace (1997). Near the root, pJP27 and pJP78 are
Korarcheota, the deepest and shortest branched extant organisms – presumably the
extant organism that most resembles LUCA (Elkins et al 2008).
Lineweaver and Schwartzman (2004) based on Pace (1997)

190 | Genes to Galaxies


Figure 8: Tree of life emerging from roots
in an RNA/Viral World. Every branch is
adorned (or infected) with viruses. Viruses
may well be remnants from an earlier
epoch in which they were the dominant
life form and no stable gene lines had
yet emerged. From the viral point of view
our vertically transferred genomes are
frozen, hardly-evolving non-participants
in the lively cut and thrust of lateral gene
transfer. Image Lineweaver 2006.
spectroscopy to look for the traces of chemi-
cal disequilibrium as the primary biomarker
(Lovelock 1979).
Are we alone?
The answer to this important question depends
on what “we” means. If “Are we alone?” means
“Are we, the life forms on Earth, part of a larger
group of life forms out there in the universe?”
then we don’t know the answer. We don’t
know if terrestrial life is the only life in the
universe…but even more problematically we’re
not sure what “life” in its most generic form is
or how we can recognize it. For more on these
doubts see Lineweaver (2006).
If “Are we alone?” means “Are we humans the
only species of life in the universe?” then the
answer is easy. No, we are not alone. There are
millions of other species of life on Earth. If we
Cosmobiology: Our Place in the Universe | 191
are not alone on Earth, we can’t be alone in
the universe.
If “Are we alone?” means “Are we humans the
only species of life in the universe with human-
like intelligence?” then we have a controversial
question and the topic of much debate. Many
physical scientists tend to believe that we hu-
mans are members of a larger group of “func-
tionally equivalent humans” and thus, we are
not alone (Sagan 1995a,b).
Many biological scientists tend to believe that
there is no evidence for such a group of “func-
tionally equivalent humans” and that our clos-
est relatives in the universe (chimps and other
apes) are here on Earth, not in orbit around
other stars. Thus, if, after examining our clos-
est relatives, we decide there are none with
human-like intelligence, then by our own self-
servingly narrow definition of intelligence, we
are alone (Simpson 1964, Mayr 1995ab). This
last version of the question “Are we Alone?” can
be sharpened and rephrased as:
Is human-like intelligence a
convergent feature of evolution?
In other words, is there a tendency in evolu-
tion to evolve toward our kind of intelligence?
If there is, then we are likely to find beings
with human-like intelligence elsewhere in the
universe. If our version of intelligence is some-
thing species-specific – something that evolved
only once in the context of billions of years of
evolution on Earth – we should not expect to
find it on other planets.
The scientists who support Sagan’s view, sub-
scribe to what I call the Planet of the Apes
Hypothesis that goes something like this: There
is a “human-like intelligence” niche. There is
selection pressure on other species (including
our ancestors) to occupy this niche. In our
absence (or on other planets) some species will
evolve into that niche and develop technology.
Carl Sagan has called the occupants of this
niche the “functional equivalent of humans”.
I call it the “human-like intelligence” niche not
the “intelligence niche” because generic intel-
ligence is poorly defined. Each animal species
with a brain seems to have its own version of
intelligence. It is also not clear to me that a
life form must have a brain to be intelligent.
All creatures that survive and reproduce could
be said to be as intelligent as they need to
be. Bacteria, for example, have worked out
complex and simple ways of accommodating
themselves to virtually every environmental
condition that exists on the planet. That’s pretty
smart. But that’s not the kind of intelligence
most people hope to find elsewhere in the uni-
verse. Our human-like intelligence, unlike any
other type of intelligence on Earth, has allowed
us to build radio telescopes and given us the
ability to hear and be heard across interstellar
distances. This ability that we humans have,
and that we are able to look for in others, is a
“species-specific characteristic”. No other spe-
cies on Earth seems to have it.
Frank Drake is a physical scientist and a
pioneer in the search for extraterrestrial intelli-
gence (SETI). When I asked him what the best
evidence for the existence of intelligent extra-
terrestrials was, he referred me to the work of
Jerison shown in Figure 9 which seems to show
that human-like intelligence, or at least a large
brain case is a convergent feature of evolution.
In this version of the evolution of human in-
telligence, Jerison analyzes the sizes of brain
cases as a function of time and finds a trend
toward bigger and bigger brains. He concludes
that there is some general trend in evolution
toward bigger brains. Compare this plot to my
plot in Figure 10, where I trace the evolution
of the nose size of the elephant. Looking back
through time, it is easy to see that the ances-
tors of the elephant had smaller noses than the
elephant. In fact, if I look at the evolution of
the elephant, I can find a definite trend toward
bigger noses, but it would be silly to conclude
that there is a general trend in evolution toward
bigger noses.
Interpreting Figure 9 as evidence for evolu-
tionary convergence on bigger brains is as
silly as interpreting Figure 10 as evidence for
convergence on longer noses. One cannot
identify a current extreme feature in a species,
plot the trend with time of its ancestors and
then generalize that trend to other lineages.
The trend that results is specific to your ances-
tors – obligatorily so, since the recipe for such
plots is 1) identify your species’ most extreme
feature (a big brain, a big nose) and make that

Figure 9: The Evolution of Relative Brain Size in Groups of Vertebrates Over the Past 200
Million Years (adapted and updated from Jerison 1976, p 96, Jerison 1991, Figure. 17). This
plot purports to show an evolutionary trend towards increasing relative brain size ( = E.Q.
= Encephalization Quotient) and is probably the most well-documented evidence for
such a trend. Average living mammal E.Q. is defined as 1. The broken lines indicate gaps
in the fossil record. Variation within groups is not shown. The lineage that led to humans
is drawn thicker than the other lineages. Lineweaver (2008)

192 | Genes to Galaxies

Figure 10: The Evolution of Relative Nose Size (= N.Q. =Nasalization Quotient, ratio of
nose length to body length) Over the Past 200 Million Years. Notice the apparent trend in
the data as, over time, N.Q. reaches its ultimate value in extant pachyderms. Notice also
that once the direct lineage that led to elephants is ignored, most of the species do not
have an increasing N.Q. This plot is meant to illustrate a point, and should not be taken
as more than a crude representation of a specious trend in N.Q. that has been largely
ignored and poorly quantified by paleontologists. Lineweaver 2008.

the y-axis of a plot 2) plot yourself in the upper useful, we should see many independent ex-
right 3) plot your ancestors who, since you are amples of it in biology, and we could cite many
the extreme, will fall on a descending line into creatures that had evolved on independent
the lower left. Thus Figures 9 and 10 are not continents to inhabit the “intelligence niche”.
evidence for any general trend toward bigger But we can’t. Human-like intelligence seems
brains or noses. to be what its name implies – species specific.
Thus, the terrestrial record suggests that we are
In addition, heads (and therefore brains) are
as unlikely to find a creature with human-like
monophyletic: a single species diversified into
intelligence elsewhere in the universe as we are
all extant species with heads (brains). Not only
to find a sulphur crested cockatoo or a naked
is human-like intelligence not a convergent
mole rat on another planet.
feature of evolution, heads are not a conver-
gent feature of evolution. Heads were once a Even so, I am a strong supporter of the SETI
species-specific feature, thus, all heads and Institute, which uses radio telescopes to search
brains have diverged from a single species that for extra-terrestrial intelligence. I do not expect
had a head. Thus, heads and brains are not the to find creatures on other planets that build ra-
generic products of evolution but are as quirky dio telescopes, but I support the effort to keep
and unique as a single species. looking. Who knows what we will find? SETI
is the exploration of new parameter space with
Humans are unique, just like every other spe-
new instruments – a proven recipe for scientific
cies on Earth. It makes no sense to concoct
discovery. However, we do not need to misin-
an imaginary set of which we are the only
terpret the fossil record to justify continuing
terrestrial member and then suppose that
exploration of our universe.
biological evolution elsewhere in the universe
evolves toward this set. This concoction is The
Planet of the Apes Hypothesis. It is testable.
Paleoneurology does not support it.
Carl Sagan said that our evolution represents
the universe becoming aware of itself (Figures.
12 and 13). If human-like intelligence were so

Cosmobiology: Our Place in the Universe | 193

Figure 11: The Schwarzeneggerization of Life: a self-serving misinterpretation of
evolution. A muscle-bound man stands as the end product of a linear progression—the
Great Chain of Being – a ladder of life that leads to male Caucasian weight lifters. One
can create such an apparent linear trend out of the crooked phylogenetic branch of
any species. Looking back from any particular species we will find the evolution of the
traits of that particular species but these traits will be different from the ones listed
along the central axis here. Precisely because we can construct such a figure from the
lineage of any species, a single example of such a construction should not be construed
as a general linear trend applicable to all life. The simple appeal of this figure is a good
example of how easy it is to be misled into believing that the important events and
the major transitions in evolution that led to us, are important events for all organisms.
The problems with this view are detailed in Gould (1989) but are perpetuated by Smith
and Szathmary (1995). The prevalence and recurrence of this mistaken interpretation of
evolution needs to be avoided as we try to use terrestrial evolution to give us hints about
the evolution of extraterrestrial life. This Schwarzo-centric tree should be compared with
Figure. 7 which itself, because it ignores viruses, may be guilty of a similar bias against
creatures who outsourced protein production. Gatland and Dempster (1957)

194 | Genes to Galaxies

Figure 12: Who are we? As you read this, photons are bouncing off the image and
entering your eyes. The photons are producing a pattern of excited retinol molecules.
This pattern is being sent from your retina through your optic nerves to the occipital
lobes of your bilaterally symmetric brain, where you have a molecular model of
yourself, and how you fit into the universe. Thus, patterns of molecules inside your
brain are contemplating themselves, and that, of course, is what this picture illustrates.
Understanding how the universe produced molecules and how these molecules acquired
the ability to think about themselves may be a central thread of how we are woven into
the universe. Drawing by Victor Juhasz.

Figure 13: This cartoon captures the status of a big-brained biped. Our big brains
enable us to ask important questions such as “What’s it all about?”, “How do I fit into
the universe?” On the other hand, our brains may be too big. They deceive us with self-
importance and prevent us from knowing the humble answer that every other creature
seems to know: “Eat, survive, reproduce”. Image Garret Hardin.

Cosmobiology: Our Place in the Universe | 195

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Cosmobiology: Our Place in the Universe | 197

The Private Life
of a Proton
Helen Johnston
V ery few things are forever.
Molecules re-arrange and re-
make themselves constantly, in
countless chemical reactions; and
even atoms can be made and destroyed in the
interiors of stars, forging entirely new chemical
elements. Only protons are truly unchanging:
every proton in every atom in the universe has
been there since the very beginning1. But over
the life of the universe, those protons may have
been through many different guises. If one of
those protons could tell its story, what a story
that would be ...
Well, here is that story.
In the beginning, there was a proton.
Actually, it wasn’t quite at the beginning. At the
very beginning was the Big Bang, a moment
of infinite temperature and density. The whole
of the universe we see today was compressed
into a region smaller than an atomic nucleus.

1 Actually, under some circumstances, protons can turn

into neutrons and vice-versa. However, it takes energy
to convert a proton to a neutron, so left to themselves
neutrons will decay into protons but not vice-versa.
Figure 1: History of the Universe. Microcosm CERN

200 | Genes to Galaxies

We have no laws of physics to describe what
was going on under these conditions, so our
description of the universe has to start a tiny
fraction of a second after time zero. After that
time, the universe began to expand, and as it
did so, it cooled.
The story of our proton begins just 0.01 sec-
onds after the Big Bang. Before that, the uni-
verse had been too hot and dense for protons
to exist: instead, it was a seething mass of pho-
tons2, electrons, positrons, neutrinos, quarks
and antiquarks. It was not until the tempera-
ture of the universe had dropped below several
million million degrees that quarks could bind
together to form protons and neutrons.
This is where we meet our proton for the
first time.
For a while, the existence of the proton is
very transitory: every time it meets an anti-
proton the two annihilate, converting their
mass-energy into a pair of energetic photons.
These photons then spontaneously convert
the energy back into mass, producing a new
proton/anti-proton pair, which speed away
from each other.
There comes a time, however, when the
universe has cooled just enough that the
photons no longer have enough energy to
produce new particles. When that happens,
most of the particles and antiparticles annihi-
late each other one last time. Our proton was
one of the few – the very few – that did not
find an antiparticle. For each lucky particle,
30 million other particles did not make it.
One second after the Big Bang, our proton
finds itself in a universe made up of energy
and matter, with essentially no antimatter.
For reasons we still don’t understand, there was
a tiny imbalance of matter over antimatter – for
every 30 million antiparticles there were 30
million and one particles. After the annihila-
tion had finished, only this small amount of
left-over matter remained: the rest had disap-
peared into radiation. So about 1 second after
2 Electrons and positrons are examples of antiparticles,
which have the same mass but opposite electric charge.
Particle-antiparticle pairs can annihilate one another and
convert their entire energy into two photons. Matter is
made of protons, neutrons and electrons, while antimatter
is composed of antiprotons, antineutrons and positrons.
the Big Bang, there was about one proton or
neutron for every billion photons or electrons
or neutrinos.
The universe is a seething maelstrom.
Protons and neutrons smash into each other,
moving much too fast to stick together. The
entire universe still consists entirely of sub-
atomic particles.
As the temperature drops, the particles start
moving more slowly. Now when protons and
neutrons meet, they can stick together; the
strong nuclear force grabs them and binds
them together into the first nuclei. All around
our proton, particles are sticking together
in clumps: first two, then three and four.
The four-nucleon clump – two protons and
two neutrons – is the most stable: a helium
nucleus. But not five: when a four-particle
helium nucleus is struck by another particle,
the whole lot is split apart again.
By the time the universe is a bit more than
three minutes old, nearly all the neutrons
have combined into nuclei, while most of
the protons (including ours) are still free.
About 90% of the universe is hydrogen, with
nearly all the rest made up of helium. There
is some deuterium3, and tiny amounts of
lithium and beryllium, but nothing else. The
first elements have been born, albeit without
electrons: it is still too hot for the electrons
to combine with the nuclei to form atoms.
Shortly afterwards, when the temperature
becomes too low for nucleosynthesis to
take place, the production of nuclei stops.
No more elements will be formed for a
long time.
This story of how the first elements were
formed is extremely well understood. As the
universe cooled, new particles could be made
out of old ones. We can measure the rates at
which these reactions occur in particle ac-
celerators, and by applying the concepts of
thermodynamic equilibrium, we can predict
which particles will be formed as the universe
cools. It turns out that the final composition
of the universe depends only on the baryon
3 Deuterium is the name given to heavy hydrogen,
hydrogen-2, whose nucleus consists of one proton and one
neutron bound together. The ordinary hydrogen nucleus,
hydrogen-1, has just a single proton.
The Private Life of a Proton | 201
Figure 2: The cosmic microwave background, observed by the Wilkinson Microwave
Anisotropy Probe (WMAP). The average temperature is 2.725 K; the colours represent tiny
fluctuations (0.0001 degrees) from this mean, with red regions warmer and blue regions
colder.
Image: NASA/WMAP Science Team
density – how many protons and neutrons there
were in a given volume of the early universe.
By measuring the abundance of elements like
deuterium in the oldest stars, we can determine
this baryon density.
It was still too hot for the electrons to com-
bine with the nuclei to form atoms, so our
proton found itself free in a sea of protons
and helium nuclei, surrounded by photons
and electrons.
The entire universe consisted of nothing but
this ionised gas: a plasma. Electrons and nuclei
moved freely about. Because electrons are very
good at scattering photons, light cannot travel
far before hitting an electron and flying off in
another direction. This has the effect of making
the universe opaque: light is scattered around
just like being inside a fog.
Nothing else much of note happens for a
long time, while the universe continues to
expand. About 380,000 years later, the tem-
perature has cooled to about 3,000 degrees.
Finally, it is cool enough for electrons to
combine with nuclei to form stable atoms
without being ripped apart again. Once it
has captured an electron, our proton is no
longer a free proton. It is now the nucleus of
a hydrogen atom.
202 | Genes to Galaxies
This period when electrons were trapped into
atoms – the recombination era4 – has one impor-
tant consequence. Once the photons were no
longer continually bouncing off electrons, they
could begin flying freely. Most have been flying
freely ever since. We can observe these photons
today as the cosmic microwave background.
Since they began travelling, the universe has
expanded by a factor of 1000, so the tempera-
ture has dropped from 3000 degrees to just 3
degrees above absolute zero.
The cosmic microwave background radiation is
almost uniform in all directions. The Wilkinson
Microwave Anisotropy Probe (WMAP) was a
satellite launched in 2001 to measure the tiny
variations in the temperature of the radiation:
the temperature over the sky ranges from
2.7251 to 2.7249 degrees Kelvin.
The universe is completely dark. There are
no stars; nothing is hot enough to produce
any visible radiation. There is no source of
light anywhere.
Once the temperature of the universe had
dropped below 3000 K, the wavelength of the
average photon making up the background
4 Actually, it should be called the “combination era”, since
the electrons and nuclei had never been united before.
Figure 3: Snapshots of a very large
volume of space in the Millennium
Simulation, which followed the formation
of galaxies and clusters. The yellow points
represent individual galaxies.
Images: G.Lemson and the Virgo Consortium

radiation had shifted into the infrared. Nothing

in the universe was emitting visible light.
This cosmic dark age lasted for perhaps a hun-
dred million years.
Our hydrogen atom moves aimlessly as
part of the gas that makes up the universe;
almost, but not quite, completely uniform. By
random chance, in some regions the atoms
are slightly closer together than in other
regions. This means they have slightly more
mass, so their gravity pulls in more material,
so they get denser still. By such means, little
by little, the universe gets lumpier.
In the dark, things were happening. The mat-
ter was distributed almost but not quite evenly
through the universe: we still see the imprint
of these tiny fluctuations in the background
radiation. As time went on, the clumps of mat-
ter grew; gravity was assembling the compo-
nents of the universe. The physics of how this
happened is extremely complicated: we need
supercomputer simulations to understand how
structures grew. These simulations show that
the matter develops into a web of filaments,
with voids separating the denser regions. We
see these filaments today in maps of galax-
ies. The 2dF Galaxy Redshift Survey, which
was done at the Anglo-Australian Telescope,
measured the distances to nearly a quarter of a
million galaxies, enabling astronomers to make
a three-dimensional map of the universe. The
distribution shows clusters and filaments, sepa-
rated by vast voids almost devoid of galaxies.
For a long time, our hydrogen atom drifts.
For millions of years the drift is barely per-
ceptible, but gradually it becomes apparent
that the gas is getting denser, and that it
is drifting in a particular direction. The gas
cloud containing our hydrogen atom is now
stretched out like a long thread. Then at last,
something has changed. Millions of light
years away in the direction the cloud is drift-
ing, there is light: the first light that has been

The Private Life of a Proton | 203

Figure 4: A slice of the universe from the 2dF Galaxy Redshift Survey: each dot is
a galaxy. Matthew Colless
seen since the universe cooled below 3,000
degrees. Far ahead, one of the first stars in
the universe is shining.
Eventually, the first objects which produced
light were born. This light not only illuminated
the darkness, but also stripped the electrons off
the atoms in the interstellar gas again. We are
still not sure which objects were responsible
for this cosmic re-ionisation. They had to be
objects producing large numbers of energetic
photons: hydrogen is ionised by radiation with
wavelengths shorter than 91.2 nm, which are
ultraviolet photons. The most likely candidates
are either quasars or the first stars. Quasars
are supermassive black holes, which are ac-
creting gas from a swirling disk and sending
narrow jets of high-speed particles and radia-
tion towards us. We know the universe was
already re-ionised by the time the universe was
1 Gy old5, at a redshift of 6, because quasars
5 Redshift describes how much the wavelength of the light
which reaches us has been stretched by the expansion of
the universe since it left the source. More distant objects
have higher redshifts, and so when we observe an object at
high redshift, the light has been travelling since a long time
in the past. The relation between redshift and age of the
universe is given in Table 1, see end of chapter.
204 | Genes to Galaxies
at higher redshift have all their blue light ab-
sorbed by neutral hydrogen gas, while quasars
at lower redshift do not. Re-ionisation almost
certainly did not happen all at once; instead,
bubbles of ionised gas formed around stars (or
quasars). As the number of bright objects grew,
the bubbles merged together and cleared up
the “fog” of neutral hydrogen, allowing the blue
light to travel freely.
Evidence is beginning to suggest that it was
stars that first re-ionised the universe. The most
distant quasars yet observed already show the
presence of elements heavier than hydrogen
and helium, which means (as we shall see) that
there must have already been massive stars be-
fore these quasars were born.
Composed only of hydrogen and helium (and a
tiny amount of lithium), these first stars would
have been very different from the stars forming
today. Theory predicts they would not only
have been much hotter than stars forming now,
but also that they could have been much more
massive. Stars forming today cannot be more
massive than about 150 times the mass of our
Sun. Beyond that mass, the star produces so
much radiation that the outward pressure of
Figure 5: Cosmic reionisation in the history of the Universe. S. G. Djorgovski et al., Caltech.
Produced with the help of the Caltech Digital Media Center.

The Private Life of a Proton | 205

Figure 6: The radio galaxy Centaurus A, showing twin jets of matter being ejected from
the central black hole. These jets can be seen at X-ray and radio wavelengths.
NASA/CXC/SAO
the radiation exceeds the inward pull of grav-
ity, and the star tears itself to pieces. The very
first stars, however, could potentially grow to
be much more massive: several hundred, per-
haps even up to a thousand solar masses. Such
stars would have extremely short lifetimes – a
million years or less – after which they would
explode, seeding the interstellar medium with
heavy elements. Their collapsing cores may
even have provided the seeds which grow into
the massive black holes we see at the centres of
quasars and galaxies.
The region towards which our hydrogen
atom is falling is now perceptibly a proto-
galaxy. At its centre is a black hole, formed
from the embers of one of the dying first
stars. Since its formation it has grown con-
siderably, by merging with other black holes,
and by sucking down enormous quantities of
gas. Surrounding it is a cloud of stars formed
206 | Genes to Galaxies
from the gas that continues to accumulate.
The gas cloud containing our proton gradu-
ally swirls towards the centre of the growing
galaxy. As smaller clumps come too close
and are pulled in, some of the gas is flung
completely away, doomed to swirl forever
in the almost empty regions of intergalactic
space. Other gas finds itself being hurled
towards the centre of the galaxy. There it is
pulled into a swirling, super-heated accretion
disk around the black hole, where it will even-
tually disappear into the event horizon and
be lost forever, or else squirted at nearly the
speed of light right out of the galaxy in twin
jets. Our proton avoids both of these fates;
instead, it finds itself near the centre of a
dense cloud, which gets denser as more gas
collides with it and compresses it.
Whether they were formed in the first stars,
or collapsed directly from the gas, or grew
from seeds of primordial black holes created
Figure 7: A series of interacting galaxies observed by the Hubble Space Telescope.
ESA/Hubble

in the first instants of the Big Bang, we know of the galaxy and the black hole are somehow
that massive black holes already existed and intimately linked.
were growing less than a billion years after the
However they began, the evidence suggests that
Big Bang. The most distant quasar currently
both the galaxy and the black hole at its heart
known has a redshift of 6.43, so it was formed
grow as a result of the merging of galaxies.
when the universe was only 0.87 Gy old. Radio
Everywhere we look, we see signs of galaxies in
galaxies are also powered by supermassive
the process of colliding, or showing evidence of
black holes, but the jet is seen side-on, so we
collisions in the not-too-distant past. And the
see radio emission from the jets. Radio galaxies
further back we look, the more common these
are known at redshifts of up to 5.19, when the
collisions seem to be. When galaxies collide,
universe was just over 1 Gy old. So the black
the stars almost never collide: their physical
holes must have been formed very early on
size is so small compared to the vast distances
in the universe. Did they exist first and then
between them that they just pass freely past
galaxies grew around them? Or did the galaxy
each other. However, the enormous gas and
and the black hole both form together? We still
dust clouds in both galaxies do collide: the
don’t know. We do know, however, that almost
gas is compressed, which triggers more star
every galaxy has a massive black hole at its
formation. Meanwhile, some of the gas and
heart, and that the bigger the galaxy, the bigger
stars are flung out in huge tidal tails, while
the black hole. This suggests that the growth
some is sent spiralling towards the centre of
the galaxy, where it can feed the black hole.

The Private Life of a Proton | 207

Our own Milky Way galaxy contains the debris
of many dwarf galaxies it has swallowed up in
the past, and it is currently in the process of
devouring a few more; the Magellanic Clouds
will be devoured within the next few hundred
million years.
Over millions of years the gas cloud gets
denser and colder, and our proton (now a
hydrogen atom) finds itself in a molecule for
the first time: two hydrogen atoms are bound
together as molecular hydrogen, H2.
The interstellar gas is the raw material from
which stars form. A cloud of gas has a tendency
to collapse under its own gravity, but this in-
ward pressure is resisted by the gas pressure.
This is sufficient to resist the collapse until a
critical threshold is passed, when the collapse
becomes unstoppable. This threshold mass
depends on the temperature and density of
the cloud, with colder and denser clouds more
likely to collapse. So stars tend to form in the
coldest, densest regions of gas; these regions
are called giant molecular clouds.
A typical giant molecular cloud might be
50–100 light years across and contain a million
or more solar masses of material. The gas is
now not just the pristine material made in the
208 | Genes to Galaxies
first few minutes after the Big Bang; the first
stars polluted the interstellar gas with heavy
elements when they exploded. So by the time
this second generation of stars begins to form,
the gas cloud already contains small amounts
of (amongst other things) carbon, nitrogen,
oxygen, and other elements. Astronomers can
measure the proportion of heavy elements in
the spectra of stars, and find that older stars
have significantly lower proportions than
younger stars. In our own galaxy, these low-
metallicity stars6 are found primarily in the
Galactic bulge and in globular clusters, while
younger, more metal-rich stars like our Sun are
found in the disk of the galaxy.
When the giant molecular cloud starts to col-
lapse, it continues under its own momentum.
More and more gas falls inwards as the collapse
accelerates. Multiple clumps develop in the
cloud, as denser-than-average regions pull in
more and more gas. Eventually the cloud frag-
ments into hundreds of small dense globules,
each of which will eventually become a star.
The collapse is fastest near the centre of each
globule where, inside a cocoon of gas and dust,
the dense core of gas is getting hotter as the ki-
netic energy of the accreting matter is convert-
ed into heat. As the density increases the cloud
becomes opaque, trapping the heat within the
cloud. This then causes both the temperature
and pressure to rise even more rapidly – the
collapsing cloud is now a protostar.
The cloud containing our proton has been
accumulating mass, getting denser and
more massive as more gas falls in. Once
the runaway collapse has started, the gas
containing our proton begins its long fall
towards the dense knot that will become the
newborn star. The gas heats up as it falls; first
6 To an astronomer, every element other than hydrogen
and helium is called a metal, so oxygen and carbon are
described as metals. Only the first generation of stars,
made from the primordial gas of hydrogen and helium, was
metal-free.
Figure 8: The young star cluster NGC 602
in the Small Magellanic Cloud, showing
hot young stars just emerged from their
birth cloud.
NASA, ESA, and the Hubble Heritage Team
the molecules are stripped apart, then the
electrons are ripped from the atoms. When
the collapse finally ends, our proton finds
itself near the centre of a young, massive star,
about 25 times the mass of our Sun.
The collapse only comes to an end when the
star finds a source of energy to balance the
inexorable inward pull of gravity. That source
is nuclear fusion: when the temperature at
the core reaches about 15 million degrees,
hydrogen nuclei can begin to fuse together to
form helium, just as they did in the first few
minutes after the Big Bang. Energy is a product
of that fusion, so as each set of four hydrogen
nuclei fuses into helium via a series of nuclear
reactions, energy is produced which increases
the temperature and pressure of the star’s core
enough that it can resist the inward pull of
gravity. A star has been born.
Our proton sits near the core but not in it.
Here, where our proton sits, a bit less than
a quarter of the way out from the core, the
temperature is lower. Unprotected by their
electron shells, protons regularly collide, but
their positive charge means they just bounce
off each other. It is only deep in the core,
more compressed by the great weight of the
star, that the nuclei are moving fast enough
to collide and form new elements: first deu-
terium, then helium.
This conversion produces enough heat to
support the immense mass of the star against
the inexorable pull of gravity.
As long as the star can continue fusing hydro-
gen to helium in its core, it can maintain its
equilibrium against the pull of gravity. The star
stays like this for 6.6 million years, steadily
converting the hydrogen in its core to helium:
the star is a main sequence star. Outside the
core, where our proton sits, no fusion is taking
place: the material of the star is still the same as
the original gas cloud from which it was born:
mostly hydrogen, with some helium and some
trace amounts of other elements left over from
previous generations of stars.
For six and half million years, nothing much
has changed for our proton. Enormous
quantities of radiation flood past every
second, produced in the core and flowing
through the star to its surface, there to shine
into space.
But this situation cannot last. Eventually the
time comes when the hydrogen in the core is
exhausted. When that happens, the core can no
longer support itself against gravity, so it starts
to collapse. When it does so, it heats up, and
hydrogen just outside the core finds itself hot
enough to fuse into helium for the first time.
This sudden increase in energy forces the outer
layers of the star to swell up dramatically: the
diameter of the star increases by a factor of
200. The outer layers, being so much larger,
also cool dramatically, so the star becomes
enormously large and red: a red giant star. If
this star replaced our Sun, it would stretch past
the orbit of Jupiter.
Meanwhile, the helium core is still collaps-
ing and heating up. Eventually, it becomes
hot enough for helium to fuse: this takes
much higher temperatures, about 100 million
degrees. But eventually the helium is also ex-
hausted: then the collapse re-commences. The
cycle repeats: each time a fuel is exhausted, the
core begins to collapse once more, which heats
it up even higher, so that even heavier elements
can fuse, which produces more energy to sup-
port the star. The fusion of these nuclear fuels
goes faster and faster as the atomic number
increases, both because there are fewer atoms
to fuse, and less energy is released each time.
At last something changes. The pressure
beneath our proton drops, and it starts to
fall inwards. The fall is stopped as the gas
beneath is more compressed, but now the
temperature is higher. Several times this
collapse and halting happens, with the tem-
perature increasing each time. At last the day
comes when, instead of bouncing off other
protons, the particles collide and stick: our
proton is now part of a deuterium nucleus.
Almost immediately, this fuses with two more
particles to form first helium-3 and then he-
lium-4. Later, after more collapse of the core,
this helium-4 nucleus fuses with two others to
form a carbon-12 nucleus.
Once silicon has fused to iron, however, there
is no next step. Iron is the most stable nucleus,
and does not release energy when it is fused:
adding anything else to the nucleus costs
The Private Life of a Proton | 209
Figure 9: Chandra X-ray image of the supernova remnant Cassiopeia A.
NASA/CXC/SAO
energy instead of producing it. The star has
reached the end of the line, and can no longer
support itself. Gravity has won.
The core of the star collapses inwards. The
inwards pressure forces electrons and protons
in the core to combine to form neutrons. These
neutrons are squeezed so tightly together that
in less than a second the whole core of the star,
weighing about one and a half times the mass
of our Sun, is compressed to a sphere only 15
km in diameter: it has become a neutron star.
Meanwhile, the outer layers of the star are still
falling, oblivious to what is happening to the
core. When these layers meet the newborn
neutron star, they bounce off it so hard that
they are ejected outwards again at a substantial
fraction of the speed of light. This creates a
shock wave which blasts the whole envelope of
210 | Genes to Galaxies
the star outwards at tremendous speed. When
this blast wave reaches the surface of the star,
it becomes visible as an enormously expanding
fireball: a supernova.
Sitting in the layer of carbon, our proton (in
its carbon nucleus) has no warning of the cat-
astrophic events that have taken place deep
below it in the core of the star. The first sign
that something has changed is that the pres-
sure beneath the layer suddenly drops; the
star begins to collapse. With nothing sup-
porting it from beneath, the outer layers of
the star, including the carbon atom contain-
ing our proton, begin to fall inwards. Seconds
later, however, the blast wave exploding
outwards through the star roars past, and the
gas is exploded outwards. All around, nuclei
are being fused with other nuclei to form
heavier elements, and bombarded by a flood
of neutrons in the wake of the blast. Within
seconds, elements up to uranium are formed,
in the crucible of a supernova explosion.
Our carbon nucleus is swept outwards as part
of an expanding shell of gas. As it expands,
the shell cools, and after about a hundred
thousand years stops glowing. The remnant
of the star, now light years behind, is visible
for a few million years as a pulsar, then it too
fades. The gas from the explosion, no longer
discernible as a shell, mingles with the inter-
stellar medium.
Without supernova explosions, there would
be no heavy elements from which to form
(amongst other things) rocky planets. Recall
hydrogen, helium and a tiny bit of lithium
were the only elements formed in the Big Bang,
and until the first stars formed nearly a bil-
lion years later, they were the only elements
in the universe. Once the first stars had been
born, heavier elements like carbon and oxygen
were created in their cores, but these elements
were locked up, inaccessible beneath layers of
unburnt hydrogen. Supernova explosions not
only liberate these elements into interstellar
space, but are also responsible for creating all
the elements heavier than iron in the explosion
itself7. All the stars in our Galactic neighbour-
hood, including the Sun, have about 1% of
their mass composed of elements heavier than
helium. All these elements must have come
from earlier generations of massive stars which
lived their lives, then exploded as supernovae,
seeding the surrounding gas with the new ele-
ments. This gas, now enriched with heavy ele-
ments, can then be incorporated into new stars.
Eventually, our carbon atom finds itself in
another cloud of cold, dense gas. A nearby
supernova triggers the collapse of this cloud.
Again, the gas is drawn inwards to where
the densest regions are pulling in ever more
material, eventually to reach high enough
temperatures that nuclear fusion begins and
stars are born.

7 There is a tiny number of elements that are formed

in different ways, like beryllium, formed when cosmic
rays split heavier nuclei in the interstellar medium, or
molybdenum, formed in the atmospheres of red giant Figure 10: Protoplanetary disks around
stars. Every other element in the periodic table is made stars in the Orion Nebula, from HST.
inside stars.
NASA, ESA, and the Hubble Heritage Team

The Private Life of a Proton | 211

 Figure 11: Every old surface in the Solar
System bears witness to having been
battered by impacts of all sizes. From top
to bottom: Callisto, Mercury and Mimas.

This time, our carbon atom is not in the

dense centre of the cloud, so by the time the
new star begins to shine, it is trapped in an
icy body at the outer edges of a giant disk
swirling around the star.
As the centre of the cloud collapses, the outer
regions flatten into a disk surrounding the pro-
tostar. The Hubble Space Telescope has taken
pictures of these disks in regions like the Orion
Nebula, showing that they are common around
young stars. It is from a disk like these that the
Solar System formed.
In the inner regions of the disk, dust and
particles condense out, then stick together,
bumping and colliding and growing in size
until the fragments, now called planetesimals,
have grown to about 1 km in size. Now their
gravity starts assisting with their growth: the
larger they grow, the more matter they attract.
The largest planetesimals sweep up all the mat-
ter within their reach, until we are left with a
hundred or so proto-planets, each the size of
our Moon or larger, orbiting the infant Sun.
Over the next hundred million years or so, this
number was reduced to the current handful of
planets as the proto-planets cross orbits and
collide in giant impacts. Every old surface in
the Solar System bears witness to having been
battered by impacts of all sizes.
Orbiting beyond the outermost planets were
the left-over planetesimals, which never coa-
lesced into a planet. We still see this disk of
left-over bodies as the Kuiper Belt, a region
beyond the orbit of Neptune containing prob-
ably 70,000 or more small icy bodies more
than 100 km in diameter. Pluto and the newly-
discovered dwarf-planets like Haumea and
Makemake are just the largest members of the
Kuiper Belt.
Six hundred million years after the planets
formed, something is happening in the end-
less cold at the edge of the Solar System.
As they orbit, the icy bodies feel new and

212 | Genes to Galaxies

 Figure 12: The near side of the Moon,
taken by the Galileo spacecraft on its way
to Jupiter. The dark areas are the maria:
impact basins filled with lava from ancient
volcanic eruptions.
different pulls; orbits that were previously sta-
ble are perturbed. Chaos ensues; some bod-
ies are flung outwards, but many others are
hurled inwards, towards the inner solar sys-
tem. The icy rock containing our carbon atom
is one of them. It hurtles towards a small
rocky world circled by one large moon...
Simulations of the formation of the planets
suggest that Uranus and Neptune probably
formed much closer to the Sun than they are
now. The four largest planets interacted with
each other and with the disk of icy planetesi-
mals which circled beyond them. The orbits
slowly expanded, until after about 700 million
years, the orbit of Saturn came into 2:1 reso-
nance with Jupiter, which means that Jupiter
orbited the Sun exactly twice for every one
of Saturn’s orbit.
This made the orbits of Uranus and Neptune
unstable, and their orbits expanded outwards
into the disk. Planetesimals were scattered in
all directions; some were flung outwards, and
some were sent careening into the inner Solar
System. This late heavy bombardment left scars
on most planets and satellites in the solar sys-
tem. It produced the great basins of the maria
on the Moon, and may have contributed to the
atmospheres of the inner planets. None of the
rocks brought back from the Moon were older
than 3.9 billion years, which is 600 million
years younger than the age of the Solar System.
Any atmospheres the terrestrial planets had
at the beginning would have been lost during
the worst of the heavy bombardment. As the
rate of impacts began to ease, however, the
planets began to cool. Gases trapped in the hot
rocks were gradually released, and combined
with the volatiles (water, carbon dioxide etc.)
brought by comets and asteroids from the
outer solar system to gradually build up an
atmosphere. On Earth, once the temperature
dropped below 100° C, water vapour could
condense out and the oceans begin to form.
Only inside stars can transmutation of ele-
ments take place, because only inside stars do
we find the enormous temperatures required.
Outside a star, a proton in the nucleus of an
atom is almost certain to stay there forever.
However, atoms can form an enormous variety
of molecules with other atoms, and molecular
bonds can form and break at much lower tem-
peratures. Carbon in particular forms bonds
with many elements, and can form molecules
of great complexity.
We don’t know how long it was after the late
heavy bombardment before conditions were
right for life to form, but the evidence sug-
gests it wasn’t long. The earliest evidence for
life comes from the study of isotope ratios
of carbon-12 to carbon-13 in rocks from 3.8
billion years ago, suggesting that life arose a
mere 100 million years after the late heavy
bombardment stopped.
The cataclysm of the impact that delivered
our carbon atom to the Earth has subsided;
the vaporised material from the icy planetesi-
mal has mixed with the existing atmosphere.
Sometime later, our carbon atom joins with
two oxygen atoms to form carbon dioxide,
the principal component of the atmosphere
of the young Earth. Soon it finds itself dis-
solved in the newly-formed oceans. The en-
ergetic UV radiation encourages many differ-
ent compounds to form and re-form, so our
carbon atom goes through a continual cycle
The Private Life of a Proton | 213
of new configurations: methane, ammonia, a molecule that can reproduce itself. Our
simple amino acids. proton has made the next step in its long
voyage, from galaxies to genes...
One day, a completely new type of molecule
emerges, built around our carbon atom. This
molecule and its descendants will eventu- Further reading:
ally transform the planet itself, changing
its atmosphere, its surface, its oceans. It is

Here are some suggestions for popular-level books covering some of these ideas.
• “The First Three Minutes: A Modern View Of The Origin Of The Universe” by Steven Weinberg
(Basic Books, 1993)
• “Big Bang” by Simon Singh (Fourth Estate, 2004)
• “The Birth of Stars and Planets” by John Bally and Bo Reipurth (Cambridge UP, 2006)
• “Cosmic Catastrophes: Exploding Stars, Black Holes, and Mapping the Universe” by J. Craig
Wheeler (Cambridge UP, 2007).
• “The Story of the Solar System” by Mark A. Garlick (Cambridge UP, 2002)
Table 1: Redshift and lookback time

Time since Big Bang

Redshift Fraction of current age 9
(in Gy = 10 years)
1100 0.0028% 380,000 y CMB
20 1.3% 0.2 Gy
Reionisation
10 3.5% 0.5
5 8.8% 1.2
Peak of galaxy
2 24% 3.3
formation
1 57% 5.9
0.5 63% 8.6
0.2 82% 11.3
0 100% 13.7 Now

214 | Genes to Galaxies

The Private Life of a Proton | 215
Research at
the School
of Physics
T his chapter will give some high-
lights of the history of the School
of Physics at the University of
Sydney and a more detailed
description of current activities, including the
fields of research undertaken here. It will also
give brief snapshots of arguably our most pres-
tigious scientists, the five Australian Research
Council (ARC) Federation Fellows who are at
present working in the School. Some words on
what the future might hold for the School com-
pletes the chapter.

Some Historical Highlights

The School of Physics occupies a beautiful
heritage building, which was built in 1924
from a design of the acclaimed architect
Lesley Wilkinson on the main campus of The
University of Sydney.
The present outstanding reputation of the
School, in Australia and internationally, had its
genesis in the appointment of Professor Harry
Messel as Head of the School in 1952. His
early achievement was to appoint a number of
bright young professors who were to emerge as
leaders in their fields. For example, the noted
theorist Professor Stuart Butler and Professor
Hanbury Brown who built an optical interfer-
ometer at Narrabri, in regional NSW, which lat-
er provided the impetus for the present Sydney
University Stellar Interferometer (SUSI). By
1960, Professor Bernard Mills also joined the
Department. He designed and built the radio
telescope at the Molonglo Observatory near
Canberra. Another star who was an alumnus
of the School, and later an academic, is Lord
Robert May, who was President of the Royal
Society.
A vibrant research environment was generated
by Professor Messel and continues today. He
appointed such leading scholars as Professor
Donald Melrose, a world-ranked theoretical
astrophysicist. Professor Melrose is currently
our only Fellow of the Australian Academy
of Sciences. The Academy elects Fellows
on the basis of their exceptional contribu-
218 | Genes to Galaxies
tions to science, which are nationally and inter-
nationally recognised.
The Present School in 2009
The legacy of Professor Messel is reflected in
the number of outstanding researchers and
teachers who are enthusiastic about work-
ing here. Over the past decade the School of
Physics has been spectacularly successful in
research, with national competitive grant in-
come more than doubling and the number of
research staff increasing from 20 to 80.
The School is also noted for its excellence
in teaching with several members of staff,
Professors Geraint Lewis and Tim Bedding,
Associate Professor Manjula Sharma, Drs John
O’Byrne and Joe Khachan all winning teaching
excellence awards in recent years. The number
of postgraduate research students has doubled
in this period and is continuing to rise. In
particular we have been successful in attracting
Honours students to work in our active and
diverse research groups, with the number (40)
increasing three-fold since 2000.
The research in the School covers all the basic
themes in experimental, observational, compu-
tational and theoretical physics. The particular
fields include astronomy and astrophysics,
medical physics, space physics, materials sci-
ence and plasma physics (both laboratory
and astrophysical), photonics and optics,
quantum science, particle and nuclear phys-
ics, computational biophysics and condensed
matter physics.
The astronomers and astrophysicists study a
wide range of research topics including cosmol-
ogy and the early Universe; the vexed questions
of dark matter, dark energy and the origin of
cosmic magnetism; using the University’s and
other world-class telescopes to investigate
asteroseismology, galactic archaeology, stellar
and galaxy formation and evolution. A related
area of research is space and solar physics,
where solar flares, the Sun’s magnetic field and
complex plasmas are modelled. Simulations of
plasma instabilities and self-organising systems
are part of a wider research effort in complex
systems, which also encompasses modelling the
dynamic functionality of the brain.

Biomedical physics is an increasingly im-
portant area of research in the School, with
academic staff investigating the interaction
and effects of radiation with matter to apply
to radiation oncology and diagnostic imaging
as well as modelling ion transport across cell
membranes. Surface modification to produce
bioactive sensors are carried out by the applied
physics group. Among other experimental
developments they are pioneering the prepara-
tion of novel nanolaminate materials for high
temperature operations in industry, using
plasma deposition.
The School has strengths in many areas of
theoretical physics, including single atom
modelling to understand the properties of mat-
ter and surfaces, and working with quantum
entanglement to advance quantum information
theory. This work ties well with effort in ultra-
high precision measurements using photons
and a new area of experimental physics re-
search called mesoscopic physics, which looks
at the quantum properties and behaviour of
atoms and single electrons using macroscopic
techniques.
One area of research that has developed a
strong international reputation is in optics
and photonics. Fundamental science is be-
ing carried out to develop a photonic chip,
to enable terabit data rates and to understand
non-linear optical signal processing. Since
2003, the School has been headquarters for
the ARC Centre of Research Excellence for
Ultrahigh-bandwidth Devices for Optical
Systems (CUDOS), led by Professor Benjamin
Eggleton. CUDOS is one of only two Centres
of Excellence headquartered at the University
of Sydney. These centres have nodes in sev-
eral institutions around the country, either
Universities or research institutions. To crys-
tallise Sydney’s leadership in photonics, we
recently launched the Sydney Institute for
Photonics and Optical Science (IPOS), which
will be the focus for expanding our high
profile in this area. Strong links exist with the
new research field of astrophotonics, bridging
astronomy and photonics, where innovative
techniques are used to build optic-fibre based
instruments for world-class telescopes.
We are also part of the worldwide collabora-
tions researching fundamental particle physics
with the Large Hadron Collider at CERN, near
Geneva in Switzerland. As well as high-energy
particle physics, there is a group investigating
accelerator-driven sub-critical nuclear reactors
as a safer option for nuclear power generation.
To add to our diversity, we accommodate a
group working on the quantitative analysis of
humanity’s impact on our environment, and
one with a focus on physics education and the
question “how should we best teach physics?”
Many of the research groups are led by ARC
Federation Fellows, which is the most prestig-
ious research fellowship offered in Australia.
In 2008 there were 6 in the School, the largest
number in any research area in the country and
more than the total awarded to several entire
Research at the School of Physics | 219
Universities. Currently we have 5 Fellows
and a brief description of their research is
given below.
As well as the Federation Fellows the School
hosts another 25 researchers who have been
awarded nationally competitive Fellowships,
including 5 ARC Professorial Fellows and 5
ARC Queen Elizabeth II Fellows. The intel-
lectual fire-power in the School is impressive.
One measure of excellence is that we published
over 450 refereed publications in 2008 alone,
including papers in the highest impact journals
such as Science, Nature Photonics and Physical
Review Letters.
A large refurbishment has recently been un-
dertaken to improve the experimental physics
facilities in the School and to accommodate 15
staff and students who have transferred from
the University’s Optic Fibre Technology Centre.
They are now members of the School and part
of IPOS. The new laboratories also provide
facilities to begin research in mesoscopic phys-
ics and nanotechnology. As well as internal
collaborations between many of the research
groups, the academic staff have multiple links
with top international research groups. These
networks are essential for maintianing our
excellent research output. A brief snapshot of
Four of the ARC Federation Fellows in
the School of Physics in 2008: Professor
Ben Eggleton, Professor Marcela Bilek,
Professor Cathy Stampfl, Professor
Bryan Gaensler.
220 | Genes to Galaxies
the research of our Federation Fellows will give
some insight to the exciting and challenging
science questions they are tackling.
Our ARC Federation Fellows
Professor Marcela Bilek
The research focus of Professor Marcela Bilek is
the synthesis of new materials and surfaces us-
ing plasma processes. In recent years, she and
her team have developed plasma deposition
systems capable of delivering sub-monolayer
quantities of constituent elements in a highly
ionised form. The ions are guided by magnetic
fields to the growth surface where the material
is forming. The energy with which they arrive
is controlled by electric fields. Professor Bilek
has demonstrated that fine control over the
composition and microstructure of the growing
materials can be achieved by tuning the con-
stituent fluxes and their ion impact energies.
The structure and properties of the new ma-
terials are studied by advanced microanalysis
methods such as infra-red spectroscopy, X-ray
photoelectron spectroscopy, secondary neu-
tral mass spectroscopy, transmission electron
microscopy (TEM), X-ray diffraction, spectro-
scopic ellipsometry etc. Our understanding of
the structure and properties is extended by ab-
initio molecular dynamics simulations, using
codes to implement density functional theory
methods. Materials of particular interest for
applications include versatile bioactive protein
immobilisation surfaces for use in biosensors,
medical diagnostic and implantable devices
and transparent conducting oxides for use as
transparent electrodes. She is also studying a
new class of materials called MAX phases for
applications in extreme temperature environ-
ments. These materials combine the properties
of ceramics and metals.
Professor Joss Bland-Hawthorn
Professor Joss Bland-Hawthorn is a world
leader in the study of galaxy evolution. In
collaboration with Professor Ken Freeman,
he developed the field of galactic archaeology
and the technique of chemical tagging, which
uses the detailed chemical and kinematic
 Complementing this astrophysical research, he
has been actively exploring new instrumenta-
tion. Most recently he has led developments in
astrophysics, exploiting optic fibre technology
in new astronomical instruments. These revolu-
tionary technologies will be used to search for
the first galaxies in the early universe, and the
existence of cosmic antimatter.
Professor Benjamin Eggleton
Professor Eggleton is Director of CUDOS
ARC
and also heads the newly formed Institute of
Federation
Photonics and Optical Science (IPOS) at the
Fellow
University of Sydney. He is regarded as a world
Joss Bland-
leading researcher and pioneer in the fields of
Hawthorn
optical physics and photonics, which is the
use of light for the transmission and process-
ing of information. Professor Eggleton has
information of millions of stars to reconstruct pioneered fundamental studies in the optics of
the sequence of events leading to the formation man-made nanostructured optical materials,
of the Galaxy. His research inspired massive known as photonic crystals and his research
stellar surveys, such as the Radial Velocity has led directly to the realisation of new optical
Experiment (RAVE) to measure the positions devices for telecommunications applications.
and proper motions of 50 million stars and the His current research focuses on the develop-
HERMES project to measure the phases-space ment of the ultrafast photonic chip, a crucial
orbits and chemical abundances of stellar as- device for the development of next generation
sociations in our Galaxy. These surveys are set communication systems. In this context, his
to dominate the field over the next decade. team has reported numerous breakthroughs,
Professor Bland-Hawthorn’s work is described including demonstrating that the speed of light
in the pre-eminent review journal, the Annual
Reviews of Astronomy and Astrophysics (in
2002 and 2005). He has also helped to develop
the science case for the GAIA satellite to be
launched in 2011 that will measure positions
and three-dimensional space motions for a bil-
lion stars in the next decade.
A parallel theme of his research is the accretion
and ejection of gas in the vicinity of galaxies.
He first showed that the mysterious high-ve-
locity clouds are actually close to us and quite
low mass, which means they cannot account
for the gas apparently missing in the Galaxy, as
was widely believed. He demonstrated that the
Magellanic gas stream is rapidly dissolving and
raining gas into the Galaxy. Over two decades,
he has demonstrated that both starburst and
black-hole galaxies generate huge energetic
winds that carry gas, metals and energy far
from galaxies.

Research at the School of Physics | 221

could be slowed down and that slow light can to measure the Faraday rotation in the emission
be harnessed for efficient nonlinear processes. from thousands of distant galaxies. With these
His team recently demonstrated switching of measurements, magnetic fields are detected
optical signals at 640Gb/s (i.e. 640 thousand throughout the Universe. The observations they
Megabits per second) in a monolithic glass are undertaking result in three-dimensional
device. This is about 60 times faster than the maps of cosmic magnetism, which are reveal-
switches currently in Australia’s telecommuni- ing what these magnets look like and what role
cation networks. they have played in the evolving Universe.
Professor Bryan Gaensler
A remarkable discovery made by 20th century
astronomers was that the Universe is magnetic.
These cosmic magnetic fields play a vital role
in controlling how stars and galaxies form and
evolve. This naturally occurring magnetism also
regulates solar activity, protects the Earth from
harmful particles, and is vital for the navigation
of birds and other species. However, despite
the ubiquity of astrophysical magnets, we do
not understand what creates them, or how they
have maintained their strength over billions of
years. And unfortunately, magnetic fields are
invisible even to the largest telescopes.
Professor Bryan Gaensler is working to open
the window to this “Magnetic Universe” by
exploiting an effect called “Faraday rotation”, in
which light from a background object is subtly
changed when it passes through a cloud of
magnetised gas. He and his team are carrying
out detailed measurements using radio tele-
scopes in Australia and in the USA, with which

9000 light years

222 | Genes to Galaxies

Professor Peter Robinson
Professor Peter Robinson carries out research
in two main areas within the field of Complex
Systems. In theoretical plasma physics he stud-
ies random and nonlinear processes for appli-
cation to both space and laboratory plasmas. In
biological physics, he studies the dynamics of
brain activity and measurements, with applica-
tions in neuroscience, sleep research, imaging,
and medicine.
What does the future hold
for the School of Physics?
The priority for the School is excellence in re-
search and teaching and to continue to improve
our performance in both areas. We are also
committed to raising the awareness of science
in the community. We have several outreach
programs to encourage science awareness and
to provide training and resources for science
teachers. One of the most exciting programs in
the Faculty of Science is the Talented Student
Program, which offers a research experience
and individual challenges for the most gifted
students entering University. Physics is proud
to be a part of this program and we encourage
these students to continue on to postgraduate
studies. However, we are also committed to
giving all our students an enriching experience
in the School of Physics.
One initiative we are developing is a suite of
postgraduate coursework programs, such as
the successful Master of Medical Physics, which
was begun in 2004. By 2010 we shall have two
other programs in place, in Applied Nuclear
Science and Optics and Photonics. These pro-
grams have links with professional placements
in industry and hospitals. Other areas being
considered are space science and astronomy.
These programs complement the postgraduate
research degrees as part of the wide-ranging
experience of studying in the School of Physics.
High quality research demands top quality fa-
cilities, particularly in experimental disciplines
where laboratories need to be increasingly
sophisticated to support cutting edge science.
High performance computing and vast data
storage capabilities are required for modelling
and simulations. To this end, a new building
for the School of Physics is being planned,
with teaching spaces for innovative learning
techniques, nanofabrication facilities, and
clean rooms to support a growing experimental
capability in the areas of photonics, quantum
science and applied physics. Our goal is to be-
come the acknowledged top School of Physics
in Australia and the region. We would be very
pleased to welcome any ISS scholars to this ex-
citing environment to study the laws of nature
and the world around us.
Research at the School of Physics | 223
Help us to Honour Excellence
The International Science School (ISS) was estab-
lished by Professor Harry Messel AC CBE in 1962
to recognise and reward talented senior high school
students, and to encourage them to pursue careers
in science. The ISS is a two-week, fully residential
program of lectures, workshops, tours and special
events - and it is all free to the participating scholars.
Thus each scholarship is valued at around A$3000.
Alumni of the International Science School can be
found in senior positions in all walks of life, with
many of them acknowledging that their╒Science
School was responsible for changing their lives, and
recalling its two weeks as an exciting developmental
experience.
The International Science School, renamed the
Professor Harry Messel International Science School
in 1999 to honour Harry for his foresight, have con-
tinued uninterrupted for almost 50 years. In order to
ensure the continuation of the International Science
School, so that future students may also benefit,
the Science Foundation for Physics established The
Messel Endowment. The Foundation aims to raise
$5Million in 2009 Australian dollars. At the time of
printing, the fundraising campaign has come a long
way: in 2009, the Endowment sits at $3.1Million.
Despite this success, for which we are enormously
grateful, the Endowment still has a long way to go,
and the Foundation is determined to achieve the
target.
The Messel Endowment is managed so that the
real value of the capital is preserved. Bequests will
also be sought to ensure the growth of the capital
in the years to come. The primary purpose of the
Endowment is to support the International Science
School. If income from the Endowment exceeds the
requirements of the Science School the funds may,
with the approval of the Science Foundation, be
used to support other initiatives named to honour
Professor Harry Messel. Examples of such initiatives
may include a Professor Harry Messel Visiting Chair
and a Professor Harry Messel Lectureship.
As acknowledged with gratitude in the front of this
book, many individuals and companies have already
contributed to The Messel Endowment, and the
2009 Professor Harry Messel International Science
School has received considerable benefit from
the Endowment. All our Endowment donors are
“A contribution of A$30,000 to The Messel Endowment will
ensure the participation of one student in perpetuity ...”
224 | Genes to Galaxies
acknowledged on our web site and in all books of
the lectures presented at future International Science
Schools, and on a permanent display in the School
of Physics.
We hope you have enjoyed your time at the
International Science School, or had your mind ex-
panded by reading the chapters submitted by the ISS
lecturers and their on-line podcasts. Many people,
after experiencing the ISS, wish to give something
back, but are not sure how to do this. Here are some
suggestions. First, you could consider coming back
as staff for the next International Science School.
There is information in the Scholar Handbook on
how to apply. Secondly, you could approach some-
one in your neighbourhood, for example a company
or philanthropic institution or even a member of
your family with the capacity to contribute, to seek
a donation for The Messel Endowment. A personal
approach is always the best method of obtaining
such support and a person such as yourself, who has
just benefited from an International Science School,
makes the best ambassador.
Finally, we realise that you may not be in a position,
at present, to give to the Endowment yourself –
however, at some stage in the future, if you are in a
position to do so, we ask that you consider it then.
A donation form has been included on the next page
to assist you if you choose to proceed with some of
these suggestions. More donation forms are available
from The Messel Endowment at www.physics.usyd.
edu.au/foundation/
A contribution of A$30,000 to The Messel
Endowment will ensure the participation of one
student in perpetuity.
Please join us today in our vision for the young
scientists of tomorrow through The Messel
Endowment.
Professor Anne Green
Director, Science Foundation for Physics
 Science Foundation
for Physics
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ISS 2009 | 225