EVOLUTION

The First Four Billion Years

E D I T E D BY

MICHAEL RUSE
J O S E P H T R AV I S

W I T H A F O R E WO R D BY

E DWA R D O. W I L S O N

THE BELKNAP PRESS OF

HARVARD UNIVERSITY PRESS
CAMBRIDGE, MASSACHUSETTS
LONDON, ENGLAND
2009
 Copyright © 2009 by the President and Fellows of Harvard College

All rights reserved

Printed in the United States of America

Library of Congress Cataloging-in-Publication Data

Evolution : the first four billion years / edited by Michael Ruse, Joseph Travis ;
with a foreword by Edward O. Wilson.
p. cm.
Includes bibliographical references and index.
ISBN 978-0-674-03175-3 (alk. paper)
1. Evolution (Biology) I. Ruse, Michael. II. Travis, Joseph, 1953–
QH366.2.E863 2009
576.8—dc22 2008030270
 Contents

Foreword vii
Edward O. Wilson

Introduction ix
Michael Ruse and Joseph Travis

The History of Evolutionary Thought 1

Michael Ruse

The Origin of Life 49

Jeffrey L. Bada and Antonio Lazcano

Paleontology and the History of Life 80

Michael Benton

Adaptation 105
Joseph Travis and David N. Reznick

Molecular Evolution 132

Francisco J. Ayala

Evolution of the Genome 152

Brian Charlesworth and Deborah Charlesworth

The Pattern and Process of Speciation 177

Margaret B. Ptacek and Shala J. Hankison

Evolution and Development 208

Gregory A. Wray

Social Behavior and Sociobiology 237

Daniel I. Rubenstein

Human Evolution 256

Henry M. McHenry

Evolutionary Biology of Disease and Darwinian Medicine 281

Michael F. Antolin
vi Contents

Beyond the Darwinian Paradigm: Understanding Biological Forms 299

Brian Goodwin

Philosophy of Evolutionary Thought 313

Kim Sterelny

Evolution and Society 330

Manfred D. Laubichler and Jane Maienschein

Evolution and Religion 348

David N. Livingstone

American Antievolutionism: Retrospect and Prospect 370

Eugenie C. Scott

Alphabetical Guide 401

Contributors 935

Illustration Credits 949

Index 951
 Introduction
Michael Ruse and Joseph Travis

The discovery of evolution is one of the greatest intellectual achievements of

Western thought, ranking with the calculus and general and specific relativity
among scientific discoveries that changed indelibly how we see our world.
From seeing nature as fixed forever in form and composition to seeing it as
forever changing, we have been transformed utterly by discovering and un-
derstanding evolution.
In science the word evolution is used to express three different but related
ideas. First, there is the fact of evolution. This is the realization that all or-
ganisms, living and dead, including humans, are the end products of a long
natural process of change through which each species is descended from
other, different ones. Although protoevolutionary ideas date back to the time
of the ancient Greeks, only in the eighteenth century did the claim that or-
ganisms evolved really start to gain currency. However, the idea was not con-
sidered a basic element of scientific knowledge until after Charles Darwin
published his On the Origin of Species in 1859. Darwin argued that all the
organisms on the planet emerged through a single, straightforward process
that operated relentlessly from the dawn of life and that continues to shape
the natural world. An enormous amount of scientific research, from paleon-
tology to molecular biology, has provided the compelling and overwhelming
evidence that evolution is indeed a fact.
Second, evolution is often used to refer to the path of life’s history on this
globe. This can refer to the history of a group of existing species, as in the
evolution of orchids, or the path through which particular traits emerged,
such as the evolution of the middle ear of mammals from small bones in the
reptile jaw. Evolutionary histories are reconstructed from a wide variety of
evidence that ranges from sequences of species and forms in the fossil record
to similarities and differences in the DNA of existing organisms. The evolu-
tion of some features, such as the hooves of ungulates, is very well under-
stood, while the evolution of others, particularly very old features like the
organelles of cells, is less well understood.
The third idea is the theory of evolution. This refers not to a suggestion
that evolution has not occurred or that the history of particular features cannot
ix
x Introduction

be reconstructed but to our ideas about the forces that drive evolutionary
change. In the Origin Darwin proposed what today is almost universally con-
sidered the major force in organic change, natural selection. But natural se-
lection is not the only important evolutionary force; natural selection operates
on the variation in shapes, sizes, and forms of organisms created by muta-
tions in their genes, and the rate and magnitude of the changes that are
driven by natural selection are governed by how those genes control develop-
ment. An enormous amount of observation and experiment has documented
the action of natural selection and some of the genetic responses to selection.
But modern discoveries in genetics and development have raised many new
questions and guided us toward some surprising answers about how all these
forces combine to drive evolution.
Outside science the word evolution refers to a natural process considered
the inspiration for a host of sociological, literary, political, philosophical,
and religious ideas. From writers exploring the animal nature of humans to
psychologists searching for the origin of human behavior in evolutionary his-
tory to theologians grappling with the implications of evolution for our un-
derstanding of the Divine, the influence of evolution outside science far
exceeds that of any other scientific discovery ever made. And as modern con-
troversies in the schools illustrate, particularly in the United States, it pro-
vokes reactions almost as strong as issues surrounding the beginning and end
of human life.
In this book we explore all these facets of evolution. Our authors present
the evidence for evolution as fact from the fossil record to genomics, illus-
trate the history of groups from bacteria to birds, and describe our current
ideas about how these histories and this evidence came to be. Our authors
also explore the influence of evolution on philosophy, religion, sociology,
psychology, and many other areas and address the current controversies
about the teaching of evolution in schools. The book covers the historical dis-
coveries, such as homology, that opened the path for discovering evolution;
the phenomena, such as industrial melanism, that played major roles in in-
spiring experimental studies of evolution; the applications of evolutionary
principles to areas seemingly far afield, such as computer science; and the
contributions of the major figures who shaped the history of evolutionary sci-
ence and the discipline as it exists today.
Perhaps most important, this book presents evolutionary science as a mod-
ern, dynamic discipline. All too often discussions of evolution outside the sci-
ence itself give the impression that the subject became fossilized in the
nineteenth century. This is particularly so when the suitability of evolution as
a subject for secondary-school students is being argued. The irony is that the
discoveries of modern science, from molecular biology to computational in-
novation, have provided compelling evidence that Darwin could only dream
of seeing. From those discoveries have also come applications that Darwin
might never have imagined, such as Darwinian medicine. Principles of evolu-
tion are being applied to a wide variety of scientific problems, from under-
standing senescence to strategies for conservation to explaining human
 Introduction xi

behavior. There are few topics in science with so many exciting new facets,
which reveal that despite all we have learned, there is much more to be dis-
covered. Not that there is further need to substantiate evolution as fact;
rather, there is much more to be done to trace the evolution of groups of
species or features, particularly complex features at the cellular and molecu-
lar levels, and to refine our theory of evolution to account more fully for the
astonishing diversity of life as we continue to discover it. The essays in this
book show not only how far we have come but where the scientific horizons
lie and how we might move toward those horizons.
This book is organized into two parts. The first part contains long essays
on the overarching themes in evolution. From the history of evolutionary
thought to the controversies over education, from the fossil record and the
origin of life to the process of adaptation, the long essays offer primers on the
major features of evolution. Many of them offer close looks at particular
areas like molecular evolution, genomic evolution, and Darwinian medicine.
The second part contains a large number of shorter essays on more specific
topics. These include essays on major groups of organisms with which most
people are familiar, topics that are important facets of evolution, major fig-
ures in the discovery and shaping of evolutionary science, and the critical
books that recount the history of discovery, development, and maturation of
a discipline.
This organization allows the reader to explore evolution according to his
or her interests and background. The reader who wishes to be immersed in
the science can focus on the major scientific themes, while the reader who is
interested in the intellectual history and influence of the subject away from
science can enter through a separate set of essays. A reader interested in very
specific topics or historical figures can find the appropriate entries, along
with essays on related topics. Our goal was to provide an exciting and com-
pelling introduction to evolution along with a basic reference work that could
point the way toward a deeper study of individual issues. The essays include
bibliographies, which serve as guides to further and deeper reading.
Although we hope that our fellow scholars enjoy these essays, we want this
volume to inform, educate, and excite readers who are not professional
scholars. We find evolution in all of the word’s meanings to be a provocative,
interesting, and indeed awe-inspiring topic, and we want our readers to
emerge with the same feeling. But beyond the excitement of studying evolu-
tion, it is important to understand and appreciate it. Evolution explains the
challenge of antibiotic-resistant pathogens and the scourge of novel infec-
tious diseases, it shows us what we can expect climate change and our own
alterations of habitat to do to the natural world, and it may offer profound
explanations of who we are and why we behave as we do. It also challenges
many of our closely held beliefs about man’s, and woman’s, place in nature.
The last of these issues is perhaps the foundation of why evolution has
proven so controversial. Survey after survey shows that fewer than 50% of
people in the United States accept that evolution is responsible for the diversity
of life on earth. It is unclear how much of that opposition is based on a poor
xii Introduction

understanding of evolution and the evidence about it and how much is based
on the challenges that it offers. Yet opposition to evolution by religious peo-
ple, especially by Christians, is by no means inevitable; some of the most dis-
tinguished believers have accepted evolution without many qualms. We are
convinced that the Christian—with the Jew and Muslim and other religious
believers—should be at the head of the queue of those who welcome evolu-
tionary ideas. Finding the idea, building and elaborating upon it, and looking
at its influence and importance are, as the contributors to this volume show
again and again, truly the best of proofs that we are made in the image of
God, celebrating creation in all its wonderful manifestations.
This book is a testament to one of mankind’s greatest discoveries, a discov-
ery that offers unparalleled insight into what creation really is. We love evo-
lution, and if we and our fellow contributors can inspire you even in a small
way with our enthusiasm, then we shall be happy indeed.
 The History of Evolutionary
Thought
Michael Ruse

The idea that all organisms (including humans) are generated by natural
means from other forms has ancient roots. Aristotle tells us that Empedocles
(fifth century b.c.e.) toyed with such thoughts. However, it was not until the
eighteenth century and the Enlightenment that evolution (as we now call this
idea of natural development) really started to gain a serious number of sup-
porters. There are reasons both for the long delay and why the idea finally
began to gain momentum.

The Early Days

The Greeks had no great religious objection to evolution, but their world pic-
ture did not have a place for any kind of significant developmental processes.
Specifically, the Greeks thought that they had irrefutable reasons to reject on-
going, incremental organic change. They—particularly the philosophers
Plato and Aristotle—thought that the world (especially the world of organ-
isms) showed order and intention and, as such, was not something that could
simply have appeared through blind, ungoverned processes of law. It cer-
tainly was not something that could have grown from simple beginnings to
the complexity of today. Plato used human fingernails as an example of order
and design: “Sinew, skin and bone were interwoven at the ends of our fingers
and toes. The mixture of these three was dried out, resulting in the formation
of a single stuff, a piece of hard skin, the same in every case.” Plato then went
on to put things in context.
Now these were merely auxiliary causes in its formation—the preemi-
nent cause of its production was the purpose that took account of future
generations: our creators knew that one day women and the whole
realm of wild beasts would one day come to be from men, and in partic-
ular they knew that many of these offspring would need the use of nails
and claws or hoofs for many purposes. This is why they took care to
1
2 The History of Evolutionary Thought

include nails formed in a rudimentary way in their design for hu-

mankind, right at the start. This was their reason, then, and these the
professed aims that guided them in making skin, hair and nails grow at
the extremities of our limbs. (Timaeus, 76d–e, in Cooper 1997, 1277)

In an incredibly influential discussion, Aristotle in De partibus animalium

(1984) identified the factors at work here as “final causes.” These are causes
that occur not just to produce or do something (the finger parts dry and make
nails) but for the sake of some kind of purpose (the nails protect the finger
ends). They show some kind of forethought or intention. For this reason, fi-
nal causes cannot be reduced to blind, unguided law, as is demanded in evo-
lution. The world, particularly the world of organisms, must in some sense
have been designed rather than just produced under its own steam by natural
processes. (Sedley 2008 is the definitive study.)
The Jews, and following them the early Christians, had religious reasons
for the rejection of evolution. It goes against the creation stories of the early
chapters of Genesis, which portray a world created miraculously by God and
then peopled by him through divine fiat over a short time span. But do not
think that religion as such was then and always an absolute bar to evolution-
ism. The church fathers (the major Christian theologians of the early cen-
turies) worked toward an understanding of the biblical text that would allow
interpretation, particularly in the face of advances of science. Saint Augustine
was eager not to let ancient creation accounts stand in the way of modern
thought. He himself, believing that God stands outside time, speculated in a
kind of protoevolutionary fashion that the Divine had formed seeds of life
that then sprang into full being when they were placed here on earth. How-
ever, one should not read too much into any of this. Like the Greeks, the
Jews and Christians were simply not looking in the direction of evolution and
would have thought final causes an unanswerable objection to significant de-
velopmentalism. As is well known, these kinds of causes became a founda-
tion of one of the major proofs of God’s existence, the Argument from
Design, which moves from design here on earth to the existence of the divine
artificer.
Why, then, did evolution start its rise in the eighteenth century? The an-
swer is simple. It was at this time that people started to challenge the
Christian picture of world history—a providential picture of a world cre-
ated by God, where humans are made in his image but have fallen and are
able to achieve salvation only through his undeserved grace. Some began
to argue that perhaps humans held their fates in their own hands and
could progressively improve their own lots. It was this idea of progress—
the belief that the world and its denizens are on a trajectory upward and
that this upward rise is made possible by (and only by) the unaided efforts
of the world’s human inhabitants—that gave rise to the idea of organic
evolution (Ruse 1996). Enthusiasts for progress extended their thinking
into nature and developed the idea of evolution—progressive change up-
ward from the simple to the complex. They then read this idea back into
 The History of Evolutionary Thought 3

human thought and social practice as confirmation of their beliefs about

progress.
The British physician and man of science Erasmus Darwin (grandfather of
Charles) was a paradigm who hymned in verse life’s upward rise to hu-
mankind:
Imperious man, who rules the bestial crowd,
Of language, reason, and reflection proud,
With brow erect who scorns this earthy sod,
And styles himself the image of his God;
Arose from rudiments of form and sense,
An embryon point, or microscopic ens!
(E. Darwin 1803, 1: Canto I, lines 309–314)
This is all the end product of the progressive development of human intelli-
gence, which causes and is reflected in humans’ scientific achievements:
How loves and tastes, and sympathies commence
From evanescent notices of sense;
How from yielding touch and rolling eyes
The piles immense of human science rise!
(Canto III, lines 43–46)
Similar ideas were to be found elsewhere, most notably in France. In his
Philosophie zoologique (1809), the taxonomist Jean-Baptiste de Lamarck
produced the first full-blown evolutionary theory—a picture of upward rise
to our own species from the most primitive forms of life, which in turn had
been produced from mud and slime through the actions of heat and electric-
ity and other natural forces.
Although the metaphysical idea of progress was the main factor behind the
rise of evolutionary ideas, it is not true that there was no pertinent empirical
evidence. Aristotle had noted that organisms of very different species seem to
share common patterns or structures—what today are known as homologies—
and the evolutionists were ready to interpret these as signs of common ances-
tries (Figure 1). Likewise, the successes of animal and plant breeders did not
go unnoticed (Figure 2). But generally the evidence took a very secondary po-
sition. The fossil record, something that today many (if not most) people
would invoke first as the proof of developmental origins, was less than help-
ful. As a systematic proof of progressive change, the gleanings from the rocks
were meager indeed. In any case, counting against the empirical side was the
fact that no one had any great understanding of what might have caused evo-
lution. Most assumed some kind of vague, upwardly thrusting force or
forces, but little more. Generally, everyone was committed to the folk belief
that characteristics acquired in one generation could be transmitted immedi-
ately to the future generations—Lamarck was so enthused by this process
that the inheritance of acquired characteristics has since become known as
Lamarckism—but beyond this was silence.
4 The History of Evolutionary Thought

The ideology of progress was what counted, and it was for this reason that
most people around 1800 would have regarded evolutionism less as a real
science and more as a pretender, somewhat like animal magnetism (mes-
merism) and the reading of character from skull shape (phrenology). Even
judged by the standards of that time, evolution was what may fairly be called
a pseudoscience. Obviously, Christian opponents of evolution disliked in-
tensely the antiprovidential underpinnings of the doctrine. But evolution was
not associated with total nonbelief, atheism, or even what later in the nine-
teenth century Thomas Henry Huxley was to call agnosticism. Most evolu-
tionists were deists who believed in God as unmoved mover, a being who had
set the world in motion and now let it unfurl without need of miraculous in-
tervention. For the deist, indeed, evolution was proof of God’s power and in-
tention rather than disproof. Everything was planned beforehand and went
into effect through the laws of nature. In Erasmus Darwin’s words: “What a
magnificent idea of the infinite power of the great architect! The cause
of causes! parent of parents! ens entium!” (1801, 2: 247). There is a
link here, especially in England, with the Industrial Revolution. People were
harnessing the forces of nature—water, coal, and others—to produce goods
through machines rather than by hand. The god of the deist was the ultimate
 The History of Evolutionary Thought 5

divine industrialist as he harnessed the forces of nature to produce the goods

of the world through law rather than miraculously or by hand.
Critics of evolution, notably the great French comparative anatomist
Georges Cuvier, made reference to empirical problems. Cuvier cited the
mummified bodies of humans and animals brought back by Napoleon’s army
from Egypt. Although they were very old, their forms were identical to con-
temporary forms and hence counted against ongoing organic change. But as
with the positive case for evolution, in the negative case it was the ideology
that really counted. Above all, for Cuvier, there was hatred of progress—
hatred of a doctrine that had led humans to think that they could do more
than they could do and had led ultimately to the terrors of the French Revo-
lution, when opponents of the existing state had tried to change all that had
proved true and safe for many generations. Combined with this, for Cuvier,
as for every other opponent of evolution, was the still-unsolved problem of
final cause. The Frenchman emphasized that this was something that could
not be ignored; indeed, it was the most important distinguishing feature of
life. The key to understanding the organism lay in the fact that it was not
6 The History of Evolutionary Thought

simply subject to the physical laws of nature but was organized. The parts
were directed to the end of the functioning whole, and each individual fea-
ture played its role in the overall, purpose-directed scheme of things:

Natural history nevertheless has a rational principle that is exclusive to

it and which it employs with great advantage on many occasions; it is
the conditions of existence or, popularly, final causes. As nothing may
exist which does not include the conditions which made its existence
possible, the different parts of each creature must be coordinated in such
a way as to make possible the whole organism, not only in itself but in
its relationship to those which surround it, and the analysis of these con-
ditions often leads to general laws as well founded as those of calcula-
tion or experiment. (Cuvier 1817, 1: 6)

Cuvier’s point simply was that the organism is far too integrated—organized
and complex—to allow significant change in any direction. It is certainly too
integrated to allow change from one species to another. Organisms at mid-
point would be literally neither fish nor fowl and hence would simply be un-
able to exist or survive. Evolution was in some sense a theoretical impossibility,
as well as empirically unfounded.
Religion was involved too. Progress goes against the Christian doctrine of
Providence. Nevertheless, although Cuvier thought that there was evidence
of Noah’s flood, neither he nor other serious scientists wanted to make the
case by simple reference to Genesis. Indeed, by the beginning of the nine-
teenth century, all were starting to realize that the earth’s history must be far
older than the traditional 6,000 years that one can work out from the ge-
nealogies given in the Bible. It is not that the Bible is false, but rather that it
needs interpretation. Some solved the problem by thinking of the six days of
creation as six long periods of time; others solved it by supposing that there
were long, unmentioned gaps between the biblical days. God’s creation there-
fore was a long, drawn-out process, but it was not evolutionary.
The controversy was at an impasse, and not much had changed by the mid-
dle of the nineteenth century. On the one side were the evolutionists, com-
mitted to progress and ardent in their belief that organic development was
the perfect complement to this ideology, with enthusiasm outstripping empir-
ical knowledge. Confirming this pattern, in 1844 the Scottish publisher
Robert Chambers wrote (anonymously) a highly popular work on evolution,
Vestiges of the Natural History of Creation, in which he argued that every-
thing was in a state of upward becoming and that what happened in the so-
cial world mirrored what happened in the biological world:

The question whether the human race will ever advance far beyond its
present position in intellect and morals, is one which has engaged much
attention. Judging from the past, we cannot reasonably doubt that great
advances are yet to be made; but if the principle of development be ad-
mitted, these are certain, whatever may be the space of time required for
their realization. A progression resembling development may be traced
 The History of Evolutionary Thought 7

in human nature, both in the individual and in large groups of men . . .

Now all of this is in conformity with what we have seen of the progress
of organic creation. It seems but the minute hand of a watch, of which
the hour hand is the transition from species to species. Knowing what
we do of that latter transition, the possibility of a decided and general
retrogression of the highest species towards a meaner type is scarce ad-
missible, but a forward movement seems anything but unlikely. (Cham-
bers 1846, 400–402)

On the other side were the opponents, committed to Providence, vocal

about the significance of final cause, and accepting that Genesis must be
modified but thinking that this could be readily done. David Brewster, gen-
eral man of Scottish science and biographer of Newton, could see the dan-
gers: “It would auger ill for the rising generation, if the mothers of England
were infected with the errors of Phrenology: it would auger worse were they
tainted with Materialism.” The problem, Brewster gloomily concluded with
reflections that still find much support in many circles today, stemmed from
the slackness of schools and universities: “Prophetic of infidel times, and in-
dicating the unsoundness of our general education, ‘The Vestiges . . .’ has
started into public favour with a fair chance of poisoning the fountains of sci-
ence, and of sapping the foundations of religion” (Brewster 1844, 503). (In-
terestingly, this kind of attack seems to have confirmed Chambers in his
views. Although, from the start, progress was the leitmotif of his book, he
felt the need to make his point ever more explicit. The passage just quoted
above is from the fifth edition of Vestiges and replaces a passage that gives
more credit to the Creator. [Figure 3])
Of course, neither side was really satisfactory. Ideology is no substitute for
real evidence, and final cause can be ignored but does not go away. Referring
all to miracle may be socially and psychologically comforting, but it is not a
good scientific solution. The time had come for a significant step forward.

Charles Darwin

Charles Robert Darwin (1809–1882) was sent to Edinburgh University to

train in the family tradition of medicine (Figure 4). After two years he
dropped out, bored with the lectures and revolted by the operations. Yet al-
ready Darwin had started to mix with scientists, especially naturalists inter-
ested in the living world. One of his acquaintances was Robert Grant, an
anatomist and an avowed evolutionist. So, quite apart from his grandfather’s
work (the young Charles read Erasmus’s major treatise, Zoonomia), evolu-
tion was an idea to which Darwin was introduced at an early age. It seems,
nevertheless, that the youthful Darwin accepted in a fairly literal form the
whole of Christianity, including the early chapters of Genesis, and that this
was a factor in his redirected choice of a career: to be an ordained minister in
the established Church of England. To achieve this end one needed a degree