Life goes on!

Harshal Ganpatrao Hayatnagarkar version 2013.12.21 CC BY-SA 3.0

Why do we feel hungry? What keeps our body temperature around 98.6 or 37 ? Why our wounds are healed, by themselves? How does our body fight diseases?

Why certain variety of wheat is more productive?

Why certain computer software perform better than others, in impossible situations?

Are we alone in the Universe? Can there be Life elsewhere?

Although not apparently so, these questions are connected and so are their answers.
The thread connecting them is Theory of Evolution

What is Evolution?

How to study evolution?

History of Life as Evolution

Summary

What next?

Credit: M. F. Bonnan

History of changes Passive process. NOT limited to biology.

NOT synonymous to progress.

NOT same as Origin of Life.

Essentially interplay of variations over time.

Explained by various theories (to be discussed later).

Origin of Life

Evolution of Life
time

This presentation is about Evolution of Life, which starts AFTER Origin of Life.

Because it is the study of history of Life, the only known phenomenon in the Universe.

Medicines

Food

Climate

Education

Technology

Economics and finance

Sociology

Exobiology

Nothing in biology makes sense except in the light of evolution Theodosius Dobzhansky

(Evolution) is a general postulate to which all theories, all hypotheses, all systems must hence forward bow and which they must satisfy in order to be thinkable and true. Evolution is a light which illuminates all facts, a trajectory which all lines of thought must follow this is what evolution is.

Why study evolution?

This is a long story, so behold !

Time

Diversity

Implications

Evolution

+ one needs tools and techniques to study each of these aspects.

Time

Diversity

Implications

Evolution

To understand so much diversity, that once existed, exists today, including the Humans and probably would emerge,

and to which
we are the witness.

Literally means Classification in Latin.

Grouping organisms in different classes (lets call them buckets for simplicity). Well, putting buckets into bigger buckets. Deriving common properties for each bucket. Originally defined by Carolos Linnaeus in 1735. Based on morphology. Grouped organisms into groups and subgroups. Organisms were created by God and Carolos only classified and named them.

Linnaean Taxonomy

Linnaean Nomenclature
Binomial nomenclature
Naming organisms by dichotomous key Meaning two words.

[Genus species]. For example Humans Homo sapiens Elephant Elephas maximu Potato Solanum tuberosum

Groups (we called them buckets earlier)

Common features abstracted. Resulted in initial hierarchy.

Final hierarchical definition

With criteria E.g. Kingdoms
Plantae, Animalia, Fungi.

abstract class Phylum extends Kingdom abstract class Family extends Order abstract class Genus extends Family abstract class Homo extends Genus class Homo_Sapiens extends Homo

harshal = new Homo_Sapiens(Harshal);

*Java programming language Only Species can be instantiated

Taxonomy has raised more questions than it answered. Organisms are similar to one another
How much similar? Why those similarities? For example, fox is similar to wolf.

As well as different
How much different? Why those differences? Fox is not wolf.

In wrong buckets - Whales were fishes once.

Classification based on appearances. And whale is NOT a fish, only if one looks INSIDE.

In addition, there are hints from the development of embryos of various species. Tail at origin tells tale of origin.

Correction of such mistakes did not leave taxonomy untouched of evolution, too. Taxonomy has itself been evolving since then.

Morphology

Anatomy

Physiology

Microbiology

300 years of journey

Proteomics

Genomics

Biochemistry

Wikipedia:Taxonomy

Linnaeus 1735 2 kingdoms

Haeckel 1866

Chatton 1937 2 empires

Copeland 1956 4 kingdoms

Whittaker 1969

Woese et al. 1977 6 kingdoms Eubacteria

Woese et al. 1990

3 kingdoms

5 kingdoms

3 domains

Bacteria

(not treated))

Prokaryota Protista

Monera

Monera Archaebacteria Archaea

Protista Vegetabilia Plantae Eukaryota

Protista Fungi

Protista Fungi Plantae Eukarya

Plantae

Plantae

Animalia

Animalia

Animalia

Animalia

Animalia

Time

Diversity

Implications

Evolution

If two objects are separating at rate of 1 inch per year Then After 1 million year, they would be 25.4 kilometers apart.

12 % of Geological time

First fishes.

All major phyla.

Prof. Carl Sagan

To give glimpse of events occurred in the history of the Universe to fit into the scale a common person can understand

From Big Bang till today Thirteen billion years of the Universes history scaled into 365 days of a year

January 1st, 00:00:00 AM Big Bang

Each month is roughly equivalent to a billion years

Courtesy - Arif Babul

But from such a remote past, what could survive to tell us the story?

Literally means Obtained by digging in Latin and studied under Paleontology.

A Fossil can be past impressions about the living being (like a thumb impression).
Impression of a leaf on a then-wet mud. An insect caught in a tree amber. Petrified skeletons of animals.

All one gets from such an antiquity is a fossil. A paleontologist must make sense out of them, such as to extract, preserve, connect and date the specimen.
Fossils can still tell the story of the organism when it was dying.
Morphology Anatomy Physiology (possibly)

Challenges

Identifying if a specimen is a fossil. Recovering a fossil as complete as possible. Identifying parts and whole of a fossil. Identifying organism of that fossil. Determining age of a fossil. Preserving for future study.

Informally, an organism still alive representing a lone species whose other relatives are extinct.

Coined by Charles Darwin himself. To understand certain anomalous species that have survived evolutionary pressure for very long time.

For example, platypus or duck-bill.

Theories have been evolving since last 200 years to answer these questions

Lamarcks Theory

DarwinWallaces Theory

Mendel's Theory

NeoDarwinism

Modern Evolutionary Synthesis

Inheritance of acquired characteristics

For example, giraffes stretched neck and passed it to progeny generations after generations.

Jean-Baptiste Lamarck

It does not hold good today.

There is no known reverse path from phenotype to genotype.

Explains origin of diversity over time i.e. Evolution Charles Darwin and Alfred Russell Wallace
Independently and then together Popular as Darwinism or Survival of Fittest

Darwin influenced by Malthusian Catastrophe

Human population tends to increase a lot faster than food supply, which may lead to catastrophic implications for entire planet.

Charles Darwin

Alfred Russell Wallace

Variation Competition

Multiplication

Origin of species

Speciation

Competition

Multiplication

Theory of Natural Selection

Adaptation

Growth

Survival

To understand Theory of Natural Selection, we should understand role of diversity and ecological niche.

Kind of approximation of term habitat. Subset of Ecosystem. Hyperspace of multiple dimensions. Dimensions can be temperature, Humidity, salinity, language and so on. For example
Salt water/fresh water. Arctic deep ocean water. Amazon rain forests. Highland forests. Top and bottom of Maple trees. Roof-tops in Manchester city. Marathi-speaking regions in India. Traffic signals in India . and almost anyplace where life-forms exist.

Source: http://hhh.gavilan.edu/rmorales/EcologySpring200 8.htm

Source: http://www.geol.umd.edu/~jmerck/GEOL388/lectures/06.html

Source: http://www.geol.umd.edu/~jmerck/GEOL388/lectures/06.html

On Galapagos Islands Darwin observed variety of finches, adapted for respective habitats.
High altitude vegetation Highland forests Lowland forests Bushes Shoreline vegetation

Even various levels of the same habitat, for example, from top to bottom of tree trunk.

Source - http://14yunhyu.wordpress.com/2013/08/31/d-2d-macroevolution/ Source http://hhh.gavilan.edu/rmorales/EcologySpring2008.htm

Species adapt to suit to their habitat. Alternatively, only suitable species survive in a habitat.
Adaptation for food, safety, nursing and so on.

Competitive Exclusion Principle OR Gauses Law

No two species can occupy the same niche in the same environment for a long time. Complete competitors cannot coexist. Thus if two organisms occupy exactly same niche, then they are the same species.

Source http://14yunhyu.wordpress.com/2013/08/31 /d-2d-macroevolution/

Source - http://hhh.gavilan.edu/rmorales/EcologySpring2008.htm

Life forms are food for others.

Visually chains and webs/networks. Mostly undiscovered. Delicate balance in ecologies.

Human interference.

Source: http://en.wikipedia.org/wiki/File:Chesapeake_Waterbird_Food_Web.jpg

Try removing few species here and there, the ecological collapse may happen (See Gaia Hypothesis). For example, cell towers and insecticides are killing bees, reducing crop output.

Population/individual becomes better suited to its habitat. Caused by variation through

Mutation (random variation in genes) Breeding (sexual reproduction) Horizontal gene transfer (Asexual borrowing. Typically occurs in bacteria).

For example, in highland forests, those finches will survive better which can crack nuts with hard shells.

Evolution of ecological and phenotypic diversity within a rapidly multiplying lineage.

Starting with a recent ancestor, this process results in an array of species with different traits with which they can exploit a range of divergent environments. For example, over generations few finches moved up the tree and few moved down.

Likely to trigger Evolutionary Radiation in local ecosystem.

Source http://hhh.gavilan.edu/rmorales/EcologySpring2008.htm Source - http://14yunhyu.wordpress.com/2013/08/31/d-2dmacroevolution/

Emergence of new species.

Species : A group of organisms capable of interbreeding and producing fertile offspring.

Consistent variation passed to offspring.

An increase in taxonomic diversity or morphological disparity, due to adaptive change or the opening of ecospace.
Essentially adaptive radiation spread across species. Essentially many branches in a phylogenic tree.

Evolutionary Explosion

A rapid radiation in a relatively short span of time. For example, Cambrian Explosion, The Internet.

Cambrian Explosion

Span of 10 million years happened 425 million years before. Blueprints of all known phyla emerged in this short span.

Darwin postulated that species change gradually and continuously. However, Stephen Jay Gould and others observed stasis and sudden speciation, called as Punctuated Equilibria.

Species accumulate changes and then suddenly radiate into new species.
Introduced and reinforced idea that species are Darwinian individuals and not just classes. Reasons are unknown.
Source - http://en.wikipedia.org/wiki/File:Punctuated-equilibrium.svg

All these variations do not survive over time. In fact, 99.9% of species that have ever existed, are now extinct, including dinosaurs.

Predation

Mating

Climate change

Externalities (such asteroid impact)

Marriages

Conflicts and Wars

Job interviews

Markets Genetically Modified Food/Organisms & Selective breeding

Individuals survive due to useful variations survive and perish through harmful ones. Units of selection
Self-reproducing molecules Genes Cells Individuals Groups Species Societies Nations

Ecological contrasts

Snow Black soot deposited on roof tops.

Altered predator-prey pattern

Black soot was getting accumulated on roof-tops, in all seasons. White moths were becoming visible even during winter, on accumulated black soot on roof-tops and predators could find and eat them. Thus increasing black moths population over white ones.
Black moth White moth Black moth White moth

Black soot from textile factories of Manchester

Black soot deposited by textile factories

Snow deposited in winter

Slow though the process of selection may be, if feeble man can do

much by his powers of artificial selection, I can see no limit to the amount of change, to the beauty and infinite complexity of the co-adaptations between all organic beings, one with another and with their physical conditions of life, which may be effected in the long course of time by nature's power of selection.
Charles Darwin

Probably origin of term Natural Selection.

Source: http://en.wikipedia.org/wiki/File:Life_cycle_of_a_sexually_reproducing_organism.svg

Fitness is NOT about being strong or healthy. Ability to survive and to reproduce, both
Collective quality of a population of species. Also thought in terms of average contribution to Gene pool. Simply, determines if a species would continue to survive.

But what makes a baby elephant as strong as its parents? OR How traits are transferred from parents to children, in general?

Mendels Laws

Law of Segregation Law of Independent Assortment.

Gregor Mendel

Discovery-rejection-rediscovery

Work published in 1865-66. Initially rejected by scientific community of his time. Later rediscovered in 1900 independently by Hugo de Vries and Carl Correns and was acknowledged.

A set of primary tenets relating to the transmission of hereditary characteristics from parent organisms to their offspring;
Units of heredity called as Factors
Today known as Genes Basis of chromosomal inheritance and genetics.

Law of Segregation
When any individual produces gametes, the copies of a gene separate so that each gamete receives only one copy.

Law of Independent Assortment

Alleles of different genes assort independently of one another during gamete formation. Also known as "Inheritance Law" True only for unrelated genes

Discovery of nucleic acids DNA and RNA.

James Watson

Francis Creek

Structure and role of nucleic acids in inheritance. Analogous to Mendels work.

Genes - Segments of DNA and RNA.

Functional units of inheritance. For example, color of eye/hairs.

What Mendel called factors then, are called as Allele today. Allele
Either of a pair (or series) of alternative forms of a gene that can occupy the same locus on a particular chromosome and that control the same character; Some alleles are dominant over others

Darwinism + Chromosomal inheritance Gene-centered view or Selfish gene theory

Holds that evolution occurs through the differential survival of competing genes as if such genes are selfish. Even further, altruistic behavior of organisms are in fact manifestations of selfish genes. Introduces concept of replicator and two instances of them Genes and memes. What genes are for organisms, memes are for cultures.

Phenotype Observable trait For example morphology, anatomy, behavior and so on. Expression of genes Extended Phenotype

Genotype Genetic make-up For example, chromosomes, nucleotide sequences in some cell organelles. Translates into phenotypes. Replication through extra-dimension of time.

For example birds nest.

Extended expression of genes.

Amino acids

Proteins

Nucleic acids (RNA & DNA)

Chromosomes and organelles

Individuals

Organs

Tissues

Cells

Groups, herds, societies and nations

Ecosystem

Planet

Brings together fields that are separated

From geology to paleontology. From molecular biology to ecology. From linguistics to political science.

Neo-Darwinism becomes subset.

It becomes possible to explain many phenomena due to borrowed learning.

Evolution A primer

Evolution = Study of variation over time and space

Space Variation across individuals at any given time. Time Variation across individuals in past and present.

Systematics

Study of the diversification of life on the planet Earth, both past and present, and the relationships among living things through time.

The history of organismal evolution

together, or terminate by extinction]

Evolution is regarded as a branching process,

[whereby populations are altered over time and may speciate into separate branches, hybridize

. This may be visualized as a multidimensional character-space that a population moves through over time.

Basically family tree of species

Further reading

Tree of Life from Phylogeny point of view

1. Single entry for all the animals

2. Common ancestor of animals and fungi

No surprise that microbes account for more than half biomass on Earth.

Tree of Life (by David Hillis, based on genome sequences) Explore more at http://onezoom.org

Human Evolution

Linux Evolution

Variation - An individual is different from others

Of same kind Attributes shared, values differ. Of different kind Attributes differ, values differ.

Classification

One combines similar individuals into a group, and then such groups into larger groups and so on, forming a hierarchy of groups called Taxonomy. Shared attributes of groups in a taxonomy In biology, species are loose groups of similar, compatible individuals, different from one another.

+
Creativity

Error in copying information

Mutation

Borrowing/snatching information
Horizontal transfer

Recombination

Sexual reproduction

Creativity

time

Macroevolution
Meteorology

Economics
Sociology Game theory Ecology Population genetics Behavioral science

Individual Microevolution
Anatomy Physiology Genetics Microbiology Chemistry Quantum mechanics

4. Growth and multiplication

Mating

Microevolution

3. Selection
Survival

1. Variation
Useful Harmful

2. Competition
In presence of limited resources 2. Radiation

3. Speciation

1. Adaptation

DNA

RNA

Proteins

Cellular Metabolism

Physiology

Structure and behavior

Individual

Species

Ecosystem

Study of changes that occur at or above the level of species, in contrast with microevolution. For example, a new species emerges or a group of species goes extinct. Explosions and extinctions - Two recurring patterns in macroevolution .

Source: http://evolution.berkeley.edu/evolibrary/article/evoscales_01

Extinction = Death of a species

Extinction of species is continuous process. Time (million years ago) Sometimes, widespread and more destructive. Either due to evolutionary pressure or external events. Great evolutionary significance.

D i v e r s i t y

E A B C D

Major causes
Asteroid impact Volcano Fall in sea levels

D i v e r s i t y

E A B C

Time (million years ago)

(A) OrdovicianSilurian 450-440 Mya (million years ago)

60-70% of all species - 2nd largest of all.

(B) DevonianCarboniferous 375-360 Mya

70% of all species. Extinction pulses within this period.

(C) PermianTriassic 250 Mya

Deadliest of all, Known as Great Dying. Killed upto 95% of all species. End of Trilobites, arguably longest surviving organisms.

(D) TriassicJurassic 200 Mya

Killed 70-75% of all species.

(E) CreteciousPaleogene 65 Mya

Killed 75% species. Known for end of dinosaurs.

Its not all that badas in creative destruction, creation follows destruction. Sometimes, more creatively

Rise in speciation in relatively smaller time window. Accelerated increase in diversity in geologically shorter time. Usually, driven by rush to fill empty niches. Could be triggered by an innovative trait and sustained by competition. For example development of
Photosynthesis. Oxygen-based metabolism. Aging. Sex. Eye. Endoskeleton and jaw. Endothermic mechanism.

Approximately 540 million ago. All major animal phyla emerged from this period. Blueprints for all vertebrates including fishes, dinosaurs and humans. Triggered by
Innovation of eye. Increase in oxygen levels. Snowball earth. Sustained by arms race thereafter.

Rise of trilobites

Arguably longest lived organisms till date 300 million years. Highest inter-species diversity.

Cambrian explosion

Devonian explosion

Triassic explosion

Paleogene explosion

540 Mya.
All major animal phyla emerged from this period Blueprints for vertebrates including humans. Triggered by Innovation of eye. Increase in oxygen levels. Snowball earth. Sustained by arms race thereafter.

440 Mya.
First major adaptive radiation of landbased life such as rise and spread of free-spore vascular plants. Rise of fishes, and known as age of fishes.

240 Mya.
After the largest extinction event PT. Rise of dinosaurs. Rise of first true mammals.

60 Mya.
Adaptive radiation of mammals, birds and reptiles.

When different organisms develop similar features to survive in a common niche. For example, streamlined body for swimming swiftly in the water.
Shark (Fish) Kronosaurus (Reptile/dinosaur) Penguin (Bird)

Dolphin (Mammal)

Whale (Mammal)

Okay, Evolution is a great story. But, what if the tape is played again?

For example (popular in sci-fi movies)

Imagine you go on a jungle safari, albeit of Jurassic age (150 Million years before present). You make a simply change, say killing a butterfly and come back to present time. Should there be any impact of that killing on future? Alternative History. Small perturbation (at one place) may lead to large effects (at other places). Observed by Edward Lorenz while modeling weather patterns that very small changes in values (such as a flap of butterflys wings) lead to dramatic changes in patterns (such as hurricane formation) over time. Hence the name.
Edward Lorenz

Chaos Effect (Butterfly Effect)

Chaos is NOT same as randomness.

Randomness necessitates denial of any pattern or order. Whereas chaos is often termed as Hidden Order.

Extreme sensitivity to initial conditions.

Vastly different outcomes over time due to slightly different initial conditions. Chaotic is property of all non-linear dynamical systems. Highlights significant path dependence. For example Weather, Stock market crashes, Epidemics, etc.

Always prevalent situation any point in space-time is an initial condition.

Analogous to sliding rule, the window of study moves thus making any point on rule as start of the window. Interesting part is about emergence of the other end of this window.

Emergence = property or behavior of a system demonstrated by none of its individual parts but collectively by them.

For example, intelligence is emergent property of brain, made from zillions of neurons, though none of them individually has this property. For example, locomotion is property of automobile, but none of its parts.
Changes in Population

Changes in Individual

Natural selection makes it possible to achieve similar goals with different routes.

For example, due to convergent evolution, vision, flight and streamlined body have been emerged in different species in the past.

Changes in Environment

Actually it may not matter in many cases whether we play the tape once or many times, due to phenomenon namely Selforganization.

A special kind of emergent phenomenon Spontaneous order arises out of local interactions of components.

For example, crystallization, galaxy formation, flocks of birds, multicellular organisms, human societies and so on. Islands of predictability in the ocean of unpredictability.

Perhaps, its an answer to every question regarding Life, or at least participatory.

Life is because-of, is a and has Self-organization.
Natural selection itself is a kind of Self-organization phenomenon.

Helps achieve similar results from different initial conditions. Thus acts as opposite of chaos.

Selforganization

Chaos

Overview of Factors

Populations Combinations Competitions

Variations

Evolution

Generations

Time

Diversity

Implications

Evolution

Highlights some important patterns in evolution

Functional integration Functional differentiation Complexity trend Information aspect of evolution

From Replicating molecules Independent replicators (probably RNA) RNA as both genes and enzymes Prokaryotes Asexual clones Protists

To "Populations" of molecules in compartments Chromosomes

Notes Can't observe RNA world hypothesis

DNA as genes; proteins as enzymes

Eukaryotes Sexual populations Multicellular organisms animals, plants, fungi Colonies with non-reproductive castes Human societies with language, enabling memes Sociocultural evolution Can observe Evolution of sex Evolution of multicellularity

Solitary individuals Primate societies

Increasing biocomplexity through Integration Smaller entities often have come about together to form larger entities.
For example Chromosomes, eukaryotes, sex multicellular colonies.

Often smaller entities

Have become differentiated as part of a larger entity.

For example DNA & protein, organelles, anisogamy, tissues, castes

Are unable to replicate in the absence of the larger entity. e.g. Organelles, tissues, castes Can sometimes disrupt the development of the larger entity. e.g. Meiotic drive (selfish non-Mendelian genes), parthenogenesis, cancers, coup dtat

New ways of transmitting information have arisen.

e.g. DNA-protein, cell heredity, epigenesis, universal grammar.

Complexity has been rising since origin of life. Cambrian Explosion

A tipping point. Accelerated pace of increase in complexity. A pattern in evolution, typically preceded by an extinction event/span.

Quasi-closed system/habitat, populations of species affect each other. In predator-prey model, changes in demand and supply. Complex relationship in presence of multiple predator and prey species. Such patterns affect environment.

For example, if a grass consumed by rabbits will affect population of not only rabbits, but also wolfs.

Bacteria

Herb

Rabbit

Wolf

Single mutation in a bacterium can significantly affect an herb, which forms significant diet of a species like rabbit and thus affecting population of wolves too, that feed upon rabbits.

Life forms are food for others.

Visually chains and webs/networks. Mostly undiscovered. Delicate balance in ecologies.

Human interference.

Source: http://en.wikipedia.org/wiki/File:Chesapeake_Waterbird_Food_Web.jpg

Try removing few species here and there, the ecological collapse may happen (See Gaia Hypothesis). For example, cell towers and insecticides are killing bees, reducing crop output.

Prof. James Lovelock

Biosphere is a self-regulating entity.

Abiota affects biota and vice versa.

Cycles in a Daisy World.

Model for climate change.

Now a fact instead of fiction.

Major contribution by humans.

By Gaia hypothesis, climate change in turn will affect humans. Rise in ocean levels, resulting into submerging of coastal cities. Frequent hurricanes and cyclones. Malthusian catastrophe Behavioral sink

Changes in seasons to affect harvest. However, humans will affect humans too.

A condition or event by which a population returns to subsistence level conditions once population growth outpaces agricultural growth Wikipedia
An Essay on the Principle of Population published in 1798. Inspired Charles Darwin, to late discover Theory of Origin of Species.

Thomas Malthus

Criticism

New knowledge and technology can avert such crisis. For example, Green Revolution. Socio-economic aspects such as birth control and urbanization play their role too.

Increasing population has its impact on itself too. An experiment to understand impact of overpopulation.
From 1947 to 1972.
Published initial result in Scientific American in 1968. Though experiment involved rats, results are indicative to humans too.
John B. Calhoun

Many rats placed in a relatively small area.

Area divided into four rooms, with decreasing amenities such as food, water and protection. Rats in each room showed different behavior.

Least resourceful room was termed as Behavioral Sink.

Rats showed destructive behavior, especially towards weaker rats such as females and babies. It resulted into inability of females to carry through pregnancy and mortality rates as high as 96 percent.

Similar indicative behavior can be seen in patches of human societies too.

Ecology crisis

Mining, petroleum and heavy industries. Automobiles and livestock. Shrinking fisheries, forests, glaciers and icecaps.

Economy crisis

Faltering growth Booming and busting bubbles Unemployment Inequality

Economy crisis Ecology crisis

Humanity Crisis

Energy crisis

Energy crisis

Depleting fossil fuel sources. No viable alternative in sight.

Evolution has brought us here. It will guide us from here.

Change is the only constant thing.

Hence evolution is omnipresent and almighty.

Evolution is interplay of scale and diversity over time. Never underestimate power of small change.
Butterfly effect An action sets the Universe on a new course, every time and all the time.

(Everything else is an illusion Bhagvadgeeta)

Prof. N Swaminathan and other colleagues. Wikipedia

Being evolutionary is not a bad idea, perhaps because being survived as fittest is not bad idea.

To be continued with Evolution: Understanding facts