an introduction to evolution dr. chrisantha fernando systems biology centre university of birmingham...

An Introduction to EvolutionAn Introduction to Evolution

Dr. Chrisantha Fernando

Systems Biology Centre

University of Birmingham

Dr. Chrisantha Fernando

Systems Biology Centre

University of Birmingham

What does Evolution explain?What does Evolution explain?

To explain how different animals and plants have become adapted to different environmental conditions over many generations.

Evolution is the process by which living things become adapted to their environment over many generations.

To explain how different animals and plants have become adapted to different environmental conditions over many generations.

Evolution is the process by which living things become adapted to their environment over many generations.

What is Evolution?What is Evolution?

Evolution occurs in populations of agents some of which produce offspring. The 'fitter' ones tend to produce more.

Over many generations, the make-up of the population changes without the need for any individual to change. Over successive generations, the 'species' changes, in some sense adapts to the conditions.

Evolution occurs in populations of agents some of which produce offspring. The 'fitter' ones tend to produce more.

Over many generations, the make-up of the population changes without the need for any individual to change. Over successive generations, the 'species' changes, in some sense adapts to the conditions.

The HorseThe Horse

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Open country, ran from predators.

Muscles tend to be foundat the upper part of the leg, later on.

Lower part is less heavy.

Easier acceleration and deceleration -> less energyon galloping.

One toe

Karl Sims’ Artificial EvolutionKarl Sims’ Artificial Evolution

Evolved virtual body plans in a simulated physical environment

Used artificial evolution in the computer Show video.

Evolved virtual body plans in a simulated physical environment

Used artificial evolution in the computer Show video.

Evidence for EvolutionEvidence for Evolution

Selective breeding for phenotypic traits, e.g. cows for milk, chickens for eggs, dogs for friendliness, mice for better teeth.

Similarities between different species allows inference of an evolutionary tree.

Moths in Birmingham during the Industrial Revolution.

Selective breeding for phenotypic traits, e.g. cows for milk, chickens for eggs, dogs for friendliness, mice for better teeth.

Similarities between different species allows inference of an evolutionary tree.

Moths in Birmingham during the Industrial Revolution.

BreedingBreedingQuickTime™ and a

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Homology Homology

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Moths in BirminghamMoths in Birmingham

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1956 1996

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Evolution by Natural SelectionEvolution by Natural Selection Natural selection is an algorithm that works iff… Multiplication. Entities should give rise to more

entities of the same kind. Like begets like: A type entities produce A type

entities, B type entities produce B type entities, and so on.

Variability. Heredity is not exact; occasionally A type objects give rise to A' type objects. Undirected.

Entities of different types have a hereditary difference in their survival. Directed.

Natural selection is an algorithm that works iff… Multiplication. Entities should give rise to more

entities of the same kind. Like begets like: A type entities produce A type

entities, B type entities produce B type entities, and so on.

Variability. Heredity is not exact; occasionally A type objects give rise to A' type objects. Undirected.

Entities of different types have a hereditary difference in their survival. Directed.

‘Natural’ Selection of Paper Gliders

‘Natural’ Selection of Paper Gliders

1.Generate 20 random sequences of folding instructions 2.Fold each piece of paper according to instructions written on

them. 3.Throw them all out of the window 4.Pick up the ones that went furthest, look at the instrns. 5.Produce 20 new pieces of paper, writing on each bits of

sequences from parent pieces of paper. 6.Repeat from (2) on.

This is Inman Harvey’s example.

1.Generate 20 random sequences of folding instructions 2.Fold each piece of paper according to instructions written on

them. 3.Throw them all out of the window 4.Pick up the ones that went furthest, look at the instrns. 5.Produce 20 new pieces of paper, writing on each bits of

sequences from parent pieces of paper. 6.Repeat from (2) on.

This is Inman Harvey’s example.

Fold TL to BR towards you

Fold horiz middle away

Fold vertical middle towards

Fold TR to BL towards you

Fold horiz middle away

Fold vertical middle away

I. Harvey.

Evolving Tables

Hornby et al

Natural Selection in the Lab Natural Selection in the Lab

Sol Spiegelman’s experiment with Q-beta replicase enzyme.

Sol Spiegelman’s experiment with Q-beta replicase enzyme.

R

RNA

R

RNA

R

RNA

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Serial Dilution, like with homeopathy

Natural Selection in the CPUNatural Selection in the CPU

Tierra (Tom Ray) and Avida. Tierra (Tom Ray) and Avida.

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Parasites Yellow

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Immune HostsRed Starting Set

“Organisms compete for CPU time to replicate”. “A reaper randomly removes organisms”.

An example Tierran OrganismAn example Tierran Organism

nop_1 ; 01 47 copy loop template COPY LOOP OF 80AAAnop_0 ; 00 48 copy loop templatenop_1 ; 01 49 copy loop templatenop_0 ; 00 50 copy loop templatemov_iab ; 1a 51 move contents of [bx] to [ax] (copy instruction)dec_c ; 0a 52 decrement cxif_cz ; 05 53 if cx = 0 perform next instruction, otherwise skip itjmp ; 14 54 jump to template below (copy procedure exit)nop_0 ; 00 55 copy procedure exit complimentnop_1 ; 01 56 copy procedure exit complimentnop_0 ; 00 57 copy procedure exit complimentnop_0 ; 00 58 copy procedure exit complimentinc_a ; 08 59 increment ax (point to next instruction of daughter)inc_b ; 09 60 increment bx (point to next instruction of mother)jmp ; 14 61 jump to template below (copy loop)nop_0 ; 00 62 copy loop complimentnop_1 ; 01 63 copy loop complimentnop_0 ; 00 64 copy loop complimentnop_1 ; 01 65 copy loop compliment (10 instructions executed per loop)

Evolutionary Dynamics in Tierra.Evolutionary Dynamics in Tierra.

Smaller self-replicating mutants require less CPU time (energy/resource), so replicate faster.

Parasites appeared 45 instructions long, able to use the code of their neighbors.

Hyperparasites appear that are even smaller and faster at replicating.

Smaller self-replicating mutants require less CPU time (energy/resource), so replicate faster.

Parasites appeared 45 instructions long, able to use the code of their neighbors.

Hyperparasites appear that are even smaller and faster at replicating.

Natural Selection as movement over a fitness landscape.

Natural Selection as movement over a fitness landscape.

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Random

F

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Smooth

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Neutrality. Neutrality. ’Constant innovation’ -- You never get stuck !

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Examples of Neutrality of GP Map.

Examples of Neutrality of GP Map.

RNA Sequence --> RNA Structure. Evolvable Hardware.

RNA Sequence --> RNA Structure. Evolvable Hardware.

William Paley and the EyeWilliam Paley and the Eye

People said evolution could not produce the eye by small improvements, but it can.

Computer experiments helped confirm this. “To suppose that the eye… could have been

formed by natural selection, seems, I freely confess, absurd in the highest possible degree,” (Darwin, The Origin of Species).

People said evolution could not produce the eye by small improvements, but it can.

Computer experiments helped confirm this. “To suppose that the eye… could have been

formed by natural selection, seems, I freely confess, absurd in the highest possible degree,” (Darwin, The Origin of Species).

Nilsson’s Computer SimulationNilsson’s Computer Simulation

The New Eye The New Eye

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The Origin of LifeThe Origin of Life

Chicken and Eggs, Catch 22’s and the Oroboros.

How did natural selection start without genes that could undergo natural selection in the first place?

How did the molecules that made genes come about in the first place?

Chicken and Eggs, Catch 22’s and the Oroboros.

How did natural selection start without genes that could undergo natural selection in the first place?

How did the molecules that made genes come about in the first place?

What was the first Self-Replicating Thing?

What was the first Self-Replicating Thing?

The Major Transitions in Evolution (JMS & ES 1995)

The Major Transitions in Evolution (JMS & ES 1995)

1. Replicating molecules to Populations of molecules in compartments2. Independent replicators (probably RNA) to Chromosomes3. RNA as both genes and enzymes to DNA as genes, proteins as enzymes• Prokaryotes to Eukaryotes5. Asexual clones to sexual populations — evolution of sex6. Protists to multicellular organisms — animals, plants fungi evolution of multicellularity7. Solitary individuals to colonies with non-reproductive castes8. Primate societies to Human societies with language, enabling memes

Ammalgamation: e.g. Chromosomes, eukaryotes, sex multicellular colonies.Specialization: e.g. DNA & protein, organelles, anisogamy, tissues, castesObligate Symbiosis: e.g. Organelles, tissues, castesConflict Mediation: Meiotic drive (selfish non-Mendelian genes), parthenogenesis, cancers, coup d’étatNew Information Transmission Techniques. DNA-protein, cell heredity, epigenesis, universal grammar.

What is Life? (Tibor Ganti,1971)What is Life? (Tibor Ganti,1971)

If you went to Mars and found a pink fluffy object, how would you work out if it was alive?

Boundary Metabolism Informational Control System E.g. single cell, multi-cellular organism. Is a

country alive?

If you went to Mars and found a pink fluffy object, how would you work out if it was alive?

Boundary Metabolism Informational Control System E.g. single cell, multi-cellular organism. Is a

country alive?

Problems in Evolution.Problems in Evolution.

How could sex evolve? Why only two sexes not three or four?

How do new species come about? How does the genotype-phenotype map

evolve, i.e. the evolution of evolvability. Can there be selection of groups or

ecosystems in the wild? Chicken coops.

How could sex evolve? Why only two sexes not three or four?

How do new species come about? How does the genotype-phenotype map

evolve, i.e. the evolution of evolvability. Can there be selection of groups or

ecosystems in the wild? Chicken coops.

Thanks toThanks to

Inman Harvey Jon Rowe All sources used for Images from the

Internet.

QUESTIONS AND DISCUSSION if you like.

Inman Harvey Jon Rowe All sources used for Images from the

Internet.

QUESTIONS AND DISCUSSION if you like.