An Introduction to Evolution
Dr. Chrisantha Fernando
Systems Biology Centre
University of Birmingham
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.
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.
The Horse
One toe
Open country, ran from
predators.
Muscles tend to be found
at the upper part of the
leg, later on.
Lower part is less heavy.
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Easier acceleration and
deceleration -> less energy
on galloping.
Karl Sims’ Artificial Evolution
 Evolved virtual body plans in a simulated
physical environment
 Used artificial evolution in the computer
 Show video.
Evidence 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.
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Breeding
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Homology
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Moths in Birmingham
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1956
1996
Evolution 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 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.
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
 Sol Spiegelman’s experiment with Q-beta
replicase enzyme.
R
R
R
RNA
RNA
RNA
Serial Dilution, like with homeopathy
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Natural Selection in the CPU
 Tierra (Tom Ray) and Avida.
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Red Starting Set
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Parasites Yellow
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Immune Hosts
“Organisms compete for CPU time to replicate”.
“A reaper randomly removes organisms”.
An example Tierran Organism
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copy loop template
COPY LOOP OF 80AAA
copy loop template
copy loop template
copy loop template
move contents of [bx] to [ax] (copy instruction)
decrement cx
if cx = 0 perform next instruction, otherwise skip it
jump to template below (copy procedure exit)
copy procedure exit compliment
copy procedure exit compliment
copy procedure exit compliment
copy procedure exit compliment
increment ax (point to next instruction of daughter)
increment bx (point to next instruction of mother)
jump to template below (copy loop)
copy loop compliment
copy loop compliment
copy loop compliment
copy loop compliment (10 instructions executed per loop)
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.
Natural Selection as movement
over a fitness landscape.
F
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Random
Smooth
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Neutrality.
’Constant innovation’ -- You never get stuck !
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Examples of Neutrality of GP
Map.
 RNA Sequence --> RNA Structure.
 Evolvable Hardware.
William 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).
Nilsson’s Computer Simulation
The New Eye
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The 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?
What was the first SelfReplicating Thing?
The Major Transitions in
Evolution (JMS & ES 1995)
1.
2.
3.
4.
5.
6.
7.
8.
Replicating molecules
to
Populations of molecules in compartments
Independent replicators (probably RNA)
to
Chromosomes
RNA as both genes and enzymes
to
DNA as genes, proteins as enzymes
Prokaryotes
to
Eukaryotes
Asexual clones
to
sexual populations — evolution of sex
Protists
to
multicellular organisms — animals, plants fungi evolution of multicellularity
Solitary individuals
to
colonies with non-reproductive castes
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, castes
Obligate Symbiosis: e.g. Organelles, tissues, castes
Conflict Mediation: Meiotic drive (selfish non-Mendelian genes), parthenogenesis, cancers, coup d’état
New Information Transmission Techniques. DNA-protein, cell heredity, epigenesis, universal grammar.
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?
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.
Thanks to
 Inman Harvey
 Jon Rowe
 All sources used for Images from the
Internet.
 QUESTIONS AND DISCUSSION if you
like.