Evolution in Action

Startling conclusions on the ultimate consequences of unsupervised tinkering

The Evolutionary Algorithm• Start with something that works pretty well.• Make tweaked copies of it.• Various copies compete against each other,

and environment. ‘Fittest’ reproduce most.• Repeat on large populations for billions of

years.• Ultimate source of the intelligence in the

genome.• A very slow way to develop software.

Double Helix

• DNA is composed of the bases A,C,G and T

• A and T always pair, C and G always pair

• Each strand can serve as a template for the other.

Mutation and DNA

• Radiation can break DNA.• Aromatic chemicals can nestle between bases

and cause insertions when copying• Other chemicals like AZT mimic bases, cause

substitutions.• UV light can fuse pairs of T’s• Copy mechanism is only 99.9999999%

perfect.

Viruses

• Some viruses integrate their genome into genome. HIV is an example.

• When a virus leaves a cell it can accidently pick up some of host DNA, transporting it to another host.

• Occasionally viruses can transport DNA from one species to another.

Transposons

• “Selfish” DNA. Stripped down viruses.

• Make copies of themselves which are randomly inserted into genome.

• Some end up making partial copies of other genes as well.

• Currently relics of transposons make up half of human genome.

Sex• Each individual has two copies of each

chromosome, one from mom, one from dad.• Sperm/egg have only one copy of each

chromosome, chosen randomly.• Chromosomes ‘cross over’ in at least two

places further shuffling genes.• Cross-over between different copies of same

transposon can cause large duplications, deletions.

Crossing Over

Normal crossover:homologous regionsswapped.

Crossover seeded by repeat:leaves one chromosome with a large insert, the other with a largedeletion.

Advantages of Sex• Allows selection to more easily work on

combinations of traits.• Allows genome of species to carry significantly

more information than genome of an individual.• Encourages fruitful collaborations.• Asexually producing species often thrive for a

time, but are slower to adapt to change.• Many organisms only reproduce sexually only in

times of stress, reproduce asexually normally.

The Value of Duplications

• Each gene has an important function. Most mutations disrupt this function.

• Duplication of a gene frees one copy to evolve another function.

• Clusters of related genes are the fastest evolving part of the genome.

Human vs.

Human

• A variation every 1000 nucleotides.• 90% of human variation is within African

populations.• There are enough humans, and the mutation rate is

high enough, that on average each base is mutated several times in each generation.

• Humans each carry hundreds of bad mutations. Most are recessive, only show up with inbreeding.

Human vs. Chimpanzee

• A difference every 100 bases.• A new transposon every 50000 bases• Two chromosome in one species fused

compared to the other.

Human vs. Mouse

• In general 40% of bases have changed.• In functional regions only 15% of bases have

changed.• Looking for conserved regions between human

and mouse helps identify functional parts of human genome.

Evolution of Multicellular Life

• Competition between cells is intense.

• Cells dividing randomly form a solid ball. Cells in the middle of ball get starved

• Beginnings of multicellular forms were cells dividing in organized fashion to form filaments, sheets or hollow balls.

A Filamentous Form

Anabaena - a filamentous algae. Filamentous forms haveevolved independently many times.

A Hollow Ball

Volvox - an algae that forms hollow balls. Baby volvosare forming inside. The hollow ball is more rare than filaments, but human embryos go through this stage.

Building a Body from DNA

• 3 billion bases of human DNA contain roughly 30,000 genes.

• The products of the genes are the parts that make up a cell.

• These genes are turned on and off in a very intricate fashion to form and maintain a human body.

• Some genes regulate other genes.

How DNA is Used by the Cell

Promoter Tells Where to Begin

Different promoters activate different genes indifferent parts of the body.

A Computer in Soup

Idealized promoter for a gene involved in making hair.Proteins that bind to specific DNA sequences in the promoter region together turn a gene on or off. Theseproteins are themselves regulated by their own promotersleading to a gene regulatory network with many of thesame properties as a neural network.

Evolution of Cancer• Human body has 1014 cells descended from a

single egg cell.• Many mutations occur in cells over your lifetime.• Mutations that favor growth of an individual cell

over growth of the organism lead to cancer.• A half-dozen genes must be disabled to have a full

fledged malignant cancer.• Cancer cells have mutations that encourage

mutation – flawed DNA repair mechanisms. • Radiation paradoxically induces cancer and cures

it.

The Peculiar Dangers of Smoking

• Smoking kills lung lining rapidly. Lung cells must reproduce a lot to keep up.

• Many opportunities for copying errors and growth competition.

• Aromatic compounds in ‘tars’ intercalate in DNA leading to frame shift errors.

• Tobacco accumulates uranium, leads to ionizing radiation and chromosome breaks.

Engineering vs. Nature

• Disadvantages of Nature– Blind forces of mutation cause 100 problems

for every benefit. Worse than a bad hacker!– Genome is cleaned up by pain of infertility,

spontanious abortion, and disease.

• Advantages of Nature– Nature just runs each experiment on a few

organisms.– It’s taken 3 billion years, but Nature has

accumulated great wisdom.

Startling Conclusions

• Evolution good• Homogeneity bad• Sex good• Inbreeding bad• Cooperation good• Smoking bad• The body is built from a 1 dimensional code.• Genetic engineering is best practiced a small scale

The End