Evolution in Action

1. Evolution in Action Startling conclusions on the ultimate consequences of unsupervised tinkering

2. 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.

3. 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.

4. 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.

5. 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.

6. 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.

7. 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.

8. Crossing Over Crossover seeded by repeat: leaves one chromosome with a large insert, the other with a large deletion. Normal crossover: homologous regions swapped.

9. 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.

10. 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.

11. 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.

12. Human vs. Chimpanzee • A difference every 100 bases. • A new transposon every 50000 bases • Two chromosome in one species fused compared to the other.

13. 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.

14. 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.

15. A Filamentous Form Anabaena - a filamentous algae. Filamentous forms have evolved independently many times.

16. A Hollow Ball Volvox - an algae that forms hollow balls. Baby volvos are forming inside. The hollow ball is more rare than filaments, but human embryos go through this stage.

18. 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.

19. How DNA is Used by the Cell

20. Promoter Tells Where to Begin Different promoters activate different genes in different parts of the body.

21. 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. These proteins are themselves regulated by their own promoters leading to a gene regulatory network with many of the same properties as a neural network.

22. 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.

23. 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.

24. 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.

25. 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

26. The End