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 Crossover seeded by repeat: leaves one chromosome with a large insert, the other with a large deletion. Normal crossover: homologous regions swapped.
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 have evolved independently many times.
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.
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.
Promoter Tells Where to Begin Different promoters activate different genes in different 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. 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.
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