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Simplifying Complexity – Evolution and Biological Complexity Part II Timothy Bonebrake – November 12, 2014 I. Reflection and review 1. Natural selection: variation in traits, differential reproduction, heredity. 2. Fewer human genes than might be expected. 3. Where does a tree come from? How does development figure into evolution? 4. In addition to the Mitchell text, this lecture will focus mostly on Carroll’s Endless Forms Most Beautiful and Jablonka’s Evolution in Four Dimensions. II. Genetic algorithms (GA) 1. Taking cues from the mathematics of the modern synthesis: GAs! 2. GA = Recipe a. Create an initial population of candidate solutions. b. Calculate fitness of each individual. c. Select individuals (weighted by fitness) to be parents for next gen. d. Pair up parents. Each parent produces offspring based on crossover/ recombination. Mutation can also occur at this stage. e. Using the offspring population as the new population go to step 2. 3. Robby the robot is an example of a GA. Genes are the can pick-­‐up strategies. a. The GA does a better job of picking up cans than intuition (Mitchell) b. Not always best strategy to pick up closest can c. Fitness increases with increasing number of generations 4. Each gene by itself is uninformative with respect to its performance. It’s the interactions of the genes that are important. 5. Can be used as a means of biology-­‐inspired optimization for many problems. III. Genetic regulation 1. As discussed last week, transcription and translation results in proteins. 2. Monogenic diseases (e.g. sickle cell), examples of genetic causes to disease. 3. However, the human genome project has not cured all disease. Why? 4. Genes are regulated by other proteins (and other genes). a. Feedback loops are common result of genetic regulation mechanisms. b. Lactose in E. coli only metabolized if gene is turned on when repressor binds with lactose inducers and doesn’t prevent transcription. 5. Most of all genomes consist of “dark matter”, DNA that is not expressed. 6. Noncoding DNA can be functional however. a. Genetic switches cause genes to turn on and off at different stages of organismal development. b. Repressors and promoters can interact to produce complex patterns. c. Genetic regulatory circuits can have many pathways (like electronic). 7. Hox genes (homeotic genes) regulate development along the head-­‐tail axis. a. Antennapedia is a famous HOX mutation which causes legs on a head. b. Hox genes are basically the same across the entire animal kingdom. c. Human HOX genes are simply replicates of Drosophila HOX genes. d. “What is true for the E. coli is also true for the elephant.” e. HOX genes may be responsible for the Cambrian explosion and emergence of animal phyla in the history of life. 8. Genetic regulation key to understanding why 20K genes = human diversity. VI. Epigenetics 1. Consider Jaynus creatures have the exact same DNA – mutations all removed. a. Evolution based on cellular heredity mechanisms. b. Variation caused by large genetic switchboards. 2. Epigenetic inheritance systems, a few examples (from Earth!) a. Gene activity of generations past can be passed through generations. b. Structural inheritance can cause changes in cellular structure (e.g. prions and mad cow disease). c. DNA methylation is perhaps the best known epigenetic inheritance. i. Suppresses gene expression ii. Can cause big changes in phenotype (like obese mice!) d. RNA interference can also cause changes in gene expression. e. Behavior and culture can be importance forms of inheritance. 3. Recall the major and minor ants from the Networks lecture. Same DNA! Huge phenotypic differences caused by differential gene expression. 4. All of these mechanisms have caused a shift in our understanding of evolution. We now tend to think of an “epigenetic landscape” rather than the gene-­‐based adaptive peaks model of Sewall Wright. VI. Evo Devo: Case study with butterfly wings 1. Butterfly wings made up of tiny cells, also known as scales. 2. Nymphalidae butterflies (~6000 species) all have a basic developmental ground plan of stripes and spots. 3. Distal-­‐less Dll has proved to be an important gene in bfly wing development. a. Also important in Drosophila development. b. A key gene at multiple points in development (body, wing, spots). c. Spots can be experimentally induced in bflys with Dll. 4. Butterfly eyespots are a key evolutionary innovation. a. Can be used to deflect predators. b. Lots of variation produced through interactions of a few genes. 5. Melanization (recall E.B. Ford) in bflys is the result of a single gene change which causes a cascade of differential gene expression. 6. “Evolution is chance caught on the wing” – Stuart Kauffman/ Monod. 7. We now also know the developmental cause of Galapagos beak finches. Changes in the expression of the Bmp4 gene cause beak thickness changes. V. Extended synthesis? 1. The Modern Synthesis did not devote much time to developmental biology. Many evolutionary biologists have argued that this was a mistake and that key points about evolution have been subsequently missed. 2. Three perspectives on evolution a. Adaptationists – natural selection is of primary importance b. Historicists – chance and history have a significant evolutionary role c. Structuralists – development drives evolutionary change (evo devo) 3. Some have also argued that evolutionary biologists have been too reductionist and that a greater attention to complex systems (e.g. “adaptation at the edge of chaos”) could provide a more synthetic and accurate view of evolution.