UTACCEL 2010 Adventures in Biotechnology Graham Cromar Part

UTACCEL 2010 Adventures in Biotechnology Graham Cromar

Part 1: Evolution

Darwin’s Voyage 1831 -1836 Adaptations of finches to various habitats is consistent with descent (with modification) from a common ancestor.

Darwin’s four tenets • • Inheritance Variability Limited resources Selection Evolution Note: Evolution is not random! Evolution has no goal or predetermined direction

Lines of Evidence • • • Fossil record Selective breeding Ontology Comparative anatomy Direct observation Comparative genomics Ontology describes the origin and the development of an organism from the fertilized egg to its mature form

Fossil Record provides many intermediate forms

Human Lineage

Selective breeding has produced this impressive range of characteristics in only a few hundred years. Note these animals are technically still the same species. Both are descended from wolves.

Comparative anatomy Vestigial structures, such as pelvic bones in the baleen whale, are evidence of evolution because they show structural change over time.

Phylogenetic Tree of Life

Hillis Plot This phylogenetic tree, created by David Hillis, Derreck Zwickil and Robin Gutell, depicts the evolutionary relationships of about 3, 000 species throughout the Tree of Life. Less than 1 percent of known species are depicted.

Species Diversity Animals: estimated 3 -30 million species | |--Invertebrates: 97% of all known species | `--+--Sponges: 10, 000 species | |--Cnidarians: 8, 000 -9, 000 species | |--Molluscs: 100, 000 species | |--Platyhelminths: 13, 000 species | |--Nematodes: 20, 000+ species | |--Annelida: 12, 000 species | `--Arthropods | `--+--Crustaceans: 40, 000 species | |--Insects: 1 -30 million+ species | `--Arachnids: 75, 500 species | `--Vertebrates: 3% of all known species `--+--Reptiles: 7, 984 species |--Amphibians: 5, 400 species |--Birds: 9, 000 -10, 000 species |--Mammals: 4, 475 -5, 000 species `--Ray-Finned Fishes: 23, 500 species We humans have an over-inflated opinion of our own importance. In fact, we are only one of millions of species. Even our close kin the vertebrates are not as successful in biological terms as the invertebrates in terms of diversity and biomass. Its still a microbial world: There are over a billion viruses in a teaspoon of sea water. There about 100 trillion cells in the human body and over ten times that many bacteria in our guts.

Evolutionary Arms Race

Happens also on a molecular scale Our immune systems are locked in an arms race with infections and rapidly develop defences against their invaders, research suggests

Introduction to Game Theory The Prisoners’ Dilemma provides insight into the difficulty in maintaining cooperation. Often people fail to cooperate with one another even when cooperation would make them better off. This applies equally to animals whose behaviour is determined by instinct. The prisoners’ dilemma is a particular “game” between two captured prisoners that illustrate why cooperation is difficult to maintain even when it is mutually beneficial. *2

Suppose there are 2 criminals- Mike and Alex. The police have caught them on a weapons’ charge which the punishment is 1 year. The police suspect they robbed a bank, but lack of evidence, therefore, they need one or both of them to confess. They separate the criminals and offer each of them the same deal: *3

• If you confess to the bank robbery. I’ll let you go free and your partner will get 20 years in jail. • If you both confess, we won’t have to go to trial so you will each get 8 years in jail. • If neither of you says anything, we’ve got you on the weapons’ charge, so you will each get 1 year in jail. *4

Payoff Matrix Alex’s Decision Mike’s Decision Stay Silent Confess Stay Silent -1-1 -20 0 Confess 0 -20 -8-8

• If Alex choose to confess, Mike will confess too, for -8 > -20. • If Ales choose to keep silent, Mike will confess anyways, for 0 > -1. • If Mike choose to confess, Alex will confess too, for -8 > -20. • If Mike choose to keep silent, Alex will confess anyways, for 0 > -1. For both criminals, their dominant strategy* is the same: They should confess, rather than risk that the other will confess if they keep silent. * The dominant strategy is the best strategy for a player to follow regardless of the strategies chosen by the other players.

Group Exercise Player 1 Cooperate Defect Cooperate 3/3 1/4 Purpose: Win the game by accumulating the most points over 12 rounds 1/1 You may not speak to your opponent to conspire or reveal your strategy. Player 2 Defect 4/1 Rules:

Questions 1. How does repeated play influence the outcome of prisoner’s dilemma? 2. What was your strategy? How did you determine it? 3. Did it work? Why or why not?