1. Simulating Evolution Robbie Rosati

2. Definition of Evolution
“The change in heritable traits in biological populations over generations.” – Wikipedia
NOT: adaptation within a generation,
improvement toward a predetermined goal

3. Mechanisms of Evolution
Natural selection
repeated trial and error
Genetic drift
genetic selection bias
At what level do these happen?

4. Genetic Drift

5. Unit of Selection Natural selection: genes
Genetic drift: function of population size

6. “Selfish” Gene Selection
The genes that are passed on serve their own interest (replication) by giving the organism beneficial traits.
Organisms are “survival machines” for their genes.
Genes can reproduce at the expense of the organism. Ex. Maternal flour beetle gene that causes the death of embryos that do not inherit the gene. Ex. Mating behavior of some spiders, praying mantises

7. Limits of Natural Selection
Lack of necessary genetic diversity
Non-fatal mutations tend to be small
- Developmental history important

10. Genetic Algorithms Mimic the process of natural selection
Sort-of subject to the same constraints
Anecdotes

11. Evolutionarily Stable Strategies
If a population behaves with an ESS, it is resistant to invasion by mutant strategies
similar to Nash equilibrium

12. Hawk-Dove game
Similar to Prisoner's Dilemma, different payoff matrix.

13. The Prisoner's Dilemma
Two members of a criminal gang are arrested and imprisoned. Each prisoner is in solitary confinement with no means of speaking to or exchanging messages with the other. The prosecutors don't have enough evidence to put both prisoners away for more than a few months, so they make them an offer:
If A and B each betray the other, each of them serves 8 years in prison
If A betrays B but B remains silent, A will be set free and B will serve 20 years in prison (and vice versa)
If A and B both remain silent, both of them will only serve 6 months in prison.

15. E(C) = (3+0)/2 = 3/2
E(D) = (5+1)/2 = 3

16. Iterated Prisoner's Dilemma
Indefinite length
Players remember past rounds, adjust strategy
Requires mutual cooperation to have the highest total reward

17. Axelrod and Hamilton (1981)
Performed IPD simulations at University of Maryland
Asked economists, sociologists, physicists, etc to mail in strategies

18. Tournaments Initial tournament of 14 strategies – 200 rounds
Second: 62 strategies – 200 rounds
Third: “ecological tournament” – rounds
Winners: Tit-for-tat, every time
Observations: no ESS

19. Recent Recreation

20. Conway's Game of Life (1970)

21. Game of Life Examples Turing-complete
First self-replicating pattern created 2010
First self-replicating pattern to preserve its instruction tape created 2013

22. Biogenesis http://biogenesis.sourceforce.org
GREEN: gets energy from the Sun, coverts CO2 into O2
RED: allows eating other organisms
CYAN: allows movement in stick direction
YELLOW: increases number of children made when reproducing
WHITE: infects any organism so that it's next child has the owner of the white segment's genes, costs energy
GREY: kills on contact, costs energy
BLUE: shield against RED, WHITE, and GREY

23. Critterding Critters are informed by sensors:
If their head is touches a food cube
If their head touches another critter
If they are able to procreate
About their energy state
About their age
About the state of their joints
What the world looks like (8x8 pixel RGBA vision)
Critters can make use of the following motor neurons (actions):
Bend joint (in two directions)
Eat
procreate

24. Related projects
BrainInWorld: neural-net organism simulator written by a physicist at Fermilab:
OpenWorm ( attempt to simulate a C. elegans nematode entirely in software
Framsticks ( : 3D artificial life simulator, more elaborate than Critterding