Aipotu: a Computer Simulation Linking Genetics,

Biochemistry, Molecular Biology, and Evolution

Brian White

Biology Department

UMass Boston

Goals of this talk

• Present Aipotu

• Recruit users – Education– Research?

• Feedback on design, model, etc.

Outline

• Simulation Goals

• Description

• Sample Evolution Run

• Questions

Connections

Genes

Proteins

LifeIndividual functions of living things

Genetics

Biochemistry

Molecular Biology

Evolution

The Phenomenon: Flower color

Experiment: Select for Black

• Start with Green/Green

• Relative Fitnesses:– Black = 10 – White = 0– Other Colors = 1

Select for Black Generation 0

Time (min:sec) 00:00

Select for Black Generation 1

Time (min:sec) 00:16

Select for Black Generation 2

Time (min:sec) 00:26

Select for Black Generation 3

Time (min:sec) 00:42

Select for Black Generation 4

Time (min:sec) 00:59

Select for Black Generation 5

Time (min:sec) 01:09

Select for Black Generation 6

Time (min:sec) 01:26

Select for Black Generation 7

Time (min:sec) 01:38

Select for Black Generation 8

Time (min:sec) 01:50

Select for Black Generation 9

Time (min:sec) 01:58

Select for Black Generation 10

Time (min:sec) 02:07

Acknowledgements

• Ethan Bolker (CS)

• CS MS Students

• My Students

• John Jungck (BioQUEST)

http://intro.bio.umb.edu/aipotu/brian.white@umb.edu

• Questions?• My questions to you:

– How would you use this in teaching?– What features would you add?– How best to model evolution with it?– How do I know if this is ‘behaving properly’?– What other experiments should I do?