Dynamics of genetic information

Processing on the cluster

Talk to the cluster people

There have been some problems in the past

Igor people

Ask Lee for a copy of the bridge thingy he showed

Email

Stata

Talk to the data analysis

Probably write in .txt

Modeling populations with electrical circuits

Figure out a specific entry point into the litterature

Fill in the Blahs

-by Tonje

Is using dna evidence (number of neutural mutations) a valid way of dating populations?

• Lee’s model from wolf paper says no
• Does geography change this?
• How does this respond to a changing geography (islands with changing bridges etc.)
• How would this respond to a disaster (flood, famine etc)? Will we loose important information? (My got feeling is yes)
• Who would care?

Will landbridges (over roads etc) and wildlife parks (which sort of functions as islands) affect species? If so how? Will we see a string founder effect here? Landscape Paper

• It feels like this will be easy to answer, my gut instinct says yes.  Might be possible to tie into the previous question.
• Is it already answered?
• Model  idea: two areas seperated by one or several roads. Compare what happens when you put land bridges in.
• Who would care?  The WCS and WCS – living landscapes, other people who deal with wildlife conservation in relation to roads etc?
• We have chosen to focus on this ( Sun. Sept 27 09)

Other places to present/publish?

• Smith Colllaborations(“Celebrating Collaborations: Students and Faculty Working Together”). Small, poster and/or powerpoint presentations of research done by students. Will need to check of they will accept this as it is not completely Smith based. Is in the spring.

-by Tonje

last night I was bouncing ideas of my two biology major room mates and got a crash course in genetics.  Here are two things that jumped out at me as easy to model.

Model currently being worked on:

• has two gene arrays instead of one.
• color can be one of 4 colors (0,75, 150, 225)
• Darker color is always dominant.
• An offspring gets one of the gene array entires from each parent
• It is random if the gene from a parent is the dominant or the non dominant gene

Second model: co dominace

• the offspring’s color code is the average of the parents

Todo next: debug these models and do more research of what is in fact goin on here, build in color for a better visual effect (3 genes, R-G-B, darker always dominant a marble has geneBlue1, geneBlue2, geneRed1 etc.  Which of the pair the offspring gets from each parent is random)

If I am messing up here, please tell m.

-by Tonje

Idea:

Add in obstacles, islands etc

Local made up

Look up a more formal

Ecology how do people measure something like spatial diversity

This mutation is good if you are in an area where people can see you

Hybrid zones

How do you measure diversity in one area vs. another

Who is going to care?

Biology

Ecology

Conservation

Founder vs. adaptive

What is the point the sim can show

First sim

Use dna evidence to date populations

Add this to founder

What kind of land bridges

Landscape species model

GIS indicator species

Corridors

Amazon test patches

Ecology/conservation

Where are they not doing mathematical

-by Tonje

Notes for making a replica of the second simulation in “What is a Wolf?

marble lives:

• A marble dies after 250 timesteps
• Everytime a marble collide with another it ages 10 steps
• 1/150 chance of producing offspring
• Two conditions

1. Asexual reproduction, gene copied from parent
2. Mating, gene copied from either a  parent or mate (1/2 chance)

• mutation happens 1/100

-by Tonje

Genetic Programming, Push, PushGP

Genetic Programming for finite Algebras

GECCO -publishing?

Finite Algebra

Boolean algebra

Primal every possible operation can be expressed by a term using only AND, OR and NOT

All Boolean functions can be made of NAND

Number of terms grow astronomically with size of underlying set

Find terms with certain properties

Discriminator term, determine primality

Malcev majority and pixley terms

Genetic Programming

Random Generation

-> Assessment

->Selection

->Variation

->Assessment

->Solution

Tournament selection

Elitism not so a good thing

Enough variation

Koza http://www.genetic-programming.com/johnkoza.html

Genetic Hitchhiking

The Push3 Execution Stack and the Evolution Control

Push v3

Open ended evolution of arbitrary computational process

Natural selection or programs expressed in syntactically trivial, semantically rich program representation.

Rich enough to express evolving programs of arbitrary architecture and even the mechanisms of evolution itself

Stack based postfix language

Trivial syntax

Evolved programs may use

Multiple data types

Subroutines

Recursion and iteration

Supports evolution of evolutionary mechanisms

Parentheses are critical for code manipulation

Dynamic

First step

Create Blog

Read what wolf and understand

Diversification of mitochondrial dna

Show what you can and can not know

Code

Geography

Panmitic population

Charles Ross

Meet

What would the biological community learn

What is wrong with the three of life

Inter fertile

Color web

Trivial Geography in Genetic Programming

Tag-Mediated Altruism

Tags and Tolerances

Varied interaction radius within a linearly structured population