Topics › Evolution

Cell evolution game - basic interface

Today I started to make a game that I've been thinking about for a quite a while now (I mention it here). The general idea is that you play as a single-celled microbe which evolves ever more complex metabolic and regulatory systems as it moves to ever more challenging environments.

Sex in Sugarscape

Since the last time I wrote about Sugarscape, I've made a bit of progress. The biggest improvement is the introduction of sexual reproduction. I can therefore recapitulate more of the results of the original simulation, and test a number evolutionary ideas.

Solar system evolution

After running my solar system simulation several times I was interested to see how robust the system was. By this I mean that despite the fact that the particles start off randomly distributed, the progress of the simulation is quite similar each time. The details weren't exactly the same each times, but in general, a star formed at the centre of the universe at about the same time and ended up with a few satellites, while several particles were sent flying off into space.

Adding ribosomes to my cell simulation

This is a description of some work I did on an older version of my cell simulation.

So far, the main adaptation that cells in my simulations have evolved has been an increase in of gene copy number. Such adaptations are unsurprising given that it's the only way cells can alter the relative amounts of each protein. In my final simulation I want to allow cells to alter gene expression using transcription factors to control rates of transcription (and thus translation).

Project:

Cell Simulation

A simulation of single celled organisms and their evolution with the focus on metabolic and regulatory pathways.

Project:

Heterocyst Simulation

An old simulation of a type of cyanobacterium and its evolution, which was originally written in QBASIC. Includes analysis of the results from this simulation

Evolving ant behaviour

Example of simple ant behaviour - spiralling

I've been thinking for a while about how to program ant behaviour in my simulation. The difficulty is that even relatively simple behaviours (such as following a pheromone trail) are difficult to code as a behaviour at the agent (or ant) level. While I probably could come with a reasonable behaviour if I thought about it and tested various parameters, it seems a lot simpler to evolve a suitable behaviour. After all, that’s what ants did.

Project:

Evolving Images

A genetic algorithm that uses overlapping transparent circles to approximate an image. Includes analysis of the effect of altering mutation rate and population size.