I was inspired by this video:
http://www.ted.com/talks/rob_knight_how_our_microbes_make_us_who_we_areAnd having learned about predator-prey simulations and saw its potential as an evolution simulation, I began looking for projects that had already gone in this direction. Scriptbots is the most promising project I have found so far and the makers seems to have much the same goals as me. A simplified evolution system that tries to figure out how to cook down evolution to its basics in animal lifeforms.
Usually evolution simulations focus a lot on neurons, but as the ted talk above explains, then microbes might have at least as big an influence on behavior is the neurons. I just got the idea recently, so I have to work out the parameters for it, and I have not even figured out how to make any kind of neuron simulations yet or any kind of evolution to improve on a basic predator-prey simulation I found for Java. But seeing how far this project has come, I thought I would share my idea here and see if you might find it inspiring and possibly move in the same direction.
Some of the main known effects of the gutflora or the microbes of our body has on us is effecting our mood, how much we want to eat, and how well we process the food we eat. If we do not process the food we eat very well, we will have a tendency to gain weight faster. There are other influences as well, but the video should explain much of it.