One reason to create artificial life is to experiment on it – to see in what way it behaves like real life and what, if anything, it can tell us about real life. While considering what sort of experiments I would like to do, and, what tests I would require to ensure that the simulation was working as expected, it occurred to me that in order to test the artificial cells, I would have to build various tools – additional programs that could slot into the simulation and extract and display information about what was going on. For example, I might want to test the function of various proteins by removing them and measuring the effect on the cell (growth rate, metabolite concentrations etc.).
It struck me that an interesting way to display the information would be to mimic the output a real-life, analogous experiment would give. For example, if I wanted to see where various proteins bound the DNA, I could simulate a DNA footprinting experiment. I then thought that this idea could be expanded to simulate a complete basic molecular toolkit for a biochemist or molecular biologist. This would of course make analysing the organism much harder that simply peering into the code and getting a print out of the variables I was interested in, but it might be more fun and could be used to teach students about various laboratory techniques. It could even be the basis of a game in which players basically play at being microbiologists (although I’m not sure how many people would find that fun, or what the competitive element would be).