Open source Digital Bacteria

FiReaNGeL writes "Scientists have constructed a software capable of simulating organisms at the molecular, single-cell and population levels. The program, called AgentCell, will soon be available, open sourced under a BSD license. "With AgentCell we can simulate the behavior of entire populations of cells as they sense their environment, respond to stimuli and move in a three-dimensional world". The researchers have designed their digital bacterial system in modules, so that additional components may be added later - "The hope is that people will modify the code or add some new capabilities". AgentCell has possible applications in cancer research, drug development and combating bioterrorism. Lots of movies and pictures are available, along with a detailed press release describing the program."

Re:This Is New?

[Rei]

This isn't really a variant on Conway's Game of Life - it's closer to a variant on Polyworld. Of course, if you want a grown up Conway's Game of Life, I wrote one called Megaconway [daughtersoftiresias.org] a while back - massive worlds made possible by using each byte to store 8 squares and doing operations in bulk wherever possible. It also keeps entropy in the world with occasional random inputs of randomness of varying sizes. My big hope, although I doubt it will occur, is that eventually it will come up with a system that is stable, self-perpetuating, and can "heal" from random damage. Who knows... I leave it running niced to 19 at all times.

Re:Combatting bioterrorism?

[ScentCone]

Rather, how long before the nice Men in Black show up at their door, confiscate the code, throw them all in jail, and get Con-gress to pass a law against this sort of thing, on the grounds that it could be used to ADVANCE bioterrorism?

Why is that tinfoil-clad perspective any better (more likely) than wondering how long it will be before they're offered jobs at Fort Dietrich or at any of a number of big contractors that are working on exactly this sort of stuff with defense in mind? They can't hire good people fast enough in that area, they pay's good, the need is real... oh, never mind. That sort of info takes all fun out of wearing the hat. My bad!

combating bioterrorism

[exp(pi*sqrt(163))]

!!!

I'd put money on this work being completely bogus. There's quite a bit of funding going to researchers from Fath^H^H^H^HHomeland Security. I'm pretty astonished by the types of reserach these people are doing which really has no practical applications whatsoever. But on paper it makes it look like the department are investing in our security. This sounds like a prime example of such a project. There simply isn't a situation involving bacteria that is both (1) something we can model on a computer and (2) relevant to combating bioterrorism. Sure, we might be able to qualitatively model a population in a petri dish, but that has nothing whatsoever to do with the reality of a terrorist releasing bacteria into the atmosphere, say. But the ignorant politicians working at the department have no way of understanding this for themselves and fund it anyway. Remember, these are the same people who think this [ready.gov] is useful.

So...politicans might be taken in by BS about the applications of these methods, but there's no need for /. readers to be decieved the same way.

Re:What about us?

[bcmm]

Trouble is, in The Matrix, Neo's brain (and, for that matter, a functional body) are physically outside the simulation.

It's also possible to have a simulation that's good enough to simulate matter behaving as a brain, in which case any life being simulated has no existence at all outside of the simulation. It's not impossible for that life to be intelligent, conscious, or self aware, and there would be no way for them to tell they were in a simulation, other than by saying that things looked like someone designed them.

I wonder if any of the theories that constants like the speed of light or the cosmological constant are changing are correct, and if so if whoever coded that kludge got in trouble...

Re:combating bioterrorism

[Frumious Wombat]

Strangely enough, sometimes theoretical underpinnings are crucial to end-user applications. Yes, maybe this should have been funded by a grant from NIH (new bacterial simulator), NSF (ibid), FDA/DoAg (food contamination), or DOE (model potential industrial organisms), rather than DoHS, but e. Coli is both (a) well-understood and (b) a real problem in our food supply. A good e. coli simulator could, as they've already demonstrated, teach us quite a bit about potential pathogens, or be generalized into an organismal simulator for other, more potentially useful, bacteria.

In principle, presume that you model various strategies of optimizing for methanogens, leading to a shorter development time for biofuels, or even optimize e. coli for better use in industrial synthesis (i.e. an e. coli that will produce 20% more HGH for the same feed input). As long as the model is directly related to experiments, this is a great idea, and will lead us towards a future where eukaryotes (such as your cells, or more plausibly food crops), can be digitally screened and optimized for their response to various promotors and inhibitors.

What's the worst that happens; someone has figured out how to get DoHS to pay for an improved version of Life, and fabulous new screensavers are developed! In all seriousness, the outcome should be much more promising than that. This is one more step to placing usable molecular biology tools into everyone's hands. You could look at individual molecules, and now you can simulate the workhorse of microbiology, without having to have petri dishes or autoclaves around until the last stages of the experiments. I, for one (remembering the smell of agar in the morning), welcome this development.