Friday, August 1, 2008

Better (artificial) living through chemistry?

Just got caught up with my Biota podcasts and GT presentations. I particularly enjoyed Bruce's presentation at Greythumb London.

I believe it was in the London GT meeting that Bruce quoted a simulation author who said that there's always an IOU you have to write. In other words, there's always going to be a part of the simulation where you wave your hands a bit. This makes some sense...if you are trying to simulate the spread of a virus in a human population, it makes sense to simulate the mobility of the population, but why waste the effort simulating the internal combustion engines that are getting people from point A to point B?

Actually, that's not such a great example, because no one would expect you to repay that IOU. We all know in abstract terms how cars allow people to move from here to there, and so it would be unreasonable to expect your poor CDC epidemiologist to have to model reality beyond the minimum needed to solve the problem.

So, do we write an IOU that we have to repay when we create simulated organisms that use genetic information to control their form and behavior without actually modeling the underlying chemistry?

I think it all depends on your perspective. If you're a biologist, or if you want to evolve something in your simulation that might exist in the real world, then you'll need a high adherence to reality in your simulation. But since all simulations fall short of reality, I think requiring accuracy is something of a losing game.

Case in point: the three body problem. If you just have three objects that interact with each other - for example, a planet, moon and sun - there's no way of exactly determining what effect each body has on the others. You can only approach a solution. So what if you have a billion bodies in interaction? And how far down do we take we model subatomic particles, and then do we store their location OR their velocity?

But let's say that we model atoms and molecules, and we have good approximations of their interactions. We ignore relativity and just use Newtonian physics. How large a world can we model? As fast as computers get, and even writing our IOUs, I'm skeptical that we could model a very large volume of space in real-time. Since it took something like two billion years for multi-cellular life to evolve in the vast oceans of Earth, I don't hold out too much hope we'd see this in a computer simulation.

But if we did, what of it? Creationists would say that the simulation was flawed and created by proponents of evolution, and both charges would be true. It might be confirming evidence of evolution, but do we need more confirmation?

So while I see this as a very interesting enterprise, I'm skeptical of this approach as yielding useful results. Interesting perhaps, but I'm not sure about useful.

My personal preference at this point is to say: hey, evolution works, and it's given us these great design patterns - such as DNA and a central nervous system. What can else can we do with those design patterns? And then, like the CDC epidemiologist, we can make a simplified simulation that yields useful results without worrying about the tire pressure of the virus' host's car.

All JMO.