[terangdom]

My prediction: We can find a subset of proteins such that they do not interfere with each other, and still large enough that they can perform useful functions.

It is possible to write threaded software in a way that everything interacts with everything and it is almost impossible to make out how anything works. That's why we don't. The halting problem never stopped us from writing software.

[jboggan]

Proteins are very "sticky". Even proteins with weakly predicted interactions exhibit significant effects upon one another when all-atom simulations are performed - this is actually a major stumbling block in getting cellular simulation right.

The most complicated piece of multithreaded software yet devised by humans does not compare in complexity to the transcription, translation, and interaction events occurring in a typical human cell. The "DNA as software" metaphor is just that, a metaphor - it is an exceedingly poor model. Cellular systems are so quantitatively enormous and convoluted (yet not chaotic!) that we have to compare them to the most complicated designs our species has recently engineered just to begin to get our heads around the problem.

I haven't kept up with the state of the art in the past two years, but I remember an experiment running a ~10k node cluster for several weeks being able to successfully simulate only the cytoplasm of a cell - and 1/1000th of its overall volume at that. And the proteins were all modeled as spheres. I'm sure the art has advanced, but that is orders of magnitude away.

[fghh45sdfhr3]

My prediction: We can find a subset of proteins such that they do not interfere with each other, and still large enough that they can perform useful functions.

The tiny, tiny amount of bioinformatics knowledge I have makes me think the probability of your prediction is ~ 0.00000000000001%. For non-trivial values of "useful". :)

Can you tell me what experience or knowledge lead you to make that prediction?

[s_baby]

http://en.wikipedia.org/wiki/Evolutionary_developmental_biol...

Biological systems are highly coupled but also very "fault" tolerant if manipulated at the right pivot points. That's why you can move a fly leg from the torso to the head by just manipulating a few transcription factors.

[terangdom]

Now I feel bad, maybe I should have voiced it in a way that sounded less sure. I base it on two things. 1. Similar genes do similar things in different species. 2. There are an incredible amount of possible proteins.