getting shape from sequence (and function from form?)

Something I’m quite interested in and hope to do some more work on in the next couple of years at least, is the ‘protein folding problem’ (see here for some fairly unhelpful background info and here for something more to the point.) Basically, it’s the question of how to get a protein’s 3D structure ‘from the ground up’ i.e. how to predict it from its primary (amino acid) sequence. It’s pretty tricky – at best, computationally it’s a ginormous task.

Philosophically, it interests me as perhaps it can say something about the issue of reductionism – specifically, can proteins just be accounted for in terms of their amino acid sequences and the interactions thereof (and hence in terms of the relevant ORFs – open reading frames – of their genetic sequences)? It seems that the answer, perhaps, is a no. I’m not quite sure what that means, but I’m intrigued at the idea that there are higher level ‘biological laws’ of some kind in addition to the familiar physical ones.

The next step (for someone trying to account for life from the bottom (quarks?) up), of working out a protein’s function from its shape is one that seems to me to be even more problematic for a thoroughgoing reductionist to make sense of; but perhaps when I find the time energy and patience to read more about it I’ll change my mind. I’d quite like to write a book on it one day, if it turns out there’s something worthwhile that hasn’t yet been said.


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