No need to worry about arguing semantics, I'm learning here. As I've said, I'm what you'd call an applied computer scientist. While I've got a good handle on tr

No need to worry about arguing semantics, I'm learning here. As I've said, I'm what you'd call an applied computer scientist. While I've got a good handle on tractability, dynamic programming, and the like, sometimes I miss the formalisms of the terminology. In some formulation of protein folding that is NP-complete, your statement (require[s] trying all possible conformations) is tantamount to P!=NP. So I'm guessing you don't have a proof of that. ;) Haha, ok, yes. You've got me there. Actually, that also clears up a few issues I was having with the original article. I tend to confound tractability and NP-complete. If I follow you now, an algorithm that can fold a protein to lowest energy is the solution. If that solution can be shown to be correct without trying all possible conformations, then it is P. If the only way to verify it correct would be to explore all fold space, then it would be NP and and P!=NP. In other words, my original assertion that protein folding is not, strictly speaking, NP relates to the fact that nature does not try all possible conformations. We could write an NP solution that does, but this is not what happens in reality. So, either nature is solving a slightly different problem (it doesn't worry about finding the global energy minimum exactly), or P=NP and the "algorithm" (in this sense a combination of physical laws) used by nature solves the same problem as our NP search of all conformation space.