[FOM] constructivism and physics (reply to Gordeew)

Dmytro Taranovsky dmytro at MIT.EDU
Tue Feb 14 15:35:49 EST 2006

Lew Gordeew wrote, 
> There is a remarkable uniqueness of the (stable) proteins' 3D shapes, and
> all of them are (claimed to) satisfy the minimal energy condition. In fact,
> these shapes determine their required properties. That's why biology and
> molecular pharmacology are so much interested in the protein folding, as
> well as the inverse protein folding problem (whose known mathematical
> simulations are NP-hard, too).

The shapes reached are generally but not always of the lowest energy.
The problem of minimal energy protein folding is NP hard, but physical
protein folding is expected to be in BQP, albeit with a large number of

There is an evolutionary advantage to proteins folding in well-defined
ways, which accounts for the uniqueness of shapes.  The most common
shape tends to be the one of the lowest energy.

Dmytro Taranovsky

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