[FOM] constructivism and physics (reply to Gordeew)

[Lew Gordeew]

joeshipman at aol.com wrote on Sun, 12 Feb 2006 19:47:25 -0500: 
> Lew, how do you know that the "solution" achieved in "natural reality" 
> is really optimal?  Might it not just be optimal among the solutions 
> that can arise from a long string folding, while there are lower-energy 
> solutions which cannot be reached by a feasible "path" starting from a 
> straightened string?

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). For it is not difficult to create an
arbitrary string of amino acids, provided that it is supposed to fold as
required - actually this is exactly what happens in the DNA double helix
machine.
  
Notably, all physical forces and conditions involved in the protein string
folding are well known and precisely measurable. So it really seems to be a
mathematical problem - how to put a string in a, say, hexagonal lattice
satisfying given conditions. There are many popular presentations of the
resulting "natural computing" in the Internet - see e.g.
http://www.psc.edu/science/kollman98.html

Regards,
L. Gordeev

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