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AllanCrossman comments on Demands for Particular Proof: Appendices - Less Wrong
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Um... that's a rather odd argument to make, considering steel, wheels, nuclear power, transistors, radio, lasers, books, LEDs...
Proteins are held together by van der Waals forces, which are much weaker than covalent bonds. Preliminary calculations show gargantuan opportunities for improvement (see Drexler's Nanosystems).
I'm not sure how this affects the argument, but the very flexibility of proteins is one of the things that makes them work. A whole bunch of biological reactions involve enzymes changing shape in response to some substance.