"The problem is this unjustified dichotomy between machine and biology."

There isn't engineering practice in place for developing programmable 
nanomachines in the way there is for fabricating circuits, but   biology 
demonstrates it is possible.  It could be we work from the bottom, learning how 
to build extremely simple machines, atom by atom, and also work from the top, 
rationalizing how to manipulate proteins in arbitrary ways.    I think we'll 
find out that our understanding of "programming" is impoverished compared to 
what living things achieve.  

http://www.pnas.org/content/109/23/8884.abstract

Marcus
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