On Thu, Jan 03, 2013 at 08:27:53PM -0500, Miles Fidelman wrote:

> you might want to google "biological computing" - you'll start finding  
> things like this:
> http://www.guardian.co.uk/science/blog/2009/jul/24/bacteria-computer  
> (title: "Bacteria make computers look like pocket calculators")

Computing with solvated linear biopolymers is really disadvantaged
in relation to moving electrons, photons, plamons, or flipping
spins. You sure have a lot of parallellism, but the linear chain
and viscous drag severely limits the possible rate of sampling.

Fundamentally you could eventually self-assemble a crystal of ~nm^3 sized
cells capable of processing/storing a single bit which would be
a provably optimal classical computer. Such a thing would make 
biology look like infinitesimal beer.

> Think massively parallel/distributed  computation focused on organism  
> level survival and behavior.  If you want to program colonies of nano  
> machines (biological or otherwise), you're going to have to start  
> thinking of something a very different kinds of algorithms, running on  
> something a lot more powerful than a small cpu programmed in c.

Obviously you need to be able to design emergent behaviour on the
edge of chaos, which is resilient/gracefully degrading (it pretty
much has to, due to noise floor and device failure) but also
nondeterministic. 

This is something which humans are really terrible at, so they
need to figure out how to make machines design such machines.

> Start thinking billions of actors, running on highly parallel hardware,  
> and we might start approaching what cells do today.  (FYI, try googling  
> "micro-tubules" and you'll find some interesting papers on how these  
> sub-cellular structures just might act like associative arrays :-)

You're probably referring to Penrose-Hameroff, which is pretty much
kook science.
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