X-Message-Number: 12941
From: "John Clark" <>
Subject: more on big computers and the protein folding problem
Date: Tue, 14 Dec 1999 13:12:23 -0500

In  #12933 Thomas Donaldson <> Wrote:

    >it's simply not true that we need a computer like the kind that IBM is
    >making to make progress in understanding protein folding

I will concede that you are absolutely positively 100% certain of that, but
the really interesting question is, are you also correct? IBM is betting
$100,000,000 that you are not.

    >It's even possible that someone will come along with an algorithm that
    >doesn't need such computer power

Yea maybe. Maybe someday someone will find a way to solve the problem
in 30 seconds just using pencil and paper, but I wouldn't hold my breath.

    >I know that most people on Cryonet don't bother to keep up with this side
    >of bioscience.

I am not most people.

     >I personally suspect that IBM is building this computer not because
     >IBM people believe that it's needed to solve the protein folding problem,

Then why are they building it?

    >but because previous work on protein folding has gotten far
    >enough that experts on the problem can now simply sit down and write
    >out the required programs.

Yes but that seems to contradict what you just said. Even blue gene isn't
big enough to solve the problem from first principles but over the last
few years we've learned a lot of useful heuristics about protein folding
that greatly simplify things, apparently enough to change an astronomically

difficult problem to one that is only amazingly difficult and solvable by blue 
gene.

On a another matter I've been hearing some talk (the current issue of Science)

of writing a computer program that completely simulates a bacteria, in 
particular
a Mycoplasma chosen because it has only 265 genes and is the simplest known
life form that has a metabolism. It would be a huge project but Blue Gene might
be able to handle it. Among other things we'd need to know the 3D shape of all
265 proteins the genes produced but some of those are already known, obtained

from laborious X ray diffraction experiments. If we really can write such a 
program
then we can truly say we understand how at least one life form works. Anyway I
was encouraged that respectable scientists are no longer embarrassed to talk

about such things. There is even talk of making the first artificial cell, one 
that
is even simpler, perhaps with only 180 genes or so.

     John K Clark        

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