X-Message-Number: 12933
From: Thomas Donaldson <>
Subject: more on big computers and the protein folding problem
Date: Tue, 14 Dec 1999 01:29:38 +1100 (EST)

Hi again!

About protein folding: it's simply not true that we need a computer like
the kind that IBM is making to make progress in understanding protein 
folding --- though with current methods it will certainly help. There's
been a lot of successful work already aimed at understanding this problem;
what the big parallel computer will let us do is to work out folding for
much larger proteins.

It's even possible that someone will come along with an algorithm that
doesn't need such computer power, but such an algorithm (other than very
approximate methods which can refined by experiment) doesn't yet exist.

I know that most people on Cryonet don't bother to keep up with this side
of bioscience. I will say, though, that I have several times discussed
new work on protein folding in PERIASTRON. A good number of clever ideas
have already been developed to study this problem; if anyone wishes they
can send me a message and I'll give them some references.

In fact, I personally suspect that IBM is building this computer not
because IBM people believe that it's needed to solve the protein folding
problem, 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. It's not needed to study the general problem
but rather to use what we already know to work out larger proteins which
cannot be worked out with a smaller computer.

After all, if you haven't noticed, for what it's worth, biochemistry 
now provides the ONLY fully developed "nanotechnology". And I put that
in quotes only because the creatures making these complex chemicals aren't
doing so as a technology in the sense we ordinarily mean it. Of course,
with bigger computers we will very soon be able to do just that, not 
with relatively small biochemicals (which have already been solved) but
with much more complex ones. (And for those who favor nanotechnology,
I say this not to denigrate work that is now going on, but simply to state
a fact. We're going to want a much wider variety of chemicals than 
proteins are likely to provide. And there's another point here too: just
because it took us some time to work these things out in biotech, it may
be wise to keep in mind that other kinds of nanotechnology, not as theory
but as actual working devices, will involve lots more work too. It's
easy enough to talk about solving those problems, but actually doing so
may involve LOTS of thinking and work... and time, too).

			Best and long long life to all,

				Thomas Donaldson 

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