X-Message-Number: 12947
From: Thomas Donaldson <>
Subject: more about computers and protein folding
Date: Thu, 16 Dec 1999 01:24:20 +1100 (EST)

Hi everyone!

I am glad that some commentators have tried to follow the protein folding
problem.

As for my statement that we do not need large computers to make progress
on that problem, perhaps I should have clarified what I meant by
"progress". There has been lots of work aimed at finding efficient means
to work out the final shape of a folded protein. This work has involved
invention and testing of algorithms to do so on smaller proteins. When
I say that the IBM computer won't help this job of finding algorithms,
I meant that exactly. But once we have some algorithms known to work on
smaller proteins, it quickly becomes very interesting to apply them to
much larger ones. (And we can do the mathematics to prove that they will
work on larger proteins even if we can't actually solve any large protein
--- that's what math is about). 

So that's why I think this new computer is a Good Thing. Not the solution
to all our problems, by any stretch, but still a Good Thing. But just
because it sounds like it works just the same as many other parallel 
computers I've known of I just can't get excited by it as an advance
in computer science. (A detailed statement of how it works, the kind
IBM might --- but probably won't --- get patents from, might reveal some
deeper thinking on the computer science problems involved, but so far
I've not heard such a statement, and I will state here that we could
do the same with practically any parallel computer, given that it has
enough processors).

Will it help us with our desire to be suspended? Not directly. But it
can certainly be useful for other things, and these in turn may be
useful even to us.

			Best and long long life for all,

				Thomas Donaldson

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