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 Rate This Message: http://www.cryonet.org/cgi-bin/rate.cgi?msg=12933