Re: A simulated cell
Tue, 14 Dec 1999 10:57:45 -0800

John Clark writes:

> 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.

It would seem that we have a ways to go before attempting this. We not only need the 3D shapes, we need to know the chemical affinities of each portion, and the mechanical properties. As a trivial first step, we'd need to know exactly how ribosomes perform protein synthesis. Very little is known about this at the mechanochemical level. They only obtained a detailed 3D map of the ribosome within the past few months. It appears that it may be something of a clockwork mechanism, with internal moving parts. I can't wait until we can really understand this molecular machine in detail.

One of Gina's forwarded articles described similar progress in the DNA transcription complex, which forms messenger RNA from DNA. They have a pretty detailed 3D shape now, not quite at the atomic level yet. It also offers tantalizing hints of machine-like structure.

Then there is the whole process of construction of these devices, via self-assembly or perhaps by simpler specialized structures. Simulating the self-assembly of 40-odd proteins and RNA particles into a working ribosome will be a real breakthrough.

As we learn more about these protein machines I think this will add further interest in the prospects for nanotech. If proteins are just enzymes, with specially-shaped active sites, that is old-fashioned chemistry. But if they are mechanical devices, Drexler's gears and cables don't look so outlandish.