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Supercomputer Sets Protein-Folding Record
Nicros writes with this snippet from Nature News:
"A specially designed supercomputer named Anton has simulated changes in a protein's three-dimensional structure over a period of a millisecond — a time-scale more than a hundred-fold greater than the previous record. ... The simulations revealed how the proteins changed as they folded, unfolded and folded again. 'The agreement with experimental data is amazing,' says Chandra Verma, a computational structural biologist at the Bioinformatics Institute of the Agency for Science, Technology and Research in Singapore. Simulating the basic pancreatic trypsin inhibitor over the course of a millisecond took Anton about 100 days — roughly as long as computers spent toiling over previous simulations that only spanned 10 microseconds."
..it's a rather poor article. It talks in very basic terms about proteins and their folding, talks a bit more about the scientist who founded the institute behind the computer, and says fuck-all about the construction of the computer itself.
Bah. For a publishing house of Nature Publishing Group's (intellectual and economic) muscle, one should expect more.
"The agriculture ministry is not in charge of Gundam" - Japanese ministry official.
That's a little unfair to Folding@Home. Shaw has a lot of resources to pour into this project - he's lured faculty members away from universities to work for him instead and has the equivalent of several large labs worth of advanced researchers. He also has an immensely larger budget than most non-profit labs, and he's self-employed so he doesn't have to answer to granting agencies or tenure committees. I think what he's doing is great but he's really one of the only people who could have pulled this off. It's difficult to know what approach will work best in advance, and both Shaw and Vijay Pande have been very innovative in approaching the problem from completely different angles.
By the way, this approach has been tried before with less stellar results - I'm thinking of the MD-GRAPE project in Japan. You're also assuming that every problem is equally well suited towards custom ASICs, but actually, molecular dynamics is far easier to do this with than many other methods. For instance, Rosetta (Rosetta@Home and Fold.It) is doing structure prediction, not folding, using a mostly statistics-based energy function and Monte Carlo sampling, and this isn't something you can trivially offload to a specialized chip. In that case, distributed computing is by far the most efficient solution.
No, Anton simulated one millisecond over the course of a hundred days. The previous recordholder took roughly the same time to do a hundredth of the work. (This was probably the RIKEN MDGRAPE-3, but again, documentation is le sparse.)
Bio questions? Ask me to start a Q&A journal. Computer analogies available for most topics!
It is complex, but you are ignoring the relative isolation between levels that exists in the human, and rat, body.
Protein folding may be complex, but most of it is irrelevant detail. What's usually important is the final shape that one ends up with, e.g. But when wants to modify that process, then the details of that process become important. This is roughly equivalent to...at the level that I work, I pay no attention to how the compiler is going to optimize my code. If I wanted to modify that I'd need to pay attention to things at a much finer level of detail.
It *is* true that people tend to oversimplify things they aren't dealing with directly. But to make it a fair statement it needs to be made fully *that* general. (This doesn't make you original assertion false, but observationally it *is* false. I've never known a knowledgeable geek that oversimplified the biochemistry of life in the way that you painted. I'm sure they exist, but they aren't, as you implied, common. If they are common among your friends, well, then you have some uncommon friends.)
I think we've pushed this "anyone can grow up to be president" thing too far.