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Well, I would argue that much of what has emerged on the Internet in the last 15 years has been novel. And a biochemist can learn the basics of Python about as
by dreish 18y ago
Well, I would argue that much of what has emerged on the Internet in the last 15 years has been novel.
And a biochemist can learn the basics of Python about as easily as a programmer can learn how to operate basic lab equipment. A biochemist could no more easily add to human knowledge about compiler optimization than a programmer is likely add anything to protein folding. If anything, I would say the opposite of what you claim is true -- programmers are more likely to be interested in leading-edge science as a hobby than the other way around.
- jmzachary 18y agoExcept that a biochemist learning Python to solve problems he/she has in protein folding research (or whatever) is a useful skill to get things done in his/her field. A programmer learning about basic lab equipment probably isn't going to help too much in developing software (although it might help him/her get more attractive dates). And protein folding is much more useful to humanity than compiler optimization. Does anyone even work on compiler optimization anymore?
- timr 18y agoAs someone who has published research on protein folding, trust me: compiler optimization is about a thousand times more useful. Protein folding is the biochemical equivalent of string theory. It's fun to talk about, but the practical applications are perpetually 20 years away.
- jmzachary 18y agoThen we are in the same club. I've published research on global optimization algorithms for protein folding. I'm not a biochemist, but I understood that protein folding actually has immediate application in understanding disease and drug design. As a computer scientist, I also understood that compiler optimization is a mature field with most of the low-hanging fruit already picked. So, I guess I'm confused and will ask respectfully what problems in compiler optimization make it a thousand times more useful than protein folding and associated medical problems?
- timr 18y ago"I'm not a biochemist, but I understood that protein folding actually has immediate application in understanding disease and drug design....what problems in compiler optimization make it a thousand times more useful than protein folding and associated medical problems?" Short answer: Compilers are used for real work, every day. Nobody is using protein structure prediction for anything practical, and they likely won't be for decades more. At this point, it's blue-sky research. Long answer: "Immediate application" is one of those bits of academic-speak that really means "is related to", but sounds better to grant review boards. While it's true that protein folding is important (after all, most biological processes are mediated by folded proteins), it's not true that protein structure prediction is important. It would be great if we could predict protein structures accurately, but we can't, and until we can, it's not a practically useful discipline. Even the very best, crystallographically determined protein structures are barely sufficient to do rational drug design, and predicted structures don't come close to that level of quality. For example: we can sometimes (very rarely) predict very small (<150 residue) protein structures to within 1 angstrom RMSD of their experimentally determined shapes (i.e. >2 angstrom resolution, in the best case). However, the interactions important to drug binding, protein design, etc., don't start until a tenth of that (scales of ~0.1 angstrom). Throw in the fact that the vast majority of proteins are much larger than 150 angstroms, and that we keep creating cheaper, faster, more automated ways of getting actual experimental information on structure, and the role of protein structure prediction looks increasingly marginalized. It's definitely a cool, fun problem -- just not a very practical one. For whatever it's worth, my first papers were on applying the state-of-the-art method (you've heard of it...I think you're paraphrasing the lab's PR) for protein structure prediction to genome annotation. To call the approach useful was/is a stretch, and that's for a much easier application than drug design (in fact, we were trying to find a practical application for protein structure prediction, and it was the most likely thing we could think of!)
- aswanson 18y agoWow. This is really enlightening; I thought that the computational method was going to open a new phase in disease treatment, but you seem to say here that the empirical method is on its way to making it useless. So the Pande group at Stanford is wasting their time. Interesting.
- thwarted 18y agoIf it wasn't for the programmer creating languages that make massive, fast computation accessible to the biochemist, there would be no Python for the biochemist to use to do their research. The programmer is just once removed from the "important to humanity" aspects. And if it wasn't for the programmers who get excited about languages and pioneer different uses of them, the biochemist would most likely never even know there is this tool available for them to use.
- Tichy 18y agoCan you show me how I can learn biochemistry in two days? I would be really interested!
- deleted 18y ago[deleted]
- dreish 18y agoNo. But if you haven't learned anything new about programming since two days after you started, you're doing it wrong.
- Tichy 18y agoWell I remember learning Python in one day. If I could do the same for biochemistry, it would be fantastic. Maybe it is only the lack of hands on tutorials that is the problem, though. There are tomes of biochemistry books, but I suspect after reading them you are still not sure what to do.
- rplevy 18y agoYou learned the rules of chess in one day, but how many chess games will you win with only one day of experience?