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2010-08-23 Science-Proteins-Foldit-Techno
2010-08-23 Science-Proteins-Foldit-Techno
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Commentary
As the authors write, "we hypothesized that human spatial reasoning could improve both the sampling of conformational space and the determination of when to pursue suboptimal conformations if the [random elements of current algorithms] were replaced with human decision making while retaining the deterministic Rosetta algorithms as [tools for players]." Was this hypothesis correct? In three of the 10 challenges the best Foldit players and the best current simulations performed similarly--that is, the two approaches got about equally close to the final folded shape of the protein. In five other challenges, the best result from Foldit was substantially better than the best a superfast computer alone could do. In only two of the 10 cases did the simulation do substantially better. These appeared to be the two hardest puzzles; neither Foldit players nor computers alone were able to get very close to the correct shape. What explains this astonishing result? How can it be that crowds of people playing a game on desktop computers do better at this
http://www.forbes.com/2010/08/23/science-proteins-foldit-technology-breakthroughs-... 01/07/2011
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important task than supercomputers programmed by super scientists? Are the scientists themselves the ones playing Foldit? Maybe, but they're not the best at it; none of the five highest-scoring players took chemistry classes beyond high school. The team behind Foldit realized that even "normal" people have a number of interesting attributes that make us well-suited to tackle protein folding challenges. --We are particularly strong at spatial reasoning, or literally seeing solutions. As is the case with all primates, a substantial portion of our brains is devoted to processing visual signals. This means that when a puzzle is posed to us in spatial terms, we can apply a lot of our cranial horsepower to it. And protein folding is, at its heart, the work of folding an initial shape into a smaller shape. --We have intuition, especially after lots of experience in a given domain like Foldit. We develop a sixth sense for smart moves in the game, and even though most of us couldn't explain where the idea for a particularly far out move came from, protein folding seems often to rely on such moves. It's very hard to program computers to make intelligent-yet-far-out moves. We can program in randomness (and the best protein folding programs do just that), but it's hard if not impossible to program in smart, intuitive randomness. As the Nature team writes, "We found that Foldit players were particularly adept at solving puzzles requiring substantial backbone remodeling... stochastic Monte Carlo trajectories [in other words, random computer guesses] are unlikely to [find] the coordinated backbone... shifts needed..." --We have great adaptivity. We can change our strategies and approaches over time based on what we learn and intuit about what's working well, and what's not. The Nature paper has some cool graphs showing how people change their mix of Foldit "moves" after the first hour, first day, and first week of playing. Again, it's hard to program computers to do this well. --In addition to being highly visual, we humans also inherently tend toward collaboration. We form teams and share knowledge among members pretty effectively, thanks to the gift of language. Many scholars believe that is what most fundamentally separates us from all other animals. And technologies like wikis are a big step forward in facilitating collaboration within geographically dispersed groups.
--While collaborating, we exercise a high degree of self-organization. The Foldit researchers found that, "Within teams, there is often a division of labor. Some players specialize in early-stage openings, others in middle- and end-game polishing." I would bet that these roles were not assigned by team captains; instead, people fell into them unconsciously over time, and also fell into effective workflows and divisions of labor within teams. This is exactly what's happened with Wikipedia, and I'd be surprised if the situation were radically different within Foldit. --Finally, we love competition. The desire to get ahead of a rival or be on the game's leader board can be a powerful motivation. Foldit's designers did a great job of tapping into this motivation. They also made the game engaging to play and provided frequent feedback to players, thereby increasing intrinsic motivation as well. Taking advantage of all these features simultaneously led to better outcomes in the dauntingly difficult domain of protein folding. By studying what people did to rack up high scores in Foldit, we may be able to improve how well computers alone work in this domain. As the authors write, "More in-depth analysis of player strategies should provide further insight ... and could lead to improved automation algorithms for protein structure prediction." I'll go a big step beyond that statement: It could be that studying how people succeed at Foldit might help us better understand not only computer simulation of protein folding, but perhaps also protein folding itself. The Foldit team did science that was both rigorous and creative, and they deserve at least as much attention they're getting. They also deserve credit for realizing that when faced with a nasty problem, the smart approach is not always to retrench--to rely more heavily on established experts and powerful computers. Instead, when the tools needed for effective problem solving can be widely and cheaply distributed, the responsibility for problem solving can also be. And as Foldit results and lots of other evidence shows, expertise--for problem solving, innovation, etc.--is emergent. It's out there in large quantities, and in hard-to-predict places. A problem solving approach that lets pockets of enthusiasm and expertise manifest themselves and find each other can yield surprisingly large rewards, even in the unlikeliest places. Andrew McAfee is a principal research scientist at the MIT Center for Digital Business. His book Enterprise 2.0: New Collaborative Tools for Your Organization's Toughest Challenges was published in November 2009 by Harvard Business Press. His website is andrewmcafee.org, and his Twitter identity is @amcafee. See Also: Rising Above Tech's Temptations Why Geeks Hate The iPad Defending The iPad's Restrictions
http://www.forbes.com/2010/08/23/science-proteins-foldit-technology-breakthroughs-... 01/07/2011