When someone whines that your playing video games is a waste of time, tell them you’re doing it for science. Researchers at the University of Washington have successfully leveraged the power of gamers to solve a biochemical puzzle: the structure of a complex protein related to the development of AIDS. By playing an online game called Foldit, teams of average citizens were able to make a breakthrough discovery in how this protein was shaped even though scientists had stumbled over the question for more than a decade. A combination of computer-created predictions and human 3D spatial reasoning transforms simple game playing into a mighty problem solving engine. Their discovery could help develop new anti-viral drugs for HIV. Watch how Foldit is played in the video below. While applications are likely to remain limited for years to come, programs like Foldit demonstrate the vast potential of crowd-sourced solutions in science. Never doubt it – video games can be powerful tools for change.
Researchers from the University of Washington described their unique method for solving the structure of the AIDS related protein in a recent report published in the journal Nature Structural and Molecular Biology. The compound in question was Mason-Phizer Monkey Virus (M-PMV) a retroviral protease that affects how the HIV strains mature and replicate. Like so many proteins, M-PMV’s crystalline structure is determined by very complex interactions between the amino acids in the molecule, as well as preferences for parts of the protein to avoid or attract water in its environment. Predicting how proteins fold up is a computer-heavy problem, and various groups have explored distributed computing solutions so that people all over the world can donate processor time towards determining protein structures.
Foldit has a very similar goal, only it’s using your brain, not your computer to help it figure out how proteins fold. In the style of a game, Foldit players are rewarded points for finding solutions to protein folding problems. There are always many different possible solutions, so Foldit rewards players, or teams of players, based on various requirements set by the game designers in the University of Washington computer science department. Essentially players look at complex proteins and use their 3D spatial reasoning skills, as well as healthy doses of trial and error, to find the the folding pattern that gives them the most points. It’s up to the UW team to determine how to award points in a way that makes the gamers’ efforts most useful.
In this study, University of Washington researchers determined that there are some conditions in which Foldit doesn’t work very well. Sometimes players get stuck pursuing dead-ends, other times they try to tweak a possible solution when they really need to make big changes to find the ideal answer. The Foldit puzzles in this study gave players starting points (called Rosetta structures) as well as the means to manipulate portions of the protein and compare them to earlier (validated) solutions. By changing the starting points, and giving players more freedom in exploring the possible folding patterns, the University of Washington enabled Foldit teams to get very close to finding the M-PMV structure. The gamers’ answers were so good that UW could then step in and use more traditional computer driven methods to find the finalized solution to the problem. Scientists had been working on M-PMV for years, this new style of guided-gaming figured it out in just three weeks.
It’s tempting to call the Foldit participants “untrained” or “typical video game players” because that makes for a good story. The truth is, however, that part of what Foldit does is teach you how to solve protein folding problems. It just does it in a way that you’ll find fun and challenging. It’s not that the University of Washington isn’t training the thousands of players who participate in Foldit, it’s that the training is so vastly different than normal scientific education. You don’t have to know why some atomic bonds lead to lower energy states when arranged in new patterns, you just have to play with these twisted proteins until you get enough points to win.
In the short term, the combination of human and computer processing that the University of Washington demonstrated could be put to extraordinary use. Humans have 3D understanding that computers just can’t handle yet, and computers have the number crunching capabilities that humans can’t possibly compete with. Put the two forces together and you’ll find new avenues for anti-viral medications (as with the M-PMV case) or possibly solve any number of other biochemical mysteries. We’ve seen similar pairings of human and computer expertise suggested for things like image tagging. There’s a whole application space waiting to be explored by inserting large numbers of humans into a problem solving system when computer power alone doesn’t cut it. Video games are a great tool for leveraging the human mind, especially as massive multiplayer online games and other internet entertainment are teaching us to enjoy solving challenges in crowd-sourced environments simply for the sake of earning more points (and prestige).
Looking further down the line, however, intellect-harnessing video games like Foldit are only going to be useful as long as there are skills that human brains possess that computer processors do not. We’ve probably got several decades of that being the case, but eventually it will change. So for now we should really enjoy the power of video games. Used correctly they can transform even the most lackadaisical layabout into a mighty instrument of science. So your mother was wrong: you’re not a coach potato, you’re a biological processor that really enjoys its work.
Speaking of which, there’s some scientific work I really need to get done. Anybody know the cheat codes to Ebola?
[image and video credit: FoldIt]
[source: Khatib et al Nature Structural and Molecular Biology 2011, University of Washington News]