Get the gamers involved

I had intended to write about this topic earlier in the semester and had forgotten all about it until I saw a reference in this week's reading by Amy Friedlander, The Triple Helix: Cyberinfrastructure, Scholarly communication, and Trust. Friedlander discusses how problems that can be cleanly parsed into discrete tasks are well suited for a distributed capacity model which allows open, but still structured, participation from the public. She provides the example of protein folding, which is the topic of an April 2009 Wired Magazine article: Gamers Unravel the Secret Life of Protein.

The protein chemistry world has a biennial World Series competition to see who can predict the shape of a protein only knowing the sequence of its constitute parts (Community-Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction, or CASP). CASP surveys labs around the world to find proteins that are about to be solved, and compile a list of puzzles online.

David Baker, whose team had dominated the competition since 1998, had been using Rosetta@home, similar to SETI@home, which farmed out computations to volunteer PCs distributed globally - providing Baker with the equivalent of a supercomputer. However, the computers were unable to complete certain puzzles, which humans should be able to solve, having better spatial reasoning. Baker's friend David Salesin, a computer scientist, brought him together with Zoran Popovic, another computer scientist and graphics expert, and the three developed what turned into a massively multiplayer competition. Gamers are given a multicolored knot of spirals and clumps, which they fold and wiggle into its optimum shape.

Baker then entered potentially accurate CASP protein structures into the biennial competition. Of 15 submissions, 7 finished "in the money" and one took first place. The gamer team, led by a 13-year old, beat the best biochemists. Baker was also hoping to find prodigies... when "Cheese" (the 13-year old) was asked how he did it, he said, "it just looks right."

Baker has given the players a new challenge to design a new protein drug with the right size and binding properties. Baker will synthesize and test the most promising structures and if any have value in the real world, the gamers will share in the credit.

The article doesn't specifically address authenticity or trust, but the gamer submissions are not automatically deemed correct, even though the game is based on laws of physics. Submissions are reviewed by CASP, and/or tested in the lab. But, given the fact that there are more ways to fold protein than atoms in the universe, and they arrange in a fraction of a second, collective efforts are crucial.