Play at Work by Adam L. Penenberg

Author:Adam L. Penenberg
Language: eng
Format: epub
Publisher: Penguin Group US
Published: 2013-09-06T16:00:00+00:00

The Contenders

For years, the researchers in Baker’s lab in Poland had been trying to fold the protein for the Mason-Pfizer Monkey Virus Retroviral Protease. Thus far, Rosetta@home had not even formulated a nibble. In a last-ditch effort, Khatib presented the protein to Foldit players. Ten days later a group of players solved it.

Michele Minett, a self-described “lowly lab technician” from the United Kingdom, is credited with having solved the 3-D puzzle while working with members of the Foldit group the Contenders. The group is informally comprised of about three dozen players from all walks of life. Some have a background in science, others don’t. A few may code but many don’t. After reading about Foldit in New Scientist, she figured it would be a “more productive way of wasting time” than, say, Minesweeper. She started playing in November 2008, six months after its release. On her woefully out-of-date computer, the game ran slowly and the display was jerky. At the time, manipulation of the protein was done manually by studying the shape of the protein and using the game tools to pull parts together or apart and change the position of side chains. Initially she played for short periods, gradually learning the techniques by experimentation and reading the conversations in the global chat window. She found the internal chat facilities “a vital part of creating and maintaining the Foldit community without which the game would not work.”

She says she asked to join the Contenders because she liked how members comported themselves in game chat and was looking for a relatively small and friendly group where she could make a contribution. A year after she started playing, she upgraded her PC, which made it possible for her to work more easily on protein puzzles. Over that period advances in the game meant it was possible to leave the program to run a sequence of instructions programmed by the player on a protein instead of making manual adjustments every few minutes. This function, called “scripting,” arose out of a function in the game called “The Cookbook” and enables players to script or code their own strategies in the game. Players can share and modify their recipes with other players. This way they can pick up strategies from other players and then automate them. The most popular recipe, “Blue Fuse version 1.1,” was made up of just a few lines of basic code that anybody could learn to write. According to Cooper, a biochemist from Baker’s lab remarked that it was an algorithm that they had independently been developing in the lab but hadn’t published yet. “Organically,” Cooper says, “the community of Foldit players had come up with the same algorithmic moves that the scientist in the biochemistry lab had come up with independently.”

Between December 2010 and January 2011, Khatib unveiled the Mason-Pfizer Monkey Virus puzzle to Foldit players with the comment: “The Folded monomer of protease from Mason-Pfizer monkey virus is currently unsolved by protein crystallographers.” As usual, they were given a deadline, this time three weeks, and provided with ten alternative starting points.

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