Online Gamers Contribute To Hiv Breakthrough

Structure of Molecule Critical for HIV to Multiply Decoded by Gamers

Biochemists have been working for years to determine the structure of a molecule known as an HIV-1 protease. A protease is an enzyme that "snips" long chains of amino acids made by a virus into smaller chains of amino acids known as virions. The virions are capable of infecting new cells and acquiring new proteins there. If the virus is never "snipped" by protease, it remains coiled into a long, inert chain that cannot infect new cells.



Protease inhibitors, as you might imagine, are a key goal of AIDS treatment. Scientists have been trying to ascertain the geometry of the HIV-1 protease for almost 15 years. Online gamers decoded the structure of the molecule in just three weeks.

Scientists already knew that the placement of the HIV-1 protease was something like a dumbbell, with two larger, folded ends connected by a more or less straight chain of amino acids in the middle. They knew that the "snipper" in both ends of the dumbbell was aspartic acid. But they did not know how the enzyme positioned itself so that the aspartic acid would break the long dormant virus into smaller active pieces.



To gain insight into the geometry of the enzyme, researchers in the laboratory of University of Washington AIDS researcher Dr. David Baker developed a game called Foldit. Their idea was to tap into the enormous intellectual energy online gamers put into their games.


Foldit is a series of games (or tutorials) about how proteins coil and uncoil inside a cell. They start with "One Small Clash" and work their way up to "Rubber Band Reversal."

Gamers are given basic information about how the individual amino acids in the protein may attract or repel each other, and then they are presented with amino acid sequences in real proteins of known geometry to "fold." They are invited to try to make a protein depicted on the screen loop or wiggle. They can double the length of the protein to form a helix. They can shake the protein, work on just segments of the protein, freeze and unfreeze segments, and introduce cross links to hold the protein together. They can make the protein more or less compact and use a voiding tool to see which areas of the protein could be worked on more.

The game generates a score based on how well the protein is folded compared to what scientists already know, and the site maintains a list of high scoring gamers. Foldit gamers may share solutions and form groups, or compete against each other individually. Scientists then use analyze how gamers made decisions about folding proteins to write new computer algorithms to explain the structure of still-unknown proteins.

Foldit has been online since 2008. The structure of the protease enzyme is the fourth scientific breakthrough made with the help of online gamers. When brute computing power is not enough for scientists to figure out a problem, Foldit and similar tools make scientific discovery possible through the use of crowdsourcing.

Foldit has been a success for figuring out algorithms for breakthroughs in biofuels and HIV research because of the combined contributions of over 100,000 gamers, but it is hardly the only example of crowdsourcing, the process of inviting public contributions to work out scientific problems.


Galaxy Zoo uses public input to identify the shapes of galaxies seen through the Hubble telescope. A Dutch public school teacher named Hanny van Arkel, who had no formal training in astronomy, had been playing the game for about a week when she noticed a strange gas cloud in IC 2497, a small galaxy in the Leo constellation. She asked a supervisor for information, and the professional astronomer was stumped. Other astronomers also were at a loss to define the object, now known as Hanny's Voorwerp, vorwerp being the Dutch term for "object."

More than five million computer users have been recruited for SETI@home, which searches for extratrerrestrial life. IBM's World Community Grid is helping Chinese researchers develop methods fo purifying water using nanotubes. The Herbaria@home project is helping British botanists identify over 75,000 plants collected in the UK, helping determine which plants are endangered. Cornell University's Nestwatch collects data about bird migrations across North America. The Climate Watch project in Australia tracks plant and animal fluctuations in the Southern Hemisphere, and tens of thousands of Americans collected beach data after the BP oil spill.

Sometimes the research is hands-on. DIYBio (Do It Yourself Bio) maintains laboratories in Boston, Brooklyn, and San Francisco where its 1,500 members can operate DNA sequencing equipment. Recently DIYBio members sequenced DNA from bacteria each had collected from 50 dollar bills donated by 50 acquaintances, to track the spread of disease by money.

Not everyone who participates in crowdsourcing works for free. Prizes range from $1 million for helping locate a new lab test marker for Lou Gehrig's disease (amyotrophic lateral sclerosis) down to $7,500 for helping develop a better smelling kitty litter.

And some crowdsourcers enjoy fame. Ms. van Arkel became the basis of a character in an online comic book. She started a Twitter feed. And in January of next year she will be memorialized as the co-author of the scientific paper announcing the discovery of her "object."

Scientists complain that crowdsourcing is not really science, and that opening up participation to the public introduces new issues in peer review, the process of approving scientific papers for publication. David Weinberger, a researcher at the Berkman Center for the Study of the Internet and Society at Harvard University, goes so far as to like the participants in crowdsourcing as "scientific instruments." More charitable assessments by mainstream scientists suggest that at least participants in crowdsourcing should be able to get some of the same reward as academic scientists, much as Hanny van Arkel has.

But far more people feel that crowdsourcing is a way to do science without being a scientist. Participating in crowdsourcing won't give anyone entry into the scientific establishment, but as van Arkel told the New York Times, it can be a life-changing thing.