Screen shot of Foldit - Courtesy of University of Washington

My wife calls me “ulterior motive man” because I have this firm belief that a single reason is rarely if ever justification for any action. Thus taking out the garbage should be done when you can button hole that neighbor kid about mowing your lawn for you.

Today the L.A. Times has a story that gives ma a reason to play an on-line game, Foldit. This game allows users to work on determining the shape of molecules and more importantly viruses. In a mere three weeks this game has done something that more than a decade of traditional bio-molecular science has failed to do, it has map a protein that the HIV virus uses to replicate itself and become AIDS.

The protein is called M-MPV. It is the part of the replication mechanism of a simian AIDS variant. It has been remarkably resistant to the normal mapping technique of Molecular Replacement (MR). MR is in the field of X-ray crystallography and it can get a little deep, but bear with me and I’ll try to break it down to understandable bites.

X-ray crystallography allows us to map the position of electrons in the material embedded in the crystal. When we know where the electrons are we know where the atoms are and can determine the bonds between them. This technique has been in use since the 1920’s and moved into the field of bio-chemistry in the 1950’s.

MR is the process of taking a known structure map and then comparing it to a new sample and looking for the differences then trying to determine what the differing molecules are. It has been very useful but it uses a ton of computing power and has some notable failures, like M-MPV.

This is where Foldit comes in. The game was invented by the University of Washington’s Center for Game Science and the department of Computer Science and Engineering. What the game allows users to do is take existing maps and then use their intuition to change some of the positions of the molecules. It also allows an iterative function where they can use combine other models. What they are looking for is a model that has the lowest energy state, which is most likely to be close to the real world structure they are mapping.

Once there is a statistically high chance of an accurate model, that model is used in MR to verify. So the gamers were unleashed on the M-MPV structure. In three weeks it produced a result that allowed a confirmation with MR techniques. What had been a mystery for more than a decade was solved in short order by a bunch of nerds (and I mean that in the very best way) playing a moderately complex game.

So what does this mean out here in the real world? Quite a lot, actually. By knowing the structure of protease proteins like the one in the study, drugs can be designed that bind to specific areas of the protein and prevent it from reproducing. No new virus proteins mean there is no expansion of the disease.

That is what the current crop of anti-retrovirals do, but they could do it a lot better. Having a solution like this for the HIV retroviral protease would allow a much more specific kind of drug to be developed and perhaps even lead to a way to vaccinate against HIV.

This is probably the first time you’ve heard of this, but it is sure not to the last. The proof that this kind game matching human intuition with complex computer models for real world outcomes has been given. Going forward it is very likely that we will see more and more of these kinds of ‘games’ that work problems that our material science and computer science alone can’t solve.

This is an important break through. The whole of the modern world is based on our increased understanding of materials and biology. Now that there is a way to speed up the process by putting human intuition into the loop a new door is open to a room full of discoveries just waiting to happen.

If you are a glass half empty person you will worry about what we humans will do with this knowledge. Our record of using new discoveries is pretty spotty, with abuse just as likely as proper use.

Still my father had a saying that is rolling around in my mind this morning it went: Technology = A great time to be alive! That is a sentiment I feel a lot and this morning especially. Now I can say that when I spend hours and hours playing a game it is not wasted time, it’s research!

The floor is yours!

PS if you are interested in the paper published on this (warning, it is pretty hard sledding) you can find it here

Bill Egnor

Bill Egnor

I am a life long Democrat from a political family. Work wise I am a Six Sigma Black Belt (process improvement project manager) and Freelance reporter for Govtrak.org