September 22, 2011

September 22, 2011
Gamers Solve Puzzle Part 2

Welcome to another day in my life. Today is Thursday and I hope you are having a safe and great week so far. Still dealing with situations going on in my life with the help of Dab the AIDS Bear.

Yesterday, I started a blog about how gamers have supposedly solved the molecular puzzle to HIV which I will conclude today.

Looking for new problems to solve The monkey-virus puzzle solution demonstrates that Foldit and other science-oriented video games could be used to address a wide range of other scientific challenges ranging from drug development to genetic engineering for future biofuels. "My hope is that scientists will see this research and give us more of those cases," Khatib said.

He's not alone in that hope. "Foldit shows that a game can turn novices into domain experts capable of producing first-class scientific discoveries," Zoran Popovic, director of University of Washington's Center for Game Science, said in today's news release. "We are currently applying the same approach to change the way math and science are taught in school."

That's something that Carter Kimsey, program director for the National Science Foundation's Division of Biological Infrastructure, would love to see happen. "After this discovery, young people might not mind doing their science homework," she quipped.

One caveat, though: Playing Foldit isn't exactly like playing Bejeweled. "Let's be honest, proteins aren't the sexiest video game out there," Khatib told me. Give the game a whirl, and let me know whether it's addictive or a drag.

Tale of a Contender The final decisive move in the Foldit Contender Group's solution to the monkey-virus puzzle involved twisting around that floppy loop, or "flap," in the structure of the enzyme. The paper published today notes that one of the Contenders, nicknamed "mimi," built upon the work done by other gamers to make that move. I got in touch with mimi via email, and here's the wonderfully detailed response she sent back today from Britain:

"I have been playing Foldit for nearly three years, and I have been in the Contenders team for two and a half years.

"Although there are 35 names on the members list on the website, when you take off duplicate names and non-active players, it comes down to about 12 to 15 people.

"The team members come from a wide range of backgrounds, chiefly scientific or IT [information technology], although our best player is from neither.

"One of the main features of Foldit is the ability to communicate via chat within the game. There is both global chat, which everyone can access, and individual group chat, which allows team members to talk easily to one another. The Contenders are spread out between Canada, USA, UK, Europe and New Zealand, so this is essential.

"Each player can work on a solo solution to a puzzle, but we can also exchange solutions between the team and add our own improvements to achieve a better result. Often the evolved solution for a team scores higher than the top solo score.

"The game is not only an interesting intellectual challenge, allowing you to use your problem-solving skills, 'feel' for protein shapes, and whatever biochemical knowledge you have to obtain a solution to each puzzle, but it also provides a unique society of players driven by both individual and team rivalry with an overall purpose of improving the game and the results achieved. A body of knowledge has been built up in the Wiki by contributions from players, and ideas are constantly fed back to the game designers.

"In the case of the Mason-Pfizer monkey virus, I had looked at the structure of the options we were presented with and identified that it would be better if the 'flap' could be made to sit closer to the body of the protein one of the basic rules of folding is to make the protein as compact as possible but when I tried this with my solo solution, I couldn't get it to work. However, when I applied the same approach to the evolved solution that had been worked on by other team members, I was able to get it to tuck in, and that proved to be the answer to the structure. I believe that it was the changes made by my colleagues that enabled mine to work, so it was very much a team effort.

"We were all very excited to hear that we had helped to find the answer to this crystal form, especially since it had been outstanding so long and other methods had been unsuccessful. The feeling of having done something that could make a significant contribution to research in this field is very special and unexpected. Foldit players have achieved a number of successes so far, and I hope we will go on to make many more.

"You may be aware that we asked for accreditation for the Foldit Contenders Team within the article, rather than being named individually.

"Many of the people playing the game are known only by their user name, even within a team.

"I would be grateful if you could refer to me as 'mimi' rather than using my full name."

More games for science:

Play a game and engineer real RNA Fight disease by playing a game Help scientists decipher a 'lost' gospel Join a worldwide planet search Look for icy worlds over the Internet Still more research games from Zooniverse SETI @ home and much more from BOINC

In addition to Khatib, DiMaio, Cooper, Popovic and the Foldit Contenders Group, the authors of "Crystal Structure of a Monomeric Retroviral Protease Solved by Protein Folding Game Players" include the Foldit Void Crushers Group, Maciej Kazmierczyk, Miroslaw Gilski, Szymon Krzywda, Helena Zabranska, Iva Pichova, James Thompson, Mariusz Jaskolski and David Baker. The authors also acknowledged "the members of the Foldit team for their help designing and developing the game and all the Foldit players and Rosetta @ home volunteers who have made this work possible."

The work was supported by UW's Center for Game Science, the Defense Advanced Research Projects Agency, the National Science Foundation, the Czech Ministry of Education, the Howard Hughes Medical Institute and Microsoft Corp. ( is a joint venture involving Microsoft and NBC Universal.) Foldit was created by computer scientists at the Center for Game Science in collaboration with the UW's Baker Laboratory.

Until we meet again; here's wishing you health, hope, happiness and just enough.

big bear hug,

Daddy Dab