Tag Archives: James Bardwell

Promoting video games for the pursuit of science

An Oct. 6, 2016 essay by Scott Horowitz and James Bardwell for The Conversation (h/t Oct. 6, 2016 news item on Nanowerk) makes the case for more video gaming projects designed to advance science. From The Conversation’s Oct. 6, 2016 essay,

In Foldit, players attempt to figure out the detailed three-dimensional structure of proteins by manipulating a simulated protein displayed on their computer screen. They must observe various constraints based in the real world, such as the order of amino acids and how close to each other their biochemical properties permit them to get. In academic research, these tasks are typically performed by trained experts.

Thousands of people – with and without scientific training – play Foldit regularly. Sure, they’re having fun, but are they really contributing to science in ways experts don’t already? To answer this question – to find out how much we can learn by having nonexperts play scientific games – we recently set up a Foldit competition between gamers, undergraduate students and professional scientists. The amateur gamers did better than the professional scientists managed using their usual software.

This suggests that scientific games like Foldit can truly be valuable resources for biochemistry research while simultaneously providing enjoyable recreation. More widely, it shows the promise that crowdsourcing to gamers (or “gamesourcing”) could offer to many fields of study.

Horowitz and Bardwell (both crystallographers) created their own game,

We teach an undergraduate class that includes a section on how biochemists can determine what proteins look like.

When we gave an electron density map to our students and had them move the amino acids around with a mouse and keyboard and fold the protein into the map, students loved it – some so much they found themselves ignoring their other homework in favor of our puzzle. As the students worked on the assignment, we found the questions they raised became increasingly sophisticated, delving deeply into the underlying biochemistry of the protein.

In the end, 10 percent of the class actually managed to improve on the structure that had been previously solved by professional crystallographers. They tweaked the pieces so they fit better than the professionals had been able to. Most likely, since 60 students were working on it separately, some of them managed to fix a number of small errors that had been missed by the original crystallographers. This outcome reminded us of the game Foldit.

They then ran a competition between their students, two trained crystallographers, and some Foldit players,

We gave students a new crystallography assignment, and told them they would be competing against Foldit players to produce the best structure. We also got two trained crystallographers to compete using the software they’d be familiar with, as well as several automated software packages that crystallographers often use. The race was on!

Amateurs outdo professionals

The students attacked the assignment vigorously, as did the Foldit players. As before, the students learned how proteins are put together through shaping these protein structures by hand. Moreover, both groups appeared to take pride in their role in pioneering new science.

At the end of the competition, we analyzed all the structures from all the participants. We calculated statistics about the competing structures that told us how correct each participant was in their solution to the puzzle. The results ranged from very poor structures that didn’t fit the map at all to exemplary solutions.

The best structure came from a group of nine Foldit players who worked collaboratively to come up with a spectacular protein structure. Their structure turned out to be even better than the structures from the two trained professionals.

Students and Foldit players alike were eager to master difficult concepts because it was fun. The results they came up with gave us useful scientific results that can really improve biochemistry.

I first wrote about Foldit in an August 6, 2010 posting (scroll down about 50% of the way).