The Determination of the Imagination

The story of online gamers solving protein structure problems for biochemists has been reported by many, including the New York Times, NPR’s 360, Youtube, and a host of blogs.  The gamers, by using their three-dimensional puzzle solving skills, have made significant contributions to biochemical research.

The problem for biochemists is predicting the shape that a protein will take.  Proteins first appear as strings of amino acids, like coils.  The amino acids then interact with each other to produce a well-defined three-dimensional structure.  It happens spontaneously and quickly, in time frames measured in billionths of a second.  The process that takes the protein from string or coil to the three dimensional structure is what’s called the  folding.  And even if the time frames were slower, proteins are far too small to be seen by a microscope.

Researchers at the University of Washington became aware of inefficiencies in the software that had been designed to find the folding patterns. They considered that one of the problems was that the computer couldn’t see the shapes. But individuals could see the inefficiencies, so perhaps individuals could also work  through the complexities of the whole problem.  And so they designed a a protein-folding video game, available on the Internet, to tempt the human imagination to solve the puzzles.  The researchers themselves had no advantage in solving the puzzles.  In fact, they weren’t good at it.   The game, called Foldit, has attracted a dedicated following of thousands of players (one who spoke on NPR was only 13).  Players actually fold different proteins into their lowest energy state (which is their final resting state) using computer tools and figures that are designed to contain the biochemical parameters of the problem.  The success of the effort was reported in a paper in the journal Nature, and the players were listed as coauthors of the paper.

The complexity of the problem is directly related to the degrees of freedom, or the number of parameters, in the space of all possible shapes.  But the Nature paper tells us that one of the reasons the human effort surpasses the software effort was that gamers (who are able to collaborate) didn’t only look at all possible shapes.  They also looked at all possible strategies.

The times article tells us that, according to one of the gamers, the complexity of a problem is somehow like “……trying to solve a million-sided Rubik’s Cube while it spins at 10,000 r.p.m.”   Also, according to the Times:

In a comparison involving 10 separate protein-folding puzzles, video game players matched the results generated by software solutions in three of the puzzles, outperformed them in five cases and found significantly better solutions in two others, according to the scientists.

Knowing the shape of particular proteins is the key to understanding how they work (even as they cause the progression of a disease like HIV).

This is certainly a new way to do science and opens the door, I’m sure, to all kinds of ways that the human community can be knitted together.  But it’s also worth noting that the success of Foldit says something about the talents of the imagination.  We’re wired for pattern recognition and for conceptualizing problems, and this is the very thing that makes mathematics possible.  That gamers explored the strategy ‘space’ as well as the structural ‘space’ is a great example of the determination of our imagination.  I’ve also learned that dopamine can make the puzzle irrisistable since its pleasurable release is now known to happen, not when we finish a puzzle, but when we start it.  But that’s another story that I’ll write about soon.