If people spent just a fraction of their play time solving real-life scientific puzzles – by playing science-based video games – what new knowledge might we uncover? Many games aim to take academic advantage of the countless hours people spend gaming each day. In the field of biochemistry alone, there are several, including the popular game Foldit.
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 non-experts play scientific games – we recently set up a Foldit competition between gamer’s, undergraduate students and professional scientists. The amateur gamer’s 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 crowd-sourcing to gamer’s (or “game-sourcing”) could offer to many fields of study.
Looking closely at proteins
Proteins perform basically all the microscopic tasks necessary to keep organisms alive and healthy, from building cell walls to fighting disease. By seeing the proteins up close, biochemists can much better understand life itself.
Understanding how proteins fold is also critical because if they don’t fold properly, the proteins can’t do their tasks in the cell. Worse, some proteins, when improperly folded, can cause debilitating diseases, such as Alzheimer’s, Parkinson’s and ALS.
Taking pictures of proteins
First, by analyzing the DNA that tells cells how to make a given protein, we know the sequence of amino acids that makes up the protein. But that doesn’t tell us what shape the protein takes.
To get a picture of the three-dimensional structure, we use a technique called X-ray crystallography. This allows us to see objects that are only nano-meters in size. By taking X-rays of the protein from multiple angles, we can construct a digital 3D model (called an electron density map) with the rough outlines of the protein’s actual shape. Then it’s up to the scientist to determine how the sequence of amino acids folds together in a way that both fits the electron density map and also is biochemically sound.
Although this process isn’t easy, many crystallographers think that it is the most fun part of crystallography because it is like solving a three-dimensional jigsaw puzzle.
The competition, and its result, were the culmination of several years of improving biochemistry education by showing how it can be like gaming. 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.
From the classroom to the game lab
Like crystallographers, Foldit players manipulate amino acids to figure out a protein’s structure based on their own puzzle-solving intuition. But rather than one trained expert working alone, thousands of non-scientist players worldwide get involved. They’re devoted gamer’s looking for challenging puzzles and willing to use their gaming skills for a good cause.