Thursday, August 12, 2010

Folding proteins for fun and science.

Earlier today on the lengthy and always semi-productive (if you count listening to podcasts as productive) bus ride home from Toronto, I listened to a lecture given by Cory Doctorow at the Perimeter Institute in Waterloo. The subject was Copyright vs. Universal Access, and while the entire hour long lecture is worth listening to — particularly his early musings on the relationship of individuals to books — a certain portion stood out for me in light of a link from Shakesville, of all places. is a game designed by computer scientists and biologists at the University of Washington that allows gamers to fold proteins according to their genetic makeup. While biologists know the genetic sequence of proteins, as well as their functions, there is still a lot to learn about why they twist and fold into their specific shapes. While a computer could calculate all possible protein shapes, it would take an obscenely long time, and it turns out that human beings, under the auspices of gaming, are faster. Points are awarded not for accurately repeating a known solution, but for how much (or little) energy it would take for the protein to fold into that particular shape. Competition comes in when you compete with other players to make the most efficient form of a particular protein.

This is an excellent example of what Cory Doctorow describes as the most radical possibility of the Internet. While many early techno-utopianists describe the ultimate power of the Internet as the ability to liberate information and provide universal access to all human knowledge, Doctorow takes it a step further. The radical possibility of the Internet, in his view, is not only in the liberation of information but in it’s ability to lower the transaction costs for participating in acts of collaborative creation. He uses the example of GNU on Linux and a skyscraper. The ‘real world’ equivalent of the way the Linux OS was built, he argues, is asking a bunch of people you don’t know if they have construction-grade steel, office chairs, carpet, window glass, hard hats, etc and if they do, if they could bring them to the construction site and pitch in a bit to help build a skyscraper that they could then all live in. Clearly this is absurd — almost no one would participate in such an endeavour, and the project would never get done.
But the Internet side-steps these issues of collaboration and donation of time and energy by lowering the transaction cost of participation. People participate in projects like (or like Wikipedia, the perennial example) not because they’re required to, but because they want to — they enjoy it. By contributing to the collaborative project, however, they are able to accomplish things that a single human being — or, in the case of, a computer program — could never reasonably get done. For Doctorow, as well as internet commentators like Clay Shirky, the most radical and exciting parts of the Internet have less to do with technology and more to do with people. As a sociologist, I can get behind that. 

And as a nanoscience student, my brother can get behind, which is apparently super addictive. It’s also already been scoured for exploits, which indicates not only has it attracted it’s fair share of internet assholes, it’s also being treated as a real game. Who’da thunk it.