Can you fold RNA?

January 28, 2011

3 Min Read
Can you fold RNA?

When I was learning biology (or rather trying to avoid learning — biology didn’t involve programming, or circuits, and my interests were pretty one sided in high school.  Two sided, actually, I was also distracted by the young lady who sat directly in front of me.  The biology teacher was a distant third at best) I learned that in a cell DNA was the boss, and RNA was the messenger.  Today scientists think it plays a much larger regulatory  role in the operation of the cell, but they really don’t know for sure.  When you’re a scientist you don’t really know anything for sure, that’s how you keep getting grants.  Plus, once you do know something for sure it’s almost certain that you’ll be proven wrong.

The image at the top is an artists conception of a complex RNA molecule.  I think it bears a resemblance to the Love Symbol, which is what the artist formerly (and currently) known as Prince changed his name to during the last decade of the 20th century.  Prince, like the scientists, also has some uncertainty, his being related to his name.  Unlike scientists however, Prince is fabulously wealthy and gets to hang out with celebrities.  Once the party of 1999 was over and the hangover dissipated Prince changed his name back to Prince.

I’ve put Prince’s symbol up also so you can compare the two.  Maybe Prince’s RNA is love symbol shaped, and that explains his musical prowess.

So, back to the point.  My editor sent me a link to a new game created by Carnegie Mellon University called eteRNA.  It’s hooked into Facebook, but it’s not about farming or running a crime syndicate.  In this game you try to design molecules of RNA that fold into particular shapes.  A state-of-the-art simulator predicts how your entry will fold, and the best entries of the week are actually synthesized in a biochemistry lab at Stanford.  The final scoring is based on how well the molecule actually folds in the lab, so in the end entries are judged by nature.

The game includes some background on how RNA folding works, and some training exercises that potential RNA folders can use to get up to speed.

The effort is described as “crowd sourcing” the scientific method.  The critical feature that makes it work is that RNA can actually be synthesized quickly so the potential winners can be evaluated and the results fed back to the players, and presumably also used to improve the folding simulator itself.

Nobel Prize winning economist F. A. Hayek wrote extensively on self organizing systems and distributed knowledge.  I think that this example is a terrific illustration of how groups of people who, individually, are not particularly knowledgeable about the problem at hand can self organize to collectively solve problems that stump the experts.

Hayek wrote about the topic in the context of economics, where individual actors, each acting in his or her own self interest, are able to coordinate the production of exceedingly complicated end products.  Products which none of the involved actors are able to grasp in their full complexity, such as the pencil or the smartphone.

Already this game has advanced the state of knowledge in RNA research.  According to project co-leader  Adrien Treuille:

One player solved a puzzle that a widely used algorithm could not. Another player has written a strategy guide that proposes an algorithm for solving design problems that is different and simpler than anything in the scientific literature.

So put on your raspberry beret and get to work designing RNA.

Steve Ravet

Design News Gadgeteer

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