Blog Post #2: Crowdsourcing in Scientific Research – It’s Not Just Foldit

Markoff’s article on Foldit brought an old, cobwebbed memory to the forefront of my mind. This business about crowdsourcing biological puzzles seemed all too familiar. Although I was sure I had never played Foldit before, I swear I’d played something like it.  Instead of tasking the player to solve protein structures, I was pretty sure it asked him or her to solve RNA structures (RNA, by the way, is the stuff that gets translated to proteins; the intermediary between DNA and protein). So, naturally, I decided to scour the Internet for an RNA folding game, to assure myself that I was not crazy.

Lo and behold, with one quick Google search, I stumbled upon the game of my memories. The game, entitled EteRNA, is indeed about using the pattern recognition abilities of the human mind to determine the ways in which RNA can fold to create their complex structures. As you’ve probably noticed, the premise of EteRNA is quite similar to Foldit, and was in fact inspired by Foldit’s success in its aims to develop new protein folding algorithms. In fact, some of the researchers that worked on Foldit also helped design EteRNA (1).

A bit about EteRNA: as a player, it is your job to learn two general facts before solving the RNA puzzles of the game. The first is that there are four types of molecules, known as “bases” that make up an RNA molecule – adenine (A), guanine (G), cytosine (C), and uracil (U). You may recognize these bases before from a high school biology class. The second rule is that A preferentially bonds with U (and vice versa) while G likes to bond with C Seems simple, right? Don’t we just need to match the As with Us and the Gs with Cs until the molecule is folded correctly? Well, it depends.

While some RNAs can be folded pretty easily that way, many do not have equal numbers of As, Gs, Cs, and Us and need to double back on themselves to reach their bonding partners. And that’s where the fun begins. RNA can perform a dizzying array of molecular acrobatics to reach its favored (lowest-energy) conformation. It is the player’s job to figure out how to utilize these properties of RNA to consistently make unique shapes.

Perhaps the coolest part about this project is that the structures players create online for a given RNA are actually then synthesized in the laboratory, to see if nature agrees with their intuition. The laboratory results are published online, so players can see the discrepancies, if any, between their computer models and the real deal, and allows developers to modify the computers to work more like nature.

EteRNA is just another example of crowdsourcing science. During my hunt for the game, I stumbled upon others such as Phylo, Eyewire, and Galaxy Zoo, which utilize the human mind to solve puzzles in genetics, protein biology, and astronomy, respectively. I highly suggest you all check them out, because it seems like crowdsourcing science is the new hot thing.

(1) http://www.nytimes.com/2011/01/11/science/11rna.html?_r=0

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One Response to Blog Post #2: Crowdsourcing in Scientific Research – It’s Not Just Foldit

  1. cstabile says:

    Thanks for your comments on crowdsourcing science and the post to the NYT article — which raised a host of issues about crowdsourcing science. For example, Markoff (NYT science and technology writer and author of the piece on Foldit as well) cites two competing views that are perhaps worth returning to in class: 1. that games like these are democratizing science, 2. that games like these are exploiting what one sociologist calls “a cognitive surplus.” The first claim is hugely inflated — how is RNA research democratized by outsourcing solving problems that have been established elsewhere? The second contains an important issue that we discussed a bit in class: is outsourcing this labor to amateurs exploitative? This is perhaps more obvious in the case of videogames, where players and fans create code and content that is then monetized by game developers and publishers.

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