wicked smaht

What's the fastest computer on Earth? Blue Gene? ASCI Q? The Earth Simulator? Your Compaq running Vista?

Technically speaking, while the latest supercomputers are unmatched in number-crunching ability (try calculating an exaflops), the most powerful processors are biological. Your brain can process more things simultaneously than can the best computer. For all their power, the Blue Genes of the world can't simultaneously drive a car while translating English to Portuguese over the phone, evaluating the age of a french fry found in the back seat by taste and texture, predicting the weather by looking at the sky, worrying about question 4 on the last Mammalogy exam and thinking about an itch on its butt.

Your brain, however, can. (The french fry is two weeks old. Take it out of your mouth.)

It'll be a while before a silicon computer can function as well as a human brain, but in the mean time, scientists have begun developing a computer that can potentially process information exponentially faster than anything we can build. How much will it cost? A spoonful of sugar.

Researchers (in this case, a few professors and undergrads at Davidson College) have recently developed a new method for computation, using E. coli bacteria. Instead of having one giant computer with lots of little circuits and chips calculating every possible solution to a given problem, each bacterium serves as an individual processor, calculating a portion of the problem individually. Since E. coli can grow practically anywhere (you have billions in your intestines and they help you digest your food) and the generation time is short (15-20 minutes for laboratory strains), you can grow your own supercomputer in a matter of days.

It works by taking a protein called flagellin from Salmonella and introducing it into the E. coli. In Salmonella, flagellin serves as a structural protein for the flagellum (in other words, it is the framework for the whip-like tail). Mammals can develop an immune response to these proteins, so the bacteria usually have several different genes which code for different types of flagellin to evade detection. When these genes are introduced into E. coli, they serve as an "on/off" switch. The bacterium is used to compute a problem by flipping segments of its DNA, and if it solves it correctly, the genes are activated for the protein that the antibiotic doesn't recognize, and the bacterium lives. If it can't solve the problem, the bacterium dies [there's some motivation for you].

In this case, the problem being solved is the classic burnt pancake problem, where a stack of pancakes, each with one side burned, must be sorted by a series of flips so that they are stacked according to size with the burnt side down. The number of combinations of flips increases exponentially with the number of pancakes, and so far the bacteria have only been able to sort out a stack of two pancakes. This may not seem that impressive, but the potential for this technology, once more developed, is huge, and just may allow us to grow our computers instead of mining them.

Once again, Biology rules. ;-)


For an interesting interactive video on how these bacterial computers work, check out:

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