Sunday, February 3, 2008

Noise and Fluctuation

Remember The Inner Life of a Cell? I've mentioned it before. Every time I see it, I think that the molecules seem a bit too anthropomorphic for my taste; they're all running around very purposefully and directly. Does anything about that strike you as being strange? It does me.

It strikes PZ Myers as being strange, too. He recently wrote a criticism of this video that captures very well the essence of its nonphysicality.

The feature that's missing from the video is noise. Every molecule in this video should be moving randomly at each moment, but with an average motion in some particular direction. I think PZ gets it right when he says,

For purposes of drama and minimizing complexity and confusion, though, the animators of that video have stripped out one of the most essential properties of systems at that scale: noise, variability, and the stochastic nature of chemical interactions.
Not only can thermal or chemical fluctuations not be ignored, there is evidence that for some systems noise can be important (PDF) to their functions.

The reason I wanted to link this was to put up a cool animation of single-molecule-imaging of a protein binding to DNA and exhibiting stochastic motion. Sadly, I couldn't find it online—here's the reference, though. Instead I'll show an also-cool animation of a simulated actin fiber pushing an obstacle. Actin generates cellular motion, basically by converting thermal fluctuations into mechanical work. Each monomer is small and can sneak in under the fluctuating obstacle to make the actin fiber longer. Slowly, eventually, gradually things move in more or less the needed direction. It's awesome but overlooked by the Inner Life video. So enjoy this low-tech animation, pilfered from Anders Carlsson.