links for 2008-03-24
Daniel Froomkin Visits Bush's Alternate Reality

P. Z. Myers Has a Quibble with the Excellent "Inner Life of a Cell" Video

It has aroused his ire. From P.Z. Myers:

Pharyngula: Buffeted by the winds of chance: why a cell is like a casino: This is what bugs me about the "Inner Life of a Cell" video. They're portraying the behavior of single molecules, and the movie has them dancing a slow waltz, steadily moving through fixed patterns. It should look more like a mosh pit filled with meth addicts; real chemistry doesn't direct single molecules, it shifts overall equilibria so that the random activity of single cells has certain probabilities of throwing them off a thermodynamic cliff into a new state. Those kinesin "feet" [on the motor transporter molecule] should have been pitter-pattering all over the place, occasionally falling into a more stable position that led them in a particular direction -- what was needed was a portrayal of a hyperkinetic ratchet. Anyone who uses a microscope or looks at the activity of small numbers of molecules or studies thermodynamics and reaction equilibria (like, say, a chemist or biochemist) ought to be familiar with the stochastic properties of the world on such a small scale.

The closest example on a macro scale that I can think of is a casino. People go in and out of a casino, and they engage in many small probabilistic events. Some people win big, some lose big, and all states in between are represented... but the house always has its small, advantageous odds in its favor. They don't shake down the crowd deterministically and demand a cut from each, instead what they have done is basically tipped the the reaction equilibrium gently to favor the transfer from one state -- your pocket -- to another state -- their bank. From the aggregate kinetics of a great many transactions with only a tiny edge in one way, they have constructed a powerful and reliable siphon hose to draw off your money. (I suspect that's also one, perhaps unconscious, reason why gambling establishments are fanatical about keeping out people with even a hint of a successful gambling system; it doesn't take much of a shift in the percentages to reverse the flow in their money siphon.)

If you watch single individuals in the casino, rather than the rising total profits for the whole institution, you wouldn't see a smooth and steady drain of money, though. Over long periods of time the trend would appear, but moment-by-moment? No. You'd see a herky-jerky random pattern of wins and losses.

And that's what I would want to see portrayed in my ideal version of an animation of the chemistry inside a cell: not a ballet, a jostling mob on an uneven floor. Show me more noise and chaos.