Science Wednesday: Instrumentation and Insight

I’m not a big fan of second-guessing the ancients’ perception of natural events. People in earlier times didn’t have incorrect ideas of what the world was like because they were ignorant — let alone stupid. Generally, their ideas were pretty much in line with the phenomena they saw, given the quality of the instrumentation they had to measure those phenomena.*

Case in point: Archaeologists have (re)discovered the gates of Hell. The literal gates of Hell. Quite frankly, even knowing all about carbon dioxide and other toxic gases emerging from volcanic caves, it’s hard not to side with the ancients on this one. You watch birds dropping dead at the entrance of an opening into the bowels of the earth, given no volcanology (the word hadn’t been invented yet), no chemistry, no physiology. Of course you’re going to build a temple and bring sacrificial animals (carefully) to the gate, saying, “Please not me, not yet.”

Which is all by way of saying that these things look pretty clear with a couple thousand years of hindsight. And if you improve the instrumentation, you improve your perception.

I’m looking forward to talking next week with Elia Zomot and Ivet Bahar at Pitt about their paper from last month showing how a molecular door in nerve cell membranes uses the relatively high concentration of sodium ions outside the cell to drive neurotransmitters inside. Kind of like an oshiya in the Tokyo subway, cramming commuters into a car. Important, because getting rid of the transmitters in the junction between nerve cells helps turn off neural signals when they’re no longer needed. That process may be faulty in conditions like epilepsy, ischemia and other stroke-associated causes of nerve damage, and Huntington’s disease.

For this task, the researchers used Anton, a PSC resource from D. E. Shaw Research that specializes in simulating the motions of all the atoms in large biomolecules. Anton allowed them to run an electronic model of the door, a protein called an aspartate transporter. First as it opened to the outside to pick up an aspartate molecule, and then as its components pivoted, clothespin-like, to release it inside the cell.

Clothespin-0157e3

Fair-use image from Wikimedia Commons, http://commons.wikimedia.org/wiki/File:Clothespin-0157e3.jpg.

Their model spanned multiple microseconds. That’s a long stretch of time in molecular dynamics. It also would have been a major computational challenge as recently as three years ago, before a D. E. Shaw Research grant made PSC’s Anton the first of its kind available to researchers outside the company.

Based on what I glean from the paper, the “old,” static images of the transporter that we had from previous crystallographic experiments had given the impression that the door opens differently than the Anton calculations show that it has to move. A subtle correction, but one that could pay off in addressing neural damage in a number of diseases.

Our own Markus Dittrich, director of the National Resource for Biomedical SuperComputing at PSC, tells me that Anton can run these kinds of simulations about 100 times faster than anything else out there. Anton handles microsecond-scale simlations with relative ease, offering even glimpses into millisecond timeframes. By comparison, the brain can perceive auditory events as short as about 10 milliseconds.

That’s amazing, even if it isn’t quite as profound a transformation as explaining cave-entrance deaths as a phenomenon of carbon dioxide poisoning rather than of the miasma arising from the land of Death. But then, they had over 600 times as long to work on the problem.

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* I’m not counting the pre-Galilean notion that heavier objects fall faster than light objects. Then as now, people can hold wrong ideas about things they haven’t bothered to measure.

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