Friday, November 30, 2007

Extreme Gene Transfer and Speciation, Part I

This is a bit off the topic of protein folding, but I feel it's an extremely important topic to think about, if you work in molecular biology.

Think of how you would explain the following riddle.

If you go in your back yard with a spoon and dig up a spoonful of topsoil, I can virtually guarantee that you will be able to find Pseudomonas aeruginosa somewhere in that soil sample.

I can do the same thing. My back yard has (some) topsoil, and I' m sure it contains Pseudomonas aeruginosa.

As it turns out, I live in Connecticut, about an hour from New York City. But if I go to any grassy area of Central Park and dig down an inch or two into the topsoil, I'm confident I will be able to find our good friend Pseudomonas aeruginosa.

Bear in mind, on a bacterial scale, my back yard is about as far from Central Park as Earth is from Venus.

Now then. If I travel 10,000 miles to Sydney, Australia, I will find topsoil there, too, and in the topsoil I am quite confident that I can (once again) find Pseudomonas aeruginosa. This time, on a bacterial scale, I have done the equivalent of traveling something like ten solar-system diameters.

One might ask how it is that an organism of Pseudomonas aeruginosa's size and limited ability to travel could possibly be found over such a wide area (encompassing my back yard in Connecticut, Central Park in Manhattan, and somebody's back yard is Sydney). True, Pseudomonas aeruginosa has a flagellum. But I don't think a flagellum helps, it this case.

Someone can say, "Well, you can explain the widespread distribution of Pseudomonas aeruginosa by the physical transport of dirt through the air, or by birds carrying the organism on their claws." This kind of answer is, if not particularly satisfying, at least within the bounds of plausibility.

But it gets more complex. If I dig through the topsoil in my back yard (or in Central Park, or in someone's back yard in Sydney), I will find not just Pseudomonas aeruginosa, but Clostridium tetani. The "wind-borne dust" and "travel-by-bird" theories suddenly aren't as plausible. Clostridium tetani is a strict anaerobe. Exposure to air kills it.

"Well," the dust/bird advocate will argue, "Clostridium tetani forms spores, and the spores can survive a journey like that."

So far, so good.

But now it gets harder. About a hundred meters from my house, there's a freshwater stream that leads to a large pond. If you dig a couple meters down in the mud at the bottom of that pond, you'll find various species of Methanobacterium. These are non-motile, non-spore-forming strict anaerobes that are killed immediately upon exposure to oxygen, and they grow only in deep sediments.

If I go to Linchuan, China (a remote village with many freshwater ponds) and dig down into the sedimentary mud at the bottom of a pond, I will find some of the same species of Methanobacterium. How did they get there?

We can (but won't) carry this sort of argument on, to include organisms that grow in deep igneous rock acquifers; thermophiles found inside rock in miles-deep mineshafts; and so on.

How did these species (many of which either have no plausible means of transport across large distance, or would be killed by transport) become widely distributed?

(to be continued)

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