Surprisingly often, scientific researchers make what (eventually, perhaps after decades) turn out to be bad assumptions. They simplify a vexing problem in order to investigate it with the available tools, and then assume that what they’ve learned describes what happens in the real world, forgetting that they began by making a simplifying assumption.

Right now I’m reading Microcosm, a wonderful layman’s science book about the bacterium E. coli. You may not know much about E. coli, but they know quite a lot about you, at least in a vague, utilitarian way, because billions of them are living in your intestines right now.

E. coli has been quite extensively studied in the laboratory. It’s right up there with mice and fruit flies as one of the favorite organisms used in research. But research can’t be done in your intestines. On p. 51, the author (Carl Zimmer) says this:

“Out of the 4,288 genes scientists have identified in E. coli … only 303 appear to be essential for its growth in a laboratory. That does not mean the other 3,985 genes are all useless. Many help E. coli survive in the crowded ecosystem of the human gut, where a thousand species of microbes compete for food.”

But I’m not here today to meditate on intestinal parasites (though that’s a topic worth meditating on). I’m a lot more interested in what happens inside of E. coli. The little critter is a jam-packed protein circus! Large molecules are whizzing around carrying out amazingly intricate and sophisticated tasks. Each type of molecule has a shape that allows it to do one specific thing (or perhaps a few related things) — but molecules quite obviously don’t “do” anything. They’re inert. They’re just bouncing around inside of E. coli, jostled by the random motion of all of the nearby molecules, and when a given protein just happens to bump into another molecule with a matching shape, the two do a little tango that changes one or both of them. The protein catalyzes a chemical reaction. And the sum total of those randomly initiated reactions is, the bacterium is alive.

Did you see the simplifying assumption in that last paragraph? It implicitly assumes that molecules are sort of like those little models that we all experimented with in chemistry class back in high school, made of sticks and colored balls. A molecule, it’s assumed, is sort of like a wired-up collection of billiard balls. They bounce off of one another. This happens quite rapidly, so there are a lot of collisions, and a few of the collisions turn out to be useful to E. coli.

The billiard ball model of atoms and molecules is a radical oversimplification. Atoms, physicists assure us, are actually fuzzy. An atom’s electron “shell” isn’t a shell at all; it’s more like a cloud. And the cloud can be described only probabilistically. It’s not possible for us to say with certainty where any given electron is. There’s a small but finite probability that a given electron in a given E. coli in your intestines right now isn’t inside of that bacterium at all. That electron might be in your foot. In some sense, it is in your foot, because in some sense it’s just a cloud of probable interactions. An electron is not a billiard ball either.

It’s known that the ball-and-stick model of large molecules is flawed. They aren’t rigid. They’re constantly flexing, stretching, wriggling. And their electrons aren’t necessarily staying in the neighborhood of the protons and neutrons. The electrons in a given molecule are sort of flowing around the interior of the bacterium, in a fuzzy dance.

Recent research suggests that colonies of bacteria may communicate with one another, in a vague, sleepy way, using tiny flashes of light. Do you suppose it’s possible that large protein molecules could do the same thing? All a photon is, is an electron changing its state. Complex molecules are quite likely festooned with electrons that are constantly changing their state, emitting and absorbing photons.

What occurred to me last night — and this is an original insight on my part, but scientists may have known it for years, I just haven’t read about it — or, on the other hand, I could be entirely wrong — is that in some sense a protein molecule can sense the shapes of other nearby molecules, even when they’re not actually bumping into one another. Because, remember, “bumping into” is an oversimplification. Several other molecules, or dozens of them, might be floating around between Protein Gus and its designated target on the DNA, the cell membrane, or whatever it’s fitted to. And yet Protein Gus might be drawn through the molecular soup toward its intended destination, either because the two are exchanging photons or for some other reason. The protein’s affinity for that destination might be strong enough to affect its wriggling and twitching so as to cause it to move in a direction that will turn out to be useful to E. coli.

To put the matter more succinctly, in some sense a large protein molecule may be alive.

This is heresy, of course. Everybody knows molecules aren’t alive. They’re inert. They’re just little wired-up collections of billiard balls, nothing more. Trouble is, this view of molecules is arrived at through studying them in the laboratory. And laboratory researchers use simplifying assumptions in order to be able to investigate problems using the equipment they have. Quite a lot of what we know about how elementary particles behave, we know from smashing them together at very high speeds. How they may behave in the interior of E. coli we really don’t know, because there’s no easy way to investigate that. Trying to draw sensible conclusions from the behavior of particles in a particle accelerator is a little like trying to investigate how prairie dogs behave in their underground warrens by capturing a bunch of them, putting them in a furnace, and then picking through the charred bones.

To a man with a furnace, the whole world looks like charred bones.

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