It appears to be Mahoney Time

This going to be a "cool things I learned in science class" post. You have been forewarned.


This morning in biochemistry class, our professor gave us the Willy Wonka factory tour of an enzyme known as ATP synthase*, which I will now recap even more briefly for your reading pleaure. Trust me, it will be quick and painless, and it's worth following the sci-talk to get to the coolness.

ATP synthase has two components, F1 and Fo.** F1 is a ring of three α-β subunit pairs, and the action happens right in between the two members of each couple. And what action is it? The conversion of ADP and free phosphate to ATP!

(If that doesn't mean anything to you, just think of it as the creation of high-energy fuel for the cell. Good news.)

Anyway, each α-β pair has three configurations - or moods, if you will: liking ADP, liking ATP, and liking nothing at all. They change mood based on the orientation of the γ stick. Don't worry about how it works. The γ stick spins around, pointing to each pair in turn, causing them to like ADP, then ATP, then nothing. This catalyzes the process of turning ADP to ATP and then letting it go.

But, in a Thomist vein (Lewis Thomas, that is, not Aquinas), we have to ask "What makes the γ stick spin?"

Well, that's where the Fo unit comes in. The Fo is a cylinder made up of α-helices, and the γ stick from the F1 sticks down into it like an axle into a gear. The actual dynamics of what happens were beyond the scope of our lecture, but suffice to say that there is a proton pump that that uses the proton gradient across the mitochondrial membrane to make the Fo unit spin. Think of it like a water wheel: because of pumps elsewhere in the membrane, there are a lot of protons outside, so when the Fo's channel opens, they all happily flow in. The Fo uses this current to power its spinning. As the Fo spins, it takes F1's γ crankshaft along with it, clacking the other end across the catalytic α-β pairs and driving the synthesis of ATP.

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If you don't see why this is cool at this point, I'm afraid you may not even see the coolness after I enthuse about it, but here goes:

ATP SYNTHASE IS LIKE A TINY MACHINE INSIDE YOUR CELLS!

Yes, an actual machine. With moving parts. How unbelievably cool is that? I'll tell you: it's very unbelievably cool.

As Julien Offray de La Mettrie wrote in his 1748 L'homme Machine, "The human body is a machine which winds its own springs." Though he was largely concerned with locating the soul in a mechanistic body, I think he would have been ecstatic to know about ATP synthase. Granted we would have had a lot of biology and chemistry to cover before he could even understand what was going on ("OK, so... humours? Right out. Now let's talk about cells...), but this little protein complex really is the perfect example of how mechanical our bodies really are. And because this is a machine involved in creating usable energy for the functioning of the rest of the cell, it's also a fantastic example of the body winding its own springs.



OK, that's enough swooning over science for now. The title of this post, in case you are wondering, is in tribute to the late Professor Mahoney of Princeton's history of science faculty. The man's enthusiasm for machines - and the reading thereof - left a fairly indelible mark on the minds of his pupils, and loomed large over all our explorations into the history of science.





Notes:
*"This is the machine that extracts the juice of the snozberries, and it's connected to the tubes full of luminiferous aether, but it's really rather complicated so don't worry about exactly how it all works. Just trust me, it works."
**That's "F one" and "F oh," not "F zero." The o stands for oligomycin, an antibiotic that poisons the Fo unit.

Making duchesses of draggle-tailed guttersnipes

A scientific wager to be adjudicated by the Royal Society? Oh, smashing good fun, chaps!

In short, "Prof Wolpert bets that the following will happen. Dr Sheldrake bets it will not: By May 1, 2029, given the genome of a fertilized egg of an animal or plant, we will be able to predict in at least one case all the details of the organism that develops from it, including any abnormalities." [Boing Boing, via Detritus].

I'm afraid the good Dr. Wolpert is doomed to lose. The whole scenario reminds me of an essay titled "An Earnest Proposal" by Lewis Thomas (in his collection Lives of a Cell), in which he proposes that, tied to the big red buttons of the world's thermonuclear arsenal, we have program that prevents their launch until we've entered every single detail of the structure of a single microorganism: Mixotricha paradoxa, an intestinal bacterium living inside the guts of Australian termites. This at first seems like a ludicrously minimal safeguard against nuclear holocaust, but the essay goes on to explain that M. paradoxa is really rather more complicated than one might expect. Its flagella are fully-formed spirochetes themselves, its cytoplasmic organelles are bacteria with enzymes that break down cellulose, and its centrioles are yet a third kind of unique creatures. Thomas imagines that, at the end of a decade of superpowers racing to collect the required information and, presumably, angrily growling at each other all the while, some hapless government scientist will finally input everything they've learned, only to receive the message: "Request more data. How are spirochetes attached? Do not fire!"

It's a charming essay, featuring Thomas' typically brilliant prose, but why do I bring it up here? Only to say that life is infinitely more complex than we tend to realize. I imagine that when 2029 rolls around, and the fine port is aged to delicious perfection, Dr. Wolpert will triumphantly present his genomic databanks and his predictive algorithms based on amino acid sequences, and Dr. Sheldrake will only need to find a single aspect left unexplained to win the case of Quinto.

Now, I happen to agree with Sheldrake on principle, too. I think that an organism's genes are the central determinant of the majority of its features, but that there are too many environmental factors involved in growth and development to comfortably state that nucleic acids are the be all and the end all in determination. Granted, a simple enough organism bred under strict laboratory controls may fit Wolpert's criteria-- in which case, I hope he enjoys his rich beverage.

I worry, too, about the implications of developing a paradigm of genetic determinism, as biology guided by such principles has the potential to be misused in some spectacularly errant ways. Being able to "blame it on the genes" could be a rather dangerous proposition for human beings in particular, as would, I believe, any model that permits us to take less responsibility for our own condition and actions. Not to say that we should shy away from the answers to these questions, any more than we should be blaming Darwin for Social Darwinism (or Nazism, as some wingnuts take great delight in doing). But we must, as ever, proceed with prudent acknowledgment of the possible repercussions of scientific research.