Colloquium today reminded me of coffee and doughnuts -- this time it was outside of its trivial context.

It wasn't exactly novel to me last year about this time when it was explained to me (although it was deliciously stimulating) but coffee cups and doughnuts have a lot in common topologically. It's easiest to start with the coffee cup (a normal one with the usual handle): imagine it's made of play dough. One -- you, perhaps -- can start pushing down at the lip of the cup portion, molding it so that eventually it resembles something that can no longer hold coffee. This exercise can further be extended to this new object, pushing the flattened portion of the cup slowly, but carefully into what used to be the handle, but is now conveniently (suddenly? magically?) looking more and more like a taurus. A few moments, and a couple of gentle pushes of the clay later, you may have shaped something that looks -- albeit remotely -- like something resembling a play dough doughnut.

Do not attempt to eat this object.

This process, not surprisingly, is called a deformation, and mod it, a lot of things look alike. Needles (but not pins), represent donuts; Coke bottles look a hell of a lot like sheets of paper; straight lines look a hell of a lot like parabolas -- note, NOT hyperbolas. Indeed, all those two-dimensional shapes you probably played with as a tot begin to look a lot like circles, and the three-dimensional ones begin to look like speheres, but remember, spheres aren't the same as doughnuts. So much for kindergarten.

Those of you who aren't willing to let go of such fond memories will argue that this seems a lot like a reductio ad absurdum, and despite how hard I wish it weren't, it really is -- so why mention this? Mathematically, it turns out to be fairly useful to magick any object into your favorite one that has the same topology (e.g., your textbook into a full martini glass, and your pencil into a pick with two pimiento stuffed green olives*). I'd be lying to you if I were to tell you I could delve deeper into the exact reasons why, but here's where things begin to get a little fuzzy*. However, that's really not why I bring this up.

A large part of today's colloquium was about an RNA. RNA's, as many people can attest to, are neat molecules. RNA's are really cool in single-stranded form**, and a lot of this coolness comes from its ability to fold back on itself, base-pairing with itself. The speaker posited (not unreasonably, I might add) that it was precisely this ability of the RNA to fold back on itself that was integral to its functionality -- that when the complementary base-pairing sequences were on the same strand of RNA (i.e., in cis with respect to each other), the RNA was functional, presumably because it stalled the ribosomes that are translating it*** by folding back on itself. Again, given his data, this is not unreasonable.

The coffee and doughnuts part comes next: during questions, C--, a fellow first year graduate student, asked if this inhibition worked if the base-pairing portion of RNA was expressed in trans -- i.e., separately from the RNA strand itself.

I should explain: imagine the RNA as a piece of red yarn which is yellow at both ends (this time, they're cis to one another, your thumb and index fingers, the ribosome complex. Pretend now that you glue the yellow portions of the yarn together. As long as your thumb and forefinger are on the red portion of the yarn prior to gluing, you can trace the yarn with your fingers until you come to the glued portion, at which point you've got to deal with two strands instead of one. You find your ribosome stuck.

C--'s question asked the following. Suppose that instead of two yellow portions at either end, there are now two pieces of yarn. Your red yarn has only one yellow portion at the end, and the other piece of yarn is the same size an color as the yellow bit on the end of the red yarn -- the yellow pieces of yarn are said to be in trans with respect to one another. Now glue the yellow pieces together, and ask if your fingers can trace over both the red and the "double stranded" yellow portion. You can come up with your own scenarios, and the speaker had already tested this possibility and come to his own conclusions. But this is not what made me think of coffee and doughnuts.

The beauty (and really, simplicity) of C--'s question is that he changed topologies on the speaker. C-- could have asked, of course, "What happens if we make the intervening sequence longer?" -- i.e., what would happen if we made the red yarn longer. It's not as interesting a question -- you'd have to test it experimentally, of course, but one would expect that things, for the most part, would stay the same. But what happens if you change the topology? What a bodacious thing to ask. What happens if you replace one piece of yarn with the topologically different (in some ubiquitous sense of the words) two pieces of yarn? As you can already begin to see from the shreds of yarn and glue you (presumably) have in front of you, things have the potential to get much hairier, and -- as with too many things -- gives me the opportunity to bring things back to what really matters: coffee and doughnuts.

*Martinis, I've recently learned, are bliss.
**A primer: DNA usually has two strands that are base-paired through the nucleotides -- A's to T's, G's to C's. It's these two strands turn and turn around a hypothetical central axis into the double helix of Watson-Crick fame. RNA tends to be lonlier: it's usually found in only one strand, and doesn't have the usual double-helix structure DNA does. However, it IS able to fold back on itself, and base pair with itself: A's to U's (remember RNA has U's instead of T's), and G's to C's.
***Another primer: ribosomes are (essentially) RNA-protein hybrids that translate single-stranded RNA into protein.

Last Sunday, April 24, was the official 90th anniversary of the Armenian genocide. For those who might not know of it, sometime between 1915 and 1917 a large number of Armenians were killed by the Ottoman Empire. Because modern day Turkey doesn't officially recognize the actions of its antecedent state, Armenians everywhere troop out in force to protest annually.

I'm sure the genocide happened, whatever the more extreme Turkish apologists say. Too many branches of my family tree mysteriously end in the years in question for anything else to be true - only one of my grandparents had parents of their own while growing up. But I've always strongly opposed the Armenian obsession with the "slaughter", as we call it internally. As I once tried to explain to some fanatics marching around in front of the Turkish embassy in Paris chanting "Turquie, Assasin!", remarkably little of any use to us (if indeed there is some sort of racial us) would happen if the current Turkish government apologized for the actions of its barbaric ancestors. Such grovelling might have been useful in the immediate aftermath of the great disaster, but insisting on "justice" 90 years on seems to me excessive. Indeed, my view is that the whole genocide thing has become a crutch Armenians have apparently decided to use to excuse a whole range of bizarre infirmities common to many armenians. Furthermore, with Sasha Volokh, I do not believe there is anything distinctive about killing 1.5 million of this race rather than the same number of some other, random people. Fiendish evil is fiendish evil - even if someone interested in rational discussion wouldn't say this to most armenians.

In any case, I'm mostly writing to point out that the appalling French left has proposed speech restrictions on denial of the Armenian genocide, to go with equally appalling restrictions on denial of the Holocaust. Clearly, Francois Hollande, socialist leader, wants to cash in on the relatively large French armenian vote in the next election. And armenians being obsessed with the issue, I suspect he's got his wish. But speaking for myself, I just wanted to note that no democrat has anything to fear from mere speech, however distressing. And thankfully, the first amendment's framers apparently agreed.

UPDATE: Just on the last point, I should say that I find it extremely strange that exceptionally wrong speech is what's usually banned. But exceptionally wrong speech, like holocaust or genocide denial, is the easiest to rebut. Wouldn't ir make more sense, from the speech prohibitionist's point of view, to ban wrong but plausible speech?

In A Lonely Place: I think it was because of Terry Teachout that I watched this movie, but halfway through it was hard to believe that this movie had existed for fifty years but I had failed to find it until now. The first half of the movie is something like The Stranger meets The Maltese Falcon; the second half is Out Of The Past meets Othello. Casablanca is still better (contra Teachout) but I can't think of another Bogart movie that is.

I have spent a lot of time lately tangling with a friend about unions, and trying to explain why a libertarian might still be general skeptical of the modern phenomenon of unionization (at, for example, Yale). F. A. Hayek seems to have grasped some of the trouble, although he goes much further in his opposition to unions than I would. Still, this is from Chapter 18 of The Constitution of Liberty:

Public policy concerning labor unions has, in little more than a century, moved from one extreme to the other. From a state in which little the unions could do was legal if they were not prohibited altogether, we have now reached a state where they have become uniquely privileged institutions to which the general rules of law do not apply. They have become the only important instance in which governments signally fail in their prime function-- the prevention of coercion and violence.

This development has been greatly assisted by the fact that unions were at first able to appeal to the general principles of liberty and then retain the support of the liberals long after all discrimination against them had ceased and they had aquired exceptional privileges. In few other areas are progressives so little willing to consider the reasonableness of any particular measure but generally ask only whether it is "for or against unions" or, as it is usually put, "for or against labor." Yet the briefest glance at the history of the unions should sugest that the reasonable position must lie somewhere between the extremes which mark their evolution.

Most people, however, have so little realization of what has happened that they still support the aspirations of the unions in the belief that they are struggling for "freedom of association," when this term has in fact lost its meaning and the real issue has become the freedom of the individual to join or not to join a union. The existing confusion is due in part to the rapidity with which the character of the problem has changed; in many countries voluntary associations of workers had only just become legal when they began to use coercion to force unwilling workers into membership and to keep non-members out of employment.