The Futile Cycle

There are some people around who say “nuke-ular” (as in, “NOOK-yoo-ler”) instead of the conventional (and correct) “nuclear” (”NOOK-lee-er”). I can accept that this is a relatively easy thing to fall into, since “nuke” is a fairly common slang word, and both words have something to do with nuclear power, nuclear weapons, and so on.

Today, a professor was giving an introductory lecture, and I was half-paying attention (I’d heard this part before). But wait, did she just say “nuke-ulotide”?? Yes, yes she did. Not “nucleotide” (NOOK-lee-oh-tide), but “nuke-ulotide” (NOOK-yoo-lo-tide). Since this was a bioinformatics course, I spent the rest of the lecture trying to stop the bleeding from my ears.

From Horowitz and Leupold (1951), “Some recent studies bearing on the one gene-one enzyme hypothesis”. Cold Spring Harbor Symposia on Quantitative Biology. 16, 65-74.

“[The proportion of indispensable functions] would seem almost by definition to be unknowable, in which case the one gene-one enzyme idea must be banished to the purgatory of untestable hypotheses, along with the proposition that a blue unicorn lives on the other side of the moon.”

Ten years later, of course, President Kennedy proposes that we go to the moon…

A paper came out in PNAS two days ago on a new ribozyme (that is, an “RNA enzyme”) that can (sort of) self-replicate and evolve!

Well, ok, it’s a bit more complicated than that. There is a certain kind of ribozyme that can attach itself to another RNA fragment of a particular sequence. The authors made this ribozyme into a version that attaches itself to a promoter, which allows its sequence to be read back and converted into DNA by reverse transcriptase. That DNA can then be read and converted back to RNA by an RNA polymerase, and the cycle continues. So, in a sense, replication (and thus evolution). Here’s a picture of the process from the paper (sorry about the small text…it’s the only way the figure will fit):

Now, this isn’t exactly new. Someone else has constructed a ribozyme that can do this. But now, there are two very different ribozymes that do similar things and replicate, so the coolest part is that now you can do “molecular ecology,” where the two RNA molecules compete with each other for resources! It’s a whole new kind of experimental evolution!

Via Terra Sigilata, the amount of diacetyl artificial butter flavoring in microwave popcorn is apparently high enough to destroy your lungs, in a syndrome called bronchiolitis obliterans. It’s been well known that the compound will destroy the lungs of workers in factories, but this is the first reported case of a consumer being affected. Now, this is one reported case in the past umpteen-year history of microwave popcorn, so the risks are probably very low, but still, beware savoring the smell of microwave popcorn.

This was an amusing press release, about using wine as a solvent for dissolving metals. I like this part of the press release:

The scientists tested red wine and a number of popular soft drinks. The effectiveness of the technique is unlikely to be affected by whether the wine is a shiraz or a malbec and diet soft drinks are just as effective as those containing sugar. Dr. Noble would also like to reassure taxpayers that the research was conducted in the scientists’ spare time. The research had the added benefit that none of the unused scientific solutions were wasted.

Via the Evilutionary Biologist, from the acknowledgements of this paper (PDF):

This manuscript has been improved substantially by the suggestions of C. Chang, B. D. Collier, C. F. Cooper…and two anonymous reviewers. Any errors that remain are their responsibility and theirs alone.

Wonderful!

I hadn’t heard this before, but comment 10 on this post was rather awesome.

The post is an interesting topic, too, about who’s the modern Asimov (in terms of science writing).

Today was the first working day of my first lab rotation.

A bit about the rotation system. Biology graduate schools tend to have a system in which, for the first year or so, graduate students formally try out a couple (usually three) different labs, doing miniprojects and getting a feel for the work and the people in each lab. It’s a great system, because it helps prevent gross personality mismatches between advisors, labs, and new graduate students (and having a good match with an advisor and his/her lab is probably the most important determinant of happiness in graduate school). In fact, I thought rotations were so obviously good that all fields did them, but surprisingly, they seem to be a relatively uncommon phenomenon. I know chemistry doesn’t do them, and apparently engineering doesn’t either. I assume physics doesn’t? Very strange. My professor was an engineering professor, and he hadn’t even heard of the rotation system. For me, I just can’t fathom joining a lab without rotations. With the advisor being such a make-or-break part of graduate school, rotations seem like such a essential part of the experience.

Anyway, this was my first time doing work in yeast, and really the first time in a while that I’ve done biology labwork (before, I did a lot of synthetic organic chemistry). And as I relearn things like sterile techniques, it reminds me of when I first learned about how to do chemistry without contamination from water or oxygen. It was essentially beginner’s jitters.

When I first started working in an organic chemistry lab, I was ultra-paranoid about having water ruin my reaction, or oxygen silently poisoning my transition metal catalysts. I concentrated very hard every time I had to transfer material from one flask to another (in a syringe, or with a metal-tube syphon), carefully checking and rechecking to make sure unreactive argon or nitrogen gas was protecting my chemicals from oxygen and water. But after some time, it just became second nature. I wasn’t as paranoid, because I became relatively confident about my experimental technique. I wasn’t less careful, but it didn’t require my consciously going through a mental checklist of what to do next (”flush the needle, take up the compound, suck in some argon, remove, stick the needle in before air gets through, stick the needle in!”). I just did it. I knew what would and would not contaminate my chemicals, and I didn’t have to worry as much.

But now I’m back with the beginner’s jitters, the paranoia of having my sterile solutions get contaminated by random bacteria or yeast getting blown around in the air. Every time I have to pipette something from one container to another, I get flustered and worried (”Did I hold the container open too long? Make sure I’m not touching anything. Close the cap, close the cap!”). But it’ll soon pass and become second nature, I expect, just as the dry and airless techniques I learned in chemistry soon became second nature.

But for the time being, I have beginner’s jitters, and a strange interesting feeling.

Nobel Intent has a wonderful post at Ars Technica that shows the difference between real science and pseudoscience by going through an issue of the journal Homeopathy and systematically destroying every article in it. It’s a six page post, and after a while, it gets repetitive (oh goody, yet another crank who doesn’t understand basic concepts in science), but there it is, a systematic deconstruction and refutation of almost every single article in that special issue. I’m amazed that the Nobel Intent authors had the patience to do something like this, but someone had to, to finally blow some reason into the minds of these strange “scientists” and the easily duped consumers.

The entire department went on a retreat this past weekend, which was a grueling but pretty wonderful experience. We have a rather large department (arond 50 labs, spread across vast swaths of biology, including microbiology, cell biology, development, neurology, virology, cancer research, metabolomics, mathematical biology, bioinformatics, systems biology, structural biology, biochemistry, infectious disease, and so on), so trying to get an idea of what’s going on here is a rather Herculean task; the retreat not only allows us first years to get a sense for all the labs and talk to faculty and older students, but it also allowed lots of grad students and professors to talk about research all day and form new collaborations. It almost seems like a third of all the research presented during the retreat was done in collaboration with another lab. It was a great thing to have almost as soon as I got to campus. I bonded with other grad students, met almost everyone in the department that was there, found other labs that were doing great research, and learned a heck of a lot of biology.

We invited a great guest speaker to the retreat as well, Charles Ofria, a computer scientist who researches the evolution of “digital organisms” — computer programs that can self replicate, compete, and mutate. He started off with the story of Core Wars, in which programmers wrote programs to fight each other for control of a computer, to Tierra, where programs could mutate and evolve, to his Avida system, which allowed Ofria to control and analyse almost any aspect of the evolution of the organisms. He was able to look at a large variety of theoretical problems, including the evolution of complex traits (e.g. critically examining the arguments of Behe’s “irreducible complexity”), fitness changes in a rugged landscape, and the ecology of programs in various systems. Fascinating stuff, really. I can see why he was hooked when he learned about Tierra; perhaps if I had learned about that really early in my life, I would have chosen a completely different intellectual path.

Anyway, after almost 15 hours of talks in two days, practically living on coffee the whole time, I’m a bit tired. Tomorrow, we get our first rotation assignments!