The Futile Cycle

I went to a talk a few weeks ago that absolutely floored me. The science was amazing, the presenter was astonishingly clear, and the whole package of the presentation was stunning.

It made me want to do biophysics.

(Of course, that wore off after about a day…only Steve Jobs has an infinitely persistent Reality Distortion Field). The talk was by Suckjoon Jun, who has a heavy Korean accent, but is still by far one of the best speakers I’ve ever seen. He beats the pants off of pretty much any native English speakers I know of.

In any case, the talk was called, “How Entropy Can Save Bacteria.” The idea is, once again, that everything you learned in high school was wrong (about bacterial replication). The classical model — which is taught in high schools and a lot of colleges — for how bacteria separate their chromosomes when they split into two cells is that the chromosomes attach to the cell wall, and as the cell wall lengthens, the two chromosomes slooooooooowly get pulled apart. Very very slowly.

This is wrong, of course. If you look at any part of the bacterial chromosome, especially the origin, you can see that the two replicated origins separate from each other at a very fast rate, much faster than the rate of growth of bacteria. This is really easy to see in Caulobacter crescentus, a banana-shaped bacterium which has its origin of replication stuck at one end. When the chromosome replicates, the new origin quickly gets pulled to the other end of the cell.

This paper basically sums up Suckjoon’s position. The idea is that entropy will physically separate the chromosomes into little balled-up tangles, because that gives each atom in the DNA the most freedom to move around. The cell then divides in the middle, and each daughter cell ends up with a nucleoid. Amazing!

The problem, of course, is that bacteria sometimes have a few really small chromosomes, called “plasmids,” and these aren’t separated so well by entropy, as Suckjoon’s mathematics showed. But there’s a solution! These are separated by the bacterial cytoskeleton (another thing not often taught about in high school and college), which was discovered only half a decade ago or so. Very cool! Now there’s a good evolutionary pressure that would explain the two different bacterial systems for separating chromosomes!

This is the kind of biophysics that’s exciting, combining evolutionary theory, questions about important biological systems, and theories that propose further experiments that people would actually care about.

Since I’m right at the start of my Ph.D. training, I’m looking for anything that’ll reduce my stumbling blocks ahead. This article on maxims to survive by is more oriented towards physicists, but is quite applicable to almost any field, including biology.

I particularly like this maxim:

Don’t make your equipment better than it needs to be. “The best piece of scientific apparatus is one that falls apart the day after you finish using it.”

I’m currently using a flow-cell that’s made of a glass slide, some scotch tape, nail polish, and a sheet of tissue paper. I could conceivably use epoxy and a syringe pump to construct a more robust, more controlled flow cell, but what’s the point? I only needed the flow cell for one experiment, and I’m doing cell biology with non-synchronized cells, which means that there’s too much noise to do anything more precise anyway. I feel like half of science is done with patched up equipment that falls apart right after that grad student or post-doc leaves.

I also used to think that people who used kits were sissies. “Just” do a phenol extraction! But really, kits are good enough. Who wants to troubleshoot a purification step if it doesn’t lead to a paper?

I installed Leopard this past week.

The pictures of Leopard boxes don’t really do it justice. There’s a weird hologram-ish thing in the background of the “X” that makes it look like it’s floating in the middle of space. No really, go check out a box in a computer store (or an Apple Store). It’s pretty nifty.

Overall, I like it a lot! Spotlight and the Finder are considerably more snappy, which is always a great quality of life improvement (yes, it’s sad, much of my life is spent on my computer). QuickLook is excellent. Spring-Loaded Dock folders are also very useful. The new ability to create Dashboard widgets from Safari is quite handy; I’ve set up weather.com and PhD comics widgets. I don’t know what else I’d use it for, though. On the programming side, I’m looking forward to automatic memory management in Objective-C.

I’m not bothered by the UI changes as much as other people seem to be. I don’t like high-contrast backgrounds anyway, so the transparent menu bar isn’t a problem, and I’m just not nit-picky enough about the dock to worry about the angle it’s at. On the other hand, I’m having trouble getting used to the over-saturated colors on little bits of the system (like the menu highlight color), and the rounded corners on everything. It’s still jarring to me that my top menu-bar isn’t white, or at least grey; I keep thinking that I’ve engaged “Exposé.”

The UI change that bothers me most is that the icons in the “Stacks” on the bottom of my computer are pictures of the contents, which means that I have to move my mouse along to hunt for the correct folder, as rarely are the mismash of icons very informative.

A note to those who use DoubleCommand and Logitech software: installing Leopard will cause problems. Logitech’s programmers have decided to try to hack OS X in ways Apple has explicitely told them not to in order to make their hardware work, instead of writing proper drivers. DoubleCommand, for some reason, causes hangups of the system during shutdown, so I’ve had to manually go through and remove every trace of it.

Confused about what the EMBL database is? What about MGD, MTB, or SNPSTR? Maybe you’re intrigued by TIGRFAM, U12DB, or VNTRDB? Do you find KNDBSPRAL frustrating?

Ok, I made that last one up. But seriously, there are a ton of biology databases these days, and I find it hard to wrap my mind around all of them. This issue of Nucleic Acids Research is pretty helpful as a starting point, though. There are some obscure databases on there, too, but they hit several of the major ones. And every article in the issue is open access!

Scientific Misconduct Blog has an excellent graph from the literature, and a wonderful rebuttal. Alas, I doubt such things would be published in this too-serious era.

You know a paper is too long when it’s a 14 page Cell paper, and it still has 23 supplemental figures, supplemental results and experimental procedures, and three extra tables.

(For the non-biologists, Cell is known for very long, in-depth papers, as compared to the absurdly short Nature and Science papers. Cell and its related journals are the bane of all biology students that are assigned reading from the primary literature.)

It’s 12 hours till I finish writing my NSF fellowship application, reading two for tomorrow’s class, and analyze my data for tomorrow’s group meeting. I’ve got a full cup of coffee, half a bag of chocolate, it’s dark, and I’m wearing sunglasses.

Hit it.

This past week was “Fall Break”, which I’d not experienced until now (my college had no such things…). My department likes to ease first years into the flow of things by massive bribery with tons of free food at colloquiums, talks, and events for the first years.

Unfortunately, that all went away during fall break, such that I was left to my own devices. My supply of ramen was non-existent (I know, should have planned better), so I had to look elsewhere. And, lacking a car and a kitchen, ’twas slim pickin’s.

So when the dining halls reopened here, my reaction was rather like this:

I use Papers to organize all of my, well, papers. I read a lot of journals regularly, because I have a lot of interests; without a good workflow, I’d get buried under a pile of PDFs (admittedly, not that heavy, but >1,000 PDFs is hard to manage, no matter what the organization folder system).

The new version is much better. It integrates with more search services, such as Google Scholar, Scopus, and Web of Science, and the organization system just got a lot easier. The search integration with Spotlight is much snappier now, there is now even better BiBTeX integration, and lots of bugs seem to have been fixed, as it hasn’t crashed for me yet. There are still some small nitpicky issues (like not being able to specify a Smart Collection that gathers all papers imported in the last month), but overall this is a much more stable and useable release. Worth the price, especially with the student discount!