The Futile Cycle

One of the topics that came up at a “town hall” meeting between graduate students and the department faculty recently was how to increase attendance of the department seminars. There were some good insights, like “attendance at each seminar is inversely proportional to the frequency of seminars”, but really, was it that hard to miss the most compelling incentive to attend seminars? It seemed like 50 scientists just could not figure out!

Today’s Ph.D. comic summarizes:

One person spoke up and mentioned, in passing, “It always seems like more people come if you put out snacks.” The comment was mostly ignored, in favor of other speculation, like “what if you send out abstracts of the relevant papers beforehand?”

Hellooo! Feed them, they will come!

When I was in college, my biology friends would all mutter “ethidium bromide” in hushed tones, as if discussing the devil incarnate. It was the evil-but-necessary chemical, the mutagen that would cause dozens of cancerous masses all over your body with the slightest bit of contact. Meanwhile, I happily worked my hours away in a chemistry lab using pyrimidine, benzene, toluene, and plenty of more mutagenic stuff than that. Pansies.

But when I started working in biology, again, safety training indoctrination told me: Ethidium Bromide is hazardous stuff. Use a fume hood. Any spill must be cleaned immediately, and so on. It’s dangerous.

Well, apparently not. (via Life of a Lab Rat) Eh. Guess I shouldn’t worry so much that we heat our running buffers with EtBr already it in. I probably do worse things to my body by being lazy about sunscreen in the summer.

For my current lab research, I spend a substantial portion of my time filming and photographing sex — baker’s yeast mating, or pheromone-y, cytoplasm swapping, petri dish action, if you will. Take a look at this classic shot:

They’re finicky, shy little things. I have to go to a lot of work to make them comfortable. Not too hot, not too cold, just the right humidity, not too crowded, not hungry or too full. I hope they appreciate my efforts!

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 week I will most likely not be posting, mainly due to my taking my “Molecular Biology of Prokaryotes” exam. It reminds me of the theoretical mathematics class I took as an undergrad; most of my time was spent staring at an empty page, waiting for inspiration to hit (or as Douglas Adams puts it, “until your forehead bleeds”).

As one of the professors here said, “When I read through the midterm, it was not obvious to me how to solve the problems.”

A lot of science is done in little glass and plastic vials, mainly because there are some things that are just too hard or unethical to do in live organisms. We even have words for the distinction between science done in a test tube (”in vitro”) versus done in a living system (”in vivo”).The gold standard, of course, is “in vivo”. You want data in vivo, because, frankly, a test tube full of chemicals (even chemicals extracted from cells) isn’t a substitute for a real living system.But really, what is “in vivo” depends on your point of view. If you’re a chemist, throwing your favorite molecule on a bunch of cells in a Petri dish is probably “in vivo” for you; after all, there’s living stuff there. But if you’re a doctor, “in vivo” means “in an animal.” Cells in a plate is just “in vitro.”And in reality, whether “in vivo” is a gold standard isn’t that clear cut. Sure, eventually you wan to see whether something happens in an actual living system, but what if you want to test whether two molecules physically interact (we’re not talking regulation here)? Then the “gold standard” would be an “in vitro” assay (i.e. chemicals in a tube), since in a live cell, there’s all sorts of things that can really jiggle up the FRET, colocalization, yeast two-hybrid, ELISA, or whatever other test that biologists and chemists like to use in living systems. There’s too much other “junk” in a living cell to really tell for sure. So you have to do it in a test tube, where you can control all the conditions.Just a though, the next time someone sneers at an “in vitro” experiment. Just smile and tell them “in vitro” is the new gold standard!

After the first week of classes in graduate school, I’m a bit wrung out. I’ve taken graduate classes before, but not too many focused on paper-reading; the other classes had maybe two or three papers per week, but the current course I’m taking assigns two or three papers per class, which means around 10 hours of reading a week, assuming a little more than an hour per paper (we have to read them inside and out, understanding them in deep, experimental detail). With having around 6 or 7 seminar talks a week, two classes, and lab work to be done, and fellowships to write, I’m glad the weekend is here.

On the other hand, though, all the classwork means that I’ve been getting a lot of exposure to some very classic papers. The “fluctuation test” paper by Luria and Delbruck, for example, is from 1943, ten years before the structure of DNA was deciphered by Watson and Crick. Luria and Delbruck try to figure out whether bacteria become immune to viruses by mutations or because by chance some survive and acquire an immunity which is heritable, and they use some pretty clever math to do it.

The basic idea they use is that of the “jackpot”. Imagine that you’re playing a slot machine, and you win very rarely, but when you do, it’s a huge, huge payout: $100 million. Let’s say you pull the lever a million times, enough that you have some chance to actually win once or twice, but not enough that you’re sure to win. Now, let’s say that you have 20 people who all go to this machine and pull the lever a million times. Because one person might win three times, and another might not win at all, each person’s winnings will vary a huge amount from the others’. That’s the “jackpot” idea, that small differences get amplified a whole lot, because the payout is huge.

Now back to bacteria. There are two possible ideas, that bacteria all have a small chance of surviving the virus randomly, but that once they survive they’re immune (and pass that immunity on to their children), or that a small fraction of bacteria have a mutation that makes them immune, but most bacteria are susceptible.

The thing is, mutations are kind of like jackpots. If you start with one cell and it divides, acquiring mutations along the way, then in the early stages where there still aren’t that many cells, one cell might get a mutation. Since bacteria multiply quickly, that cell will then have lots of descendents that are also mutated, and so there’s a huge “payoff” for having an early mutation, because that change gets amplified. The number of mutations early on is random, so in two different experiments, there’s a good chance that the number of mutations you find in one is very different from the number in the other.

On the other hand, in the surviving and adapting viewpoint, there’s a low chance of surviving no matter how you go about it, and that characteristic doesn’t get amplified when bacteria have descendents. There’s no “jackpot” effect, and so the level of immune bacteria wouldn’t vary as much from experiment to experiment.

So, Luria and Delbruck did the experiment a lot of times. They took a small number of bacteria, grew them up, and tested them for immunity against a virus; and they saw the jackpot effect. Thus, mutations are the underlying cause for the resistance to virus. Bingo!

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.

Yesterday was the first day of orientation for the department, and today, I leave for a departmental retreat, wherein the first-year students get bashed over the head with tons of talks, plenty of poster sessions, free food, drinks, and lots of interaction with the professors, post-docs, and older graduate students.

During the retreat, I’ll also be thinking about this post from “GTD in Academia”, especially the comment about developing a toolkit. (It reminds me very much of the part of Surely You’re Joking, Mr. Feynman, where Feynman talks about his mathematical toolbox and differentiation under the integral sign.) The post focuses on ecology, but of course the advice is more general than that.

Develop a toolkit. You’re going to know how to design experiments and analyze data and think broadly and synthetically about ecology. But you should also develop a toolkit to distinguish yourself from all of the other ecologists who can do those things. Your toolkit might include modeling or null model analyses or genetic techniques or specialized statistics. Just make sure you have one, and make sure everyone knows what it is. MK–make yourself unique and indispensable part of the group.

So I keep wondering, what kind of toolbox can I develop? Even as I try to find a topic that I’m interested in during the retreat, and lab rotation choices, I’ll be thinking hard about that.

All of the professors that I’ve admired have their own little niche that they create with their unique expertise, their esoteric collection of abilities. Howard Berg, for example, is really good at machine-work, and so he was able to hand-make the parts needed for a 3D E. coli chemotaxis tracking microscope, which led to his great theoretical contributions to that field. David Evans is spectacularly good at dissecting molecules down to their basic, synthetically manageable parts, to make clever insights about reaction mechanisms via molecular orbital theory, and visualize asymmetric induction at a very sophisticated level in his head, allowing him to manage the beautiful, almost pedagogic syntheses of really complicated molecules. Martin Nowak is really good at paring away the complexity of a problem to get at the underlying mathematical structure and model, in order to gain very deep, and yet strangely simple and beautiful insight. They’re not expertises in the sense that they’re one-trick ponies; it’s more that they have some sort of edge on the competition that just allows them to break through and do the work better and faster.

I need to find my own toolbox to really succeed and do well. But what? I’m decent at math, programming, physics, chemistry, and biology, but not a big deal on any of it. No subject really scares me, though; I know I can learn more of anything if need be, so I have some help there. But what’ll be my edge? Finding that will be my goal this year. Jack-of-all-trades, master-of-none is not the way to succeed in grad school, I think. Still, until I find that straight-flush, lots of jacks aren’t that bad either…

By tips, I mean pipette tips. Alex Palazzo has an amazing data set on the order of pipette tip usage in his lab.