The Futile Cycle

Since right now it’s both fellowship-writing and graduate school application season, I figured this was as good a time as any to post about this.

For those undergrads out there considering whether to enroll in a four-year combined Baccalaureate/Masters program, a word of advice: if you’re planning to try for a Ph.D. in the sciences later, the Masters may not be worth the hidden cost: you may lose a year of eligibility for applying to graduate fellowships during your Ph.D. program.

If you’re planning to do a Masters in, say, philosophy, and then you want to do chemistry for your Ph.D., then fine, no worries, get your M.A. and be joyful. On the other hand, if you plan to go do your Ph.D. in the same field as your Masters, it’s probably not worth it.

First of all, you’ll get a Masters in most Ph.D. programs after a year or so, regardless of whether or not you pass the qualifying exams. Secondly, your Masters work is sufficiently related to your Ph.D. work such that you may not be eligible to apply for many graduate fellowships—such as the NSF, DoD, or DoE fellowships—as a second-year Ph.D. student. Since getting the fellowships is a bit of a crapshoot, the extra year of eligibility in graduate school is quite helpful.

The main reason to get that Masters in chemistry (or whatever science) would probably be if you want to take time off before graduate school and get a job, in which case the Masters might come in handy (I’m assuming), and that advantage might outweigh your possible fellowships eligibility loss later on.

In any case, the choice ultimately comes down to personal factors, of course, but this is an often-overlooked factor when people consider the four-year Masters program in college.

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?

This PhD Comic hits too close to home, especially since I’m applying for an NSF fellowship right now. For the planned research summary, I have to supply keywords, background, detailed methodology, anticipated results, broader impacts, and citations and references all in two pages of 12 pt. Times New Roman font, with 1 inch margins.

But since I’m begging for money, I guess I can’t really complain too much. I’ve learned a lot of tricks for beating the page limit, though. Hyphenating long words at the ends of lines is really key; it can save you several lines of text. The most painful thing to include in the proposal is a citation to a book with a really long title, because there’s really no way to get around putting the entire title in the citation. The long title, however, almost always wraps the text to the next line, taking up two whole lines…

I was recently talking to a faculty member in my department who is working on recruiting underrepresented minority students to apply to graduate school. She mentioned that the NIH was really riding graduate schools (such as Harvard, Yale, and Stanford) hard to increase their ethnic diversity, since right now they’re mostly composed of whites and Asians.

At least in our department, the balance between men and women is pretty even, but the ethnic diversity is essentially nil. There are whites, Asians, and Asian-Americans. A few Southeast Asians round out the total. Almost no African-Americans (or Africans) that I’ve seen (maybe a post-doc somewhere?), maybe a few of Hispanic descent. No native Americans that I can recognize (though I often find it difficult to tell).

The Ivory Tower really is a sea of ivory faces.

But that’s apparently the way it is in all biology departments across the nation. The professor told me that across the nation, there were only 500 African-American applicants to graduate schools in biology programs. 500 in the entire nation. Looking at the ETS numbers, nearly 40,000 students taking the GREs in a year said they wanted to enroll in biology or biomedical research graduate school. Let’s say only 25,000 students actually applied to graduate school, to be conservative (that’s less than two thirds). African-Americans would make up only 2% of the student pool (and these are just applicants). There’s something definitely amiss with this situation.

That’s not something that can be fixed by the faculty at one university department or another. The government needs to do something, because this is a collective action problem. The NIH shouldn’t just pressure the graduate schools; they should throw money at the situation, if they really feel there’s a problem (and I think there is). Establish scholarships. I mean, with $10 million, they could establish 100 fellowships that fund at the level of the NSF or DOD fellowships, giving 3 years of a $30,000 stipend. Maybe they could even cut back the war spending 0.01% and use that money to provide 500 fellowships. The situation will be difficult to change for any one university; just putting the pressure on them will make them squabble over the 500 prospective students that are out there.

As everyone probably already knows, the 2007 Nobel Prize in Medicine or Physiology went to Mario Capecchi, Martin J. Evans, and Oliver Smithies for developing a way to create transgenic mice by targeting genes. Smithies and Capecchi developed the methodology for creating cells which had specific genes knocked out, while Evans developed a lot of the methodology for using these techniques in stem cells to create live mice that would carry these induced mutations. The knock-out mouse is now one of the most versatile models we have for testing questions about genes and diseases. A good explanation of the process that they developed is explained here.

I know a lot of people just skim the press release, but there are some really interesting nuggets in the “Advanced Information” section of the announcement. For example, Evans first tried to use cancer cells to make mice, but (as you would expect), the cells were just too sick to actually make a good organism. So he actually went through and found the cells the we now use as “Embryonic Stem Cells,” which he used to create mice that were a mosaic of cells of two different mice.

Another thing was that Capecchi and Evans both wrote grants proposing this research (on gene targeting) to the NIH and the UK Medical Research Council (respectively), but both were rejected, because the reviewers thought it would be too hard and unlikely to succeed!

Finally, though this isn’t mentioned on the Nobel website, Capecchi had a really hard life as a child. His mother was arrested and put away in a concentration camp during World War II (for being an anti-Fascist bohemian), and he was left alone for four years as a street urchin. Fortunately, he was later found (very sick and malnutritioned) by his mother (who survived). He moved to the US, went to school, then college, worked under Jim Watson at Harvard, and then went on to have a massively successful career (though, as I mentioned above, not without a few hiccups along that path as well). It’s an amazing life story, and the Nobel Prize surely can’t go to a better person.

Part of the problem with looking at a field like computational biology or systems biology (which I have some interest in) is that it’s hard to figure out how to narrow the field into one project that I can do for graduate school.

In synthetic organic chemistry, this was a relatively easy proposition. Pick a molecule, not too big, not too small, with interesting complexity, and make it. Then you’re done with your Ph.D. (course, this is much easier said than done). In traditional biochemistry, molecular biology, or cell biology, you’d focus on one protein, one pathway, one set of activities, one phenotype, and then figure out what they do, how they interact, what affects them, etc. When you generate enough publications and have a good, detailed story to tell about the systems, you’re done.

But computational biology feels like a whole ‘nother thing. It’s probably because I’m still not quite as familiar with that field, but it seems very methodological, more than anything else, and so it’s hard to find a particular angle to break down the problem and get a story out of it for a thesis. There’s not just one specific model system to work on, or one biochemical system that one can mine. At some point, it feels a little arbitrary, that you choose a system hoping that your hammer will find a nail you can hit; it could be that you choose wrong and just get screwed (I couldn’t help myself with that pun).

I remember reading about Eugene Shakhnovich’s work on protein folding, and he always had a particular angle to hit the topic with: his lattice folded proteins. One of the professors that I talked to at my new university tends to focus on bacterial chemotaxis. I need a good focus point by which to approach the field. Large-scale topics for data-mining, such as the ENCODE project, just seem too big for me to do as part of my Ph.D. project, and it would probably make my Ph.D. drag on and on in a way that would both make me depressed and make my work harder.

Perhaps I can find a particular algorithm to work on, if I decide to do a “big biology” sort of project. A particular technique, perhaps? I feel like doing a particular methodology is the only manageable way to approach “looking at systems-level behavior.” Otherwise, you’re relying on luck (pick a system and hope you can use your hammer). Because systems biology isn’t really a field, right? It’s just a methodology.

Maybe that’s why people like the reductionist mode of research so much? At least it’s easy to find a story to tell. I guess it’s a little like history. Everyone wants a handle, some sort of focal point. So you get focal points, like Alexander the Great, or Napolean. Even when studying social trends and situations, such as poverty and crime, you get the Italian Mafia, Tammany Hall, Five Points. Focal points.

So here I am, trying to wade through the literature and find a good focus.

From now until around May, I’ll be on the hunt for a Ph.D. advisor. Amusingly, I came across this Nature article on what makes good mentors at the same time that PhD comics had this strip:

Commencement was today, and I am now officially graduated, with an AB and AM in Chemistry and Chemical Biology, class of 2007! The last few days were very interesting, especially since the university made a whole-hearted attempt to make us feel the weight of the long train of tradition (perhaps for our future pocket cash?). I felt more of that this week than I had ever in the past four years, because of all the alumni coming back, the ceremonies and antiquated little quirks that made the university slightly weird (probably retained on purpose for distinguishment), and the gathering of the students together in Memorial Church for the Bachelor’s service that has (supposedly) been held every year for centuries.

Well, it’s been a long four years, but they were great ones. I loved learning from devoted professors, great peers, and having access to some of the great resources that make this university wonderful. Learning about NFkB from biologist Thomas Maniatis, studying organometallic chemistry and transition state structures from chemist David Evans, learning how to set up a sucrose gradient from biochemist Guido Guidotti, deriving wave mechanics with string theorist Cumran Vafa, analyzing bioethics with philosopher Michael Sandel, and learning how to build an economic model from economist Edward Glaeser – these are all wonderful experiences that I’ll take with me to graduate school and beyond. These people are a marvel to watch and learn from, and their infectious enthusiasm for the material that they study is one reason why I love science so much.

There is little that I truly regret about my undergraduate experience. Perhaps I could have worked harder in my coursework; maybe I could have made a few more friends and gone to a few more parties. Perhaps I could have been a bit more proactive with my research experience. I really should’ve taken my time drinking that white russian at my friend’s party. But, really, I thoroughly enjoyed my time here, and I think I learned a lot, not just about science, but about life and people. I built lasting friendships and relationships. That’s probably the most important thing I take away from here; after all, the education, though grand, probably isn’t qualitatively any better than other colleges and universities. Instead, it was the remarkable and unique collection of students and faculty that truly made my undergraduate experience memorable.

There has been a lot of back and forth recently on physics blogs about the tenure process, sparked by Rob Knop’s airing of his grievances on academia’s tenure system, specifically about the criteria by which it is awarded. Reading the comments on that post, as well as Mark Trodden’s response and Chad Orzel’s post, gives me the impression that the general consensus about tenure is that it is the worst process for evaluating professors, except for all the other possible ways.

From growing up the son of a professor, I get the impression that the academic system is most broken and at its worst when it is used to bludgeon junior professors into submission under the giant thumb of a particularly powerful and autocratic senior faculty member or cartel of senior faculty. In this case, the tenure process becomes politics-driven and full of fear-mongering; it’s then no surprise that it would exacerbate in-fighting and personality conflicts, increase racial and sexual discrimination or tension, and cause in faculty depression, stress, and general unhappiness.

This might be categorized under a larger umbrella of any situation in which the senior faculty (or just the department in general) treat the junior faculty as fodder, rather than as respected colleagues. My dad once told me about rumors of a high-level university hiring ten junior faculty to fill one tenure spot, which is just plain disrespectful.

I get the feeling that the situations in which the tenure process breaks are similar to the ways in which graduate school and post-docs can get broken: when professors treat their lab members as fodder and labor, rather than as valuable students or research associates under their mentorship. The lack of respect seems to be the main lynch-pin in all of this.