P.C. Shannon

Yesterday, you were reading the mad ramblings of a mere graduate student. Today, you are reading the mad ramblings of an official PhD candidate. Woohoo!

Unfortunately, I didn’t actually get any money. Doh!

I’m really quite pleased with this. A lot of my troubles in grad school have come from a lack of a clear plan, but now I have one. And it’s not just my own crazy, hare-brained ideas; it has actual faculty input. I feel like I should have done this a year ago. But then, who knows what my project would be or if that really would have avoided any of the turbulence of the last year. Certainly the genomes that are central to my project weren’t available then.

There comes a time in every grad student’s life when he must propose a dissertation topic, and that time is finally upon me. It has been astoundingly difficult for me to figure out exactly what is involved in making a proposal, and I can’t decide if that’s due to miscommunication, benign neglect, or design.

When my class had our qualifying exams last year, there was big meeting and everything was laid out for us pretty clearly. There has been no such meeting for proposals, which makes sense because it’s a much smaller deal than quals (though no less necessary for attaining the Ph.D.). My first inclination to explain my own lack of information is to think that my boss expects the department staff to tell us about it while the staff expects my boss to handle it—miscommunication. It’s equally likely that no one realizes I’m adrift—benign neglect. (I have tried a couple of times to arrange meetings with my professor to get this straightened out, but he seems oblivious to my confusion.) My sneaking, paranoid suspicion is that we students are intentionally left in the dark. The Ph.D. is supposed to teach us to be independent researchers, so why not leave it up to us to take the final steps to becoming doctoral candidates on our own?

I think that’s giving the faculty too much credit; they have better things to do than actively trying to make our lives difficult. And lest anyone get the wrong impression, I’m really just amused—not upset—by these circumstances, at least since I found the answers and got them confirmed by the department’s staff. It’s just par for the course for grad school. See Piled Higher and Deeper for more evidence.

I’ve taken the structure for my dissertation proposal from my grad school bible, Getting What You Came For, which suggests a three-part format. The proposal starts with a brief introduction and then lays out the research problem. This is followed by a review of all of the relevant literature and an in-depth description of the research methods and techniques that will be used. The format could just as easily have been stolen from the NIH R01 grant, which follows a similar pattern.

My great epiphany from this experience is that no research project should be undertaken without a proposal. It doesn’t have to be as grandiose as even the ten-page proposal I’m preparing for my dissertation, but it should contain all the same parts: a clear statement of the problem, the questions involved, and the goal or end result of the project; a review of the literature; and a clear description of the techniques that will be used. In a perfect world, it should also include a timeline and milestones. This proposal (perhaps without the lit review, which can be very time consuming) should be circulated and agreed to by all involved parties.

Too often I feel like I have floundered in my own endeavors because I didn’t fully understand the project that I was working on. I didn’t have a larger context to put it in. I didn’t have a clear idea of the project’s goal or expected result. Having a clear proposal for each project would have helped tremendously, and it’s something I intend to do for new projects going forward.

The usual trajectory for graduate school in science is that you spend the first year or so taking classes. Then in the second year, you take a preliminary or qualifying exam in order to become a doctoral candidate. After candidacy, you do some research, write a dissertation, defend it, and thus earn your PhD. There’s no Master’s degree involved; it sort of a consolation prize if you muster out after some point (I’m not sure exactly when one becomes eligible for the Master’s and when quitting is just quitting).

Presently, I find myself in the early stages of the preliminary exam — prelims. In my program (and I think this is pretty common in the life sciences), the exam basically consists of preparing an NIH-style grant on an original research topic. This is the proposal. Then you have to give a presentation on the proposal to a committee of three faculty members whose identities you don’t know until you walk into the room. You have to defend your proposed research, and the committee gets to quiz you over any general science knowledge they like — basically, they will back you into a corner in order to figure out what you don’t know. This is the oral exam.

At this early stage, I don’t even have a research topic yet. Instead, we have to prepare a pair of abstracts on proposed research topics. Then the committee will choose one of the two topics for the proposal. This is no small feat as the topics can’t be related to the research we’re already doing in the lab, but they have to related to our tracks within the program. In my case, this is “Biosensors, Biotechnology, and Bioinformatics.” Plus there are all sorts of other recommendations and guidelines about the experiments that frequently lead towards good, basic science. Unfortunately, basic science is not one of the three B’s in the BBB track, so it’s difficult to make it all come together.

On the other hand, I really appreciate what the grant-writing style of the exam is trying to accomplish. Obviously it’s practical experience for writing grants, especially since NIH fund so much of the life science research in this country. Prelims have also gotten me into the library, pouring through journals, exploring other topics outside of my little microcosm of bioinformatics. It’s broadened my horizons and opened my eyes to what practicing scientists actually do. It may be hell, but like so many hellish things in life, it’s also a good experience.

I’ve got two projects going in lab at the moment. One is the same thing I’ve been working on for a while: mining the structural data in AANT. You can read the paper describing the database (PubMed or PDF) for more background.

I have also been drafted, at least temporarily, by the selection facility to operate the Tecan robot workstation and do some aptamer selections. There’s a paper in review that describes the process. I’ll let you know when it gets published. Sadly, it doesn’t have my name on it.