P.C. Shannon

In grad school, I TA’d for a professor who claimed that students finished his class knowing genetics as well as those at Harvard. He gave out these detailed definitions for terms and made the students write them down verbatim. On the tests, he give them the definitions with some words missing, and they had to fill in the blanks. It struck as a very rote, grammar school type of pedagogy, and I’m not sure that any of the students came away from the course with a very deep understanding of genetics. After all, just because you can recite a definition doesn’t mean that you understand what you’re saying. It’s the difference between knowing and truly understanding.

I bring this up in response to a recent editorial in Wired, “Your Outboard Brain Knows All,” in which Clive Thompson talks about our increasing reliance on computers to store key facts. He cites a study that found a number of young people didn’t know their own phone number and instead had to look it up on their phones. I usually know my own number, but I was dating Caroline for years before I’d memorized hers. Moreover, I love looking stuff up on Wikipedia or IMDB. But Thompson raises a good question: “Does an overreliance on machine memory shut down other important ways of understanding the world?”

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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.

Last time, I said that I had clear vision of my future. I want to lay that out now, as much for my benefit as anyone else’s. I want to work in systems biology. I’m really interested in the range of interactions within a cell, and I want to contribute to applying results from high-throughput studies, such as microarray analysis, to real biological problems, primarily cancer and other diseases.

Wow, this has really turned into a personal mission statement. I’ve also realized that while I’m not currently working on anything that could even loosely be termed “systems biology,” I am studying cellular interactions, so at least I’m kinda on course.

Wikipedia is telling me there’s something called “computational systems biology,” which nominally sounds like it’s right up my alley. But when it comes down to it, I’m much more interested in applications than in pure research. So if I need to develop new algorithms, then that’s great, but if I just need to process data, then so be that’s great, too, so long as my efforts are contributing meaningfully to the research.

I’m also interested in synthetic biology, but there are two problems with pursuing this area immediately. One is that it’s still a very bench-oriented enterprise. I don’t think we’ll ever get away from that as there are just too many random factors to handle computationally. Second and more significant, it’s still a very academic discipline, and I don’t want to be an academic. I think that systems biology now will pave the way for me to enter synthetic biology later, when it becomes a field in which biotech and pharmaceutical companies are interested.

I’m very interested in working at Genentech. The biotech company was just named as the best place to work by Fortune and as one of the top twenty smartest companies by Baseline. The Fortune article sacred me off a little bit, just because I wasn’t sure if I had the passion. But after writing this little “personal mission statement”—as touchy-feely as that sounds—I’ve found that I do.

Sometimes I have a very hard time getting motivated about my research. I don’t have any problem doing homework for my classes, and once I get into my research, it’s fine. It’s just sometimes I can’t seem to find the energy to get started. I had thought that maybe this was a sign that I’d perhaps made a bad decision somewhere along the line, but I realized the other day that the source of my anxiety is not my research, it’s my career after grad school.

For a long time, I didn’t have a clear vision of what I want to do after graduation and after my post-doc. I do now. But it’s still not always clear to me how to get from here to there. Part of the problem is that I feel like a career in science doesn’t follow a clear progression. While that can be true of any job, I feel like it happens far more often than not in science careers. Or maybe I just feel like things never work out for me the way I want them to.

Really, I need to be doing everything I can now to stack the deck in my favor. I know where I want to be in two years (when I’m doing my post-doc) and in four (or whenever the “real” job starts). So I need to make sure that the path I’m on now gives me the best chance to make that vision a reality.

I’ve started doing some of that. My in-laws provided me with a contact at GlaxoSmithKilne, who provided me with another. I’ve also been in touch with a researcher at Genentech. All three have been very helpful. However, I need to do some more research and make more contacts.

I think that, at least until I get established, I will always have some anxiety about my career. Doing this sort of due diligence will take some effort and it will take me out of my comfort zone, but it will be worth it, especially as it will help me achieve my goal. Certainly, I feel more confident now about my career than I have in a long time.

I’ve been on a major slump lately, as far as my research goes. Everyone traditionally has a post prelim period where they don’t get much done, but this has lasted for months. I just am not very excited about my current project, but it hasn’t been clear to me exactly why I’m not excited.

I guess part of it is that the research doesn’t seem to present any particular challenge, because it seems clear to me that it will work. I also don’t really see where it’s going, what the larger implications are. So we’ll be able to predict X, Y, and Z. That’s useful, but what can I do with it at that point? Not much.

I did experience a brief swell of enthusiasm when it was time to start moving from the computational phase to the experimental portion, simply because I’ve hardly done any bench work in grad school. But that faded, too, especially as even ordering the chemicals I need has become a headache.

But I found myself quite elated yesterday when I had an idea for an experiment to make a synthetic goober, which is how Andy likes to refer to my aptamer designs. What I realized is that last year, when I had my own research, I was really excited about the implications and possibilities of it, even if we were in the very earliest stages. I could see that it had a future, and it was a tantalizing vision that I wanted to be a part of. Thus far, I haven’t had that sort of feeling about my current project. Now I kinda of do, so today, I’m a little more motivated and a little more excited.

Nonetheless, I need to find a second project to work on, if only to avoid putting all my eggs in one basket.

I won an IGERT Fellowship. The program is administered locally at UT, but the funds come from the National Science Foundation or some other federal group. Funding is for 2 years. I’m not sure how many people applied (there are at least two people in my lab who didn’t get it), but they only select six each year. Free money. I love it.

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.

…away from home, anyway. I joined the Ellington Lab this week. I have a slew of computational projects stemming from my rotation project. I’m also supposed to get another wet lab project because there’s currently no funding for the computational stuff so I need to “pay the bills” somehow until new grants come in. I’m excited about it, but it’s very overwhelming. I think I was handed about twenty journal articles in the first hour, and I have yet to really sift through them. I’m still trying to get my feet under me in the lab. I’m so accustomed to the corporate world where there’s a fair amount of supervision (and also someone looking after you) that it’s a bit of a shock to be thrown in open water and forced to swim. I’m still just doggy paddling, but before too long I should find my pace.