P.C. Shannon

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.

Ok, I don’t actually hate science, but I certainly feel that way sometimes when doing experiments. Here’s an example. In my system, I have some RNA (an aptamer, in fact) that has been labeled with a fluorescent dye. I also have a shorter piece of DNA that is complimentary to the aptamer, so it will bind to the aptamer. The DNA is labeled with a quencher that prevents the dye from emitting its signal. Basically, when the DNA is present, the aptamer doesn’t glow, and when the DNA is absent, it does glow.

At least, that’s the way it should work. In some of my experiments, the more DNA I added, the brighter the aptamer glowed. This is the exact opposite of what should happen. It’s like the TV turning off when you press the on switch, only you can’t blame it on faulty wiring. Maybe it’s more like water flowing uphill, since these are basic physical properties of matter we’re talking about.

Nonetheless, it’s very frustrating. Fortunately, that project was canceled recently, due in part to the confounding results I was getting.

I’ve been having some trouble getting back on track with my other projects. I’m not sure why, exactly. Sometimes simply having to do something makes it unappealing, no matter how interesting it might be if it weren’t a requirement.

But in the last few days, I’ve felt really on top of things. I’ve been very productive. I worked on my mountain bike and have gone on a few short rides. I’ve taken care of various projects around the house. I’ve even made some progress on my main research project. Hopefully, I can keep things on track and maintain my forward momentum.

Plus, I always have Piled Higher and Deeper to console me in any event.

I'm amazed at how the brain works. For instance, there's a word that I've been trying to remember for the better part of a year. I'll want to use it in a conversation, because it perfectly captures what I want to say, but I can't, because I can never remember it. This word means “that which is directly observed” and is frequently used in high school discussions of the scientific method (which makes this problem all the more embarassing). I've actually come across it once or twice in this quest, but I can't seem to hang on to it. I keep thinking it is or is similar to “epistemological” because the first sound is the same and they both have to do with knowledge.

How can I know that? How can I know what a word means and what it sounds like but not know the word itself? It's really quite amazing.

I looked the word up before I started writing this, but now I've forgotten it again. Which leads me to my real conclusion: I'm just getting old.

That word, by the way, is “empirical.”

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 had one of those kids selling magazines come to my door today. Usually I turn them away, but I guess because I knew some of my subscriptions were coming up for renewal, I took a look at his wares. I bought a renewal for Wired for two years for $50 even though a single year is only $10. I figured the money was going to a good cause, something about getting kids off the streets, but I couldn't shake the feeling that I had been fleeced. Sp of course I turned to the Internet.

The company that handles the subscriptions, American Community Services includes their website on the order form. Of course, it looks reasonably legit. So I stuck their name into Google and came up with this site, which basically says, yes, it's a scam. The kids are lying to you about earning points for a trip or whatever, but they're also being exploited by the people who put together the sales crews and the clearing house. I also found this story about one of these kids assaulting an elderly woman. Nice.

Time to cancel my order.

P.S. In preparing my cancelation form, I discovered that on the back of one of the forms, it explicitly states that salespersons are prohibited from saying that they are working for prizes, scholarships, or anything of the things that they say!

The Texas Longhorns are headed to our first BCS bowl: The Rose Bowl on January 1, where we'll face the Michigan Wolverines. We ended up fourth in the BCS standings, behind three undefeated teams. This is a big win for Mack Brown, especially following 4 consecutive losses to OU. The game itself should be great, I can hardly wait. Hook 'em, Horns!

More details at the Longhorn Football site.

I have a lot of anxiety over what I’m going to do after I finish grad school. Even though I’m only starting my second year, I’ve still spent some time browsing job listings online at sites like Nature Jobs. This is not necessarily representative because in my field, I think a lot of recruiting is done at conferences and via word-of-mouth. In fact, I think it’s only fueled my anxiety because most of the bioinformatics lobs listed are for coders and technicians — people with Bachelors and Masters degrees — which is not what I want to do.

Strangely, it took me a while to figure out that rather than being paranoid about limited opportunities available to me (as listed online), I need to position myself as a bioinformatics researcher as opposed to a mere technician. This is similar to the difference in the software industry between a coder and an engineer. What I need to be doing, I realized, is not just taking one bioinformatics course and farting around on my computer. I need to be developing my toolbox so that I have a variety of ways of solving new problems rather than just getting headaches while trying to reinvent the computer science wheel. (Much of the foundation of computer science was set out years ago by people who are much smarter than me, so I couldn’t possibly recapitulate it all.)

This curriculum was driven home recently by an editorial in the journal Bioinformatics by Pavel Pevzner, a name I recognized from browsing bioinformatics books on Amazon.com. Pevzner’s argument is that undergraduates in molecular biology need to take an introductory algorithms class, but his broader point is that biologists need to understand the logic behind bioinformatics and not just “cookbook” their way thru computational biology.

The bioinformatics class that I’m currently taking does a good job of explaining the algorithms that are used. The students in there certainly understand sequence alignments better than most practicing biologists. The professor is not just giving us a recipe, he takes us through the algorithms. The problem for my educational goals is that, out of necessity and aim, he only hits a few algorithms that are currently employed. He can’t build the toolkit that I want to have. He does a good job of explaining the current state of the science, but he’s not preparing us to advance that state. It’s just beyond the scope of his course.

The class is a good starting point, a solid foundation that I have already applied to my research. But from here, I definitely want to take at least a basic algorithms class and I’d like to take something more advanced, too. But I also want to take some high level statistics and math courses, too, because a lot of bioinformatics is statistical modeling and such, so I need that background as well. The only problem is that I don’t want to have to subject myself to taking a slew of undergraduate classes if I can avoid it. So maybe I’ll just audit all of the class, we’ll see. Certainly having this plan has alleviated much of my anxiety.

I’m off to Duke University today to visit the lab of Homme Hellinga. Homme has this cool program called “Dezymer” that can be used to computationally design new binding proteins and enzymes. This is really cool stuff, and I’m super excited about it. If you want the nitty-gritty technical details, see this paper in Nature or this one that just came out in Science. For anyone keeping score at home, these are the top journals in biology if not all of science. It’s a big deal.