P.C. Shannon

On Wednesday night, both Caroline and I had our cars broken into. This has happened to me before, but this time was much more unsettling. Previously, some crackhead smashed the window on my pickup truck and nabbed my portable CD player, which I paid $20 for at Best Buy. The real pain there was having to replace the window.

In the current circumstance, our cars were sitting in front of our house, and there was no “breaking in” per se as both cars were unlocked. The theives—who we figure were just some kids from the neighborhood—took some CDs from my car, nothing from hers. The unsettling part is that this happened in our tranquil little subdivision miles from downtown and other sketchy areas.

I keep thinking about the part in Fahrenheit 9/11 where Michael Moore goes to Canada and starts walking into people’s homes to see if they lock the doors or not (the film makes it seem as though there are no locked homes in Canada). He starts a conversation with one guy, asking the man has ever experienced a break-in. Just some liquor, probably taken by local teenagers.

I guess that’s my conundrum. I’m not really upset about the actual theft—although it is annoying to have to repurchase like 8 CD—my mind is filled with images of home invasions and Elizabeth Smart and so on. (And for all the worried parents out there, we do lock the doors at night.) But I don’t want to have to lock my car at night. I want to believe that we live in an area where such precautions are unnecessary.

But clearly that’s not the case. I guess the solution is to only keep burned copies of my CDs in the car.

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.

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’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.

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.

Whenever I talk to music fans — indie rock fans in particular — from other cities, they’re always jealous of me living in Austin. Not because it’s the self-anointed “Live Music Capital of the World,” but because we play host to the South by Southwest Music and Media Conference (SXSW) every March. “It must be so awesome,” the music fans rave, “to go to South by Southwest every year.” Fuck no! SXSW sucks ass. For starters, you can’t get a seat in any restaurant in town for 10 days. But more importantly, all the cool bands that you wait all year to see all come into town on the same weekend. They’re spread across however many dozens of venues all over town, and those are all packed to the gills. You can drop $80 or $100 on a wristband, but that doesn’t guarantee you admission to anything, and people who went to the actual conference get to jump in line ahead of you. The bottom line here is, if you’re lucky, you might be able to get in to see 2 or 3 bands in a night, but you’ll miss 8 or 10 other bands you’re dying to see. The net effect is that there are no good shows in Austin for the three months prior to the conference and for three months afterwards because they all get crammed into that one weekend. Adding insult to injury, SXSW was started as a way to promote local acts, but since it’s turned into an industry confab, local acts are few and far between on the showcase schedule.

That’s why all the good shows in Austin are in the fall and winter, when SXSW is just a hazy memory. Enter the Austin City Limits Music Festival (ACL), which has grown in popularity since its inauguration three years ago. This year, I was afraid it was turning into the SXSW of the fall, sucking all the season’s good road acts into one unreachable weekend. Plus the idea of seeing favorite bands — bands that should be playing small and mid-sized clubs — on huge outdoor stages under the blazing September sun with drunken frat boys wandering aimlessly about was not particularly appealing. But I figured I had to experience ACL at least once in order to properly bad mouth it. Plus, you know, the Pixies.

So Caroline and I bought three-day passes at the last minute. We went down on Friday evening, along with everyone else who was going after work. I have to hand it to the city and the festival organizers, the bus system was well organized and efficient. It’s no mean feat carting 75,000 people a day into Zilker Park. We saw Franz Ferdinand that first night, and they put on a great show. Of course, it would have been much better inside and at La Zona Rosa or Stubb’s. And there wouldn’t have been the frat boys in front of us who only knew the words from the chorus of Franz’s one radio song. He kept singing it whenever they started a new song, even if it wasn’t that song. When they finally did play his song, “Take Me Out”, he and his buddies left right away, even though the band was only a third of the way through their set. Such rudeness, but what do you expect. Thanks, ACL.

Saturday I made the mistake of going to the festival around 1 in the afternoon, without Caroline and mainly to see the one-woman act Cat Power. She’s much more suited to someplace otherworldly, like the Scottish Rite Theater where I had seen her previously. Chan Marshall even apologized for how much her set sucked. I couldn’t tell how bad it was because I was stranded a good 50 yards from the stage. I’m more inclined to blame the venue. I’ll say this much, an ice-cold Lone Star on a hot afternoon is wonderful. Of course, that left me cranky and dehydrated by the end of the day. The Pixies suffered from the same problems as Cat Power and Franz Ferdinand — bad sound outdoors and an unappreciative or indifferent crowd.

By Sunday morning, there was serious talk of skipping the third day, Saturday having been such a hellacious experience. But somehow we rallied and managed to get to the festival in time to see one of the few local bands, Spoon, and another long-time favorite of mine, Cake. Same shit, different day. In fact, it was so bad that during the first half of Cake’s show, the crowd had to chant “Turn it up” after every song.

I think I would have come away with a better impression had I not suffered the long day on Saturday. In the end, it was a bit of a pain in the ass to see a few good bands put on shows that were mediocre at best. I did enjoy being outside in the evenings, when it was nice, enjoying some good music with my girl. But it was also expensive — $90 for the three-day pass, plus the $4 beers and $5 fish tacos. I would have much preferred to see the same bands in more appropriate venues, which also would have cost me much less. The real testament is this: will we go again next year? I don’t know, it depends on the line-up. But we’ll definitely buy passes earlier in the summer, when they’re cheaper, and only go in the evenings. Will it be worth it, since a lot of the bands I’d…

Caroline and I got engaged a couple of months ago. Our official wedding websites are at The Knot and The Wedding Channel. You can see a (blurry) picture of her ring on the phone-blog and our engagement pictures here.

I taught my first two classes of the new semester today, and it went pretty well. The big thing I learned today is that you have to set the mood from the first time you walk in the door — or at least the first time you open your mouth. So I greeted everyone and asked them all their names. I made a sincere effort to learn the students names and call on them by name. They seemed to respond very well to that. They were a little bashful about coming up to the board to work problems, but they did it and seemed to take to it well.

Setting this kind of friendly, jovial classroom environment is a big step for me. I’m usually kind of quiet and reserved. I’m certainly in the habit of waiting for others to set the mood and then fitting myself into that. Of course as the instructor, it’s up to me to set the mood.

I really enjoy teaching, at least in a smaller classroom where you can interact with the students. I don’t envy the professor, having to stand before 115 blank faces and drone on for an hour about Mendel’s experiments. The part of teaching I hate the most is the grading, which the prof — lucky bastard — doesn’t have to do. I suppose there isn’t a way to have your cake and eat it, too.

Anyway, the course website is here, and you can see the website for Dr. Iyer’s lab here. He does very cool stuff with microarrays, a.k.a. gene chips. He got his PhD from Harvard and did his post-doc in the Brown Lab at Stanford, which played a big role in developing microarray technology.