P.C. Shannon

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.

The conventional wisdom is that intellectual property is generally a good thing, although it can lapse into the absurd. Shakespeare is in the public domain, but just about anything printed in the last 100 years is not, even though the vast majority of it is long out-of-print. In the present tense, IP laws are intended to protect innovation and allow inventors to profit from their ideas. This is thought to drive innovation, and innovation ultimately benefits everyone. However, I've come across two examples recently where IP laws, while perhaps protecting innovation, nonetheless are not working in the public interest.

The first example comes from everyone's favorite evil corporation: Microsoft. Gates and company had some ideas about how to stop e-mail spam. They joined forces with AOL and maybe even Yahoo, and presented their ideas to IEEE, the body that approves standards for electronics and communications. IEEE considered the idea only briefly because they learned that Microsoft intended to file for a patent on their idea. IEEE can't very well make a patented process into a standard because that would force everyone to pay a licensing fee to the patent-holder. So someday we may be free from spam, but thanks to Microsoft, that day won't come soon.

While spam is certainly annoying, the second example is much more serious. A technology called DNA microarrays allows researchers to examine how genes are turned on or off in a cell across its whole genome. It's a very powerful tool and has the potential to give us great insights into the biology of cancer. In fact, there have probably been enough microarray experiments conducted on human DNA to date to be a tremendous boon to cancer researchers. Unfortunately, it's locked away in the intellectual property of dozens of companies. Each has just a piece of the puzzle, which is useful but not nearly as powerful as the whole picture.

To be fair, microarray experiments are expensive. The companies that do this work went into it with the intention of making a buck in addition to curing disease. As more or less a believer in capitalism, I think that's their right. It's just a shame that every once in a while, we can't put aside our materialism for a greater good. On the other hand, without the lure of riches, the microarray data wouldn't exist in the first place.

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…