P.C. Shannon

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.

Honestly, I’m not sure what the hell “web 2.0″ even means (although there are definitions from Tim O’Reilly and Wikipedia and an article about how it’s just hype). I could talk about the browser is the new desktop, the web is the new o.s. Instead, I’m simply going to say that I need new tools to manage my information.

I’ve been an Outlook addict for years, but it’s a huge beast that takes forever to load. That’s just not very efficient if I only need to glance at a calendar. I’m also tired of having to click in eight different places just to change the due date on a task. I don’t use Outlook for e-mail, and I don’t have a lot of appointments, so it’s mainly a to-do manager for me at this point. If I fall behind and need to reschedule a dozen tasks, I want to do it quickly.

Also, I’ve developed another crazy impulse to really learn and use linux as a day-to-day operating system. Outlook is the main anchor that ties me to Windows, so I started looking for ways to get away from Outlook. I wanted to move to a system that was platform independent.

These criteria led me to Remember the Milk, which has really changed the way I work. RTM is a web-based task manager that has a lot of the features I wished Outlook had. It also has features that I didn’t even know I wanted Outlook to have, like multiple lists.

For calendar functions, I switched to Google Calendar. I now have the calendar at my fingertips, thanks to a gadget for Google Desktop. Logically, I had to try out Gmail next. (With all these Google services, I sometimes wonder if I’m not just trading one evil empire for another.)

I haven’t really gotten into Gmail yet, but I can already see how it’s just a better way to handle e-mail. Never deleting anything, efficient search, and tagging messages. We don’t use the Internet like we did in 1992, so why are we still handling e-mail the same way?

The next application I wanted to replace is my reference manager, which keeps track of important and interesting scientific papers. It’s also indispensable for writing papers because it automagically formats your references. I’m never going to get this functionality in linux; it’s one of the things that will demand I boot into Windows and run Word and EndNote.

But I did find a better way to manage a library of articles: Connotea, which is to EndNote what RTM is to Outlook. Put another way, the desktop applications are slow and clunky; the web-apps are slick and intuitive. They work much more like your brain works, much more naturally. They work the way you want them to instead of forcing you to learn how to use them.

If that’s what “web 2.0″ means, then I’m all for it. The downside, of course, is that my Internet connect has become the syringe in my arm, and I can’t get a damn thing done without it.

P.S. I haven’t found a decent replacement for the Outlook address book. I want something that is basically RTM for contacts. I also am not terribly interested in auto-update services like Plaxo. I can conceive of how to roll-my-own, and it shouldn’t be terribly difficult. I just don’t have the time to learn AJAX and Ruby-on-Rails, the software technologies to make it truly “web 2.0″. Any suggestions?

I was driving around on empty this week. Somehow that got me to thinking about the diesel car that Wesley had in high school, Old Smokey. Man, we had some good times in that car and its successor, Old Yeller. So then I started trying to remember what I did during my summers in high school. I have pretty clear memories of each of summers during college, but not so much high school. I didn’t work. I went to band camp a couple of times (yes, I’m that big of a geek). But the summer between my junior and senior years in particular is a big blank, which leads me to one inescapable conclusion: I did jack shit.

Here’s the thing, though: we’re all, like, grown up now. Wesley is, like, a doctor. But not just any old doctor. No, he’s a fancy MD/PhD kind of doctor. Who’s married. To a lawyer. And owns a house. And has a kid.

What the hell? When did that happen? I guess sometime in the last 14 or so years.

Speaking of 14 years ago and memorable summers in high school, the summer of 92 shall live in infamy. Not only did it have a pretty profound effect on my life for, like, 10 years, it was also the summer I stole my dad’s car. Good times.

Recently I was watching the ST:TNG episode “Genesis“. The science in this episode is all on the level of the Heisenberg compensator, which is to say, laughably bad. (Someone did point out once that a Heisenberg compensator doesn’t necessarily mean one can determine both a particle’s speed and position, it just compensates for the fact that you can’t.) But Dr. Crusher’s estimation of the number of genes in the human genome was pretty accurate, at least for 1994.

Estimations of the number of genes make for an amusing measure of scientific progress. I’ve heard that in the 60’s, the number was estimated in the millions. According to Star Trek, it was down to 100,000 by the mid-nineties. (It’s also interesting to note that at that time, the Human Genome Project would have been considered to be only a third of the way into it’s fifteen year lifespan, but it actually finished in 2001, four years ahead of schedule, because the technology improved so drastically during the project.) I noticed recently that my genetics textbook, which was probably written in 2001, estimates the genome to be between 40,000 and 60,000. The current estimate is much more like 27,000.

For comparison’s sake, the fruit fly Drosophila melanogaster has about 12,000 genes. The bacterium E. coli, which is famous for killing people at Jack in the Box but also thrives in your intestines, has about 3000 genes.

We’re far more than twice as complex as a fruit fly, or nine times as complex as a lowly bacterium. Clearly there are other mechanisms that contribute to complexity, so that it doesn’t scale linearly with gene number. We already know about several, but we’re also finding new ones.

The picture is somewhat more complicated because the idea of a gene has changed over time, and, in my opinion, is fairly nebulous. The word “gene” actually has two different meanings, even in the halls of science. In one sense, it means “allele.” Alleles are different types (or flavors) of one gene. So when someone says, “he has the gene for sickle cell anemia,” they really mean he has the allele for it. The average person has the non-sickle cell allele.

The other meaning is “locus,” which is the physical position of the gene in the genome. You might hear, for example, that the gene for color blindness is on the X-chromosome, which really means that the locus is there.

When we talk about how many genes there are in the genome, we’re really talking about loci and not alleles. Some of the recent discoveries about gene regulation—the mechanisms that make us so much more complex than fruit flies even though we only have about twice as many genes—turn traditional notions about these mechanisms on their ear. They may even require another revision to the number of genes in the human genome.

You’ve seen the Pokemon Kid on Google Video. Maybe you’ve seen some of the webcam karaoke videos. But now some genius has combined two of humanity’s greatest passions: lip syncing to American pop music and the various American Idol incarnations. It’s Google Idol! Vote for you favorites from around the world.

To the best of my knowledge, Austin is the origin of the current resurgence in rollerderby. We have two leagues, TXRD and Texas Rollergirls. I’m not sure what the beef between them is, but I assume there is one, since there are two of them and they never play against each other. Even though both leagues have been around for a few years, Caroline and I have only ever been to one match, a bout in the Texas Rollergirls league.

In January, the A&E channel premiered their Rollergirls show, which followed the TXRD league. I don’t know if I would have followed the show if I didn’t live in Austin, but thanks to the magic of Tivo, we saw all the episodes. For me, part of the interest was just in supporting local, uh, culture. It was also strangely fascinating to see very familiar places on television.

It has been even stranger seeing the girls from the show around town. Most of our encounters have been at the regular 80’s dance night on Sundays at Elysium. The experience was kind of a cross between seeing a celebrity and (because the show exposed their private lives, as much as any “reality” program does) running into an old friend.

Any lingering notions I had that reality show were real, however, was shattered by witnessing the girls’ behavior. I don’t want to name names, but one girl, who came across as very mild mannered and reserved on television, turns out to be really very crazy. Another, who was one of the more colorful characters on the show, I can only describe as even skankier in person.

For Caroline’s birthday, we went to a TXRD bout, and finally got to see our televised friends in action live. It was a blast. Going to rollerderby is kind of like attending the female version of a hockey match, because you spend half the game just waiting for a fight to break out. And fight they did! One girl got her shirt torn off and was ejected from the game.

Being familiar with girls on both teams, we couldn’t decided which one to cheer for. I ended up taking my father’s route and cheering for a good game. I was not disappointed. The bout was close throughout and undecided until the very end.

Rollerderby leagues are springing up all over the country, from New York City to Phoenix, Kansas City, and even Caroline’s hometown of Richmond. I like to think that it started right here. Now that I’ve had a taste of the all-girl rollerderby, I’m hooked and ready for more.

Bruce Campbell is the best known of a stratum of middle-class actors who make their living primarily in straight-to-video movies. I think there must be a similar stratum of actors who work mainly in syndicated TV shows and make guest appearances on network shows. At least, that’s what a keen mind for trivia, a sharp eye for faces, and a lifetime of bad television have led me to believe.

For example, actors from a Star Trek series who have appeared in an episode of either Stargate series. On SG-1, both Q and the holographic doctor have had recurring roles, and Counselor Troi made an appearance as a Russian scientist. Chief O’Brien has been on Atlantis, along with one of the Agents Johnson from Die Hard. Somewhat more obscurely and back on SG-1, Lt. Barclay shows up in one episode, and the art collector who kidnaps Data played the documentary filmmaker. All this is to say nothing of Ben Browder and Claudia Black, who played lovers on Farscape, showing up in the last season, nor of Wayne Brady’s notable guest appearance (which was sadly devoid of improv, singing, or him smacking MacGyver in the face and shouting, “I’m Wayne Brady, bitch!”).

But that’s kid stuff, really. Let’s try a harder category: Star Trek actors who have appeared on The O.C.. The holographic doctor, again. He’s in damn near everything; he was in an episode of E.R. where he played the escrow agent or something for the nurse who tried to kill herself by ODing on barbiturates. Also, Chief O’Brien’s wife plays the headmaster at Harbor, the private school in The O.C..

But the most wonderfully mashed-up set of guest stars ever—even surprassing Hulk Hogan on The A-Team—was on an episode of MacGyver. In it, Mac is helping Shaft, who’s both a sex machine to all the chicks and running a program to rehabilitate gangs in South Central. Seriously. Commander Chipotle from ST:Voyager is also working for Shaft, but he goes vigilante to stop the rich white dudes who are supplying cocaine to the gangs. It’s up to Mac and Shaft to talk him down. No, really. It wasn’t some crazy dream. It was one of the most magical hours of my life.