The Futile Cycle

Hmm…so it seems that the Apple iPhone will come with VPN support, and it also opens PDFs. Which means that if I bought one, I could browse science journals and read papers on the iPhone using my university’s institutional subscription.

But alas, I am a graduate student, and have no need for such a device for the cost. Dead trees are still far cheaper for reading things while traveling. Plus, who wants to be on call from the Boss all the time?

Physicists have their “H-Bar” (the real one is at Caltech’s Faculty Club…I think astrophysicists could potentially make some awesome – but nerdy – drinks there, like a Supernova, Black Hole, or a Golden Nebula). But what about molecular and cellular biologists? We could also have a landmark with a geeky name: “Pub Med”, “The Exon Junction,” maybe the “Beta Barrel.” Or even just, “The Beagle.”

And what about chemists? “The Electron Cloud”? Or they could have a bunch of bars named “The Molecular Orbital”, with two bars awarded HOMO and LUMO status every year, and the singles scene could give SOMO ratings.

I see that Jorge Cham has drawn this conclusion:

But clearly, the formula is only true theoretically. In practical terms, the formula is more like Net Effect on Research Productivity N = log(R/P), where R is the Readily Available Information and P is the number of ways to procrastinate. Since P is much greater than R, we have N really, really negative.

Via Small Things Considered, I found a very nice summary article on how to use Error bars in experimental biology. It has very little math, but does a good job in emphasizing the different roles of standard deviation, standard error, and the confidence interval, as well as how to eyeball the significance level of differences using both CIs and standard error bars. Plus, it mentioned something I hadn’t realized previously:

The CIs (or SEs) do not give the information needed to assess the significance of the differences between means of the same group at different times because they are not sensitive to correlations within the group.

Very useful. This is in my permanent library.

I was in the middle of an interesting article on two documentary film-makers doing an exposé of Michael Moore, when I saw this sentence:

They were kicked out of Moore’s Traverse City (Mich.) Film Festival after questioning his nonprofit’s investments in defense contractor Halliburton and drug maker Eli Lilly.

Now, I understand that the main point is about Michael Moore’s hypocrisy, but I didn’t think I’d see the day where “Eli Lilly” and “Halliburton” were uttered in the same breath. I mean, as bad as drug companies can be, can one really compare them to a defense contractor?

This is an amazing book review that I find highly entertaining. Cosma Shalizi is an excellent writer:

There is the problem of conjectural conspiracy: an isolated hypothesis almost never leads to anything we can test observationally; it is only in combination with “auxiliary” hypotheses, sometimes very many of them indeed, that it gives us actionable predictions. But then if a prediction proves false, all we learn is that at least one of our hypotheses is wrong, not which ones are the saboteurs. So far as deductive rectitude is concerned, we are free to frame whichever auxiliaries we like least, and save our favorite hypothesis from execution at the hands of the Tribunal

Physicists, computer scientists, and mathematicians have long had arXiv, which is an online pre-print archive for prepublication of manuscripts, and for discussions, editorials, and commentaries that wouldn’t be published elsewhere. I don’t know anywhere else where a Cosma Shalizi and William Tozier’s cheeky A Simple Model of the Evolution of Simple Models of Evolution essay would be published.

Now, biologists have sort of the same outlet. Nature Precedings (no, that is not a typo) has gone online, and it looks like there’s some interesting stuff already. Its interface is a little cluttered, but so far the site looks very promising. It’s almost like an amalgamation of arXiv, PLoS ONE, and Digg, in terms of the way things are presented and what can be done with them. I’ll be watching to see what happens.

(EDIT: added accidentally omitted co-author)

Commencement was today, and I am now officially graduated, with an AB and AM in Chemistry and Chemical Biology, class of 2007! The last few days were very interesting, especially since the university made a whole-hearted attempt to make us feel the weight of the long train of tradition (perhaps for our future pocket cash?). I felt more of that this week than I had ever in the past four years, because of all the alumni coming back, the ceremonies and antiquated little quirks that made the university slightly weird (probably retained on purpose for distinguishment), and the gathering of the students together in Memorial Church for the Bachelor’s service that has (supposedly) been held every year for centuries.

Well, it’s been a long four years, but they were great ones. I loved learning from devoted professors, great peers, and having access to some of the great resources that make this university wonderful. Learning about NFkB from biologist Thomas Maniatis, studying organometallic chemistry and transition state structures from chemist David Evans, learning how to set up a sucrose gradient from biochemist Guido Guidotti, deriving wave mechanics with string theorist Cumran Vafa, analyzing bioethics with philosopher Michael Sandel, and learning how to build an economic model from economist Edward Glaeser – these are all wonderful experiences that I’ll take with me to graduate school and beyond. These people are a marvel to watch and learn from, and their infectious enthusiasm for the material that they study is one reason why I love science so much.

There is little that I truly regret about my undergraduate experience. Perhaps I could have worked harder in my coursework; maybe I could have made a few more friends and gone to a few more parties. Perhaps I could have been a bit more proactive with my research experience. I really should’ve taken my time drinking that white russian at my friend’s party. But, really, I thoroughly enjoyed my time here, and I think I learned a lot, not just about science, but about life and people. I built lasting friendships and relationships. That’s probably the most important thing I take away from here; after all, the education, though grand, probably isn’t qualitatively any better than other colleges and universities. Instead, it was the remarkable and unique collection of students and faculty that truly made my undergraduate experience memorable.

Genentech’s CEO, Dr. Arthur Levinson, gives an interview in the Wall Street Journal on drug pricing and development. It’s a great article, and it can answer a lot of questions that people might have for the seemingly outrageous prices of biological drugs such as Avastin, Herceptin, and Lucentis, all of which are made by Genentech. There’s nothing here that people in the biotech industry wouldn’t already know, but it’s a wonderful look inside for the general public. Levinson also has a great point about generic biologics:

Makers of pharmaceutical pills can show chemical equivalence easily. But if you are producing a biological, it is not made by chemical synthesis. It is made by a Chinese hamster’s ovary cell or an E. coli bacterium — a very complex route. We do not yet have analytical techniques to tell you that a copy is clinically identical to the innovator’s drug. Our recommendation to the FDA would be to simply require a clinical trial to make sure that the drug is behaving in the clinic as expected.