Science twit

Dear all,

Blogger is still doing the weird thing where the cursor, after I tapped "enter" key twice, will not have moved, but the typing will show up at the right spot. It's still disconcerting.

In other news, the martial arts exam day is coming up. I am about three lessons away from it and everyone who's testing (there're around ten of us) is starting the rounds of "Are you ready?" Today I went through two hours of lesson before staying behind to run through the entire exam material with Cathe, to get the "feel". I am certainly feeling it now (as opposed to norm, where I feel it the day after). A nap would be nice, but sadly I still have a bunch of chores to do. Blogging is currently my break / procrastination method of choice.


Looking back on my week's notes in Twitter, I seem to have rapidly converted notes about random things happening to me in the week mostly to notes about random bits of science that I've encountered. The benefits of being in a lab is such that, when your coworkers suddenly start snickering over something you can bet that it's a) something weird and b) something inevitably nerdy.

To demonstrate, I give you Exhibit A, Squid Mating Habits, based on this article from Science. 

There are of course really cool bits of science too, like the fact that Foldit gamers cracked the AIDS enzyme structure (yep, that game; remember that, guys?). I kept feeling like I should be installing Foldit on one of my computers but then, when would I play it? In any case it's awesome that they solved in three weeks (for frame of reference, usually solving a protein structures takes years upon years of word). This is public-sourcing that I can get behind.

...then there are of course the slightly depressing things. Like an article trumpeting gene therapy that can reduce HIV that, first of all, targets a gene that'll reduce the viral load regardless of the virus, and, secondly of all, is based on a small sized trial that has no controls. Then my labmate pointed out that most people probably aren't familiar with what "Phase I" and "Phase II" trials mean and I ponder the day when I'll have time to diagram this out for people, along with how the gene to protein thing works. There's also the article about the concern that giving antibiotics to livestock increases antibiotic resistant bacteria in the world, which is something that we've been teaching in Genetics 100 for awhile but know it hasn't made its way into the general public. The crown of all this, of course, is a comment I saw which reminded why I don't read comments on news anymore, that goes: "... with the economic woes of our country, we need to cut back on research. How many years has cancer been researched? Still no cure."

I will do a cartoon of what cancer is some day. I swear I will. (Unless Victoria beats me to it, of course, since she's a better cartoonist.) 

But back to the general life thing (yes, "life thing") -- fall quarter started for us on Thursday, but move-in day was last weekend and I was encountering hapless freshman asking me for directions to dorms (which I, being a grad student, of course had no clue about). Wendy and I went out to the student center for udon come Monday and already the walkways were full of sorority and fraternity booths. At one point we were swarmed by a group of blonde girls in identical blue shirts and we thought they were from a sorority. Turns out? They're from Chase. Doing what, I'm not sure, but both Wendy and I were left more than a little bemused. As far as I know Chase does not have a sorority, though this could be no longer true.

I continued to wade my way through the systems biology book and marvel at science jargon. I think it is imposed because of word limits on everything. By which I mean, instead of saying "heterogeneous variation in rate across time" people can just say "heterotachy", which is shorter but will mean absolutely zip to people outside of the field, yet because the proposal / article / what-have-you has to be a certain length, but require more and more information for it to be "convincing" to the peers, people have to increase the amount of words they make up to shorten their language. My PI calls it "tightening" the language. According to him I can tighten my writing style more. I am considering ranking the papers I read now according not just "impact factor" (how interesting the science is) and "robustness" (how careful / well-done are the experiments), but also by "density" or "brick-ness", to account for the banging-head-against-wall feeling I experience when reading some of the articles. 

Density would be defined by the number of times it takes a person to understand one paragraph, on average, in that article, where understanding, I think, I will define as the ability, after reading, to paraphrase the content of that paragraph to scientist from a different field and have the content be understood. Personally, I would avoid anything that has a "density" greater than 10.

(I was going to have "density" be the number of minutes it took to understand one sentence on average, but then I realized that people have different default reading speeds. While it's true that this can be corrected by a factor if we were to have everyone read the same paragraph first to estimate their default reading speed (DRS), I realized that people also have different reading speeds depending on what they read. For instance, some people liked reading the US history book from high school while, for me, it required liters upon liters -- a volume unit so with the right factor you can convert it to the corresponding amount of caffeinated beverages that must've been consumed -- self control to wade through. Therefore I figured -- times it takes to understand -- if you're in the field and reading that article, it's assumed that you already possess some ability to understand this sort of material, if needed to, grad school application or even GRE can be a numerical cut-off as needed.)

(Okay this is getting too long now I will continue some other time.)