Social Networking for the Geek Set

March 29, 2008 at 7:57 am | | science community, wild web

Recently I went to a talk on networking that was put on by the people behind Nature Network. It was interesting to see how the editors of Nature saw the future of social networking in the sciences.


I’m generally not a big fan of social networking. Had a Friendster account when it was still in early beta (2000?). That’s about it. Sites like LinkedIn and Nature Network make sense to me though, I just signed up. Do you folks use social networking sites for scientists? Any other suggestions?

Oh, and please drop by my profile if you sign up.

who would patent the atomic bomb?!?!

March 28, 2008 at 8:29 am | | news, science and the public, science community, stupid technology

The US Government would. Alex Wellerstein at Harvard has compiled some of the 2,100 patents that came out of the Manhattan Project … secret patents. Here’s a great one:


Ah, the METHOD FOR PRODUCING, SEPARATING, AND PURIFYING PLUTONIUM. Better patent that one so no one else does it in their basement and sells plutonium on their own. Right.

I hear an interesting piece on NPR about this story. My favorite part was the realization that spies could have taken advantage of these patents, even though they were secret, by submitting their own patents: the Patent Office would then basically reveal they already have a similar patent. Ha! Good luck for the US that no one was smart enough to try that!

I’m sure there’s a smart reason to patent the frikkin’ atomic bomb while you’re making it, but I still don’t know that reason.

filter your RSS feeds using Pipes

March 20, 2008 at 10:51 am | | great finds, science community, software, wild web

I read all my TOCs via RSS in Google Reader. Normally, this is just marvelous. However, some journals (e.g. Science and Nature) include a lot of junk along with the real science articles: news and whatnot. Also, PNAS has so many articles, it’s really hard to get through them all.

So I’ve started filtering some of those TOC RSS feeds using Yahoo! Pipes. (Click the image above for an example—the filter function is found under “Operators.”) So PNAS was easy, because they include the subject category in the title of each feed item. For Nature and Science, I need to find a way to filter out the news and fluff pieces somehow. Maybe there’s a keyword in those entries I can find.

Anyway, I just wanted to pass this along, because it’s really helpful. I know there are other RSS filters, but I like the versatility and ease of Yahoo! Pipes. Lemme know if you find any cool tricks!

Here’s a library of my edited feeds.


March 19, 2008 at 8:15 am | | news, science and the public

acc.jpgOne of the greatest science-fiction writers of all time, Arthur C. Clark, died today at his home in Sri Lanka. Not only was he a great “hard” sci-fi writer, but he shaped our scientific world by promoting the use geosychronous orbit, which is essential to global communication today.


happy pi day!

March 14, 2008 at 10:31 am | | nerd

Glad we caught this one (unlike last Pi-Approximation Day).

That’s all.

think gum

March 11, 2008 at 8:32 am | | lab safety, pseudoscience, software, stupid technology

Finally, a gum that will clean my teeth and my synapses! My PI found this wonderful product:


This gum must have brain-boosting powe, with all its “proven” ingredients (including rosemary and peppermint). It does have 20 mg of caffeine (which is a little less than a cup of green tea of a Coke), which I’ve found does help concentration; but coffee makes my breath smell so much better! This caffeine is “natural,” which is nice because I’m sick of getting my caffeine the only other way possible: via that intravenous injections of SynthCaffTM eight times a day.

You know, at first, I was just going to make fun of this product. But then I read the story. Hey! This kid went to Cal and now he’s a PhD student here at Stanford. I’m quite impressed with his entrepreneurial spirit. I’m really happy that this gum isn’t secretly made by Clorox or ExxonMobil or something.1

OK, back to making fun of it. I still think the gum is bunk: it uses the label “science” to sell a product to the gullible public, like my mom. (Just kidding, Mom.) But I’ll try it…

Well, the flavor is really good: a nice mixture of herbs and it has a green taste that transforms to an almost spicy pleasant-bitter, with a hint of spruce; the flavor lasts longer than some brand-name gums. Is my writing getting any better? I can see the fourth dimension and smell “yellow.” Is that normal? I feel like taking the rest of the day off and watch each blade of grass discover its little world. Seriously, though, I do feel a little light-headed.2

Well, I guess this product is no worse than all the other “mind-boosting” drinks and pills out there; and it tastes good! I did feel a little different after chewing it for 15 minutes, but no different than after half a cup of coffee, wondrous coffee.

Jeez, I almost recommend it. (That’s embarrassing.) But I recommend it if you want a nice flavored gum with some caffeine that will make you light-headed and feel happy … and your French press is broken.


1 Great stocks to own, terrible companies to make you gum.
2 My spelling got a lost wose [that was supposed to be “worse,” for instance] after chewing the gum, for some strange reason. And my HTML editing just got an order of magnitude more destructive

Are graduate student stipends too low?

March 7, 2008 at 10:37 am | | grad life, news, stipends

According to a article in the Stanford Daily, over 60% of graduate students at Stanford consider finances “stressful,” and over 40% consider graduate school “a financial risk.” Source. These figures are apparently from the Graduate Student Council’s 2007 survey of graduate student life, which unfortunately I could not find a copy of on the GSC website.

I did some investigating myself. According to the Stanford Registrar’s “Guide to Graduate Student Life,” the estimated living costs (per quarter) of a Stanford graduate student are:

Housing (Rent, Utilities, Furnishings): $2,941

Food: $1,835

Personal (toiletries, entertainment, and clothing): $856

Transportations (Fares, Parking, Insurance, and Vehicle Expenses): $300

Medical (Insurance, Co-payments, and Meds): $766

Books (For courses and outside research): $591

Total: $7,289/quarter ($29,156/year)


So, according to the Stanford Registrar’s office, the estimated living expenses for a graduate student are $7,289/quarter ($29,156/year). In chemistry since we generally don’t take classes after our first year and our P.I.’s pay for almost all research expenses, we’ll consider a chemistry (or natural sciences) living expense (minus books) to be $6,698/quarter ($26,792/year).

The minimum graduate Research Assistantship at Stanford (which is what the Chemistry Department pays for us as a stipend) is $6,953/quarter (or $27,812/year). This is between a shorfall of $336/quarter (or $1,344/year) from the registrar’s estimated expenses and a surplus of $255/quarter (or $1,020/year) from the chemist’s expenses.

Of course, we’re TAXED on our stipends, and the amount of federal tax we owe on our standard RAship (based on the 2007 tax tables for $27,812 – $5,350 standard deduction) is $2,587/year. That brings our annual salary down to $25,225. This is a shortfall in either scenario.

coffee physics

March 4, 2008 at 10:38 am | | EDSELs, great finds, literature

OK, is this a joke? Or is the author simply a bullshit artist?


Source: (Buffo, R. A.; Cardelli-Freire, C. Flavour and Fragrance Journal 2004,19, 99-104.)

I can forgive the εR-equals-zero-instead-of-unity mistake, but what does that have to do with CO2 release? And the glass-transition temperature? Seriously? Of a coffee bean?

edsel.jpgMy favorite part is that neither of those two ridiculous statements is cited.

OK, this wins an EDSEL for “Most creatively incorrect physical analysis of food chemistries.”

FRETing about forster vs. fluorescence

March 2, 2008 at 7:19 pm | | everyday science, open thread, tutorial

fret-plot.jpgUntil recently, I thought FRET stood for “Förster resonance energy transfer”; I figured that “fluorescence resonance energy transfer” was a bastardization used by biologists. But a friend challenged me on that point, claiming that fluorescence was more specific and meaningful than Förster. I was all confused.

My reasoning was this: Förster’s equation for long-range dipole-dipole nonradiative energy transfer is a specific case of RET; other cases (e.g. Dexter electron exchange) have different mechanisms and follow different scaling laws. Moreover, because fluorescence is not necessary in the FRET mechanism, I thought it was misleading.

But how true is all that? Does Dexter ET count as RET? Is FRET the only way to transfer the potential to fluoresce from one molecule to another? My friend claimed that Dexter should not be called RET, because it is electron exchange instead of Coulombic.

So I refer to the experts.

Bernard Valeur, in Molecular Fluorescence, says:

The term resonance energy transfer (RET) is often used. In some papers, the acronym FRET is used, denoting fluorescence resonance energy transfer, but this express is incorrect because it is not the fluorescence that is transferred but the electronic energy of the donor. Therefore, it is recommended that either EET (excitation energy transfer or electronic energy transfer) or RET (resonance energy transfer) are used.

That doesn’t help solve the Förster vs. fluorescence dilemma, but instead adds another term (EET, gross) to throw into the mix. But I think this sorta supports my using “Förster” because “fluorescence” is misleading and too broad. Anyway, good ol’ Bernard goes on to carefully describe the different RET mechanisms and formulas.

So what does Joseph R. Lakowicz say? First, he calls it “fluorescence resonance energy transfer,” but then echoes Valeur that RET is a preferable term because “the process does not involve the appearance of a photon.” But Lakowicz also differentiates RET and Dexter electron exchange (because the latter is purely quantum-mechanical).

In Turro’s Modern Molecular Photochemistry, the energy-transfer chapter starts right in with a “Golden Rule” for the transitions between states, and demonstrates that the probability includes an exchange term and a Coulombic term. (Valeur’s book also includes a nice mathematical explanation of the two terms; it might even be in Lakowicz somewhere!)

So now I’m mostly reconvinced that FRET should be Förster resonance energy transfer, not fluorescence. That is, RET is the general term for nonradiative excitation-energy transfers, and FRET is a specific mechanism—the specific mechanism applied in practically all biophysical measurements using RET to study distances.

What do you think? Am I way off?

UPDATE: IUPAC says I’m right.

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