Everyday Scientist

p-r-o-d-a-a

I’ve written a few posts where I criticize/make fun of papers, and figures, and acronyms. And some people didn’t like it. And some people thought I was snobby. And some people thought I was wrong.

This is my apology post. And I will apologize by making fun of myself. (Easy to do…)

I am a co-author on a recent paper: “Long-Wavelength Analogue of PRODAN: Synthesis and Properties of Anthradan, a Fluorophore with a 2,6-Donor-Acceptor Anthracene Structure.” Basically, we made and characterized an anthracene version of a popular fluorophore, 6-propionyl-2-dimethylaminonaphthalene (PRODAN). The point of the paper doesn’t matter so much here, but I have to make fun of our nomenclature: “PRODAN”—or even its word form, prodan—is an acronym of the structure, with the “N” standing for the naphthalene in the structure. So why would “Anthradan” make any sense as a name? Does the “n” in Anthradan still stand for “naphthalene”? Clearly not. A decidedly silly name.

Actually, I had suggested the name “PRODAA” for our new structure, in order to fit with the previous naming scheme. But my advisor reasonably criticized my plan: How do you even pronounce PRODAA?? OK, so my idea was even worse. “Anthradan” won simply on the grounds that it was able to be pronounced.

(OK, so some may see this not as a mea culpa post, but as a veiled attempt at promoting my own research and paper. But, gimme a break: I’m trying to make fun of myself here without pointing out all the real flaws in my research. That would be unfair: I have insider information!)

scientific article filtering

The wave of social bookmarking is finally reaching scientific journal articles. What YouTube, de.licio.us, and digg are to stupid videos and strange websites, now biowizard, CiteULike, and BioInfoBank are to scientific articles. (See also my previous post about CiteULike.) I suspect Connotea, with some social features already existing, is on its way to more filtering of scientific articles, too.

I welcome this progress. I find it pretty tedious reading journal tables of contents every day/week, which is necessary to keep up with new ideas that you hadn’t thought of (and thus are hard to search for in a database). Also, with journals such as PLoS One (which publishes anything—whether it’s interesting or not), filtering of journal articles will become more and more useful to pinpoint only articles you’re interested in reading.

The ranking mechanism of these science social bookmarking sites is far from perfect. But it’s a good start. Go check them out and make it easier for me to find papers I want to read!

[Note: My favorite site is still CiteULike. Connotea is nice and probably less buggy, but it seems to progress at a much slower rate, probably because CUL programming is open-source and collaborative. I can’t imagine biowizard really being that helpful in the long run, because it doesn’t have any of the functionality of CUL or Connotea and only applies to biology. I’m going to stick with CUL until someone else wins unequivocally (then I’ll export my library). I’ll update you as things change.]

news update: photonics, publishing, and elephants

Just a few (sciency) news updates today…

Publishing

This month, NPG launches its new (sub)journal Nature Photonics. It might have some cool articles in the future. Also PLoS One launched at the end of 2006 and will be an open-access journal that publishes any submissions that pass very limited scientific criteria (i.e. not including the impact or “coolness” of the paper). Who know? It might even work. If there were a good way of filtering the papers after they’re published, this open-access fad might be the new paradigm.

Invisible Cloak (not)

OK, everyone’s calling it an invisible cloak, but the “metamaterials” technology isn’t really even close. But it just got closer, with Opt. Lett. 2006, 32, 53–55. The authors report a metamaterial with a negative refractive index for visible (780-nm) light. And it’s really cool because … hey wait … where’d you go??

Stupid Elephant Picture

Many newspapers etc. have been publishing a picture of an elephant fetus in the womb (allegedly).

Cool eh? But it’s bogus! (Yeah, I was fooled, too. I saw it in Nature, where they claimed it was “enhanced with computer graphics.” Riiiiight. That should have tipped me off.) Actually, it is a silicon model of this ultrasound image:

I guess that’s cool.

citeulike

I recently found a cool website: CiteULike. It allows you to easily post scientific articles that you find interesting. To post an article you find, you simply stay on the page with the article (or abstract) and click a CiteULike bookmark, which automatically imports the various fields (e.g. authors, title, journal, etc.) into your library; then you simply add your own “tags” (or categories) and submit the post. I love it!

This site has a two-fold benefit: (1) you can share this library with others who are in your field (see my Watchlist), and (2) you can rank them according to how much you want to read them and remember to read papers.

CiteULike was written by Richard Cameron in 2004 and is run by him. And it’s free! I was so happy to find CiteULike, because I came up with the idea a few weeks ago, but I don’t have enough programming experience to write such a website (I took a C++ in high school, but didn’t really do the homework).

There are probably several other sites like this one, but the only other one I’ve found is Connotea, which was commissioned and now part of Nature Publishing Group. I checked out Connotea, and even imported my CiteULike library (tags include). But I prefer CiteULike’s style and features, especially the ability to rate and sort how interested I am in reading each article (maybe that feature exists in Connotea, but I can’t find it). I hope that CiteULike eventually becomes an open-source, collaborative effort; but until then, I’m still really happy with it.

So start you own library and send me a link!

reporting from the GRC

I’m here at the Gordon Conference on Single Molecule Approaches To Biology in New London, NH. When I get back to CA, I’ll get back to writing the blog…