Everyday Scientist

royce makes a funny

Prof. Royce Murray’s recent editorial in AC is fun. I actually do find these type of sarcastic instructions for writing a paper helpful. To an extent. These devices are great reminders of the essentials to making a paper readable. I might find even more helpful a template of a paper that tells you what each paragraph and caption should say. Maybe I’ll make that someday for teaching purposes…

My fav line is: “Diagrams are worth a thousand words, so in the interest of writing a concise paper, omit all words that explain the diagram, including labels. Let the reader use his/her fertile imagination.”

Another anti-suggestion from Royce is: “It should be anathema to use any original phrasing or humor in your language, so as to adhere to the principle that scientific writing must be stiff and formal and without personality.” Which reminds me of this line from an old Chem. Rev. paper: “Evans boldly put 50 atm of ethylene (C₂H₄, trans-C₂H₂D₂, or C₂D₄) in a cell with 25 atm of O₂. The apparatus subsequently blew up, but luckily not before he had obtained the spectra shown in Figure 8.”

I think Royce should have added another rule: Make sure your TOC art is unreadable, phallic, or filled with math formulas (or even just “Maths“).

P.S. I see that CBC scooped me on Royce’s editorial!

c&e news archive

Well, Paul inspired me to go check out the C&E News Archives. I looked for some p-chemists at my (PhD) alma mater. I was happy to find an article about my PhD advisor, W.E. Moerner:

The best one I found was on Steve Boxer, mostly because of the photo and caption:

And several articles on Zare, like this one.

History is fun.

UPDATE: A quaint story about a growing department at Stanford.

Also, a cool pic of my old building, from 1961! That building still has those same windows.

JOOT: the journal of one try

Today my labmate suggested someone start the Journal of One Try. It could have two sections per issue: “worked” and “didn’t work.”

JOOT would be dedicated to publishing scientific experiments tried only once. It would be an excellent resource for young graduate students to see if they should try an experiment (i.e. if it’s been published in the “worked” section) or try a different route (if it’s been published in “didn’t work”).

This is different than the Journal of Irreproducible Results: The results in JOOT would be reproducible … probably … just no one tried. Because it worked (or didn’t) the first time. Also, it wouldn’t be silly or funny science, simply experiments no one had the patience to try again. And this is different from the Journal of Negative Results, because many of the results would be positive. Well, once.

Maybe I’ll start that journal someday…

nature highlight

My colleague’s JACS paper was highlighted in Nature. I’m especially excited about that, because I’m a coauthor. ;)

The strange thing is that, despite our suggestions otherwise, the Nature folks chose a not-the-most-interesting figure from the paper. Of course, I’m more than happy that they showed any of our awesome figures! But, instead of showing one of the super-resolution images that Hsiao-lu made, the highlight shows a proof-of-labeling image, which is diffraction-limited. That said, they did select one of the live-cell images. I suppose it could be worse: they could have picked one of the controls. Or not displayed a figure at all.

Thanks Nature. I don’t mean to look a gift horse in the mouth.

Well, I’ll highlight our paper here. And choose my favorite figure (it’s protein localization in a little-bity bacteria):

i hope this isn’t faked….

… because it’s so beautiful! Schaller et al. have used the Sheetz-Spudich sliding assay to watch collective motion of moving biomolecules. Like watching flocks of birds:

Or crazy swirling patterns:

For these awesome results, I’m awarding the authors an EDSEL for “Coolest paper (if it isn’t faked) of little filaments spinning around in circles of 2010.”

Not that I have any reason to think that these results are faked. They just seem so crazy and beautiful. Animated, even.

how to tell if your horse is dead?

(In reference to How to tell if your rabbit is dead.)

Apparently, you can’t tell.

By the way, one of those organisms is my friend.

(source: “Evolution: What Is an Organism?“)

acs feeds broken?

I was forced to update all my ACS feeds in my RSS reader (Google Reader). None of the ACS feeds I follow had updated for a couple days. I think ACS switched over to Feedburner and their old feeds stopped updating. Anyone else have this problem?

And TOC images seem brokenish with the new feeds…

UPDATE: Alex updated us on the issues. I’m happy that ACS is migrating to a better system. They really tried to redirect, but there are some problems. I think the new feeds seem to be working well now!

TOC ROFL

My (very nerdy) friends started a internetted-web-blog to celebrate/mock hilarious/terrible table-of-contents images: TOC ROFL. (In reference to NCBI ROFL.) I might even submit my own once in a while; you can too!

how do you read PDFs?

I now have a longer commute, with at least 30 minutes of quality reading time. I don’t really want to carry my laptop everyday, so I’m seeking a better way to read journal articles. I’m not going to print them out, so don’t suggest reading them on paper. :)

[poll id=”3″]

Of course, cost is a factor, but I don’t want to go for the cheapest option if I end up never using it! My guess is that the Kindle DX is the best for reading PDFs, but loses on other fronts (e.g. large, expensive, limited, only grayscale). The iPad is a versatile color reader and I can sync with programs such as Papers or Mendeley (soon for the latter), but it is very expensive. Also, the screen isn’t as nice for reading print. The iPhone is way too small to read PDFs.

Man, I need to test-drive these devices for a month!

Other options?

even JACS is excited about the new Tron movie

I thought this TOC looked pretty awesome.

my world is crumbling!

What the what?!?

JACS will now consider Communications of any length up to 4 journal pages and will include the Abstract in the PDF and print versions, starting with Volume 132, issue 27 (July 14, 2010). Authors should refer to the online Information for Authors and use the Communications template when submitting Communications.

Four pages is not a letter. That’s an article, dammit. And abstracts for letters. WTF? No no no. This is all wrong.

What’s the best part of JACS Comms? That they’re short and sweet. You can actually read the damn things, instead of just reading the abstract and looking at the pretty pictures (like we all do with full articles). No longer. Now JACS Comms will be long and complex. Boo.

Instead of destroying the sanctity of the blessed JACS Comm, ACS should have added an intermediate category between Comms and Full Papers.

This is almost as bad as when ACS defaced the elegant JACS by adding images!

(Unlike FSP, I really am a curmudgeon.)

lost my library proxy

Stanford already took away my off-campus access to journal articles. I thought I’d have a couple months of access after I graduated, but I guess not. So keeping up with the literature means going to campus and sitting in the library like an undergrad.

I suppose I could rent articles, but I’m too spoiled by free access! Ah well, I’ll catch up reading my PDFs, then keep up better once I start my postdoc in a couple months.

obscure paper

I was recently looking for a prep for p-bromophenylphosphine, and I found exactly 1 reference for it’s synthetic prep that’s cited by every paper that uses it.

It happens to be in (possibly) the most obscure journal in the world – “Phosphorus and the Related Group V Elements.”  It had all of 6 volumes in the 70’s before it merged with the “International Journal of Sulfur Chemistry” to form “Phosphorous and Sulfur and the Related Elements.”

I finally found TWO places in the world that had hard copies – the North Carolina State University library, and, of course, the National Library of Australia.

I’m beginning to think what I want must be some obvious synthesis, and that I’m just an idiot.  However, I did fail organic chemistry and am now working in a synthesis lab, so the “idiot” part is probably appropriate…

Energy and Fuels RSS

Apparently, if you believe the Google (or is it Topeka?) statistics, I’m the only person who reads the RSS of Energy and Fuels on Google Reader.  As opposed to the 364 of you currently reading this on Google Reader.

vulva (hehe)

This is fit for NCBI ROFL:

“Where the sun does not shine: Is sunshine protective against melanoma of the vulva?” Journal of Photochemistry and Photobiology B: Biology 2010.

I suppose that if you research the vulva, you’re going to be very tempted to make silly jokes.