go get your own alligator!

January 15, 2010 at 1:16 pm | | literature, science community

“They cannot argue with this data,” she said. “I have three lines of evidence. If they don’t believe it, they need to get an alligator and make their own measurements.”

(via Randy and Eric.)

acronym fail

January 6, 2010 at 9:10 am | | literature

Strange choice for the name of the fluorescent probe.

The “SS” stands for the disulfide bond; the “A” for acetylnaphthalene. I think. Fortunately, the authors never used the phrase “ASS probe” in the paper.

to be unpublished

December 23, 2009 at 11:53 am | | history, literature

Footnote 20 is great.

Lipscomb, W. N. J. Chem. Phys. 1954, 22, 985-988. (Thanks Mike.)

how to respond to referees

December 15, 2009 at 10:42 am | | how-to, literature, science community

Now that I’ve listed some pointers on how to write a referee report, I want to discuss how to respond to reviews of your own manuscript. Again, I’m still a novice at this, so I’d love input from the audience!

  1. Try not to be offended. It’s hard not to, but try not to hate the reviewer when they criticize your manuscript. Usually, I get one referee who says the paper is great and another who says it’s crap. It’s hard not to want to hurt that latter type. Bad. But they might be partially right, so correct the issues they find that have merit, and defend your original manuscript against the foolish criticisms.
  2. Organize your response. I like to make tables with one row being the referee’s comment and the other being my response, with each comment on a separate row. Any way you do it, respond to each referee point-by-point. In your cover letter to the editor, summarize the major requests by the referees and the main changes in the revised manuscript.
  3. Stand your ground when you’re right. Don’t make changes that make your manuscript worse. If the referee is wrong about something, say so (gently). Your goal is the editor seeing that you are right. If you’re too rude in your response to an incorrect referee, the editor may think you protest too much and become suspicious.
  4. …but don’t pull an Einstein. Sometimes referees find a problem with your science or reasoning that, no matter how much it pains you, is worth seriously considering. Referees can make your papers much better, so it is important to listen to them.

Number 1 is the one I have the most problems with. I don’t understand why some referees have to be so unreasonable and wrong when writing their reports. I usually draft very snarky responses, only to replace them with polite disagreement before sending my revisions to the editor. And complain to friends a lot. Not sure if that helps me or keeps me angry.


how to referee a paper

December 11, 2009 at 8:55 am | | how-to, literature, science community

Here are some pointers about how to referee a scientific journal article. I’ve picked these up both from having refereed papers myself (with my PIs) and more importantly from reading referee reports (good and bad) of my own manuscripts.

  1. Be timely. Editors often proceed with the publication process after getting back only two (or sometimes one) review. If yours is the third to come back, it may be too late. I’ve learned the hard way that, if you take too long to submit your review, your hard work might be all for naught. Of course, it is totally inappropriate to sit on a review purposefully to give yourself time to scoop a competitor.
  2. Be positive. Authors will be more willing to make the changes you suggest if you “sandwich” the constructive criticism between positive comments about the manuscript. It’s easy as a reviewer to only see the bad and forget that the science and writing took a lot of effort from the authors.
  3. Organize your criticisms. At minimum, split the changes you’re asking for into essential and minor. For instance, don’t bury a serious problem you found among a bunch of nit-picky points. First list the essential changes that need to be made in order to make the manuscript publishable, then you may list typos and minor points if you wish. This way, the authors (and editors) will immediately understand your assessment of the paper, and not get offended by what feels like an endless list of complaints. Remember: you’re a referee of the science, not an editor. UPDATE: Also, as MRW says in the comments, write your report so it can be responded to point-by-point.
  4. Do unto others… Remember what you appreciate in a review of your own manuscripts (and what drove you mad), and go from there. The authors are not your enemies—even though some of them torture you with their unclear writing and lackluster science—treat them like you would want to be treated.
  5. But be a good filter. Don’t let fatally bad science into the literature.

The best referees are the ones that help the authors make the paper better. Try to be that kind of referee. The worst are the ones that don’t read the manuscript closely enough, then unfairly criticize it. The just plain unhelpful are the ones who just say “publish as is.”

I’m sure I have a lot more to learn, but these are some things I’ve picked up so far. Others?

(Later, I’ll talk about how to respond to referee reports of your own manuscripts.)

how Cy5 switches

December 7, 2009 at 9:10 am | | literature, single molecules

Xiaowei Zhuang and Roger Tsien have published a JACS paper on how Cy5 photoswitches: “Photoswitching Mechanism of Cyanine Dyes.”


Nothing surprising here: this is the mechanism that Tsien proposed informally a couple years ago. But now they have published evidence that the thiol (e.g. BME, a component of the oxygen-scavenging system) attacks a polymethene bond.

I think this paper is a nice characterization of the photochemistry involved in Cy5 photoswitching.

open letter to journals about RSS

November 25, 2009 at 9:14 am | | literature, open thread, science community, wild web

Dear all journal publishers,

If the RSS feed to your journal is missing a TOC image or a full list of the authors, you need to correct that.


Reading just titles can be hard, especially when you skim through many journals. TOC images make that much more enjoyable. It’s the way to go, and if your journal does not include TOC images, you’re behind the times.

Also, it’s very simple to include all authors in the RSS feed. First authors only is not helpful: it’s very helpful to be able to check who the corresponding author is on a paper you might be interested in. (I’m talking to you ACS.)

Mitch’s ChemFeeds is great, but I doubt it can add TOC artwork to journals that don’t request it from their authors!

Happy Thanksgiving, everybody!

this is crap!

November 1, 2009 at 11:11 pm | | literature

No, just kidding. But I like the acronym: iSCAT (for “interferometric scattering”).

Sandoghdar, et al. High-speed nanoscopic tracking of the position and orientation of a single virus. Nature Methods.

They tracked both the scattering from a virus and the fluorescence from a quantum dot attached simultaneously, with a precision of a few nanometers. And they could measure differences in the orientational tumbling of viruses of various sizes as they diffused around on a surface (on a supported lipid bilayer).


self promotion

October 28, 2009 at 1:29 pm | | cool results, literature

But what is a blog for anyway? Advertising! Here’s my most recent paper:


“Azido Push−Pull Fluorogens Photoactivate to Produce Bright Fluorescent Labels” J. Phys. Chem. B

Sorry for the lame post, but I’ve been too busy to write cool things…

AC now has letters

September 22, 2009 at 9:13 am | | literature, science community

Anal. Chem. has begun accepting shorter publications as letters. I think that’s probably a good idea: another option when publishing a short, timely, interesting result.

epi tube as a lava lamp

September 18, 2009 at 7:51 am | | crazy figure contest, literature

Nice, a lava lamp in table-of-contents artwork.


Oh, wait. That’s an epi tube.

protect the non-born-oppenheimer!

September 9, 2009 at 12:49 pm | | crazy figure contest, literature, wild web

This is how the table-of-contents artwork showed up in my RSS reader:


Oops. It turns out that the artwork was supposed to look like this:


It takes some balls to make your TOC “artwork” a big, complicated equation.

how not to choose a title 101

September 8, 2009 at 3:12 am | | great finds, literature

It’s easy for one to find amusement in a poorly conceived figure or in a t-shirt attempting to show the structure of PCP but failing quite miserably or in the egregious cover of an Oxford University Press promotional booklet for ACS publications. But let us not overlook the gems of humor that we encounter everyday in the form of journal-article titles. Throughout the process of writing my dissertation, I have accumulated countless EndNote libraries, the entries of which are fertile grounds for laughter. I challenge you to improve upon these categories (or add new ones):

Greatest disregard for the importance of being concise:

Bennett, M. A.; Yoshida, T. J. Am. Chem. Soc. 1978, 100, 1750-1759.

long title
Most dizzying:

Arroyo, M.; Bernès, S.; Brianso, J. L.; Mayoral, E.; Richards, R. L.; Rius, J.; Torrens, H. J. Organomet. Chem. 2000, 599, 170–177.

Most [{(=flamboyant=)}]:

López, O.; Crespo, M.; Font-Bardía, M.; Solans, X. Organometallics 1997, 16, 1233-1240.

Most clichéd:
Gaydos, C. A. Neurology 2001, 56, 1126-1127.


Longest running series (most pretentious?):
ten Brink, G.-J.; Arends, I. W. C. E.; Hoogenraad, M.; Verspui, G.; Sheldon, R. A. Adv. Synth. Catal.
2003, 345, 1341-1352.

longest series
Most in need of an editor (and a vacuum pump to remove those 0.88 +/- 0.04 molecules of methylene chloride):

Usón, R.; Forniés, J.; Espinet, P.; Garcia, A.; Tomas, M.; Foces-Foces, M.; Cano, F. H. J. Organomet. Chem. 1985, 282, C35-C38.

I still have four chapters of my dissertation to write and only four days before a draft is due to my committee.  I can’t help but to ask myself, Is this the best use of my time?

oh. my. god.

August 27, 2009 at 4:31 pm | | literature

The Chemical Structure of a Molecule Resolved by Atomic Force Microscopy


Holy cow.

This is the second coolest thing ever done with pentacene!

(Thanks for the tip, Jian.)

ozone hole and global weirding

August 20, 2009 at 9:00 am | | literature, news, science and the public

Nature has a nice News Feature on how humans first caused an ozone hole in the atmosphere, then banded together to fix it. Really pretty inspiring what we can do when we need to. (The scientific story is also interesting.) And a lesson to how we can work together to solve the specter of global climate change and global weirding.

ozone-no-reg ozone-reg

The images on the left show a computer model of what the ozone hole (blue) would have looked like if we had done nothing; the ones on the right are what we’ve (probably) done by eliminating CFCs from the atmosphere. The large ozone hole would have been seriously catastrophic: Living in NYC or Tokyo would mean getting dangerous sunburns in 5 minutes of sun exposure. Ouch.

I think the ozone hole offers two lessons. (1) That climate science is not BS. And (2) that humans can cause and solve global atmospheric problems. The first probably won’t convince any global-warming skeptic, because they could claim that it was the same faulty science then as now, and that there never was a ozone hole.

But the second lesson should inspire all but the most adamant doubters. Humans are powerful enough to dramatically alter Earth’s environment, sometimes in catastrophic ways. Moreover, we can collaborate internationally to solve global problems. Why are we not inspired to slow global weirding (and solve other international problems such as abject poverty)?

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