lobsters chelate

December 28, 2009 at 10:51 pm | | crazy figure contest

As a Mainer, I appreciate this table-of-contents artwork:



to be unpublished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.)

check out this cool link

December 19, 2009 at 11:29 pm | | nerd, science community, wild web

Check it out here. I promise you won’t be rickroll’d.

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.)


December 8, 2009 at 8:39 am | | lab safety

I don’t know how I didn’t find this earlier (or maybe I did, and forgot).

ACS has a really nice set of safety sheets for common chemicals, called Chemistry Laboratory Information Profiles (CLIPs). They are designed to be more straightforward than MSDS reports and useful for teachers and students (and physical chemists).

It doesn’t look like these have been updated since 2004, but they’re still useful. I just wish there were more. For your convenience, I’ve downloaded all the CLIP sheets and combined them in one PDF document. Enjoy.

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.

avoid mistakes in lab

December 4, 2009 at 11:26 am | | everyday science, how-to, lab safety, open thread

Nick at BiteSizeBio gives of a list of ways to make fewer mistakes in lab.

1. Use a checklist.

2. New protocols and SOPs: write out your own version.

3. Annotate. If you make a mistake in a protocol, annotate your copy so that you won’t make the same mistake again.

4. Repetitive pipetting: be consistant and use bookmarks.

5. Don’t multitask too much.

6. Get set up before you start.

7. Prepare in bulk.

8. Don’t spend so long in the lab.

9. Get enough sleep.

10. Take responsibility.

I’d like to add a few of my own, from my vast experience making mistakes:

Clean up after yourself as you go and maintain a tidy workspace. Obvious, but often forgotten. Tidying up will make your next experiment easier, and shows respect for your fellow labmates.

Label samples with sufficient information. When you come back tomorrow (or in a month), having a dozen ambiguously labeled epi tubes means you’ll probably have to start over (or screw up your experiment by grabbing the wrong one).

Write down a plan (in your lab notebook!). Maybe even a decision tree to plot out the experimental path you will take, what to do if unexpected results occur (i.e. anticipate the unexpected), what data you will collect in the experiment, and what controls are necessary. This will help avoid that terribly frustrating situation where you realized during data analysis that you collected only (n-1) of the necessary data points and have to start all over the next day.

Ask questions! If you don’t know how to use a piece of equipment, don’t know how to properly use or store a chemical, don’t know a protocol, or are simply stumped by a problem, ask a labmate. Most people would rather answer a question or demonstrate a technique than find out you broke a piece of shared equipment. Of course, respect your labmates: plan ahead and ask someone on their schedule, read manuals and protocols before asking for help, and avoid going to the same person every time.

When something isn’t working, take a deep breath and think. No matter what Murphy says, often the problem is minor and obvious. Before you start twisting knobs on a laser that isn’t lasing, confirm that the shutter is open.


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