Everyday Scientist

interrupting student

A (grad?) student walked into a seminar lecture, went up the the speaker in mid-sentence, and said, “Sorry to interrupt, but can I borrow some chalk?”

Everyone in the seminar room started chuckling at the kid. It was strange and awkward.

What a dumdum.

f1000

UPDATE2: OK, it turns out that the daily(ish) email isn’t too terrible. I now use it and I’m no longer upset that they don’t have an RSS feed. I correct myself and now fully endorse F1000!

Faculty of 1000 is extremely powerful with a lot of potential, but simultaneously completely worthless.

F1000 is like mini-peer-review post-publishing: it uses its “Faculty,” experts in various fields, to rate publications that those experts think are worth reading. It’s like … nay, it is … getting suggestions on what to read in the recent literature from a large group of experts. That is very cool. Of course, there are various databases like Cite-U-Like and Mendeley that are trying to mine their data to find interesting papers, but there’s something great about getting little mini-reviews from actual people.

OK, so why am I annoyed? F1000 doesn’t have an RSS feed! So I have to remember to go and check the website every week. Even if I happen to remember, there’s no way to mark which reviews I’ve already seen and the new ones. What is this, 2002?

UPDATE: rpg comments below with some good news: F1000 is actively trying to get RSS on the site. The comments also explain why it’s a challenge. I eagerly await RSS.

new chemistry dictionary for Word and OO.o

Check it out: azmanam has a new version of the chemistry dictionary for Word:

http://www.chemistry-blog.com/2011/01/19/chemistry-dictionary-for-word-processors-version-3-0/

Now you can eliminate all those red squiggly lines under half the words in your document.

Enjoy!

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!

CV of failures

Nature Jobs has encouraged folks to spread the word of their failures, as well as their successes. So I made a CV of my failures. I’m probably forgetting a lot of failures, but I’m not really motivated to spend a lot of time trying to remember. Anyone else want to air their dirty laundry?

rip paul barbara

Doug at Nanoscale Views brought my attention to the news that Paul Barbara died very recently. That is sad and surprising. He was a fun, exciting, and important scientist. RIP.

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):

should i join the postdoc union?

Postdocs at Berkeley (in fact the whole UC system) formed a union a few years back. Recently, the union negotiated a better contract with UC, which brings the postdoc pay up to … wait for it … the NIH minimum! That’s actually a big step. (Read more about it in Nature.)

Pro:

• I can listen to Woody Guthrie without feeling guilty
• it supports a good cause: I do think that postdocs need someone looking out for their interests
• it is a relatively small amount of money to ensure that postdocs have representation

Con:

• it costs 0.28% of my paycheck to join (although that’s only around $100)
• my money might go towards those terrible political ads on TV
• the general possibility of making my relationship with my PI more adversarial

I’m conflicted. Thoughts?

caveat grumptor

Royce Murray doesn’t like blogs.

No that’s an oversimplification of his editorial. Actually, his worry is that science blogs are more fun and easier to read than real science journalism (which, by the way, is hard to find); meanwhile, bloggers have no required credentials, no accountability, and might just be lying to everyone.

Damn straight.

UPDATE: In case it isn’t clear, Royce Murray is one of my favorite chemists and teachers. UNC is my Alma Mater, and I really appreciated his class. While most bloggers are pretty unhappy with Royce’s editorial, I wasn’t offended. I basically agree that neither the public nor scientists should be getting information from blogs without a grain of salt. Especially this blog. I’m sarcastic 83% of the time.

crick’s lost letters

Some revealing letters of Francis Crick have been found—mostly to Maurice Wilkins—and they discuss Rosalind Franklin. Here are some of the excerpts that I found interesting. For instance, this letter from Wilkins to Watson and Crick after they proposed the double-helix model:

My dear Francis,

I gather you have got the coordinates of your model or some worked out. Do you think we could have a copy of what you have?

The crystalline data is clearing up nicely. To think that Rosie had all the 3D data for 9 months & wouldn’t fit a helix to it and there was I taking her word for it that the data was anti-helical. Christ.

We have redone a lot of the 3D more accurately on mouse & will need all the extra accuracy for dealing with some of the finer points.

Regards & to Odile too.

Yours

M

P.S. I think I have a flat.

But “Rosie” had been focusing on the A structure of DNA, which generated clearer crystal diffraction pattern images. Unfortunately for her, crystalline DNA-A wasn’t helical. Crick agreed when he eventually saw her data:

This is the first time I have had an opportunity for a detailed study of the picture of Structure A, and I must say I am glad I didn’t see it earlier, as it would have worried me considerably.

All in all, it sounds like Franklin was generally unfriendly to her colleagues (and competitors). Wilkins wrote to Crick of Franlkin’s leaving King’s College:

I hope the smoke of witchcraft will soon be getting out of our eyes.

It sounds like her colleagues didn’t like her too much. But there was friction from the beginning: Wilkins thought that Franklin was going to work for him … or at least they would work together on DNA … and Franklin had been told that she would work independently. What a mess.

I feel bad for Franklin having to deal with these sexist jerks. Watson and Crick were probably the most annoying, because they didn’t do any experiments; instead, they’d listen to Franklin (and others) present their data, then run off and make a model. Annoying. Intellectual thievery almost. (And Watson and Crick admit as much, referring to it as “burglary” in one of their letters.)

But on the other hand, it seems Franklin made some serious mistakes interpreting her data and was quite abrasive. No angels here. No devils (or witches?) either.

I suspect that if everyone had worked together and been friendly, Watson and Crick would have proposed the correct structure much earlier. Not only that, but I think Franklin would have been given more credit by the boys. But that’s just my speculation. I just know that I’d prefer to collaborate with folks than fight with them.

NRC finally releases updated school rankings

Phew. That was a long wait. Since 1995.

But the wait wasn’t really worth it. NRC released basically a gimungous table of data, and didn’t actually give departments rankings. I don’t have time to wade through all this data. Someone needs to tell me that my department(s) are better than Harvard.

To make things worse, their spreadsheet doesn’t work on MS Excel 2008 on Mac (only on 2004). Maybe I’ll update sometime if I can wade through the data. In the meantime, see if your school has posted its own analysis. (Berkeley has. It looks like Stanford is still in the process of manipulating the data to make themselves look awesome.)

UPDATE:

Here are the top chemistry programs (ranked on research activity):

And programs containing the word “biophysic”:

So there. You can go make your own tables. I find this very confusing.

UPDATE: Not surprisingly, there are some serious errors being found in the piles and piles of numbers being released by the NRC ranking. And come to think of it, since when does Stanford chemistry have 50 faculty members??? Something is very wrong…

NRC should just list schools according to the US News and World Report rankings and keep their data hidden. jk.

the simpsons have their own nobel predictions

This was on The Simpsons last night:

(the screenshot is from 1 min 22 sec on Hulu)

I may update my predictions to reflect the venerated opinions of cartoon writers.

By the way, seeing my PhD advisor and a member of my dissertation committee listed on The Simpsons feels really strange.

(My/our real predictions are here.)

2010 nobel predictions

In previous years, I’ve awarded Edsel-Nobels, which no one really cared about. Maybe this is the year I’ll make predictions for the actual Nobel. Paul at Chembark already started his predictions, and everyone else will be buzzing about it soon enough.

In no particular order (and without much forethought):

1. Solar: Grätzel
2. Super-resolution optical microscopy: Betzig [awarded in 2014], Hell [awarded in 2014], Zhuang, Hess
3. Cloaking: Pendry
4. Birth control: Djerassi
5. Laser-induced fluorescence: Zare
6. Inorganic: Gray, Lippard
7. Single-molecule spectroscopy: Moerner [awarded in 2014], Orrit, Rigler, Xie
8. Chaperonins and protein folding: Horwich, Hartl, Lindquist, Ellis
9. DNA fingerprinting: Jefferys
10. Electrochemistry: Bard, Nocera
11. Polymer synthesis: Matyjaszewski, Wang
12. NMR and membranes: McConnell
13. Discovery of kinesin: Sheetz, Vale, Brady
14. Nano: Whitesides
15. Peace: Twitter
16. Cross-coupling: Suzuki, Heck, [awarded in 2010] Sonogashira
17. Electron Transfer in DNA/Electrochemical DNA Damage Sensors: Barton, Giese, Schuster
18. Pd-catalyzed Alkyne/Alkene Coupling and Atom-Economy: Trost
19. Nuclear hormone receptors: Chambon, Evans, Jensen, O’Malley
20. Two-photon microscopy: Webb, Denk, Strickler
21. DNA microarrays: Brown
22. NLO: Harris (as predicted by The Simpsons)

So there. The only one I’m confident about is Twitter.

Please feel free to add more in the comments. I will probably continue to update this…

UPDATE: Paul now has updated odds. Very impressive. He’s put a lot more thought into this than I. I’ve added cross-coupling to the list. Additions are in italics.

UPDATE: Can you name all the Chemistry Nobel winners?

UPDATE: Thompson has released their predictions.

UPDATE: The Simpsons also have some predictions.

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!