Archive for January, 2007

One of my favorite sports blogs is UniWatch, where you can learn about team uniforms in mind-numbing detail. In general, chemists are an awfully dressed bunch and our lab-related gear is pretty standard. That said, we do have interesting clothing when commencement time rolls around. Here’s my review of the doctoral regalia of the top chemistry grad schools, UniWatch-style:

Berkeley - Tight. The blue-on-blue motif works, and the gold piping gives the outfit impressive flair.

MIT - An absolute disaster. Who even knew that MIT’s school colors were red and gray? Despite having the same colors, Ohio State University’s gowns don’t look half as bad. The Beavers should go back to the drawing board.

Harvard - Elegant and identifiable. My only complaint is that the gowns have been made with different shades of crimson over the years. The ones that are closer to maroon look better than those that skew toward magenta. And it’s not just a side effect of lighting—you can see both side-by-side in this photo. Adding some gold trim might improve things, too.

Stanford - These gowns are more like cloaks; there’s a definite English thing going on. For example, take a look at these people from Leeds and Sir Fraser himself. All in all, I’ll give Stanford a thumbs up, with added props for choosing to be different.

Princeton - The orange bars are nice, but the color needs to be used in moderation. I would lose the faux stole that goes down the front of the gown.

Scripps - All black. What a cop out. While it works for New Zealand’s rugby team, the motif doesn’t look so good on Ph.D. scientists. I expect more from an institute that prides itself in its synthetic creativity.

Caltech - See above.

Columbia - The baby blue works, and the crowns are a nice historical touch (the school used to be known as King’s College).

Illinois - Ack!

Northwestern - Regal elegance. The royal purple gowns look great with black bars, but maybe my opinion is a little bit biased.

Finally, here are some things to keep in mind at commencement:

Do: Accessorize with an appropriate weapon.

Do not: Refer to your chemistry professor as “a Mack Daddy” in the commencement announcement.

Do: Wear your mortar board at a jaunty angle (especially if you’re a synthetic genius).

Do not: Use your mortar board to express your chemical nerdiness. Especially if it is going to embarrass you in front of the entire UCLA chemistry faculty.

Move over, Bingel cyclopropanation… I’ve got a new favorite reaction.

While thumbing through a review article on the chemistry of some “extraordinary Maillard flavor compounds,” I came upon this little diddy:

Magnificent! While I don’t want to make a habit of encroaching on Milo’s territory of posting organic reaction mechanisms, you’ll find one after the jump. See if you can figure it out before peeking…

. 

Read the rest of this entry »

While chemists were home for the holidays, Dalibor Sames rang in the New Year by retracting more data from the Journal of the American Chemical Society. For those of you keeping score, that makes a total of eight retractions and partial retractions for Dr. Sames & Co.

This latest move was especially surprising because Bengu Sezen was not an author on the publication. While she was listed in the acknowledgments for “helpful discussions,” that would appear to exclude any experimentation. Dr. Benjamin Lane was the first author on the paper, and his name may sound familiar to you. Lane was interviewed by Science magazine for its initial story on the Sames retractions back in March of 2006. From that article:

Benjamin Lane, a former Sames group member now working as a chemist with the pharmaceutical company Biogen in Cambridge, Massachusetts, says some of Sezen’s work has been replicated and has been used by chemists in the pharmaceutical industry. Says Lane, “She has done some good things and made an impact on the field.”

So, the plot thickens. From the newest partial retraction:

For comparison purposes, this article refers to a palladium-catalyzed arylation of free azoles in the presence of magnesium oxide, published previously in a separate communication. Although the magnesium oxide procedure has recently been found irreproducible (J. Am. Chem. Soc. 2006, 128, 8364), this fact does not affect the conclusions of this paper. Consequently, the magnesium oxide protocol has been removed from the Supporting Information. Also, Figures S5 and S8 have been replaced with corrected versions.

The previous retraction notice also stated that MgO could not be used as a base to give product, but cited Lane’s 2005 paper as showing that both Grignard reagents (RMgBr) and Mg(HMDS)₂ are appropriate bases. What exactly was retracted remains a mystery. The authors don’t offer specific details in the “addition/correction” notice, and the editors of JACS have overwritten the old supporting information so you can’t track the changes. It appears that the MgO reaction was compared against the new reactions in the paper, apparently in the context of kinetic studies. What is important—and completely ignored—is whether Lane’s paper used data from the old Sezen paper or if he repeated the previously-published experiments to generate new data.  If it turns out to be the latter, that would be odd.  And if I’m missing something obvious here, let me know.

Like its predecessors, the latest retraction also bypassed the JACS RSS feed and the daily ASAP alert e-mails. Why do the editors of JACS choose to post Sames’ retractions in this manner? By putting different information in their feeds, e-mails, and print editions, the editors are making it hard for their readers to process information. It seems to run counter to the whole idea of why the scientific literature exists.

As far as the significance of this latest retraction, here’s how I see it:

1. The development is especially bad for Dalibor Sames. He keeps his name in the news by retracting more data, and it will be hard to pin these results on Sezen because she isn’t listed as an author.

2. The fact that Sezen isn’t listed as an author in this work suggests a number of possible explanations:

i) Sezen performed these latest retracted experiments but was not credited in the paper as having done so.

ii) The “irreproducibility” goes beyond Sezen.

iii) Something happened in 2006 where this C-H activation chemistry ceased to work. For instance, the reagents they used in their lab were contaminated with a catalyst that worked and they finished that bottle. This would be the best possible explanation for everyone, but would still leave Sames on the hook for the aftermath.

iv) Experiments were sabotaged. (The use of the passive voice here is intentional.)

3. The editors of JACS, once again, have made some questionable moves. They have completely overwritten the retracted data instead of just posting the updated supporting information under the addition/correction notice. As far as I know, the generally-accepted, “standard procedure” in scientific publishing is to place a conspicuous note in the PDF file of the old publication and link to the correction notice. Furthermore, JACS has again allowed a Sames retraction to bypass their daily ASAP updates, which does a good job of making the news less visible. This practice of having addition/correction notices (which include retractions) bypass the ASAP system is not standard procedure. For instance, you can find addition/correction notices like this one on ASAP right now. In fact, there were four addition/correction notices on the JACS when when I made the last Sames-Sezen post a couple of weeks ago, and one of those had been sitting there since December 24, 2006. I have no problem with the editors sending retractions straight to the printers, but the notices should simultaneously go through the ASAP RSS feed and e-mail alerts. I mean, is there any reason they shouldn’t?

4. I have obviously lost some credibility as a blogger for missing this latest retraction. It had been out for over a week before I got the initial post up. I’ll blame JACS, but the fact of the matter is that I will have to change the way I read journals. What other important articles have I missed because they didn’t show up on ASAP?

4a. Thank you to the kind person who sent an e-mail alerting me to the retraction. It goes to show you how important blog readers are as sources of interesting info. If you see something of note, please speak up. Leave comments, use the wall, or send an e-mail. And “interesting” doesn’t necessarily mean “bad.” Pass stuff along that is remarkably good, bad, funny, strange, or inspiring. Anything goes.

Finally, in case you missed them, the Sames-Sezen retractions drew two mentions in the news this week. First, the outgoing Deputy Editor-in-Chief of C&EN, Pamela Zurer, raised an indirect reference to the case in her farewell editorial (C&EN, Jan. 22, p.5):

Misconduct in research is another complex issue the scientific community has yet to fully come to grips with. Although chemists like to think such unethical behavior is rare in our discipline, News Editor William Schulz reported on a couple of troubling cases in the past year and is digging into yet another. As I wrote in 1996, “The real question is not how often scientific misconduct occurs, or whether the scientific record is ultimately self-correcting. It is how the community behaves when faced with unpleasant allegations against one of it established members.”

Second, Nature singled out Sezen and Sames, by name, with regard to a story on the current status of some high profile cases of (alleged) scientific misconduct. Sames was clearly given a reprieve by the editors, as the section discussing the Columbia case was simply titled “Bengu Sezen”:

In March 2006, Dalibor Sames, a chemist at Columbia University in New York, withdrew two papers and part of a third from the Journal of the American Chemical Society (JACS).

.

Work done by graduate student Bengü Sezen, he said, couldn’t be reproduced. The work was in the field of carbon–hydrogen bond functionalization, which aims to selectively break bonds within a molecule. The case got a lot of coverage on the ever-lively chemistry blogs, and a few press outlets mentioned the issue, including Nature (440, 390–391; 2006).

.

Sames is not commenting further until an inquiry is completed, and Columbia University says that it is against its policy to “comment on the existence or non-existence of any internal investigation into allegations of research misconduct”. But Sezen has vigorously defended herself in e-mails to the editor of JACS and the press.

So, that’s that.  Next time on this “ever-lively chemistry blog”: something less unhappy.

Some recent discussions in the chemical blogosphere have wandered into particularly contentious areas. Whether trading news about scientific misconduct or sounding off on minorities in science, bloggers and commenters want to know how much they can say without getting into trouble. Fortunately, the Berkman Center for Internet and Society at Harvard Law School has the answers. They developed chillingeffects.org to help Average Joes and Janes on the Internet understand laws regarding what you can and can’t say online.

So, how many of the protections enjoyed by the press also apply to bloggers? All of them. Just remember that when you post stuff online, you are publishing information. Online publications are governed by the same laws that govern information published in more traditional media. Blogs have the right to report newsworthy things, but at the same time, bloggers are also open to defamation and violation-of-privacy lawsuits. You generally want to keep two things in mind: make sure what you say is both true and newsworthy. Don’t make stuff up, and don’t go digging into areas where someone would have a reasonable expectation of privacy.

On the plus side, you only have to worry about what you say. Legal precedent has established that owners and operators of sites are not responsible for statements posted by third parties. That means that bloggers are not responsible for defamatory comments left on their blogs. (So keep on posting, Wolfie.) At the same time, commenters don’t have “freedom of speech” on someone else’s Web site; their comments can be deleted by the site’s owner at any time.

While those are the main points, I highly recommend surfing through the Chilling Effects Web site when you’ve got some free time. And should you ever find yourself having to figure out a cease-and-desist letter, they’ve got a great section on those, too.

While the law may treat bloggers as members of the press, the rest of the world has been reluctant to do the same.  Fortunately, that’s changing. A recent article in The Washington Post notes that 2 out of the 100 seats for the media at the Scooter Libby trial are being distributed to bloggers. With this new vote of confidence, it will be interesting to see whether bloggers improve their journalistic standards by doing things like taking the time to verify information, obtaining permission before using copyrighted images, and publishing corrections when circumstances warrant them.

As far as chemistry goes, the American Chemical Society has pretty much poo-pooed the idea of blogs being a legitimate news medium. As proof, look no further than national meetings, where the ACS offers complimentary registration and access to a media room (complete with wireless Internet access) to the people lucky enough to be deemed journalists. Seeing as how the ACS is coming to Boston this Fall, I thought it might be interesting to use their facilities to post dispatches from the lectures and maybe even get short interviews with anyone being offered to the media. Upon closer inspection, it appears that the ACS won’t let me:

Press/Media Registration: Press registration is complimentary for credentialed members of the news media (restricted to reporters and editors working full-time for print or broadcast news) who are approved by the ACS Office of Communications. Press representatives may pick up their badges with valid media credentials from the Press Room (Moscone Center, Room 232) during the meeting.

That stinks, and it makes little sense as a blanket policy. For instance, by their definition, no freelance reporter will be granted press registration. Furthermore, a reporter from the Harvard News Office could get credentialed but not a student-reporter from the Harvard Crimson, despite the fact that the latter probably has a much greater readership. If the ACS truly exists as an organization to promote chemistry, I think that encouraging intrepid bloggers to cover interesting chemistry would be a good idea. I mean, who’s going to do a better job of covering chemical lectures: some random reporter working full-time for the Sunnyville Post or some nerd on the Internet who actually understands chemistry?

Maybe I’ll send a letter to the ACS Press Office to see if they’ll step into the 21st century and reconsider their restrictions. I’m not looking for a free ride…I’ll happily pay for registration, just give me access to the Internet at the meeting site. Pretty, please?

UPDATE: Mitch found a more extensive write-up of the ACS’s Media Accreditation Policy.  Web entities can get media registration so long as they have a news component, and freelancers just need a note from mommy.

Expect more news posts on ChemBark in 2007.  If I can save some money on registration, the drinks will be on me.

Over at The Chem Blog, Kyle has a post on the latest chemistry rankings by the National Science Foundation and US News and World Report. I guess we’re approaching the deadline in the contest to come up with the stupidest way to quantify scientific quality, because the Chronicle of Higher Education (sub. req’d) just reported another “new standard for measuring doctoral programs.”

The company that developed the system calls it completely objective and, for a mere $30,000 per year, will provide the data to university deans interested in keeping tabs on their faculties. The new system bases rankings on “scholarly output,” which accounts for “the number of book and journal articles published by each program’s faculty, as well as journal citations, awards, honors, and grants received.” These numbers are plugged into highly scientific equations to generate highly bogus final rankings. I guess the equations are something like: 1 Nobel Prize = 3 Priestley Medals = 10 ACS Local Section Awards, and 1 Letter to Nature = 3 JACS Comms = 10 Org Letts. Someone should tell them that using math doesn’t equate to being objective.

Anyway, rather than tell you how stupid the new system is, see for yourself. Here are the top 5 chemistry departments using data from 2005:

1. Harvard
2. Yale
3. MIT
4. Northwestern and UCSF (tie)

Interestingly, their system also ranks Jimmy Carter and William Henry Harrison as the best presidents of all time, and Vanilla Ice as the best rapper.

School rankings, impact factors, h-indices, j-factors…they’re all bull. If one thing is clear, it’s that the greatest value of these numbers is in marketing. The annual college rankings sell a lot of US News magazines, and it seems like all the scientific journals are trumpeting their impact factors to attract both subscriptions and submissions.

Don’t take the bait.

One of the major objectives of Harvard’s new Origins-of-Life Initiative is to build a community of scientists who can draw on each other’s expertise to figure out how life started. This approach makes a lot of sense when you consider the interdisciplinary nature of the problem. I really enjoy the collegiality that the new program has offered; it’s quite refreshing. In our department (chemistry and chemical biology), each research group essentially exists on its own island. The chemistry professors at Harvard seldom collaborate with each other on research projects, and inter-group interaction is uncommon. We don’t have departmental problem sessions, organized chats about science, or student colloquia.

In contrast, the Origins program not only offers a full schedule of seminars, but also a number of informal “chalk talks” where incomplete research is presented and discussed among the students and professors who show up. The newest feature of the program is a series of “lab visits,” where everyone tours the laboratory of one of the other researchers in the program. Last month, we took a walk up Garden Street to Observatory Hill and the Harvard-Smithsonian Center for Astrophysics.

Most of the origin-of-life projects in astrophysics concern hunting for planets around distant stars. About 200 exoplanets have been discovered, and there’s a good possibility that their composition can be studied spectroscopically. The researchers are especially interested in finding Earth-like planets and signs of distant life. Right now, the limitations of their techniques make it very difficult to find any planets other than large ones that are close to their stars (so-called “Hot Jupiters”). It’s interesting stuff.

What amazed me about the visit was how astrophysicists have a completely different culture from chemists. The first thing that struck me was that although grad students had advisors, the student offices were located in a central building instead of in the research labs. I got the sense that the students had their own vibrant community in addition to their individual labs, which has definite advantages. It is always nice to have a diverse set of acquaintances who are willing to engage you in scientific discussions. When you spend all day in one research lab, you are often surrounded by people who are experts in the same area and think alike.

Much like chemists get classified into organic and physical, the astrophysicists divide themselves into observers, theoreticians, and instrumentalists. The observers’ research is mostly limited by the time they can reserve on the best telescopes. Getting telescope time is a highly-competitive process: only 1-in-4 proposals are allocated time on NASA’s land telescopes. That number shrinks to 1-in-7 for the telescopes in space. Some schools even sponsor telescopes so that their faculty will have priority on them.

Because resources are tight and government instrumentation is used to collect the data, NASA lights a fire under the butts of the observers by opening the data they requested to the general public a year after it is collected. That means you have a limited period of time to find something interesting before any nerd with an Internet connection can scoop you.

I love the openness of their system. There is no comparison in organic chemistry, where despite the fact that most of our research is funded with taxpayer money, we generally resist sharing our data with anyone until it is published. And once published, some people are still unwilling to grant outsiders’ requests for help or data. Would you be willing to scan your lab notebooks and post them online?

Finally, I thought I’d share one interesting piece of scuttlebutt from the astronomical community. The word on the street is that the slated “Return to the Moon” is not very popular among scientists and stands a reasonable chance of getting scrubbed if the Dems take back the White House in 2008. So if you we’re looking for one, that’s another reason to vote donkey in the next election.

I missed this since I read JACS by the ASAP alerts and every single addition/correction from Sames has been allowed to bypass the system. A tip of my hat to the kind person who e-mailed it.

Edit: I don’t have the time right now to investigate the e-mail’s note that the original supporting information file has been altered so that you cannot compare the new SI with the old, but I wouldn’t be surprised. I’ll get to it tonight, but feel free to investigate this lead on your own. On the surface, it doesn’t look good.

Edited again:  The supporting information files from 2005 and 2007 appear to be identical.  They are also many many pages long, and I’m busy, so you probably won’t get a post from me today.  Sorry.

The Chemmy Award for the Most Outstanding Chemistry Department of 2006 goes to:

Princeton University

In the comments thread announcing the Chemmy Awards, Excimer noted that “although all these awards are subjective as hell, the Outstanding Academic Department is really out there. How can one honestly be 100% objective about such things?”

He’s absolutely right; there’s no way to definitively peg what department had the best year. This award was made to mimic how various sports leagues recognize a general manager or team executive of the year. We’re just asking, “which department made the best personnel moves or exceeded expectations for the past year?” Of course, this is going to make it harder for the “top flight” departments to win this Chemmy. The bar is higher for them, as we’ve come to expect schools like Berkeley, MIT, and Stanford to do amazing things.

So, why Princeton? They’ve made a number of big strides forward in the recent past. Coming on the heels of Sorensen’s arrival from Scripps in 2003, Princeton was able to attract superstar David MacMillan this year. Princeton also gained a resident chemistry blogger in 2006, Carmen Drahl, who’s noted that the school has vastly improved its instrumentation this year. A new chemistry building is also in the works, with completion scheduled for 2010.

In terms of losses, the sophomore organic class at Princeton might suffer with the impending departure of Maitland Jones. He is closing down research operations in preparation for a move to Greenwich Village to teach orgo at NYU. For those interested, The Chem Blog had a post this summer chronicling the movement of some other professors. Yale had a particularly rough year, which included the loss of Hartwig to Illinois.

So, when I think of up-and-coming schools, Princeton is the first that comes to mind. I’ll stand by it as deserving of the award for 2006, but feel free to post your thoughts on other departments that will soon be surging up the rankings.