ChemBark

It’s time to start attacking the ChemBark mailbag. Let’s begin with this little gem sent in by Excimer:

Photo credit: Excimer

Excimer writes:

I’m currently reading the sci-fi classic series Cities in Flight by James Blish, and hooray! there’s organic chemistry in it. Unfortunately, it looks like this.

Indeed. You’ve gotta love the: (i) Texas carbon, (ii) doubly-bonded hydrogen, and (iii) calcium–carbon bonds. I guess this sci-fi classic is heavier on the fiction than the science.

It seems that VWR and I have very different opinions as to what constitutes “IMPORTANT Information”:

A dinosaur squishy toy attached to a 15%-off coupon for a new balance only musters an 8.2 out of 10 on my scale of importance, but thanks for writing.

Just about every chemistry blogger—including me—has lamented the increase in the number of businesses that advertise their products as “chemical free”. This rampant war on chemicals is as distressing to our field as it is to common sense—no product is free of chemicals.

But while I’ve seen plenty of anti-chemical ads, I’d never seen an anti-chemistry ad…until now:

Photo credit: Megan!

My fabulous labmate Megan snapped this photo at the Jamba Juice on historic Colorado Blvd in Old Town Pasadena. For those who might not be familiar with Jamba Juice, it is a fast food chain that sells overpriced fruit drinks to people who want to pretend they are living a healthy lifestyle. Imagine a less successful, fruity version of Starbucks. The slogan on their trough reads:

“ALL THE ENERGY, WITHOUT THE CHEMISTRY.”

Well, hot damn. No chemistry…whatever that means. And here I thought “chemistry” actually had a positive public image (e.g., “that football team has good chemistry”). Oh well. Not for long.

Jamba Juice even has a handsome anti-chemistry commercial too:

Oh no! Taurine? Inositol?! I don’t want anything to do with those!

Give me real fruit juice (for $6.99 + tax) and I’ll forget about the fact that real fruit juice naturally contains inositol, and taurine naturally accounts for 0.1% of our body weight.

Argh! I’ll stick to soda to wash down this stupidity.

Matt at ScienceGeist is hosting a blog carnival this week on “Our Favorite Toxic Chemicals.” The idea is to generate posts about chemicals that have reputations for being toxic, but that also have important applications and non-toxic manifestations (e.g., in low concentrations). All of your favorite chembloggers have posts up, including Excimer, who has returned from a long blog hiatus.

I should have my contribution up by Friday. What I love about this carnival is that the posts will live for eternity, standing ready to drop some knowledge on any curious soul who runs a Google search for one of these molecules.

In other news, I have been busy going around the department in preparation for a visit next week from a very special guest. On my recent travels from office to office, I came upon a number of these signs in the hallway outside of a research lab:

CHEMICAL FREE ZONE!!

NO labcoats, gloves, tlc plates, NMR samples or other chemical contaminants

The extra exclamation mark lets you know that they mean business. I’ll refrain from identifying the lab to protect my colleagues, but the scene definitely made me cringe. I understand it when marketers raise the “chemical-free” dagger, but a lab of chemists? Et tu, Brute?

In a subsequent discussion on the matter, a member of a different lab pointed out that my concern was probably a trifle, because this building was a laboratory not generally accessed by the public. Under these conditions, the sign is widely understood to succinctly communicate that contaminated items should not be brought into the office space.

While I think such an argument is tenable, it is preferable (and relatively easy) to avoid the controversy completely. If we—chemists—can’t be bothered to find a suitable alternative to “chemical-free”, then why should we expect the same from laymen? It seems like a sign that says “No lab equipment or samples in this room” would get the job done with only a slightly less economical use of words.

And finally, a kind chemical engineer sent me a link to the following paper, in which a freshly-minted Harvard professor railed against “chemical free” in 1995:

Chemistry and the chemical industry often are misunderstood by the general public. It is not uncommon for products to be advertised as “chemical free” or for a product to be labeled dangerous because it contains chemicals. As chemists, we know that these claims are incorrect. Unfortunately, many people in today’s society do not have the chemical training necessary to determine whether or not such claims are valid.

I guess J. Chem. Ed. was where bloggers blogged before there were blogs.

While the transgressions in the Sames-Sezen and Breslow sagas are very different, we can use both events as probes for how the ACS (through C&EN and JACS) deals with unethical behavior. A lot has changed in the past six years.

The first set of three Sames-Sezen retractions was published in JACS on 1 March 2006. I remarked at the time that these “addition/correction” notices had completely bypassed the ASAP page as well as the daily JACS e-mail feed. This move by the journal may have been unprecedented, and it certainly was not common. The move reeked of sweeping the scandal under the rug. Feeding into this perception was the fact that in spite of the magnitude of the situation, C&EN did not run a story on the retractions until the afternoon of 15 March 2006. Coincidentally—<rolls eyes>—the magazine happened to beat the New York Times to press by a couple of hours. Keep in mind, the ACS Publications division knew these retractions were coming for quite some time, yet once they were finally released, it took an additional two weeks for C&EN to write up a bare-bones story.

In contrast, C&EN ran a story reporting the withdrawal of Breslow’s offending paper less than a day after it was pulled from the JACS site. In both cases: (1) blogs reported the transgressions before anyone else and (2) once the papers were finally withdrawn, online traffic and discussion flared up quickly. The difference this time around was that C&EN did not wait to jump in and provide “official” coverage. It seems that C&EN might have learned a few lessons from 2006: (1) although these stories do not paint chemical research in a positive light, they are important to cover, (2) chemists are interested in these stories, and (3) these stories will not go away, so there’s no sense in waiting to report them.

This apparent change in approach makes sense to me, and I applaud it. In contrast, the editorial decisions made by JACS with regard to retractions—both then and now—are beyond my comprehension.

The recent Breslow perspective was published online and, I assume, in print since it was assigned page numbers (vol. 134, p. 6887-6892). Despite the publication of the paper in print—an action that cannot be reversed—JACS completely pulled the paper from its Web site. The site Retraction Watch noted that it is unusual for a journal to take this step, especially preemptively, before it has completed an investigation. It is more common to leave a copy of the retracted paper online, with a note that refers to its withdrawal. Retraction Watch points to an example where JACS has left a retracted paper online with a notice, and a different example where a paper was retracted and essentially had its DOI commandeered by the subsequent addition/correction notice. The original paper, which had been assigned proper page numbers, now appears as Supporting Information. The case is similar for another JACS article brought into question by the chemical blogosphere: the infamous NaH-as-an-oxidant paper. This paper never made it off the ASAP page—it has no proper page numbers—but it remains online as the Supporting Information for a subsequent retraction notice.

So, what is the pattern? Perhaps we can throw out the Breslow retraction because JACS wanted to avoid liability associated with copyright infringement, but what about the different treatment of the two other retracted papers that made it into print? Odd.

And if we go back to 2006, things get even more strange. Bengu Sezen’s 2004 paper in JACS remains online with a note about the retraction written under the title of the PDF. Fine. But take a look at the addition/correction notice:

After the departure of the first author, the laboratory of the corresponding author (D. Sames) has been unable to reproduce the key results in this publication. Accordingly, the corresponding author withdraws this paper, and deeply regrets that the chemical community was misled by its publication.

Now, look what you’ll see if you open a print edition corresponding to that addition/correction. A kind reader from Montreal sent me a scanned image of the page in question.

After departure of the first author, we were unable to reproduce the key results presented in this paper. The parent coupling between pyrrolidine and iodobenzene does proceed; however, the efficiency is far lower (GC <4%) than originally claimed. The authenticity of spectral data provided in the Supporting Information cannot be confirmed. Accordingly, we withdraw this paper. We deeply regret that the chemical community was misled by this publication.

The two publications are strikingly different. Also, I am not sure whom the “we” referred to in this case. Perhaps that is one reason why Sames and/or JACS decided to make the modification. Whatever the reason, the first version of the retraction completely disappeared from the JACS Web site.

So, in the Breslow and Sames cases, we have situations where the print versions of the Journal are different from the online versions. In the former case, an unfilled hole exists online. In the latter example, the Web and paper editions disagree, and there is no notice of this disagreement.

Why would a journal want to do this? My first thought turns to legal considerations. The original Sames-Sezen addition/correction notices were published under the names of all the co-authors on the paper. We know from Sezen’s comments to the press that she vehemently denied anything was wrong with her work, so she would seem to have a strong claim that she was misrepresented by both Sames and JACS.

But, I don’t know for sure. Everything above is a hot mess, and I don’t think JACS has any firm editorial policy regarding how to deal with retractions. That said, I could easily have overlooked something. Feel free to take me to task in the comments. Regardless, I think many of these actions are inconsistent with one of the central tenets of scientific publishing. Aren’t journals supposed to constitute a permanent record of information? If not, then why can’t we all correct errors we find in our papers by overwriting them online?

Today’s image was kindly sent in by Santiago, who stumbled across this scene at the Globus department store in Geneva, Switzerland:

(click to enlarge)

Kiehl’s makes beauty products, and what could be more beautiful than phenanthroline, right? I sure hope there is plenty of carbon monoxide in my skin cream—especially carbon monoxide that’s missing four electrons.

But not all is wrong in the world of chemical art: check out the cool gate at Yale that See Arr Oh found. The chemical structure represents a tetrapeptide that spells out Y-A-L-E (tyrosine-alanine-leucine-glutamic acid). Pretty cool.