ChemBark

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 In both cases: (1) blogs reported the transgressions before anyone else and (2) once the papers were finally withdrawn, online traffic and discussion flared up quickly.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?

You all know that origin-of-life research is near and dear to my heart, and you’re probably sick of how often I lament that the problem has not taken root in chemical academia despite the fact that it almost certainly requires a chemical solution. One of the few PIs at a top university who has dabbled in the field is Ronald Breslow, University Professor at Columbia and a past president of the ACS. Breslow just published this little diddy as a perspective in JACS:

First of all, how often do you see a single-author paper in JACS anymore? It is kind of refreshing. It also means that you can attribute 100% of the content to Breslow, including the ChemDraw structures:

What the hell is that? If I drew that structure on a slide in grad school, my committee would have eviscerated me.

Anyway, let’s get down to the science. Breslow’s premise is that you can take alpha-methyl amino acids found in non-racemic mixtures in meteorites—generated by selective destruction of one enantiomer by circularly polarized UV light—and “use” these compounds to generate non-racemic mixtures of sugars (which are also found as moieties in nucleic acids). Since meteors hit the early Earth with great frequency, maybe one or more of these chiral amino acids was the origin of life’s homochirality. It is an interesting idea and one worth keeping in mind. We could argue all day about how unlikely the scenario is, but this field needs to collect more neat ideas accompanied by simple demonstrations. That said, I take issue with the premise of the paper as outlined in the Introduction:

In 1969 a carbonaceous chondritic meteorite landed in Murchison Australia carrying many organic compounds. These compounds were apparently able to survive the frictional heating as the meteorite passed through our atmosphere since they were initially at ca. 10K, and chondritic meteorites are pieces of rock, with low thermal conductivity, from the asteroid belts that surround the sun. When the meteorite was split open the interior was still cold enough to freeze water.

Among the compounds identified were the amino acids alanine, valine, aspartic acid, glutamic acid, proline, and leucine, which were racemic, with equal mixtures of the L and D forms, along with achiral glycine. However, five amino acids were found that had methyl groups instead of hydrogens on their alpha positions (Figure 1), and these had a range of small excesses of the enantiomers originally described as the L amino acids (in modern terminology they are the S enantiomers). Since that time, these and other α‐methyl amino acids with small excesses of the S enantiomer have been found in the Murchison, Murray, and Orgueil meteorites (ref 1).

The whole point of why the Murchison meteorite is so interesting is that while the “natural” amino acids in it were initially thought to be racemic, subsequent analyses revealed them to have enantiomeric excesses.  I could be missing more recent analyses, but I don’t think so. Breslow should check out these seminal papers (1 2) and revise his background before the paper is “truly” published in JACS.

It is things like the odd ChemDraw structures and completely wrong information in the background that make me question the quality of peer review in JACS (and in all of chemistry, for that matter). I think one should also question the fairness of the editors, for I cannot imagine that this paper would have made it anywhere near publication in JACS if the author were Assistant Professor Joe Schmoe from Sunny Valley Technical College. But that said, the editors of JACS are the sole arbiters of what is “worthy” of publication in JACS, so I’ll just accept it and move on.

Normally, I wouldn’t blog about an otherwise run-of-the-mill paper about the origin of life, but this paper has really taken off in the world of popular science thanks to what amounts to a poetic thought by Breslow used to close the paper:

An implication from this work is that elsewhere in the universe there could be life forms based on D amino acids and L sugars, depending on the chirality of circular polarized light in that sector of the universe or whatever other process operated to favor the L α‐methyl amino acids in the meteorites that have landed on Earth. Such life forms could well be advanced versions of dinosaurs, if mammals did not have the good fortune to have the dinosaurs wiped out by an asteroidal collision, as on Earth. We would be better off not meeting them.

Since you are a reader of blogs, you will recognize this paragraph for what it is: a silly piece of fluff meant to close an otherwise esoteric piece on a humorous note. I’ve got no problem with that. We can argue over whether the joke is funny, but the attempt at humor is obvious…

…except to the staff in the ACS Pressroom, for they issued the following press release to promote the paper. I am copying it here verbatim because these things are intended for distribution—and because it is ridiculous.

Could “advanced” dinosaurs rule other planets?

“Evidence for the Likely Origin of Homochirality in Amino Acids, Sugars, and Nucleosides on Prebiotic Earth”
Journal of the American Chemical Society

New scientific research raises the possibility that advanced versions of T. rex and other dinosaurs — monstrous creatures with the intelligence and cunning of humans — may be the life forms that evolved on other planets in the universe. “We would be better off not meeting them,” concludes the study, which appears in the Journal of the American Chemical Society.

In the report, noted scientist Ronald Breslow, Ph.D., discusses the century-old mystery of why the building blocks of terrestrial amino acids (which make up proteins), sugars, and the genetic materials DNA and RNA exist mainly in one orientation or shape. There are two possible orientations, left and right, which mirror each other in the same way as hands. This is known as “chirality.” In order for life to arise, proteins, for instance, must contain only one chiral form of amino acids, left or right. With the exception of a few bacteria, amino acids in all life on Earth have the left-handed orientation. Most sugars have a right-handed orientation. How did that so-called homochirality, the predominance of one chiral form, happen?

Breslow describes evidence supporting the idea that the unusual amino acids carried to a lifeless Earth by meteorites about 4 billion years ago set the pattern for normal amino acids with the L-geometry, the kind in terrestial proteins, and how those could lead to D-sugars of the kind in DNA.

“Of course,” Breslow says, “showing that it could have happened this way is not the same as showing that it did.” He adds: “An implication from this work is that elsewhere in the universe there could be life forms based on D-amino acids and L-sugars. Such life forms could well be advanced versions of dinosaurs, if mammals did not have the good fortune to have the dinosaurs wiped out by an asteroidal collision, as on Earth. We would be better off not meeting them.”

What. The. Hell. Some booger-eating PR guy on 16th Street jumped to the end of the manuscript and took Breslow’s joke at face value. Then, his/her editor never thought to question the idea, and sent the press release out in the weekly PressPac. Now, the ACS is the laughing stock of the world of scientific publishing and popular science writing.

I guess we’ve learned nothing from the NASA/Wolfe-Simon/Arsenic Life episode. Why the hell do these things always seem to happen to origin-of-life chemistry?

:/

See also:

Just Like Cooking
Chemistry-Blog
Pharyngula
David Bradley’s Sciencebase
The Awl

This article from 1965 might be the first example of the publication of a purely farcical chemistry paper in a respectable journal. This article also appears to have completely eluded the attention of blogs, most likely because bloggers were especially lazy in the 60s. The unmistakable quality of the paper is certified by a consequent letter to the editor, in which a concerned member of the Canadian Medical Association wrote:

I was appalled to read J.S. Greenstein’s Very Original Article on “Armpitin”…I am very sorry to observe that the official journal of Canadian doctors has published this article.

The paper describes the development of armpitin as a powerful contraceptive agent. While the author provides a structure for a portion of the molecule, he refuses to provide the full details of its synthesis because he “intends to make a fortune.”

The results seem unsurprising. I would wager that a majority of us have collected anecdotal evidence that a repetitive string of NOs can be very effective at preventing pregnancy. The author reports he serendipitously stumbled into the field of contraceptives while designing deodorants. One deodorant led to a noticeable increase in libido without concomitant increase in pregnancy. His initial studies proceeded from there:

With typical male self-assurance, we undertook to examine the females for the causative factors leading to their infertility. We employed every known gross anatomical, histological, histochemical, biochemical, endocrinological, physiological and psychological test of reproductive capacity and could find no evidence of malfunctioning of the female reproductive systems and accessory structures. We could only conclude, reluctantly, after months of exhaustive investigation, that the females were normal in all respects, and that we should turn our attention to the males.

When we took the trouble to examine the ejaculates obtained by masturbation, artificial vagina, or by post-coital recovery from the site of deposition, the answer to the enigma stared back at us through the narrow barrel of the microscope tube: THERE WERE NO SPERMATOZOA IN ANY OF THE SEMEN SAMPLES.

Yeah, this paper was actually published in a respectable journal—and in 1965, when by all accounts, people were humorless. (There is simply no other rational explanation for the popularity of Jerry Lewis.) What shocks me more than anything is that the content of the paper is 98% pseudo-legitimate technobabble and only 2% punchlines, yet the editor allows the damn thing to go on for 5 pages. That said, the list of references is particularly amusing. The author acknowledges “A. Gabriel” for divine inspiration in the form of a personal communication, and also cites a paper on orgasm by C. Men as well as a child’s guide to erotica by M. Goose.

While I regularly advocate that Carl Djerassi should be recognized by the Nobel Committee, I don’t think that Dr. Greenstein’s seminal contribution rises to the same level.

Yesterday, I attended an interesting symposium that featured a slate of talks by five undergrads here at Caltech. During a presentation on the formation of dendritic structures during the recharging of lithium batteries, I was momentarily distracted by a citation to the following paper:

 Kahanda, G.L.M.K.S.; Tomkiewicz, M. J. Electrochem. Soc. 1989, 136, 1497.

That has got to be a record for the chemist with the most middle names. His full name—which can be found in his Ph.D. thesis on the electrochemical morphogenesis of zinc and silver—is Galathara Lekamge Mahendra Kumara Samarakone Kahanda. Remarkably, it appears that he is related to a computer scientist with an even longer name: Galathara L.A.U.K.S. Kahanda. Well, either that, or he found a two-for-one deal and traded in his “M”.

You think these guys know Govindjee?

My advisor passed along a paper for me to read that blew my mind. The corresponding author has but one name…

So…

Fashion has Fabio;
Music has Madonna;
Biochemistry has Govindjee.

A quick bit of research from his Web site reveals:

I use only one name; Govindjee is my given name; my family name is “Asthana”, but I do not use it. My wife uses “Rajni Govindjee” as her name, and our children use “Anita Govindjee” and “Sanjay Govindjee” as their names. My departmental friends call me “Gov”.

I like his style. It balances out all of the German chemists who—back in the day—added fake middle initials to distinguish themselves from one another in the literature.

Wow…there has been a lot of criticism of the “arsenic-based life” paper.  A lot.  There’s so much that I’m not even going to try to link to all of it.

As you know, I’m a pretty affable person.  I never have a bad word to say about anyone, and the last thing I would do is kick someone while she’s down.  That’s just not my style.  Consequently, I’m not going to tell you about the time I had lunch with Dr. Felisa Wolfe-Simon a couple of years ago when she was a postdoc at Harvard.

You see, a good deal of my graduate work was in the field of origin-of-life chemistry.  I was a fellow of the nascent Origins-of-Life Initiative at Harvard and participated extensively in the program.  I am fascinated by the challenge of the problem and believe that the matter of how life originated on Earth is the second greatest mystery in the planet’s history.  (The first is how the arsenic paper made it past the editors of Science.)

A couple of years ago, the great Albert Eschenmoser came to give a talk at one of the monthly Origins Forums at Harvard.  Thanks to the largess of the director of the initiative, I snagged an hour with Prof. Eschenmoser and the honor of taking him to lunch.

I invited my partner-in-OoL-crime to the chat, and after the two of us had a nice discussion with Eschenmoser about our research, we were joined by a fourth person for lunch: Dr. Felisa Wolfe-Simon.

My knowledge of FWS was limited.  I knew her only as the girl with hot pink hair who asked a lot of questions at OoL talks.  I think there should be a strict limit of two questions per person per seminar, unless I need to go to the bathroom, in which case there should be a one-question limit.  And short of trying to gain employment as a marker buoy in Boston Harbor, I can think of no good reason to dye one’s hair magenta.  Whatever.

Lunch was short…and uncomfortable.  At one point, FWS brought up trying to incorporate arsenic into DNA.  (Remember, this was years ago.  I assume it was before she started her work at Mono Lake.)  FWS said she wanted to make DNA with arsenic atoms as the backbone.

Eschenmoser asked if Felisa had any experience in synthetic chemistry.  She responded that she had none, at which point Eschenmoser recommended that she not undertake this work as it would be very synthetically challenging.  FWS’s response was that it might be a good thing for her to have no synthetic experience: with no knowledge of the challenges, she would not be daunted by such a hard task.

I love when people justify ignorance…of anything.  And I didn’t think she was joking.  I buried my gaze into my avocado sushi roll and occasionally exchanged uncomfortable glances with my labmate.  In the words of John McEnroe…you CANNOT be serious!  Did she not know to whom she was speaking?  This was Albert Eschenmoser, a titan of organic chemistry.  I felt embarrassed that I was even involved in this conversation…and in the chemistry building at the finest university in the world.  Ugh.

Eschenmoser took her comment at face value and went on the reinforce the point that this task would require extensive synthetic skill.  Lunch was over quickly after that.  My labmate said he would never forgive me for wasting his time.  I can’t blame him.

What does all of this mean?

1) I am a jerk.  Sorry.

2) Wolfe-Simon is not an organic chemist or anything close to one.  I have no trouble understanding the lack of attention to detail in the chemistry presented in the Science paper.

3) Wolfe-Simon has been looking for arsenic-based biomolecules for quite some time.  I don’t want to try to read too far into the tea leaves, but sometimes when you are really looking hard for something, you think you’ve found it when you haven’t.  She missed some obvious experiments, but my guess/hope was that she didn’t do so maliciously with an intent to deceive.  She is one of the most enthusiastic, effervescent scientists I have ever encountered.   I think that she may have been so excited to have found what she was looking for that she got a little ahead of herself.

Still, I don’t condone this behavior from an experienced scientist.  Regardless of whether her conclusions stand, the work is shoddy.  What really bugs me is that papers like these end up harming the field of prebiotic chemistry.  I have said before—on blogs and in seminars—that prebiotic chemistry does not get the attention the subject deserves.  One of the big reasons it doesn’t is because chemists don’t respect the field.  People trumpet the simplest results as major discoveries and chew up space in Science and Nature that would probably best be left for less sexy but more robust results.  This paper is going to do nothing but reinforce this image, and that’s a damn shame.