ChemBark

I have used this blog to opine that the American Chemical Society—and chemists in general—need to do more to improve the public image of chemistry. I think one effective method to advance this goal would be to design an ad campaign in the fashion of Dow Chemical’s “Better Living Through Chemistry.” Of course, it is easy to sit behind a computer monitor and shout at the ACS to do this. It is much more difficult to get the job done. So, in an effort to increase my credentials for yelling at the ACS, I decided to give it a shot myself. After all, how hard could it be to come up with a good idea for a pro-chemistry ad campaign?

It’s hard.

It is easy to come up with examples where chemistry and chemicals have helped society, and you can patch together some tag lines, but it is hard to make everything fit together. I was looking to: (i) do something visually appealing, (ii) introduce a decent slogan, and (iii) educate the public with a small, digestible morsel of the good of chemistry. Here’s what I came up with:

I am not enamored with it at all, but I’ll stand behind it as a first draft. Even if it’s thoroughly mediocre, at least it is something. If we continue to do nothing, the public image of chemistry and chemicals will continue to deteriorate, and it won’t be long before the chemical industry and research funding suffer serious consequences.

Anyway, I think you could extend the idea with other cool pictures and stories (e.g., “a chemical saved my life” with a patient on Gleevec or “a chemical saved my car” featuring some lubricant…whatever).

Credit: I took the photo above from the page of Flickr user treesftf, who kindly made it available for use with a CC-BY license. Also, I completely fabricated the story.

Part of the fun of having a blog is monitoring its traffic, and more traffic equals more fun. I say this because, eventually, someone is going to read this blog and finally create a respectable chemistry journal where all of the correspondence—including letters to the editor, original submissions, referee reports, responses to referees, editorial decisions, and reader comments—is signed and available online. That post was from 2007. What is the delay, people? Let’s make this happen.

Long ago, I had the fanciful idea of running an ad for ChemBark in C&EN. What better way could there be to reach out to so many chemists? Unfortunately, I quickly learned that I couldn’t even afford a single line in those mind-numbing walls of text at the end of the magazine. If you want an ad in the middle of the magazine, the minimum you’ll have to shell out is $3,560 according to this notice (16 April 2012, p. 54).

And what kind of magic was I expecting from an ad in C&EN, anyway? Oh yes…all 150,000+ readers would be so intrigued by a URL under a head shot of Ed the Dog that they would race to their computers and hit the site. Once they had the chance to read my biting criticism of Swiss department stores and admire my poor skills at Photoshop, they’d fall in love and become addicted to blogs, for sure!

Ummm, no. And it is through such a lens that I have wondered what other advertisers have hoped to achieve with expensive print ads—especially those who list random compounds they have available. I think my bewilderment hit an all-time high last month when this ad from Quanta BioDesign was published in back-to-back issues:

“Non-Quenching Fluorescein!” certainly grabbed my attention, and the first thing I felt compelled to do was look at the structure to see what was different about this fluorescein. That is when I noticed something was terribly wrong. At least, I think.

That’s not fluorescein, right? It has a methylene group where an oxygen should be. Wait, is that why this molecule is special? Wait, that shouldn’t even exist…it would tautomerize (such that one of the methylene hydrogens would move to the carbonyl group to make the ring system aromatic).

I was confused, so I went to the Web site and searched for Product #10885. It turns out, there is no product #10885.

So, let me get this straight…this company paid $6,150 (x at least 2 weeks) to run an ad with a wacky structure for a product that doesn’t exist?! I wish I had that kind of money to throw away. I’d save up and get Ed on the back cover.

I have found so many errors in ads run in C&EN that I could probably make a decent living proofreading them on commission. And I sometimes wonder how much money a chemistry blog could make if it wanted to get serious about selling ads. C&EN has a weekly circulation of ~164k and lists a rate of $6,150 for the ad above. Could a blogger like Derek Lowe, who reports traffic of 15-20k pageviews per day, make $615 from running that ad? Seems reasonable to me, and I’d just as well see people throw money at Derek.

Someone should run the experiment, but it won’t be happening here anytime soon. I purposely make sure I’m losing money on this site in an attempt to show I’m not in this for financial gain. That said, just to be on the safe side, I have still reported the blog to my employer as a potential conflict of interest. My job provides me with access to nice things like journals, which are useful to the blog and would cost a pretty penny if I were a professional journalist working from home. I think you can mount a reasonable argument that a revenue-free ChemBark meshes well with the educational mission of a non-profit research university.

Incidentally, the “ads” that you see running on ChemBark are fake. Several weeks ago, I added space for a 150 x 150 pixel image to the left sidebar and a 500 x 80 pixel image to the footer of the page. The ads that you have seen in these positions—for instance, the one linking to the assistant editor position listed at Nature Chemistry—have all been designed by me, for fun. They were neither solicited nor purchased, and I will continue to use these ads to link to things I like. Click them and warm yourself with the knowledge that no one is making a penny.

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?

This image has been plagiarized from an unknown source

Since I’ve already given my advice to the ACS regarding how to deal with the space-dinosaur situation, it is only fair that I offer some thoughts to Ronald Breslow as well. Once faced with the facts, JACS pretty much had no other option than to pull the paper. In contrast, Breslow has a variety of options to pursue. Here is what I think is his best course of action:

(1) Stop talking, for the moment. While the “space dinosaur” aspect of the story has gone through the news cycle, the self-plagiarism aspect of the story is only just beginning. By giving comments to every Tom, Dick, and Harry that asks for an interview, you are only perpetuating the agony by ensuring a steady trickle of fresh, negative stories.

To make matters worse, there is probably significant bad news on the horizon: JACS is either going to verify that you violated their ethical guidelines, or there is likely to be considerable backlash from the same group of people who exposed the duplication in the first place. Your reputation is going to depend on integration of the area under the curve of bad-news vs. time. The bad news is coming, the only thing you can do to improve the outcome is to minimize the time that these stories are in the spotlight. You want all of the bad news to crash down like a ton of bricks, then once that happens, you can immediately start re-stacking them.

(2) Get a feel for JACS‘ timeline and act in concert with the journal. The ball is pretty much in JACS‘s court, as they have acknowledged starting an investigation. I have to imagine that this investigation will involve Breslow in some way, so these interactions can be used to get a sense for what is going to happen when.

(3) Try to shape the outcome by admitting some wrongdoing. The case at hand is probably a textbook example of duplication/self-plagiarism. Stuart Cantrill‘s highlighter pen and JACS‘s swift action in pulling the paper—rather than leaving it up—verify this assertion. I think the best way to mitigate the damage is not by fighting everything tooth-and-nail, but by admitting some fault and arguing that the offense is not that serious. You see this behavior all the time in the sports world. In soccer, you’ll see a defender raise his hand after a nasty tackle to admit the foul and wrongdoing in an attempt to avoid further punishment (i.e., getting booked). In poker, players with bad hands will purposely lead out with a small bet in hopes that the other player will just call the defensive bet instead of betting more.

Here, Breslow might volunteer to retract the paper and issue a public apology to avoid worse punishment.

(4) Publicly embrace whatever punishment JACS doles out. This step goes hand-in-hand with the previous advice, but whereas step #3 is designed to influence the punishment, this piece of advice is designed to influence public opinion. Those that see the JACS paper as a violation of ethics will want to be sure that Breslow is punished and learns his lesson. If no such punishment is publicly acknowledged, there will always be questions over whether Breslow was able to “get away” with it.

This perceived lack of justice is the main problem that Dalibor Sames’ reputation has suffered in the wake of the Bengu Sezen scandal. Sezen was exposed and punished to what is probably the fullest extent possible. Her reputation is absolute garbage. On the other hand, it appears that Sames has suffered no significant punishment for his role as a careless manager. He ignored the warnings of several of his subordinates—and in some cases, fired them rather than pursuing the matter—yet it appears that he never lost funding, and wasn’t sanctioned by JACS or Columbia. To my knowledge, he’s never spoken publicly on the matter. Perhaps as a result of this perceived injustice, Sames is a pariah in academic chemistry. When was the last time you saw him invited to a department to give a talk?

In contrast, look at the case of Leo Paquette, who was accused of plagiarizing information from a grant application. Paquette, while maintaining that he never intentionally stole ideas, accepted the (significant) punishment of renouncing all government funding for several years. Whether or not he did the crime, he certainly “did the time”. As a result, he enjoys a rather positive—albeit, slightly tarnished—reputation among organic chemists.

(5) Polish your story—hopefully, the truth. I have no idea what the truth is in this case, but I can see several possible stories that don’t strike me as particularly evil. For instance, Breslow could say he was very proud of this work with homochirality and wanted to share it with an audience larger than that of Tet. Lett. He might have felt the special issue of Isr. J. Chem. and the perspective that JACS asked him to write were perfect opportunities to showcase this work. He could continue to say that while he did cut-and-paste material from the original paper, he thought that he had made enough changes to the manuscript to avoid self-plagiarism. Next, Breslow could admit to making a mistake, in hindsight, and apologize for it. This story would pave the way to voluntarily retracting the JACS paper to free the journal from being held liable for copyright violations…etc.

(6) Sit for an in-depth interview when the punishment comes out. Once again, the best way to handle the impending storm is to get it over with quickly. Pull the Band-Aid right off. You can do this by sitting for one, high-profile, definitive interview. Every subsequent interview request could then be directed to the original one. You see this strategy employed all of the time in politics and showbiz: a star will get into trouble, then sit with Barbara Walters, Diane Sawyer, or Larry King for an hour-long broadcast that gets millions of viewers. Examples: Chris Brown, Pete Rose, Michael Jackson, Mel Gibson.

Don’t fall into the trap of giving an in-depth interview to a young science reporter or, even worse, a hard-nosed blogger. These people have no name-recognition and the interview won’t be regarded as the definitive interview. You are looking for a Barbara Walters—someone  well known who will ask the hard questions (that you expect), but let you tell your story. You do not want a Tim Russert—someone that will work to move through a laundry list of specific questions designed to probe every contentious detail about the issue at hand. The obvious reporter to target is C&EN‘s Rudy Baum. He is the head honcho at the magazine, and he’s already assigned himself the story for C&EN. Since C&EN is the official organ of the ACS, I don’t think the magazine will want to do anything to soil the reputation of Breslow, JACS, or the office of ACS President. Just look at how Baum’s story reporting the withdrawal of the JACS paper ended:

Breslow is a titan in the chemistry enterprise and a major figure at ACS. He served as the society’s president in 1996 and was the recipient of the society’s highest award, the Priestley Medal, in 1999. He is a member of the National Academy of Sciences and a recipient of the National Medal of Science (1991).

That’s a pretty fair/nice way to close a story about the start of an investigation about self-plagiarism.

(7) Keep your chin up. Remember that you’ve got strong records of achievement in research and service to chemistry. The community appreciates your many, many contributions; it just wants to ensure that all of us are held to the same ethical standards. You’ll move past this episode, as you have similar sticky situations in the past.

JACS has removed Ronald Breslow’s “Space Dinosaur” paper from its Web site. Users who click to view the PDF are greeted with the following message:

10.1021/ja3012897
This article was removed by the publisher due to possible copyright concerns. The Journal’s Editor is following established procedure to determine whether a violation of ACS Ethical Guidelines to Publication of Chemical Research has occurred.

This is an interesting move by the editors. While the paper has not yet appeared in print, its presence on the ASAP site constitutes “official” publication. There is something unwholesome about making the paper vanish. After all, isn’t that why we have addition/correction notices? Otherwise, why wouldn’t we go just into the original documents and change them?

Update (9:05 PM) — The guide “Notice to Authors of JACS Manuscripts” verifies that the ASAP version constitutes official publication of the paper:

Authors must consider that the publication date for a paper is the date of first disclosure, either the Just Accepted date, ASAP date, or date on which the issue is posted on the web.

I guess it is possible to un-ring a bell.

The Breslow “dinosaur” story has intensified to a crescendo. What started as bewilderment over a silly press release issued by the ACS about an otherwise unremarkable paper, has morphed into serious accusations of misconduct in the form of self-plagiarism by a living legend of chemistry. The conversation has transpired almost completely on chemistry blogs and microblogs (e.g., Twitter). In an effort to keep track of everything, I have collected a list of pertinent links below, which I plan to curate as the story evolves.

It seems that once again, the collective chemical Internet has uncovered a serious case of misbehavior in our field. This amateur journalism was a truly distributed effort, with multiple sites contributing new facts and insights, and with each site building on the work of the others. The cooperation and openness of the system are two of the reasons I value blogs and blogging. It is heartening to see that small groups of people can catalyze positive change by drawing attention to obvious problems and stimulating thoughtful analysis.

Links Regarding the “Space Dinosaur” Paper by Ronald Breslow

General – Twitter – Commentary and links – #spacedino hashtag – Major contributors: @stuartcantrill, @NeilWithers, @Chemjobber, @SeeArrOh, @ChemBark, @Dr_PaulC, @edyong209, @Sci_ents, @sciencegeist

6/9/2010 – Tetrahedron Lett. – “A likely possible origin of homochirality in amino acids and sugars on prebiotic earth” – Original paper (?)

27/4/2011 – Tetrahedron Lett. – “Erratum to “The origin of homochirality in amino acids and sugars on prebiotic Earth” – Erratum notice

27/4/2011 – Tetrahedron Lett. – “The origin of homochirality in amino acids and sugars on prebiotic earth” – Corrected paper, republished

18/5/2011 – Isr. J. Chem. – “Formation of L Amino Acids and D Sugars, and Amplification of their Enantioexcesses in Aqueous Solutions, Under Simulated Prebiotic Conditions” –A review published by Breslow in the Israel Journal of Chemistry

25/3/2012 – J. Am. Chem. Soc. – “Evidence for the Likely Origin of Homochirality in Amino Acids, Sugars, and Nucleosides on Prebiotic Earth” – Breslow’s perspective paper in JACS

11/4/2012 – ACS Press Room – “Could ‘advanced’ dinosaurs rule other planets?” – Sensationalist press release from ACS referring to the above paper in JACS

11/4/2012 – Just Like Cooking – “Space Dinos! Prebiotic Chemistry Meets Paleozoic Commentary” – Coverage of paper vis-a-vis the bungled press release by See Arr Oh. Possible self-plagiarism is mentioned in the comments thread

11/4/2012 – Chemistry-Blog – “Taking a dinosaur’s name in vain” – Initial analysis of the paper vis-a-vis the bungled press release by Mark

11/4/2012 – Smithsonian Magazine – “Dinosaurs From Space!” – Analysis of the dinosaur idea with respect to evolution

11/4/2012 – Pharyngula – “Adding dinosaurs always makes research sexier” – Analysis of the evolution idea and the press release

12/4/2012 – Boing Boing – “The threat of intelligent space dinosaurs”

12/4/2012 – ChemBark – “Breslow and Dinosaurs in JACS, Oh My” – Analysis of the science in the paper and the bungled press release

12/4/2012 – Sciencebase –”Alien Dinosaur Chemists” – Analysis of the press release vis-a-vis the paper

14/4/2012 – ChemBark – “A Terrible Week for Chemistry” – An attempt at humor

24/4/2012 – Chemistry-Blog – “Space dinosaurs, the saga continues” – Mark posts about the self-plagiarism in JACS, includes Stu’s famous highlighter work. Note that Mark has alerted JACS about possible misconduct by e-mail.

25/4/2012 – ChemBark – “What the ACS Must Do Regarding the Dinosaur Paper” – An editorial calling for correction of the press release and retraction of the paper in JACS

25/4/2012 – In the Pipeline – “Breslow’s Chirality Paper: More Than Just Alien Dinosaurs” – Derek covers the story

25/4/2012 – Nature News Blog – “Eminent chemist denies self-plagiarism in ‘space dinosaurs’ paper” – Daniel Cressey, a reporter at Nature, begins to probe deeper. Breslow is interviewed and defends his paper.

25/4/2012 – Everyday Scientist – “self-plagiarism and JACS” – Sam returns to post thoughts on self-plagiarism

25/4/2012 – Chemical Connections – “I’m still here” – Stu checks in regarding recent and future personal events

25/4/2012 – Curious Wavefunction – “Would Ron Breslow’s dinosaurs be typing this post?” – Discussion of humor in papers, self-plagiarism, and evolution

25/4/2012 – Science 2.0 – “Former ACS President Denies Charges He Plagiarized Himself” – A general piece/note/report

26/4/2012 – ChemBark – “Breslow Dinosaur Paper Pulled by JACS” – First report that JACS has pulled the PDF of the “space dinosaur” paper and launched an investigation

27/4/2012 – Chemistry-Blog – “The case of the disappearing (space) dinos” – Mark comments on the pulled paper

27/4/2012 – Retraction Watch – “JACS temporarily pulls ‘space dinosaurs’ paper for alleged duplication” – Ivan O. reports on the pulled paper and previous retractions involving JACS

27/4/2012 – Nature News Blog – “‘Space dinosaurs’ paper withdrawn amid self-plagiarism allegations” – Daniel Cressey follows up on his earlier piece

27/4/2012 – Chemjobber – “Pentagon, defense industry, legislators respond to professor’s warnings” – Humor from CJ: fake press release regarding possible attack of Earth by alien dinosaurs

27/4/2012 – C&EN – “Breslow Paper in JACS Questioned” – Editor-in-chief of C&E News reports on the pulled paper in the official newsmagazine of the American Chemical Society. The article was updated on 30/4/2012 with a comment from Breslow.

27/4/2012 – Skepchick – “Is it still plagiarism if you copy yourself?“ – A good discussion of self-plagiarism

29/4/2012 – ChemBark – “My Advice to Breslow“ – Advice on damage control regarding chemistry papers

30/4/2012 – Curious Wavefunction – “The anatomy of peer review: Why airing dirty laundry in public is important” – A fantastic post on two scientists’ quest to correct the scientific record in the wake of another infamous paper by Breslow

1/5/2012 – Just Like Cooking – “Same (Space) Science, Different (Dino) Day” – See Arr Oh points out other similarities among many of the recent origin-of-life papers written by Breslow

3/5/2012 – ChemBark – “How C&EN and JACS Have Changed Since Sames-Sezen” –A look at how ACS Publications handled the Sames-Sezen retractions in 2006 vs. the Breslow “space-dinosaur” retraction in 2012

Please draw my attention to new or missed items by using the comments.