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.

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.

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.

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.

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.

Problem #1: The Dinosaur Press Release

We previously analyzed Breslow’s homochirality paper in JACS and its accompanying press release. The content of the paper was interesting, but the press release missed the point. Perhaps in an effort to engage a wider audience, the Press Room ran with a fanciful, poetic thought on dinosaurs that appeared at the close of the paper. In the process, they almost completely ignored the crux of Breslow’s scientific work. I am not alone in this analysis; the release was instantly ridiculed on Twitter and on many chemistry blogs, yet the ACS Press Room left the story on its front page and in its PressPac for a full week. While some news reports recognized the situation for what it is (1 2 3), other news outlets have run with the release (1 2 3 4 5), and as a result, are perpetuating the bizarre idea.

Solution #1: Issue an Updated Press Release and Draw Attention to It

The ACS must strive to communicate science accurately to the public and in a manner consistent with the spirit of the research. Breslow’s paper had little—if anything—to do with dinosaurs. The press release was an absolute farce. To not correct the focus of the release and allow it to snowball in the mainstream press is completely antithetical to one of the fundamental purposes of the ACS as outlined in its National Charter: “to foster public welfare and education.”

The ACS Press Room must pull the original release, issue a corrected version, and forward it to all news organizations that picked up the story. Furthermore, an employee should be assigned the task of posting links to the updated release in the comment threads for any news stories on the Internet where a corresponding comment threads also exists.

A certain degree of courage is required to publicly acknowledge a mistake, and even more is required to step boldly into the light and attempt to repair any damage that was caused. It is much, much easier to hide, do nothing, and wait for the story to die down. But while it is a thankless task, our society has a duty to spend a day fixing this damage before it moves on.

Problem #2: Ethical Concerns Regarding the Paper in JACS

It has been noted on Twitter—as well as in comment threads here, on See Arr Oh’s blog, and Chemistry-Blog—that it appears that large portions of Breslow’s paper in JACS have been self-plagiarized from not one, but two previously published papers (1 2). The most thorough analysis was conducted by Stu from Nature Chemistry, where he took a pen to the Breslow paper and highlighted the portions that were lifted “>97-98% verbatim from” the previous publications. The five pages of Breslow’s perspective are COVERED in ink (1 2 3). [These three photos are a must-see. Incidentally, I highly recommend following @stuartcantrill's Twitter feed.]

Some commenters have asked whether self-plagiarism is that big of a deal. I can see tenable arguments for either side of this question, and in cases where this is true, it makes sense that any journal should be allowed to set its own policy. The policy for JACS is stated in the ACS Ethical Guidelines to Publication of Chemical Research:

Authors should not engage in self-plagiarism (also known as duplicate publication) – unacceptably close replication of the author’s own previously published text or results without acknowledgement of the source. ACS applies a “reasonable person” standard when deciding whether a submission constitutes self-plagiarism/duplicate publication. If one or two identical sentences previously published by an author appear in a subsequent work by the same author, this is unlikely to be regarded as duplicate publication. Material quoted verbatim from the author’s previously published work must be placed in quotation marks. In contrast, it is unacceptable for an author to include significant verbatim or near-verbatim portions of his/her own work, or to depict his/her previously published results or methodology as new, without acknowledging the source.

Note that this policy makes no distinction among articles, communications, and perspectives, so it should be assumed to apply to any publication in JACS. Furthermore, it is clear from the format and tone of Breslow’s manuscript that it was intended to be a “proper” report of research rather than an essay. The “perspective” label  can offer no wiggle room here. To me, the paper seems like a textbook case of self-plagiarism.

Solution #2: Retract the Paper

Ronald Breslow is a powerful member of the chemical elite, and he has led a distinguished career associated with a strong body of research. He has achieved the rank of University Professor, won the highest honor of the American Chemical Society, and even served as the President of our Society. But no scientist should be above the rules. The unfortunate duty of Peter Stang, the editor-in-chief of JACS, is clear. He must:

(1) Delay the publication of Breslow’s paper in print. It is unfortunate that the paper has been published, but unless the originality of the paper is verified, it must be held in limbo as an ASAP.

(2) Investigate the manuscript for self-plagiarism—a case that, unfortunately, seems open-and-shut.

(3) Force the retraction of the manuscript and make a public notice of doing so.

(4) Sanction Breslow, privately, by suspending him from publishing in JACS for a period of at least one year.

No person would relish taking these steps, especially against someone who wields the power and influence of a man like Ronald Breslow. But to take no action would make an absolute mockery of the ethics of publication in ACS journals. Stang must summon the courage to protect the integrity of our field’s flagship journal; the situation demands it.

Once your group gets to a certain size, you do not really have to worry about the cost of failure anymore. The successes more than make up for it. It’s not a bad thing, it’s just the way it is and not enough chemistry professors who want to be big shots but are at middling chemical departments realize it.

What I mean is someone like Robert Langer takes credit for the successful grad students and the succesful companies, and there are just so many of them, that the ones who fail are forgotten about in light of the success. The better you can manage everything, the bigger your empire will be. Plus it helps to be in a university that attracts students who are very motivated.

If you’re in charge of a small group, then the failure of a graduate student to get any papers will be magnified since you don’t have too many offsetting grad students that are publication machines. In fact, you might have none. I’ve seen a few profs with medium-sized groups that were taking off, but were blinded by their own hubris, forgot that they were not in a top ten school, and decided to ‘fire’ two or three students or postdocs who weren’t performing well enough (not getting a Jackass or Andjewandte or not coming in on the weekend). Not only does this cause potential students in a non top ten school avoid you (since they care more about lifestyle and not monastic scientific pursuit), but it magnifies the failures of your remaining students (should they happen) as your own failures. Automatically, you’re now an average scientist for the rest of your career and not Robert Langer. Not that there is anything wrong with that, as you can do very good science and pay more attention to individual students, but that’s not what some of the more ambitious types wanted before they cannibilized their group. The lesson is get big as fast as possible with as many driven types as possible and then just sit back and manage your success. You have to get rid of someone who creates a bad group dynamic or is lazy or just plain stupid of course, but once it starts being every second person who works for you, then you’re not doing it right (unless you’re in a really crappy department). Once you’re going, you can move to better and better departments and become bigger and bigger and have to worry about failure even less.

The same effect used to work in pharma. If you’re the CEO of a start-up, when your drug fails, your failure is huge. You’re out of business. If you’re the CEO of a big pharma company and a few candidates fail Phase II, it’s no biggie because you’re got good phase III data on that one cholesterol lowering candidate that will pay the cost of failure for the others.

That’s some biting analysis, filled with all of the cynicism and bitterness one expects of a recent product of graduate school in chemistry. Of course, none of the analysis had to do with the topic of that post—pictures of professors working in labs—so just to make sure Eugene’s thoughts didn’t get lost in the shuffle of the other thread, I wanted to unpack them here.

While it’s more than a bit cynical, the point that Eugene makes about large groups’ affording their PIs protection from a degree of failure is absolutely correct. PIs are judged by the magnitude and number of their accomplishments, not by unspectacular failures. In all of the farkakte metrics used to judge research productivity (e.g., paper count, h-index, total citations), I have never seen someone divide the metrics of accomplishment by the number of graduate students and postdocs required to achieve them. The situation is not unique to chemistry. Reggie Jackson is remembered as one of baseball’s greatest hitters, despite the fact that he holds the dubious honor of being the MLB’s all-time leader in career strikeouts. But people don’t remember the 2,597 strikeouts; they remember the handful of home runs he hit in the clutch.

Getting back to chemistry, let me start by stating that I think it’s great when professors establish themselves to the point that they have the flexibility to fail. It is a deserved product of success, and everyone should be so fortunate in their jobs. Getting to this point probably also helps take the heat off of students in the lab. And when students “fail” (or flounder or whatever), I don’t think you can blame the PI solely (or even primarily). A lot of factors influence these outcomes, ranging from things that can be controlled (intelligence, lab skills, motivation, work ethic, design of experiments) to those that can’t (bad luck, family issues, medical issues).

What worries me about “superlabs” is that by their design, one or more students is probably destined to be ignored not because of his or her personal failings in lab, but because the number of available professor-hours in a year is limited. Eugene is making the point that professors in superlabs need only pay attention to a fraction of their students because their accomplishments will be enough to support the machinery of the superlab and ensure its continued existence. In this model, a professor actively makes a decision to ignore some students. That idea is extraordinarily cynical, but I am not at all sure it can be ruled out.

My view is that one needn’t adopt as cynical a view to show what is effectively the same outcome. That is, I will assume that professors want to pay attention to all of their students, but sometimes, they just can’t. I assume that professors sleep, eat, commute, attend to personal hygiene, spend time with their families, watch television, and do other “normal” stuff we expect of human beings. These activities require time, and together, probably account for more than half of the day. Even if you are going to spend the entire balance of time performing “work”, there is a lot of work to get done. You’ve got to teach, prepare for class, hold office hours, write grants, write reports, serve on committees, go to departmental meetings, meet with speakers, referee papers, keep up with the literature, travel to conferences, give talks, and write letters of recommendation. I am sure I have missed some things, but that is already a lot of stuff and it doesn’t even begin to address advising students—or ancillary work such as consulting or running start-ups. It is an absolute miracle that people can do all of these things and run groups of 10+ students and postdocs, let alone 30+ or 40+. In these cases, it’s almost inevitable that some students will fall by the wayside.

In an era where we have a surplus of freshly minted chemists and a dearth of jobs, I think our field should consider whether it wants to encourage the model of superlabs run by single professors. I personally like the idea of incorporating senior investigators into these research groups to serve as “minibosses” that can provide hands-on expertise and advising. In defense of Langer’s superlab, which might be the biggest in all of chemistry, it is my understanding that he does employ a group of senior scientists as lieutenants to oversee his various subgroups. But, by and large, I don’t think this idea is very common in chemistry. I think a lot of people feel the money for one senior scientist is better spent on multiple students and postdocs, and the delegation of authority is something many professors loathe to accept. While every lab is different, as time goes on, professors’ increasingly jammed schedules are bound to take a toll on advising. Graduate schools must watch out for their students, because many overextended professors will not.

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