Archive for the ‘Ethics’ Category

How Should the Online Community Handle Suspicious Papers?

Saturday, August 17th, 2013

The latest news regarding the Dorta paper in Organometallics is that Emma Drinkel’s mother wrote an e-mail to Fredrik von Kieseritzky that is posted to his chemistry blog, Synthetic Remarks. You will recall that Emma Drinkel was the first author on the OM paper, and she was on the receiving end of the infamous instruction to “just make up an elemental analysis”.

Dr. Drinkel’s mother wrote:

From: Mary-Anne Drinkel [mailto:xxxxa@xxxx.co.uk]
Sent: 15 August 2013 21:04
To: Fredrik von Kieseritzky ‘xxx@xxx.com’
Subject: Emma Drinkel – the Dorta Affair

Dear Dr Kieseritzky

I hope you don’t mind me contacting you, but I would just like to thank you for your comment on ChemBark. My name is Mary-Anne Drinkel, and I am mother of Emma. We are very proud of our daughter she has worked hard and conscientiously to earn her first class degree at Durham, her PhD at Zurich, and presently her Post doctorate work in Brazil- we know that fabricating data would be alien to her. I cannot believe that her good reputation, built up over these years can be destroyed in a week. I know nothing of the academic community, but the hostile and aggressive comments left on the blog sites are unbelievable. I don’t know if Reto Dorta was careless or has done a very bad thing, but I do know that Emma is the innocent party in this affair. How many PhD thesis could withstand the hostile scrutiny that Emma’s has been subjected to, with these bloggers determined to find evidence of wrongdoing – boasting about who broke the news first.

Emma’s husband has a new industry position in Switzerland, and they will be moving back to Europe very soon; this means Emma will be applying for jobs – she fears this affair will affect her chances, as she would be honest with prospective employers about her situation. They had decided to leave the academic world long before this episode because the competitiveness and political environment of university life was not for them. Emma is devastated that her good name at Durham and Zurich University will be forever tarnished by this affair.

My husband and I have felt so sad and so helpless as these events have developed – when I saw your comment that was sympathetic to Emma’s plight, it was the first bit of humanity I had witnessed in the whole affair, and I am grateful to you for that. Emma will get through this, she is resilient and has the support of her husband, family and friends – but we feel so angry that Emma has been subjected to this through no fault of her own.

Once again thank- you,

Best wishes,

Mary-Anne Drinkel

Credit: Synthetic Remarks

I sympathize with Dr. Drinkel, but when you are an author on a paper, you share responsibility for its content. This responsibility is especially serious for the first and corresponding authors on a paper. With that said, it could easily turn out that Dr. Drinkel’s only transgression might have been a failure to carefully read the published version of her article—which most chemists probably don’t do anyway.

As it stands, it is impossible and unproductive to attempt to assign blame to specific people. We don’t know who wrote what parts of the paper, who was responsible for submitting it, and who reviewed the galleys. What we do know is that the paper is suspicious. It is a fact that the editorial remark to “just make up an elemental analysis” was published in the Supporting Information. It is a fact that the elemental analysis data in Dr. Drinkel’s thesis are different from the data presented in the paper.

The integrity of data is the foundation of scientific research. The community has a serious interest in maintaining the integrity of its data and pointing out cases where the validity of a particular set of data should be questioned. I don’t think that investigations into possible misconduct are best left solely to journals and universities. Time and time again, we have seen journals state that they do not have the resources to conduct thorough investigations of suspicious data, and once they have acted, the punishments are never made public. Where is the accountability?

Universities, often by law, are required to conduct thorough investigations of possible scientific misconduct. But the details of these investigations—even when they definitively identify egregious misconduct—are also often swept under the rug. It can be pointed out that journals and schools have little incentive to identify and publicize misconduct that has occurred on their watch. The community is not served well by this secrecy, and there would seem to exist an important void in the process for journalists, blogs, and social media to fill. These stakeholders can help identify suspicious data, misconduct, and the scientists responsible for it.

On the flip side of the coin, when suspicious data or behavior are identified, scientists who have not engaged in misconduct can get dragged in the mud. There will always be people who read a blog post on a suspicious paper and lump all the authors together without much thought. Obviously, Dr. Drinkel’s mother—as well as another commenter—is upset with my coverage of her daughter’s paper. My question is how would they have handled this situation and similar ones in the future?

The Committee on Publication Ethics has developed a set of recommended procedures for journal editors to deal with suspicious papers. How should chemistry blogs write about them? Should we just post links to these papers without comment? Should we write about them but close the posts to comments? Should we moderate the comments to remove unfair opinions and speculation? Should we black-out names and delete comments that attempt to identify the authors? Should blogs avoid writing about suspicious papers altogether and just rely on journals and universities to tell the community what they think we should know?

I bet there are a variety of opinions out there; I would love to hear yours.

Dorta Paper Link Roundup

Tuesday, August 13th, 2013

For chemistry news stories that generate a lot of fragmented discussion online, I like to post a list of links to facilitate keeping track of everything. This post may be updated; I think there’s a good chance we will hear more about this story down the line….

Coverage of the Dorta-Drinkel paper in Organometallics

12 July 2013 – Organometallics – “Synthesis, Structure, and Catalytic Studies of Palladium and Platinum Bis-Sulfoxide Complexes” – Original published article

6 August 2013 – ChemBark – “A Disturbing Note in a Recent SI File” – Our original report

6 August 2013 – Reddit – “Check out page 12 of the supporting info…”

7 August 2013 – In the Pipeline – “New Frontiers in Analytical Chemistry”

7 August 2013 – Chemistry-Blog – “When Authors Forget to Fake an Elemental Analysis”

8 August 2013 – Reddit – “A Disturbing Note in a Recent Supplemental Information file for a published chemistry paper”

8 August 2013 – Reddit – “Editor-­in­‐Chief of Organometallics Responds to Paper by Reto Dorta”

8 August 2013 – ChemBark – “Organometallics Responds to the Dorta Situation”

8 August 2013 – In the Pipeline – “Make Up the Elemental Analysis: An Update”

8 August 2013 – Retraction Watch – “Insert data here … Did researcher instruct co-author to make up results for chemistry paper?”

8 August 2013 – Science Careers – “Note to Self: NEVER do This”

9 August 2013 – ChemBark – “The OM Paper vs. Drinkel’s PhD Thesis”

9 August 2013 – Slashdot – “Request to Falsify Data Published in Chemistry Journal”

9 August 2013 – Chemical & Engineering News – “Insert Data Here … But Make It Up First”

9 August 2013 – Chemjobber – “The Dorta Affair and others…”

12 August 2013 – Reddit – “[Recap] A failure in peer review enrages /r/chemistry”

16 August 2013 – Synthetic Remarks – “In Defense of Emma” – includes an e-mail from Dr. Drinkel’s mother

16 August 2013 – Reddit – “Emma’s Mother Responds to the Dorta “just make up an analysis” Affair. It’s a reminder that we need to be careful who we criticize in these controversies.”

17 August 2013 – ChemBark – “How Should the Online Community Handle Suspicious Papers?”

20 August 2013 – Der Spiegel Online – “Fälschungsverdacht gegen Schweizer Professor: ‘Erfinde einfach eine Analyse'”

 

Use the comments to call out other links; I’ll add them to the main post.

A Disturbing Note in a Recent SI File

Tuesday, August 6th, 2013

ChemBark InvestigatesA recently published ASAP article in the journal Organometallics is sure to raise some eyebrows in the chemical community. While the paper itself is a straightforward study of palladium and platinum bis-sulfoxide complexes, page 12 of the corresponding Supporting Information file contains what appears to be an editorial note that was inadvertently left in the published document:

Emma, please insert NMR data here! where are they? and for this compound, just make up an elemental analysis…

This statement goes beyond a simple embarrassing failure to properly edit the manuscript, as it appears the first author is being instructed to fabricate data. Elemental analyses would be very easy to fabricate, and long-time readers of this blog will recall how fake elemental analyses were pivotal to Bengu Sezen’s campaign of fraud in the work she published from 2002 to 2005 out of Dalibor Sames’ lab at Columbia.

The compound labeled 14 (an acac complex) in the main paper does not appear to correspond to compound 14 in the SI. In fact, the bridged-dichloride compound appears to be listed an as unlabeled intermediate in Scheme 5, which should raise more eyebrows. Did the authors unlist the compound in order to avoid having to provide robust characterization for it?

ChemBark is contacting the corresponding author for comment, and his response will be posted in full when we receive it.

This story points to very real concerns that young researchers can be instructed and pressured to fabricate data. Would a scientist be so concerned that a journal would reject his manuscript over a piece of missing characterization data that he’d feel pressure to make something up?

Expect more as this story develops…

Noyori on Ethical Conduct in Chemistry

Wednesday, January 9th, 2013

Breslow CEN Dinosaur Fake CoverA kind reader of the blog brought my attention to a piece of commentary in Advanced Synthesis & Catalysis titled “Ethical Conduct in Chemical Research and Publishing”. The lead author of the piece is none other than Ryoji Noyori, who won a share of the 2001 Nobel Prize in Chemistry for his work in asymmetric catalysis. Noyori is the Chairman of the Editorial Board of the journal, while the second author is the Editor of the journal.

I agree with a lot of what Noyori has to say, because a lot of it is obvious:

The research supervisor – group leader, principal investigator (PI), however he or she is called – is the main person to pass on the tradition of science to the next generation. Senior scientists have an obligation to instill strong ethical and moral values in their progeny…However, the education of graduate students should not be the sole responsibility of the research supervisor; each department should have a collective responsibility for the education of its students and for the activities of its professors. It is regrettable to see that in many departments the professors each form their individual kingdoms with a minimum of departmental cohesion.

also:

Fraud is hard to detect in a manuscript and is usually discovered only after publication, if at all. This should lead to retraction of the article.

Yep. The majority of the six-page article is full of statements like the above, which are pretty hard to argue against. But every now and again, Noyori makes some statements that strike me as mostly right, but a little odd:

When the careers of students depend entirely on the relationship to their professor, and only successful results count, then there is a large temptation for abuse on both sides.

I’ll agree that this relationship is very important, but to the point of using the word “entirely”? That’s not an assertion I would make.

It is hard to understand the logic behind committing fraud in spite of the apparent short-term gains. Scientific progress is achieved on the basis of previously published results. Fraudulent results cannot obtain a place of significance in the advancement of science, because they are not reproducible. Therefore, scientific fraud is a suicidal act for the career of the perpetrator. Integrity is an essential requirement for conducting scientific research.

This statement strikes me as naive. I think I understand many of the reasons why people commit fraud, just as I can understand why someone would murder someone else. In both cases, these reasons do not justify the crime, but there is still reasoning and logic at play.

Now, on to two passages that greatly interested me:

Another form of self-plagiarism is to cut and paste large segments of text from previous publications. The case of the Breslow publications offers important insights into the question of self-plagiarism. Ronald Breslow is one of the most highly respected chemists alive, and has made an enormous contribution to chemistry in his distinguished career of over 50 years. He published three personal review articles on the origins of homochirality. Many people are irritated by attacks on Breslow, since it is the right of every scientist to repeat their own ideas in different contexts, especially in talks or review articles. Indeed Breslow was unaware of any misconduct, since he has specifically made changes so as not to infringe on copyright laws. Nevertheless, the invited Perspective in JACS was withdrawn “at the request of the author due to similarity to his previously published reviews..” This is a difficult matter. “Self-plagiarism” can in fact be highly beneficial to the community. Eminent scientists travel worldwide and present almost the same lecture to many audiences; the goal is to have the largest possible dissemination of the ideas and results. The bottom line in publishing similar overviews should be whether it serves the advancement of science by reaching different and larger audiences. Copyright law needs to be respected, but other solutions in the interest of science should be sought to facilitate the widest dissemination of seminal reports. In conclusion, the repetition of a sentence or parts of a sentence is not considered plagiarism or self-plagiarism.

I cannot believe that the top editors of a journal are going to the mat for Breslow’s duplicate publication. I think most editors view the case as a classic example of self-plagiarism that is wholly unacceptable. “Self-plagiarism” is not simply restating your own ideas; it is lifting identical or minimally-altered pieces of writing for re-publication in a new article without clearly indicating that this material was published previously. The reasons self-plagiarism is unethical are: (i) it wastes resources, like the financial resources of the second journal and the time of those scientists assigned to referee material that has already been refereed once before, (ii) it traps the second journal in an adverse legal position with respect to copyright law, and (iii) it uses deception to “game” a system where publications are viewed as the principal metric of accomplishment in research.

And there is a huge difference between giving scientific talks and publishing scientific papers. Justin Bieber can perform “Baby” to audiences in Ottawa, Newark, and Richmond, but he can’t get away with publishing the song over-and-over on subsequent albums under different labels. Noyori’s opinion here is nothing short of bizarre.

If Noyori truly feels that “self-plagiarism can…be highly beneficial to the community”, I suggest that everyone submit self-plagiarized material for duplicate publication in Adv. Synth. Catal. I think he and the other editors will quickly change their tune.

Finally, here is the editors’ requisite thumbing-of-the-nose to blogs:

The Internet has become a major medium of communication in research and is contributing to the democratization of the global science community. Society is conditioned to consider that the printed word is valid; unfortunately, this trust cannot be extended to the Internet. Scientific results put onto the Internet without peer review have a serious problem with credibility. The American Chemical Society guidelines contain a section on publishing outside the scientific literature, but more comprehensive ethical guidelines are needed for publishing in the social media. More harmful is the publishing of irresponsible criticism and slander, even in the blogs of highly respected journals (see the Comments to the C&EN article on Breslow, cited below). Ethical guidelines condemn personal criticism and yet one often sees unscientific accusations, rumor or innuendo in the Internet. The mass media tend towards sensationalism and are not considered scientific, but irresponsible personal accusations on the Internet in an alleged scientific context are damaging to the individuals and to the entire image of science.

What a surprise: the editors of an expensive peer-reviewed journal denouncing the prospect of publishing scientific research for free on the Internet. Also, I love how they criticize “irresponsible criticism” on blogs without specifically citing what they find wrong. They only drop a numbered reference to the web page for the Breslow duplication story at C&EN, which has a comments thread that is heavily moderated by the editors. Someone please identify the slanderous comments that Noyori thinks are so irresponsible. Is this the best he could do?

How C&EN and JACS Have Changed Since Sames-Sezen

Thursday, May 3rd, 2012

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?