Archive for the ‘Mailbag’ Category

How JACS Treated the Anonymous Tip of the Rodriguez–Marks Paper

Monday, November 11th, 2013

ChemBark InvestigatesBy the time the chemist who noticed the suspicious data published in the Rodriguez–Marks paper had contacted ChemBark, the chemist had already anonymously notified the Journal of the American Chemical Society with the concerns. A member of the staff at the journal responded to this initial message with the following:

To Whom It May Concern:

Thank you for your message regarding J. Am. Chem. Soc. 2009, 131 (16), pp 5902–5919. Indeed JACS takes ethics quite seriously. We would be pleased to investigate your concerns. Before proceeding, however, we ask that you reveal your identity.


The implication of the official response from the journal was troubling. It implied that for the investigation to proceed, the whistleblower would need to reveal his/her identity.

Surely a journal that grants anonymity to referees would appreciate why a reader who was calling attention to possible misconduct by a well-known, powerful chemist would want to remain anonymous. Furthermore, JACS is a member of the Committee on Publication Ethics (COPE), and the source reports he reminded the journal that “COPE supports a whistleblower’s right to remain anonymous”. Beyond COPE, Ivan Oransky (co-editor of the blog Retraction Watch) has also summarized why editors shouldn’t ignore anonymous tips.

To its credit, the journal responded favorably to the source’s gentle reminder about COPE’s policy, and the investigation was allowed to proceed.

After the paper in question was retracted, ChemBark asked JACS Editor-in-Chief Peter Stang by e-mail:

When the source initially contacted the journal in August with these concerns, the journal office responded to him/her “We would be pleased to investigate your concerns. Before proceeding, however, we ask that you reveal your identity.”

As you know, the source refused to identify himself/herself and defended his/her right to anonymity in the process. While the journal eventually relented and proceeded with the review, the initial implication was that the source would need to identify himself/herself for an investigation to proceed. Was the request and wording of the initial response from the journal “standard procedure”? Is the journal worried that such a response could have a chilling effect on the identification of suspicious or irreproducible data? Why would the identity of the source matter if the concerns are reasonable?

Dr. Stang’s response included the paragraph:

I will say, however that the request for the individual to identify themselves was unnecessary. The  identity of the “whistleblower” was immaterial to the issues raised and did not  prevent JACS from considering the allegation and taking action. All ACS  Journals take all cases of alleged research improprieties very seriously and have established procedures for reviewing and taking appropriate actions, where warranted, to preserve the integrity of the scientific record. Institutions and funding agencies  also have established departments, policies and procedures for handling  allegations of data fabrication by researchers. Upholding the scientific record requires the vigilance of all participants in the research community.

All credible reports of suspicious data should be thoughtfully considered by the corresponding journal, whether reported anonymously or not. Journals should be grateful to anyone who attempts to correct the scientific record and understanding of why a tipster might want to remain anonymous. While JACS‘s initial response was troubling and “unnecessary”, it would appear as though the editors have taken steps to correct how they handle anonymous tips.

That is an encouraging outcome.

Fish and Chips for Chemists

Wednesday, May 1st, 2013

This image of a fish-and-chips shop in Glasgow was kindly sent in by longtime reader/commenter Eugene. (Thanks!)


While “organic” oil is great, a silicone oil might help control customers’ gas.

I wonder if this restaurant is owned by the same people as the Boston dry cleaners boasting about their “organic” solvents?

WWWTP? – Markovnikov Edition

Tuesday, April 16th, 2013

Perfectionists take note: even titans of catalysis make embarrassing mistakes with their chemistry. Just look at this little oopsie that was caught by an astute reader in the Midwest.

It seems like there might be a bit of confusion hanging over the chemists developing methods for anti-Markovnikov hydroamination of alkenes at the Center for Enabling New Technologies Through Catalysis (CENTC):


Ummm….yeah….that’s not the difference between Markovnikov and anti-Markovnikov addition.

Those of you who’ve taken sophomore organic chemistry will remember that Markovnikov’s rule states that protic functional groups (e.g., H-NR’R’) will typically add to double bonds such that the hydrogen adds to the less substituted carbon (and the other group, e.g., -NR’R’, adds to the more substituted carbon.) What Hartwig and coworkers have drawn as the Markovnikov product is still anti-Markovnikov. The products they’ve drawn might charitably be called conformational isomers, but they’ve failed to note any 3-D structure.

Of course, the true Markovnikov product would place the amine on the same carbon as the R group.

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.


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?

ACS Sheds More Light on Leadscope Case

Friday, December 21st, 2012

ChemBark InvestigatesIn today’s mailbag, an astute reader of the blog writes to bring our attention to a new post on the American Chemical Society’s Web site regarding some of the details of the ACS v. Leadscope case.

The post is written in a Q & A format that might be an homage to the “tough questions” survey that ChemBark recently sent to the candidates for ACS President. While it would appear that the ACS both asked and answered the questions found in the post, some of the questions match those posed in the presidential survey and in ChemBark‘s posts about the recent ACS v. Leadscope verdict and settlement.

First off, let me applaud the ACS for this giant leap forward in transparency. We, the members of the Society, need these details to help us function as an informed electorate. It is a pity that we’ve had to wait until the matter was almost completely resolved to get many of these basic facts.

So, what is new? Let’s start with the money. It seems that after losing the initial verdict, the ACS owed Leadscope $26.5M in damages plus another $7.9M in the defendant’s legal fees. By not immediately paying these sums as the Society pursued the appeals process, the ACS accrued another $11M in post-judgment interest. Thus, prior to the verdict in the Ohio Supreme Court, the ACS was on the hook for >$45M. After that verdict erased the defamation judgment but upheld the judgment of unfair competition, the ACS was still on the hook for >$26M. Leadscope and ACS soon settled for a $22.6M payment to end the litigation.

Now, how much of this does the ACS have to pay? Not all of it. It turns out the ACS has insured itself to reduce its financial exposure in these and similar issues, but it is unclear what is covered. From the post:

The ACS has a comprehensive suite of insurance, including primary commercial general liability and umbrella general liability coverage. As a result of this insurance, ACS has been reimbursed for over a million dollars in attorney’s fees. In light of the Supreme Court’s ruling, we are working with our legal counsel to determine the amount ACS will be responsible for paying and then we will work with our insurance providers to determine what portion, if any, may be covered by insurance.

Of course, the ACS’s legal fees far exceeded $1M…they are over $9M for the case, and the ACS does not say how much it pays for their insurance coverage.

The ACS still claims that shelling out $22.6M is not that big of a deal, which is incomprehensible to me for a non-profit of their size:

ACS paid the settlement using funds from the Society’s substantial cash reserves and investments. Nevertheless, ACS recognizes that paying $22.6 million to settle litigation begun over a decade ago is a very negative outcome to this litigation.

One of the reasons why large nonprofits strive to maintain financial reserves is to cover large, unexpected financial losses. Members and others should be assured that the settlement in this case will not result in higher ACS member dues or increased prices for ACS products, programs or services. The settlement in this case will neither restrict ACS staffing levels nor impair the ACS’s continued ability to achieve its mission.

In a bizarre twist, the ACS tries to make the argument that the cost of the settlement is not that big of a deal by comparing it to the much greater sum that the ACS finds itself shelling out for post-retirement benefits plans:

The decline in the Society’s unrestricted net assets from 2008 to the present has been largely driven by accounting charges related to the Society’s postretirement benefit plans.1 The plans have become underfunded due to historically low interest rates, which have caused the discount rate to decline. The discount rate is used to calculate the postretirement benefit plan liabilities. The rate has declined from 6.5% at December 31, 2007, to 4.0% at November 30, 2012, and resulted in accounting charges of $153 million during this period. If, as most observers expect, interest rates eventually rebound to higher levels, the accounting charges related to these plans will reverse and the Society’s unrestricted net assets will increase accordingly. Other factors impacting unrestricted net assets include the Society’s net from operations, investment gains/losses and non-operating gains/losses.

How on Earth is the ACS spending this much money on benefits? This seems like yet another matter that deserves more study.

And finally…

11. This whole case seems like it was a very bad idea. If ACS had it to do all over again, would it still file suit? Will there be management changes as a result of this outcome?

In hindsight, it is very easy to second guess the 2002 recommendations made by the Society’s in-house and outside lawyers and the Governing Board for Publishing, as well as the 2002 Board’s decision to file suit.

However, given the information available to ACS management and governance at the time and the advice provided by legal counsel, ACS elected to file a suit in an effort it believed was necessary to protect valuable ACS intellectual property. ACS and its in-house and external counsel believed that its claims were valid and supported by evidence. Prior to and during the pendency of the Leadscope case, ACS management and governance engaged in a robust and thorough decision-making process. Moreover, the decision to pursue this case was not made by any one individual but rather was authorized after a careful and thoughtful analysis of the nature of the Society’s claims by internal and external legal counsel, ACS senior management, and the ACS Board of Directors.

There will be no management changes as a result of the Leadscope outcome.

This is why we have elections, my friends. The people in charge at ACS answer to nothing else. They are free to do whatever they want, however carelessly, as long as we (the electorate) allow it.