Archive for the ‘Scientific Culture’ Category

Response to ACS Nano Editorial on Reporting Misconduct

Wednesday, October 23rd, 2013

ChemBark's Jackie Jaws, the Jaded JACS RefereeYesterday, the entire editorial board of ACS Nano published an editorial on how scientific misconduct should be reported and dealt with. The piece took square aim at chemistry blogs, and I’ve decided to publish my thoughts as an open letter to Paul Weiss, the Editor-in-Chief of the journal:

Dear Professor Weiss,

Yesterday, I read your editorial titled “Be Critical but Fair”, within which you and the other editors of ACS Nano outline an official policy that calls on those who discover suspicious data to report their findings directly to the journal (where they can be scrutinized privately) as opposed to blogs and social media (where the findings will be scrutinized in the open). It is with candid disdain that I write this (public) blog post to explain why I believe your policy is misguided, and ultimately, damaging to the institution it seeks to protect.

Before going further, I want to thank you for the job that you and the rest of the board perform as editors. You are the primary stewards of the chemical literature, and the gravity of this responsibility is immeasurable. I imagine there are times when the extra salary you receive as editors does not adequately compensate you for the hassles of the job. I have no taste for this stress, but I am glad there are scientists among us willing to step up to the plate. Thank you for your service.

It is because of the immense responsibility of your job as a steward of the chemical literature that the community has an interest in analyzing your actions and holding you accountable for them. Everyone makes mistakes—from lowly chemistry bloggers to exalted editors-in-chief of ACS journals—but the true tragedy of any mistake is when we fail to learn from it. Recently, the process of peer review at your journal failed in a most spectacular manner. Similar high-profile cases recently occurred at your sister journals (e.g., Nano Letters and Organic Letters), and these cases of suspected misconduct are slowly working their way through the process of editorial review.

One common vein to this recent rash of suspicious papers is that they were brought to light on chemistry blogs. As you may already know, I am the editor of one of these blogs, ChemBark. I read with particular interest the comments you directed at those who discuss misconduct on blogs and Twitter:

In science, we face a similar problem: the numbers of blogs, twitter messages, etc. in which individuals accuse others of academic fraud are steadily rising. Although one might think that this trend is generally beneficial for the purity of science, there are also obvious risks involved. Thus, in this Editorial, we outline some general behavior guidelines that we believe should be followed in such cases. In general, we need to respect our law, in dubio pro reo, which tells us not to condemn anyone before wrongdoing has been proven. It is easy to tweet a message like “X committed fraud and manipulated data”, but how do we know that this is, in fact, true, and that instead, it was perhaps person Y who sent the tweet who just wanted to damage an unwanted competitor? We are convinced that it is important to “clean” the scientific literature from manipulated data, incorrect statements, plagiarism, etc. However, when these issues arise, they need to be investigated with good scientific conduct. In other words, be critical but fair.

The implication of your last statement is that the coverage of scientific misconduct by ChemBark was unfair, and I take great offense to this postulate. I use this word because you have not cited a single shred of specific evidence in support of your statement. When has a chemistry blogger ever raised serious suspicions about the validity of data in a paper only to be later proven incorrect? If a researcher submitted a manuscript to ACS Nano that did not include even one specific piece of data in support of his conclusions, the journal would reject the manuscript immediately. It is a shame that the editors do not hold their own writing to a similar standard.

You said on Twitter that the journal has a policy never to cite blogs or tweets, as if this represents a valid defense of why you couldn’t provide specific facts in support of your ideas. First, your tweet was absolute rubbish. Stuart Cantrill, chief editor of Nature Chemistry, immediately pointed out you wrote a previous editorial that cited the Retraction Watch blog. Second, why on Earth would you have a blanket policy not to cite blogs or tweets? Is ACS Nano so recalcitrant to changes in the publishing industry that it feels ideas voiced online can be ignored or reapportioned in print without credit? I hope not.

The true reason that your editorial did not cite a single instance of a blogger’s leveling false accusations of scientific misconduct in chemistry is that no such instance exists. To imply otherwise is dishonest sophistry that does not befit the editors of a major chemistry journal. In the very rare instances where commenters make weak accusations in the discussion thread of a blog post, the comments are ignored or ridiculed. Despite the fact that the majority of popular chemistry blogs serve as places for civil and thoughtful analysis, your editorial treats blogs as shady underground operations where anonymous bloggers are free to wreak havoc on innocent scientists. Again, I challenge you to find one anonymous chemistry blogger who has broken a story of possible misconduct. I use my real name on ChemBark, and Mitch Garcia blogs under his real name at Chemistry-Blog. Your editorial could have easily cited our work in reporting suspicious papers, but of course, doing so would not have fed into your desired narrative.

Returning to your statement above, you note that “we need to respect our law, in dubio pro reo, which tells us not to condemn anyone before wrongdoing has been proven.” First off, your translation isn’t even correct. A more accurate translation is “when in doubt, favor the accused.” This tenet is why our legal system requires proof “beyond a reasonable doubt”, and the idea has nothing to do with trying cases in public versus private. The fact that you drew on our legal system—which is famous for holding trials that are televised or open to members of the public—to support your policy is ridiculous.

While bloggers who report cases of possible misconduct are indeed accountable to the law, that law is not “in dubio pro reo”. Rather, bloggers are accountable to defamation law. If any chemistry blogger were to raise baseless accusations of misconduct against a scientist, the blogger would open himself to (i) financial ruin from an adverse finding in a civil claim, and (ii) professional ruin in the court of community opinion. Bloggers need to be careful about what papers they choose to highlight regarding scientific misconduct, but this is no different from how newspapers and magazines need to be careful about how they handle their coverage of crime in everyday life. Do we want newspapers to abstain from reporting major crimes until a trial by jury has concluded? No, that’s crazy. There is a public interest served in covering these stories, and news outlets play a valuable role in gathering, distilling, and reporting this information. As both a chemistry blogger and a human being, I need to make sure that the facts I report regarding possible scientific misconduct are accurate and the opinions I voice are rooted in reason. That’s the bottom line, and I am accountable to the very intelligent readership of the blog and to our legal system (should someone have a problem with my coverage). No blogger can expect to level spurious claims of misconduct and get away with it.

Your editorial continues with a statement that peer review is “the best way to avoid potential academic fraud” and correctly notes that the system sometimes fails. When it does, you implore readers who find evidence of misconduct to report it directly to you so you can conduct an investigation in private. You note:

The difference between this formalized accusation investigation and reports in blogs or on Twitter is that, during the investigation, the authors of the article under dispute have a fair chance to explain, and the decisions are made by known experts in the field. After we have made our decision, all are welcome to comment on it in any blog, even if they have different opinions; this is their privilege. We strongly suggest that such comments be made without the cloak of anonymity, using real names and affiliations, so that direct and open discussion of the work can be understood by others.

I hope you can appreciate the irony of how you begin by extolling the virtues of (anonymous) peer review and conclude by haranguing bloggers and commenters to register their opinions “without the cloak of anonymity.” It takes a lot of gall to make those statements in the same line of thought.

Furthermore, the idea that the public should not be free to point out deficiencies of a (publicly) published paper without first receiving clearance from the editorial board of ACS Nano is preposterous. The notion is antithetical to the freedom of inquiry espoused by the academic community and the freedom of speech held sacred by American society. Unless I am mistaken, the “A” in ACS Nano stands for American. In America, it is not a “privilege” to comment publicly on a subject; it is a right.

Your assertion that commenting on papers is a “privilege” smacks of the elitist, opaque, closed-door, Old-Boys’-Club approach that many lament has become standard operating procedure in too many areas of chemistry. Many young chemists decry that success in our field is not so much about what you do, but whom you know. Blogs are helping to level the playing field by putting users on equal terms and democratizing the flow of information. In order for any self-governing and self-policing body to operate effectively, members of the community must stay informed about important issues they face. There can be nothing more important to chemistry than the integrity of our data; it is the foundation on which our knowledge is built. Private systems of dealing with misconduct do so in a darkness where—even if an investigation takes place on the level—those outside will always have their doubts. The open system afforded by blogs shines a light on problems so all can see, participate, and judge for themselves. While private peer review of papers may make sense to eliminate errors before they’ve been published, once a paper is out in the open, it should be fair game for comment. There is no point in dragging problems back inside only to leave a trail of blood and a multitude of questions behind.

I would like to think that the private system you espouse could also function efficiently, but recent history has proven otherwise. Despite the importance of maintaining the integrity of the scientific record, the chemical community has been routinely kept in the dark about cases of scientific misconduct. Journals, universities, and governments seem to share as little as possible about their investigations. Just look what happened with the Sezen–Sames retractions. The case involved a shocking rampage of deceit and was probably the worst scandal to hit organic chemistry of all-time, but it took a FOIA request from me and C&EN to release the details of the case to the community. How can chemists be expected to learn from and prevent scandals without knowing any of the specific details? It’s ridiculous! Do you pledge to release all of the specific details of your investigations that result in adverse findings against an author?

Journalism—including that provided on chemistry blogs—is one way to address this vacuum of information. The Founding Fathers of the United States protected the freedom of the press in our Bill of Rights because they knew that an informed electorate was essential to the efficient operation of our government and the prevention of tyranny. A (small) part of what I’ve tried to do with ChemBark is to shed light on cases of scientific misconduct in our field such that these cases can be discussed and analyzed by the wider chemical community. It is unfortunate that there exists a need for bloggers to invest some of their time in this effort, but experience has repeatedly shown that chemists cannot rely alone on journals, universities, and governments to keep them informed.

Regardless of how persistent you are in your attempt to intimidate the blog community into keeping silent, bloggers will continue raising these issues. The health of our science is at stake, and the importance of its protection far exceeds the cost of however you and your colleagues decide to punish us for openly analyzing important issues in our field.

In summary, I believe your editorial is unfair and completely misguided. I am dismayed that it represents not only your personal opinion, but the professional opinion of every member of your editorial board (who signed it). You all have perverted an embarrassing, spectacular failure of peer review at your journal into a condemnation of the community that exposed and prevented the proliferation of your error. Chemists should be outraged at your editorial, and I hope they see through this shameless attack on those of us who use blogs and social media to analyze articles rather than the traditional method of grumbling in solitude. In the future, I suggest your effort will be better spent listening to the constructive feedback bloggers and their readers provide rather than attacking them for conducting their analysis in a public forum. Finally, on Twitter yesterday, you mentioned a willingness to engage further in a discussion of the merits of open vs. closed review of problematic published papers. I do not hold grudges and would be happy to participate in whatever forum you deem appropriate. Please keep me informed if you remain interested in hosting such a symposium.

Yours in chemistry,
Paul

Doctor? No.

Wednesday, October 16th, 2013

bracher_office_doorI generally like to be respectful of people. Toward this end, I try my best to address people properly. You’ll find that I’m pretty liberal in using “Dr.” when addressing letters and e-mails, because you never know when someone is going to get upset at being called “Mister”. In contrast, few people seem to get upset at being called a doctor when they are not. When I was applying for faculty positions last year, I am certain I conferred Ph.D. degrees on a multitude of unsuspecting departmental staffers whose job it was to assemble the applicants’ files.

On the flip side, I have a personal aversion to signing anything as “Dr.” I always check “Mr.” when filling out forms, and I cannot bear to end an e-mail with “Dr. Bracher.” As I am now a teacher, this has established a weird dynamic where students address their e-mails to “Dr. Bracher” and I return them by signing “Paul.” I know this has got to weird the students out because I remember fretting over how to address professors when I was in college. Do you call them “Professor”, “Doctor”, or by their first name? I am pretty sure I always opted for “Professor.”

In my undergrad research lab, it was always a big deal for students when the boss started signing his e-mails to you by his first name. It was an unmistakable signal that you had made it and was regarded as a rite of passage in the lab. In contrast, my graduate and postdoc advisors were pretty much known exclusively in the lab by their first names. Of course, the undergrad-professor dynamic is much different from the dynamic with grad students and postdocs, but it’s always interesting to see how these differences manifest themselves.

Some students attempt to solve the e-mail problem by using the non-direct “Hi,” “Hey,” or “Hello there” salutation. Of course, in trying to avoid any awkwardness, this device mostly just draws attention to it. Would you walk up to a professor and address her as “Hey”? Some of my colleagues sign their e-mails to students as “Dr. D” (or similar), which is an interesting compromise between formal and informal. At the same time, it makes me question what I should address these professors when we are in front of students. Can I say “John” (as I normally would), or should I say “Dr. Doe”?

While I don’t especially care what people call me and would never be offended by any of the standard choices, I prefer “Paul”. But after two months in St. Louis, it seems as if I’m going to be “Dr. Bracher” to the vast majority of students. To friends, colleagues, and those online, I will still be “Paul”, while to family at home, I have always been “P.J.” All are fine with me.

Yesterday, I found myself reconsidering whether to sign my e-mails to students as “Dr. Bracher” to make them feel more comfortable. My conclusion was not to change—signing “Dr. Bracher” would probably make me feel just as weird as if they were to address their e-mails to “Paul”. Anyway, the decision of what to call myself has got to be one of the few privileges to which I am entitled in this new job.

–Paul

Chemistry World and Others on Dodgy Data

Thursday, September 5th, 2013

ed_baseballcap_150Hello, friends. Pardon the radio silence of late. My first semester of teaching just started at SLU and my head is already spinning. I’ll have a full post on that subject soon, but I wanted to weigh in on a few recent pieces regarding the cases of suspicious data that were reported here and elsewhere.

Reporter Patrick Walter wrote a story earlier this week for Chemistry World that examined whether blogs are appropriate venues for policing the chemical literature for misconduct. I was interviewed for—and quoted in—the story, which I feel is thorough, is balanced, and represented my positions accurately. As you might imagine, I argue that blogs are indeed appropriate venues to report suspicious data and to analyze how the community should respond to misconduct.

There are plenty of people who disagree with me—to varying extents—and the article raises their concerns as well. That is fantastic, because this is a discussion that we need to have. I am happy to engage in thoughtful debate on the subject (see posts here and here) in hopes that we, as a community, can arrive at a more efficient system for removing manipulated data from the literature and preventing their publication in the future.

Mitch André Garcia, who runs both Chemistry-Blog and the chemistry subgroup of Reddit, is one of the people who took exception to my post on the manipulated spectra in Organic Letters. Here is what he wrote on Twitter:

I’m left scratching my head here. How do the nanochopsticks he reported qualify as “acceptable to cover” for being “egregiously manipulated and…in a high impact journal” but not the erased impurities in the Anxionnat/Cossy spectra reported here? Seems pretty hypocritical. And if we can’t agree on whether these cases meet his standard for “egregiously manipulated” and “high impact”, how are we supposed to agree on anything?

My view on the matter is that anyone who wants to raise concerns publicly about data may do so, with the full realization that they are putting themselves on the line. If I raise concerns about the integrity of data in a paper, I am accountable to defamation law and the high intelligence and ethical standards of the readership here. I can only bring information to people’s attention. If that information is wrong or doesn’t support my opinions, I will be excoriated in the comments and lose credibility. If what I publish is defamatory, I will probably also be sued. The root cause of the outrage among chemists about these papers cannot be attributed to blogs; the data speak for themselves.

A few days ago, John at the blog It’s the Rheo Thing posted some cautionary advice to “activist [bloggers] that are confronting examples of fraud, plagiarism and other publishing infractions in the technical literature”:

What goes around, comes around. Many are pleased to bring the axe down hard on someone’s head, and hold as many people responsible as possible (from ALL the authors to the principal investigator and maybe even beyond that), but we need to keep in mind that publishing scientific research is a human effort and as such, will be imperfect at times even when no harm, deceit or other nefarious activity is intended. Many of the commentators screaming for blood are young professionals you have yet to run a large, established research group, but who think that they will be able to do so flawlessly in the future. Of course that won’t happen. You will have failings and shortcomings and things will go wrong despite your most fervent intent to prevent it. Most people do not have a problem with that.

Most people. But there will be plenty of others wanting your head on the same chopping block and with an added level of glee since you were responsible for bringing so many down yourself. It’s human nature. We can’t change it, this perverse desire to bring down the people bringing down others. Worse yet, these efforts to trap you may be entirely without merit. That won’t matter. “A lie can travel halfway around the world while the truth is still putting on its shoes” (Mark Twain). Your name and reputation can be placed in the same trash heap as those truly deserving it far more easily than you can ever imagine. Despite your noble intents and purity of heart.

User “juicebokz” on Reddit called John’s post “a letter to ChemBark”, and I feel compelled to weigh in with the following points:

Do you seriously think that the responsibilities of running a modestly popular blog don’t weigh on me? Do you think that I don’t consider whether I am treating the subjects of these sorts of posts fairly? These posts are not aimed at destroying scientists; they are aimed at protecting science. I do not take joy in the downfall of others, but I am not going to let a miscreant’s potential downfall prevent me from discussing a topic that I feel is important. Should any researchers be “brought down” for data fabrication, I will not be the person responsible for bringing them down. They will have been the people responsible for their own downfall.

And I am by no means a perfect person. Everyone makes mistakes and does things of which they are not proud. The point is that you have to pay for your mistakes, then dust yourself off and go about living a productive life. Should anyone gather the motivation to search through my past, or present, they’re going to find stuff that will embarrass me…but they are not going to find any fabrication of data.

As for drawing attention to co-authors who very likely did not actively participate in the fabrication of data, I still stand by the position that authors must share the responsibility for the content of their papers. “Share” does not mean “share equally”, but all authors should at least read through their papers and keep an eye out for things that are obviously wrong. When you are a corresponding author, ensuring the integrity of the data in your papers must be one of your priorities. If you think I’m alone in this view, please go back and read Smith’s editorial in Organic Letters. Any punishment doled out regarding fabricated data in a paper should be proportional to (i) one’s active involvement in the fabrication and (ii) one’s responsibilities as a conscientious scientist and/or manager. These responsibilities should be the subject of more discussion among chemists.

Finally, does anyone really think I am helping my career by reporting on scientific misconduct? Do you have any idea how uncomfortable it is to send e-mails to the editor-in-chief of a high-impact journal in my field asking for comment about how he’s going to deal with manipulated data in a paper written by one of his associate editors? Was it lost on people that Smith’s response to my inquiry was addressed “Dear Bracher”? It’s certainly not the most cordial of salutations. I asked a follow-up question by e-mail and was not given the courtesy of a reply.

I don’t like these sorts of awkward interactions, but asking hard questions is part of doing a thorough job of reporting, so I’ll just bite the bullet. I can only hope these interactions don’t come back to hurt me down the road, but that’s a possibility. At the end of the day, I would love not to have to write about scientific misconduct because (i) chemists have stopped doing it or (ii) universities, journals, and government have created a good system for dealing with it.

Now, how do we make that happen?

Some Very Peculiar NMR Spectra in Organic Letters

Monday, August 19th, 2013

A close examination of the Supporting Information attached to this paper from 2011 in Organic Letters reveals some pretty interesting NMR spectra:

compound_5d_hnmr_zoom

(compound 5dfull spectrum)

Hmmmmm. I have collected hundreds of NMR spectra, and I can’t ever recall seeing a spectrum in which intensity was not a reasonably continuous function of chemical shift. That is, values of chemical shifts had only one associated intensity each, and no spectra had missing chunks of signal.

Here are some other interesting pieces of spectra from the same paper:

compound3j_hnmr_zoom(compound 3jfull 1H NMR spectrum)

 

compound3j_cnmr_zoom(compound 3jfull 13C NMR spectrum)

 

compound_7c_zoom  (compound 7cfull spectrum)

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You can check out all of the spectra in the SI for yourself—the file is open access.

So, what is going on here? One explanation is that we’re seeing something very scientifically interesting. I hope this is the case. Another explanation could be user error, or a malfunction on the part of the instrument and/or software used to collect and analyze the data.

Yet another explanation could be that unexpected or undesired peaks (e.g., those corresponding to impurities in the samples) have been erased from the spectra. Some of you might think this suggestion is outlandish—why would a chemical researcher manipulate spectral data in this regard?—but I cannot take credit for conceiving of this idea. I believe the first time I was alerted to this (highly unethical) practice was by the Editor-in-Chief of the journal in which this work appears.

Organic chemists and readers of this blog will recall that earlier this summer, Amos B. Smith III—the Editor-in-Chief of Organic Letters—penned an editorial documenting that he hired a data analyst to examine spectra and other data submitted to the journal for possible manipulation. The editorial included the statement:

I write to alert the organic chemistry community to a serious problem related to the integrity of data being submitted for review and publication by Organic Letters and to outline steps that the Journal is taking to address this concern. Recently, with the addition of a Data Analyst to our staff, Organic Letters has begun checking the submitted Supporting Information more closely. As a result of this increased scrutiny, we have discovered several instances where reported spectra had been edited to remove evidence of impurities. Such acts of data manipulation are unacceptable. Even if the experimental yields and conclusions of a study are not affected, ANY manipulation of research data casts doubts on the overall integrity and validity of the work reported.

I wish to reiterate that I have no definitive idea of what happened in the production of the spectra in this paper; this post only notes that they don’t look normal. In an effort to ascertain more about the spectra, five days ago, I reached out by e-mail to the first author, corresponding author, and Editor-in-Chief of the journal.

Dr. Bruno Anxionnat, the first author of the paper, did not respond. His former PI and the corresponding author on the paper, Professor Janine Cossy, replied with the following statement:

Dear Professor Bracker

There is probably a mistake as I know that the 1st supporting information with some spectra were wrong and I asked an other student to reproduce the experiments and sent back an other SI with the right spectra, may be the 1st SI was not changed by the right one.

Right now, I am abroad and can not check but I am going to check with the Organic Letters editorial office and I will tell theñm to contact you

Sincerely yours
Janine Cossy

I will note that Professor Cossy is an Associate Editor of the journal in addition to being corresponding author on the paper. You may recall that Smith’s editorial in Org. Lett. addressed the responsibilities of corresponding authors quite clearly:

In some of the cases that we have investigated further, the Corresponding Author asserted that a student had edited the spectra without the Corresponding Author’s knowledge. This is not an acceptable excuse! The Corresponding Author (who is typically also the research supervisor of the work performed) is ultimately responsible for warranting the integrity of the content of the submitted manuscript.

The responsibility to foster a research environment where all involved can confidently present their results, even if they are not optimal, resides with each research supervisor and Corresponding Author. At times, the inherent power of a research advisor’s position can create an atmosphere that leads some to embellish results.

In my e-mail to Professor Smith seeking comment, I made sure to mention his recent editorial. He sent back the following note:

Dear Bracher,

Thank you for bringing these discrepancies to my attention. As with any allegation concerning published articles, we have shared your concerns with the author, who is as you note an Associate Editor. Organic Letters has standard procedures for handling inquiries regarding the content reported in published articles, which are in play here.  As you may be aware, COPE (http://publicationethics.org/) provides  journal editors and publishers with guidelines for handling such issues.  Speculation and comment are premature at this time.

ACS and ACS Editors hold the conviction that the observance of high ethical standards is vital to  the entire scientific enterprise. Guidelines for a course of conduct by  those engaged in the publication of chemical research, specifically, editors, authors, and manuscript reviewers are set forth in ACS Ethical Guidelines to Publication of Chemical Research http://pubs.acs.org/userimages/ContentEditor/1218054468605/ethics.pdf.

Amos Smith

So, there you have it. The matter is being examined more closely, and it would appear the ball is in Organic Letters’ court. Interestingly, there are a few more papers (listing Anxionnat as first author and Cossy as corresponding author) where you might notice similar-looking spectra:

Anxionnat, B.; Pardo, D.G.; Ricci, G.; Cossy, J. Eur. J. Org. Chem. 2012, 4453–4456. (paper, SI)

Anxionnat, B.; Robert, B.; George, P.; Ricci, G.; Perrin, M.-A.; Pardo, D.G.; Janine Cossy. J. Org. Chem. 2012, 77, 6087–6099. (paper, SI)

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Go have a look and judge for yourself.

 

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.

The OM Paper vs. Drinkel’s PhD Thesis

Friday, August 9th, 2013

ChemBark InvestigatesAs part of our investigation into the controversial paper published by Reto Dorta and coworkers in Organometallics, ChemBark contacted a source in Europe who was able to obtain a copy of the Ph.D. dissertation of the first-author of the paper, Dr. Emma Drinkel. Chapter 4 of the thesis carries the title “Synthesis, Structure and Catalytic Studies of Novel Palladium and Platinum Bissulfoxide Complexes”, and the chapter appears to describe the vast majority of the work reported in the publication in Organometallics.

The entire thesis is 174 pages long. ChemBark has made the editorial decision not to republish Drinkel’s thesis in its entirety, but rather, to provide a set of small excerpts that highlight important information, including a number of discrepancies with the paper in Organometallics. We are also republishing excerpts from the SI of the paper. I believe that this approach constitutes “fair use” with respect to copyright law, because (i) there is a time-sensitive need for the community to be informed about this important case, (ii) these excerpts represent a small fraction of the whole of the published works, and (iii) republication of these excerpts does essentially nothing to deprive Drinkel or ACS Publications of financial gain.

ChemBark’s excerpts from Chapter 4 of Emma Drinkel’s Ph.D. Thesis
ChemBark’s excerpts from the Supporting Information of the OM Paper

Drinkel’s thesis is dated “Zurich 2011”. In her curriculum vitae included at the end of the thesis, Drinkel reports her Ph.D. studies as having spanned “09.2007-09.2011”. Dr. Drinkel’s LinkedIn profile reports that she was at Zurich until December 2011, and she began work as a postdoc at Universidade Federal de Santa Catarina (Brazil) in July 2012. It is worth noting that the Organometallics paper was received by the journal on January 7, 2013—a full year after Drinkel departed from Zurich. This piece of information is interesting when one considers whether “just make up an elemental analysis” could mean “perform an elemental analysis” versus “fabricate the elemental analysis data”. Of course, the (arguably) ambiguous instruction could have been written many months prior to submission of the paper—while Drinkel was still in Zurich—or Drinkel could have carried all of her samples from Switzerland to Brazil.

A brief examination of the dissertation reveals that much of the information published in the supplementary file of the OM paper is identical to the information published in Chapter 4. This includes most of the characterization data and the prose used to describe the experiments. But a rapid comparison is hindered by what appears to be the root cause of the confusion between the main paper in OM and its corresponding supplemental file: Drinkel misnumbered some of the compounds in her thesis. The numbers in the discussion section of chapter 4 are shifted relative to the data reported for the same compounds in her experimental section. For example, compound 14 in the thesis’s experimental corresponds to compound 15 in Figure 13 from the thesis (pasted below). This compound is labeled 14 in Scheme 5 from the OM paper and 154 in the OM supporting information. The same problem goes for compound 16a/15a/15a/165a and others.

Figure 13 from the Thesis

Figure 13 from the Thesis

 

Scheme 5 from the Main Paper

Scheme 5 from the Main Paper

 

The numbering discrepancies in Drinkel’s thesis not only went unnoticed, they were exacerbated when the OM authors built their paper off of the chapter and decided to delete the label from compound 14 in Scheme 5. This is the compound associated with the now-infamous instruction to “just make up an elemental analysis”.

The written response from the editor-in-chief of Organometallics on the SI’s controversial statement regarding compound 14 included the following:

The author has explained to us that the statement pertains to a compound that was “downgraded” from something being isolated to a proposed intermediate. Hence, we have left the ASAP manuscript on the web for now. We are requiring that the author submit originals of the microanalysis data before putting the manuscript back in the print publication queue.

Indeed, there are no data for 14 written in the experimental section of Drinkel’s chapter 4—its preparation occurs as an intermediate in the preparation of 15 (using the numbering from Figure 13). With that said, the discussion section of chapter 4 mentions:

When 5a was treated with only 1 equivalent of AgBF4, unlike in the Pd case, the stable complex 14 was formed. No crystals could be grown to confirm the structure, but the 1H NMR spectrum of the complex shows the ligand is still symmetric. There is precedence for this type of chloro-bridged Pt dimers in the literature with phosphine ligands.

This statement from the thesis might appear to refute the claim in the letter that the authors could not isolate 14 and that it was simply a proposed intermediate, but the text of the main paper states that NMR was taken “in situ” after the first reaction. With that said, no NMR data are provided for compound 14 in the Supporting Information file, and an instruction is given to Emma (Drinkel) to insert these data. Perhaps the instruction to “insert” was given because the instructor already knew the data existed (based on what was written in the discussion section of the thesis)?

Beyond the problems associated with misnumbering, there are several discrepancies between the data reported in the thesis and the data reported in the SI of the Organometallics paper. All of the examples that I could find related to elemental analyses. Specifically:

SI-5b vs Thesis-5b

Compound 5b from the SI

Compound 5b from the SI

 

Compound 5b from the Thesis

Compound 5b from the Thesis

 

SI 11a vs Thesis 9a

Compound 11a from the SI

Compound 11a from the SI

 

Compound 9a from the Thesis

Compound 9a from the Thesis

 

SI 12 vs. Thesis 12

Compound 12 from the SI

Compound 12 from the SI

 

Compound 12 from the Thesis

Compound 12 from the Thesis

SI 165b vs. Thesis 15b

Compound 165b from the SI

Compound 165b from the SI

 

Compound 15b from the Thesis

Compound 15b from the Thesis

 

You can see that the authors chose to “count” different associated solvents when calculating the expected values for the elemental analyses, and they reported different observed results in the paper vs. the thesis for some compounds. Were these samples run multiple times? Since the original data have been demanded by the journal, I guess we’ll find out.

 

Stay tuned for continuing coverage…

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Note: In the reporting of this story, we wanted to give both the first author of the paper (Emma Drinkel) and the corresponding author (Reto Dorta) the chance to comment on the discrepancies we found in the data prior to the publication of this post. ChemBark first attempted to contact Professor Dorta by e-mail on Tuesday night (St. Louis time) and received no response. Dorta also has yet to respond to a second message, sent Thursday afternoon, that sought comment on the discrepancies reported in this story. A message seeking comment was also sent to Dr. Drinkel, at the same time, through her Facebook account. Should either author respond to our requests for comment, the responses will be posted in their entirety.