Archive for the ‘Scientific Misconduct’ Category

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)

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)

Go have a look and judge for yourself.

 

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.

Some VERY Suspicious TEM Images in Nano Letters

Wednesday, August 14th, 2013

Mitch at Chemistry-Blog has a new post about a set of very suspicious TEM images that was published recently in the journal Nano Letters.

The associated paper reports the fabrication of pairs of gold nanorods in “chopstick” structures where the two rods touch at their tips and form an angle that the authors say they can tune. Some of the TEM data can be viewed for free in the associated SI file. If you zoom in on the images, it appears that the background immediately around many of the rods is different from the rest of the background field. Hmmm…

from Nano Lett.

from Nano Lett.

 

from Nano Lett.

from Nano Lett.

 

User “spookyjeff” on the chemistry subgroup of Reddit commented:

That is some impressively bad photoshop. Allegedly.

To which user “FubarFreak” replied:

I’m going to go with MS paint

Mitch also reports that Leonard Pease, the last author on the paper and an assistant professor at the University of Utah, told Mitch “an investigation [is] underway at the University of Utah into this matter and [he] strongly encouraged [Mitch] not to publish this story until the University completed its investigation.” Pease also “informed [Mitch] that legal action might be pursued by the University of Utah if [he] published this story.”

Longtime readers of ChemBark will recall that Columbia University never explained to the community what happened after it was finished with its investigation of Bengu Sezen. FOIA requests filed by ChemBark and another news organization were required to report the full extent of Sezen’s misconduct to the public. One lesson there [of many] was that you cannot count on universities to investigate or publicize the results of investigations into suspicious data and other possible scientific misconduct. Journalists, sources, blogs, and social media have helped fill this void by making valuable contributions toward identifying suspicious data and ensuring research misconduct is investigated and punished.

Fortunately for Mitch, ensuring that one’s facts are true is an absolute defense against libel in the United States, and the truth is that the above images were published by the authors in Nano Letters.

Finally, if the images in Nano Letters turn out to be manipulated, we should consider the question of “just how lazy/inept was the offender?” Michael on Facebook tried his hand at “fixing” the authors’ figures and produced the following:

michael1  michael2

michael3

Very nice—no more boxy awkwardness and mismatched backgrounds. He reports that “after installing the photoshop trial it took about 5 minutes to do 2 or three images.”

Elsewhere: Chemistry-Blog (original report), Reddit, Chemjobber

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…

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.