Archive for the ‘Academic Politics’ Category

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?

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.

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.

Organometallics Responds to the Dorta Situation

Thursday, August 8th, 2013

As was first reported—I believe—by “Dr. MJP” in the comments thread of ChemBark’s original report on the Dorta paper, the editor-in-chief of Organometallics is distributing a letter to parties who have contacted the journal regarding the troubling comment on page 12 of the Supporting Information. ChemBark has confirmed the contents of the letter, which is reproduced below:

Wednesday 07 August

Dear Friends of Organometallics,

Chemical Abstracts alerted us to the statement you mention, which was overlooked during the peer review process, on Monday 05 August. At that time, the manuscript was pulled from the print publication queue.

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.

Many readers have commented that the statement reflects poorly on the moral or ethical character of the author, but the broad “retribution” that some would seek is not our purview. As Editors, our “powers” are limited to appropriate precautionary measures involving future submissions by such authors to Organometallics, the details of which would be confidential (ACS Ethical Guidelines, http://pubs.acs.org/page/policy/ethics/index.html). Our decision to keep the supporting information on the web, at least for the time being, is one of transparency and honesty toward the chemical community.

Other stakeholders can contemplate a fuller range of responses. Some unedited opinions from the community are available in the comments section of a blog posting: http://blog.chembark.com/2013/08/06/a-­disturbing-­note-­in-­a-­recent-­si-­file/#comments

If you have any criticisms of the actions described above, please do not hesitate to share them with me.

Thanks much for being a reader of Organometallics, and best wishes,
John Gladysz
Editor-­in-­Chief

I’ll have another post on this story tomorrow; I just wanted to post the above letter for the sake of keeping a complete record on the blog. The letter has also been posted on Chemistry Blog and In the Pipeline.