Retraction Watch

Tracking retractions as a window into the scientific process

5th retraction for Voinnet follows correction, EoC to PLOS Genetics paper

with 14 comments

PLOS GeneticsAfter correcting a paper due to problematic figure panels, researchers led by high-profile biologist Olivier Voinnet have now retracted it, after “further analysis of the paper revealed flaws in the interpretation of” another figure.

PLOS Genetics published the retraction notice September 3 for the 2013 paper on the molecular details of embryonic stem cells in mice. First author Constance Ciaudo and Voinnet assume “full responsibility for the mistakes on this paper,” according to the note.

Questions about the figures in “RNAi-Dependent and Independent Control of LINE1 Accumulation and Mobility in Mouse Embryonic Stem Cells” had been raised on PubPeer earlier this year; the paper was among many other papers co-authored by Voinnet that were questioned on the site

Shortly after the first PubPeer post about the 2013 PLOS Genetics paper, a commenter using the name of first author Ciaudo said she had become aware of “potential problems” with a figure, and that Voinnet was contacting the journal’s editor.  

One month after issuing the correction, PLOS Genetics posted an Expression of Concern about the paper, which mentions the same figure panels included in the correction, along with another figure:

Concerns have been raised regarding some of the data in the PLOS Genetics article “RNAi-Dependent and Independent Control of LINE1 Accumulation and Mobility in Mouse Embryonic Stem Cells”, notably in panel A in Fig 4, in panels A and F in S4 Fig, and with the statistical analyses used to produce Fig 2. The authors have responded to these concerns, acknowledging that some errors were made in figure preparation and with some statistical tests, however a final resolution has not yet been reached, and the matter is being evaluated by the authors’ institution.

Now, a couple of months later, the paper has been retracted. Here’s the full retraction notice:

At the request of the authors, PLOS Genetics is retracting this publication following an investigation into concerns that were raised regarding the assembly of Fig 4 and S4 Fig, and the statistical analysis used in Fig 2A. The text below has been agreed to by the authors and editors.

The corresponding author, Olivier Voinnet, was originally alerted to errors that occurred during the assembly of Fig 4 (panel A) and S4 Fig (panels A and F). These errors have been corrected using the original raw data, and a correction notice was published accordingly.

Further analysis of the paper revealed flaws in the interpretation of the transposition data presented in Fig 2A. In the originally submitted version, the L1 copy number was only presented for the DCRFlx/Flx P10 and DCR-/- P30 cells, and a T-test performed on the two datasets showed that the L1 copy number was statistically higher in DCR-/- cells than in control cells. During the last stage of the review process, additional datasets were added and a second T-test was then used to establish the statistical analysis published in the final version of the paper. However, it was later realized that T-tests are not appropriate for comparing more than two datasets. At the recommendation of the ETH statistics helpdesk, a suitable Analysis of Variance (ANOVA) test with multiple comparisons was then conducted on the DcrFlx/Flx P30 and Dcr-/- P30 datasets, providing a p-value of 0.0501, which is at the margin of the threshold of significance. The ANOVA test conducted on the DcrFlx/Flx P10 and Dcr-/- P30 datasets revealed a statistically significant p-value of 0.0018. The statistical issue regarding the L1 copy number in DCR-/- versus control ES cells is currently being addressed using a new set of cells and a direct GFP-based transposition assay. This issue will hopefully be clarified in the near future via the submission of an amended study for peer-review.

Based on the present uncertainty revealed by the corrected statistical analysis of the L1 copy number—a key element of this paper—and on the previous errors in the figures, the authors have collectively decided to retract this study. Constance Ciaudo and Olivier Voinnet take full responsibility for the mistakes on this paper and wish to apologize. They also wish to state that none of the above-mentioned mistakes involved any of the co-authors from the Curie Institute, whose contributions to the paper were restricted to the bioinformatics analysis of small RNAs (NS, CJC, EB) and the generation of reagents including an ES cell line required for the study (EH, IO). All authors regret the inconvenience caused.

The study has been cited 16 times, according to Thomson Scientific’s Web of Knowledge.

Our total count for Voinnet now stands at 12 corrections (including one from this newly retracted paper) and five retractions.

In July, Voinnet was suspended from Centre national de la recherche scientifique (CNRS) for two years following investigations into problems with his research. An inquiry by ETH Zurich found “errors of varying severity” in 20 of the 32 studies they looked into.

Voinnet won the Rössler Prize in 2013 and was awarded the EMBO Gold Medal in 2009.

We’ve reached out to Voinnet and Ciaudo for a comment on the retraction. We’ll update with any response.

Update, 10:00 a.m. Eastern, 9/8/2015: In a statement on the retraction, a spokesperson for PLOS Genetics said that they were tipped off by a “member of the community”:

The overall history of this retraction is given in the retraction notice itself, and we hope that readers will find this to be a clear and informative explanation. Prompted by an alert from a member of the community, and after further investigation by the authors and journal editors (during which time an Expression of Concern was posted to inform readers), it was felt that the conclusions of this article were no longer considered reliable.  Following this decision, PLOS Genetics supported the authors in retracting the article, which we believe was the responsible step to take.

As a community journal, we rely on and value the input of our readers, editors and authors. If readers have concerns about research published in PLOS Genetics, we would always encourage them to contact the journal office directly. We investigate all concerns in accordance with the guidelines issued by the Committee on Publications Ethics (COPE) and aim to resolve questions promptly.

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Written by Ross Keith

September 8th, 2015 at 9:40 am

Comments
  • HeiDi September 8, 2015 at 10:25 am

    Reading all the comments regarding Voinnet’s work and corrections I can’t help but feel that this isn’t just a noble quest for scientific rightness.
    Rather, it feels like a terrible form of systematic harassment from a few zealous / jealous competitors, fueled by hatred. Not nice. At all.

    • Neuroskeptic (@Neuro_Skeptic) September 8, 2015 at 10:49 am

      With respect, how it feels isn’t the point. What matters are the facts: this is science after all. Thanks to the “jealous competitors”, we now know more facts than we previously did.

      • HeiDi September 9, 2015 at 10:48 am

        There is a clear difference between (i) organized fraud, deception, fabrication of data and (ii) different forms of slopiness.
        Not that slopiness is acceptable, it isn’t. But, Science or not, systematic bashing is not acceptable either. It really seems that the treatment the guy receives is a bit more than what he may deserve. Note that I don’t work in his field at all. I’m completely unrelated to this guy. However, I find your military approach to the thing a bit childish.
        Nothing is ever Black or White.

        • herr doktor bimler September 9, 2015 at 5:58 pm

          your military approach to the thing
          Now I am imagining Neuroskeptic in charge of an armoured infantry division.

    • LMW September 8, 2015 at 11:01 am

      If the original data are available and support the figures and conclusions, a lab has the ultimate defense (no mater how zealous any competitors may be).

    • Turingsbrain September 8, 2015 at 8:10 pm

      It was never about a “noble quest’ – it is about the process of self-correction which is part of science. Unfortunately, Voinnet et al. require a lot of external prompting for performing the corrections, which then seem to lead to retractions. It’s the emergence of a concerning pattern. I am just curious to see which publishers will be proactive about this, and actually follow through with the necessary steps so that the scientific record will be corrected.

    • cvdolan September 9, 2015 at 4:22 am

      The “witchhunt card” … It is based on the notion that the retraction of papers can be achieved by the concerted effort of bad people. Happily the antidote to the poison that these people spread is simple: See LMW’s reply.

    • My opinion September 9, 2015 at 4:57 pm

      HeiDi, your opinion is valid, as are all. I do not know Dr. Voinnet, but I do know one thing, as an unpaid, unerappreciated scientist: I feel quite angry to know that this reputed gentleman and apparent specialist won some of the globe’s most reputable prizes, received a great salary, benefits and travel expenses to present – most likely – the same “sloppy” science at meetings, with all costs paid for (tax payer’s money?). So, while I do agree that scientist bashing is most likely not the most gentlemanly form of treating a peer, as a peer (of sorts), I tell you straight: Dr. Voinnet has lost my respect, and trust. Science has a cost, and so does sloppiness. If Dr. Voinnet is so noble, then why does he simply not retrun the funding that he, in my opinion, received unfairly? And why does he not come forward to RW to speak his mind and his opinion, freely, and openly?

      • HeiDi September 10, 2015 at 2:43 am

        I do understand your point of view. It’s justified. As mentioned above, I don’t work in Voinnet’s field at all. My opinion might well be different if I was a competitor and if I knew the guy. It’s just how things look like from the outside. For the last retracted paper there were comments that t-tests were used rather than 1-way Anova thereby leading a non-significant result with p=0.051 or something like that. That’s not serious. If we were to remove from the literature all papers which do not use proper statistical analysis, not to mention all those that do not use stats at all, and sometimes end up in high-profile journals, there wouldn’t be much left. That’s why I said it looks like systematic bashing. But, you’re right, the opinion depends on your own standpoint.

  • fernando pessoa September 8, 2015 at 10:53 am

    It is about the data.

  • Query September 8, 2015 at 11:20 am

    Could PLOS elucidate whether the “member of the community” was anonymous, or not.

  • 6th retraction September 23, 2015 at 4:15 am

    The 6th retraction appears for Voinnet on September 22, 2015.

    Original
    Extreme resistance as a host counter-counter defense against viral suppression of RNA silencing. Raphaël Sansregret, Vanessa Dufour, Mathieu Langlois, Fouad Daayf, Patrice Dunoyer, Olivier Voinnet, Kamal Bouarab, PLoS Pathogens (2013) 9(6): e1003435
    DOI: 10.1371/journal.ppat.1003435
    http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1003435

    Retraction
    Sansregret R, Dufour V, Langlois M, Daayf F, Dunoyer P, et al. (2015) Retraction: Extreme Resistance as a Host Counter-counter Defense against Viral Suppression of RNA Silencing. PLoS Pathog 11(9): e1005207. doi: 10.1371/journal.ppat.1005207

    Last sentence of the retraction notice: “Kamal Bouarab and Olivier Voinnet, as the corresponding authors, take full responsibility for the publication of this erroneous paper and regret deeply the inconvenience caused.”

    • Query on funding/prizes September 23, 2015 at 12:18 pm

      I have a question regarding research funding when a paper is retracted. For example, this 6th retracted paper states: “RS is a fellow of the FQRNT. KB and FD are supported by Discovery grants from the Natural Sciences and Engineering Research Council of Canada (NSERC). OV was supported by an award from the Bettencourt Foundation and the Louis D. Prize from the French Academy of Science. PD was supported by the Agence National pour la Recherche (ANR-08-JCJC-0063 and ANR-10-LABX-36). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.”

      In particular the KB and OV support since KB and OV took direct responsibility for these errors. Why would they not be expected to return a fraction of the funding they received? In essence, this paper does not exist in the literature any longer, at least formally speaking, so the funding received for the research that culminated in this paper represents squandered money.

      I continue to be firmly of the opinion that there must be a severe financial punishment to OV, whose 6 retractions and multiple EOCs and corrigenda/errata have basically been a waste of public and private funding. Not to mention the generous prizes and their associated money.

  • A curiosity September 25, 2015 at 1:31 am

    An interaction that is archived publicly between the first author, Raphaël Sansregret, and Leonid Schneider:
    http://imgur.com/n7kIEtT

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