Retraction Watch

Tracking retractions as a window into the scientific process

Cell Press dismisses fraud allegations in high-profile genetics papers

with 8 comments

Screen Shot 2016-08-03 at 18.54.35Cell Press has dismissed accusations of image manipulation in two well-cited papers. 

In June 2015, we reported that the publisher was investigating anonymous allegations of more than a dozen instances of manipulation of images in the papers published in Cell and Molecular Cell in 1999 and 2001, respectively. 

After assessing the original high-resolution versions of images from the laboratory notebook of Maria Pia Cosma, the first author of both papers, the journals have not found enough evidence to determine that fraud had occurred. 

Here’s the editorial note, issued last week for both papers (and also reported by Leonid Schneider):

Concerns about duplicated images in Cosma et al. (Cell, 1999) and Cosma et al. (2001, Mol. Cell 7, 1213–1220) were brought to our attention by a reader. We, the editors of Cell and Molecular Cell, have investigated the matter, communicating with the corresponding author, Dr. Kim Nasmyth; the first author, Dr. Pia Cosma; The Research Institute of Molecular Pathology (IMP), where the research in question was conducted; and the Center for Genomic Regulation, Dr. Cosma’s current institute, which conducted its own investigation. The IMP located Dr. Cosma’s notebooks and provided her with high-resolution copies. As part of our investigation, Dr. Cosma brought those copies to the Cell Press office, where we went through them with her, identifying data for the figures in the paper. The notebooks contained original images, alternate exposures, and/or replicate data for most of the figures in the papers, providing support for the reported findings. In a few instances, original data could not be located, making it difficult to assess the concerns raised about those specific data panels.

While we understand the reasons that the figures in the paper were flagged by the community, in our judgment the burden of proof for determining inappropriate data handling or image duplication has not been met. Furthermore, the available original data support the findings of the papers. With these things in mind, based on the information available to us at this time, we have decided not to take any further action. This statement is to notify the community of our investigation and findings.

The Cell paper, “Ordered Recruitment of Transcription and Chromatin Remodeling Factors to a Cell Cycle– and Developmentally Regulated Promoter,” has been cited 541 times, according to Thomson Reuters Web of Science. The Mol Cell paper, “Cdk1 Triggers Association of RNA Polymerase to Cell Cycle Promoters Only after Recruitment of the Mediator by SBF,” has 109 citations to its name so far.

As we noted in June 2015, the images in question also appear in a Molecular and Cellular Biology paper, “Mutations in the Extracellular Domain Cause RET Loss of Function by a Dominant Negative Mechanism,” which has been cited 44 times so far.

We reached out to the American Society for Microbiology, the publisher of Molecular and Cellular Biology, who said they wouldn’t be able to comment before press time.

Comments about the papers first surfaced on PubPeer in March 2015.

A on the thread about the Cell paper signed by Cosma said:

The figures were made after scanning pictures of multiplex PCR amplifications ran in agarose gels. The final pictures were submitted as print out documents and finally re-scanned. This is a 16 year-old paper, at that time, journals had no clear guidelines on how to present gel data.

In a comment on the same thread for the Cell paper, representatives of the Center for Genomic Regulation (CRG) in Barcelona, Spain, where Cosma is currently based, wrote that they had commissioned M. Rodriguez Sanchez of the Polytechnic University of Catalonia in Barcelona to carry out an investigation into the papers.

As we reported last year, Rodriguez magnified the images and scrutinized them using Photoshop. Any difference he took as evidence against duplication. Ultimately, he concluded that all 30 allegations from PubPeer that he examined were false.

Last year, Craig Peterson from the University of Massachusetts Medical School told us the Cell paper was particularly influential:

It was one of the first papers to use ChIP to monitor sequential recruitment of transcriptional regulators to a eukaryotic gene, yeast HO.

At the time, Peterson added that he understood why people might think the bands in question might be duplicated, but didn’t believe that these issues would refute the conclusions of the original paper even if they were true.

Kim Nasmyth, the last and corresponding author of both papers from the University of Oxford, UK, told us last year:

If someone comes to me with clear evidence for wrongdoing then I will be more than happy to respond. However, I am not aware that this has happened. For all I know, the allegations are part of a personal vendetta against Pia.

Meanwhile, additional papers co-authored by Cosmas are now also being questioned on PubPeer.

We’ve reached out to Cosma, and will update the post with anything else we learn.

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Written by Dalmeet Singh Chawla

August 8th, 2016 at 9:30 am

Comments
  • Anonymous August 9, 2016 at 8:16 am

    As ever, take all instances of anonymous post-publication peer review with a very large pinch of salt. One never quite knows the motivation of the peer(s).

  • fernandopessoa August 9, 2016 at 9:19 am

    What does motivation have to do with data?

    Kim Nasmyth:

    “If someone comes to me with clear evidence for wrongdoing then I will be more than happy to respond.”

    What about looking at the data?

    • Anonymous August 9, 2016 at 11:43 am

      Because mud sticks.

      • fernandopessoa August 9, 2016 at 1:35 pm

        It is not mud, but what the authors published.

        • Anonymous August 9, 2016 at 2:32 pm

          …and the Editors of Cell Press find no evidence of malpractice in these data. Do you accept this conclusion?

          • Sir Duke August 9, 2016 at 2:53 pm

            The authors and the editors succeeded in “muddying the waters” while most peers would have immediately retracted the studies based on the available data.

  • John Krueger August 9, 2016 at 1:30 pm

    The position by “Anonymous” echoes the ludicrous ‘explanation’ for a discrepancy that respondents would often proffer to ORI: i.e, that “someone is making the allegation because they don’t like me.” (Seriously, you just can’t make this stuff up!) Data is data, it provides its own testimony enabling researchers to fairly assess the merits of any made claims against it, irrespective of motivation. Mud does not stick to teflon.

  • Sir Duke August 10, 2016 at 5:28 am

    Among the additional papers being questioned at PubPeer are a couple of papers from EMBO. They usually handle these cases quite differently (read: in an ethically and scientifically sound manner) than Cell Press and I saw that Bernd Pulverer, Head of Scientific Publications at EMBO are investigating the papers (https://pubpeer.com/publications/7B8AF80BA03943EA70B307946CCC23#fb46558), so I wonder whether RW has contacted him about their investigation?

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