More than a dozen members of the editorial board at Scientific Reports have resigned after the journal decided not to retract a 2016 paper that a researcher claims plagiarized his work.

As of this morning, 19 people — mostly researchers based at Johns Hopkins — had stepped down from the board, according to Hopkins researcher Steven Salzberg. Salzberg organized the response after learning of the issue from colleague Michael Beer, who has accused the 2016 paper of plagiarism.

Monday morning, Richard White, the editor of the journal (published by Springer Nature), sent an email to Salzberg and the researchers who had threatened to resign if the paper wasn’t retracted, saying:

Given your concerns, we have revisited this assessment and thoroughly reconsidered the issues raised with our Head of Editorial Policy and the Research Integrity Group at Nature Research, but we do not think retraction is warranted. We believe that the paper makes an original contribution to the literature in that it takes existing methodology and applies it to a new question or issue, in this case applying the algorithm developed by Michael Beer to recombination. The original paper was reviewed by experts in the field who understood and agreed that the paper was a new application of Beer’s previously-reported methodology and thus an incremental scientific advance that warranted publication. Beer’s work (including the PLOS Computational Biology paper) was cited and discussed multiple times in the original paper in the appropriate context.

Not surprisingly, the resignations are starting to flow. Hopkins professor Ted Dawson told us:

I resigned as soon as I learned that Scientific Reports elected not to retract the paper. It seems Scientific Reports has a unique publication policy — “If you are caught plagiarizing someone else’s work in Scientific Reports, all you need to do is apologize and publish a corrigendum.” I don’t think this is something the community should support or we are condoning this behavior.

“Very disappointed”

According to Beer, large portions of the 2016 paper simply reworded his work and restated the same equations that underlie his previously published algorithm, designed to better identify regulatory sequences in DNA. The 2016 paper, by researchers based at the Shenzhen campus of the Harbin Institute of Technology in China, used the technique to identify recombination spots in DNA; Beer’s was called gkm-SVM, and the China group named theirs SVM-gkm. Although the paper references Beer’s work, he told us the wording in the abstract made stronger claims to novelty.

In his email, White explains that the journal corrected the paper late last year, adding an acknowledgment to Beer’s work:

When concerns were first raised following publication, we undertook a reassessment of the paper and consulted reviewers and we concluded that the paper’s claims about the contribution to the algorithm development, notably in the original abstract, were unjustified and needed to be corrected. The original paper indicated that the software had been previously published (citing the PLOS Computational Biology paper and providing a link to the software in the ‘Tree Structure’ section of the Methods). But following our assessment and discussions, we concluded that the paper should have been clearer that existing methodology is applied to a new biological question, appropriately citing Beer as the original source of the algorithm in the abstract. Equations 2-6 were used without appropriate referencing and this was also addressed in the corrigendum, with citations added to equations 2-6 for the PLOS Computational Biology paper. As such we think that the corrigendum appropriately corrects the publication record by ensuring the contribution of the paper is accurately represented, and that previous work is appropriately credited and cited.

But this decision didn’t resolve the issue. Late last year, one of Beer’s colleagues at Johns Hopkins, Aravinda Chakravarti, resigned from the journal’s editorial board, citing the journal’s response as one factor in his decision. When we covered the case earlier this year, Chakravarti told us:

I was deeply disappointed in SR’s judgement on this paper and am baffled why they would insist on publishing this manuscript.

After our story about the journal’s decision to correct — not retract — the paper appeared, Beer forwarded the article to some colleagues at Hopkins, including Salzberg. Salzberg is not on the board of Scientific Reports, but he decided to go through the list of members and contact everyone at Hopkins. He ended up sending a letter with 21 names to the journal, all of whom willing to resign if the paper wasn’t retracted. (Their letter to the journal also included a side-by-side comparison between the 2016 paper and the work it allegedly plagiarized.) Since then, researchers at other institutions have signed on as well.

Yesterday, after reading White’s email that the journal didn’t plan to retract the paper, Salzberg responded, cc’ing Beer and other letter signatories:

We are very disappointed by this decision. You have decided to reward plagiarism by allowing the authors to make a few minor revisions, and keep their paper in the literature. When a student plagiarizes, we don’t give him a chance to revise and resubmit: we give him a failing grade and sometimes take even stronger disciplinary action, up to and including expulsion. Your journal is thus setting a very poor example. I would mention also that the paper in question did not create any new software, but simply used Dr. Beer’s software and pretended that they had invented it. Your response does not indicate that your advisors or reviewers understood this additional act of plagiarism. My colleagues will let you know shortly of their decisions. I am not a member of the board so I cannot resign, but I will no longer review for your journal, and I will encourage others not to as well.

Please see an update on this post.

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