Over a dozen editorial board members resigned when a journal refused to retract a paper. Today, it’s retracted.

Following a massive editorial protest, Scientific Reports is admitting its handling of a disputed paper was “insufficient and inadequate,” and has agreed to retract it.

The 2016 paper was initially corrected by the journal, after a researcher at Johns Hopkins University, Michael Beer, accused it of lifting some of his earlier work. After we covered the story, nearly two dozen Hopkins researchers threatened to resign from the journal’s editorial board if the journal didn’t retract the paper — and many followed through with that threat after the journal reaffirmed its initial decision. In response, the journal said it would assemble a “senior editorial committee” to review its decision-making.

That committee, it appears, has determined that the journal erred in its initial decision. According to a statement from the journal provided to Retraction Watch:

We have now undertaken further assessment of this case, including seeking additional independent advice from external ethics experts.The conclusion of this review is that the original and corrected versions of the article include ambiguous sentences and textual overlap without adequate attribution which failed to give due credit to a previously published article by another research group, and should be retracted. The review also concluded that the correction made following the initial review was insufficient and inadequate. As a result of this issue, we are now developing updated and more extensive guidance for all of our editorial staff on handling allegations of plagiarism and will also be developing further guidance for authors on how to avoid plagiarism.

A representative of the journal declined to provide us a copy of the external committee’s report.

It’s unclear whether this move will be enough to prompt the editors who have resigned to rejoin the journal. Hopkins researcher Steven Salzberg, who organized the response after learning of the issue from Beer (but was not a member of the editorial board), told us this was “excellent news:”

…I’m very pleased (and relieved) to see that Nature’s Scientific Reports has done the right thing here.

Beer, too, told us he was happy with the result:

I would have been very surprised if an unbiased scientific review panel had not reached the conclusion that this was plagiarism…I’m a little surprised that it took this long. But I believe that this end point is the appropriate one.

Salzberg noted:

I have not asked any of the academic editors who resigned what they would do if Scientific Reports retracted the article, but I will let them know as soon as the embargo is lifted. Each of them is independent, of course, but I would not be surprised if some of them agree to re-join the editorial board. I would certainly support them if they choose to do that.

I also hope the journal will contact all of them and invite them to re-join. We have not heard this news from the journal yet, perhaps because they wish to keep it under embargo until tomorrow.

The number of people who resigned from the journal in response to its handling of this paper is only a small fraction of the journal’s large editorial board.

Here’s the retraction notice for “Recombination spot identification Based on gapped k-mers,” which cites the paper by Beer and his colleagues:

This Article reports an application of methodology originally reported in Reference 33 to recombination spot identification. Reference 33 (Ghandi, M. et al. PLoS Comp. Biol. [2014]) of this Article introduced a feature set called gapped k-mer for regulatory sequence prediction; this Article applied these gapped k-mer features to recombination spot identification, and a computational predictor was constructed for recombination spot identification.

The original and corrected versions of the Article include ambiguous sentences and textual overlap without adequate attribution, which failed to give due credit to the authors of Reference 33. The original and corrected versions of the Article are therefore being retracted by the Editors. The authors do not agree with the retraction.

The paper has been cited 17 times, according to Clarivate Analytics’ Web of Science, including once after it was corrected in December, 2016.

We contacted last author Bin Liu based at Harbin Institute of Technology, and will update the story if he responds. Last year, he denied the accusations that his paper had plagiarized from Beer’s work.

The now-retracted paper is an application of a previously published algorithm designed to better identify regulatory sequences in DNA. Liu and his colleagues used the technique to identify recombination spots in DNA, calling it SVM-gkm. Beer claimed that large sections of the 2016 paper simply reworded his paper and restated the equations that underlie his software—named gkm-SVM.

The retraction went live at 2 AM New York time, 6 AM UTC. The publisher sent us an advanced copy of the notice and a statement at 11 AM New York time yesterday, noting that it was under embargo. We contacted Salzberg and Beer under the condition that they would not reveal details about the retraction before it was published.

Salzberg concluded:

My only other comment is that I think the journal acted much too slowly, and did not take the original claims of plagiarism seriously enough. Based on their statement, I hope that they will be more alert to this issue in the future.

Beer noted that since the journal had decided to correct, not retract, the paper, he had been unwilling to work with them, and had advised others to do the same — but with this retraction, he might be open to changing his mind. And added that he’s grateful to the people who helped advocate for this outcome:

I think this process is incredibly important. I think integrity of the scientific publishing process is incredibly important. If it were just me complaining to the journal, nothing would have happened…I’m thankful to my colleagues who didn’t need to speak up, but they brought this result…It’s not until a sufficient group of people say ‘this is a problem’ that it gets on the radar of the journal.

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