Retraction Watch

Tracking retractions as a window into the scientific process

17 Johns Hopkins researchers resign in protest from ed board at Nature journal

with 26 comments

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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Written by Alison McCook

November 7th, 2017 at 11:02 am

Comments
  • EJNP November 7, 2017 at 12:26 pm

    Just because they cite the original paper, doesn’t mean it’s not plagiarism. Come on Nature!

  • ICC November 7, 2017 at 2:52 pm

    I applaud this principled stand of Prof. Beer’s colleagues. Furthermore, this is a very important story.

    Just my 2c in observing this kind of stuff happening every single day in my field:
    In reporting plagiarism to open-access and/or pay-to-play journals, I have also encountered extreme resistance in trying to get an acknowledgement of the facts that can be deduced from (even for the most blatant cases in which an iThenticate report is unambiguous). I presume this resistance to acknowledge plagiarism (of both blatant and subtle types) has to do with the fact that the journal already took the authors’ money, thus going back for a retraction is “just too much effort” and/or “not worth the headache” for them.

    For example in the notorious AIP Advances we have this “erratum”:
    http://aip.scitation.org/doi/full/10.1063/1.4791777
    which states that “[the authors] did not properly reference material taken from several previously published works” and then proceeds to place citations around all plagiarized and/or duplicated text. The age of scientific pay-to-play open-access is truly mind-boggling.

  • Steven Salzberg November 7, 2017 at 3:54 pm

    In addition to setting a terrible example by rewarding plagiarism, Nature’s Scientific Reports is demonstrating contempt for the thousands of scientists who serve on their editorial board and who perform the vast majority of reviewing work for them. My colleagues and I are calling on all editors for this journal to resign unless the journal’s Managing Editor reverses his decision and retracts the plagiarized article.

    In the meantime, I hope that scientists will cease submitting papers to Sci. Reports. I am announcing to all my scientific colleagues that I will not count publications in Sci. Reports as real papers; thus when I’m asked to review scientists for promotion or to review proposals, I will simply ignore any papers (after today’s date) that appear in this journal, just as I do for low-quality predatory journals.

    • mph November 7, 2017 at 5:54 pm

      i had sincere doubts from the beginning. Appreciate your efforts.

    • Anon November 7, 2017 at 6:55 pm

      Don’t you think that if you ignore such papers, you are unfairly harming disadvantaged persons/less informed people… they are still valid papers, in most instances. Perhaps consider some sunset period and more broadly announcing this?

      • Bobber November 8, 2017 at 4:15 am

        Exactly.

    • K. Hayes November 8, 2017 at 3:43 am

      Dr. Salzberg,

      Thank you for taking a hard-line stance on this issue. It is unfortunate that some see plagiarism as a lesser form of scientific misconduct that can be remedied after publication with some quotation marks or a corrigendum. I am heartened to see such a show of solidarity from the Hopkins community and encourage others to follow suit, as Sci Rep’s actions are clearly unacceptable in this regard. The amount of plagiarism I see in the papers I review is astounding and l know first hand what it feels like to have someone else take credit for your research. Keep fighting the good fight.

    • MR Berlin November 10, 2017 at 10:09 am

      Dear Dr. Salzberg, what about judging papers by scientific merit instead of the journal they happen to appear in?

    • JHU soph November 11, 2017 at 9:32 pm

      As a student at Hopkins, I am proud that our professors will not accept anything less than the utmost integrity in conducting research. Thank you for standing up against plagiarism in the scientific community.

  • imohacsi November 7, 2017 at 4:40 pm

    Well, Scientific Reports does not technically lists novelty as a necessary requirement for publication, just being “technically sound and scientifically valid”, so replication studies like this are welcome…

  • Miguel Roig November 7, 2017 at 5:29 pm

    Not being a complete outsider to this area of research, and in spite of the similarities between both sets of equations, I can’t really determine whether those equations were plagiarized (though they sure look like they have). As such, I personally can’t possibly tell whether the new paper makes an original contribution. Again, it is an area totally unfamiliar to me. However, even if this paper was making an original contribution, the textual similarities between the two papers are highly problematic and they raise serious questions about Springer Nature’s regard for the scholarship of science. Assuming that the new paper is making a novel contribution (a questionable assumption given comments in this and related threads), does the blatant violation of fundamental elements of scholarship (e.g., the use of original prose, proper attribution) not represent a serious concern for these journals any more? If so: ‘Houston, we have a MAJOR friggin’ problem!!!’

    • Miguel Roig November 7, 2017 at 5:43 pm

      I meant to write ‘Being a complete outsider …”

    • Tobias Kildetoft November 8, 2017 at 4:21 am

      As far as I have been able to tell from various comments, the paper does make a novel contribution, by applying previously developed methods to a new problem.
      However, the authors have then way overstated their own contribution, using such language as “we develop…” and similar in regards to these methods, which they themselves had nothing to do with and just apply.

      • Miguel Roig November 8, 2017 at 7:21 am

        Ok, let’s assume that the paper does make a novel contribution. Given its other lapses, the editors’ refusal to retract this paper sends an unambiguous message best articulated by ICC’s comment above. This entire episode is very disappointing; I would have expected better from this publisher.

  • Vladimir Svetlov November 8, 2017 at 6:41 am

    I deeply resent the use of term “predatory” applied to pay-to-publish publications. Let’s call them what they are – prostitutory journals, the girlfriend experience of science.

  • rfg November 8, 2017 at 12:09 pm

    The problem is not that Scientific Reports is open access, “pay-to-play,” and a megajournal. There are more problems IMO with the traditional, closed access, fire-walled subscription, editor as gatekeeper publishing models.

    Like it or not open access is the future, and there will be more megajournals beyond Scientific Reports and PLOS ONE not fewer.

    But, open/closed access is a red herring.

    The problem is using the so-called CORRECTION to cover-up plagiarism, a form of scientific misconduct. This happens much too often in both open access and closed access journals, and for not only plagiarism, but also fabrication and falsification as well as less ethical shortcomings (undisclosed CoI, lack of human and animal use approvals, etc.)

    I applaud the stand of the Hopkins scientists for their protest against this shoddy practice by journals and editors.

    The only appropriate action is RETRACTION, with clear indication that the retraction is for ethical concerns.

    • Vladimir Svetlov November 8, 2017 at 9:50 pm

      Well, you future looks very similar to the present with OA being it. If the current subscription model would go away, what is there to keep pay-to-publish OA afloat – as opposed to the free or nearly free post-publication review (e.g. Biorxiv)? So far even the best among OA experiments proved unable to compete with legacy journals. The vast majority of OA journals are simply profiteering from the established academic tradition, where the science is paid for by grants and the work of reviewers comes free. The break from the tradition comes in the form of abandoning the notion of novelty or originality, opening the door for mediocre at best and fraudulent at the worst of scientific endeavors. And unlike legacy journals, OA journal embroiled in scandal will not look to repair its reputation (as it has none), but close, reopen under a new name and a new address somewhere in a strip mall in Iowa.

    • rfg November 9, 2017 at 12:17 pm

      “The vast majority of OA journals are simply profiteering from the established academic tradition, where the science is paid for by grants and the work of reviewers comes free.”

      How is this any different than than the subscription model of the legacy journals? The only difference – a big one IMO is that there are no paywalls with open access – scientists in developing countries or at institutions without huge library budgets can freely access the scientific content.

      I recommend this video on open access from visionary Jorge Cham:

      https://www.youtube.com/watch?time_continue=357&v=L5rVH1KGBCY

      The correction mechanism is abused by open and closed access journals alike.

      • Vladimir Svetlov November 9, 2017 at 1:21 pm

        How subscription model differs from OA? Let me put it in simple terms: it’s akin to the difference between an established brand and a knock-off. Subscription sells a brand, a reasonable (based on past performance) anticipation of quality and novelty of research, appearing, say, in Nature, Science, and Cell. So the brand-name journals care about tarnishing the brand with substandard papers. Not totally an error-prone mechanism (they do fall for sensationalist claims every now and then), but there is a built-in mechanism for prioritizing quality. OA, on the other hand, sells the right to publication to an author in every given case, not the whole portfolio to the subscriber. The driving mechanism is to attract paying customers, driven not by desire to secure timely access to the high profile papers, but by vanity. Hence no requirement for novelty and originality, just the minimalist (and often unenforced) request for “technically sound” work.
        I recommend for your perusal a visionary work called Masha and the Bear (available on Netflix). It contains as many insights into scientific publishing as video recommended by you, but is far more entertaining.

        • ICC November 9, 2017 at 3:23 pm

          Exactly. A basic analysis basis on the introductory principles of economics shows that OA’s only possible future is pay-to-play scams.

          Another example where the “driving mechanism is to attract paying customers … just the minimalist (and often unenforced) request for “technically sound” work.” fails to produce/recognize real research is in the mathematical sciences. Tautological work is technically sound work in every sense of the work. “2=2.” This is a sound statement. It is based on a sound approach. It is true in the sense of formal logic.

          So, should every author be able to pay a hefty fee and add publications to his CV? Publications that are just math exercises (e.g., undergraduate calculus homework problems)? Changing a “2” to a “5” and an “x” to a “y” here and there, while maintaining “truth” of the work in the formal-logic sense? Based on my observations of OA/pay-to-play, the answer is a resounding “YES!”. I see this over and over in all these journals (often with a heavy sprinkling of plagiarism) … what a joke!

          • Vladimir Svetlov November 9, 2017 at 3:40 pm

            I agree. Although I should clarify that in rare cases OA isn’t outright damnable, such as a legacy journal (NAR) turning OA, or non-profit OA, with costs offset by donors, such as iLife. Anyway, you’ve given a perfect example of technically sound work that contributes nothing but noise. In biology we have that too, although sometimes it’s more difficult to spot, given the idiosyncratic nature of experiments. Paper in question is one example of that – using already published method in regard to a different (“novel”) subject. Plagiarism aside, it is like saying that you made contribution to math by demonstrating that arithmetics works not only for counting apples, but kittens too. General lack of standards (or their enforcement) leads to technically “sound” work that is sound only in appearance. For ages one could get away with irreproducible data by citing “strain differences” – in essence the unknown variables nobody cared to find out about. Things are changing in this regard but slowly. And prostitutory OA journals don’t even pretend to enforce standards of reporting, data availability, etc.

  • Morty November 8, 2017 at 2:24 pm

    I am afraid that if one should avoid all journals that accept plagiarism, there will be a shortage of journals to publish in. Plagiarism is widespread and journals do not care. It is sad, but unfortunately a reality.

    • Patrik Bavoil November 9, 2017 at 9:30 pm

      Journals do care! At least, journals that care that the science they publish be of the highest standard possible, and thankfully there are still a few of these, those journals care. Plagiarism, duplication, data manipulation, just like theft and malpractice, are criminal activities that unfortunately are rarely punishable by law. The fact that SR decided to ‘correct’ the crime rather than retract it, makes SR accessory to the crime. I therefore applaud my colleagues at Hopkins for taking the stand they are taking and I will never review a paper for SR either.

  • rfg November 9, 2017 at 5:22 pm

    “Although I should clarify that in rare cases OA isn’t outright damnable, such as a legacy journal (NAR) turning OA, or non-profit OA, with costs offset by donors, such as iLife.”

    So, if a closed access journal turns to prostitution that’s OK?

    Or, if a generous donor pays for the prostitution that’s OK, too? Convenient that you should mention eLife [I’m assuming iLife is a typo].

    How about when a traditional publishing house like Springer-Nature acquires an open access publisher, BioMed Central. Does that legitimize the house of prostitution?

    Sure there are “low-quality predatory journals” and these should be avoided.

    There are several non-predatory OA publishers that maintain similar standards to the legacy journals, such as BioMed Central and MDPI. One could argue about megajournal PLOS ONE, but the other PLOS journals are similar to legacy journals in terms of standards.

    Perfect standards no. Similar to glam journals Science, Nature and Cell – absolutely.

    • Vladimir Svetlov November 9, 2017 at 6:14 pm

      What visionary video told you about non-profit prostitution? The distinction isn’t between closed and open access, but between legacy journals and OA mimics, and between non-profit OA and prostitutory/for-profit OA. I specifically referred to for-profit OA as pay-to-publish, being aware of nuances not covered on YouTube. Having experience in the field naturally leads to a nuanced position, which you take as a weakness of the argument, when compared to a polarized and uninformed one.
      To the facts: Springer and Nature merged with an expressed point of lending Nature brand name to BMC(then owned by Springer) which is vastly profitable. But they take care not to dilute Nature brand name. And no, BMC and MDPI do not have similar standards to legacy journals, not Nature or Science, not NAR or EMBO. The funny thing is that Genome Biology, the most decent journal under BMC umbrella, doesn’t use BMC in the title, trying to distance itself from the rest of BMC catch-all crowd. Do you know they used to have BMC Cough? I immediately suggested further expansion into BMC Itch, BMC I Don’t Feel So Good, and BMC Poop.

  • rfg November 10, 2017 at 10:24 am

    Dr. Svetlov,

    My life experience has not taught me that a company making a profit is equivalent to prostitution. Perhaps your life experience differs.

    Ironically, a strong argument for the open access model is the obscene profits made the subscription journal publishers (30-40% margins for the big houses). You can find facts in Cham’s video linked above or you can watch another Masha and the Bear cartoon (your choice).

    The cost of publishing OA Are much closer to the actual costs of publishing a paper, and as you yourself have noted OA publishers struggle to maintain viability even with what appears to be large publication charges.

    The additional benefit is that papers published OA are freely available to all, not just those at elite institutions with large library budgets. That’s a good thing considering that the public pays for OA or subscription journals one way or the other. If this point of view makes me a bit of a communist or socialist, so be it.

    I also stand by my view that the standards of some OA journals are equivalent to glam journals. It might just be my life experience again, but I’ve received much more detailed and useful reviews from some PLOS journals that the three minute non-expert editorial review that leads to rejections of 90% of manuscripts submitted to Nature, Science and Cell journals.

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