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I recently discovered that a paper I reviewed a while back and rejected as a result of major methodological flaws had been resubmitted to another journal and published without addressing any of the significant errors that required the paper to be rejected in the first place. Is there anything I can do that doesn't violate the confidentiality of the peer review process to address the problem?

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    Inform to the editor of the published journal or make a comment to the published paper. – Kay Mar 7 '16 at 5:17
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    There is no need to do anything. If you wish, you may submit a comment to the journal without mentioning the peer review. – Anonymous Physicist Mar 7 '16 at 6:19
  • Regarding the confidentiality of reviewers, I asked about that at MO some time ago, i.e. under what circumstances a reviewer may disclose his identity. I was surprised by the diversity of of replies ranging from "that's not the reviewers business" over "it's the reviewers decision" to "I always sign my reviews with my real name". So you may consider it an option to contact the editorial board, the handling editor or even the authors directly. – Dirk Mar 7 '16 at 7:38
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Two things are unclear about your question Is there anything I can do that doesn't violate the confidentiality of the peer review process to address the problem?:

  1. What is the goal of any intervention?
  2. Why do you think that anything should be done?

If, for example, you aim for retraction, I guess this could be difficult. You may go for this on the ground that you can prove that the authors were aware of the flaws you pointed out and submitted the paper knowing that there was something wrong. The journal may have some rule that the authors have to certify that the results are true to the best of their knowledge. If this really is so, you may have some angle of attack. If you aim for correction by the authors, it could also be difficult. However, you could consider writing a letter to the editor, pointing out what is wrong and then ask if the journal would publish such a letter. Some journals I know have such formats. You could also do follow-up research on the same topic and write a paper yourself where you refer to the paper with flaws and describe what wrong there.

For the second question, it sounds like you feel that "What's published and peer-reviewed should be true." While this resonates with me, it's not something that is close to true now and probably never will be. Mistakes happen. You may then trust in the scientific community that the flawed paper will be perceived as such in the long run and find peace with this particular paper.

Finally, the premise that confidentiality of the peer review process may permit some actions is not totally clear. As I wrote in a comment, I asked a question about this on MO and got very different responses.

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  • What is the goal of any intervention seems pretty obvious to me: removing junk from the literature, or at least mark it as such. – Cape Code Mar 7 '16 at 10:15
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    That's also two different goals. Anyway, was not clear to me. – Dirk Mar 7 '16 at 10:20
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I think the first question you need to ask yourself is what have the authors done wrong. Disagreements between authors and reviewers about methodology are fairly common. I see two situations. The first is you believe the paper is wrong and needs to be retracted. The second is you believe the authors have intentionally mislead the reader (since you told them about the error in your review).

You should be able to make the claim that the methodology is flawed from the published manuscript. As that claim would only be based on the published manuscript, it would not violate the confidentiality of the peer review process. You should follow whatever procedure the publisher has for reporting issues.

If you believe the authors engaged in ethical misconduct by ignoring your review, you should be very careful. You should talk to colleagues to make sure that the methodology is in fact flawed. Once you are sure of the flaw, you then need to approach colleagues about the "hypothetical situation" of whether it is potentially unethical if the authors knew about the flaw prior to publishing the work. Once you are confident that there is a flaw and that it was potentially unethical to publish the work, you should go through the editor at the journal you reviewed for. Let the editor know about the misconduct and hopefully they will follow up on it. If the editor chooses not to follow up on a claim of misconduct, then you should follow up on that. In this case, where the journal refuses to follow up on a claim of misconduct, I think it is reasonable to violate the confidentiality of the peer review process to the extent required to show the misconduct to an outsider (e.g., COPE).

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    Yes. And, further, we can wonder whether not-so-competent authors would necessarily be convinced of their own incompetence even when it is explained to them. Thus, without deliberate intent, in what sense is failing to believe referees' comments/critiques "misconduct"? Incompetence, arguably, but it's more dangerous to start declaring that incompetence is an ethical failure, etc. – paul garrett Mar 8 '16 at 21:49
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There are plenty of similar cases where a rejected paper gets published in some other journal. But if a reviewer had pointed out some mistakes, then it is a bad attempt to submit to another journal without making a correction or giving proper evidence. In my point of view, the author must have disobeyed the statement during journal submission, if they have anything like,

"whether this manuscript was rejected by another journal. If yes, then why?"

So inform the methodological flaws you noticed to the editor of the published journal with a request to being confidential. And let the editor to reply in that matter.

Another best way would be you can write a commentary note to the published paper to make a discussion. In this case you will have to justify the drawbacks of the used methodology.

Another possible way would be to remain silent.

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    I have never seen a policy like that. Maybe it happens in other disciplines? – Anonymous Physicist Mar 7 '16 at 6:17
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    I have seen a question like that in a minority of biology journals. – user2390246 Mar 7 '16 at 8:02
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    The author may have said the manuscript was rejected because Reviewer 2 thought the method was flawed. The editor could have then confirmed that the method was fine and even asked additional reviewers to check the method. – StrongBad Mar 8 '16 at 21:04
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    For that matter, an author may believe and claim that their earlier submission was "rejected because referees were idiots", no matter what evidence referees give, etc. – paul garrett Mar 8 '16 at 21:46
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    @paulgarrett, or just venue shopping. – vonbrand Mar 8 '16 at 22:08

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