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A while ago, we read a paper published in a quite credible journal (impact factor around 3), which we believed had a few very basic but significant mistakes in the methods and final results.

The journal's guide for authors mentioned the possibility to submit a discussion ("Discussion: A short commentary (1000-3000 words) discussing an article previously published in XXX."). Together with a colleague, we decided to write a discussion manuscript highlighting the problems of the paper in two pages. We did it twice, actually—one time very polite, and a second time more to the point.

Although each time all of the reviewers agreed on the highlighted problems and one reviewer even recommended publication "as is," both times it was ultimately rejected, because the editor focused on a comment of the reviewer like: "was not general enough", or because "it is more a discussion, and not an original research contribution." (But this was actually exactly what was intended, and fully in agreement with the objective for this type of manuscript in the guide for authors.)

It is OK if a manuscript is rejected (I am a PhD student because I like to learn new things), but it should be rejected for the right reasons. The arguments against the article did not seem to consider properly the submission type, "discussion" instead of "original research article." Furthermore we have the feeling that the editor could be embarrassed to publish a discussion highlighting a paper with such errors that could be recognized by frankly any above-average high school student. (although the paper has been cited quite a number of times, apparently without anyone noticing the mistakes).

It is probably not worth the effort, but it became a matter of principle. We contacted a few other people (not our friends) in the field for a quick opinion about the manuscript, and they confirmed our impression that it has probably been rejected out of embarrassment. This seems quite a disgrace, but what can one do about it?

Should we publish the manuscript together with the reviewer comments on our group website? Submit the manuscript to a competing journal? Would it make sense to contact the publisher (Elsevier) to complain about the editor in chief?

I should also mention that the writers of the original article are, according to their group website, co-sponsored by a big company which gains obvious advantages from their erroneous findings. Is there maybe an ombudsman to which we could go to?

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    Have you written to the EIC directly describing the type of article you were trying to submit? What did you cover letter say? – Bill Barth May 6 '15 at 14:09
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    Have you been in contact with an editor, or with the editor in chief? If the first, you could escalate to the editor in chief. If not, there is likely little you can do, beyond fleshing your paper out to become a full research article (pointing out the errors in the original article), then submitting it either to this journal, or to a different one. Let the EIC deal with people laughing at his journal. – Stephan Kolassa May 6 '15 at 15:54
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    @Alexandros, if there is a paper out there with substantial errors, regardless of OP's characterization, wouldn't you like to see it corrected? – Bill Barth May 6 '15 at 16:37
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    @Alexandros, if the journal claims to accept these discussion articles, then it should follow its own guidelines. Also, his blog post is not archival, and a discussion article would be. If it's bad enough, it may lead to a correction or retraction. – Bill Barth May 6 '15 at 16:51
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    Have you tried contacting the authors to hear what they have to say? I would like to hear from someone who found an error in my model. Some journals actually contact the original authors whenever there is a comment on one of their papers (see e.g. Physical Review). – Miguel May 6 '15 at 21:21
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The first step to take, if not already done, is to answer back to the Editor in Chief, politely explaining that the status of your submission (discussion letter) seems to have been overlooked. Stress again, politely, that the policy of the journal allow explicitly such letters, and that it would be better for everyone that they either enforce this policy (and not reject letters on the ground that they are not full research articles) or remove it from the guide to the authors. Given the answer you get, there are several possible follow-ups if your letter keeps being rejected.

You can contact the authors and see what they have to say. In fact, it would be something to be done before any of the propositions below. They may acknowledge the mistake and publish an erratum by themselves, acknowledging you, and this would make things right in the best way. If they do not answer in a satisfactory way, at least they will have been warned and your case will be stronger.

You can appeal to an ethics committee on your field, if one exists, disclosing both your letter explaining the error, the written exchanges you have had with the journal, and the conflict of interest you spotted for the authors of the original paper. Do not make assumption, just present the fact and let the committee judge for itself.

You can try to publish your letter in another journal, in order to make the official record straight. Depending on the existing venues, you may have to add some flesh to your letter and grow it to a full paper, even if short. You are right in your principles, such mistakes should not be let unknown, and a blog post is too personal and too unofficial to make it right. People should get the information on the mistakes you spotted while using the databases usually used in your field.

But, given you are a PhD student, before you take any step I very strongly advise you to ask your advisor (or another senior researcher you can trust) about it. Depending on your field, your situation, the stature of the author the work of who you criticize, you could end up in pretty bad situation if you do not beware. I cannot tell from the information you gave, but you also have to protect yourself, and unfortunately this is not always achieved by doing the right thing.

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    I agree that contacting the authors before submitting a comment letter is the most diplomatic solution, it gives them the chance to submit an erratum, as you say, and also clearly states the the OP is acting in good faith. It is very easy to interpret a comment letter as an attack, especially if the tone is not right. Making enemies in academia is a bit like shooting yourself in the foot, especially if your field is particularly small. – Miguel May 7 '15 at 10:15
  • I like your suggestions. Also the warning for the risk of some sort of revenge. We discussed with our supervisor about this but decided to continue. I ve send the letter today. – Sarmes May 7 '15 at 21:30
  • @Miguel your responses are itching my brain, you are right it would have been kinder and better to write the authors. Before this all. Ill come back on this. Sorry to flag, fat fingers on a phone – Sarmes May 7 '15 at 21:43
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I can understand the editor's decision not to publish your discussion if the mistakes highlighted should have been identified by the reviewers.

However, it does seem out of context to send the discussion of a paper published in a said journal to a different journal of which the first one was published in. As for a solution, in your stead I would not really know what to do either. If you have a relatively significant connection to authors in your domain via social media (e.g. Twitter, ResearchGate), you could consider uploading your manuscript there.

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