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I was invited to review a paper in which the journal's Editor-in-Chief is a co-author. I do not mind, but raised the question that this peer-review is no longer blind. The co-author can see who wrote the reports.

I do not say the editor takes advantage of his position, but the peer-review is not actually the same.

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    The details will depend on the journal, but I know that some have special procedures in place for this case. It is not in itself a necessity that the Editor in Chief knows the identity of each reviewer. – quid Nov 1 '17 at 14:06
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    As far as I know sometimes editors can write what they want without reviews but of course it doesnt carry the same prestige and is not considered "scientific" in the same sense as if they wrote some journal where they are not editors but must follow review procedure. – mathreadler Nov 1 '17 at 17:14
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In such cases, the editor-in-chief should recuse himself from having anything to do with the review process. This gives the associate or deputy editor for the given paper essentially full control of the process. (In general, I don't think the editor-in-chief is aware of exactly who is assigned to which manuscript.)

One would hope that the editor-in-chief would know the quality and standards required to publish a paper in her own journal; however, should the paper fail to meet those requirements, you should, of course, call that out in the review.

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    How would they maintain blind review in such a case? The editors have the author list. – Ray Nov 1 '17 at 16:39
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    @Ray: I don't really understand. To whom is the review supposed to be "blind?" (In almost all of the papers I've been asked to review, I know who the authors are ahead of time!) – aeismail Nov 1 '17 at 17:14
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    @aeismail most journals I have heard of review is supposed to be double blind to avoid social, economic or any other unscientific bias. – mathreadler Nov 1 '17 at 17:16
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    @mathreadler: As I said, in all of the journals I review for (chemistry, physics, chemical engineering), the reviews are blind to the authors only. – aeismail Nov 1 '17 at 17:20
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    @EmilJeřábek For the reviewers, yes. But the editors who look at all the reviews and rebuttals and make the final decision do have access to the author list (and need to, so the authors can communicate with them to clarify any issues that arise). And making the final accept/reject decision when the EIC is a co-author definitely involves a conflict of interest. – Ray Nov 1 '17 at 17:42
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I've reviewed a paper by section editors in their own journal. I can't speak to common practice, but for this particular paper, in this particular journal, the practice was to simply assign the paper to the editor of a different section. My assumption is that confidentiality was maintained. I imagine the handling for an editor-in-chief would be similar, and that the paper would go to a section editor who would handle everything.

In this particular instance, I can't say I was real happy with the outcome. There was a major mistake of interpretation of the manuscript. The other two reviewers simply missed it (don't get me started about referees who choose to do no work!!), and just about recommended acceptance with no revisions, and my recommendation was much more harsh . The author acknowledged the error and rewrote the results and discussion-- changing the paper from "Earlier investigators found 'A', but using this new method, we find the exact opposite of 'A'" to "We find 'A', just like everyone else", making it a much less important contribution. I felt that if the author were not a section editor, the paper would not have been accepted to that high profile of a journal. I don't think I'd referee under those circumstances again.

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    "The other two reviewers simply missed it (don't get me started about referees who choose to do no work!!)": Please, avoid accusations you cannot really prove: as much as the authors missed the mistake, also the reviewers could. – Massimo Ortolano Nov 1 '17 at 21:56

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