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I just received the feedback from the Editor-In-Chief that my paper has been rejected for publication in this high-ranking journal.

There are several concerns raised by one of the reviewers. Therefore, it would not be possible to accept this paper for publication.

Based on the reviewers' comments, two of them seem to be in favor, as they raise no "substantial" concerns (they raise 5 and 4 points, respectively), i.e. their findings are mostly of a cosmetic nature (rephrase that, elaborate this, color the figures differently, correct a spelling mistake), and their recapitulation of the work is more precise than that of the third reviewer.

Now the third reviewer raises 6 points of concern. 4 of them are very valid remarks, however, they are not fundamental problems, at least, I don't perceive them as such, because they are easily amended (by at most 2 sentences each) and present no conceptual fallacies, i.e. as I see it, the particular parts are not clear to the reader and need additional explanations and more appropriate emphasis. The fifth concern addresses the structure of the paper, the reviewer proposes another ordering of the sections. The final point states the need for a discussion, which I indeed drafted, but chose not to include in the paper. It is not irrelevant, but it is not crucial for the problem, solution or background and could possibly distract the reader from the focus of the paper. In addition to space constrictions, this discussion was left out before submission.

Between submission and the decision, there was a change of the Editor-In-Chief at the journal. This might be the reason the review took longer than usual (10 instead of 6 weeks). Perhaps that could even influence the accepting policies...

After the first review, I'm used to getting rather harsh comments, either rejecting the paper or proposing another review cycle, it doesn't matter. The important part is usually that I get meaningful feedback about my paper and improve it. In this case, however, the reviewers' comments resemble something I would expect after the second or third review cycle, i.e. something that I can alleviate in a morning.

The problem is that I don't understand the reason for rejection. Even when I address all the reviewers' suggestions, I would still feel that nothing crucial has changed. Furthermore, when rejected, I can't submit the same paper to the same journal. I obviously intend to submit the paper to another journal. However, before doing so, I consider emailing the Editor-In-Chief and asking for more information regarding his decision. As things are now, the reviewers' comments state neither fundamental fallacies which imply that the paper is of low scientific value nor point how I could realistically improve on it. Is this a good idea?

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    I would correct the mistakes and submit somewhere else. Since your paper is already out of the editor's sight (and mind), she probably does not want to go back into it. Of course, you can write a polite email and ask but I doubt you will receive any substantial input. – mmh Feb 16 '15 at 11:44
  • In many journals with high impact factor the editors will be biased towards papers that will bring in more citations. This means that some papers which are scientifically sound will be left out. While this is ideally done during editorial checking, if the editor is unsure he might send the paper for review to get the referees to comment on its (insert euphemism for "bring more citations" here) before making a final decision. If the reviews did not convince the editor this might be the reason he decided to reject the paper. – Miguel Feb 17 '15 at 22:28
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I have never been an EIC but I have spoke to some, I have been a reviewer of many papers, and I have had the similar experiences as you described.

It is probably useless to further inquire about your paper. The EIC decision could have been based on the private communication channels of the review process. The reviewer might have been lukewarm about your paper - maybe it was not a case of a substantial error but that the result was uninteresting. It could also be the case that the new EIC did not have the time for a careful consideration of your paper, of balancing the different reviews and based her decision on the less positive one. EIC are usually very overloaded and some of them explicitly use the rule of deciding based on the most negative review. If it is any of these two cases, you will not receive any further information from the EIC regarding your paper.

My personal experience is that I was only able to change a EIC decision once, when the negative review was reasonably detailed and I could show that some of the main points made by the reviewer were 100% opposite of what was already written in the paper. The other occasions where I asked for more info or criticized what I thought was a wrong interpretation of the paper, I would receive a polite answer that the decision was made.

Now, I wait a week until the frustration and the anger of how "dumb is this reviewer" subsides, make the the changes I think are reasonable and send to the another journal.

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The editorial board's job is to keep out the worst papers, keep in the best papers, and make some (sometimes subjective) decision on which of the remaining to publish and which to reject.

Note that it does not include helping your write your paper better. (Note that while good referee reports often do provide sufficient feedback for you to revise your paper accordingly, the main goal of the reports are to inform the editorial board to allow them to come to a decision.)

EICs being busy as they are generally will not bother to carefully respond to requests for more information: all the info they can provide to you are already provided to you. It is possible that they made their decision in part on confidential reports by the referee to the editorial board (yes, most journals I referee for allow me to write a few sentences in private to the board that the authors don't get to see), and so cannot reveal that to you. It is possible that they are just so backlogged with submission right now that anything negative will cause them to reject.

You are much better off finding a somewhat senior person in your field, show him or her your paper and all the referee reports, and ask for his or her opinion. Chances are one of the following is true:

  1. There are certain things that the referees wrote between the lines that you didn't quite understand yourself, and with this explained you can figure out how to much improve your paper.
  2. There are nothing strictly wrong about your paper, but maybe you were too ambitious in your original choice of journal (importance/sexiness of results and so on), and the senior person can point you to a more appropriate one.
  3. The senior person can, in an unbiased way, agree with you that your paper should not have been rejected, and that the EIC made a mistake to reject you. Then you just pretty it up and submit it to the next journal.

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