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We have a paper that is a second round R&R at a Journal that is a cognate field which is less technical than ours. The editor has been extremely conscientious and supportive through the process, but has made several suggestion that reveal he doesn’t really understand some of the deeper methodological details of our approach. In particular they are concerned that X could be playing a role but this is definitely not the case.

I don’t want to respond saying X can’t explain our results because textbooks prove otherwise. We could probably handle this but this is the second round in which they have suggested X is an issue/explanation, despite us gently explaining in our first round response and adding a footnote explaining why X was not an issue. So we need to find a better way of persuading him that this isn’t an issue.

In particular, I am interested in solutions that avoid the need to explicitly contradict him.

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  • What options do you have if you can't do that without being explicit? – Buffy Feb 4 '20 at 21:00
  • I’m not willing to publish nonsense and so we would have to be explicit but I am concerned, given the tone of previous correspondence, that the editor will react badly. I don’t believe they realise they don’t understand these techniques well. – dothyphendot Feb 4 '20 at 21:02
  • Actually, I was thinking wider. Is this the only suitable journal? But no, don't publish nonsense. – Buffy Feb 4 '20 at 21:03
  • No, but the journal is the top journal in its field and so we are keen to publish there. – dothyphendot Feb 4 '20 at 22:06
  • Are you sure the editor read the footnote? – Anonymous Physicist Feb 5 '20 at 1:36
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I think you just lay out the facts as you see them, pointing to supporting evidence as necessary. If the editor can't be convinced then how you say things isn't going to matter much. Let the facts speak for themselves. Point up the flaws in X as applied to your work. And if you need to reference textbooks, do so, even citing page numbers.

You may lose the battle, but it may not be winnable at this journal. If the reviewer is wrong, but is someone trusted by the editor you have a losing situation. If you sense that then withdraw politely and go to another journal.

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In most cases when you get an editorial/referee comment that is a misunderstanding of the paper, it behooves you to add something in the paper to address this possible misunderstanding. The fact that you have already added a footnote dealing with the matter, and this is insufficient, means you will have to consider expanding this to a larger explanation in the body of the paper. Unless you think it would detract from the quality of your paper, I would suggest expanding your footnote into one or two paragraphs in the body of the paper, explicitly raising this objection and putting forward the evidence that X cannot explain the results. There is no need to be concerned about trying to avoid contradicting the editor --- if he is wrong, your argument should contradict him.

Ultimately, either the editor will accept the explanation in your paper, or not. If you have gone to the trouble of addressing the argument explicitly, and the editor is still not convinced you are correct, he can at least be assured that the argument is there for the reader to consider. Hopefully this will be enough to get your paper through peer review, but even if you don't, it might make your paper better to add this point as an explicit argument in the body of the paper, which will be a benefit if you submit to another journal.

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