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In my field, it's common that once the first round of reviews are complete and the manuscript is revised, the revised document includes detailed responses to all peer reviewers' comments. There are some comments by another reviewer I do not agree with, and some comments that I do. Some comments are incredibly constructive and some are obviously "my group doesn't do research this way, so neither should you."

When reviewing the revised manuscript, what is the etiquette involved in addressing this? For some light context, the manuscript is about a technique that is relatively new to my field and is slowly catching on, but not without a serious uphill battle. The other reviewer is clearly someone who is opposed to "shaking things up" and taking this new technique seriously, while I am open to it but still unconvinced that it works.

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What is more important to you, etiquette or good science? Stepping in to controversies can bounce back on you. But not saying what you think seems sub-optimal.

My preference would be to call it like I see it and if it ruffles a few feathers then that is OK. Einstein's special relativity paper ruffled feathers among the most prominent physicists of the day, who were committed to the aether theory.

If it is nuanced in your view, then say that. If it is unproven, then say that. Referring directly to the comments of another reviewer might be the only way to state the case you see. My preference would be to not be bashful about this, while avoiding attacks.

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I would probably not address the other reviewer's opinion directly, but you can be strategic and persuasive in your comments and refer to their review, similar to how you might respond to a review as an author.

If everyone in your field weaves underwater baskets with bamboo, but the paper is weaving their baskets with hemp, and this other reviewer is a bamboo purist, you need not write:

Reviewer 2 is a ridiculous old buffoon for insisting on bamboo and the editor should ignore those comments, the way of the future is clearly hemp!

However, you can add your own praise of the paper and address the controversy, and perhaps even suggest a reference or two to the authors even if they haven't included them, and even propose a middle ground. An example might be:

Though there is resistance in the field to use of hemp for underwater basket weaving, recent advances have suggested hemp is superior to bamboo in some contexts (NewRef1, NewRef2), as the authors also note by citing (Author's reference 54). The authors might improve their paper by referencing the recent discussion on these controversies in (ReviewofBasketMaterials).

Alternatively, if you find the authors already addressed the concerns of that reviewer in their revision I think you can just call those changes out directly:

I appreciate how the authors have addressed concerns about use of hemp in their underwater baskets by referring to (Author's reference 54 and 55) that establish this as a suitable approach.

You may even acknowledge your own skepticism of the technique and how this paper addresses it for the field, if you find it persuasive:

Although the field is still overall resistant to use of hemp, the authors make a convincing case for this approach that strengthens the significance of their paper for the field.

To me, these are strong signals to the editor yet they are not overly confrontational to the other reviewer. I think it's possible to do both good science and keep to etiquette, which is more about how you communicate things rather than what you say. The other reviewer can remain convinced their opinion on techniques is correct, but that should not be sufficient to rejecting a paper if other reviewers (you) are accepting and the authors at least speak to the possible controversy.

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