Shall I write a rebuttal letter or just transfer my manuscript? How shall I write the letter?

Question

I recently submitted a paper to a peer-reviewed journal and received feedback from two reviewers. Reviewer #1's feedback was rather nonspecific, but Reviewer #2's comments were quite perplexing.

This reviewer accused my paper of lacking novelty, stating it merely echoed previous findings but using new methods. Paradoxically, they also recommended that I reconsider my tone, claiming it lacked support from prior research.

In an even more baffling turn, Reviewer #2 appeared to completely misconstrue the methodology of my paper, launching extensive critique based on this misinterpretation. They also alleged the presence of multiple typos and non-standard usage in tables and figures, but didn't specify any instances. To top it all off, I received a letter recommending transfer.

My advisor opined that the comments were largely baseless and agreed to write a rebuttal letter in the name of her. I'm now in a bit of a muddle, unsure about the best way to respond to such a perplexing reviewer. The incoherent and contradictory feedback suggests to me that it may have been given by multiple individuals, possibly lacking foundational knowledge in this field. This is the only explanation I can think of for the confusing logic and conflicting statements in these comments. How should I best address this situation?

(PS: Our field is short of reviewers)

Answer 1

Rule one of responding to referee reports: Referees misunderstanding your manuscript is a "you problem" not a "referee" problem.

If a referee has misunderstood what you wrote, then what you wrote was not clear enough. Try to understand why the referee misunderstood your intended meaning and improve your writing accordingly. Once you have done this the rebuttal will pretty much write itself.

Answer 2

The hardest part of science is taking something that is clear to you and making it clear to others. You did not do that part correctly if a referee did not understand your paper.

So the first step is to go through the referee comments one by one and address them. Whatever you choose to do, don’t gamble that transferring a manuscript that has been misunderstood without changes will result in a different outcome. If you transfer to a journal by the same publisher, the new referees will likely have access to the old referee reviews, and you’re not ahead. If you restart the process with another publisher, you might have the same referee as you have now.

In my mind, it is slightly better to resubmit with a rebuttal precisely because it will go to the same referee and you can address specific points of the report; a new set of referees often generates a new set of problems.

Answer 3

Sometimes you do get an unhelpful review. When you do, your job is to convince the editor that the review was in fact unhelpful; it is their job to decide what to do after that -- either to get another reviewer or to proceed based on the one sensible review.

You are well within your rights to respond like this:

[Reviewer:] Multiple typos and non-standard notation make this paper very difficult to read.

Response: We have tried to standardise our notation more wherever we notice it -- for example, replacing "stdev" with $$\sigma$$ as our notation for standard deviation in figure axes -- but, without specific examples of what the reviewer finds fault with, we are not able to improve our paper accordingly.

The flip side is that if you're going to write something like this, then wherever the reviewer has said something specific and actionable, you better well have done something. Add or remove paragraphs as asked -- your paper isn't going to tank just because it was changed 5-10% in response to a reviewer, and if it's good work people will reach out directly to you, whereupon you can tell your side of the story. Do what you must to get the paper past review -- that gives you the credibility to tell the editor that some things the reviewer said simply could not be done.