Responding to referee reports - part 1

When referees recommend rejection of your manuscript, it's normal to feel angry and reflexively attack the negative referees, but this is rarely the best course of action.  I have refereed hundreds of papers and managed to get many of my own manuscripts past difficult referees and into high profile journals. Here are some of my thoughts on how best to respond to difficult reports.

Your response to the referee reports should be targeted at the editor handling your manuscript. Ultimately it is the editor who will decide whether your manuscript is accepted or rejected. Therefore when you craft your response letter, keep in mind what the editor wants!

The editor is looking to publish papers of interest to the readers of the journal, papers that are correct, papers that will be well-cited. Your response therefore needs to convince the editor that your manuscript meets these criteria. The editor's job is NOT to simply tally the referees' recommendations and go with the majority opinion. In rare cases, usually for controversial topics, the manuscript may be published even when all referees recommend rejection!

While the referees are anonymous to you, they are known (and were likely picked by) the handling editor because he or she thinks they are experts on the subject of your manuscript. Therefore it is unwise to directly attack the referees, as you are implying that the editor made a bad choice. The opinion of referees that are more senior and experienced will be weighted more heavily than a report provided by a junior researcher or student.

Perhaps the worst type of referee report to receive are very brief reports that (perhaps incorrectly) summarise your work in one or two sentences and then recommend rejection based on subjective reasons. You spent months (or even years!) working on a project, only for someone to skim your manuscript in 10 minutes and dismiss your work out of hand. While editors do not like this kind of report either, they are still of use. What is not said by the referee can be just as useful as what is said.

A brief, dismissive referee report indicates they did not find your work interesting enough to engage with it and provide detailed criticism or questions. This suggests your manuscript, as currently written, is not of interest to (some) readers of the journal. This is sufficient grounds for rejection from high profile journals such as Physical Review Letters, even if your results are all correct and of interest to specialists working on your research area. 

Therefore your response should not be to attack the referee for not fairly considering your manuscript or not being an expert in your research area (the referee could be a leader of your field without time to write a more detailed report!). Instead, you should carefully revise your manuscript to improve the presentation and make your results more accessible and interesting to the journal's readership. You should explicitly highlight these revisions in your response to the editor.

On the other hand, long and detailed reports can be viewed favourably by the editor even if the referee is recommending rejection or significant revisions. A detailed report indicates that the referee was at least interested enough in the manuscript to spend time to read it carefully and provide detailed criticism. Thus, the manuscript is of interest to (some) readers of the journal, and the main challenge is to address any technical criticisms (regarding correctness or novelty) raised by the referee.

I will write more on this later.