Why make more in-depth changes than the reviewers asked for?
Before I start, it is important to identify what the end goal of publishing is. It might feel that the main priority right now is to get the paper accepted. Fair enough; when applying for positions having more publications is often seen as corresponding to a stronger CV. But is the size of your publication list necessarily the most important goal? I would argue that looking beyond the publication itself, and instead considering how the work is received, as being much more important. A scientific career is built on making important contributions to the field, and publishing clear and readable papers substantially help with achieving impact (e.g. the prestige of the journal, the number of citations, reputation of the work, etc.). Reviewer comments can be very useful for finding the best and clearest way to present a set of research findings.
Read, and re-read the full set of reviewer comments
It is really important to first get a complete picture of the reviewers’ mindset as they read the paper. Although it can be hard to do (emotionally), it requires carefully reading the whole set of comments, and asking ‘how did the reviewer come to reach their conclusion?’. It’s best to avoid getting distracted by thoughts like: ‘well they are clearly an idiot’, and instead to think about what structural factors and wording used in the manuscript could help explain where the reviewer’s concerns come from. That is, ‘why did they not understand this passage?’. Clues to such questions are often scattered throughout the reviewer’s comments, such as in the minor line-by-line edits that give insight into where a given question may have come up. Therefore, it can really help to read the reviewer comments several times. I generally read through a decision letter once, when I first get it, and then again a few days later once I’ve had a chance to digest the decision.
Consider the comments beyond the line numbers
When reading review comments and making revisions, try to look beyond the line numbers. A reviewer might write ‘Line XX: something is wrong here’. But it might not actually be at Line XX where things have gone wrong. The issue, be it clarity or giving sufficient information, might need to be resolved in text that appears earlier. Ask yourself: what led to the reviewer suggesting this? Some common reasons include having too little information or too many concepts in the introductory paragraph(s), having the wrong order of information in the methods, or having a mismatch in the logical flow across different parts of the manuscript. Sometimes it is necessary to cut some information from elsewhere to better focus the reader on the most important points. It is not uncommon to want to provide a comprehensive background containing all of the ideas that played a role while developing the work, but extraneous information can come at a cost of painting a clear picture on what the work is about, and tangential ideas earlier in a manuscript can lead to confusion later.
How to deal with comments you disagree with
It is very possible that at least one reviewer’s comment will either be incorrect or disagree with your opinion. Do not ignore these! They are often the most important comments to consider. First, to be clear, as an author you should be able to have the final word on what is in your manuscript (and if the editor disagrees, they may reject the paper, but they should not make you write something you disagree with). However, keep in mind that the reviewer is representing many other readers, some of whom may also disagree with your perspective. It can therefore help to either acknowledge the alternative perspective, or to find ways to steer the reader away from alternative perspectives. Here again, look beyond the line where the comment was made, and consider how this comment arose as the reader developed their own picture of the study through their reading of previous sections.
Should you revise the manuscript if it was rejected outright?
It is really important to go through this process even for manuscripts that were rejected outright. There’s a very good chance that the same editor(s) or reviewer(s) will come across it again, and an unchanged manuscript will not only be rejected again, but your reputation might also be tarnished (at least a little) in the eyes of these repeat reviewers. In my lab, I encourage all of the students to draft (roughly) a response to reviewer comments (see the next post) and make the necessary changes to the manuscript even if the paper was rejected outright. At the very least, this serves as practice for future revisions, and for improving the clarity of the writing in future papers.