As mentioned on the benefits of optional open peer-review history, 80% of PeerJ authors choose to make their review history public. A benefit of this is that other scholars, especially early career researchers, now have an example of how to respond to reviewer comments. Along with performing good peer-review, academic rebuttals tend to be things that get left out of traditional graduate school and post-doc training. Being able to read public academic rebuttal letters is an immensely valuable resource for this reason.
It's also important to keep in mind what a journal's editorial criteria are, and whether both the reviewers and authors have respected those boundaries. A rebuttal is an opportunity to review the editorial policies. Learn more about PeerJ's editorial criteria.
Continuing with the reviews of the PeerJ paper on the review benefits page, let's look at how the author, Associate Professor Rob Edwards, handled his rebuttal to some of the reviewer comments (or download the full rebuttal).
We'll go over two aspects of writing a rebuttal letter:
Although not a requirement, a cover letter has set the tone for this academic exchange. First, the author appropriately thanks the reviewers for their time and comments. Next, the author gives a high-level response to what seems to be the main concerns of the paper. Finally, the author has signed the rebuttal on behalf of his co-authors.
In each sample the review comments are in blue, while the author response is in yellow (add by us for emphasis, not the author).
We're showing just one snippet above, but the author has copied all of the reviewer comments (reviewers 1 and 2) and pasted them into a new document. He has then addressed each point line by line. Also notice the reviewer comments have been italicized (or could have been bolded) and the author responses are non-italicized. This greatly helps the reviewers and academic editor to quickly scan the rebuttal letter making their volunteered job easier and hopefully a little more enjoyable!
It doesn't hurt to remain civil, no matter how dramatic a reviewer may have been in their comments. Remember, the academic editor will also see the reviewer comments and know when they're being tough, but correct or just being plain uncivil. So, keep your author responses polite as well. In this case Dr. Edwards explicitly adds "Agree. Therefore I ..." or "Of course, you're right, so I've added..." and similar throughout his rebuttal. This is professional and the right way to respond to feedback.
There are two reasons a reviewer may be confused about something. Either they read it too quickly, or they were genuinely confused (by the writing style, the method chosen, etc). As an author you'll never know which of course, but it's likely that readers will be doing the same as well. Rather than debate that confusion, this may be an opportunity to expand the manuscript's discussion section. If the discussion is already lengthy then an explanation of the reason to the reviewer may be sufficient along with a short explanation of why you feel the longer discussion should not be added to the actual manuscript.
The dreaded "I believe more experiments are required" reviewer request. The initial gut reaction is to scream expletives and shout out loud at the reviewer. Go ahead and do that. Go on, we'll wait for you. Now that you've got that out of your system you can proceed to how to respond in writing.
In this case there is no magical formula, you may actually need to perform additional validating experiments or similar. The main thing to check is - "Do your conclusions truly follow from the experiments and results previously performed? If not then you have two choices: 1) perform the additional experiments or 2) re-write your conclusions to be in line with the thresholds of experimental validity. Sometimes that could mean the paper is no longer worthy of publishing, in which case you've learned something. Hopefully a simple re-write or explanation of why an additional experiment is not needed or impossible is enough though.
The key thing to remember in your responses is that a little politeness, consideration for confusion, and short explanation is usually all that is needed to satisfy publishing requirements. Editors and reviewers are just as busy as you, and everyone appreciates getting clear respectful answers to alleviate a busy schedule. For authors this usually translates into a more pleasurable peer-review process and almost guarantees a faster turn-around decision time.
In case you missed it, do check out the benefits of optional open review at PeerJ and how to perform a good peer-review.