Q: How should I respond to peer reviewer comments that I strongly feel are biased?
Since I have no knowledge of the specifics of your paper or the reviewer's comments, I can only suggest a general approach. Biased comments can generally be of two types:
1. The reviewer may have pointed out many flaws/errors in your paper which you think might not be reasonable, and suggested that you fix them;
2. The reviewer may have been completely negative and may have dismissed your paper in a general way without specifically addressing areas that need to be improved.
In case your reviewer’s comments fall in the first category, here is the approach I would suggest:
1. Address each of the reviewer’s comments point-by-point:
a. If it’s a useful suggestion, acknowledge that it is helpful and explain what changes you have made in the manuscript in response to this comment (clearly indicate page number, paragraph number, etc.).
b. If you disagree with the reviewer’s suggestion, then offer a well-framed rationale for doing so.
2. It is a general practice to mark in a different font color all changes you have made to the manuscript based on reviewer comments for the convenience of the reviewer. Hence, consider doing this and indicate to the reviewer that you have done so.
In case your reviewer’s comments fall in the second category, that is, if you feel that the reviewer’s comments are extremely negative and have not been substantiated with evidence, you could politely explain this to the journal editor and ask for more detailed recommendations from the reviewer. In extreme cases, you can write to the journal editor requesting that another reviewer be assigned for the paper on the grounds that this reviewer’s comments are not constructive in any way.
Be sure to read Do's and don'ts for responding to peer reviewers' comments.