The Courtier’s Reply is useless. It ignores the real target of an argument.
The Not My Theology Reply is legitimate, though it may be beyond the scope of the present discussion. If someone’s argument does not apply to your philosophy but it does apply to the philosophy of others, then that argument probably wasn’t intended for you. But you might still want to make the Not My Theology reply just to clear things up for people.
The Straw Man Reply is legitimate only if someone misrepresents the view he intends to attack. Remember that many arguments are not intended to attack every variety of your worldview there is.
I’ll make this very brief and to the point. Jerry Coyne wrote something on his website. (The details don’t even matter, but if you’re curious, you can read the article here.) A scientist named Ben Allen disagrees with something Coyne wrote. Allen submits a comment critical of Coyne’s claim in the combox on Coyne’s website. Allen is subsequently blocked from his site. Because of the scientific nature of the disagreement and Allen’s scientific credentials, however, Allen attracts the attention of PZ Myers, who agrees to publish Allen’s critique as a guest post on Myers’s blog. The comments on Allen’s post are as interesting as the post itself: many other people report being blocked by Jerry Coyne for similar reasons. And readers of this blog will remember that I described my own experience being blocked by Jerry Coyne over a minor issue.
I have great respect for Jerry Coyne’s intelligence and knowledge of biology. I have no respect for his thin-skinned moderation and comment blocking policy, however. Virtually all Christian apologists I’ve interacted with have been much more tolerant of publishing criticisms in their comment boxes, Twitter feeds, discussion forums, etc. than Jerry Coyne is. Jerry Coyne is not acting like a freethinker who has nothing to fear and everything to gain from the honest pursuit of truth.
Jerry Coyne should be ashamed of himself. Kudos to PZ Myers for helping to expose Coyne’s behavior.