Based on the title of this book I would have expected a bit more engagement with the philosophy of knowledge. How do we know something is true, and what do we mean when we say something is true? What could make us abandon our claims, and realistically, would we ever do so?...
Coyne begins his last chapter with the statement of an audience member to him after his public lecture: “I found your evidence for evolution very convincing—but I still don't believe it.” Well, nothing says that our job is to convince people of the “truth” of evolution—I don't think it's my job—but we would like people to understand it. Coyne does a very good job in this book of presenting the actual evidence for evolution. He is less complete on the philosophy and methods that underlie science, particularly in specific disciplines. And one would have liked to see more about dealing with people who are apprehensive about the “truth” of evolution. For the last question readers are referred to Brian and Sandra Alters' Defending Evolution: A Guide to the Creation/Evolution Controversy , which is (another unfortunately titled book) about how to listen to such people, win their confidence that you are sensitive to their worldviews, and develop answers that may make sense to them in their own terms. Maybe some of Coyne's reluctant audience members can be reached in different ways.
While Brian and Sanrda Alters' book has some great suggestingions, I think Coyne deserves a little more credit for dealing with this issue. No, Coyne does't really get into philosophy, but he does, repeatedly, hit on what makes a scientific explanation from a religious one:
"A well-understood and testable hypothesis like sexual selection surely trumps an untestable appeal to the inscrutable caprices of a creator."
He doesn't always phrase the argument in such a contentious way, but this is the heart of the issue. Of course, a designer could have made things the way they are, but then again, the designer could have done things differently. Intelligent design has to appeal to the unfathomable motives of an unavailable designer, while evolution, like all good science, produces explanations (and predictions) for why we expect things to be this way and not the other.
Hence, intelligent design advocates attribute the peacock's tail to a designer's whimsy (how do you test that?), while biologists can explain it from a well-defined theory that generates testable predictions.
This distinction that Coyne makes between arbitrary faith-based explanations for natural phenomena, and the testable, non-arbitrary explanations of scientific theories, is more effective, I think, than any philosophical discussion of the nature of truth.
See here for my review of the book.