Keller's confusion regarding Intelligent Design (the theory that living things exhibit signs of having been designed by some intelligent being) becomes evident in his discussion of Francis Collins' book The Language of God. Collins, the director of the National Institutes of Health and "an eminent research scientist" (The Reason for God, p. 91) is a theistic evolutionist, someone who believes that God created the universe but also has a "firm belief in evolution as a biological mechanism" (The Reason for God, p. 91). Keller states in his book that Collins "believes in evolutionary science and critiques the Intelligent Design movement that denies the transmutation of species" (p. 91, emphasis mine). However, this is an inaccurate description of what Intelligent Design theorists hold. For example, in his book Darwin Devolves: The New Science About DNA That Challenges Evolution, biochemist Michael Behe, a prominent Intelligent Design advocate, asserts that "...chance plus selection can indeed give rise to both new species and genera [the two lowest levels of biological classification], just as Darwin envisioned...But, as a first approximation, Darwinian processes...cannot produce descendants that differ from their ancestor at the level of family or higher" (p. 156). In other words, Intelligent Design theorists do not deny that one species can change into another species through "Darwinian processes," just that such processes do not function at the higher levels of biological classification. In short, Keller mischaracterizes Intelligent Design by saying that it denies "the transmutation of species."
Incidentally, Collins also seems to misunderstand Intelligent Design, or at least he did when he wrote The Language of God. According to Logan Gage in a review of Collins' book:
Collins gets hung up on a common misperception about ID [Intelligent Design] in biology, namely that it is an argument from ignorance. Collins thinks ID theorists look at nature, see extraordinary complexity, and conclude God-musta-done-it...But this is hardly the ID argument. Rather, ID maintains that certain aspects of nature exhibit positive signs of intelligence.
So, to be fair, if Collins, a scientist, doesn't quite understand Intelligent Design, perhaps it is not totally surprising that Keller, a nonscientist, would be confused.
Keller's misconception about what "natural selection" means appears later in Chapter 6 of The Reason for God. In the chapter, Keller makes what I think is a reasonable point--given that it is not entirely clear whether the first two chapters of Genesis are meant to be understood in a literal or figurative sense, theologically orthodox Christians can, legitimately, have differing views on creation and evolution. He notes, however, that representatives of these different views
...often imply that their approach is the One True Christian Position on Evolution. Indeed, I'm sure many reading this will be irritated that I don't take the time here to adjudicate between the competing views. For the record I think God guided some kind of process of natural selection, and yet I reject the concept of evolution as All-encompassing Theory. (p. 97-98, emphasis mine).
In other words, Keller seems to believe that Darwin's notion of natural selection is consistent with the idea of divine guidance. However, as Nancy R. Pearcey and Charles B. Thaxton state in their book The Soul of Science: Christian Faith and Natural Philosophy:
We hardly need to point out that Darwin was firmly rooted in the mechanistic tradition [of biological theories]. His theory of natural selection is implacably mechanistic, and the only reason to stress the point is that so many people have tried to wed his theory to design and purpose.
When one of Darwin's contemporaries, the botanist Asa Gray, tried to find a divine plan within the theory, Darwin protested that this was not what he meant at all. If each variation is determined [i.e., guided] to lead to some desired end, he argued, then there is no need for natural selection. The whole point of natural selection is to demonstrate how the appearance of design might emerge from undesigned random changes... (p. 114).
In other words, if God is guiding the process, it would not qualify as "natural selection." Keller is, essentially, advocating the same view of natural selection that Asa Gray held--a view that Darwin explicitly rejected.
In short, while Keller has some interesting and valid points to make about creation and evolution in The Reason for God, it is clear that he also lacks--or, at least, at the time of writing the book, lacked--a grasp of some of the subtleties involved when discussing these topics. Nevertheless, despite this problem, I would still strongly recommend The Reason for God as a generally effective presentation of the case for Christian faith, despite the shortcomings of the author's discussion of Intelligent design and natural selection.
Image of Timothy Keller from Wikimedia Commons