Keller takes the stance that the science/religion dichotomy is a false one. He spends a fair amount of time pointing out that significant numbers of scientists, in fact, believe in God. To counter claims that science has disproven the miraculous he makes the point that science, which is based on methodological naturalism, can only address the natural. Therefore, science cannot be used to disprove the supernatural, whether that be God or miracles. He asserts that God cannot be proven or disproven. While I agree with this last statement, the Intelligent Design (ID) movement would counter that science can be used to detect design in nature, providing some support for a creator (think fine-tuning arguments).
Keller addresses evolution, admitting that he believes in some type of God-directed process of natural selection. He does not view evolution as contradicting the Biblical account of creation, unless it is accepted as an "All-Encompassing Theory". I certainly agree with him here. It is important to understand the genre of the Biblical literature we are reading as well as the ancient near east (ANE) worldview in which it was written. Christendom has a history of interpreting scripture in ways which inevitably bump up against new scientific discoveries, leading to reinterpretation of the Biblical text in ways that do not conflict with them (think geocentric vs. heliocentric view of the universe).
In a bookclub meeting I attended tonight at church, we discussed this very issue of Christianity reinterpreting scripture and readjusting its view of the world as science has progressed. An important question was raised about how to prevent ourselves from taking stances based on scripture which turn out later to be wrong. I don't know for sure that we can avoid it. However, humbly being willing to hold our beliefs with some tentativeness and to revisit our positions based on new evidence would certainly go a long way. Hopefully, we are allowing our faith and science to inform each other, instead of compartmentalizing them.