Alvin Plantinga, a seasoned philosopher of religion and critic of atheistic and naturalistic belief, develops the following thesis in his 2011 work Where the Conflict Really Lies: "there is superficial conflict but deep concord between science and theistic religion, but superficial concord and deep conflict between science and naturalism." In essence, Plantinga argues that the enterprise of science functions better given certain theistic assumptions than it does given certain natrualistic assumptions. Such a claim is a direct assault on the naturalist's stronghold, for the core of naturalist doctrine is powered almost exclusively by the authority of science. Plantinga, of course, is well-aware how close to the artery his argument cuts: He colorfully writes, "Naturalists pledge allegiance to science; they nail their banner to the mast of science; they wrap themselves in the mantle of science like a politician in the flag" (p. 307). Certainly, if naturalists are as wedded to science as Plantinga takes them to be, and if Plantinga's central thesis is remotely successful, then naturalists have something of a crisis on their hands.
Plantinga systematically develops each of the major claims in his thesis throughout the book. He begins by discussing how the alleged conflict between science and theism is merely superficial, goes on to argue that science and theism are deeply concordant, then claims the concord often attributed to science and naturalism is actually superficial, then finally argues that science and naturalism are in deep conflict. Although each of these discussions is substantive, interesting, and, in characteristic Plantinga style, entertaining, I will only discuss the argument I found most interesting--the argument that science and naturalism are in deep conflict--and encourage the reader to pick up the book him or herself to learn more about the others.