A metaphysical naturalist maintains that the natural order is all there is. As Carl Sagan put it, the cosmos is all that was, is, or ever will be. This belief in philosophical naturalism is supposed to be what we should believe instead of Christian theism.
Is naturalism the inevitable, logical result of scientific thinking? It seems hard to deny the legitimacy of science as a way of knowing. Even young-Earth scientific creationists do not say that the Christian faith is true and that science is just wrong. Rather, they say that if science had been done right, it would have upheld the traditional teaching drawn from a literal (I would say hyperliteral) reading of the book of Genesis.
In my view, there is a profound problem with naturalism. In order for natural science to be possible, a natural world must be analyzable in scientific terms. However, scientists must also use scientific methods to discover the truth about the natural world. The contention of the argument from reason is that if the world were truly what naturalism says it is, there would be matter, but there would be no scientists to discover the properties of matter.
Victor Reppert, “Confronting Naturalism: The Argument from Reason” in Contending With Christianity’s Critics, ed. Paul Copan and William Lane Craig (B&H Academic: 2009) p. 27