The naturalist assumption that the only valid method of inquiry is the scientific method has generally succeeded in becoming the primary view among academics worldwide. However, when we really consider what is being said we should not be so quick to acquiesce to the claims of naturalists. According to their argument the only kind of knowledge that can be considered useful is that which can be empirically verified. The problem with this assertion is that the premise itself cannot be subject to empirically verification. It is a metaphysical assertion. Therefore, the assertion itself ought not be embraced on its own terms.
In one of his many essays, the philosopher, Alvin Plantinga addressed well the problem that naturalists face. He wrote:
According to an idea widely popular since the Enlightenment, science (at least when properly pursued) is a cool, reasoned, wholly dispassionate attempt to figure out the truth about ourselves and the world, entirely independent of ideology, or moral convictions, or religious or theological commitments. Of course this picture has lately developed some cracks. It is worth noting that 16 centuries ago, St. Augustine provided the materials for seeing that this common conception can’t really be correct. It would be excessively naïve to think that contemporary science is religiously and theologically neutral. Perhaps parts of science are like that. The size and shape of the earth and its distance from the sun, the periodic table of the elements, the proof of the Pythagorean Theorem–these are all in a reasonable sense religiously neutral. But many other areas of science are very different. They are obviously and deeply involved in a clash between opposed religious world views. There is no neat recipe for telling which parts of science are neutral with respect to this contest and which are not; what we have is a continuum rather than a simple distinction. But here is a rough rule of thumb: the relevance of a bit of science to this contest depends upon how closely that bit is involved in the attempt to come to understand ourselves as human beings.
Indeed, the proposition that human action can be studied in exactly the same way that we study things like physics has likely set our understanding of the social sciences back about one hundred years or more. Such an assumption reduces human behavior to a purely mechanical level that flies in the face of all that we know about ourselves. It assumes that choices we make are not really choices at all, but merely some sort of crude bio-chemical responses to outside environmental stimuli. Yet such a proposition is always at odds with what we already know about ourselves. Namely, we make choices and we know we are the ones making those choices.
As a result, there is more than a little poor reasoning about human action. Think of our language today. We readily speak of various addictions as if something from beyond had befallen us rather than to speak of the poor choices that gave rise to the destructive behavior. As a result, we speak of the homeless alcoholic rather than the hobo of yesteryear. Moreover, by ignoring the reality of human choice we devise all sorts of programs and policies aimed at solving a wide variety of human ills that will not work and will likely produce far greater ills. For example, the creation of social security was seen as a grand fix to provide for people in their old age. The result was that people became more prodigal based on the assumption that someone else would provide for their future. In truth, social security was a financially fraudulent scheme that could never work in the long-term. It was wrong when it was established and it will always be wrong. Maturity in action demands that the individual plan and prepare for his own future. Until we begin to get back to a better philosophical foundation for thinking about ourselves we are not likely to address the problems of today accurately.
 Alvin Plantinga, “Methodological Naturalism Part 1”, Origins &Design, 18:1.