Most of us know that some of today's biologists (especially) and other scientists are outspoken atheists, and it is easy to assume that atheism itself is at the heart of today's naturalism in science. But according to science historian Hunter, these atheists are Johhny-come-latelys; it was not scientific evidence but theological considerations that led scientists of the 17th through 19th centuries to restrict themselves to naturalistic explanations of the workings of the universe. Here's a sample...
What we need, to begin with, is a clear understanding of what naturalism is. Naturalism's adherents think it is a scientific discovery, and its detractors think it is atheism in disguise. In fact, it is a rationalist movement built on a foundation of religious thought and traditions that mandate a world that operates according to natural laws and processes. In this theological naturalism, religious justifications are freely used, but all explanations must be naturalistic. There are problems with many naturalistic explanations, but this is not why naturalism is ailing. It is ailing because it cannot contemplate the possibility that it might be wrong. It cannot evaluate these problems from a larger perspective...
This restriction of explanation leads to an unavoidable blind spot. Theological naturalism is ailing because it has no choice but to pursue all problems as equals... Theological naturalism lacks the resources to look at all sides of a problem. It lacks the wisdom to know its own limitations.
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