Reasonisfaith: “All I’m trying to say to you is that scientific naturalism presumes to explain all things in terms of natural science.”
First, let’s note again that the following terms all equate to each other: metaphysical naturalism, philosophical naturalism, ontological naturalism and scientific naturalism. They each equate to the others, all are a form of atheism and all are distinct from methodological naturalism, which is not necessarily atheistic.
But second, and more importantly, the intended role of naturalism in science is simply to define the limits and boundaries of scientific inquiry — science is limited to those subjects which can yield natural explanations of natural processes.
Naturalism is not intended to deny the **existence** of supernatural processes (I.e., miracles) or explanations, only to rule those as outside the realm of science.
Is that really so hard to “get”?
At the very least, all naturalism—methodological and otherwise—implies atheism. And most fervent believers in naturalism agree with this.
But even if “methodological naturalism” is not necessarily atheistic, there is a problem: if the Bible is true, then the natural system—which appears in its usual state to be a closed system—experienced an act of interference from outside the system when God the creator sent his only begotten Son to die on the cross and to be risen on the third day. Among many other supernatural acts.
In other words, if the Bible is true then the so called boundary between the natural and the supernatural is temporary at best and imaginary at worst.