Philosophical or metaphysical naturalism refers to the view that nature is the “whole show”; There is no supernatural realm and/or intervention in the world. In the strict sense, all forms of nontheisms are naturalistic, including atheism, pantheism, deism, and agnosticism.
However, some theists, especially scientists, hold a form of methodological naturalism. That is, while acknowledging the existence of God and the possibility of miracles, they employ a method of approaching the natural world that does not admit of miracles. This is true of many theistic evolutionists, such as Douglas Young and Donald MacKay. They insist that to admit miracles in nature to explain the unique or anomalous is to invoke “the God of the gaps.” In this sense they are bedfellows with the antisupernaturalists, who deny miracles on the grounds that they are contrary to the scientific method.
Metaphysical naturalists are of two basic kinds: materialists and pantheists. The materialist reduces all to matter and the pantheist reduces all to mind or spirit. Both deny that any supernatural realm intervenes in the natural world. They differ chiefly about whether the natural world is composed ultimately of matter or of mind (spirit). Those who hold the latter often admit the possibility of supernormal events by tapping into this invisible spiritual Force. However, these are not supernatural events in the theistic sense of a supernatural being intervening in the natural world he created.
Metaphysical naturalists reject miracles outright. They vary only in the basis for their criticism of the supernatural. Benedict Spinoza believed miracles are impossible because they are irrational. David Hume claimed that miracles are incredible. Rudolph Bultmann held that miracles are unhistorical and mythical. Based on the un-repeatability of the miraculous, Antony Flew argued that miracles are unidentifiable. Immanuel Kant contended that miracles are not essential to religion. All of these allegations have been carefully analyzed and found to be without foundation.
As for views that admit the existence of a supernatural God but deny miracles (such as deism), many critics have pointed out their basic incoherence. For if God can and has performed the greatest supernatural act of all—creating the world out of nothing, then there is no reason to deny the possibility of lesser supernatural events (i.e., miracles). For making water out of nothing (as God did in Gen 1) is a greater supernatural event than making water into wine (as Jesus did in John 2).
Modern science has pointed to its own miracle—the origin of the material universe out of nothing. The evidence for the big bang origin of the universe is strong. This evidence includes the second law of thermodynamics’ expanding universe, the radiation echo, and the discovery of the large mass of energy predicted by the big bang theory. If so, then matter is neither eternal nor all there is. And if there is a Creator of the whole universe from nothing, the greatest miracle of all has occurred.
Two premises common to all forms of secular humanism are nontheism and naturalism. These can be treated together, since if there is no supernatural being (Creator) beyond the natural universe, then nature is all there is. Often naturalism means that everything can be explained in terms of chemical and physical processes. At a minimum it means that every event in the universe can be explained in terms of the whole universe (the whole system). Naturalists believe there is no need to appeal to anything (or Anyone) outside the universe to explain any event in the universe nor to explain the whole universe itself.
But the very scientific naturalists who insist on explaining everything in terms of physical and chemical laws cannot explain their own scientific theories or laws in terms of mere physical and chemical processes. For a “theory” or “law” about physical processes is obviously not itself a physical process. It is a nonphysical theory about physical things. A physics professor was once asked: “If everything is matter, then what is a scientific theory about matter?” His response was, “It is magic!” When asked his basis for believing that, he replied “Faith.” It is interesting to note the inconsistency that a purely materialistic worldview resorts to faith in “magic” as the basis of their materialistic beliefs.
Another argument revealing the inconsistency of pure naturalism was offered by C. S. Lewis. Quoting Haldane, Lewis wrote: “If my mental processes are determined wholly by the motion of atoms in my brain, I have no reason to suppose that my beliefs are true . . . and hence I have no reason for supposing my brain to be composed of atoms”. If naturalism is claiming to be true then there must be more than mere natural processes; there must be “reason,” which is not purely a natural physical process.
This premise that “every event has a cause” is at the philosophical heart of scientific research, for scientists—certainly naturalistic ones—are trying tfind the natural explanation or cause for all events. But if every event has a cause, then it follows that the whole universe has a cause. For the universe as conceived by modern science is the sum total of all events at a given time. But if each event is caused, then every event is caused. And if the universe is the sum total of every event, then the whole universe is caused. For instance, if each tile on the floor is brown, then the whole floor is brown. And if each part of the table is wooden, then the whole table is wooden. Likewise, if every event in the universe is an effect, then adding up all the events (effects) does not equal a cause. Rather, the sum total of all caused events needs a cause to explain it.
t is not sufficient for the naturalist to say there is something “more” to the universe than the sum of all the events or “parts,” for then he is not really explaining everything in terms of the physical “parts” or events but in terms of something beyond them. It is, however, perfectly consistent for the non-naturalist to insist that all the events of the universe cannot be explained solely in terms of the physical universe of events. But naturalism is not able to explain either itself or the universe on a purely naturalistic premise.
(from Encyclopedia of Christian Apologetics by Norman L. Geisler)