A naturalist may refer to one who holds any of these philosophical positions, but most often refers to one who studies or enjoys nature.
Superior predictions regarding religious belief
Naturalism provides predicts about religious belief that are superior to what we would expect if theism were true: 
- If theism were true, there is no reason that God would be hard to find. Naturalism predicts God would be hard to find (because he does not exist).
- Theism would predict that only one religion would exist. Naturalism predicts that people would have a wide range of beliefs.
- Theism would predict that religious dogma would be stable over thousands of years. Naturalism predicts dogma to change based on social pressures.
- Theism predicts that their morality is progressive and transcendent. Naturalism predicts that morality reflects social conditions with some progressive and some regressive rules.
- Theism predicts that their sacred texts would contain advanced practical knowledge. Naturalism predicts that sacred texts would me a collection of different styles.
- Some forms of theism predict that life would be designed. Naturalism predicts that life developed through evolutionary processes without an overall direction and with many design shortcomings.
- Theism predicts minds can exist separately from bodies. Naturalism predicts minds cannot exist apart from a physical body.
- Theism predicts that needless suffering (natural evil) would not occur. Naturalism predicts the universe is "a mess".
Various arguments naturalism were true, it would not provide a suitable basis for knowledge.
- Main Article: Evolutionary argument against naturalism
Alvin Plantinga argued that belief in naturalism, particularly if it is separate from theism, is problematic.
- "The most famous version of the argument from reason is epistemological: if naturalism were true, we could not be justified in believing it."
- "To have trustworthy convictions, we have to have properly functioning noetic equipment (i.e., a brain, spinal cord, sensory apparatus, etc., that recognize reality). But can a strictly materialistic, non-teleological, evolutionary process produce such reliable equipment? [...] In order to accept the naturalistic evolutionary explanation for the development of our noetic equipment we have to be agnostic about its reliability. All we would really know is that it works for evolutionary purposes, not for the purposes of discerning truth from falsehood. Evolutionary naturalism, it turns out, is a self-defeating argument. If we believe the theory, we have no reason to believe the theory is true. "
"But then with me the horrid doubt always arises whether the convictions of man's mind, which has been developed from the mind of the lower animals, are of any value or at all trustworthy. Would any one trust in the convictions of a monkey's mind, if there are any convictions in such a mind?"
Apologists are right in that naturalism does not allow for absolutely certain knowledge. However, this does not undermine naturalism because the apologist is asking for an unreasonably high degree of certainty. Just as we assume we are not a brain in a vat and that we are not being tricked by Descartes's evil genius, we can provisionally accept that we perceive and understand reality, at least to a limited extent. Plantinga essentially claims that we do have faithful perception of reality and then goes about trying to find the best explanation for it - however, his premise has not been justified! In this way, the argument is similar to the transcendental argument.
The argument depends on evolution being unlikely to result in a mind that faithfully perceived reality. However, Alvin Plantinga's formulation contains many ad hoc assumptions in its probability analysis that are not justified. His conclusion is doubtful at best.
Also, since our perception of reality has (at least) multiple small flaws and cognitive biases, this suggests that a perfect God was not involved in its design.
A mind that directly perceives reality seems to be a simpler and more effective design than one that works with a substitute reality. This simple approach demands less resources and presumably would be favored by evolution.
Ontological argument from reason
- "Today, I want to focus on the ontological argument from reason, which asserts that there cannot be reasoning in a naturalistic world, because reasoning requires libertarian free will, and this in turn requires a unified, enduring self with active power. "
"If anything extraordinary seems to have happened, we can always say that we have been the victims of an illusion. If we hold a philosophy which excludes the supernatural, this is what we always shall say."