A metaphysical theory which holds that all phenomena can be explained mechanistically in terms of natural causes and laws. Naturalism is opposed to supernaturalism which is a teleological metaphysical theory. Supernaturalism attributes, not only a supernatural source to the universe but holds that the universe has special moral or spiritual purposes. The naturalist sees the universe as a vast machine or organism, devoid of general purpose, though integral parts of the universe may function harmoniously and appear to have been designed to so function. The supernaturalist sees the universe as having been created for a purpose, and generally believes that nothing happens without a divine or moral purpose. To the naturalist, Nature is indifferent to human needs and desires. To the supernaturalist, God has filled the natural world with everything we need and should desire, as well as with many things we don't need and shouldn't desire. The latter, too, serve a purpose: they are here as moral challenges and reminders of our place in the grand scheme of things.
As stated above, naturalism is a metaphysical theory. Metaphysical theories are theories about the ultimate nature of reality. Metaphysics is often divided into ontology, cosmology and theology. Ontology is the metaphysics of being. [What is being? Why is there something rather than nothing? What kinds of being are there? etc.] Cosmology is the metaphysics of the cosmos or universe. [What is the nature of the universe? Has the universe existed forever? If it hasn't, how could something come from nothing? etc.] Theology is the metaphysics of god and the supernatural. [Does God exist? What is the nature of God? Can there be more than one God? Is God the Creator of the universe? etc.]
The difference between the mechanistic and teleological views, may be seen by considering the sex drive in animals from each perspective. To the teleologist, the sex drive is designed to reproduce the species. The pleasure which accompanies sex is the main inducement to carry out the divine plan of reproduction. If sex were generally painful, it would be avoided and the members of the species would not pursue it and hence would become extinct. Some theologians maintain that to engage in sex for the purpose of reproduction, is the only proper sexual motive. To frustrate the reproductive purpose of sex is considered perversion and hence immoral. Birth control and homosexuality are considered moral evils under this view. This is not to say that a naturalist cannot consider birth control or homosexuality, moral evils. Some naturalists do consider them evil, but not for the same reasons as the supernaturalist. A naturalist might consider birth control a moral evil if practiced deceitfully. It is also conceivable that some naturalists might even consider it a duty for superior beings, however they might be defined, to reproduce, and for inferior beings, however they might be defined, to practice birth control. A naturalist might also be an ethical emotivist and find homosexuality morally wrong because of repulsive feelings, homosexuality evokes in said naturalist. But, by and large, I would think that most naturalists would consider homosexuality as natural as heterosexuality, and neither one of them inherently moral or immoral. To the naturalist, the sexual urge is purposeless. It was not designed to motivate animals to reproduction. Rather, animals with a strong sexual drive reproduce and hence flourish. There is, therefore, no way to frustrate the purpose of sex, since sex, in general, has no purpose. Of course, the desire to have sex with a particular person is purposive. That is the purpose: to have sex with a particular person, whatever gender that person might be.
To the teleologist, bee pollination of orchards is divinely designed. To the mechanist, bees just do their thing and, as a result, orchards get pollinated. If no animals existed which do what bees do, orchards wouldn't exist, either. The world would be a different place, but it would still be a world. Different mechanisms mean different worlds. The choice is not between this world or none at all, but this world or some other one.
To the teleological supernaturalist, pedophiles and sexual predators exist for some sort of divine purpose. To the mechanistic naturalist, child molesters and child murderers are purposeless. Their desires may be natural but that does not mean that they should be fulfilled. Both the supernaturalist and the naturalist are likely to hold pedophiles and sexual predators accountable for their evil behavior. The naturalist, however, need not feel any need to try to explain why such evil exists. Some naturalists might seek causal explanations which deny that evil is chosen behavior by evil persons with evil desires. All naturalists might agree that the desires themselves are explicable entirely by causal mechanisms outside the scope of personal responsibility. But, not all would agree that acting on the desires is completely explicable without reference to the freedom and responsibility of the evil doer.
The supernaturalist, with his moral and spiritual purposes inherent in every aspect of reality, must come up with some sort of explanation for the existence of evil. The branch of theology which tries to explain such things is called theogony. In theogony it is considered reasonable and acceptable to say of evil, "the ways of the Lord are mysterious, indeed." Or, as God allegedly said to Job (who asked "Why me?"), "Hath thou an arm like the Lord?" In short, "I'm God; I don't have to explain myself to anybody". Evil exists and since God is good you can be sure that there is a good reason for evil. Take it on faith.
Spinoza maintained that teleology represented the primitive thinking of our pre-scientific ancestors. The pursuit of final causes led nowhere in the human quest to understand Nature. Only when humankind gave up the anthropomorphic way of thinking which understands the weather, geology, physics, etc., in terms of divine purposes, could progress in knowledge of Nature be made. I think history has proved Spinoza right. Teleological theories such as supernaturalism are scientifically superfluous. On the other hand, Spinoza's attack on teleology was complete: he did not believe that human behavior was to be explained differently from anything else in Nature. There is no freedom and no responsibility in human behavior, he thought. Human behavior is to be explained in terms of mechanistic causes, just as the behavior of all natural phenomena are to be explained. To a deterministic naturalist such as Spinoza, "good" is just a word we use, to describe things which give us pleasure, and "evil" is just a word we use, to describe things which cause us pain.
Naturalism is often confused with atheism, materialism, positivism, empiricism, determinism and scientism.
Atheism is the view that there is no god. A naturalist may believe in some sort of god or supernatural beings, but denies that there is anything in nature which can't be explained without reference to the supernatural. God, as the Creator of Nature as a separate reality, is an unnecessary hypothesis to the naturalist. The Deistic founders of the United States of America were advocates of naturalism.
Materialism is the metaphysical view which holds that only material, physical, empirical reality exists. Materialists deny that spiritual reality exists, except as a delusion. A materialist might believe in god, but not in the non-physical God of Western religions. If there is a god, god is a material entity or reducible to such an entity.
Positivism is a philosophical attitude which holds that metaphysics, more or less, is bunk. Positivists don't deny the existence of supernatural phenomena; they maintain that it is a waste of time to try to understand or speak of such things.
Empiricism is an epistemological theory [theory of the nature of knowledge] which holds that the origin of all knowledge is sense experience. Some empiricists have believed in God, others have not. Some empiricists are naturalists; others are not. Some empiricists are atheists; others are not. Some are materialists; others are not.
Determinism is the metaphysical theory which holds that all events are determined by mechanistic causes. Determinism is opposed to metaphysical libertarianism which holds that at least some human behavior is explicable in terms of the freedom and responsibility of the agent. A naturalist might be a determinist, such as Spinoza; so might a supernaturalist, such as those who believe in predestination. Both naturalists and supernaturalists might believe in free will and human responsibility for at least some of our behavior.
Scientism is the self-annihilating view that only scientific claims are meaningful, which are not scientific claims and hence, if true, not meaningful. Thus, scientism is either false or meaningless.
In short, naturalism is the foundation of modern scientific theorizing. Reference to moral or divine purposes have no place in science. The scope of science is limited to explanation of empirical phenomena without reference to forces, powers, influences, etc., which are supernatural. Modern science is inherently naturalistic. If naturalism is correctly understood, one realizes that neither science nor naturalism deny the existence of God, free will, spiritual phenomena, Providence or creation by God. Neither science nor naturalism deny the meaningfulness of metaphysical theories. Atheists deny the existence of God. Determinists deny the existence of free will. Materialists deny the existence of spiritual phenomena. Positivists deny the meaningfulness of metaphysical theorizing.
For the record, I consider myself a naturalist, an atheist, a materialist, a metaphysical libertarian, and a positivist. I don't think science is the place for supernaturalist speculation such as creationism. The evidence seems overwhelming to me that there is no Being responsible for the creation of the universe and that what does exist and is knowable by humans is limited to empirical phenomena. I think metaphysics is, more or less, bunk. And, I believe that pedophiles and sexual predators may not be responsible for their desires, but they are responsible for acting on them: they could control their evil behavior, but they choose not to. And the evil they do is not an insignificant part of some divine plan but is a significant part of the human drama, though purposeless and indifferent from Nature's point of view.
further reading
Philosophical Materialism by Richard C. Vitzthum
Science and Religion: Some Historical Perspectives, John Hedley Brooke, The Cambridge History of Science Series (Cambridge University Press, 1991).