Naturalism removes Animist preconceptions require that all natural events have a purposeful agent behind them. It removes supernatural preconceptions that spirits, both benign and malevolent, manipulate nature. It removes Aristotelian preconceptions that events unfold according to their purpose - fire "wants" to go up, and stones "want" to go down, because that is where they belong, they seek their "natural places". It removes religious preconceptions that god is behind all natural events. It removes teleological expectations that nature has an conscious, agency-driven agenda and purpose which it is trying to achieve. It removes New-Age preconceptions that everything unfolds and develops for a reason (i.e., a mystical, hidden reason). One could argue that naturalism does have one fundamental preconception - which is that it is preferable to avoid imposing human preconceptions on our observations. That is a charge that I can live with. It's like admitting you have just one flaw - and that flaw is excessive modesty :).
Naturalism does not approach nature randomly, naively, and blindly, though. Obviously, there are filters that underlie this interpretation of the universe. Without some sort of expectations and preconceptions and categories, all experience would be a blinding mix of colors, sound, and movements. It would be as William James described the experience of the infant, "as one great blooming, buzzing confusion". We investigate and categorize according to our interests, not randomly or purely objectively. Because of our human self-interest, we find some things more worthy of inspection than others, some questions more interesting than others. Naturalism generally assumes the rules of logic are valid tools for learning and understanding, that the world is real and is full of objects and forces, both with properties that can be described and understood, that these objects that interact with each other, of processes that unfold in a manner that can be understood, that the world is knowable and comprehensible, that the universe is orderly, having regularity, pattern, and structure known as "laws of nature", that all phenomena have natural causes (some known, and some yet unknown), unexplained things can be used to explain other phenomenon (e.g. gravity is thus far unexplained but it is used to explain the movement of planets and the bending of light), etc. It does not presume to catelog all of the entities, properties, and phenomena which exist in the universe, but that when we encounter them, they can be understood as natural entities, properties, and phenomena.
People who defend the religious worldview say that their view and Naturalism are just different ways of viewing the world and different ways of interpreting same evidence. They assert that proponents of both worldviews have their respective biases and filters which restrict the set of possible conclusions they will reach upon consideration of the evidence. This is emblematic of just how weak a position that the religious worldview is. They may admit that their worldview is not a science, but then they say the same thing about Naturalism - that both are just belief systems - trying to drag Naturalism down to the level of Faith by incorrectly equating them. These arguments are not valid. Naturalism is backed by actual science that makes predictions and could, or can, be falsified. It has multiple independent lines of evidence supporting it, while the religious worldview isn't a scientific theory - it can't be tested at all. There is no equivalence whatsoever. Its defenders are free to make whatever claims they want and are absolved from the requirement to prove them.
However, even with these assumptions, Naturalism is a respectful, humble, and wise way to approach the unknowns of the universe. It avoids imposing ill-informed human biases on nature, and allows nature to reveal its secrets to us. It is an approach that systematically avoids extraordinary explanations. It is, by definition, limited to "ordinary" (or natural) explanations, and it is open to the real possibility that the domain of natural explanations can and will expand as we increase our understanding. In the last 500 years, it has been shown to be the "correct" world view time and again. Going back 2500 years to the ancient Greeks, the explanations of the world that have held up over time are those that were based on an empirical and naturalistic world view (with some notable exceptions, such as "atomism", which was deduced mostly apriori but turned out to be roughly correct). The most rational explanation for the success of science is that the Naturalistic world view, which is intimately tied up with science, is correct. If one has even a single pragmatic bone in their bodies, the success of naturalism in explaining the world we live in (and the failure of all other approaches) speaks volumes!
Everyone is a naturalist at the most basic level. For everyday events, like hearing a noise and looking for its source, or watching out for obstacles to walk around, to looking for food and shelter, to interacting effectively in social situations - we all use the evidence provided by habit, nature, and our senses to try to determine how best to react. Animals do this without thinking - they have no "belief system" in place that allows them to navigate the world, and humans don't need one either. Unique among the animals, humans are driven to figure out how the world works. One thing that sets us apart from the rest of the animal kingdom (with the possible exception of ants, beavers, and a few other creatures) is that we are able to exploit the natural order of the world, leverage it, make tools to manipulate it, and control it. And we do this by understanding the way it works, and then applying that knowledge. Supernatural explanations don't help us accomplish this at all. Even the most devout Christians use this naturalistic approach in all other areas of their lives. Christians make fine mathematicians, engineers, accountants, and even scientists (though the overlap of Christianity and Scientists is smaller than average). It is ONLY in the religious sphere that they add on the superfluous and needless layer of religious belief. It can be completely stripped away with no diminution in our ability to survive, prosper, and be happy in the world.
Religious apologists frequently try to shift the burden of proof to Naturalists, off their own shoulders. OK, we can take that challenge. For the last several centuries, since the Renaissance, and arguably since ancient Greece, Naturalism has made claims for how the world works, and those have been validated and shown to be correct each and every time. Anything new that we have learned about about the world, about the universe, has come through Naturalistic discovery, not religious. Religion is stagnant and unable to discover new information. It has systematically inhibited and sabotaged intellectual growth, and seen forward thinkers as heretics. As an approach to thinking about the real world, as a source of knowledge, as an epistemology, Naturalism continues to chip away at religious (including Christian) explanations of "how things work". Prior to the intellectual advances spearheaded by Naturalism, Science, Empiricism, and Rationality, conventional wisdom informed by religion was that Earth was the center of the Universe, disease was caused by demon possession or "bad air", stars were fixed in the sky in a "firmament" hanging over the flat surface of the Earth, storms and earthquakes were the acts of an angry god or gods, wars were won or lost based on a a deity's whim, comets were signs from heaven, the earth was 6000 years old, that we all descended from Adam and Eve, that slavery, rape, and torture of outsiders were acceptable, that snakes could talk, and that followers of other religions and neighboring tribes were practically sub-human and needed to be either exterminated or, at least, conquered.
Many philosophers and scientists have concluded that the best explanation for our ability to develop successful scientific explanations for such a wide range of phenomena in terms of natural causes is that there are no genuine instances of supernatural causation. As Keith Augustine wrote in "In Defense of Naturalism"
Barbara Forrest, for example, describes Naturalism as "a generalization of the cumulative results of scientific inquiry". In other words, the best explanation for the success of science is that Naturalism is true. Given the proliferation of successful scientific explanations for phenomena, Forrest concludes that there is "an asymptotic decrease in the existential possibility of the supernatural to the point at which it is wholly negligible". If Naturalism were false, there would be some phenomena that could not be explained solely in terms of natural causes. However, because science can explain all of the "uncontroversial phenomena" we have encountered (i.e., known to have actually occurred) in terms of natural causes, there probably are no phenomena which cannot be explained in terms of natural causes. Therefore, Naturalism is probably true.However, because this is an inductive conclusion, we can never be 100% sure, but as sure as we can be of anything in our experience. The possibility of it being wrong asymptotically approaches zero.
Individual theories may be disproved, but the overall body of science is fundamentally “right”. Its theories are able to explain what we currently see, to anticipate events that will occur in the future, and to predict discoveries about what occurred in the past (as in geology, astronomy, and paleontology). Its epistemological basis is nature itself, rather than mythology, tradition, personal testimony, or revelation. Apologists insultingly disparage the naturalistic worldview as "man centered" while theirs is "god centered". On the contrary, naturalism is not man-centered but focuses on all of nature, which includes man. It is universe-centered. Ironically, the Christian worldview, which claims to be god-centered, is really the man-centered worldview, since god and the bible which are the source of its epistemology, are both man-made inventions.
The increase in knowledge that results from the application of the naturalistic worldview passes through the rigorous filter of the scientific method. It is coherent (it does not contradict itself), self-correcting, consistent, reliable, open and responsive to criticism, and it makes continual progress and theoretical refinement. Further, there is no compelling reason to disbelieve it. The religious alternative is a concoction of ad hoc, dogma-driven, just-so stories that attempts to insert god as the central figure of the universe. Religious explanations contribute no new empirical success to any field they attempt to address. The explanations provided by religions are specifically suited to provide cover for what has already happened in the universe, but are utterly unable to make any worthwhile predictions or theoretical explanation for future events, and are completely incapable of being tested. They also fail in their complete inability to retrodict past events in the geological or biological history of the earth, and in any past cosmological events. They fail because they are terrible models of the universe, and so have none of the predictive power of a useful theory.
No credible competing acceptable explanation, including the religious explanation, has been proposed. And the religious explanation is missing a key ingredient required of all claims about the real world - it is not supported by evidence. This doesn’t constitute irrefutable deductive proof (which is probably not possible for any explanation of reality), instead utilizing “inference to the best explanation”, meaning that among the only set of available explanations Naturalism is by far the strongest both because of its explanatory power, and because all the evidence collected over a span of hundreds of years supports it.
Religion, on the other hand, has done nothing to advance intellectual progress in explaining the source of natural phenomena. They do no research outside of clarifying of old texts, commenting on each others writing, or trying to find fault with non-religious thinking. On the contrary, it has a history of suppressing scientific discovery (Galileo's assertions about atomism and heliocentrism, discoveries in evolutionary biology, new information from geology about the age of the Earth, discoveries from astronomy about the size, age, origin, and extent of the universe, advances in neuroscience that are beginning to uncover the source of consciousness, anthropological and psychological advances in the study of morality, current scientific attempts to unravel the mystery of life and the origin of the universe, and more). Only reluctantly and belatedly does organized religion accept the findings of science that go against entrenched dogma. The primary books they publish for the general public are of two flavors - praise-the-lord books for the already converted, and Apologist books to convert skeptics. So, when they are not celebrating amongst themselves, they are trying to sell something.
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