Naturalism comes in two unpopular flavors: Philosophical Naturalism and Methodological Naturalism. Other flavors, including Materialism and Physicalism, may be categorized as very unpopular because such a small minority of the world's population buys into them. This includes a great number of taxpayers who don't (willingly) buy into public schools due to the influence of these philosophies (aka secular religions) being used to indoctrinate students rather than to educate them.
While subtleties certainly exist between Materialism, Physicalism and Naturalism (MP&N), for all practical purposes most of us know them through Carl Sagan's famous (or infamous) declaration:
"The Cosmos is all that is or was or ever will be."
Infamous? Let's just say that most viewers of his Cosmos series were amazed that he could pack 3 lies into 12 words. Apparently, nobody told him that either the Cosmos or its Creator has always existed and it's not the Cosmos. Given the 2nd Law of Thermodynamics alone, he should have been well aware of that fact. Add an expanding universe (which is actually accelerating in its expansion) and his excuses for MP&N are very thin indeed. Nature certainly didn't have a natural cause given that nature couldn't cause anything if it didn't exist all of those billions and billions of years ago just before its explosive expansion. (Speaking of nature, natural selection can't select anything that doesn't already exist, but we're getting ahead of ourselves. Physics preceded biology in much the same way that Mind preceded matter so we recommend going to charlesdarwin.org to learn more about that.)
Does all of this mean that science and science education must include God in the equation?
No, it does not. While the inference from the scientific data to a Creator may be compelling, a mathematician never enters his or her equations.(1) The Empirical Sciences that describe observable, predictable and repeatable (i.e. natural) phenomena in the Cosmos will, for most rational people, infer a Law-Giver, however, the Empirical or Natural Sciences are limited in scope and only describe how nature operates or functions. They cannot describe the origin of nature by means of natural processes although many still try.
When it comes to the Historical Sciences and questions of ultimate origins (i.e. unobservable, unpredictable and unrepeatable unique events in the distant past) scientists should remain professionally agnostic, apart from their personal beliefs, and be very much open to the idea that Cosmos is not all there is or was or ever will be.
The NSF, for example, should not be in the business of funding metaphysical research programs that promote secular religions or world views just as public schools should not be in the business of indoctrinating students into a secular or atheistic world view. Both institutions are supported primarily through the taxation (without representation, all too often) of theists and could be easily defunded by the most rational among us for what they perceive as fruitless, if not harmful, dead ends.
Finally, scientists should never assume that everything within nature had a purely natural cause which should then be attributed to Naturalism's god-of-the-gaps, "Pure Chance", through some unpredictable process that we should, in all honesty, call Unintelligent Design. (Do random mutations come to mind?) The creation of the entire universe in the finite past with all of its evidence for fine-tuning should give everyone more than enough reasons to be skeptical of such a claim. Besides, while there is nothing like a good theory of origins, "it just happened by an unpredictable and unrepeatable process" is nothing like an good theory of origins.
While the origin of space-time, matter and energy in the finite past is problematic for the MP&N world view, the belief that life itself arose purely by natural chemical reactions is extremely questionable given that the simplest possible organism is irreducibly complex. 99.9 percent of such an organism would immediately begin to decay due to natural chemical reactions and would significantly, if not completely, decompose well before the final one tenth of one percent arrived immediately to stop the process of decay. This is why Biogenesis continues to be such a well established Law of nature making rational belief in abiogenesis to be completely implausible. Given the billions and billions and billions(2) of organisms that have existed for billions of years on Earth, Biogenesis is as solid as a scientific Law can possibly get. And yet, those in the scientific community deluded by their MP&N ideology may already have spent billions(3) trying to create just-so-creation-stories-without-a-Creator about the origin of life in order to demonstrate how life may have arisen without any intelligence whatsoever. Ultimately, they will only demonstrate how much intelligent genetic engineering was required for that first organism.
When you think about it, if it weren't so serious, it would be funny:
Naturalism - Nature could not have had a natural cause if at time = 0 natural causes didn’t exist.
Physicalism - See above. Everything physical could not have had a physical cause.
Materialism - Just who put the material in Materialism, anyway?
Nothing = Something that can fluctuate in a quantum vacuum and produce everything.
Quantum mechanics = Something that God knows a lot more about than we do.
Multiverse = Something that requires an omnipotent, eternally existing universe generator … aka God.
Bottom line? MP&N were dead on arrival over 12 billion years ago (give or take 6 decimal points among friends). Whenever these philosophies come up in a discussion, take the opportunity to discuss the real Enlightenment and the one who declared, "I AM the light of the world."
History = His Story of creation, fall and redemption
Comparative Religion - There is no comparison to the Father, Son and Holy Spirit.
The real question is why MP&N's god-of-the gaps, "Pure Chance", should ever be invoked when the real Creator has revealed Himself to us throughout history and ultimately in the flesh.(4)
(1) It a good idea, however, to give credit to the mathematician for his or her work: Newton's equations of gravity, Ohm's Law, Einstein's e=mc2, or Maxwell's equations that connect his Creator's proclamation "Let there be light" to partial differential equations.
(2) Extra billions courtesy of Carl Sagan
(3) If not billion$ and billion$
(4) "What was from the beginning, what we have heard, what we have seen with our eyes, what we have looked at and touched with our hands, concerning the Word of Life— and the life was revealed, and we have seen and testify and proclaim to you the eternal life, which was with the Father and was revealed to us" (1 John 1:1).