Many naturalists are naturalists for the very reason that they believe that talk of God or the supernatural is superfluous. That is, it is seen by them to be unnecessary to posit anything ontologically “outside” the universe. To ask for more and more explanations on top of the material universe is to upset the principle of parsimony. “Why can’t the universe simply be, with no rhyme or reason?” the naturalist wonders.
The nature of this position is that the naturalist is basically calling the universe a brute fact. A brute fact is simply something that admits of no explanation. To ask the “why” question of a brute fact is to receive the answer “it just is that way, for no reason”. Now, this is obviously not a satisfying answer, but whether or not a position is satisfying says nothing regarding its validity. So, the question should be posed regarding whether or not admission of a brute fact is logically valid. My position: it is not.
To illuminate my position, let us take us detour aimed at an explanation of, well, explanation. To ask for an explanation of something is to ask for a reason whereby that thing becomes intelligible. Let me utilize an example from mathematics to illustrate my point. (Warning: nerdy math terms ahead.) In Calculus there is a concept known as a derivative. A derivative basically tells you the rate of change at the exact moment of a function, it’s also known as the instantaneous rate of change. Now, in order to understand instantaneous rate of change, one first needs to understand the average rate of change, because instantaneous rate of change is just the limit, at a specific point, of the average rate of change. But, in order to comprehend the average rate of change, one first needs to understand rate of change itself, also known as slope (remember slope from algebra?). (Ok, the mathematical nerdage is over, go take a walk, or something, and come back.) All this is to say that the concept of a derivative is explained by average rate of change, which is explained by slope. This means that a derivative is made intelligible by average rate of change, which is made intelligible by slope.
This leads us to the conclusion that explanation is somewhat of a transitive relation. That is, if A explains B, and B explains C, then A in turn explains C. This means that the explanation of C is ultimately dependent on A. To return to our math example, this means that the concept of a derivative is ultimately dependent on the concept of slope. This is all to say that explanation, and intelligibility, is imparted by higher members of an explanatory series to the lower members. A imparts explanation and intelligibility to B, and B imparts it to C. So notice that if A does not impart explanation to B, then B has no explanation to impart to C. Taking derivatives into account, if slope is unintelligible, then it has no explanation to give to derivatives, and derivatives would likewise be unintelligible.
So, how does this all affect the position of admitting of brute facts? Well, it means, quite frankly, that brute facts are impossible. Remember that a brute fact admits of no explanation; that is, there is no reason whereby its existence becomes intelligible. But, this means that it has no explanation to give, or impart, which means that it cannot be a participant in an explanatory chain, and certainly cannot be the first member in an explanatory chain. Yet this is exactly what the naturalist wants, namely, explanation to terminate in the brute fact of the existence of the universe. But we’ve seen that this is exactly what cannot be done. That is to say, explanation cannot terminate in the universe, as a brute fact.
Moreover, we can demonstrate this in another facet. If explanation is imparted in an explanatory chain, then we can formulate the following proposition: If (x) is intelligible, then the explanatory chain leading down to (x) contains no brute facts. Why can we say this? Because if (x) is intelligible, then it has a reason whereby it is rendered intelligible—otherwise it is unintelligible. And since explanation and intelligibility are imparted, we can say that for (x) to be intelligible, every member in the explanatory chain leading down to (x) must also be intelligible—again, otherwise intelligibility is not imparted at some point in the chain—and therefore every member is not a brute fact.
So, remember that explanation, for the naturalist, terminates in the universe. That is, all explanations end up leading to the existence of the universe, which admits of no explanation and is a brute fact. But this would mean, per the contrapositive of our above proposition, that if the universe were a brute fact, then any explanation that ultimately ends in the universe—you know, everything contained in the universe, e.g., matter, energy, stars, planets etc.—would be unintelligible. However, these things inside the universe are intelligible, and since they are intelligible, we can assuredly say that the universe is not a brute fact.