A typical argument for atheism goes like this (in simplified form): Both the atheist and the theist start with a "brute fact", i.e. something that "just is." The theist argues from the existence of the universe ("What caused the universe?") to God (something that "just is.") The atheist responds that if we must accept something that "just is", why not say it is the universe rather than hypothesizing something beyond it like God? That merely, ala Ockham, multiplies hypothetical entities unnecessarily. The universe "just is" and there is no need for God.
It isn't true that the cosmological arguments for God put forward by the great classical philosophers like Aquinas considered God as something that "just is." Indeed, the whole point of the arguments are to establish the existence of something that is much more than something that "just is."
But that is beside the point of the present post, which is to explore the notion of brute facts or things that "just are." My conclusion is that brute facts are intellectually dangerous things, and destroy far more than their deployers suppose. They want to aim the cannon of brute facts at God, but the consequent explosion blows up not just God but our understanding of the universe itself.
Consider what it is to be a "brute" fact. Something that is "brute" is something unintelligible; that is why animals are called "brutes", because they do not possess reason. A "brute" fact is a fact that is unintelligible beyond the bare fact that it is. Clearly, if a fact is brute, there is no point in asking anything more about it, since there is nothing more about it that we can know.
Here is the rub. How do we know a brute fact for what it is when we encounter it? What distinguishes brute facts from intelligible facts? Intelligible facts are facts for which we can find an explanation, you say. But there is nothing to say that brute facts can't appear to have an explanation when they really don't. That, in fact, is the whole point of the atheist's brute fact argument against the theist: His argument is not that God doesn't really explain the universe should He exist, but that the universe in fact does not stand in need of an explanation in the first place because it is brute.
Newton's theory of gravitation appears to explain why the moon orbits the earth and planets orbit the sun. Perhaps, however, those celestial movements are really only brute facts; then Newton's theory only appears to explain the solar system. You scoff because it is clear that Newton's theory does in fact explain the solar system; it is ridiculous to suppose that it is just by chance that all the planets and their moons happen to orbit in accordance with Newton's theory.
And I would agree, but only because I do not accept the notion of brute facts. For smuggled in your reply is the assumption that you have some idea of the nature of brute facts: Brute facts wouldn't appear to happen in such a way that they conform with some intelligible law. In doing so, however, you have implicitly denied the notion of brute facts, for brute facts are facts about which you can say nothing at all further than the fact that they are (or might be). We can't say what they are like or what they are unlike or how they might appear or how it is impossible for them to appear. Any supposition along any of these lines is to contradict the brute nature of the supposed brute fact: It is to concede that the fact is in some measure intelligible; if we can say how brute facts cannot appear to us, then we have conceded that brute facts are in some measure knowable beyond the fact that they are, and therefore are not brute.
One of the virtues of David Hume was that he took the notion of brute facts seriously. And he saw that if we allow the notion of brute facts through the door, then we have destroyed the intelligibility of causality altogether and not just for the universe or God. For we never see causality itself, says Hume, only one event following another. And if we don't presuppose that the universe is intelligible, that is, if we take it that brute facts might be lurking around every corner, then the fact that one type of event tends to follow another might just be one of those brute facts waiting to temp us into false conclusions about causality. We might mistake our becoming accustomed to breaking glass following the flight of a brick for insight into a casual relationship between flying bricks and broken glass, when in fact their relationship might just be a brute fact.
Kant, of course, noticed that Hume's position not only undermined the traditional arguments for God but also any possibility of an actual understanding of the universe, including that of modern science. Kant furthered the Humean project by offering an explanation as to why we tend to (falsely) infer causality into the universe. Kant reflects on the fact of experience, and claims that the only way we can have connected experience is for our cognitive faculties to organize it out of the blooming, buzzing confusion around us. In other words, our minds are constructed so as to read into nature notions like causality and substance so that we can deal with it. A very clever advance on Hume, which saved science from Hume's skepticism, but at the price of recasting the subject of science from being nature itself to merely how nature appears to us given our cognitive apparatus.
The point here is to be wary when an atheist deploys the brute fact artillery. For those who start firing with brute facts typically do not understand that their shells will land on them as much as anyone else. In particular, they don't realize that the brute facts they deploy to destroy God will destroy the science they love so much as well.