[W]hile one may be an atheist before he can fully “explain how and why the universe came into existence,” he is immediately and continuously under an intellectual duty to engage in providing a cogent answer to these problems. Atheism cannot be merely passive or destructive. It must fill the intellectual gap it creates, not simply revel in sacking others epistemological systems.Kowal is, of course, wrong. By rejecting notions about gods atheism does not create an intellectual gap: we merely observe that gaps religion fails to fill. We do not know for example how and why — or even if — the universe came into existence, but after examining religious "explanations" we still do not know.
It takes a little experience to detect Kowal's equivocation in the above quotation. An explanation in this context is an ontological statement: it is a description of how the world actually is and how it works. An explanation is not an epistemological statement: it is not a statement about how we know whether one explanation or another is actually true, whether one description or another actually corresponds to reality. When atheists reject religious "explanations" we are sacking not religious epistemology, but religious ontology, and we are sacking their ontology in part because it scientific epistemology rejects it.
Indeed we cannot sack religious epistemology because the religious simply don't have one: none of them ever talk about how we can have a rigorous, determinable and shared method of separating statements into true and false*. Drill down to the fundamentals of any religious "explanation" of the world and its primary justification will be: thus-and-so is what the author happens to believe about God; if you do not already happen to share his beliefs, he will be unable to persuade you.
*If you kill everyone who disagrees, I suppose you will generate a consensus of what people believe — or at least admit — to be true.
One person happens to believe that God is infinitely loving and powerful, and though we rarely understand, everything happens for the best. Another happens to believe that an infinitely loving and powerful God nonetheless respects our autonomy and free will. Another happens to believe that God is indifferent or unconcerned with human affairs. Another happens to believe that God is malevolent. Another happens to believe that God himself is above our parochial notions of good and evil. One happens to believe that Genesis is a literally and factually accurate account of cosmology. Another happens to believe it's more-or-less physically correct but couched in poetic language. Still another happens to believe it's allegory and metaphor having nothing whatsoever to do with the creation of the physical world.
The problem with religion is not that it fails to provide explanations. The problem is that religion provides too many explanations. We want one explanation, we want to know that that particular explanation really is correct, and we want to know it's correct even if it contradicts what we happen to believe.
Atheists don't sack religious epistemology — there isn't one. Atheists use evidentiary and scientific epistemology to sack religious ontology. Indeed that's all that scientific epistemology actually does: it's a fundamentally negative epistemology. We are certain some element or elements of a theory — a set of statements about the world — are false if the theory entails false statements about observation. (And if some theory does not entail any statements about the world that are in principle falsifiable by observation, it is not a theory: it is not about the world.)
We are not certain that those theories that survive are true, but we are astonished (in a philosophical sense) that any theories about the world survive this filter, and that usually only one theory (or a family of theories with a single identifiable essential character) survives this process: the process itself does not by definition guarantee a single result. Furthermore, we are philosophically astonished that entirely different people — with different upbringing, local culture, habits, outlook and biases — almost always come to the same conclusion.
Scientific epistemology does not quite do the job philosophers expect: they would like to see a method that, like deduction, separates individual statements into certainly true and certainly false. Scientific epistemology only separates theories-as-a-whole into definitely false and not definitely false. But half a loaf is better than none, and neither philosophy nor theology gives us anything but arbitrary Just-So stories, separating statements into what we do or do not already happen to believe, a job we do not need any epistemology at all to achieve.
Worse yet, religious "explanations" are not explanations. All they do is relabel mysteries about the world as mysteries about God.
Theist: Why is the world the way it is instead of somehow different?
Atheist: I dunno. The world just happens to be the way it is.
T: That's no explanation at all!
A: Perhaps not. Do you have something better?
T: Of course! The world is the way it is because God wanted it this way.
A: Why did God want the world to be the way it is instead of somehow different?
T: I dunno. God just happens to want what He wants.
Of course, the theist will rarely be quite so honest in his last reply. The usual response is to point to some hefty volume of incomprehensible mystical blather. It is the rare atheist who will actually read this blather, but some do, and they invariably find that the tome does not actually explain why God happens to want the world to be the way it is. There are more tricks, and a clever theist can keep a naive and gullible atheist running around in circles for decades, but it all boils down to the same thing. All of theology consists of inferring what God wants from occasionally observing how the world actually is, or more frequently from how the author wishes the world to be.
Atheism by itself is merely the position that religion and theology have themselves failed to provide satisfying explanations, and failed to provide anything bearing even a passing resemblance to a system of knowledge. They have covered their abject failures under the most immense and rococo edifice of bullshit ever conceived by the mind of man (and thus deserving a certain measure of horrified fascination). If we want to know, and not merely comfort ourselves with self-serving fantasies, we must first admit we simply do not know, and set forth on a voyage of discovery, a voyage we are by no means certain to complete or even survive.
Religion demands that we burn the ships in the harbor because we cannot complete the journey before we set out.