In his comments theObserver has some interesting points to make on Longenecker and Heschmeyer's ideas about philosophy and Catholic theology. I have slightly edited the comments for style and formatting.
The Roman Catholic church asserts atheists do not understand Catholicism; that "liberal" theology is responsibly for a breakdown in the indoctrination - sorry - the catechizing of children; that once we fully understand the true teaching of the Church, we will all fall on our knees before the Pope.
The whole debate centres on the primacy of epistemology vs ontology. The thought the church pillaged from the classical philosophers was primary ontology in nature: what things exist and what is their nature. Epistemology was always secondary and usually boiled down to "because we said so" or "it's a mystery." Thomas Aquinas and his Five Ways are largely ontological and drawn from Aristotle.
But the entire foundations of the Greek-Christian worldview collapsed during the scientific revolution when the sheer scale of the mistakes in the Aristotelian-derived understanding of the natural universe became apparent. The switch from ontology to epistemology then is best understood as an attempt to fix the mistakes of the past, and we are therefore justified in dismissing the ontology-based arguments of Thomas Aquinas (who continues to have a greater influence on the Roman Church that biblical Jesus) as invalid. Heschmeyer claims that "no atheist has satisfactorily rebutted [Aquinas' five ways] arguments," but what is there to rebut? Aquainas claimed knowledge about the nature of the universe that he simply could not have. Heschmeyer offers no argument why we should even take the time to read the Five Ways, let alone treat it seriously. Even if we accept logical proof for the existence of God(s), we end up with polytheism which, let's be honest, no one really cares about because the conflict is, as noted in Larry's earlier post, primarily political.
Catholics and other Christian sects have no method of epistemology whatsoever and therefore must resort to medieval ontology, which we are then expected to take seriously. Catholics can only settle disputes by appealing to the authority of the Pope and through coercing dissenting voices into silence, a process currently underway in traditional strongholds of Catholic power. The entire history of the Christian church is of debates settled by force, political expediency, or blind chance.
But of course, it's easier for the priests and bullshit artists to whine about Logical Positivism than to deal with their lack of sound epistemology; that a large part of their scholastic traditional is by post-enlightenment (even post-romantic standards) nearly completely worthless, deserving only a footnote in a history of science textbook. Priests can sneer, but the burden is on the church to explain why their ontology-based scholastic traditional is worth engaging with, not least because if accepted, it leads to a huge shift in how we treat gender equality, reproduction, homosexuals, other species, free speech, artistic freedom and so on.
Most atheists are willing to accept that science is not the only form of knowledge, that film, art, literature, etc. have lessons to teach too. But these forms of art are highly subjective - it's the meeting point of an individual mind and an external text. That is to say, I might relate to a piece of fiction and learn from the thoughts and actions of a character while the same passage may be meaningless to another.
Interestingly, most atheists are happy to accept this subjectivity, but most of the religious people I have spoken with are not. Religious people seem to like their rules and their regulations, and they have a general problem accepting subjectivity and pluralism of thought and experience in matters other than claiming religious experiences. It was Aquinas after all who produced entire volumes detailing hierarchies of thought crimes and "unnatural" acts along with their appropriate punishment. Yet Catholics frequently accuse atheists of crude reductionism.
In Europe we are heading into a "year of faith," a year long, European-wide saturated marketing campaign paid for by the Roman church and aimed at revitalizing its brand and increasing its political power. And that largely sums up the Roman church - a glorified political party asserting knowledge it simply cannot have while whoring itself through the same manipulation techniques used to sell soft drinks and cars.