jeeprs, i am not responding to your post to refute it, but simply because I'd like to have your quote in my response.
So while everyone is bagging out 'religion' you ought to realize that science has basically demolished the idea that 'the universe is made of atoms'. All the lay-people seem to assume that we have a 'realistic picture' of 'what the universe is about' but this is far from true. The picture we have of the universe is intrinsically incomprehensible and 'queerer than we can suppose'. So it is all very well to bask in the imagined comfort of 'scientific logic' but when push comes to shove, it doesn't add up to any kind of coherent picture of reality whatever. Multiverses, string theory, and all the rest of it. Sure all of these theories have some validity in the hands of the mathematical physicists who are qualified to comment on them, but to the rest of us, it means (what is that great technical term) diddly squat. So the days when we had Science with its great material certainties and religion with its obscure dogmas and rituals are so nineteenth century. What is unfolding is going to be unlike anything we have previously conceived of and it will have many religious or spiritual implications also.
I find the conversation so far a bit confusing. All concepts and ideas have an historical origin, all originate within a specific cultural milieu. Nonetheless, some concepts are culture specific and some (esp. those that help us analyze physical phenomenon) are trans-cultural. The basis for the transmission of an idea from one culture to another is its utility (I'm not trying to draw the debate within the various "utilitarian" threads here, honest.)
Certain concepts that were authored by the ancient Greeks survived the transition into medieval Christianity, which however hostile it might have been to its antecedents also recognized the efficacy of it's arguments. Likewise, certain concepts that originate in various and extended religious cultures have made their presence felt in modern, secular science. Just as the idea of an "atom" predated the modern discovery of a particle now so-named, so other concepts sharpened and defined in religious debate find new applications in scientific discourse. Some of the ideas present in the analysis of QM first rose to prominence in scholastic arguments. (Imagine Duns Scotus as a modern physicist, yowza!)
That these ideas do not contradict certain spiritual beliefs is hardly surprising. It would be surprising if they did. Nonetheless, the spiritual beliefs are not necessary for the concepts to operate.
My objection to an idea like ID is not that it is contradicted by the scientific method, but that its addition or subtraction does not affect the utility of that method. It remains scientistic rather than scientific. If one chooses a strong scientific approach to atheism, and reduces all knowledge to that concretely acquired by the scientific method, there is no theoretical support for ID. However, science has no rebuttal to the faith-based claims made by the religious culture-specific idea of ID. And of course, there are much more subtle theoretical undertones to some quasi-scientific/religiously-inspired rhetoric. (Incidentally, my use of the word "rhetoric" is not meant as pejorative, I use it in its technical sense.) Honestly, given the fine-tuned pedantry necessary to partake in current scientific debates and its resemblance to the same sort of squabbles that took place in medieval Christendom, it seems like the perfect conduit for the transmission of certain religious ideas. I'm surprised that they are not more prevalent.
(NB: One thing that I haven't seen come up, but that occurred to me is this: Is it possible for someone who upholds the intellectual virtue of scientific method to regard the idea of divinity in anything other than historically relative terms? The ideas of fundamentalism and scientific method seem far more incompatible than do science and more flexible forms of religiosity.)