We see the phenomenon most obviously with the evolution/ID debate in North America. It's the fact that the essence, the base, the fundamentals of religion and science are at odds. We see it more and more (usually from the BBC, is my impression) that there's a continuing skirmish happening in the Arab world as well, with the Quran on one side, and geologists, biologists, astronomers, epidemiologists, and virtually everybody else on the other. The more fundamental adherents to Islam think that Mecca is the centre of the world (which is only possible if the planet is flat), and that the sun really does orbit the earth.
At its root, it's a question of questions. Who can ask them, why they do, who/what/where to ask, and the kinds of answers you can expect.
My religious experience was bounded by a healthy respect for science. In my most religious days, I wanted to be a forensic scientist (this is WAY before CSI made it sexy). It involved the coolest bits of police work and detective work, asking questions and getting answers. Getting answers from the evidence, but also from other people. Getting answers from math, and from physics, and from experiments, as well as from interviews and other scientists. I saw no contradiction between my faith and my aspirations. Chiefly, I think, because I would be using the "how does is work" questions' results to answer the "what happened" question. There would be no big fundamental questions, only minutae and details.
I've since moved on, but the disconnect between the technical applications of science and the higher orders of thinking, and how that relates to religious belief, has become more evident over time. In fact, every time I read someone's hateful venom directed at scientists, I'm struck by the fact that the computer the attack was written on owes a great deal to science.
A few notable theologists aside (and I apologist to hardcore atheists for putting the words "notable" and "theologists" together), the greatest religious virtue is that of being unquestioning. Faith, by its very nature, makes assumptions that cannot, indeed should not, be checked. God is real. God loves you. God cares what happens to you. God will answer your questions, and will listen to your prayers. God made you.
None of this is provable, to put it simply. There is no proof. I once taught at an Islamic school (an interesting time, to say the least and to give a nod to the Taoist saying), and the children offered me proof that god was real, he should be called Allah, and the Quran is his holy book. Apparently the lines on your palm look like the numerals "90" and "9", and apparently there are 99 names for god. Therefore, he made you.
I pointed out that the lines on people's palms predate written Arabic, and that it wasn't proof. I also pointed out that religion doesn't require proof. I was summarily dismissed (about this and a great deal of other things).
And that's the difference. Religion doesn't require proof. That's supposed to be the point. It was alluded to in the movie Constantine. John Constantine says he believes. Gabriel points out that he doesn't believe, he knows, and that makes all the difference (movie's not great, but the point is sound).
The conflict we see is greater than the church (in its various incarnations) railing against the loss of authority. The problem is deeper than the ethical misuse of scienific advances. The crisis in faith is far more serious.
In the last 200 years, science has done a great deal by encouraging investigation, by searching for theses and theories, by testing them and by modifying them. The basic model is much like evolution itself, where theories are found strong enough or useful enough to survive and propagate, or they are found weak, and ill-suited to the rigours of the environment, and they either adapt or fail. It's a profoundly simple analogy (and wrong, chiefly in that it's an intellectual exercise, where natural selection prizes intellect as a survival trait, rather than an evolutionary force), but it'll do.
Religion, by its very nature, prohibits this kind of discourse, investigation, testing and evaluation, if only because the most fundamental aspects of it are NOT, most emphatically NOT subject to investigation, and that is supposed to be their strength.
And this seems to have been okay for a while. Obviously people (religious ones) were upset at the constantly expanding knowledge base that scientific enquiry was providing, but for the most part, they were content to reap the benefits (I say for the most part. There are obvious bones of contention: contraception, blood transfusions, heliocentrism, germ theory. And initial resistance has usually given way before evidence.) of scientific advances. They have been smug and content in, initially, the gaps in scientific knowledge, and now in the sort of "exclusive" domain of priests and clerics. Even scientists have made concessions to religious folk, as Stephen Jay Gould did with his "non-overlapping magesteria". And in a sense, he was right. But not in the way that he or the religious folk prefer to think of it.
Science and reason are tools in the search for truth. Empirical, verifiable, testable, repeatable, and useful truth. Religion is the guardian of Truth. Mysterious, unknowable, untestable, ineffable, and ultimately useless Truth. It's theirs, and they can have it. Science doesn't want it. You can't measure it or use it to discover anything else, so, meh. Religion's all about being certain about things you can't know for sure. A contradiction (one of many), to be sure, but not one that seems to bother the believer.
Religion's turf has been constantly receding. It's been a controlled retreat, for the most part. The funny thing is that, a few notable instances aside, as far as science is concerned, it's not a contest. It's just figuring shit out. Unfortunately for clerics, when you figure shit out on your won, you don't need an authority as much. But religion sees it as losing the war, and has opened up another front. At least in public perception in North America, they are. And in the muslim world. And this, as much as everything else I've written, is the point I was getting to.
Religion is fighting science with science. They're equipping themselves with degrees, and they're taking on "big science". They're claiming that their own religious science is just as good. We ask a question, we check the scriptures, and then we (and this is the part that I have yet to see any evidence of) run some tests. If the science is in accordance with the Holy Book, the science is good. If not, we must have made a mistake, because of the inerrancy etc., and so we do not run the test again, because what if the tests are right? That's the purpose of ID. To give a scientific veneer to dogma.
But what if the tests are right?
Another attack on "big science" is an attempt to turn science's greatest strength into a weakness in the court of public opinion. Scientists are never sure, because the next test or theory or whatever might change things. But religion is ALWAYS sure, because some old book or some old man said so.
Finally, another attack is to jealously guard religion's last bastion (and the walls are eroding), and claim that religion is good, and everything else is evil. Science is the fruit of the devil. The forbidden fruit was knowledge. Ignorance is bliss. Stem cell research makes baby Jesus cry. Atheists kill people. Darwin was a Nazi. Science is dogmatic, and ID researchers are just squirrels trying to get a nut.
The problem (for religion) is that all three tactics will eventually fail. They must fail. If they don't, people are dumber than a bowl of socks. Religion is playing a game it doesn't understand with equipment it doesn't know how to use. They're severely handicapped. First, you can't not ask a question in scintific discourse for any reason as obscure or banal as religious truth. If that were the case, there'd be no germ theory.
You also can't go from "no proof needed" to "seeking proof to verify the unverifyable" without sacrificing what's most fundamental about your beliefs. For millenia, you've said you can't know god. That reason is the enemy. That god did it. And now you're trying to use scientific language to "prove" the unprovable.
The second attack contradicts the first. They're working at cross-purposes. You deride the scientific method for it's uncertainty, and then you try to use it to prop up your fairy tale.
And finally, the last one is just stupid and deliberately obtuse. God has ceded to man in most things: the causes of sickness, the nature of the mind, the nature of the universe, the design of living things, the age of the planet, the efficacy of prayer, and almost anything else that we've tested. To say that science is evil, that it causes human suffering, is to ignore the bulk of the evidence. Sure, science has given us better ways to kill, but it's also given us better ways to communicate, to travel, to heal, and to think. Science, to put it bluntly, is kicking god's ass.
Fukuyama said that history was over (so did Marx). It was the end of Marxism, and capitalism would lead all into a bright, shiny utopia. First, he was wrong about Marxism. It's still kicking around. And the arrogance to think that anything as small as economic theory would define history is laughable.
The battle between the real and the imaginary is still being waged. The imaginary is losing. That MIGHT be the end of history, but I doubt it.
I have faith that we'll find new things to fight about.