I blogged on something related to this topic recently. The heart of the problem is that we're already in a great "dark age", whether by Christian or Classical standards - namely, we've forgotten that there are many sciences, and that those pertaining to the workings of the physical world have traditionally (and rightly) been understood to be the lowest.
If this is the sign of a dark age, then I pray to God that the world will never again see enlightenment. Whatever shall we do without crusades, superstition, religious wars, inquisitions, and the burning of 'heretics.'
Indeed, for the physical sciences to have any sound application, there has to be some involvement from the practice of the philosophical and theological sciences.
And yet, while you claim that this is non-existant (we are in a 'dark age' afterall), our culture and society continues to advance to heights never dreamt possible by past generations. Someone out there seems to be finding useful applications...now I dont know if they'd meet your definition of 'sound', but ultimately anyone's opinion as to what is sound is irrelevant, progress speaks for itself.
By this I don't mean some kind of "Church censor" - rather, I think that genuinely "educated people" need a robust classical liberal arts education as their foundation. The idea that someone is truly "educated" while lacking proper training of the intellect and the will (ex. liberal arts background, plus good religious formation) is absurd - defects in either of those prerequisites are going to make the provisional conclusions of such "scientists" suspect from the beginning.
And yet the so-called educated people are completely inept and incapable of intelligently discussing the science at hand. I have heard from these so-called educated people that they dont agree with the theory of relativity for philosophical reasons...so what if you dont agree, it's how things are, get used to it...looks like it's time to change your philosophy if the theory of relativity contradicts it, because your philosophy must be wrong. Of course, these people probably have no understanding of the theory or what it entails, as I'm guessing most never even made it through a Differential Equations course, yet despite the fact that they don't understand 17th century mathematical concepts they want me to believe they're educated because they've read a few philosophers?
It is because of nonsense like this that is so often seen comming out of the academic community you praise (consider the early opposition to the use of cadavers in medical research or modern opposition to stem cell research if you need some more examples) that scientists have rejected their input for the uninformed and uneducated postulating that it is.
That this is a real problem is obvious to anyone paying attention. Now, it seems higher education has been reduced to a kind of glorified tradesmanship - qualitatively not much different than being a mechanic, just dealing with more "complicated schtuff." Not that there's anything wrong with being a tradesman, of course (around here, we need more of them, actually) - simply that this sort of background doesn't qualify one to deal professionally with "ideas."
Since these so-called 'mechanics' actually researched, discovered, and developed the 'ideas' I would submit that no one is more qualfied than them to deal professionally with said ideas. The fact of the matter is that the philosophers and theologians are simply unable to play on the same field as modern scientists. Theology and philosophy have become irrelevant. For while we may be unable to prove to the standard of the mathematician the existance of our physical world and that we can interact with it, it's existance would seem to be the most reasonable of assumptions to make. And thus with this one assumption, and this one assumption alone, all of science is born. The theologian and philosopher are now at a disadvantage because they require several more assumptions, and with each assumption the chance for error is greatly multiplied, thus their fields are less precise and in the end nothing more than mere opinion. They often play around with several ideas, but none of them have any evidence to support them, none of them are the equal of a single scientific observation.
We have a philosophy that our society has settled on: empiricism. It requires the fewest unprovable assumptions and therefore is the most objectively reasonable. We no longer have a need for philosophers and theologians.
On it's own, the physical sciences provide us with observations, and provisional conclusions. The quality of those conclusions, goes well beyond observation - claiming that "science disproves the existence of God" is not a conclusion based purely on observation, and anyone saying as much is a damned liar.
And to say that the existance of God can be proven is a conclusion based purely on subjective opinion, and anyone saying otherwise is a damned liar. However, the fact that God can be neither proven nor disproven basically means that the existance of a deity is an unknown variable and thus should not be used in our calculations or considerations. Science may not disprove the existance of God, but science does make God irrelevant.
Sadly, you can see the problem quite concretely when you read some of the ignorant stuff this type of activistic-atheist will spout. It goes beyond the quality of their reasoning (the whole philosophy problem) - they often don't even understand the subtleties of what they're attacking.
What you see in this case is the principles of science being upheld, and not allowing theists to introduce unnecessary unknown variables into scientific theories.
The fact of the matter is that the scientific community has explained away every instance where irreducible complexity has been applied and, of course, chaos theory dictates that the entire concept of irreducible complexity is flawed. What is being reacted against is creationists with an anti-scientific agend using the fact that science has yet to answer every question in exquisite detail to conclude that a deity must have been involved. Rather than adopting the scientific position that in the absence of evidence, ignorance must be assumed, these pseudo-scholars would have us assume divine intervention in the absence of evidence. If you want to claim 'intelligent design' it is not enough to prove that natural evolution was impossible (which they haven't done), all that demonstrates is general human ignorance of the subject, you must also prove the existance of some such being...until you do that, your opinion is theological rather than scientific.
Ultimately, what science does is keep people honest by requiring a certain standard of evidence.