And another thing I think we need to be aware of is that not every instance of design we see in nature needs to be directly attributed to God. Certai… - William A. Dembski

The fine-tuning of the universe, about which cosmologists make such a to-do, is both complex and specified and readily yields design. So too, Michael Behe's irreducibly complex biochemical systems readily yield design. The complexity-specification criterion demonstrates that design pervades cosmology and biology. Moreover, it is a transcendent design, not reducible to the physical world. Indeed, no intelligent agent who is strictly physical could have presided over the origin of the universe or the origin of life.

The fact is that for complex systems like the bacterial flagellum no biologist has or is anywhere close to reconstructing its history in Darwinian terms. Is Darwinian theory therefore falsified? Hardly. I have yet to witness one committed Darwinist concede that any feature of nature might even in principle provide countervailing evidence to Darwinism. In place of such a concession one is instead always treated to an admission of ignorance. Thus it's not that Darwinism has been falsified or disconfirmed, but that we simply don't know enough about the biological system in question and its historical context to determine how the Darwinian mechanism might have produced it.

The question rather is how we should do science and theology in light of the impending collapse of Enlightenment rationalism and scientific naturalism. These ideologies are on the way out. They are on the way out.