Naturalism is the view that the physical world is a self-contained system that works by blind, unbroken natural laws. Naturalism doesn't come right out and say there's nothing beyond nature. Rather, it says that nothing beyond nature could have any conceivable relevance to what happens in nature. Naturalism's answer to theism is not atheism but benign neglect. People are welcome to believe in God, though not a God who makes a difference in the natural order.
I believe, said Austerlitz, they know they have lost their way, since if you do not put them out again carefully they will stay where they are, never moving, until the last bath is out of their bodies, and indeed they will remain in the place where they came to grief even after death, held fast by the tiny claws that stiffened in their last agony, until a draft of air detaches them and blows them into a dusty corner.
A physicist that I know commented that many other scientific disciplines, such as geology, anthropology, astronomy, are also challenged by biblical fundamentalism, but their people seem to be able to get on with their work without worrying unduly. Only Darwinians seem thrown into a frenzy that sends them running to litigation and demanding censorship. His explanation was that it's a rival religion.
In the abstract, it might be tempting to imagine that irreducible complexity simply requires multiple simultaneous mutations - that evolution might be far chancier than we thought, but still possible. Such an appeal to brute luck can never be refuted.. Luck is metaphysical speculation; scientific explanations invoke causes.
The very comprehensibility of the world points to an intelligence behind the world. Indeed, science would be impossible if our intelligence were not adapted to the intelligibility of the world. The match between our intelligence and the intelligibility of the world is no accident. Nor can it properly be attributed to natural selection, which places a premium on survival and reproduction and has no stake in truth or conscious thought. Indeed, meat-puppet robots are just fine as the output of a Darwinian evolutionary process.
The theory of phlogiston was an inversion of the true nature of combustion. Removing phlogiston was in reality adding oxygen, while adding phlogiston was actually removing oxygen. The theory was a total misrepresentation of reality. Phlogiston did not even exist, and yet its existence was firmly believed and the theory adhered to rigidly for nearly one hundred years throughout the eighteenth century... As experimentation continued the properties of phlogiston became more bizarre and contradictory. But instead of questioning the existence of this mysterious substance it was made to serve more comprehensive purposes... For the skeptic or indeed to anyone prepared to step out of the circle of Darwinian belief, it is not hard to find inversions of common sense in modern evolutionary thought which are strikingly reminiscent of the mental gymnastics of the phlogiston chemists or the medieval astronomers. To the skeptic, the proposition that the genetic programmes of higher organisms, consisting of something close to a thousand million bits of information, equivalent to the sequence of letters in a small library of one thousand volumes, containing in encoded form countless thousands of intricate algorithms controlling, specifying and ordering the growth and development of billions and billions of cells into the form of a complex organism, were composed by a purely random process is simply an affront to reason. But to the Darwinist the idea is accepted without a ripple of doubt - the paradigm takes precedence!