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.
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.
To establish evolutionary interrelatedness invariably requires exhibiting similarities between organisms. Within Darwinism, there's only one way to connect such similarities, and that's through descent with modification driven by the Darwinian mechanism. But within a design-theoretic framework, this possibility, though not precluded, is also not the only game in town. It's possible for descent with modification instead to be driven by telic processes inherent in nature (and thus by a form of design). Alternatively, it's possible that the similarities are not due to descent at all but result from a similarity of conception, just as designed objects like your TV, radio, and computer share common components because designers frequently recycle ideas and parts. Teasing apart the effects of intelligent and natural causation is one of the key questions confronting a design-theoretic research program. Unlike Darwinism, therefore, intelligent design has no immediate and easy answer to the question of common descent.Darwinists necessarily see this as a bad thing and as a regression to ignorance. From the design theorists' perspective, however, frank admissions of ignorance are much to be preferred to overconfident claims to knowledge that in the end cannot be adequately justified. Despite advertisements to the contrary, science is not a juggernaut that relentlessly pushes back the frontiers of knowledge. Rather, science is an interconnected web of theoretical and factual claims about the world that are constantly being revised and for which changes in one portion of the web can induce radical changes in another. In particular, science regularly confronts the problem of having to retract claims that it once confidently asserted.
Constrained optimization is the art of compromise between conflicting objectives. This is what design is all about. To find fault with biological design - as Stephen Jay Gould regularly does - because it misses some idealized optimum is therefore gratuitous. Not knowing the objectives of the designer, Gould is in no position to say whether the designer has proposed a faulty compromise among those objectives.
Scientists rightly resist invoking the supernatural in scientific explanations for fear of committing a god-of-the-gaps fallacy (the fallacy of using God as a stop-gap for ignorance). Yet without some restriction on the use of chance, scientists are in danger of committing a logically equivalent fallacy-one we may call the chance-of-the-gaps fallacy. Chance, like God, can become a stop-gap for ignorance.