“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.”

“Whenever explaining an event, we must choose from three competing modes of explanation. These are regularity, chance, and design... To attribute an event to design is to say that it cannot reasonably be referred to either regularity or chance.”

“Even if we have a reliable criterion for detecting design, and even if that criterion tells us that biological systems are designed, it seems that determining a biological system to be designed is akin to shrugging our shoulders and saying God did it. The fear is that admitting design as an explanation will stifle scientific inquiry, that scientists will stop investigating difficult problems because they have a sufficient explanation already.But design is not a science stopper. Indeed, design can foster inquiry where traditional evolutionary approaches obstruct it. Consider the term "junk DNA." Implicit in this term is the view that because the genome of an organism has been cobbled together through a long, undirected evolutionary process, the genome is a patchwork of which only limited portions are essential to the organism. Thus on an evolutionary view we expect a lot of useless DNA. If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function. And indeed, the most recent findings suggest that designating DNA as "junk" merely cloaks our current lack of knowledge about function. For instance, in a recent issue of the Journal of Theoretical Biology, John Bodnar describes how "non-coding DNA in eukaryotic genomes encodes a language which programs organismal growth and development." Design encourages scientists to look for function where evolution discourages it.Or consider vestigial organs that later are found to have a function after all. Evolutionary biology texts often cite the human coccyx as a "vestigial structure" that hearkens back to vertebrate ancestors with tails. Yet if one looks at a recent edition of Gray’s Anatomy, one finds that the coccyx is a crucial point of contact with muscles that attach to the pelvic floor. The phrase "vestigial structure" often merely cloaks our current lack of knowledge about function. The human appendix, formerly thought to be vestigial, is now known to be a functioning component of the immune system.”

“Even if the intelligent design of some structure has been established, it still is a separate question whether a wise, powerful, and beneficent God ought to have designed a complex, information-rich structure one way or another. For the sake of argument, let's grant that certain designed structures are not simply, as Gould put it, "odd" or "funny," but even cruel. What of it? Philosophical theology has abundant resources for dealing with the problem of evil, maintaining a God who is both omnipotent and benevolent in the face of evil.”

“IDers argue that such traits, involving many parts that must cooperate for that trait to function at all, defy Darwinian explanation. Therefore, by default, they must have been designed by a supernatural agent. This is commonly called the "God of the gaps" argument, and it is an argument from ignorance. What it really says is that if we don't understand everything about how natural selection built a train, that lack of understanding itself is evidence for super-natural creation.”

“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.”

“Fallacies do not cease to be fallacies because they become fashions.”