Given that I am not a biologist, I risk going out on a limb in commenting on the controversy over intelligent design. As I've written before, I tend to be agnostic on the question of whether macroevolution actually occurred, although I strongly disagree with Darwin's assumption that a simple mechanism like natural selection can explain the irreducible complexity of especially human life and the multiple levels of causality operating within God's world. The only defence of intelligent design I've read thus far is that of Nancy Pearcey in Total Truth, and I did not find her altogether presuasive for reasons that I may get into at some point.
As I see it, a key reason why intelligent design cannot function as an alternative to Darwinian evolution is that it does not offer an alternative explanation for the rise of distinct species at particular stages in prehistory and appears to remove the issue from the realm of empirical investigation. After all, creatio ex nihilo occurred "in the beginning" (Gen. 1:1); everything else comes about through the subsequent unfolding of creation. It is the nature of this unfolding that is at issue. If proponents of the "special creation" of human beings and other species are arguing for multiple instances of creatio ex nihilo after God's initial creative act, they are going well beyond the teachings of scripture and, in any case, are arguing for something that cannot be empirically verified.
There's another reason why intelligent design is flawed, and this is picked up by James W. Skillen, commenting on a much longer article by Calvin College Professor Uko Zylstra. Here is where those multiple levels of causality come into play. In Intelligent Design as Science, Skillen writes:
In essence, what Zylstra does is to argue that the whole of reality begs for an answer deeper than science can provide of why anything exists at all and why things exist in the way they do, with millions of kinds of creatures conforming to various kinds of laws-physical, chemical, biotic, psychic, logical, historical, economic, and more. If some theorists hypothesize that everything can be explained in terms physical and chemical processes plus time and chance, their theory is reductionistic. But if intelligent-design theorists simply add the hypothesis that a designer, standing outside the physical and chemical processes, needs to be posited to account for irreducible complexity, they still haven't accounted for the biotic laws that hold for the development of living things. . . .
The key issue in the debate between evolutionary theorists and intelligent-design (ID) theorists, says Zylstra, is that of causality. “The ID theorists want to posit an intelligent cause in addition to 'natural causes.' The difficulty with this, however, is that both evolutionary biologists and ID theorists assume a reductionist ontology with regard to natural causes. Natural causes are seen as physical and chemical causality. . . . I don't believe that positing intelligent design as a causal agent for such irreducible complexity is the appropriate response,” says Zylstra. What hasn't been taken into account is the biotic mode of existence. “Life phenomena are not material in nature. Life is a mode of being, a function of living things. Biology textbooks generally promote this major misconception by the frequent reference to 'living matter'. But the expression 'living matter' is an oxymoron. Matter itself is never alive. . . . We always find whole living organisms. Matter is fundamentally physical and chemical in nature and thus subject to chemical and physical laws.” The inadequacy of ID theory, Zylstra believes, is its “failure to recognize the life function of living things,” which exist in accord with biotic laws and not only physical or chemical laws.