Stephen Meyer’s response to the charge that Darwin’s Doubt makes only a negative “God-of-the-gaps” argument (i.e., “We can’t explain it, therefore God did it”) is helpful in concisely explaining why this isn’t the case:
True, the book does offer several evidentially based (and mathematically rigorous) arguments against the creative power of the mutation/natural selection mechanism.... (However, it is probably more accurate to characterize this “absence of knowledge” as knowledge of inadequacy, since it derives from a thorough assessment of causal powers—and limitations—of various materialistic evolutionary mechanisms). In any case, the argument presented in the book is not...a “purely negative” and, therefore, fallacious argument based on the inadequacy of various materialistic evolutionary mechanisms (or gaps in our knowledge).
Instead, the book makes a positive case for intelligent design as an inference to the best explanation for the origin of the genetic (and epigenetic) information necessary to produce the first forms of animal life (as well as other features of the Cambrian animals such as the presence of genetic regulatory networks that function as integrated circuits during animal development). It advances intelligent design as the best explanation not only because many lines of evidence now cast doubt on the creative power of unguided evolutionary mechanisms, but also because of our positive, experience-based knowledge of the powers that intelligent agents have to produce as digital and other forms of information as well as integrated circuitry.
Meyer sums up the argument in his book this way:
Premise One: Despite a thorough search and evaluation, no materialistic causes or evolutionary mechanisms have demonstrated the power to produce large amounts of specified or functional information (or integrated circuitry).
Premise Two: Intelligent causes have demonstrated the power to produce large amounts of specified/functional information (and integrated circuitry).
Conclusion: Intelligent design constitutes the best, most causally adequate, explanation for the specified/functional information (and circuitry) that was necessary to produce the Cambrian animals....
Unlike an argument from ignorance, an inference to the best explanation does not assert the adequacy of one causal explanation merely on the basis of the inadequacy of some other causal explanation. Instead, it asserts the superior explanatory power of a proposed cause based upon its established—its known—causal adequacy, and based upon a lack of demonstrated efficacy, despite a thorough search, of any other adequate cause. The inference to design, therefore, depends on present knowledge of the causal powers of various materialistic entities and processes (inadequate) and intelligent agents (adequate).
The rest of the post is worth a read.