Don’t miss Casey Luskin’s gentle but nonetheless devastating dismantling of The Language of Science and Faith: Straight Answers to Genuine Questions, by Karl W. Giberson and Francis S. Collins. Writing in the current issue of Touchstone magazine, ENV’s Luskin explains why the pair of authors have failed to make a persuasive case, aimed at Christians, for theistic evolution.
The basic problem is that their scientific argument is so badly outdated:

The authors’ main scientific argument for neo-Darwinism is based on the existence of “pseudogenes,” which they call “broken” DNA (p. 49). In their view, it is “not remotely plausible” that “God inserted a piece of broken DNA into our genomes” (p. 49). Therefore, the existence of pseudogenes “has established conclusively that the data fits a model of evolution from a common ancestor” (p. 43).
But there’s a serious problem with this argument. As pro-ID biologist Jonathan Wells explains in his book The Myth of Junk DNA, scientists have discovered many examples of pseudogenes that are not “broken” but, on the contrary, perform important functions in the cell. A 2011 article by Ryan Charles Pink, et al., in the journal RNA (vol. 17, p. 792) also notes that while “pseudogenes have long been labeled as ‘junk’ DNA . . . recent results are challenging this moniker.” The paper goes on to say, for instance, that “many pseudogenes are transcribed into RNA” and “harbor the potential to regulate their protein-coding cousins.” Likewise, a 2003 paper by Evgeniy S. Balakirev and Francisco J. Ayala in the Annual Review of Genetics (vol. 37, p. 123) states that “pseudogenes that have been suitably investigated often exhibit functional roles.”
Thus, if history is our guide, Giberson and Collins are likely to find their argument for “broken” DNA overturned by future discoveries.

Not too far in the future, however. Casey was writing that shortly before the release of the ENCODE results. More:

Another of their main arguments for evolution has already been challenged by mainstream science. Collins and Giberson maintain that the creative power of mutations is revealed by the evolution of “feathers from scales.” (p. 38) The classical evolutionary model of feather origins did claim that feathers evolved when reptilian scales mutated to become frayed, eventually giving some advantage for flight.
But that model was abandoned when biologists discovered the great differences between feathers and scales: feathers develop as hollow tubes that grow out of special follicles in the skin, whereas scales are flat, folded skin which develop quite differently. The cover story in the March 2003 issue of Scientific American states outright that difficulties with the scale hypothesis show that the “long-cherished view of how and why feathers evolved has now been overturned.” Its authors, two leading evolutionary biologists named Richard Prum and Alan Brush, further admit:
Although evolutionary theory provides a robust explanation for the appearance of minor variations in the size and shape of creatures and their component parts, it does not yet give as much guidance for understanding the emergence of entirely new structures, including digits, limbs, eyes and feathers. (“Which came first, the feather or the bird?”, p. 86)

Read the rest here.