This recent reviewer seems to have come away with thoughts similar to my own...
Carroll's argument against design eschewed the real question of how genes came into existence through natural processes. There are no grounds for assuming that the processes through which genes might degrade are the same processes through which they could be built up (Ref 1). In simple terms, genes are long stretches of DNA that carry the information necessary to code for the production of functional proteins. Intelligent design theorists claim that a piece-meal assembly of information-rich genes using the basic building blocks of DNA exceeds the capacities of Darwinian selection and is better explained by appealing to the activity of an intelligent agent (Refs 3,4). If anything, this very principle should have been Carroll's first point of contention if he was to say anything against ID. From a philosophical perspective the possibility remains that a designer may have supplied an organism with more genetic information than may have been needed for life- what one may call an "all the options, all the bells and whistles" approach. Such a designer could have been interested in placing non-functional genes in the genome for a future role in his or her design. We all install software into our computers that may not be operational until some later date when we finally choose to use it. Computers can now be accurately scheduled to start a process at a specified instant in the future, similarly to the programming of a recording on a video-recorder.
One may rightly ask what evidence Carroll could furnish to support the premise that non-functional genes were necessarily derived from functional counterparts found elsewhere in nature. Indeed empirical evidence in support of an evolutionary continuum was severely lacking throughout the presentation.
Ice Fish and Pocket Mice seem to be the best examples Darwinist can come up with for evolution as their lectures never seem to evolve past micro evolutionary examples for the theory. Eugenie Scott uses the simplistic example of the pocket mouse as well...lecture review can be found here.
Their theory (at the macro level) is based primarily on historical inference, which basically means they come in with a priori assumptions and are hardened against the concept of design. They simply cannot accept that there are *no* significant examples of empirical evidence supporting the macro evolutionary changes they claim are fact beyond question.
More about these micro/macro evolutionary changes at this link.