You'll likely remember Tom from our Hegel podcasts and his several posts on this blog. His blog has switched names now to Owl of Minerva.org, and one of his interests is how the conception of reason by Hegel and the phenomenologists differs from the one prevalent in our culture, i.e. thinking clearly in the context of scientific naturalism (that's my formulation, not Tom's). This latter conception of reason is what leads directly to the sentiment that anyone religious is being irrational.
In his post on Intelligent Design theory, he gives a brief defense of "transcendental reason," which he defines as "deciphering the ultimate purpose behind the patterns of things we observe." In Aristotle's terminology, this means looking for final causes. Using a slightly different but I think equally secular tack as Thomas Nagel (as discussed at the outset of our quantum physics epsiode), Tom suggests that since naturalism is ultimately unsatisfying--incomplete (Nagel's rationale for this is clearer in light of his take on philosophy of mind), there's a future for this transcendental conception of reason. I quote:
But natural science does not give us and cannot give us an empirical explanation of itself, of its own character as a rational social institution, appearing over time, historically. It cannot explain its own rationality as a result of natural mechanisms.
I grant that the transcendental conception of reason with which the cruder proponents of Intelligent Design theory operate may be more flawed and less plausible today than naturalistic instrumentalism at explaining human life, but neither is the instrumental sense of reason adequate to this task. Naturalistic thinkers would be foolish to assume that Intelligent Design theory is simply Biblical Creationism in disguise, denying the possibility that it could draw wider public support among intelligent persons. It can do this by appealing to many such persons across the political spectrum who are frustrated with the dominance of instrumental reason in science, business, and technology, with its reductive understanding of culture, humanistic knowledge, and public institutions.