To be sure, we Thomists do hold that teleology provides the basis for an argument for God’s existence, viz. Aquinas’s Fifth Way. But that argument is very different from Paley’s, and acknowledges – with Aristotle and against Paley and his successors – that the existence of teleology in nature does not directly entail an ordering intelligence. That requires further argumentation. (As the analytical Thomist Christopher Martin has noted, modern philosophers tend to assume that getting from natural teleology to God is easy, but establishing that there really is such a thing as teleology in nature in the first place is hard – whereas Aquinas’s view was that the existence of natural teleology was obvious, and the real philosophical work comes in showing that such teleology really requires an explanation in terms of God, as Aristotle thought it did not. See my book Aquinas for my most extended treatment of this issue.)
The philosopher of biology Andre Ariew is one contemporary thinker outside the Aristotelian-Thomistic orbit who has noted the difference between Paley’s understanding of teleology and Aristotle’s, and acknowledged that Darwinian criticisms of Paley do not necessarily show that there is no such thing as teleology in the Aristotelian sense. Another is physiologist J. Scott Turner, whose recent book The Tinkerer’s Accomplice: How Design Emerges From Life Itself argues for the indispensability of the notion of unconscious “intentionality” in understanding certain biological phenomena.
Our friend John Farrell has just posted an interesting Q and A between himself and Turner over at his blog, wherein Turner expresses the view that “we’re on the verge of a major philosophical shift in biology.” Check it out, then go buy the book.