With regards to the information in http://www.discovery.org/scripts/viewDB/filesDB-download.php?command=download&id=546 There isn't much not easily refuted there.
The bottom line is that the author has worked backwards to prove his points by taking easily proved, observable facts and manipulating them to support his argument.
It's akin to saying "If the sun is hot then ID is correct" - hmm, the sun is hot! Great!
Evolution has simpler and more logical explanations for most or all of what he's using to support his ID opinions and none of what he proposed is actually testable in a real way.
Thank you for reading it. Sometimes I hate it when other posters give me a mound of material to read instead of explaining something briefly themselves.
I want to mention one last point, and then I'll drop the whole discussion (It's almost bedtime). What I want to focus on here is not the testing of Darwinism and design against the broad body of biological data, but the related question of which theory can accommodate the greater range of biological possibilities. Think of it this way: Are there things that might occur in biology for which a design-theoretic framework could give a better, more accurate account than a purely Darwinian and therefore non-teleological framework? I think the answer is "yes". But that's just my humble opinion.
Last but not least, let's be clear that design can accommodate all the results of Darwinism. Intelligent design does not repudiate the Darwinian mechanism. It merely assigns it a lower status than Darwinism does. The Darwinian mechanism does operate in nature and insofar as it does, design can live with its deliverances. Even if the Darwinian mechanism could be shown to do all the design work for which design theorists want to invoke design (say for the bacterial flagellum), a design-theoretic framework would not destroy any valid findings of science. To be sure, design would then become superfluous, but it would not become contradictory or self-refuting. ID may turn out to be a flash-in-the-pan. But I'd like to see where ID scientists take their arguments in the future. Below is a list (which I hear is growing) of scientists/researchers who are quite skeptical of methodological naturalism/Neo-Darwinism:
http://www.discovery.org/scripts/viewDB/filesDB-download.php?command=download&id=660
Again, thanks for the feedback. G'night.