If I understand Denton's "argument" correctly, he's saying that birds could not possibly have evolved from dinosaurs, because their lungs are so different. Specifically, a unidirectional flow could not evolve from a circulatory flow. This is a variation on a common ID argument, that feature A, B, or C could not possibly evolve, there is no possible evolutionary pathway to A, B, or C, therefore God must have designed this feature ex nihilo.
Without going into the details of avian anatomy, which I leave to those more knowledgeable, it is easy to see the flaws with the structure of this argument.
First, it rests on an assertion that there is no possible evolutionary pathway. Thus, to disprove it, it is not necessary to figure out exactly how the thing evolved, just that one can imagine a possible evolutionary pathway. Even I can well imagine a possible evolutionary pathway from a circulatory system to a unidirectional one, and I bet sandor can too.
Second, it a god-of-the-gaps argument from ignorance. Yes, everything else evolved, as you have shown, but God designed bird's lungs. (And apparently, the tail of a E. coli) but not much else. So instead of a grand, all-powerful God, you get a teeny little tinkering God.
And it presumes that science will not solve the problem. But history shows that science does tend to solve problems eventually (for all I know it may have solved this one already) and that is how we progress. Just because at one time we didn't know where lightning came from did not mean we should stop researching it, attribute it to God, and be done. If God created lightning, it is still worth learning exactly how. In the same way, whether or not God made birds, it is worth continuing to research and find out how. With Denton (and sandor's) God, that would make God even smaller and more puny, because they have made the mistake of opposing God and science. If you assume rather that there is a God, and science studies how he made things, God never has to shrink as our knowledge expands.
Finally, Denton makes the mistake of assuming that if he disproves ToE (which he has not done) the default is his magic poofing hypothesis. Even if ToE were wrong, that would not imply that Magic Poofing is right. It would mean further research to find out what hypothesis is correct. So far, the one hypothesis that has stood the test of time and continues to explain all the relevant phenomena, including bird lungs, is ToE.