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Pebble wrote:As I understand Behe's argument loss of function mutations are by far and away the most common occurrence and where gain of function appears this can most often be explained by reactivation of dormant coding sequences - probably by loss of function of repressor genes. The ID group can then claim that evolution works backwards - getting rid of unnecessary protein encoding rather than creating novel proteins.

It seems to me there is a more basic conceptual problem with Behe's idea: His distinction between "gain of function" and "modification of function". While that might make some sense generally, in terms of promoting ID over evolution (assuming that is his true motivation in writing this paper ) I think he oversells this idea. What I think he wants to imply is that only "gain of function" mutations would confirm evolution as a plausible mechanism for speciation and other major phenotypic changes. But it seems to me successive cumulative "modifications" by themselves are sufficient to explain this. If we think of the type of morphological changes we observe thru the fossil record, modification of existing structure by far predominates over the emergence of novel structures. I'm not sure I can even think of an example of the latter. Fins gradually become legs which gradually become wings or arms. Fins, legs, wings and arms don't just emerge "de novo." There's no reason to require that "emergence de novo" occur at the molecular level, either.