First of all, this was a very well presented opening post Aaron,even though it showed me that anatomy wasn't my forte.
And for this reason, I will let you and GM grind out the discussion about the specific issue of whales vestigial part, but this has become a very good example of what I am saying about the paradigm-based approach of evidence. Clearly, the femur's and buds of whales will only be seen as evidence of evolution only for a person who already believes in evolution.
The one part I thought was very interesting in your OP, and that I feel comfortable in discussing, is this section about vestigial organs:
She rightly states that an organ labeled vestigial isn’t necessarily a useless organ. Yablakov takes up this issue in his discussion of the cetacean pelvis. Historically, vestigiality is defined by a drastic change in form and function from an ancestral state. However, if usefulness isn’t a critical criterion, one wonders how you can discern a vestigial organ from a specialized one — a question that Yablakov poses. If your only criteria is to find examples where an organ exists in an altered state from the ancestral one, then vestigiality becomes a meaningless term. Why not call the front flippers vestigial forelimbs? Or call feathers vestigial scales? If you consider feathers specialized structures adapted to a specific purpose and not vestigial scales, why call the cetacean pelvis vestigial? The most you could say is that it has a specialized function different from the previous function, and if its structure were closer to that of a typical quadruped, it would not be able to perform its adapted function.
This is in fact a rather good formulation of what had been going in the back of my head for a while now: I can understand that a vestigial organ should not be obliged to have no function, but it seems to me that within an evolution perspective, there should be some vestigial features that have no purpose or function at all, I would even go as far as suggest that this should be a majority. We should expect some features to have had a single function, lost it's usefulness with evolution, and hasn't had the time to evolve other functions.
Yet if the vast majority (if not all) of claimed vestigial features have functions, and usually pretty specialised function, it begs the question as to why we should consider them any more or less vestigial then feathers being vestigial scales, etc. and it brings into question if the issue of vestigiality has any relevance at all.
(Might I suggest that we make this a great debate thread with Aaron, GM, myself and another evolutionist ? perhaps Percy ?)
Edited by slevesque, : No reason given.