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Originally Posted by Jaranath

Quite possibly more than any other scientific idea, evolutionary biology is grounded on solid principles of skepticism. It's because of the application of that skepticism in and to the work of countless biologists that evolution stands not only "close to fact" but as close to fact as any scientific theory currently established. The fact that you are apparently capable of conducting proper scientific research (sorry, haven't reviewed your publications but I'll take your word for it) and yet seem incapable of applying those methods to questions of faith and evolution (re: our prior discussion on testing the supernatural), and from that inability conclude arrogance, incompetence and religious-caliber faith on the part of those who do apply those standards fairly is, well, again, frustrating.

First, my point is that evolution doesn't apply skepticism. It picks and chooses ideas where it deems convenient and slaps it together in an elaborately put together puzzles. I'm quite capable of applying these methods to evolution. I'll do it below with Ambulocetus, which scientists use to establish that gap species exist in whales.

Let's look at the article that the OP originally pointed to. Tiktaalik is another creative addition to a community that cares for fantastic explanations but not skepticism.

http://www.nytimes.com/2006/04/06/sc...ewanted=2&_r=1

From the article:

Dr. Novacek responded: "We've got Archaeopteryx, an early whale that lived on land, and now this animal showing the transition from fish to tetrapod. What more do we need from the fossil record to show that the creationists are flatly wrong?"

Who is Novacek? NYTimes goes to lengths to show that he's unbiased and not part of the research of Tiktaalik, which implies that good 'ol scientific skepticism was applied. (which will later be shown to be dubious) From that same article above:

Michael J. Novacek, a paleontologist at the American Museum of Natural History in Manhattan, who was not involved in the research

Why did I mention him? You'll see. Let's look Ambulocetus, an "early whale that lived on land." Creative little pictures show it as a transitional whale-to-walking mammal. Here's one:



The scientific community has all but accepted it as fact, webbing and all. Here's an image of the fossils discovered, which were remarkably complete:



In the Nature article discussing the discovery of Ambulocetus, Dr. Novacek explains:

Ambulocetus can be clearly allied with archaeocetes and other cetaceans, based on features of the middle ear, muzzle, skull roof and teeth. Behind the skull, however, the specimen shows an extraordinary combination of features that anticipate, but do not fully embody, the aquatic adaptations of cetaceans. M. J. Novacek. “Whales leave the beach.” Nature 368: 807. 1994.

Hmm, wasn't Novacek supposed to be an external scientific source for NYTimes' story on Tiktaalik, showing that he had no vested interest--and therefore was an unbiased expert opinion? Except he does have an obvious interest, because Tiktaalik reinforces the findings from Ambulocetus. Hence, Novacek will obviously be predisposed to defending Tiktaalik, for sake of the credibility of his own work in Nature. See the backscratching at play? Publications and their review editors aren't necessarily objective. There's an element of politicking, and they bring their own interests into the peer review process--because let's face it, if somebody comes with a paper that refutes your own publication, it's a threat to your own scientific prestige.

But wait, you'll say. That doesn't disprove Ambulocetus from being a transitionary fossil. After all, as noted above the skull is incontrovertible proof that it's a whale fossil. Therefore, Ambulocetus proves that land mammals came from whales, right? The problem is, similarities in skull structure don't always establish a phylogeny. From another whale article in Nature:

Both morphological and molecular data are vulnerable to the problem of homoplasies--reversals to ancestral conditions or parallel changes in different lineages that can camouflage the true phylogeny …. For example, the ear region of the skull, traditionally considered to be a good source of highly stable characters, shows some glaring homoplasies among the ungulates and cetaceans Zhexi Luo Nature 404(6775):235–237, March 16, 2000)

To contextualize this, Zuo was searching a sister taxon, raising the concern that Mesonychids are not in fact a sister taxon, based on molecular comparison studies. Similar skulls can deceive people to drawing false conclusions on phylogeny. Which means Ambulocetus' skull isn't necessarily incontrovertible proof for being part of the whale phylogeny.

Scrutinzing other parts of the bone:
a) Legs. According to Robert L. Carroll, Patterns and Process of Vertebrate Evolution, Cambridge University Press, 1998, p.333, Ambulocetus had powerful legs suited to walk on land. No fossil evidence that shows it had webbed feet for swimming. Why then, are there fins on that pic above, when skin/membrane tissue wasn't preserved, even from the updated 1996 fossil? As a matter of fact, the thing had hooves--not a terribly efficient swimmer. Nor does the lack of attachment points for femur ligament/muscles prove it was a transitionary fossil--but simply that it wasn't an efficient walker. A waddler, if you will. The forelimbs had flexible wrists--something whales don't have. Big pelvic bones, combined with a well-developed ulna show that its limbs were well-suit for traveling on land.
b) Skull. In spite of claims that it's a whale skull, there's no blowhole. But ah yes, that part just didn't evolve yet (such a convenient way to explain away any and all differences with ceteceans).
c) Backbone. Land mammals have backbones ending at both the pelvis (elephant) and also at the tail (cat). Whale anatomy has the backbone ending right down to the tail. Ambulocetus' backbone ends at the pelvis, which is evidence that it isn't a whale. That is more compelling than a simple analysis of the tail length, which Thewissen et al uses to establish that Ambulocetus swam.

Little is known about the tail, but there is always many caudal vertebrae in primitive cetaceans and their relatives, whereas the length of individual elements varies widely. The only caudal vertebra known for Ambulocetus is elongate, suggesting that the tail was much longer than in modern cetaceans. J. G. M. Thewissen, S. T. Hussain, and M. Arif. “Fossil evidence for the origin of aquatic locomotion in archaeocete whales.” Science 263: 210-212. 1994

If it walks like a land mammal, doesn't have backbone structure consistent with a whale, no blowhole, etc, then couldn't it be just another type of extinct mammal? What rules that possibility out? Nothing. Nor does sharing similar skull traits establish that a fossil is transitionary. I suppose a platypus is transitionary for something millions of years ago, since it has a jarring mishmash of mammal and avarian traits?

Speaking of platypus, isn't it possible that many of these so-called transitionary fossils are like Platypus--that is, species that didn't fall under tidy taxonomic categories? And since the Ambulocetus' traveling/habitat characteristics are oft-compared to a Sea Lion, what negates the possibility that it wasn't transitionary, but was a completely separate from cetecean phylogeny? Even if it's possible that Ambulocetus was transitionary from the findings, it's nowhere near fact. There are other possibilites--they're simply blocked out since they wouldn't be consistent with their own presuppositions.

That skeptical enough? I could go on about the other ones (Pakicetus, Basilosaurus, etc) but you get my point.