As for vertebrates, although the jawless fish have genes for generating the thrombin-catalyzed conversion of fibrinogen to fibrin, they lack several clotting factors, including two thought to be essential for the activation of thrombin in mammals. Fish in general lack genes for the "contact factor" proteases, the predecessor forms of which make their first appearance in tetrapods. The full complement of factors known to be operating in humans does not occur until pouched marsupials (opossum), at least one key factor still absent in egg-laying mammals such as platypus.Via Pharyngula, uh, via csicop.
Behe's other example, the flagellum of certain bacteria, has also taken a beating since the Dover Trial.
Darwinism Refuted tells us*:
The complicated structure of the bacterial flagellum is sufficient all by itself to demolish the theory of evolution, since the flagellum has an irreducibly complex structure. If one single molecule in this fabulously complex structure were to disappear, or become defective, the flagellum would neither work nor be of any use to the bacterium. The flagellum must have been working perfectly from the first moment of its existence. This fact again reveals the nonsense in the theory of evolution's assertion of "step by step development." In fact, not one evolutionary biologist has so far succeeded in explaining the origin of the bacterial flagellum although a few tried to do so.DR is correct in that no one has described step-by-step evolution of the flagellum. Molecules don't leave much in the way of fossils so there is no trail heading back. If someone walks across a muddy field, we expect footprints and similar evidence. If someone swims a similar distance, no one expects to evidence of such a thing.
DR is incorrect in stating, "If one single molecule in this fabulously complex structure were to disappear, or become defective, the flagellum would neither work nor be of any use to the bacterium."
Nick Matzke at Panda's Thumb shows that many molecules can be removed. A screenshot of only some of the proteins involved and how necessary they are:
He summarizes with:
Total number of proteins listed: 42If you noted that 55% is still pretty high, I agree. Still, 45% is plenty reducible.
(this table excludes the chemotaxis proteins; there are ~10 chemotaxis proteins in standard E. coli, but the number can range from 0 to 10+ in various bacteria)
Total number thought to be indispensable in modern flagella: 23 (55%)
More at Panda's Thumb:
The relevance to flagellum evolution? Variants of at least seven T3SS proteins are also found in the flagellum, within a subsystem called the protein export system. This sits within the basal body and funnels replacement flagellin subunits to the filament, using a mechanism remarkably similar to the T3SS. In fact, the two systems are so similar that the flagellar protein export system is now considered to be a subclass of the T3SS (Trends in Microbiology, vol 14, p 157).A good video of the evidence.
Such similarities, or “homologies”, are strong evidence that the two systems evolved from a common ancestor - analogous to the way that the arrangement of bones in the limbs of horses, bats and whales reveal their common ancestry despite their very different outward appearance and function. Similar homologies can be seen in the DNA sequences of genes, and in the amino acid sequences and 3D structures of proteins - all are clear evidence of shared descent.
Ken Miller - quoted in the video above - discusses the subject at his website.
* Defeating Darwinism also considers the eye an example of irreducible complexity:
For an eye to be able to see, the 40 or so basic components which make it up need to be present at the same time and work together perfectly. The lens is only one of these. If all the other components, such as the cornea, iris, pupil, retina, and eye muscles, are all present and functioning properly, but just the eyelid is missing, then the eye will shortly incur serious damage and cease to carry out its function.DR seems unaware of all the animals that exist without eyelids. Someone should tell them about fish, lizards and snakes.