As far as Dawkins being 'old school' people couldn't agree more. Problem is it seems none of them can agree with each other either...
Dawkins is old school in the sense that he hasn't evolved (pun intended) much beyond the population genetics and morphological phylogeny arguments of the 1960s. His new book "The Ancestors Tale" is a little better, but still barely touches on the explosion of molecular genetics knowledge.
Far worse, Dawkins has used evolution to promote his own strident atheism. He is indeed guilty of introducing his religion into science, so his pointing fingers at Creationists and IDers for doing the same thing is hypocritical.
Behe's book "Darwins Black Box" was published in 1996 so allow me to do some quick double-nought cipherin' here... 2005 -1996= 9. So now research that is nine years out of date is antiquated is it? I guess that must mean all those 'real' biologists have now come up with credible models of how bacterial flagellum and the blood clotting cascade evolved. I mean since they've had all of 9 years to do it?
Much of the reference material in Behe's "Black Box" is from 1990 or earlier, see the Notes section of his book.
Behe's "irreducible complexity" argument is a useful critique of evolution. Behe has helped draw attention to the question of the evolutionary origin of the molecular machinery found in living organisms today. This is certainly not all his doing, but he has been a positive factor.
However, for each of Behe's irreducibly complex systems, a simpler system using the same proteins has been found. For the bacterial flagellum, the bacterial Type III Secretory System has many of the same protein components. In fact, for almost any type of flagellum, similar systems exist with secretory functions or virilence (infection) functions. Here is a
LINK. So, if a flagellum can be assembled from components which are used in other simpler systems, it is not an irreducibly complex system.
So the nucleotide which allows humans and apes to produce vitamin C is "missing"?
A single nucleotide is missing (deleted) from the human gene which encodes the protein, called GLO, which makes vitamin C. Working copies of the GLO gene are found in most mammals except primates.
I am assuming you know the basics of DNA -> RNA -> amino acids (protein). DNA comes in an "alphabet" with four nucleotide 'letters': A, T, C, G. Three nucleotides strung together make a triplet or "codon" for one of the 20 different amino acids. For example, G-C-A is a codon for the amino acid Alanine. The DNA code for a single protein consists of hundreds of codons strung together, each codon made from three nucleotides.
If a single nucleotide in one codon is deleted, the meaning of all the downstream codons is changed. For example consider the codon string
GCA UGC GAC UUC
which codes for the amino acids
Alanine, Cysteine, Aspartic Acid, and Phenylalanine.
If we delete the second nucleotide, C, we get
GAU GCG ACU UCX
which codes for the amino acids
Aspartic Acid, Alanine, Threonine, and Serine.
This is a completely different protein from the first example. This sort of nucleotide-deletion mutation is called a "frame-shift" mutation because every codon triplet downstream of the mutation is shifted by one nucleotide.
So, the single nucleotide deletion in the human GLO gene for vitamin C renders the gene completely inoperative (at least, for making vitamin C). Evolution predicts that the exact same nucleotide is missing in apes, who need vitamin C in their diet just like humans do. This was recently confirmed in chimpanzee, macaque and orangutan genomes. Most other mammals have functional Glo genes and don't need vitamin C in their diet.
So, this same vitamin C mutation being identical in all primates is not only explained by evolution, it was predicted by evolution. Many other similar mutations have been found. Some are common only to humans and chimpanzees.
What is the ID explanation for this? Did the designer purposely put the exact same defects in all primates?
For a detailed discussion of this type of finding, see
LINK.
This is what is commonly observed in genetic mutation.
It is not common to find the same exact mutation in different species unless they are related. If we assume roughly 1000 nucleotides in the GLO gene, the chances of a deletion mutation ocurring in exactly the same place in five different species is 1:1,000,000,000,000,000. Obviously this is not a random occurence.
Is there empirical evidence to prove it was ever there in a common ancestor? Is there empirical evidence for a common ancestor?
The common defect
is evidence of common ancestry. Very strong evidence, since it is difficult to come up with a plausible alternative.
If not, is the theory of a common ancestor falsifiable?
Certainly.
Darwin predicted that all life has a common ancestry. He made this prediction knowing nothing of biochemistry. We now know all life stores genetic information in the same way, using the same exact molecules, the same genetic code, and the same machinery for assembling proteins from genetic information. If these mechanisms were different in bacteria, humans, and redwoods, Darwin would be proved wrong.
If the human genome was closer to that of bears than chimpanzees, a theory of common ancestry for humans and chimpanzees would be proved wrong. Recent work has shown that human and chimp genomes are 96% identical. In fact, some mutations have been found which are
only common to humans and chimpanzees.