Now Meyer begins a short section called “Common Ancestor Genes?” He start these three paragraphs by saying:
Nearly all of the scenarios developed in the papers that Long cites start with an inferred common ancestral gene from which two or more modern genes diverged and developed. (page 214)
That’s a pretty stout claim. I intend to review that claim in detail. It’s not because I don’t believe him… OK, yes, it’s because I don’t believe him.
The first article in Long’s paper is: Evolution of the intron-exon structure of eukaryotic genes. What do the authors have to say about their work?
To study the origins o f exon shuffling, we identified in our database those regions of genes which were homologous to prokaryotic genes. These are ancient conserved regions (AC1L)  which represent complete genes or portions of genes that descended in a relatively unchanged manner from a common ancestor. These regions have no introns in the prokaryotes, but they have introns in the eukaryotic versions.
Phylogenetic analysis o f eukaryotic genes that exist in both nuclear and organellar versions revealed that these genes are products of ancient duplications, which probably antedate the prokaryote/eukaryote divergence. If introns are in identical positions in such genes, they are good candidates for ancient introns.
So the authors did not assume that the genes were from a common ancestor, but determined that through careful analysis. The authors point out several examples of evidence that support the idea that genes are common between wildly different organisms. For example, this paper  points out that five introns are in identical positions in both nuclear and chloroplast GADPH. This is evidence that GADPH evolved in the ancestor of prokaryotes and eukaryotes.
Let’s take a second or two here and reiterate the problem with Meyer (and most creationists). Meyer makes a claim here. It probably took him 10-12 seconds to write that sentence. I am fairly confident that he did not actually read the articles. So far, it’s take me 40 minutes to find the paper, download it, read it, reread for details, then write the few short paragraphs that I have.
By extension (and assuming I can even get all these articles), it’ll take me 81 hours to do this for all the papers. The Gish Gallop is alive and well in the creationist playbook. An unsupported claim that must be thoroughly debunked and requires something on the 4 orders of magnitude more effort to debunk than it took to write (292,800 seconds vs 12 seconds).
Sorry, but my time is worth more than that.
I’ve shown here that at least one paper does not assume an ancestral gene. Indeed, I would very much like a creationist to find ONE paper in this list that assumes an ancestral gene. I very much think that the vast majority (75% or more) instead describes the evidence which leads to the conclusion that ancestral genes exist.
Meyer then comes along and says why those things are not actual evidence for common ancestry.
As I noted in Chapters 5 and 6, standard methods of phylogenetic reconstruction presuppose, rather than demonstrate, that biological similarity results from shared ancestry.
I very much disagree with this. Because the phylogentic sequences are not the ONLY piece of evidence that supports common ancestry. All the actual evidence that exists supports common ancestry and none of it supports instantaneous design of organisms like intelligent design does.
Here’s a long discussion of the evidence for common ancestry. Now, when creationists talk about it, then will (as Meyer is doing) pick at one part and pretend that none of the rest of it exists. Meyer, for example, says that we assume that common ancestry is true because of the arrangement of certain patterns in DNA.
But is that really an assumption? Instead, is it evidence to support a claim?
The latter is correct. Consider that molecular evidence (gene sequences such as mentioned above) match many of the predictions made about common ancestry before molecular techniques were possible. For example, Thomas Huxley proposed that birds were descendants of dinosaurs in the 1870s. He was just looking at the anatomy. And here, over 100 years later, is the molecular evidence that supports that idea.
We think that common ancestry is true not because we assume it to be true, but because there is a large amount of evidence to support it. When creationists talk about common ancestry they do not mention all of the evidence, they mention one piece and then claim it is a circular argument.
What creationists have to deal with is the fact that common ancestry exists. This isn’t a wild fantasy, it’s real and their notions absolutely cannot deal with it.
Once again, I will ask that someone, anyone, tell me the page numbers in Darwin’s Doubt where Meyer supports Intelligent Design? The entire book is not evidence for Intelligent Design. The entire book, so far, is a poorly written and researched attempt to discredit evolution. Since the majority of the claims that Meyer has made so far are totally wrong, this isn’t a book against evolution. It’s a fantasy.
I would like one more point, but it’s so stupid that it deserves it’s own post. Meyer is truly lost his mind.
 Long, M., Betrán, E., Thornton, K. & Wang, W. The origin of new genes: glimpses from the young and old. Nature reviews. Genetics4, 865–75 (2003).
 M. Long, S. de Souza, W. Gilbert, Evolution of the intron-exon structure of eukaryotic genes.Current opinion in genetics & development 5, 774–8 (1995).
 Kersanach R, Brinkmann H, Liaud M -F, Zhang D-X, Martin W, • • Cerff R: Five identical intron positions in ancient duplicated genes of eubacterial origin. Nature 1994, 367:387-389.
 Intelligent design means that various forms of life began abruptly through an intelligent agency, with their distinctive features already intact – fish with fins and scales, birds with feathers, beaks, and wings, etc. (Pandas 1993, 2nd edition, published, pp. 99-100)
Chunks of Pandas are currently on the Discovery Institute website. The authors of Pandas include DI fellows Stephen Meyer (VP of the DI, director of the DI’s Center for Science and Culture, organizational head of the ID movement), Michael Behe, Dean Kenyon (YEC), and Nancy Pearcey (YEC). Dembski and Wells coauthored a new edition. Phillip Johnson, Dembski, Behe, etc. all endorsed the old edition of Pandas in print, and Behe defended Pandas as “intelligent design” in court. – Nick Matzke