Douglas Theobald's Test Of Common Ancestry Ignores Common Design
In my prior post, I explained why Doug Theobald used the wrong null hypothesis for testing common ancestry. The odds of two lengthy genes arriving at a highly similar DNA sequence by chance, or even evolutionary convergence, is extremely small. Unless there's an underlying political motive, it shouldn't take a paper in Nature to show that obvious point. Common descent is a much better explanation for these genetic similarities....
Unless, that is, you admit the possibility of common design. If you ignore common design, then the explanation for similarities between gene sequences must be common descent. Doug Theobald's recent paper in Nature gets to his conclusion only by ignoring the possibility of common design and then equating common design (wrongly lumped with "creationism") with unguided evolutionary development -- a straw man comparison that is completely false.
Why is common design at least as good an explanation for functional genetic similarities as common descent? It's simple. As Paul Nelson and Jonathan Wells observe, "An intelligent cause may reuse or redeploy the same module in different systems, without there necessarily being any material or physical connection between those systems. Even more simply, intelligent causes can generate identical patterns independently" (see their chapter, "Homology in Biology," in Darwinism, Design, and Public Education).
Likewise, in their new book Intelligent Design Uncensored, William Dembski and Jonathan Witt include a lucid discussion of why mere functional biological similarities do not demonstrate the superiority of common descent over common design:
According to this argument, the Darwinian principle of common ancestry predicts such common features, vindicating the theory of evolution. One problem with this line of argument is that people recognized common features long before Darwin, and they attributed them to common design. Just as we find certain features cropping up again and again in the realm of human technology (e.g., wheels and axles on wagons, buggies and cars) so too we can expect an intelligent designer to reuse good design ideas in a variety of situations where they work.So functional genetic similarity can be explained by common descent, or common design. They both explain how similar functional genetic sequences can appear. As noted in my prior post, ID is not necessarily incompatible with common ancestry, but common design is an equally good explanation for why two taxa can have highly similar functional genetic sequences. After all, designers regularly re-use parts, programs, or components that work in different designs. As another example, engineers use wheels on both cars and airplanes, or technology designers put keyboards on both computers and cell-phones. Or software designers will re-use subroutines in different software programs. So common design can explain this data equally well.
(William Dembski and Jonathan Witt, Intelligent Design Uncensored: An Easy-to-Understand Guide to the Controversy, p. 85 (InterVarsity Press, 2010).)
It's only by ignoring other possible explanations for functional genetic similarity, such as common design, that Theobald can claim that common descent is supported.
Koonin Unwittngly Uses Common Design to Refute Theobald's Paper
It turns out that a recent paper by a non-pro-ID scientist, Eugene V. Koonin, correctly criticizes Theobald's paper by unwittingly using common design as an alternative explanation for sequence homology.
Koonin and Yuri Wolf wrote a paper in Biology Direct which sought to show that one can generate similar sequences - for which convergent evolution is a highly unlikely explanation - without common ancestry. In essence, they used their own minds (i.e. intelligence) to analyze the genes found in all organisms. Then, they used their own minds (i.e. intelligence) to generate a gene hypothetical sequence which is similar to the real genes found in living organisms. Finally, they noted that these sequences are highly similar to actual genes, yet there is no common ancestor.
They thus wrote:
This experiment demonstrates that the phenomenon observed by Theobald  is, indeed, entirely a product of "our ability to accurately predict the sequence of a... related protein relative to an unrelated protein" regardless of the actual history of the corresponding sequences. Alignments of statistically similar but phylogenetically unrelated sequences successfully mimic the purported effect of common origin. Thus, the nature and origin of the similarity between the aligned sequences are irrelevant for the prediction of "common ancestry" of proteins under Theobald's approach. Accordingly, common ancestry (or homology, in the modern, post-Darwinian sense) of the compared proteins remains an inference from sequence similarity rather than an independent property demonstrated by the likelihood analysis.And in this case, how did they generate "statistically similar but phylogenetically unrelated sequences" which "successfully mimic the purported effect of common origin"? It's quite simple: They used their minds to analyze sequences and construct algorithms to generate new ones that were similar -- i.e., they used intelligent design. As they wrote, "we designed and performed the following computational experiment..." (emphasis added)
(Eugene V Koonin and Yuri I Wolf, "The common ancestry of life," Biology Direct, Vol. 5:64 (2010).)
Wolf and Koonin may not acknowledge this fact because they're not ID proponents. Regardless, their critique of Theobald confirms the central point of this post: intelligent design is an equally potent cause to produce similar genetic sequences in comparison to common ancestry.
Koonin and Wolf conclude:
A formal demonstration of the Universal Common Ancestry hypothesis has not been achieved and is unlikely to be feasible in principle. Nevertheless, the evidence in support of this hypothesis provided by comparative genomics is overwhelming.So it's impossible to test Universal Common Ancestry, but the evidence in support of it is "overwhelming"? That doesn't make sense to me--but what does make sense is that arguments for universal common ancestry are becoming increasingly incoherent, and their conclusion is only valid to the extent that they ignore common design.