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Can Neo-Darwinian Processes Account for Complexity in Nature?

In their critique of William Dembski, Wesley Elsberry and Jeffrey Shallit write, "there is abundant circumstantial evidence that Darwinian processes can account for complexity in nature, but Dembski excludes this evidence because it does not pass his video-camera certainty test." This badly misrepresents Dembski's argument. Looking at all the theoretical work Dembski is doing to test the ability of Darwinian processes to generate specified complexity (see his papers at www.evoinfo.org) it should be clear that Dembski is NOT demanding "video-camera certainty" but rather is willing to test the ability of present-day causes to generate high CSI empirically, and theoretically, and then apply his findings to make inferences from the historical record. That's exactly how historical scientists ought to study these things.

But is their claim of "abundant circumstantial evidence that Darwinian processes can account for complexity in nature" correct?

Earlier this year I posted an article titled, "The NCSE, Judge Jones, and Bluffs About the Origin of New Functional Genetic Information," which tried to answer this question. My article looked at standard papers cited by critics of ID when trying to establish that neo-Darwinian mechanisms can produce new functional genetic information. After a lengthy analysis of claims made by those papers, I concluded the following:

The NCSE's (and Judge Jones’s) citation bluffs have not explained how neo-Darwinian mechanisms produce new functional biological information. Instead, the mechanisms invoked in these papers are vague and hypothetical at best:
  • exons may have been "recruited" or "donated" from other genes (and in some cases from an "unknown sou[r]ce";
  • there were vague appeals to "extensive refashioning of the genome";
  • mutations were said to cause "fortuitous juxtaposition of suitable sequences" in a gene-promoting region that therefore "evolve";
  • researchers assumed "radical change in the structure" due to "rapid, adaptive evolution" and claimed that "positive selection has played an important role in the evolution" of the gene, even though function of the gene was not even known;
  • genes were purportedly "cobbled together from DNA of no related function (or no function at all)";
  • the "creation" of new exons "from a unique noncoding genomic sequence that fortuitously evolved" was assumed, not demonstrated;
  • we were given alternatives that promoter regions arose from a “random genomic sequence that happens to be similar to a promoter sequence,” or that the gene arose because it was inserted by pure chance right next to a functional promoter.
  • explanations went little further than invoking "the chimeric fusion of two genes" based solely on sequence similarity;
  • when no source material is recognizable, we're told that "genes emerge and evolve very rapidly, generating copies that bear little similarity to their ancestral precursors" because they are simply "hypermutable";
  • we even saw "a striking case of convergent evolution" of "near-identical" proteins.
  • To reiterate, in no cases were the odds of these unlikely events taking place actually calculated. Incredibly, natural selection was repeatedly invoked in instances where the investigators did not know the function of the gene being studied and thus could not possibly have identified any known functional advantages gained through the mutations being invoked. In the case where multiple mutational steps were involved, no tests were done of the functional viability of the alleged intermediate stages. These papers offer vague stories but not viable, plausibly demonstrated explanations for the origin of new genetic information.

    My article was originally posted on Evolution News & Views in a series of 8 parts, and Dr. Elsberry responded to the first part of my article, the introduction. One of his main points of contention was over my observation that a scientific paper Judge Jones cited in the Kitzmiller ruling to demonstrate "the origin of new genetic information by these evolutionary processes" did not even contain the word "information" in its body. (The paper was Manyuan Long, Esther Betrán, Kevin Thornton, and Wen Wang, "The Origin of New Genes: Glimpses from the Young and Old," Nature Reviews Genetics, Vol. 4:865-875 (November, 2003).) Dr. Elsberry calls my charge "hypocrisy" but perhaps he is not aware of the background here, which shows that it is in fact Judge Jones who is using double standards.

    In his ruling, Judge Jones repeatedly (and wrongly) claimed that ID had not published peer-reviewed scientific articles. A variety of these peer-reviewed scientific articles were documented to him during the course of the trial, including a 2004 paper that Darwin-doubting scientists Michael Behe and David Snoke published in the journal Protein Science. That paper cast doubt on the ability of gene-duplication to produce new functional protein-protein interactions. But Judge Jones dismissed Behe and Snoke's article paper because "it does not mention either irreducible complexity or ID."

    While Judge Jones is correct that their article does not contain those words, the article does bear directly on those topics as it tests the complexity inherent in enzyme-substrate interactions. Even an anti-ID article in Science acknowledged that the evolution of protein-protein interactions bears on the question of irreducible complexity and the ID argument. (See Christoph Adami, "Reducible Complexity," Science, Vol. 312;61--63 (Apr. 7, 2006).)  By Judge Jones's standards, the lack of the exact phrases "intelligent design" or "irreducible complexity" should preclude one from arguing that the paper supports ID or irreducible complexity. But Judge Jones doesn't hold evolutionists to the same standard.

    What makes this ironic is that Judge Jones claimed that the review paper by Long et al., "The Origin of New Genes: Glimpses From the Young and Old," accounted for "the origin of new genetic information by evolutionary processes" in a peer-reviewed scientific publication. Yet the body of this article does not even contain the word "information," much less the phrase "new genetic information." The word "information" appears once in the entire article -- in the title of note 103.  This reveals a double standard applied by Judge Jones to pro-evolution versus pro-ID papers as regards peer review.

    I'm perfectly comfortable with someone citing Long et al. regarding the origin of new genetic information, even though it doesn't contain the word 'information." Consistently, I think that Judge Jones' accusation against Behe and Snoke's paper is fallacious. I'm trying to be fair, and the fact that Long et al. does not contain the word "information" should NOT preclude it from bearing on the topic. Thus, I didn't dismiss Long et al. but posted a lengthy 10,000+ word analysis of the paper. Wesley Elsberry attacks me for allegedly committing what he considers to be a hasty dismissal of this paper -- but clearly that's not what I did. And why doesn't he critique Judge Jones for hastily dismissing Behe's paper?

    Instead, Wesley Elsberry writes:

    Luskin hasn't even gotten around to much more than a quote-mine, some projection, and a double dollop of hypocrisy. Nor do I have any expectation that the parts yet to be published will do any better than Luskin's initial poor showing.

    As of the posting of my response to Elsberry and Shallit, Dr. Elsberry has responded to none of the rest of my substantive critique of Long et al. But I would encourage readers to my critique of Long et al. and decide for themselves whether Elsberry's premature criticisms are fair or charitable. In fact, when facing criticisms like these, perhaps now I better understand why William Dembski never felt compelled to write a lengthy response to Elsberry and Shallit's old critique of his work in the first place. Were it not for the occasional inquiries I receive about their paper, I would not have written my response to Elsberry and Shallit myself.