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Who Misrepresented Who? A Response to John Farrell

It's a common debate tactic to overstate or misstate your opponent's argument. While John Farrell's response on a Forbes.com blog to my recent article "A Positive, Testable Case for Intelligent Design" accuses me of making that mistake, it is in fact Mr. Farrell who badly misrepresents my arguments. Mr. Farrell chides me for not contacting Dartmouth evolutionary biologist Mark McPeek before writing a response to his paper. This is ironic and hypocritical, since Farrell did not contact me before writing a response to me. I'm not upset about that, but perhaps that explains why Mr. Farrell got so much wrong.

First, Dr. McPeek's paper admitted that "elucidating the materialistic basis of the Cambrian explosion has become more elusive, not less, the more we know about the event itself," but in my 2009 commentary on McPeek's paper, I did not claim that, as Farrell put it, this was in-and-of-itself, a "boost for intelligent design." In fact, the recent article I wrote to which Mr. Farrell is responding is titled "A Positive, Testable Case for Intelligent Design" where I explain that the argument for ID stands on its own as a positive argument and not merely based upon refuting unguided evolution.

Second, Mr. Farrell alleges that I claim that McPeek's paper was pro-ID, and quotes McPeek in response stating "No, this paper does not make an ID argument for the Cambrian Explosion." I have no objection to Dr. McPeek's statement whatsoever because I never claimed anywhere that his article makes an "ID argument for the Cambrian explosion." Indeed, my original commentary on McPeek's paper made it expressly clear that Dr. McPeek is not pro-ID and was not arguing for ID. As I wrote:

The authors give no indication that they themselves support intelligent design (ID), and it seems they are still hopeful for a 'materialistic' explanation for the Cambrian explosion.

Likewise, my recent post on "A Positive, Testable Case for Intelligent Design" reiterates that "Dr. McPeek makes it clear that he is in fact not an ID-proponent." How much clearer could I have made it?

What my original commentary did note was that McPeek and his co-authors "give a witty nod to some observations and arguments made by ID proponents." Farrell misrepresents this line as if I am claiming that McPeek's paper is wholly pro-ID, but that's not what I said. Yet McPeek's article does give a nod to some observations and arguments by ID proponents about the nature of the Cambrian explosion. Don't take my word for it. Read McPeek's paper yourself:

[A]s explained on an intelligent-design t-shirt.
Fact: Forty phyla of complex animals suddenly appear in the fossil record, no forerunners, no transitional forms leading to them; ''a major mystery,'' a ''challenge.'' The Theory of Evolution -- exploded again (idofcourse.com).

Although we would dispute the numbers, and aside from the last line, there is not much here that we would disagree with. Indeed, many of Darwin's contemporaries shared these sentiments, and we assume -- if Victorian fashion dictated -- that they would have worn this same t-shirt with pride.

(Kevin J. Peterson, Michael R. Dietrich and Mark A. McPeek, "MicroRNAs and metazoan macroevolution: insights into canalization, complexity, and the Cambrian explosion," BioEssays, Vol. 31(7):736 (2009).)

My original article then went on to critique McPeek's attempt to provide a materialistic explanation for the Cambrian explosion. My disagreement with McPeek's argument does not in any way imply I said he was arguing for intelligent design.

Testing Common Ancestry

Pretending there is no answer to the question, Mr. Farrell asks, "Where does Luskin derive the idea that there are 'genes and functional parts not distributed in a manner predicted by ancestry'?"

If one takes a time to read the technical literature in evolutionary biology and systematics, one finds that it's extremely common for phylogenetic trees to contradict one another. In particular, molecular trees often conflict with one another, or conflict with trees based upon morphology. One gene gives you one version of the tree of life, and another gene will yield an entirely different version of the tree. All of this shows that genetic similarity is appearing in places not predicted by common ancestry. An excellent discussion of this problem can be found here. Many papers have reported on this problem. Here is a sample of 10 papers discussing sharp conflicts between molecular trees:

  • James H. Degnan and Noah A. Rosenberg, "Gene tree discordance, phylogenetic inference and the multispecies coalescent," Trends in Ecology and Evolution, Vol. 24(6) (March, 2009). This paper notes that: "A major challenge for incorporating such large amounts of data into inference of species trees is that conflicting genealogical histories often exist in different genes throughout the genome."
  • Michael S. Y. Lee, "Molecular phylogenies become functional," Trends in Ecology and Evolution, Vol. 14(5): 177-178 (May, 1999). This paper observes that "the mitochondrial cytochrome b gene implied...an absurd phylogeny of mammals, regardless of the method of tree construction. Cats and whales fell within primates, grouping with simians (monkeys and apes) and strepsirhines (lemurs, bush-babies and lorises) to the exclusion of tarsiers. Cytochrome b is probably the most commonly sequenced gene in vertebrates, making this surprising result even more disconcerting."
  • Mushegian et al., "Large-Scale Taxonomic Profiling of Eukaryotic Model Organisms: A Comparison of Orthologous Proteins Encoded by the Human, Fly, Nematode, and Yeast Genomes," Genome Research, Vol. 8:590-598 (1998). This paper explains that "different proteins generate different phylogenetic tree[s]" when one looks at the phylogenetic trees of major animal groups.
  • Rokas et al., "Conflicting phylogenetic signals at the base of the metazoan tree," Evolution and Development, Vol. 5(4):346-359 (2003). This study recounts conflicts in the metazoan tree, stating: "The robust reconstruction of metazoan history has proven to be a difficult task."
  • Rokas et al., "Animal Evolution and the Molecular Signature of Radiations Compressed in Time," Science, Vol. 310:1933-1938 (December 23, 2005). This paper acknowledges that "[t]he phylogenetic relationships among most metazoan phyla remain uncertain." Again, the problem lies in the fact that trees based upon one gene or protein often conflict with trees based upon other genes. Their study employed the many-gene technique, and yet still found that "[a] 50-gene data matrix does not resolve relationships among most metazoan phyla."
  • Antonis Rokas and Sean B. Carroll, "Bushes in the Tree of Life," PLoS Biology, Vol 4(11):1899-1904 (November, 2006). This paper offers a striking admission of deficiencies in the tree of life, acknowledging that "a large fraction of single genes produce phylogenies of poor quality," observing that one study "omitted 35% of single genes from their data matrix, because those genes produced phylogenies at odds with conventional wisdom." What about the technique of simply adding more data? They suggest that "certain critical parts of the TOL may be difficult to resolve, regardless of the quantity of conventional data available." This means that the excuse that problems exist because of "insufficient amounts of available sequence data" is not panning out and more data is not fixing the discrepancies. The paper suggests that "[t]he recurring discovery of persistently unresolved clades (bushes) should force a re-evaluation of several widely held assumptions of molecular systematics." Rokas and Carroll are Neo-Darwinists, and thus one assumption they unfortunately do not re-evaluate is common descent. They suggest the problems can be fixed by using less studied types of molecular characteristics--in short, they appeal to new untried techniques. Perhaps the inability to construct robust phylogenetic trees using molecular data is because common descent is not the answer.
  • Nardi et al., "Hexapod Origins: Monophyletic or Paraphyletic?," Science, Vol. 299:1887-1889 (March 21, 2003). This paper finds that the molecular data indicated that six-legged arthropods, or hexapods -- i.e. insects -- are not monophyletic, a striking conclusion that differed from virtually all previous wisdom. As the article stated "Although this tree shows many interesting outcomes, it also contains some evidently untenable relationships, which nevertheless have strong statistical support."
  • Cao et al., "Conflict Among Individual Mitochondrial Proteins in Resolving the Phylogeny of Eutherian Orders," Journal of Molecular Evolution, Vol. 47:307-322 (1998) This paper finds that molecular-based phylogenies conflicted sharply with previously established phylogenies of major mammal groups, such as ferungulates, rodents, and primates. The article concludes this anomalous tree "is not due to a stochastic error, but is due to convergent or parallel evolution.
  • Mindell et al., "Multiple independent origins of mitochondrial gene order in birds," Proceedings of the National Academy of Sciences USA, Vol. 95: 10693-10697 (Sept. 1998). This paper describes the difficulties encountered when evolutionary biologists have tried to construct a phylogenetic tree for the major groups of birds using mitochondrial DNA. Trees based upon such mtDNA molecules have conflicted with traditional notions of bird relationships. Strikingly, they even find "convergent" similarity between some bird mtDNA and the mtDNA of distant species such as snakes and lizards. The article suggests bird mtDNA underwent "multiple independent originations," with their study making a "finding of multiple independent origins for a particular mtDNA gene order among diverse birds."
  • Finally, a 2009 article in New Scientist titled, "Why Darwin was wrong about the tree of life," states:

    "For a long time the holy grail was to build a tree of life," says Eric Bapteste, an evolutionary biologist at the Pierre and Marie Curie University in Paris, France. A few years ago it looked as though the grail was within reach. But today the project lies in tatters, torn to pieces by an onslaught of negative evidence. Many biologists now argue that the tree concept is obsolete and needs to be discarded. "We have no evidence at all that the tree of life is a reality," says Bapteste.

    According to the article, the basic problem is that one DNA sequence would yield one tree, while another sequence would yield a different tree:

    The problems began in the early 1990s when it became possible to sequence actual bacterial and archaeal genes rather than just RNA. Everybody expected these DNA sequences to confirm the RNA tree, and sometimes they did but, crucially, sometimes they did not. RNA, for example, might suggest that species A was more closely related to species B than species C, but a tree made from DNA would suggest the reverse.

    For the record, this is not the kind of data expected under common ancestry.

    The article discusses proposals attempting to save common ancestry, largely entailing ad hoc appeals to a process called lateral gene transfer, where bacteria swap genes, thereby muddying any phylogenetic signal. Yet the article observed that conflicts between trees occurs even among higher branches of the tree of life where such gene swapping is not observed to take place, stating: "More fundamentally, recent research suggests that the evolution of animals and plants isn't exactly tree-like either."

    Among these higher branches, the article found that "The problem was that different genes told contradictory evolutionary stories." This led one scientist to admit that even among these relationships of higher organisms, "We've just annihilated the tree of life." Likewise, as the first paper cited above from Trends in Ecology and Evolution stated, "conflicting genealogical histories often exist in different genes throughout the genome."

This is the sort of data that runs counter to the nested hierarchy predicted by common descent.

How does this data interface with intelligent design? ID is not incompatible with common descent, and ID is certainly not incompatible with finding patterns of traits that fit within a nested hierarchy. When designers design various structures using 'variations on a theme,' such structures can often be classified as a nested hierarchy.

However, designers also can re-use parts in a way that is not required to fit a nested hierarchy. When we find re-usage of parts in a way that cannot be explained by a phylogenetic tree and common descent, this is the sort of data we might expect under intelligent design, but not common descent. And in fact we find much data that is not predicted by common descent. As this short discussion has shown, there's a lot of data that fits into that category.

Some other data that does not fit neatly with common descent include:

Mr. Farrell Fails to Stay Positive

Farrell quotes McPeek stating: "I'd have to know what mechanisms the creator was using to produce that outcome and see if I can replicate those mechanisms." But the entire point of my article, "A Positive, Testable Case for Intelligent Design," is to propose a comprehensible mechanism for biological origins that we can understand and study in nature: intelligent design. Our observations of the world around us show that the mechanism of intelligent design is capable of:

  • Producing high levels of complex and specified information
  • Introducing systems "fully formed" into the environment without less-advanced precursors
  • Reusing parts that work in different designs
  • Producing structures that have a function

So ID proposes a mechanism that we can understand from observations of the world around us, and it uses that mechanism to explain what we see in nature. This is exactly how historical sciences operate: they observe causes at work in the world around us, and then use those causes to explain the historical record.

ID invokes a legitimate mechanism we understand by observing the world around us: intelligence. But Mr. Farrell quotes Dr. McPeek claiming that ID arguments "all fall into one of two categories: (1) the argument by analogy ... or (2) science has no explanation for this, so it must have been designed." Again, neither of those are my argument.

First, the argument for design is not one of mere analogy. Modern information theory allows us to mathematically describe the precise informational properties found in designed objects, and in DNA. Information theorist Hubert Yockey observes that DNA contains a code which is mathematically identical to language:

"It is important to understand that we are not reasoning by analogy. The sequence hypothesis [that the exact order of symbols records the information] applies directly to the protein and the genetic text as well as to written language and therefore the treatment is mathematically identical."

(Hubert P. Yockey, "Self Organization Origin of Life Scenarios and Information Theory," Journal of Theoretical Biology, Vol. 91:13-31 (1981).)

Similarly, my argument goes far beyond mere analogy. Properties of life such as specified complexity, fully formed abrupt appearance of species in the fossil record, re-usage of genes in diverse organisms, and function for "junk" DNA are quantifiable properties that depend not on mere analogical reasoning. They match the precise patterns we commonly observe in human-designed objects.

Second, to reiterate, the entire point of my article is that ID makes a positive argument that does not merely depend on refuting evolution. Mr. Farrell and Dr. McPeek appear intent on missing my entire argument if they wish to characterize it as a negative one.

Mr. Farrell Gets Medieval

In his conclusion, Mr. Farrell cites a couple medieval philosophers to suggest that "Leaving a Designer out of the methodology of science as a matter of principle has a long, healthy tradition in Christian natural philosophy." There are two glaring problems with this argument.

First, Mr. Farrell ignores that employing a designer also has a healthy tradition in philosophy. After all, some of the greatest philosophers in history, including Plato appealed to intelligent agency to explain what they observed in nature. Many later Catholic philosophers, such as Thomas Aquinas, also used explicit design arguments.

Second, Farrell's quotes don't respond to my argument. My article cited over a dozen concrete and specific areas where ID thinking helps science to make advances. These pertain to fields like genetics, paleontology, physics, and cosmology. Moreover, it cited dozens of technical scientific papers published by ID proponents helping to make these very advances.

Farrell's citing of a couple medieval philosophers does not rebut my arguments as to how ID can contribute to 21st century science. But it does show the inability of ID critics to grapple with the positive case for design.