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Confusing Evidence for Common Ancestry with Evidence for Random Mutation and Natural Selection

Intelligent Design and the Origin of Information: A Response to Dennis Venema

In this article, Part 7, we:
• Explain why evidence for common ancestry is not evidence for a Darwinian evolutionary pathway
• Investigate Venema's citation of a paper that shows genomic similarity across many vertebrates, showing why this is at best evidence for common descent, not natural selection
• Discuss how common design could explain much of this data as well as common descent, if not better

Other Installments:
Part 1: Intelligent Design and the Origin of Biological Information: A Response to Dennis Venema
Part 2: Why Did One Theistic Evolutionist Part Ways with BioLogos?
Part 3: What Is a Proper Test of Intelligent Design?
Part 4: The False Dichotomy Between Intelligent Design and Natural Causes
• Part 5: Richard Lenski's Long-Term Evolution Experiments with E. coli and the Origin of New Biological Information
Part 6: Another Bogus Claim of "Novel Function Arising Through Mutation and Selection"
Part 8: Critically Analyzing the Argument from Human / Chimpanzee Genetic Similarity
The debate over evolution and intelligent design can be confusing because some keys terms in the discussion are ambiguous. Some people use "evolution" to refer to something as simple as small changes in the sizes of bird beaks. Others use the same word to mean something much more far-reaching. Used one way, "evolution" isn't controversial at all; used another way, it's hotly debated.

Dennis Venema's series for BioLogos on the "Evolution and the Origin of Biological Information" illustrates what happens when a would-be defender of Darwinian theory gets tripped up by such ambiguities. Venema seems to misunderstand exactly which type of "evolution" counts as evidence against intelligent design. He cites evidence for common ancestry, wrongly thinking that it demonstrates Darwinian pathways, and thus refutes ID.

Used equivocally, "evolution" is simply too imprecise a term to be useful in a scientific discussion. In truth, neo-Darwinian evolution is not a single idea. Instead, it is made up of several related ideas, each supported by specific arguments:

  • Evolution #1: First, evolution can mean that the life forms we see today are different from the forms that existed in the distant past. Evolution as "change over time" can also refer to minor changes in features of individual species -- changes that take place over a short amount of time. Even skeptics of Darwin's theory agree that this type of "change over time" takes place.
  • Evolution #2: Some scientists associate the word "evolution" with the idea that all the organisms we see today are descended from a single common ancestor somewhere in the distant past. The claim became known as the Theory of Universal Common Descent. This theory paints a picture of the history of life on earth as a great branching tree.
  • Evolution #3: Finally, some people use the term "evolution" to refer to a cause or mechanism of change, the biological process that Darwin thought was responsible for this branching pattern. Darwin argued that natural selection had the power to produce fundamentally new forms of life. Together, the ideas of Universal Common Descent and natural selection form the core of Darwinian evolutionary theory. "Neo-Darwinian" evolution combines our knowledge of DNA and genetics to claim that mutations in DNA provide the variation upon which natural selection acts.
Intelligent design does not conflict with evolution if by "evolution" one simply means "change over time," or even that living things are related by common ancestry (Evolution #1 or Evolution #2). However, the dominant theory of evolution today is neo-Darwinism (Evolution #3), which contends that evolution is driven by natural selection acting on random mutations, an unpredictable and purposeless process that "has no discernable direction or goal, including survival of a species." It is this specific claim made by neo-Darwinism that intelligent design directly challenges.

Venema's series claimed to demonstrate "a natural mechanism that does add functional, specified information to DNA sequences (and in some cases, creates new genes de novo): natural selection acting on genetic variation produced through random mutation." He further wrote "If any natural mechanism can be shown to produce 'functional, information-rich genes and proteins,' then intelligent design is no longer the best explanation for the origin of information we observe in DNA." These could potentially be valid ways of testing ID, and I recently responded to Venema's two primary empirical examples here and here. However, the fifth and sixth posts in Venema's series both discuss comparative genomics across vertebrate and invertebrate species, claiming that shared functional genetic similarities demonstrate that Darwinian evolution was at work. The two posts share a common theme:

  • They confuse evidence for common ancestry with evidence for a Darwinian pathway; and
  • They ignore that common design can also generate the shared functional genetic similarities discussed.
For example, in Venema's fifth post he cites evidence showing that vertebrates tend to have four times as many paralogous genes as urochordates, and notes that "these modern paralogs are still present in four-fold syntenty groups that span about 25% of the human genome." Venema then claims:
In other words, gene duplication and divergence to produce new CSI [complex and specified information] appears to be commonplace in evolution, including the evolution of our own species. Far from being rare exceptions, multiple lines of genomics evidence point to new structures, functions and information being produced through natural means. If the Intelligent Design Movement wishes to contest that natural mechanisms cannot produce new information, they need to address this widespread and compelling pattern.
But since Venema has cited no evidence for natural selection and random mutation, there is nothing for intelligent design to contest.

What Venema has discussed is shared functional genetic patterns across various classes of vertebrates. None of this evidence says anything about, as he claims his series would show, "a natural mechanism that does add functional, specified information to DNA sequences ... natural selection acting on genetic variation produced through random mutation." At best, these shared functional similarities that Venema has cited provide evidence of common ancestry, which is not incompatible with intelligent design. Michael Behe, for one, reminds us that evidence for common ancestry is not evidence of a Darwinian pathway:

[M]odern Darwinists point to evidence of common descent and erroneously assume it to be evidence of the power of random mutation.

(Michael J. Behe, The Edge of Evolution: The Search for the Limits of Darwinism, p. 95 (Free Press, 2007).)

In Darwin's Black Box, Behe elaborates on the point:
Although useful for determining lines of descent ... comparing sequences cannot show how a complex biochemical system achieved its function -- the question that most concerns us in this book. By way of analogy, the instruction manuals for two different models of computer put out by the same company might have many identical words, sentences, and even paragraphs, suggesting a common ancestry (perhaps the same author wrote both manuals), but comparing the sequences of letters in the instruction manuals will never tell us if a computer can be produced step-by-step starting from a typewriter. ... Like the sequence analysts, I believe the evidence strongly supports common descent. But the root question remains unanswered: What has caused complex systems to form?

(Michael J. Behe, Darwin's Black Box: The Biochemical Challenge to Evolution, pp. 175-176 (Free Press, 1996).)

To reiterate, there are two main problems with Venema's argument in his fifth and sixth posts:
  • At most, Venema has cited evidence for common ancestry, not natural selection acting on random mutations.
  • Moreover, designers regularly re-use useful functional components in different designs. This is especially seen in software engineering where programmers will re-use programming algorithms repeatedly in different programs because they perform the same function. In the same way, the shared functional genetic components cited by Venema could be evidence for common design just as much as they are evidence for common descent. Thus, Dr. Venema's examples of synteny for gene locations across various vertebrate groups at most this shows shared functional genetic similarities that could result from common design just as much as common descent. But designers are not always required to re-use parts that work in a pattern that fits a nested hieararchy. This leads us to the third problems with Venema's case for common descent:
Even in this case, the argument for common descent through a nice, neat nested hierarchy is not entirely clear. According to the paper Venema cited:
The phylogenetic trees for the gene families are not consistently nested, as would be expected in the case of allo-tetraploidy or two widely spaced auto-tetraploidy events. Finally, tree topologies of genes within paralogy blocks are not always congruent, indicating that the process of gene loss and rediploidization spanned the duplication events.

(Paramvir Dehal, Jeffrey L. Boore, "Two Rounds of Whole Genome Duplication in the Ancestral Vertebrate," PLoS Biology, Vol. 3(10):1700-1708 (October 2005).)

In other words, the phylogenetic trees for the gene families discussed in this paper often don't fit a nested hierarchy predicted by common descent. To explain away all the data that doesn't fit with the expectations of common descent, the authors cite gene loss and rediploidization as occurring between and after two widely spaced whole-genome-duplication events across many millions of years. Isn't that convenient: when the data fits the expected tree, we infer common descent; when it doesn't, we can invoke gene loss and other factors to explain away the contrary data.

What we're seeing are shared functional similarities distributed in a pattern that doesn't always fit a nested hierarchy. Is there a cause that can generate the same pattern in unrelated systems? There is one: common design.

But whether the data does or does not support common ancestry is immaterial to the question of whether Venema has found concrete evidence that all of these genes diverged by natural selection and random mutation. In fact, the authors of the paper he cites make it clear that they don't even know whether these supposed whole genome duplication provided advantages which natural selection could select:

It remains unclear to what extent such large-scale genomic events have driven macroevolutionary change versus the regular accumulation of small mutations, as is the central tenet of the classical model of evolution.
They further observe that "the vast majority of duplicated genes were subsequently deleted, indicating that relatively few genes may have been responsible for the increased complexity seen in vertebrates." So it seems that they are not even sure to what extent natural selection was driving the evolution of these supposed new duplicate copies of genes.

The following is the incredibly low level of detail they provide for the alleged Darwinian evolution of vertebrate genetic structure: "We imagine that rapid and extensive evolutionary change could possibly be an emergent property of having all genes duplicated at the same time, allowing this expanded gene repertoire to evolve together." Such vague assertions of evolutionary processes in no way demonstrate the efficacy of random mutation and natural selection. Instead, without providing any evidence that natural selection and random mutation could produce observed vertebrate diversification, they simply assert that it happened. It's easy to tell stories when the underlying mechanisms are assumed rather than demonstrated.

Perhaps their imaginations are simply more powerful than those of ID proponents, who find it difficult to "imagine" such "rapid and extensive evolutionary change" across thousands of genes when precise, detailed Darwinian pathways are never given.

In the end, ID is not incompatible with common descent, but Venema has confused evidence for common ancestry with evidence for natural selection and random mutation. This paper doesn't show a Darwinian pathway; it simply asserts it existed. There's no evidence against intelligent design here. There isn't even unequivocal evidence for common ancestry.