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Forbidden Question: Common Descent or Common Design?

Jonathan Witt
Photo credit: Michael Maggs, CC BY-SA 2.5 , via Wikimedia Commons.

Kids often look like their parents. That isn’t surprising. They’re closely related. Evolutionists expand this logic, pointing to similarities across species, classes, and phyla to argue that we are all descended from a common ancestor, the seed of Darwin’s great tree of life. DNA, for example, crops up everywhere in the living world. Why? According to evolutionists, it’s because we are all descended from one or a few single-celled organisms that contained DNA. And by evolved, they mean evolved blindly — without intelligent guidance. 

More than a few times I have encountered this common features/common ancestor conclusion presented as if it were self-evident truth. But it actually involves a basic confusion.

To say that similarities prove common descent ignores a logical possibility: that common features may instead be due to a common design strategy. Think of cars. A Tesla and a Cadillac share many features — four wheels, synthetic rubber tires, brakes, two axles, windshield wipers, headlights. But of course, none of that means that Teslas blindly evolved from Cadillacs, or vice versa. Designers re-use design features proven to work for specific engineering needs, even while they innovate in alternative directions, as Tesla CEO and engineer Elon Musk has with his electric cars.

We see this pattern even across disparate technology platforms. In one case, the wheel is used and adapted for a water mill. In another case, for a gear in a watch. In another case, for a bicycle. In still another case, for a pizza cutter. In yet another, for a truck. And in another, for a self-balancing scooter (aka “hoverboard”).

So, what about with living things? Might a designer of life have used and reused various good design concepts in widely different biological contexts? The only way to jump straight from biological similarities to common descent via blind evolution is to rule out the design hypothesis from the start — to treat it as the idea that must not be considered, the thought that must not be thought. But if we are seeking the truth about the history of life on Earth, we shouldn’t let ourselves be bullied into ignoring one option and accepting the other as unquestionable dogma. 

To rule out the design hypothesis from the start is to commit the fallacy known as begging the question. For some, it’s just an honest mistake, such that if you point it out, the person will realize the logical error and stop doing it. For others, it’s a tactic to shut down debate and protect modern evolutionary theory from critique.

Off Limits

For those confronted with the logical error, one countermove is to say that the design hypothesis “isn’t science” — as if there were a single, inarguable definition of science. Actually, what’s called the demarcation question in science — the line between what is and isn’t science — is a complex and hotly debated issue among the experts on the question, namely, philosophers of science. Different fields of science offer overlapping and sometimes contradictory definitions of what constitutes science. 

For instance, some definitions rule out any hypothesis that invokes unobservable entities. But that would rule out a great deal of what’s going on in quantum physics, which has made all kinds of interesting breakthroughs. Other scientists insist that repeatable experiments done in laboratory conditions constitute the heart and soul of science, and that without such experiments, you don’t have science. But this definition rules out all historical sciences — from cosmology to archeology to forensics to evolutionary biology, since the historical sciences all make claims about unrepeatable events in the past. 

Philosopher of science Stephen Meyer, who received his PhD in the history and philosophy of science from the University of Cambridge (and directs the center where I serve as a senior fellow), argues that modern evolutionary theory and intelligent design are “methodologically equivalent.”1 Both are trying to answer the same questions about past events. Both employ what’s known as inference to the best explanation

The one difference between them methodologically is that modern Darwinism appeals to a question-begging rule, according to which origins biologists must consider only material causes — never intelligent causes. But, Meyer notes, the very point at issue is blind evolution versus intelligent design, so this extra rule, known as methodological materialism, amounts to a refusal to engage the evidence and arguments of the opposing position. 

Such a move should not impress anyone, regardless of the sophisticated-sounding terminology used to describe it. Ruling out the design hypothesis by saying it “isn’t science” just dresses up the question-begging in a lab coat. It’s still question-begging. And it doesn’t shed any fresh light on how new plant and animal forms arose in the history of life. Science should be about truth-seeking and evidence, not rigged games.

What does the evidence suggest is the best explanation for the origin of new plants and animals in the history of life? Some form of blind evolution? Or does important evidence in nature strongly suggest that intelligent design was involved? And what new findings might count in favor of one option over the other? Those are the kind of questions characteristic of an unfettered, truth-seeking scientific culture.

What Story Does DNA Tell?

Return to the example of DNA. We find it in everything from bacteria to Beethoven. DNA is digital information that codes for biological machinery and form. We are told that chimpanzee DNA and human DNA are 98 percent similar, supposedly just what we should expect if humans evolved from a chimp-like ancestor. But that percentage figure drops if you compare bigger units of DNA. And since DNA codes for function, we should expect chimps and humans to share a lot of similar DNA software. 

Even prominent evolutionist Francis Collins conceded this point in his book The Language of God.2 After all, our DNA codes for things like blood and bone and muscle, for arms and legs, fingers and toes, eyes and ears, mouth and nose. These are all things chimps and humans both have. Should we be shocked that the designer stuck with a superb software system when it came time to design human beings? No, and all the more so since there are major functional advantages to having a biosphere with a shared system of biological information across kingdoms, phyla, and families.

But Collins and others say other genetic evidence does cinch the case for common descent. One example they give is what is colloquially referred to as junk DNA — stretches of DNA that don’t code for proteins. But today the whole idea of junk DNA is in retreat as geneticists discover more and more uses for the stuff. Collins himself now admits the whole business of junk DNA was badly oversold. As journalist Marvin Olasky reported in World magazine: 

Speaking at the J. P. Morgan Healthcare Conference in San Francisco, Collins threw in the towel: “In terms of junk DNA, we don’t use that term anymore because I think it was pretty much a case of hubris to imagine that we could dispense with any part of the genome, as if we knew enough to say it wasn’t functional. . . . Most of the genome that we used to think was there for spacer turns out to be doing stuff.”3

Neo-Darwinism led evolutionists to assume that most of our DNA would prove to be junk left over from evolution’s trial-and-error process. In contrast, intelligent design theorists predicted that “junk DNA” would prove to have function. The common-descent hypothesis led to a failed prediction. The common-design hypothesis made no such prediction.

Collins advanced a second line of evidence that chimps and humans share a common ancestor, evidence that also has run into trouble. Collins writes that human chromosome 2 is the result of the fusion of two chromosomes similar to those found in chimps. He notes that chimps and other great apes have 24 pairs of chromosomes, whereas humans have just 23. Collins says that if we assume common ape/human ancestry and a fusion event for chromosome 2 in humans, it nicely explains why we have one fewer pair of chromosomes than apes do — something “very difficult to understand . . . without postulating a common ancestor” between humans and apes.4

But there are two problems here. First, if there was a fusion event, it doesn’t necessarily point to shared ancestry with chimps. Casey Luskin summarizes the matter well in the book Science and Human Origins. “At most, the chromosomal fusion evidence strengthens something we already knew — that chimps and humans have high genetic similarity,” he writes. “Such functional similarities may just as easily be the result of functional requirements implemented via common design.”5 Second, and as Luskin also explains, it turns out that it’s not even clear that chromosome 2 is the result of a fusion event between what used to be two separate chromosomes. As a paper in Genome Research reported, the sequence of DNA in question is shorter than expected if it were the result of a fusion event, and the sequence has diverged “from the prototypic telomeric repeats” far more than expected.6 The authors of the paper then offer some possible explanations for the unexpected finding, none of which involve consideration of the possibility that humans are intelligently designed and not the result of blind evolution from ape-like ancestors. The design hypothesis, remember, is the thought that must not be thought. 

Evolutionary Trees Springing Up Like Dandelions

If we step back from chromosome 2 in humans and look at genetic evidence more broadly, we find a bigger problem with the idea of the macroevolution of all life from a common ancestor. Finnish bioengineer Matti Leisola and I highlight that problem in our book Heretic: One Scientist’s Journey from Darwin to Design:

In 1965 one of the most important scientists of the last century, Linus Pauling, and biologist Emil Zuckerkandl, considered by some as the father of molecular biology, suggested a way that macroevolution could be tested and proved: If the comparison of anatomical and DNA sequences led to the same family tree of organisms, this would be strong evidence for macroevolution.7 According to them, only evolution would explain the convergence of these two independent chains of evidence. By implication, the opposite finding would count against macroevolution.

So what were the results? Over the past twenty-eight years, experimental evidence has revealed that family trees based on anatomical features contradict family trees based on molecular similarities, and at many points. They do not converge. Just as troubling for the idea of macroevolution, family trees based on different molecules yield conflicting and contradictory family trees. As a 2012 paper published in Biological Reviews of the Cambridge Philosophical Society reported, “Incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species” (emphasis in original).8

Another paper, published the following year in the journal Nature, highlighted the extent of the problem.9The authors compared 1,070 genes in twenty different yeasts and got 1,070 different trees.10

These results are unexpected, even bizarre, on the assumption that all life evolved from a single common ancestor through a long series of small, random genetic mutations over millions of years. But if Darwinian evolution only explains modest differences among closely related species, and if the various similarities and differences across plants and animals of widely varying types are primarily due to an intelligent designer reusing genetic information for common purposes and fresh DNA sequences for innovations, the persistent failure of a single tree of life to emerge makes perfect sense: there is no evolutionary tree of life, because common descent isn’t the case. A common designer is. 

Editor’s note: This essay first appeared in the Summer 2021 issue of Salvo Magazine.


  1. Stephen C. Meyer, “The Methodological Equivalence of Design and Descent: Can There Be a Scientific ‘Theory of Creation’?”, Discovery Institute (July 2, 2003): discovery.org/a/1696.
  2. Francis S. Collins, The Language of God (Free Press, 2006), 134.
  3. Marvin Olasky, “Admission of Function: Junking Slurs about ‘Junk DNA,’” WORLD Magazine (July 9, 2016): https://world.wng.org/2016/06/admission_of_function.
  4. Collins, The Language of God, 138.
  5. Casey Luskin, “Francis Collins, Junk DNA, and Chromosomal Fusion,” in Science & Human Origins (Discovery Institute Press, 2012), 95–96.
  6. Yuxin Fan et al., “Genomic Structure and Evolution of the Ancestral Chromosome Fusion Site in 2q13-2q14 and Paralogous Regions on Other Human Chromosomes,” Genome Research 12 (2002), 1651–1662, doi:10.1101/gr.337602.
  7. Emil Zuckerkandl and Linus Pauling, “Evolutionary Divergence and Convergence in Proteins,” in Evolving Genes and Proteins: A Symposium, ed. Vernon Bryson and Henry J. Vogel (Academic Press, 1965), 101.
  8. Liliana Dávalos et. al, “Understanding Phylogenetic Incongruence: Lessons from Phyllostomid Bats,” Biological Reviews of the Cambridge Philosophical Society 87 (2012), 991–1024, doi:10.1111/j.1469-185X.2012.00240.x.
  9. Leonidas Salichos and Antonis Rokas, “Inferring Ancient Divergences Requires Genes with Strong Phylogenetic Signals,” Nature 497 (May 16, 2013), 327–331.
  10. Matti Leisola and Jonathan Witt, Heretic: One Scientist’s Journey from Darwin to Design (Discovery Institute Press, 2018), 84.