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Critically Analyzing the Argument from Human/Chimpanzee Genetic Similarity

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

In this final article, Part 8, we:
• Again discuss why evidence for common ancestry is not evidence for a Darwinian evolutionary pathway
• Falsify Dr. Venema’s reasoning that a 5% DNA difference between humans and chimps tells us anything about whether random mutation and natural selection could produce both species from a common ancestor, or even whether they share a common ancestor
• Show that Dr. Venema is overstating what we currently know about the degree of intraspecies genetic variation within humans
• Suggest that the percent genetic difference between humans and chimps may be much greater than 5%, and might not be accessible by Darwinian evolution

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 7: Confusing Evidence for Common Ancestry with Evidence for Random Mutation and Natural Selection
Part 8 (This Article): Critically Analyzing the Argument from Human/Chimpanzee Genetic Similarity

In his series on “Evolution and the Origin of Biological Information,” BioLogos-affiliated scientist Dennis Venema challenges ID to “address” a “widespread and compelling pattern,” which supposedly demonstrates common descent. But as we saw in the previous article, this pattern is not evidence for natural selection and random mutation, so there is nothing here that challenges ID. The problem exists in Venema’s sixth post, which makes the mundane point that humans and chimps share many genetic similarities:

[W]hile the total genetic differences between two species is an overestimation of the genetic changes needed to cause the differences, it is still a useful measure because we know that all of the meaningful changes must be accounted for within it.

Applying this test to humans and our closest (living) evolutionary relative, the chimpanzee, reveals that at a whole-genome level, we are over 95% identical. This value is even an underestimate, since it “counts” mutations that duplicate or delete sections of DNA as if they were separate mutations affecting individual DNA “letters” even though it was created by only one genetic change. Indeed if we use the same criteria to compare the diversity which exists within our own species, we humans are only 98% identical to each other. By whatever measure used, we are but a hand-breadth away from our evolutionary cousins at the DNA level.

Assuming Venema’s numbers are all correct, the short response to his point is So what? None of this bears on the question of whether natural selection acting on random mutations could produce these genetic changes.

As a longer answer, multiple levels of response are possible.

Initially, I must point out that Venema’s post provides no citation for his claim that human intraspecies genetic variation is as much as 2%. I contacted Dr. Venema privately and asked for citations that back this claim, but neither of the two papers he provided proposed an official percentage of human intraspecies genetic variation. One paper suggested that there are about 10 million single nucleotide polymorphisms (SNPs) and about 1.5 million insertion and deletion polymorphisms (INDELs) in the human genome.[1] But the other paper, published in 2011, provided the highest estimates for human intraspecies genetic variation, stating: “Like known SNPs, which affect ~15 Mb of DNA … our INDEL variants affected 11.9 Mb of the human genome.”[2]

Looking at the latter article, if we add those amounts together and round up to about 27 million base pairs, that implies that only about 0.9% of the human genome is known to vary — not 2%. This statistic is corroborated by the National Institutes of Health website which states “Human DNA consists of about 3 billion bases, and more than 99 percent of those bases are the same in all people.”

Perhaps someday Dr. Venema’s claim that “humans are only 98% identical to each other” will turn out to be correct. Perhaps it won’t. The fact of the matter is that we really don’t know at present the exact nature or amount of human intraspecies genetic variation. It thus seems premature for Venema to assert — especially without supporting citations — that humans have 2% intraspecies genetic variation. Presently, we don’t know that to be the case.

This problem of making premature claims that we don’t know are correct plagues Dr. Venema’s discussion of human and chimp genetic variation:

First, Venema claimed his series would show “a natural mechanism that does add functional, specified information to DNA sequences” namely “natural selection acting on genetic variation produced through random mutation.” But shared functional genetic similarity between humans and chimps is (at best) evidence for common descent, not evidence for natural selection and random mutation.

Second, Venema has misstated comparisons of human/ape “whole genome” similarity and human/human DNA similarity. Far from being “but a hand-breadth away from our evolutionary cousins at the DNA level,” the evidence shows that the genetic differences between humans and chimps amount to “35 million base-pair changes, 5 million indels in each species, and 689 extra genes in humans.”[3] Such a level of differences is not known to exist for human/human intraspecies genetic variation.

Third, two articles deal with human-chimp genetic similarity in more detail: “The myth of 1% human-chimp genetic differences” or “Human-Chimp Similarity: What Is It and What Does It Mean?These articles ask whether human/chimp genetic similarities are good evidence for common ancestry. As the journal Science has reported, it notes that human/chimp genetic differences are much more than the “1%” genetic difference we typically hear about. Geneticist Richard Buggs observes that “The percentage of nucleotides in the human genome that had one-to-one exact matches in the chimpanzee genome was 84.38%.” A 2020 paper that compared alignable coding and non-coding DNA and found that human-chimp genetic similarity is 96%. However, this is undoubtedly an overestimate of human-chimp genetic similarity because (a) it did not consider non-alignable DNA, and (b) it used a version of the chimp genome which used the human genome as a scaffolding. Depending on how you measure it, human-chimp genetic-similarity is likely between 84 and 96 percent, but none of this means that we share a common ancestor with chimps. 

These articles explain that functional human/ape genetic similarities might result from common design rather than common descent. The two pieces also ask what is the metric for demonstrating Darwinian evolution based upon genetic similarity. There doesn’t seem to be one, and the argument often appears arbitrary.

Moreover, as biologist Ann Gauger, mathematician Ola Hossjer, and statistician Colin Reeves explain in the book Theistic Evolution, genetic differences between humans and chimps are much greater than is often assumed:

All told, based on current knowledge, there is at least a 5 percent difference in our DNA, and that does not count rearrangements in the DNA, where segments of the DNA appear flipped end to end in relation to chimp DNA, or where one segment of human DNA is in a different location than in chimpanzees. (p. 481)

They go on to explain that the percent nucleotide similarity does not tell the whole story about human-chimp genetic differences since many of the most crucial differences lie outside the protein-coding DNA:

[C]ounting raw difference is not the best way to calculate how different we are genetically speaking … We now know that when, where, and how our DNA is used matters much more than an overall count of nucleotide differences. Human-specific differences in gene regulation, as we will see, are what make us unique. (pp. 481-482)

They recount that some of these crucial differences between humans and chimps include:

  • Human-specific genes, of which there may be over 600 genes unique to our human genome;
  • Multipurpose genes, which can build diverse different types of proteins via alternative splicing which are not always predictable by nucleotide sequence alone;
  • Differential gene expression, where notably, “there are substantial differences in gene expression between humans and chimpanzees, particularly in the brain” (p. 484);
  • Noncoding DNA differences, including differences in SINE elements, LINE elements, and long noncoding RNAs, which also seem to be important for human brain development;
  • Gene regulatory networks, which again may lead to important differences between chimp and human brains, since, “17 percent of the neural network in the cortex of the brain is unique to humans, even though our total genomes may differ from chimpanzees by only 5 percent” (p. 490); and
  • Physiological and anatomical differences, which include differences in timing of development, teeth, brain formation, musculature, diet, mode of locomotion, neck structure, rib cage structure and gait, shoulder design, pelvis and hip orientation, inner ear canals, hands (made for tool use rather than knuckle walking) — which are among some of the 26 important anatomical and physiological differences recounted by a paper in Nature (Bramble and Lieberman, 2004).

Third, whatever shared functional genetic similarities do exist between humans and chimps, they might be explained by common design just as well as by common descent. In fact, had the now-refuted statistic that humans and chimps are only 1% genetically different turned out to be correct, why should that demonstrate common ancestry? Why is a 1% genetic difference any better than a 5% genetic difference for demonstrating common ancestry? At what point does the comparison cease to support common ancestry? How about a 10% difference? 25%? Is there an objective metric for falsification here, or are we seeing a fallacious argument for human/chimp common ancestry?

Intelligent design is certainly compatible with human/ape common ancestry, but the truth is that the genetic difference expressed as a percent says nothing about whether humans and chimps share a common ancestor. The genetic similarity between humans and apes does not demonstrate Darwinian evolution, unless one excludes the possibility of intelligent design (and all other non-Darwinian evolutionary scenarios). Just as intelligent agents “re-use” functional components that work over and over in different systems (e.g., wheels for cars and wheels for airplanes), genetic similarities between humans and chimps could also be explained as the result of the re-usage of common genetic programs due to functional requirements of the hominid body plan. Even Francis Collins (who frames the question theologically) admits this is the case:

This evidence alone does not, of course, prove a common ancestor; from a creationist perspective such similarities could simply demonstrate that God used successful design principles over and over again.

(Francis Collins, The Language of God, p. 134 (Free Press, 2006).)

I elaborate further on this point here.

Waiting for Millions of Mutations?

There’s a final problem with Venema’s argument. He suggests that “we are but a hand-breadth away from our evolutionary cousins at the DNA level” and thus evolving humans and chimps from a common ancestor is no problem for random mutation and natural selection:

The differences we see, when examining these two genomes, are consistent with small changes, of the sort easily accessible to evolutionary mechanisms.

This is an incredibly weak argument.

First, as noted, we’re not talking about “small changes” but rather, as the journal Science explained, at the very least these differences entail “35 million base-pair changes, 5 million indels in each species, and 689 extra genes in humans.”[3]

Second, Venema has badly overstated the case for Darwinian evolution, as no one has any idea if these changes are “easily accessible to evolutionary mechanisms.” In fact, we still don’t understand what the vast majority of these differences mean. When speaking of human/chimp genetic differences, David Haussler, a biomolecular engineer at UC Santa Cruz, writes “To sort out the differences that matter from the ones that don’t is really difficult.”[3] And there are good reasons to believe that some (or many) of these differences might encode features not amenable to stepwise Darwinian evolution under known timescales.

In 2008, Michael Behe’s critics Rick Durrett and Deena Schmidt tried to refute him in the journal Genetics with a paper titled “Waiting for Two Mutations: With Applications to Regulatory Sequence Evolution and the Limits of Darwinian Evolution.” But Durrett and Schmidt found that to obtain only two specific mutations via Darwinian evolution “for humans with a much smaller effective population size, this type of change would take > 100 million years.” The critics admitted this was “very unlikely to occur on a reasonable timescale.”[4]

In other words, if any of the 35 million base pair changes between humans and chimps entail adaptive changes that require two or more specific mutations before providing any advantage, then they would be extremely unlikely to evolve by random mutation and natural selection in the mere 6 or 7 million years since we shared our alleged most recent common ancestor with chimps.

Durrett and Schmidt found that it would take too long to wait for two specific mutations to gain an advantage. How does Venema know that there aren’t many differences between humans and chimps that would require two (or perhaps many more–dozens, hundreds, millions?!) mutations before any benefit arises?

Venema’s claim that the genetic differences between humans and chimps are “easily accessible to evolutionary mechanisms” is difficult to accept, because frankly, no one knows that this is true. We should not assume that naturalistic evolutionary explanations are correct; we should test them, and hold on to them only if they are valid.

References Cited:

[1.] Ryan E. Mills, Christopher T. Luttig, Christine E. Larkins, Adam Beauchamp, Circe Tsui, W. Stephen Pittard, and Scott E. Devine, “An initial map of insertion and deletion (INDEL) variation in the human genome,” Genome Research, Vol. 16: 1182-1190 (2006).

[2.] Ryan E. Mills, W. Stephen Pittard, Julienne M. Mullaney, Umar Farooq, Todd H. Creasy, Anup A. Mahurkar, David M. Kemeza, Daniel S. Strassler, Chris P. Ponting, Caleb Webber and Scott E. Devine, “Natural genetic variation caused by small insertions and deletions in the human genome,” Genome Research, Vol. 21: 830-839 (2011).

[3.] Jon Cohen, “Relative Differences: The Myth of 1%,” Science, Vol. 316:1836 (June 29, 2007).

[4.] Rick Durrett and Deena Schmidt, “Waiting for Two Mutations: With Applications to Regulatory Sequence Evolution and the Limits of Darwinian Evolution,” Genetics, Vol. 180:1501-1509 (November 2008).

This post has been updated, October 2021.

Casey Luskin

Associate Director, Center for Science and Culture
Casey Luskin is a geologist and an attorney with graduate degrees in science and law, giving him expertise in both the scientific and legal dimensions of the debate over evolution. He earned his PhD in Geology from the University of Johannesburg, and BS and MS degrees in Earth Sciences from the University of California, San Diego, where he studied evolution extensively at both the graduate and undergraduate levels. His law degree is from the University of San Diego, where he focused his studies on First Amendment law, education law, and environmental law.



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