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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. Moreover, as geneticist Richard

Buggs has explained, the genetic similarity between humans and chimps may be even lower than 95%:

To compare the two [human and chimpanzee] genomes, the first thing we must do is to line up the parts of each genome that are similar. When we do this alignment, we discover that only 2400 million of the human genome’s 3164.7 million “letters” align with the chimpanzee genome — that is, 76% of the human genome. Some scientists have argued that the 24% of the human genome that does not line up with the chimpanzee genome is useless “junk DNA.” However, it now seems that this DNA could contain over 600 protein-coding genes, and also code for functional RNA molecules.

Looking closely at the chimpanzee-like 76% of the human genome, we find that to make an exact alignment, we often have to introduce artificial gaps in either the human or the chimp genome. These gaps give another 3% difference. So now we have a 73% similarity between the two genomes.

In the neatly aligned sequences we now find another form of difference, where a single “letter” is different between the human and chimp genomes. These provide another 1.23% difference between the two genomes. Thus, the percentage difference is now at around 72%.

We also find places where two pieces of human genome align with only one piece of chimp genome, or two pieces of chimp genome align with one piece of human genome. This “copy number variation” causes another 2.7% difference between the two species. Therefore the total similarity of the genomes could be below 70%.

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).