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Human-Chimp Similarity: What Is It and What Does It Mean?

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Image credit: Hannes Richter via Unsplash.

For years we’ve been told that human and chimp DNA is some 99 percent identical. The genetic similarity statistic is then used to make an argument for human-ape common ancestry, and human-ape common ancestry is then employed in service of the larger philosophical point that humans are just modified apes, and nothing special. It all amounts to an argument against human exceptionalism. This sort of thinking is embodied by Bill Nye (“The Science Guy”) in his 2014 book Undeniable:

As our understanding of DNA has increased, we have come to understand that we share around 98.8 percent of our gene sequence with chimpanzees. This is striking evidence for chimps and chumps to have a common ancestor. 

p. 248

BioLogos-affiliated biologist Dennis Venema has also argued that we are “but a hand-breadth away from our evolutionary cousins at the DNA level.” But is this really true? In response to the newly released episode of Science Uprising on human origins, we have recently received questions about the true degree of human-chimp similarity. With that in mind, let’s review some past coverage on the issue. 

The “Myth of 1% Genetic Difference”

In 2007, not long after the chimp genome was first sequenced, the journal Science published an article, “Relative Differences: The Myth of 1%,” which called the idea that humans are only 1 percent genetically different from chimps a “myth” and a “truism [that] should be retired.” It observed that the genetic differences between humans and chimps amount to “35 million base-pair changes, 5 million indels [sequences of multiple nucleotide bases] in each species, and 689 extra genes in humans.” The article further reported that if we consider the number of copies of genes in the human and chimp genomes, “human and chimpanzee gene copy numbers differ by a whopping 6.4%.”

The old statistic that we are about 99 percent or 98 percent similar to chimps pertains only to alignable protein-coding sequences. In fact the statistic first originated based upon similarity between humans and chimps in just one single gene! But many non-coding sequences are highly dissimilar, and there are sequences of the human and chimp genomes that are so different that they can’t be aligned for comparison. For example, there are some parts of our genome, such as the human y chromosome, that are radically different from the chimp genome.

Geneticist Richard Buggs has tried to refine the methods for comparing human and chimp genomes. In a 2018 post, he observes that “The percentage of nucleotides in the human genome that had one-to-one exact matches in the chimpanzee genome was 84.38%.” In 2020 he co-published an article in the journal Frontiers in Genetics providing a different method of estimating of human-chimp genetic differences, finding that human-chimp genetic similarity is about 96 percent. This paper’s estimate of ~4 percent genetic difference includes both coding and non-coding DNA, but it does not include centromeric DNA. If that DNA were included, the percent of genetic similarity between humans and chimps could drop to as low as ~93 percent, but probably not lower. Computational biologist Steve Schaffner has roughly estimated human-chimp genetic similarity to be ~95 percent. However, one criticism I’ve heard of all current estimates is that they are based upon versions of the chimp genome that used the human genome as a “scaffolding,” potentially making certain sections of the chimp genome more humanlike than they ought to be. This could also artificially inflate the degree of human-chimp similarity.

What this means is that until more accurate and complete versions of the chimp genome are produced, any estimate of human-chimp genetic similarity will undoubtedly be refined in the future, and current numbers may very well be overestimates. Nonetheless, any of the above estimates of human-chimp genetic similarity — 96 percent, 95 percent, 93 percent, 84 percent — carries meaning in different contexts. But what exactly do they mean? 

High Degree of Functional Similarity Does Not Mean Common Ancestry

Whatever the exact percentage of human-chimp genetic similarity (however you want to measure it) turns out to be, let’s grant that it will be fairly high, probably 84 percent or greater. Does this necessarily require the conclusion of common ancestry? Is the case for common ancestry, based upon the degree of similarity, an objective or rigorous argument that’s capable of being falsified? For example, if a 1 percent genetic difference implies common ancestry, but then that statistic turns out to be wrong, then does a 4 percent genetic difference mean common ancestry is false? How about 7 percent or 10 percent genetic difference? 25 percent? At what point does the comparison cease to support common ancestry? Why does the percent genetic similarity even matter? It’s not clear that there is an objective standard for falsification here, any identifiable reason why a particular percentage of genetic similarity should be taken to indicate common ancestry. 

Indeed, Dennis Venema even seems to acknowledge this point, writing in 2018:

No one is more interested in the “% genome identity” thing than folks trying to cast doubt on common ancestry. It’s just not a precise value that scientists are interested in, because it doesn’t answer interesting scientific questions in the way other values do… (emphasis added)

That’s quite a bold quote from Professor Venema when earlier he was seen emphasizing how humans are a mere genetic “hand-breadth” away from chimps, as part of a case for common ancestry. This is in keeping with numerous other evolution apologists over the years who have cited the “1%” statistic in favor of human-chimp common ancestry. They are the ones who invented and promoted this fallacious argument, and we are simply responding to it. Yet somehow us Darwin-skeptics get blamed for spreading a fallacious argument.

Perhaps Dr. Venema has changed his mind about the import of the statistic—which he is fully entitled to do. Whatever the case, we agree with his point here that the “% genome identity” provides no rigorous argument for common ancestry and does not answer very many interesting questions within this particular debate.

The case for human-chimp common ancestry is further significantly weakened once one realizes that there are other potential explanations for functional similarities: notably, design based upon a common blueprint. 

Intelligent agents often re-use parts and components that perform common functions in different designs. It’s a good engineering design principle to follow! Everyday examples of this include wheels used on both cars and airplanes, or touchscreen keyboards used on both phones and tablets. 

It should be noted that common design, as an argument, is not intended to prove species were specially created or designed separately. Rather, it’s a rejoinder put forth to defeat the evolutionist assertion that genetic similarity necessarily indicates common ancestry. Genetic similarity doesn’t necessarily indicate common ancestry because intelligent agents can and do independently use common parts in different designs to fulfill common functional goals. High genetic similarity could reflect design with a common blueprint rather than common ancestry. Biologist Ann Gauger, mathematician Ola Hössjer, and statistician Colin Reeves explain this well in Chapter 15 of the 2017 book Theistic Evolution:

[T]here are some basic differences between the way evidence is approached by evolutionary biologists and design biologists. The chief assumption made by evolutionary biologists is that the genetic changes responsible for evolutionary change are random, and therefore, if a group of species share a trait in common that is not found in other related species, it is presumed that the common ancestor of the group developed that trait, and they all share it because of common descent. On the other hand, if genetic change is directed rather than random, the trait is most likely shared because the organisms use similar solutions to a physiological need.

p. 496, emphasis added

Humans and chimps thus have similarities that reflect functional constraints due to design based upon a common blueprint. Gauger and her team indicate what this means for some of the basic molecular, cellular, metabolic, and physiological similarities between humans and chimps:

First, our basic building blocks, the proteins out of which our cells are made and the enzymes that carry out cellular metabolism, are very similar to those of chimpanzees, almost identical in many cases. One can think of our genes as being like the bricks and mortar, nails and wood, shingles and wires out of which houses are made. Two houses may look different but be composed of the same basic building blocks. By analogy, the building blocks out of which we are made, the genes, are very similar for chimps and humans, even if our bodily forms are different.

Second, the vast majority of our DNA does not code for protein but functions like an operating system, determining what files (genes) should be used when, and where. The routine processes of life are carried out by this operating system, and we share these basic routines with chimps. Thus in many respects our operating systems are the same as those of chimps. 

p. 481

Of course some will cite shared NON-functional (as opposed to functional) genetic similarities between humans and chimps as better evidence for common ancestry. I agree that non-functional shared DNA could be a potential argument for common ancestry, but I’m skeptical that many of the DNA elements cited in these arguments are actually non-functional. As we saw recently, a new paper in Genome Biology and Evolution declared, “The days of ‘junk DNA’ are over.” Even pseudogenes, commonly cited as a form of genetic junk that supports common ancestry, have had their “junk” status severely questioned in recent years — see herehereherehere, and here for discussions. 

Is Genetic Similarity by Percentage a Good Measure of Overall Human-Chimp Similarity?

Since many of the building blocks used by humans and chimps are similar, it’s no wonder that our protein-coding DNA is also so similar. Common design can explain these similarities. But it’s important to bear in mind that one can use identical building blocks — bricks, mortar, wood, and nails — to build very different houses. So it’s not just about having similar building blocks, but how you use them. This is where genetic similarities between humans and chimps probably aren’t so meaningful, when you consider how the building blocks being used can be very different. 

Gauger and her colleagues thus explain that the percentage of 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 some of the crucial differences between humans and chimps:

  • Human-specific genes, of which there may be over 600 genes unique to our human genome;
  • Multipurpose genes, which can build diverse types of proteins via alternative splicing which are not always predictable by nucleotide sequence alone, meaning “6 to 8 percent of genes that have been studied display splicing differences between chimps and humans” (pp. 483-484); 
  • Differential gene expression, where notably, “there are substantial differences in gene expression between humans and chimpanzees, particularly in the brain” (p. 484; see also Oldham et al., 2006Varki et al., 2008);
  • Noncoding DNA differences, including differences in SINE elements, LINE elements, and long noncoding RNAs, which also seem to be important for human brain development (see for example Paz-Yaacov et al., 2010 or Johansson et al., 2021);
  • 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; see also Oldham et al., 2006); 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 the many important anatomical and physiological differences recounted by a paper in Nature (Bramble and Lieberman, 2004).

And this leaves aside the vast cognitive and behavioral gulf between humans and chimpanzees. We are the only species that uses fire and technology. We are the only species that composes music, writes poetry, and practices religion. We are also the only species that seeks to investigate the natural world through science. We write papers about chimps; not the other way around. All of this is possible because we humans are the only species that uses complex language. 

The human race has unique and unparalleled moral, intellectual, and creative abilities. Regardless of the level of similarity of human protein-coding DNA to chimps, clearly that similarity is only a small part of the story. If anything, it testifies that protein-coding DNA sequences are only one of multiple crucial interacting factors that determine an organism’s biology and behavior.