Critics Change the Topic: Do Human-Human Genetic Differences Matter?
Editor’s note: For the full “Chimps and Critics” series by Dr. Luskin, see here
One of the common yet unexpected reactions from critics to the discovery that humans and chimps are 15 percent genetically different is to change the topic. These critics want to focus on something else — human-human There’s still a lot we don’t know about human-human genetic differences, but it in no way affects the fact that we are 15 percent genetically different from chimps. This 15 percent difference refutes those who use the “1 percent” icon as an argument for evolution. We can’t dismiss the differences between humans and humans, or humans and chimps, as junk. But we also can’t assume that all types of genetic differences have the same kind of “meaning” or operate based upon the same “function per nucleotide” ratio. Critics need to stop casually dismissing these genetic differences as junk, because the evidence shows they are functional. What all this means for evolution remains to be seen — but one thing is clear: critics have not addressed or refuted my arguments, and in fact have badly misrepresented my arguments. How? We’ll explore that in a final post. genetic differences. I call this a “reaction” rather than an “objection” because these folks generally don’t contest the newest evidence about human-chimp genetic differences. Before going further, let’s remind ourselves of what the relevant arguments have been.
We’re Refuting an Icon of Evolution
For decades, prominent voices have frequently used the supposed “1 percent” genetic difference between humans and chimps as an unsophisticated argument for human-chimp common ancestry and human evolution, and against human exceptionalism. For example, we saw how Bill Nye said 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.” Or we recalled how the Smithsonian Institution claims that “DNA evidence … confirms that … humans and chimpanzees diverged from a common ancestor between 8 and 6 million years ago” since “there is only about a 1.2 percent genetic difference between modern humans and chimpanzees.”
Years ago I noted that sometimes evolutionists are unaware of their own arguments, and they need to be reminded of what they’ve been saying. So there are many other scientific sources that we’ve documented saying this same thing. In 1998, the journal Science used the statistic to diminish the specialness of humans:
We humans like to think of ourselves as special, set apart from the rest of the animal kingdom by our ability to talk, write, build complex structures, and make moral distinctions. But when it comes to genes, humans are so similar to the two species of chimpanzee that physiologist Jared Diamond has called us “the third chimpanzee.” A quarter-century of genetic studies has consistently found that for any given region of the genome, humans and chimpanzees share at least 98.5% of their DNA.
In 2012, the Financial Times posted a typical argument, claiming that human-chimp genomes are highly similar, very junky, and all of this supports common ancestry:
If the theory of our evolutionary origins were true, we would expect species that split off from each other recently to have similar genes. And this is exactly what we find: we share 98 per cent of our DNA with our nearest living relative, the chimpanzee. This applies not only to the DNA that actually makes us work but equally to our vast amount of functionless so-called “junk DNA”, and even the remnants of ancient viruses that once worked their way into our genomes.
As I was writing this post, Amazon delivered a book I recently learned of titled 99% Ape: How Evolution Adds Up, published in 2008 by University of Chicago Press, and co-authored by seven university professors. It claims that of “the roughly 3 billion letters of the genetic code … The difference is just 1.06%” meaning the difference is “1% of 3 billion.” (p. 15) Don’t miss what they just said: they are explicitly applying the “1%” difference statistic to the entire genome. We now know that that statement is false and it is an ideal example of how these statistics have been misused.
The book then uses the supposed small percent genetic differences to argue for human-chimp common ancestry. 99% Ape states that Darwin “believed that the resemblance between humans and orang-utans was evidence of ‘common descent’, or evolution” (pp. 11-12), and claims that “small genetic changes can add up to significant changes in appearance, behaviour, and intelligence like those that took place over the short space of about 6 million years since chimps and humans parted company from our common ancestor.” (p. 15) The back cover says, “Darwin was mocked for suggesting that humans have apes for ancestors, but every scientific advance in the study of life in the last 150 years has confirmed the reality of evolution.” Really?—“Every scientific advance in the study of life” supports evolution? Those are very strong words for a book published by the University of Chicago Press, and this “99% ape” statistic is clearly intended as a forceful argument for evolution.
So the supposed 1 percent genetic difference between humans and chimps has become an icon of evolution — a cherished argument used by many evolution defenders. That’s what this conversation has been about from the beginning: I’m not trying to argue that the 15 percent genetic difference between humans and chimps somehow confirms or refutes common ancestry or human evolution in general; I am simply pointing out that the factual basis for this common iconic argument for evolution is wrong — and it’s wrong by more than an order of magnitude.
Not a Valid Argument for Evolution
The “1 percent” argument is not just wrong, it’s also logically fallacious. And so a secondary point I’ve been making is that the exact percent genetic similarity between humans and chimps, whatever it may be, is a fascinating number but, by itself, it’s really not relevant to addressing questions about evolution.
From the beginning of this conversation — consistent with my past discussions — I’ve been clear that I don’t think the percent genetic similarity between humans and apes tells you anything about whether we share a common ancestor with chimps. As I wrote in 2021: “the ‘percent genome identity’ [i.e., percent genomic similarity between humans and chimps] provides no rigorous argument for common ancestry and does not answer many very interesting questions within this particular debate.”
This is because functional genetic similarities between humans and chimps could be explained by common ancestry, or by common design. Common ancestry is not the only way to explain genetic similarities. Intelligent agents can re-use functional code in different designs. Common design can explain shared functional genetic similarities just as well as common descent can.
Again, I’ve been very consistent on this point. Even way back in 2008 I wrote: “the percent difference says nothing about whether humans and chimps share a common ancestor. The percent genetic similarity between humans and apes does not demonstrate Darwinian evolution, unless one excludes the possibility of intelligent design.”
My point is this: I’ve never claimed that the mere percent genetic similarity between humans and chimps helps us discriminate between evolution or intelligent design. So if critics think that by citing human-human genetic similarities that somehow they are able to challenge my argument against evolution, then they misunderstand what I’m saying. In this conversation, I’m not making an argument against evolution. I’m showing that their argument for evolution — citing the supposed “1 percent” genetic similarity between humans and apes — was wrong.
Do Human-Human Genetic Similarities Matter?
As noted, some critics have responded to this new evidence showing humans and chimps are 15 percent genetically different by changing the topic. Their claim is that certain humans are genetically different from others by up to 10 percent.
This is also a very new claim based upon newly published and more complete human genomes. A 2023 paper in the journal Genomics Proteomics Bioinformatics compared the complete (“telomere-to-telomere”) genome sequence of a male human of Han Chinese descent to the complete sequence of a human genome called “CHM13.” It reported that when these two human genomes were compared, they showed “~330-Mb exclusive sequences, ~3100 unique genes, and tens of thousands or nucleotide and structural variations” and that “280–350-Mb sequences (~ 10%) in each haplotype are not or poorly aligned to others.” They state: “All these alignment results indicate that ~10% of sequences in each haplotype are of unique and represents most of the inter-individual genome diversity.” Critic Zachary Ardern highlights this, stating that the difference represents “a remarkable approximately 300+Mb each (9% of the genome!).”
CHM13 does not come from a normal “human” person. It’s an immortalized cell line used in research that originated as a “hydatidiform mole” — essentially a botched human pregnancy where each cell contains two copies of each of the father’s chromosomes and none from the mother. Because it has essentially complete homozygosity, this has enabled improved sequencing of its genome — although one might rightly ask if telomeric sequences in a cell line like this still resemble telomeric sequences in a normal human. Nonetheless, as we reported, CHM13 is the genome used in the Progressive Cactus alignment of Yoo et al. (2025) which showed about 15 percent genetic differences from the complete chimp genome. (Our calculation of 14.9 percent genetic difference between humans and chimps is based upon 1.6 percent single nucleotide variation added to 13.3 percent gap divergence. It derives from analysis that uses a different human genome, not CHM13.)
I’m skeptical that all of the 3,100 “unique genes” have been clearly confirmed as genes. Regardless, the claim is that these human genomes are about10 percent different from one another, which is said to make the statistic that humans and chimps are about 15 percent different much less interesting or impressive.
A Lot Can Be Said in Response, Starting with the Obvious
1. Evidence regarding human-human genetic differences doesn’t refute, affect, or answer any of our arguments about human-chimp genetic differences.
Those who are talking about human-human intraspecific differences haven’t justified the continued use of the “1 percent” icon of evolution. My argument was narrow: those who have claimed we are only 1 percent genetically different from chimps were wrong on the facts. But icons of evolution don’t die easily.
The critics want to suggest that if 10 percent differences can evolve between humans then surely 15 percent differences can evolve between humans and chimps. Perhaps that’s true, perhaps it isn’t. At this point I really don’t know. But it doesn’t matter: I have not made an affirmative argument that these differences are too great to evolve. I only said that “it may be possible to do an analysis of whether there is enough time in the fossil record for these genetic differences to evolve by random mutations and other unguided evolutionary mechanisms.” But I noted that this will be a difficult analysis to do, and I don’t yet know what the outcome of such an analysis would be:
Unfortunately, this analysis will be complicated by the fact that many the differences go beyond mere point mutations that could be studied through a relatively straightforward molecular clock analysis. From an evolutionary perspective, many of the large-scale “gap differences” between humans and chimps represent insertions, deletions, duplications, inversions, and other large-scale mutations. In order to do a waiting times analysis, one would have to calculate how often such mutations arise, and the likelihood of them arising by unguided evolutionary mechanisms in the time allowed by the fossil record (usually given as about 4 to 8 million years since our supposed most recent common ancestor we shared with chimps).
It may be a challenging analysis, but now that we have the necessary raw genome sequence data, at least we could start thinking about how to do it.
Perhaps such an analysis would pose a challenge to evolution, or perhaps it would not. I really don’t know, and it’s not really relevant to what I’ve been arguing.
Two critics — Zachary Ardern, and especially Joel Duff — have recently argued that even 15 percent genetic differences between humans could potentially evolve in the time allowed by the fossil record. Duff, a professor of biology at the University of Akron and a theistic evolutionist, spends a lot of time answering certain creationists who say this new evidence of 15 percent genetic differences between humans and chimps definitively refutes evolution. But I haven’t argued that we know yet whether the 15 percent genetic difference between humans and chimps is a problem for unguided evolution. Duff claims that I have argued otherwise, but he has misstated my position.
I do want to report, however, that I contacted Dr. Duff about his misstatements and he responded very graciously and apologetically. I believe it was an unintentional mistake, and I really appreciated his response to me.
But There’s More to Say
2. 10 percent may not be a typical degree of human-human genetic difference.
Ardern notes that “A more recent paper (Liao et al. 2023) suggests on average 4.4% of sequences in pairwise human genome comparisons are either not assembled or can’t be aligned.” Duff acknowledges that “most people probably aren’t 10 percent different, probably more like 3 to 4 percent different.” So this 10 percent genetic difference between humans may not be typical. This is a new area of research, and more data is needed.
3. Differences in human-human alignable DNA are much lower than in humans vs. chimps.
As we’ve discussed, alignable sections of the human and chimp genomes show about 1.6 percent difference. But the 2023 paper reports that alignable sections of these human genomes are far more similar than that:
Furthermore, in the perfect alignments longer than 50 kb, the weighted average identity between the two haplotypes of YAO is 99.94%, higher than that of 99.83% between YAO and CHM13, suggesting more nucleotide-level variations between YAO and CHM13
In other words, the single nucleotide variation between alignable portions of DNA is as low as 0.06 percent different (when comparing the two haplotypes of the Han Chinese individual) or 0.17 percent different (when comparing CHM13 to the Han Chinese individual’s genome). This is consistent with the NCBI’s longtime statement that “Between any two humans, the amount of genetic variation — biochemical individuality — is about .1 percent.” That’s a very small genetic difference, somewhere between 9 to 26 times less than the comparable type of genetic difference between humans and chimps.
As we saw, some critics argue that the non-alignable DNA can be dismissed because it’s genetic junk. Are we conceding this point by focusing on the fact that alignable DNA differences in humans are much smaller than they are between humans and chimps, implying that they matter a lot more than non-alignable DNA differences? Not at all. There’s good evidence that function exists throughout the genome, both in the alignable DNA that is full of single nucleotide differences, and in the non-alignable DNA that includes may differences in repetitive DNA and other larger-scale differences. We’ll elaborate that in a moment.
4. We already have prima facie evidence that the vast majority of the human genome has function.
To repeat, there’s good evidence that the vast majority of the human genome is functional. In 2012, the ENCODE project found evidence for “biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions.” It stated, “The vast majority (80.4%) of the human genome participates in at least one biochemical RNA- and/or chromatin-associated event in at least one cell type.” We could go on and on citing evidence of function throughout the human genome. This is prima facie evidence that the vast majority of the human genome is functional — including evidence of numerous types of function for repetitive DNA.
5. There is evidence that the character of non-alignable genetic differences between humans and humans can be different (and of a lesser degree) than the character of differences between humans and chimps.
The major non-alignable genetic differences between humans and humans, or between humans and chimps, often involves different numbers of copies of repeat sequences of DNA. Critics dismiss these differences as mere junk DNA, but it’s well-known that this kind of DNA difference can perform important functions in terms of both sequence and structure. As we previously saw, repetitive DNA can perform important functions as “non-B” DNA, where the number of copies present can form different structural shapes of the DNA which is important for formatting genome function. According to a paper in Nucleic Acids Research, this non-B DNA is known to be “important regulators of cellular processes” and has “unequivocal importance for genome function.” Indeed, a 2025 paper in Nature Communications noted that different shapes of DNA causes changes in gene regulation, which is crucial for genome function.
In short, the number of copies of DNA repeats has a major influence on the 3D shape of chromosomes, and the 3D shape of chromosomes has a major impact on gene regulation. So the number of copies of repeats matters.
But how much do they matter? If they matter a lot in causing differences between humans and chimps, then why don’t they cause greater differences between humans? There’s still a lot we don’t know about genomics and this hasn’t been studied very much yet. But there is already some evidence that the nature of differences in repetitive DNA between humans and chimps can be different (and greater) than the nature of differences in repetitive DNA between humans and humans.
Consider Figure 5 from the open access 2024 Nature article “The variation and evolution of complete human centromeres.” It’s a complex figure so I’ve extracted certain key portions below:
Image from Figure 5, Logsdon et al., “The variation and evolution of complete human centromeres,” 629: 136–145 (2024), used under creative commons license
What you’re seeing here is an analysis of both the number and types of repeats present in the centromeric DNA of chromosome 5 in humans and chimps. In the diagram, “CHM1/CHM13” and “Human” are all different human genomes, and you can compare them to the centromeric DNA on the same chimp chromosome at the far right. What you see is that even between homologous human chromosomes, the size of the DNA in megabases (Mb) — i.e., number of repeats — can vary greatly. But the color of the DNA — which essentially represents the sequence / type of those repeats — between humans and humans is basically the same.
Now compare the human centromeric DNA for chromosome 5 with that of the chimp. Here, again, we see differences in size, meaning that the length of the DNA (e.g., the number of copies of repeats) is different. But the color of the DNA in the chimp chromosome is different from what we see in homologous DNA in humans. What this means is that in chimps, not only is the length of the repetitive DNA different compared with humans, but so is the sequence of that repetitive DNA.
In both cases (humans vs. human and human vs. chimp) you find large amounts of non-alignable DNA — what has been counted up as the “gap divergence.” But between humans, the non-alignability stems largely from the number of repeat copies, whereas between humans and chimps it stems both from the number of repeat copies and the sequences of those repeats.
What exactly does this mean, biologically speaking? I don’t think anyone knows for sure. But what is clear is that there can be different characters in the types of non-alignable genetic differences. In this example, between humans the nonalignability stems primarily from differences in the number of copies of repeats, whereas between humans and chimps it involves both numbers of repeats and the sequence of those repeats. So the differences between humans and chimps are of a different and greater character than are the differences between humans.
This is just one example. But it shows that not all differences — including non-alignable “gap divergence” differences — are equal. We mustn’t assume that the percent of non-alignable DNA between humans necessarily has the same degree of differences compared with non-alignable DNA in humans and chimps.
A Crude Assumption
6. Big differences in DNA need not equal big difference in function — but that doesn’t mean it’s junk DNA.
In this conversation there are some crude assumptions that permeate the critics’ thinking: They seem to assume that the number of nucleotides involved in a function should be proportional to the amount of “function” that’s being encoded. Then, they seem to assume that if a stretch of DNA has a low “function per nucleotide” ratio, then it can’t be very important and can be dismissed as junk. On both counts their assumptions are flawed.
Sometimes “a little bit” of DNA might encode “a lot” of function. For example, within gene-coding DNA, a single nucleotide change might make a large difference. This would represent a high “function per nucleotide” ratio.
But in other genomic contexts, “a lot” of DNA might encode “a little” function. For example, with repetitive DNA, a lot of DNA differences might be involved in changing the 3-D shape of the chromosome in the nucleus, and this might result in relatively small-scale changes in gene regulation.
In all the cases we’re talking about, the DNA can be functional and shouldn’t be considered “junk.” Yet different types of DNA are designed to operate differently, with different “function to nucleotide” ratios. We can’t dismiss DNA as junk even in situations where a lot of DNA may be responsible for only a little bit of function.
An analogy here may help. Imagine a professional NFL football team, which has lots of people employed or connected to the team. Now some people who work for the team might have a major impact on the team’s success. For example, the quarterback is probably the most important player and has a high “impact per person” ratio. In fact any player on the field probably has a major impact on the team’s success. This could be analogous to DNA segments that directly encode genes.
But in other cases, there are people who work for the team but have a lower “impact per person” ratio. The team probably employs janitors, marketing experts, and ticket-counter operators. They all contribute to the team’s success, but probably not at a level nearly as high or as crucial as the players on the field. These might be very roughly analogous to DNA involved in gene regulation.
Lastly, there might be people connected to the team who make a difference, but at a much lower “impact per person” ratio. For example, think of the fans. Thousands of fans may attend games. The loss of any one fan might not hurt the team. In fact, the team could probably withstand the loss of large percentages of fans and not go bankrupt immediately. Yet, both individually and collectively, the fans have a major impact upon the team. Their purchasing of tickets, merchandise, and food at games is what ultimately funds the team’s revenue. Individually, each fan probably has a very low “person to impact” ratio, but they aren’t useless. In a biological context, this is like noting that repetitive DNA which plays structural roles in determining the 3-D shape of the chromosome may have a low “function per nucleotide” ratio, but it plays a functional role and certainly isn’t junk.
The point is this: In some cases, many of the genetic differences between humans could be in DNA with a low “function per nucleotide” ratio, meaning that the DNA is functional but it equates to small phenotypic differences. We should not assume that these differences in non-alignable low “function per nucleotide” DNA represent junk DNA, nor should we assume that it must encode major phenotypic differences. There’s a middle-ground position that’s being ignored: The non-alignable DNA differences between humans could represent different numbers of repeat copies which, though involving large numbers of nucleotides, may have small-scale effects on gene regulation by changing the 3-D shapes of chromosomes.
Critics in this conversation seem to think you can dismiss or ignore DNA with low “function per nucleotide” ratios. But you can’t say DNA is junk just because it has a low “function per nucleotide” ratio. In fact, this DNA may be doing precisely what it is designed to do.
The Bottom Line
There’s still a lot we don’t know about human-human genetic differences, but it in no way affects the fact that we are 15 percent genetically different from chimps. This 15 percent difference refutes those who use the “1 percent” icon as an argument for evolution. We can’t dismiss the differences between humans and humans, or humans and chimps, as junk. But we also can’t assume that all types of genetic differences have the same kind of “meaning” or operate based upon the same “function per nucleotide” ratio. Critics need to stop casually dismissing these genetic differences as junk, because the evidence shows they are functional. What all this means for evolution remains to be seen — but one thing is clear: critics have not addressed or refuted my arguments, and in fact have badly misrepresented my arguments. How? We’ll explore that in a final post.
