The “1 Percent” Deception

Human & Chimp DNA Icon of Evolution Bites the Dust

How many times have you heard the claim that the human and chimpanzee genomes are only “1 percent different”—and that this shows that humans and chimps share common ancestry? It’s been cited so often that it has become what the late pro-ID biologist Jonathan Wells would call an “icon of evolution.”

In April, a groundbreaking paper in Nature provided a definitive disproof of this statistic, though it obscured that fact with opaque language. The paper published complete sequences of ape genomes, including chimpanzees, bonobos, gorillas, and orangutans.¹

You might be thinking, “Weren’t these ape genomes sequenced long ago?” The answer is yes, but also no. Yes, genomes from these species had been sequenced in the past, but, as the paper explains, they were incomplete. “Owing to the repetitive nature of ape genomes, complete assemblies have not been achieved,” said the technical paper. “Current references lack sequence resolution of some of the most dynamic genomic regions, including regions corresponding to lineage-specific gene families.” In other words, the previous ape genome drafts “lack” many of the DNA sections which were unique to that species—i.e., the sections that made them different from humans. An explainer article in Nature thus notes that previous comparisons between human and ape genomes “only focused on relatively small differences” and “excluded” the sections that entail “large-scale structural differences.”²

Moreover, most earlier versions of these ape genomes used the human genome as a template—effectively making apes appear more similar to humans than they really are. The technical paper puts it this way: “human reference biases were introduced” due to the “mapping of inferior assemblies to a higher quality human genome.” Thus, one could expect that these newly complete ape genomes would reveal much greater differences compared to the human genome. And they did.

Summarizing the Results

Now, for the first time we can attempt a much more accurate assessment of the true degree of difference between the human and chimp genomes. The results are striking:

• Between 12.5 and 13.3 percent of the chimp and human genomes exhibit a “gap difference” where the two genomes are so different that they cannot even be aligned—i.e., there’s a “gap” in one genome compared to the other. This represents a minimum of 12.5–13.3 percent difference between the human and chimp genomes.

• There are also significant alignable sections of the two genomes that show “short nucleotide variations” (SNVs) which differ by about 1.5–1.6 percent.

• We can add up these two types of differences and calculate a 14.0–14.9 percent total genetic difference between human and chimp genomes. This is an order of magnitude greater than the oft-quoted “1 percent.”

We can do the same kind of calculations for all of the ape genomes sequenced by this new study and show their total genetic differences from humans:

• Sumatran Orangutan (Pongo abelii) vs. Human: ~19.0–20.1 percent different

• Gorilla (Gorilla gorilla) vs. Human: ~19.8–29.3 percent different

• Bonobo (Pan paniscus) vs. Human: ~14.0–16.0 percent different

• Chimpanzee (Pan troglodytes) vs. Human: ~14.0–14.9 percent different

In fact, the higher numbers—for example, 14.9 percent total genetic difference in the case of chimps—are arguably the more relevant because they represent how dissimilar the whole human genome assembly is to the ape genomes. These represent a much greater degree of difference than the usually cited statistic that we are only 1 percent genetically distinct from chimpanzees!

Buried Lede

What you just read was a plain summary of the evidence. Human and chimp genomes exhibit about a 15 percent total difference. With other apes, the differences stretch up to 29.3 percent. That’s the punchline. But I had to really dig through the technical paper and its supplemental data and do my own calculations to arrive at those numbers. Although these calculations were fairly simple to do based upon the data presented in the paper, what’s strange is that as you read the technical paper, you find that a direct comparison between the human and ape genomes isn’t there.

These are huge findings for the wider culture about human uniqueness and the truth about our genetic similarities to apes—yet the technical Nature paper, as well as an explainer article in Nature that is supposed to help the non-expert understand the implications, fail to clearly bring out these points. The data points were buried in technical jargon deep in the supplemental data. The lack of clarity is simply astonishing. Why wouldn’t they clearly state these statistics for the public to understand?

Remembering the Icon

As Jonathan Wells taught, “icons of evolution” are widely promoted arguments for evolution that get recycled over and over again—but they aren’t true. How do we know the 1 percent statistic is such an icon? Science popularizer Bill Nye “The Science Guy” provided a great example when he wrote 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.

As of this writing, the website for the Smithsonian National Museum of Natural History likewise states:

DNA is thus especially important in the study of evolution. The amount of difference in DNA is a test of the difference between one species and another—and thus how closely or distantly related they are.

While the genetic difference between individual humans today is minuscule—about 0.1%, on average—study of the same aspects of the chimpanzee genome indicates a difference of about 1.2%.³

Similar statements are found within the Smithsonian Museum itself—I took this photo there in 2023.

A caption below it declares that: “DNA evidence ... confirms ... that modern humans and chimpanzees diverged from a common ancestor...” As my colleague David Klinghoffer has shown, many sources have cited this statistic:

• Nature: “We share more than 98% of our DNA and almost all of our genes with our closest living relative, the chimpanzee.”⁴

• Scientific American: “Most studies indicate that when genomic regions are compared between chimpanzees and humans, they share about 98.5 percent sequence identity.”⁵

• American Museum of Natural History: “Humans and chimps share a surprising 98.8 percent of their DNA.”⁶

• Science: “[H]umans share about 99% of our DNA with chimpanzees, making them our closest living relatives.”⁷

• National Geographic: “Chimps, Humans 96 Percent the Same, Gene Study Finds.”⁸

Many similar examples exist. A 2008 book from University of Chicago Press titled 99% Ape: How Evolution Adds Up claims that across “the roughly 3 billion letters of the genetic code …. The difference is just 1.06%.” This “1 percent” human-chimp genetic difference statistic has been widely promoted and is widely believed—it’s undeniably an icon of evolution.

Critics Respond: “Nothing to See Here”

Given how much rhetoric the evolution camp has invested in this argument, we can expect that they won’t give it up easily. And that’s exactly what we’ve been seeing since this study came out.

The first response was to challenge the numbers. Some have questioned whether human and chimp DNA could not be aligned merely due to “technical failures.” However, in the main Nature paper, a failure to align the DNA is equated with a “technical” problem, and the standard reason for such a “failure” is simply that the DNA is so different that it can’t align. Thus, “technical failures” are prima facie evidence of real differences between the genomes.

The second response—which is far more common—seeks to dismiss these newly discovered genetic differences between humans and chimps as mere junk DNA. These critics don’t dispute the basic evidence showing that humans and chimps are 15 percent genetically different. They just claim these differences are meaningless. Intriguingly, many of the folks making this argument have views that align closely with theistic evolution.

For example, Joshua Swamidass, a Christian biologist at Washington University in St. Louis and defender of human-chimp common ancestry, argued that much of the human DNA that doesn’t align with chimp DNA is “trivial” because it is “repetitive” and represents mere “cut-and-paste repetitions.” Joel Duff, a Christian theistic evolutionist, YouTuber, and biology professor at the University of Akron, admits that human and chimp genomes might be 15 percent different. But he states that the non-alignable DNA largely “makes no difference” because repetitive DNA differences “don’t even do anything” and therefore the 14.9 percent statistic is “a meaningless number.” Another Christian biologist and evolution-supporter, Zachary Ardern, claims that “not all unaligned regions are real differences” and compares differing numbers of copies of DNA repeat sequences to a “typo” that is not relevant “in terms of functional information.”

In other words, these critics assume that the repetitive DNA that’s different between humans and chimps is junk—and that having one copy of a repeat is functionally no different from having two copies or three copies or four. Added copies are just the result of “cut-and-paste” and don’t make any difference. And because they think it’s junk, they would have us believe that we can dismiss much of the newly discovered genetic differences between humans and chimps as “meaningless.” But the critics don’t really know that this is true—they’re just parroting the language of the highly dubious evolutionary junk DNA mindset (see articles in Salvo 31, 32, 33, and 34, where I wrote about “The Encode Embroilment”). And indeed, much science contradicts their claims.

A new paper in Nucleic Acids Research—published by some of the same researchers involved with sequencing these new complete ape genomes—shows that the critics’ arguments are wrong. The researchers studied the precise repetitive DNA that is different between humans and chimps and found that it can perform a myriad of functions, including structural roles as “non-B” DNA,⁹ which is known to contain “important regulators of cellular processes” and to have “unequivocal importance for genome function.”¹⁰

In short, differences in the number of copies of repeat sequences can affect the 3D shape of chromosomes, such as the size and shape of DNA loops, which can in turn influence transcription factor binding, gene expression, and other genome functions. So when critics dismiss repetitive DNA differences as junk, they’re not just making an argument from ignorance. They’re contradicting science that we know to be true.

A final response has been to try to distract from the evidence by changing the topic. Specifically, critics have cited genetic differences within the human species, which can be up to 10 percent in some cases. This is an interesting question, but it’s entirely irrelevant to the subject of genetic differences between humans and apes. For decades, prominent evolutionary voices have used the supposed “1 percent” genetic difference between humans and chimps as an argument for human-chimp common ancestry. We now know their numbers were wrong—by more than an order of magnitude. Discussing human-human intraspecific genetic differences is interesting, but it can’t rescue this icon of evolution.

“Zombie Science”

Jonathan Wells predicted these types of responses—he predicted that evolutionists would keep defending their icons even in the face of contrary evidence. He even quipped that these icons are like “zombies”—they don’t die easily but rather keep being repeated and defended, long after they have been refuted.

If that’s true, then don’t expect the 1 percent statistic to go away anytime soon. Nonetheless, the old 1 percent human-chimp genetic difference myth is now the latest icon of evolution to be refuted.

May it rest in peace.

Notes
1. Yoo et al., “Complete Sequencing of Ape Genomes,” Nature, 641: 401–418 (2025).
2. Lukas Kuderna, “Complete Ape Genomes Offer a Close-Up View of Human Evolution,” Nature, 641: 313–314 (2025).
3. “What Does It Mean to be Human?” Smithsonian National Museum of Natural History.
4. Chris Gunter and Ritu Dhand, “The Chimp Genome,” Nature 437, 47 (Sep. 1, 2005).
5. “What Does the Fact that We Share 95 Percent of our Genes with the Chimpanzee Mean? And How Was This Number Derived?” Scientific American (Mar. 1, 2004).
6. “DNA: Comparing Humans and Chimps,” American Museum of Natural History, Hall of Human Origins.
7. Ann Gibbons, “Bonobos Join Chimps as Closest Human Relatives,” Science (Jun. 13, 2012).
8. Stefan Lovgren, “Chimps, Humans 96 Percent the Same, Gene Study Finds,” National Geographic (Aug. 31, 2005).
9. According to Google’s AI, non-B DNA “refers to any DNA structure that deviates from the standard double helix form. Non-B DNA structures are not just structural oddities; they play important roles in various cellular processes.”
10. Smeds et al., “Non-Canonical DNA in Human and Other Ape Telomere-to-Telomere Genomes,” Nucleic Acids Research, 53: gkaf298 (Apr. 14, 2025).

Stalled at the Smithsonian by Casey Luskin

An exhibit on human origins at the Smithsonian’s National Museum of Natural History (NMNH) in Washington, D.C., vastly overstates the genetic similarity between humans and apes and needs to be corrected. “There is only about a 1.2 percent genetic difference between modern humans and chimpanzees,” declares the NMNH’s Human Origins exhibit. It continues, claiming: “You and chimpanzees: 98.8% genetically similar.” On May 27, 2025, I contacted the Smithsonian urging them to correct the exhibit:

I’m writing to request corrections to statements at the Human Origins exhibit (“Exhibit”) at the Smithsonian Institution’s National Museum of Natural History (“NMNH”) about the degree of genetic difference between humans and apes, which are no longer scientifically accurate…. [T]he Exhibit asserts the following statements as fact:

(1) Humans and chimpanzees are “98.8% genetically similar.”

(2) Humans and gorillas are “98.4% genetically similar.”

(3) Humans and orangutans are “96.9% genetically similar.”

According to data reported in a scientific paper, Yoo et al. (2025), recently published in Nature, these statistics are scientifically false.

My letter ended stating: “I urge you to correct the Exhibit to reflect more current, accurate scientific data.”

Soon thereafter I received a reply from Smithsonian’s Director of Public Affairs, Randall Kremer, as follows:

Understanding of evolutionary science continues to expand based on scientific discovery and advances in technology. The museum’s exhibit panel presents genetic similarity between humans and a variety of organisms across the diversity of life. Our review of the Nature paper will continue to factor such new discoveries into relevant updates to the hall.

In other words, we’ll see. In the meantime, I’m not getting my hopes up too much for a correction, and the public continues to be misinformed about the scientific evidence.