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Gibber! Gibber!

Chugley

Humans and chimpanzees are NOT 99% identical

The final nail in the coffin of human evolution

by Robert Carter

The first estimates of human-chimpanzee genetic similarity were made in the 1970s. DNA from the two species was mixed and repeatedly heated and cooled in a test tube. By passing light through the tube, the amount of DNA alignment was estimated by how cloudy the solution became at different temperatures. This gave us the first claims of “98 to 99%” identity.¹ John Ahlquist, whom we interviewed in Creation magazine, was one of the main researchers on that project. The problem with this method, he realized, is that it only measured the DNA that would align. Huge areas of dissimilar DNA could exist, and they would not have been able to see it.²

Most evolutionists simply accepted the “98 to 99%” figure without question and it has been broadcast across essentially all media platforms ever since. The only serious challenge came from the creationist community,³ with only an occasional admission from the evolutionary side. In one of those, the author acknowledged the “myth of 1%” and said that the real number is much less.⁴

Everything seemed to go in circles for a long time. Then evolutionary biologist Dr Richard Buggs wrote a blog post in 2018 where he concluded that less than 85% of the human and chimpanzee genome matched letter-for-letter.⁵ This was based on a paper he was about to publish with one of his newly minted PhDs, Josiah Seaman.⁶ That paper seemed to indicated a 96.6% similarity, but that occurs only after cutting out the centromeres, telomeres, all copy number variations, about 300,000 small insertions and deletions (accounting for about two million letters in each genome), and an additional percentage of DNA that resisted alignment.²³ Yes, humans and chimpanzees do share a lot of DNA, but when you include what they don’t share, the percent identity drops significantly, into the low 80% range.

New study with complete data

All this prior work (by Drs Ahlquist, Tomkins, Buggs, etc.) was based on incomplete sequencing. We did not have a fully sequenced human genome until the summer of 2023,⁷ let alone a high-quality chimpanzee genome. Indeed, the early versions of the chimpanzee genome were even assembled on a scaffold of the human genome, automatically making them look more human like. However, a major new study has completed each great ape genome to a very high standard.⁸ Like the newest human genome, they are (nearly) complete, from one end to the other. Older versions had major gaps, had faked centromere data, and were highly problematic around the numerous repetitive regions. These ‘telomere-to-telomere’ versions solved these problems.

The assembly of these genomes was no trivial matter. Even after all that work, they had to develop a filtering protocol that rejected certain DNA variants, and they had to hand-curate multiple sections that did not ‘behave’.

The alignment was even more difficult. They identified 175 inversions larger than 10,000 nucleotides, one chromosome fusion, and one large translocation.⁹ They also saw 632 inversions that were unique to one species only.

Analyzing the data

The ‘percent difference’ data are reported in Yoo et al.’s supplemental information (figure 1).

They did not provide any error bars, just the average for each genome pair. They also broke up the data among the autosomes and the X and Y chromosomes. The blue bulges on the right in figure 1 represent giant gaps in the Y chromosome alignment. The purple bulges on the bottom represent the differences found among the two genome copies within the same individual. I worked up their data to get a complete estimate of divergence between the species (figure 2).

From that, it was possible to generate a bar chart that showed the within- and among-species differences (figure 3).

99%? Not even close!

This is a big deal. First, many commentators have claimed this proves the human and chimpanzee genomes are only about 85% identical.^10,11,12 They are spot on, but you would not know that from the major headlines. Nor can you easily find the information in the published paper. Instead, you must drill down into more than 100 pages of detailed supplementary information to find the relevant information.

Second, creationist researchers like Dr Jeffrey Tomkins have been vindicated. While the earlier studies were stymied by a lack of trustable sequence data, the newest genomes show how different we are from all apes.

However, third, there are vast stretches of sequence that are nearly identical between humans and chimpanzees. At random, I found one that stretched for several hundred thousand bases and was nearly 99% identical.¹³Our opponents will misdirect and obfuscate to their dying breath.

Fourth, our opponents will misdirect and obfuscate to their dying breath. Case in point, in a recent video a commentator named Gutsick Gibbon claimed that I agree with her about human-chimpanzee similarity.¹⁴ No, while I agree with her that Tomkins is human and made mistakes (I have also pointed out glaring mistakes in her work and several errors in my work as well¹⁵), I do not agree with her that humans and chimpanzees are highly similar.

Fifth, God could have created us 99.9999% identical to chimps, or he could have made us 50% identical, or even less. The biblical creation model makes no prior claim on this. We should expect a high similarity because of the obvious structural, behavioural, physiological, and nutritional similarities between us. But how much? Nobody can know! Note that the evolutionary community was also unable to come up with an estimate before the numbers were run. They have no prior commitment to which ape species would be more like us. The debate about which species was more genetically like us lasted until the 1980s. Many people wanted orangutans to win and resisted the notion that chimps were our evolutionary cousins. Some paleontologists were arguing for the primacy of orangutans as late as 2009, although by that point they were a very small minority.¹⁶

The four numbers

Finally, there are four things that we need to know:

1. What is the percent similarity among the parts that align?
2. What is the percent similarity when you include the parts that don’t?
3. How many mutations must have occurred over evolutionary time to account for these differences?
4. How long would it take to functionally integrate new mutations into the genome?

The answer to the first question is now known: about 98%. The answer to the second question is also now known: about 85%. That third question is now where the debate should be, and the fourth question might be the biggest Achilles’ heel of all for evolutionary theorists.

The evolutionary model here is unlike ours in that it is ‘one-tailed’. They will gladly accept high similarity levels, but there is a cliff on the other side of the argument. If we are too dissimilar, they cannot explain the differences in their 6.5 million years. They do have the ability to back up the time to the most recent common ancestor, but even that ability is limited. A few years ago, some scientists were arguing for 13 million years.¹⁷ Some wanted to push the time even further back, but the paleontologists would have none of that because that would necessitate putting early apes in with the dinosaurs. They are stuck. The difference must be low. Period.

How much ‘difference’ can they explain?

Given an evolutionary conveyor belt of new mutations entering in, old mutations being removed by selection and drift, and really old mutations going to ‘fixation’ (i.e., 100%), they expect the mutation rate to approximate the fixation rate.

Here’s how the calculations work out:

• Given a haploid mutation rate μ, the number of new mutations per generation is simply 2Nμ, where N is the population size.¹⁸
• For a new neutral mutation, the probability of fixation is proportional to its frequency in the population. Since there are 2N copies of the genome in the population, and since, by definition, a new mutation starts in one copy of one chromosome, the frequency of that mutation is 1/(2N).¹⁹ The rate of fixation (r) would be proportional to the number of mutations that appear (2Nμ).
• Thus, r = 2Nμ/2N = μ

If the mutation rate is 100 per individual per generation, that equates to 50 mutations per haploid genome per generation. They would thus expect the human genome to accumulate 50 fixed differences per generation.²⁰ Over 6.5 million years (~300,000 generations) they would expect 15 million differences between each species and our common ancestor, or about 30 million differences between us and them today.

30 million differences / 3 billion letters = 1%

THIS is why they have been quoting that 1% figure all these years, and this is why they have been resisting anything else. If the number is much greater, things do not work out in their favor. When the difference grows past that level, their models break down. It is simply too hard to explain so many differences, even in their ‘millions of years’ mindset.

But even a 15% difference could still be explained if large insertions and deletions cause sudden changes. Consider that the chimp Y chromosome is only half as long as the human Y. Does that amount to 30 million differences, or one? For example, if a single deletion erased the heterochromatic arm of the chimp Y chromosome, a 0.5% difference between our two genomes would instantly appear. What other large changes could be effected by such things?

Yet, we are not talking about changes in ‘junk DNA’. Multiple functional genes are in the unaligned regions. Even though about 99% of human genes are found in the other species, Yoo et al. found 185 gene families unique to humans and from around 1,400 to 2,000 gene copy-number differences among the species.²¹ True, many of the duplicated areas deal with highly repetitive, non-coding DNA, but these areas have increasingly proved to be functional, as we and others have pointed out many times.²² There are also fully functional genes in these areas, specifically ones that deal with brain function.²³ About 55% of each genome, on average, is composed of repetitive elements (LINEs, SINEs, LTRs, etc.).²⁴ These, too, are proving to have functions, so they cannot be ignored in any comparison.

Given many millions of point mutations and tens of thousands of insertions, deletions, inversions, and duplications, can they explain this in an evolutionary context? They can explain some in their models, but those models are often quite simplistic (like the equations above). Random mating is a critical assumption, but it is never true, and non-random mating only slows down how fast new variants spread. There are also questions about population growth and how it affects all calculations. Given that the human population has been expanding (since the Flood or since the invention of agriculture, take your pick), ZERO genetic variants have become fixed in the human genome for the last 10,000 years in the evolutionary timeline. How does ‘no evolution for 10,000 years’ affect the evolutionary forecast?

But the fourth question above is perhaps the most fundamentally important question in evolution. Why? Because evolution needs new genes to arise and activate. Humans and chimpanzees do not just differ at the nucleotide level. Our genes are not used in the same ways and our brains have very different wiring pathways. Those changes would not just have to arise. No, they would have to arise, spread out and replace whatever original gene was in that place, and then integrate themselves into the already complex regulatory processes that exist.The ‘fact’ that they have been trumpeting from the rooftops since the 1970s turns out to be no fact at all. The real difference is NOT 1%. No, it is 15x greater.

This is a massive problem even for the “1%” crowd. Now that we know the human and chimpanzee genomes are more than 10 times more different than they thought, the problem of evolution only becomes that much more difficult. This is one of the greatest scientific discoveries that supports the biblical creation model. It does not mean, however, that evolutionists will never be able to explain what we see. It does mean, though, that they will be scrambling for cover. The ‘fact’ that they have been trumpeting from the rooftops since the 1970s turns out to be no fact at all. The real difference is NOT 1%. No, it is 15x greater.

Published: 3 July 2025

References and notes

1. See the discussion in Carter, R.W., Reassessing human–chimpanzee genetic similarity, J. Creation 38(1):93–103, 2024. Return to text.
2. This was one of the things that broke the Darwinian mindset and caused him to turn to the Bible. See Wieland, M., Convert to creation: Margaret Wieland interviews bird expert and former renowned evolutionist Dr Jon Ahlquist, Creation 40(3):36–39, 2018. Return to text.
3. Tomkins, J. and Bergman, J., Genomic monkey business—estimates of nearly identical human–chimp DNA similarity re-evaluated using omitted data, J. Creation 26(1):94–100, 2012. See ref 1 for a fuller list of citations. Return to text.
4. Cohen, J., Relative differences: the myth of 1%, Science 316(5833):1836, 2007. Return to text.
5. Buggs, R., How similar are human and chimpanzee genomes? Richardbuggs.com, 14 Jul 2018. Return to text.
6. Seaman, J. and Buggs, R., FluentDNA: nucleotide visualization of whole genomes, annotations, and alignments, Frontiers in Genetics 11:292, 2020. Return to text.
7. Rhie, A. et al., The complete sequence of a human Y chromosome, Nature 621(7978):344–354, 2023. Return to text.
8. Yoo, D. et al., Complete sequencing of ape genomes, Nature 641(8062):401–418, 2025. Return to text.
9. Yoo et al., ref. 7, supplementary information, p. 101. Return to text.
10. Luskin, C, Letter to the Smithsonian: Correct your signage on human-chimp genetic similarity! evolutionnews.org, 27 May 2025. Return to text.
11. Buggs, R., How much of a human genome is identical to a chimpanzee genome? richardbuggs.com, 6 May 2025. Return to text.
12. Tomkins, J.P., Chimp genome markedly different from human, icr.org, 29 May 2025. Return to text.
13. Carter, R.W., Reassessing human–chimpanzee genetic similarity, J. Creation 38(1):93–103, 2024. Return to text.
14. Gutsick Gibbon, I killed this creationist argument, youtube.com, 28 May 2025. Return to text.
15. Carter, R., James 3 vs the anticreationists, biblicalgenetics.com, 16 Jan 2024; youtube.com/watch?v=FIY7FTTFZyg. Return to text.
16. Grehan, J.R. and Schwartz, J.H., Evolution of the second orangutan: phylogeny and biogeography of hominid origins, J. Biogeogr. 36(10):1823–1844, 2009. Return to text.
17. Venn, O. et al., Strong male bias drives germline mutation in chimpanzees, Science 344(6189):1272–1275, 2014. Return to text.
18. The formula includes a “2” because the genome is diploid. The mutation rate is usually given as the haploid mutation rate, for historical reasons. Return to text.
19. Again, a 2 is in the denominator because there are two copies of the genome per individual in diploid species. Return to text.
20. Given random mating, which never happens, and a stationary population size, which is clearly not true for humans. Without these assumptions the evolutionary model cannot deliver even a 1% difference. Return to text.
21. Yoo et al., ref. 7, supplementary information pp. 66–67. Return to text.
22. See our ‘Vestigial’ Organs Questions and Answers. Return to text.
23. Kuderna, L., Complete ape genomes offer a close-up view of human evolution, Nature 641(8062):313–314, 2025. Return to text.
24. Yoo et al., ref. 7, supplementary information p. 78. Return to text.