If Humans and Chimps Are 15 Percent Genetically Different, What Difference Does That Make?

Think about how often you've heard it said that the genetic difference between human beings and chimpanzees is only slightly more than 1 percent, and therefore humans are 99 percent similar to chimps.  It is also said that this proves that chimps--and also bonobos--are our closest living evolutionary relatives.  This seems to be confirmed by the fact that chimpanzees and bonobos are more genetically similar to humans than to gorillas.  This 1 percent difference between humans and chimps fits the evolutionary timeline of five to eight million years since humans and chimps diverged from their last common ancestor.

But now an article published last May in Nature (Yoo et al., 2025) reports that a complete sequencing of ape genomes shows that the genetic difference between humans and chimps is a lot greater than 1 percent--more like 15 percent!  And yet perhaps I shouldn't say this article "reports" this because if you read the main article, you won't see this claim of a 15 percent difference.  You have to go to the Nature website and print out the "Supplementary Data" for the article, and even then, you have to work through the technical jargon to find the 15 percent difference.  Casey Luskin has posted a helpful article at the Discovery Institute website that digs deep into the "Supplementary Data" to uncover this remarkable finding.  You would think that such a surprising discovery would be prominently announced in Nature and in press releases: "The Chimp-Human Genetic Difference Is Not 1% But 15%!"  I think Luskin is right to suggest that the editors at Nature must have worked hard to hide this finding because it refutes the popular claim about "only a 1% difference" separating humans and chimps.  

Luskin says this refutes one of the "icons of evolution," as Jonathan Wells called them--that is, widely believed assertions about evolution that the proponents of "intelligent design theory" and "young-Earth creationism" deny.  It's not surprising, therefore, that creationists like Ken Ham have cited Luskin's article as proving that the creationists are right to deny that there is any common evolutionary ancestry linking humans and apes.  Ham explains that Bible teaches us that God created the "ape kind" and the "humankind" separately and created humans as a unique kind made in the image of God.

And yet I don't see that this newly discovered "15% difference" provides any support for the intelligent design theorists or the creationists in their denial of evolutionary science.

But first we need to understand how this new research allows us to calculate genetic difference and similarity.  The title of the article in Nature is "Complete Sequency of Ape Genomes."  The emphasis is on "complete," because the first human and ape genome sequences were incomplete.  They excluded extremely repetitive sequences and large-scale structural differences such as inversions and duplications of genomic sequences.  So the first reports of only 1% differences between human and chimp genomes were based on incomplete drafts of the genomes.  But now the complete sequency in this article allows for a fuller comparison of similarities and differences in the sequences.

The authors found two kinds of differences--"gap divergence" and "single nucleotide variation" (SNV).

Luskin prepared this figure to illustrate the difference between "SNVs" and "Gaps" between two genomes.  Gaps represent nucleotides or segments of nucleotides that don't exist in one of the genomes.  SNVs represent places where the nucleotides are different for the two genomes.  In this illustration, we have 30 nucleotides of the target genome with 3 SNVs and 9 gaps relative to the query genome.  So SNV divergence is 10%, and gap divergence is 30%, which means a total divergence of 40%.

If you go to the Supplemental Data for the Yoo et al. article, you will see that Figure III.12 shows the SNVs in comparing the genomes for humans, chimpanzees, bonobos, and orangutans--the four "great ape" species who belong to the Hominidae family.  When the human genome is the "target" genome, the "gap divergence" for the gorilla genome is 27.3 percent, for the Sumatran orangutan it's 16.5 percent, for the bonobo it's 14.4 percent, and for the chimpanzee it's 13.3 percent. 

Figure III.11 shows the SNV divergences, which are 2 percent for the gorilla, 3.6 percent for the Sumatran orangutan, 1.6 percent for the bonobo, and 1.6 percent for the chimpanzee.

If we add the gap divergences to the SNV differences, we get these total degrees of difference between human and ape genomes: 29.3 percent for the gorilla, 20.1 percent for the Sumatran orangutan, 16 percent for the bonobo, and 14.9 percent for the chimpanzee.  That's how we get the estimate of almost 15 percent difference between the chimp and human genomes, which is a lot higher than the purported 1 percent difference.  

It should be noted that these comparisons are for the 44 non-sex chromosomes in the human genome--that is, excluding the X and Y chromosomes.  As compared with chimps, the human X chromosome has a 4.4 percent gap divergence and 1.1 percent SNV divergence, while the human Y chromosome has an amazing 56.6 percent gap divergence and 3.9 percent SNV divergence.

Although this new research shows that the genetic differences between humans and apes are greater than had been previously reported, this does not deny the evolutionary story of the common evolutionary ancestry of humans and apes.  The genetic similarity between humans and apes is still very great--85 percent!  And humans are more genetically similar to chimps and bonobos than they are to orangutans and gorillas, which supports the claim that chimps and bonobos really are our closest living evolutionary relatives.

ALL IN THE GENES?  OR FOUR DIMENSIONS OF EVOLUTION?

There is an obvious problem here, however.  All of us have seen chimpanzees in zoos.  And many of us have seen bonobos if we have gone to zoos in San Diego, Milwaukee, or Cincinnati that have bonobos.  Those zoos often have displays that say something about the 1 percent difference between humans and chimpanzees.  Now those displays might have to be changed to read 15 percent.  But even so, when we look at those apes and compare them with humans, it's very hard to believe that the difference is only 1 to 15 percent.  It's simply not true that humans and apes are 85 percent the same.  The gap between the mental achievements of human beings and those of the apes is staggering.

Most human beings don't believe that evolutionary genetics can fully explain that gap, and that's why so many people reject the science of evolution, and why so many believe that the superiority of the human mind over the ape mind can only be explained by the supernatural work of an Intelligent Designer or Divine Creator.

They are right to believe that evolutionary genetics cannot fully explain the achievements of the human mind.  But that's because genetics is only a small part of evolutionary science.  As I have indicated in some previous posts, there are four levels of evolutionary inheritance--genetics, epigenetics, culture, and symbolism (Jablonka and Lamb, 2005).

The genetic inheritance system is the foundation for the Neo-Darwinian theory of evolution. But genetic reductionism and determinism fail to see how gene action depends on the complexity of interacting causes within the genome, within cells, within organisms, within groups of organisms, and within ecological circumstances. Except for a few single-gene genetic disorders, "genetic astrology"--the idea that genes directly control specific traits--must be dismissed as foolish.

The epigenetic inheritance system is evident in the differences between specialized cells. Brain cells, liver cells, and skin cells are very different, although the nucleus of each cell has the same genome. Their differences are epigenetic, rather than genetic, because they have arisen through their developmental history in which there were different patterns of gene activation and interaction within the cell. This developmental information is passed on as these cells divide to produce more cells of the same kind. It is possible for evolution to occur through heritable epigenetic variation even without genetic variation. Just as a musical recording transmits interpretations in musical performances of a musical score, so does an epigenetic inheritance system transmit interpretations of the information in DNA, so that there is a Lamarkian inheritance of phenotypes instead of genotypes. One version of such inheritance that is now under active study is DNA methylation: strands of DNA are chemically modified during development, and these modifications can be transmitted through reproduction.  The chemical modification in epimutation is not in the DNA itself but in the chromatin marking. Methylated DNA has a small methyl group attached to some of its bases. The pattern of methylation influences which regions of DNA are expressed. The different kinds of cells in the human body have the same DNA, but the different patterns of methylation regulate the expression of DNA.

The behavioral inheritance system is the transmission of information among animals through social learning. For example, among some animals (including human beings) mothers transmit food preferences to their offspring, because information about what mother is eating is transmitted either in the womb or through suckling, so that the offspring inherits a preference for that food. More complex forms of social learning come through animal culture. For example, some chimpanzees can discover how to open nuts with a stone and then pass on this practice within their group so that it becomes a social tradition. Different communities of chimps in Africa have different cultures based on distinctive profiles of traditional practices transmitted by social learning. As opposed to genetic evolution, cultural evolution is not blind but targeted to functional change.

The symbolic inheritance system is uniquely human because it shows the qualitative leap that defines our humanity as based on our capacity for symbolic thought and communication. Other animals can communicate through signs. But only human beings can communicate through symbols. The evolution of human language was probably crucial for the evolution of symbolism. Symbolic systems allow us to think about abstractions that have little to do with concrete, immediate experiences. Symbolic systems allow human beings to construct a shared imagined reality. These symbolic constructions are often fictional and future-oriented. Art, religion, science, and philosophy are all manifestations of human symbolic evolution. 

To explain why humans are somewhat similar to the great apes and yet radically different from them, we have understand how all four levels of human evolution have shaped human beings to be the unique animals that they are.

COMMON DESCENT OR INTELLIGENT DESIGN?  OR BOTH?

Although Casey Luskin is an advocate of intelligent design theory as the best alternative to evolutionary science, he stresses that he is not pointing to the new estimate of 15 percent difference between humans and chimps as evidence that refutes evolution.  As long as the five to eight million years since humans and chimps diverged from their last common ancestor is enough time for this 15 percent difference to evolve, then the evolutionary story of common ancestry is still defensible.  

But still, Luskin suggests, intelligent design theory has a better explanation for this genetic similarity--85 percent--between chimps and humans:  "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."

There are two mistakes in Luskin's reasoning, however.  First, he mistakenly assumes a dichotomy between common descent and common design, as if they were mutually exclusive.  As I have noted previously, one of the leading advocates of intelligent design theory--Michael Behe--argues (in The Edge of Evolution) that the genetic similarity between humans and chimps is evidence that human beings evolved from primate ancestors shared with chimpanzees.  He explains that intelligent design is required to explain the emergence of the higher taxonomic levels of life (kingdoms, phyla, classes) but not the lower levels (orders, families, genera, species).  This means that the evolution of species could be fully Darwinian.

Behe is an intelligent-design evolutionist, because he insists: "The possibility of intelligent design is quite compatible with common descent, which some religious people disdain.  What's more, although some religious thinkers envision active, continuing intervention in nature, intelligent design is quite compatible with the view that the universe operates by unbroken natural law, with the design of life perhaps packed into its initial set-up" (166).  Luskin refuses to recognize Behe's position.

Luskin is also mistaken, however, in assuming the plausibility of the arguments for intelligent design.  He thus ignores my objection that the arguments for intelligent design are fallacious in two respects.  First, intelligent design reasoning depends completely on the fallacy of negative argumentation from ignorance, in which intelligent design proponents argue that if evolutionary scientists cannot fully explain the step-by-step evolutionary process by which complex living forms arise, then this proves that these complex forms of life must be caused by the intelligent designer.  This is purely negative reasoning because the proponents of intelligent design can offer no positive explanation of their own as to exactly when, where, and how the intelligent designer caused these forms of life.  

The second fallacy is the subtle use of the fallacy of equivocation--in the equivocation between human intelligent design and supernatural intelligent design.  We have all had the experience of seeing how human intelligent agents create artificial products by intelligent design.  But it does not follow logically from this that we have all had the experience of seeing how supernatural intelligent agents create artificial products by intelligent design.

CREATED BY GOD IN HIS IMAGE?  OR EVOLVED IN THE IMAGE OF PRIMATES?  OR BOTH?

Ken Ham (2025) argues, on the contrary, that even if we have not seen with our own eyes God creating everything out of nothing, this has been revealed to us through the Bible; and part of that revelation is that God created all the "kinds" of plants and animals separately, and He created the "chimp kind" to be utterly different from the "humankind," which was created in His image.

But as I have said in my previous posts on Ham and his two museums in Kentucky--the Creation Museum and the Ark Encounter--he mistakenly assumes that he is conveying the clear meaning of the Bible and that the Bible's clear teaching is incompatible with Darwinian evolution.

The Bible says nothing about God creating apes and humans as separate "kinds."  The Book of Genesis never mentions apes.  Actually, in the whole Bible, the Hebrew word for "ape" appears only twice (I Kings 10:22, 2 Chronicles 9:21), and never in the context of creation.  And while Genesis speaks of God creating plants and animals "after their kind," it never identifies human beings as a "kind."  Consider Genesis 1:26--"And God said, Let us make man in our image, after our likeness."  The phrase "after our likeness" takes the place of "after their kind," suggesting that in being created in the likeness of God, man is not bound by a "kind."  So there is no Biblical basis for Ham to speak of "humankind."

Moreover, the Hebrew word min that is translated as kind in the King James Bible is ambiguous.  In the Latin translation of the Bible, min is translated as the Latin word species.  Consequently, for almost two thousand years, Biblical believers assumed that God's creating "kinds" meant that God created each "species" separately, and that each species was eternally fixed.  But then after Darwin published his Origin of Species in 1859, in which he argued against the "theory of special creation" that God had created each species separating, some Christians began to believe that the created "kinds" in the Bible referred not to "species" but to some higher level of taxonomy.  Then, in 1941, the Christian biologist Frank Marsh coined the word baramin (combining the Hebrew words for "created" and "kind") as the best term for "created kind."  He argued that a "created kind" was not at the taxonomic level of "species" but at or near the level of "family."  This allowed Biblical believers to accept Darwin's theory of the origin of "species" by natural selection while also believing that God had created the "families" of plants and animals to be fixed and separate.  So, for example, we could say that God originally created the "family" of the finches, but within the limits of that "family," the separate species of finches endemic to the Galapagos Islands evolved by natural selection to be adaptive to those islands.

Notice what this means for the taxonomic classification of human beings.  If the "kind" of human beings refers to their taxonomic "family," then in modern taxonomy, human beings belong to the "family" of Hominidae, which includes chimps, bonobos, gorillas, and orangutan.  Even the young-earth creationist Todd Wood (2010) accepts this Hominidae classification of humans with the great apes, although he identifies the "human holobaramin" as the genus Homo.

This idea of "created kinds" was crucial for Ham in solving an old problem with Noah's Ark.  If the Ark carried all the "kinds" of land-based plants and animals, how could the Ark be big enough to hold all of the land-based species--which could be numbered in the millions?

Ham's creationist researchers have solved this problem by calculating that among these land-dependent vertebrate species, there are fewer than 1,400 known living and extinct kinds (that is, families).  This allows them to estimate that Noah had to have fewer than 6,744 individual animals on the Ark.  Once these animals left the Ark, speciation by natural selection within kinds could create all the living and extinct species that we know today.  The Ham's Ark Encounter is designed to show how as many as 6,744 animals and 8 human beings (Noah and his extended family) could survive on the Ark for almost a year.  But notice that this is a speculative reading of the Bible that never defines "kind" in this way.  This is not the clear meaning of the Bible, as Ham claims.  Indeed, if you go to the Ark Encounter in Kentucky, you might notice one display that speaks of the need for "Arktistic license" in making up details in the story of the Ark that have no basis in the Bible.

Since the Bible is so obscure in its creation story, and since so much of that story sounds like a figurative folk tale that was not meant to be a literal account of natural history, many Christians (like C. S. Lewis, Francis Collins, and Deborah Haarsma) have decided that the Bible could be read as allowing for theistic evolution or evolutionary creation.  According to this conception, God created the universal laws of nature at the beginning of the Universe, but then He allowed all the forms of life to emerge by natural evolution.  God is the "primary cause" of everything.  But the evolutionary process unfolds through the "secondary causes" of nature.  Even Darwin himself accepted this metaphysical conception of "dual causality" that reconciles belief in God as First Cause with acceptance of evolutionary science.  At various points in the Creation Museum and the Ark Encounter, there are displays that acknowledge that many if not most Christians accept some version of this theistic evolution.

But what about the creation of human beings in the image of God?  If the "image of God" refers to the God-like intellect of man, then we might argue that the extraordinary mental capacities of human beings could have evolved through the evolution of the primate brain.  I have argued that the evolution in the size and complexity of the primate brain passed over a critical threshold so that now there are 86 billion neurons in the human brain, and of that total, 16 billion are in the cerebral cortex, which includes 1.3 billion neurons in the prefrontal cortex.  That emergent evolution of the brain created the uniquely powerful human mind.  We were created in the image of the primate brain.

Even if we are only 15 percent genetically different from chimps, we are different in kind from chimps because we have the mental capacities for language, morality, and symbolic abstraction that they do not have at all.  That's the difference that makes all the difference.

REFERENCES

Behe, Michael. 2007. The Edge of Evolution: The Search for the  Limits of Darwinism. New York: The Free Press.

Ham, Ken. 2025. "Study Finds Chimp DNA Is Not '99% Identical' to Ours." Answers in Genesis. Ken Ham Blog. May 27. Online.

Jablonka, Eva, and Marion J. Lamb. 2014. Evolution in Four Dimensions: Genetic, Epigenetic, Behavioral, and Symbolic Variation in the History of Life. Revised edition. Cambridge: MIT Press.

Luskin, Casey. 2025. "Fact Check: New 'Complete' Chimp Genome Shows 14.9 Percent Difference from Human Genome." Science and Culture Today, May 21, online.

Wood, Todd Charles. 2010. "Baraminological Analysis Places Homo habilis, Homo rudolfensis, and Australopithecus sediba in the Human Holobaramin." Answers Research Journal 3: 71-90.

Yoo, Dong Ahn, et al. 2025. "Complete Sequencing of Ape Genomes." Nature 641: 401-418.