Humans and chimpanzees are 99.4% identical…or are they?

Are humans and apes essentially identical? The answer to this question will depend heavily upon the philosophical assumptions one brings to the data.

Recently, the city buses in my neighborhood gained a new set of brightly-colored advertisements along their sides. In bold letters, they proclaimed that humans and chimpanzees are 98% identical: “Come and meet your relatives.”1 I’m not sure how effective these advertisements were at attracting visitors to the new monkey display being advertised, but they made an impression on my seventh-grade daughter. When precise-sounding statistics like this make it into advertising campaigns, they are likely to be lodged in the minds of everyone from children to grandparents. But where do these numbers come from? And what do they really mean?

Even a cursory examination of the percentages given for human and chimp genome similarity quickly reveals that any perception of precision is an illusion. The 98% number appears commonly,2 but so do other numbers. For example, 99.4% is another published figure that sounds more precise and makes humans and chimps even closer.3 When comparing portions of the chimpanzee and human genomes, one paper suggested they are 98.77% identical.4 On the other hand, some early published comparisons of portions of the human and chimpanzee genomes lowered the estimate to 95%.5

When a draft copy of the more or less complete chimpanzee genome was published in 2005,6 the conclusion was that the human and chimpanzee genomes are 96% similar. Despite the fact that this estimate is significantly lower than most previous ones, this new number prompted Emory University primate scientist Frans de Waal to proclaim, “Darwin wasn’t just provocative in saying that we descend from the apes – he didn’t go far enough… We are apes in every way, from our long arms and tailless bodies to our habits and temperament.”7

Of course Darwin did go quite far enough without the aid of modern DNA sequencing technology. The oft-proclaimed mantra that he never said humans descended from apes8 is simply untrue. In The Descent of Man, Darwin dedicates the whole of chapter 6, “On the Affinities and Genealogy of Man,” to making the argument that humans are apes and therefore, like all other apes, descended from the common ancestor of all apes, which was an ape itself. One of Darwin’s greatest supporters, Thomas Henry Huxley, had made this argument in print by at least 1863,9 only four years after the publication of Darwin’s The Origin of Species and well before Darwin published The Descent of Man.

Within the confines of Darwinian thinking, similarities between organisms, often referred to as homologies, are treated as evidence of common ancestry. Thus, two organisms that have more things in common than some third organism are thought to have a more recent common ancestor than either does with the third creature. For example, frogs and cows both have camera-type eyes, four legs and many other features in common, and earthworms lack these traits; thus, frogs and cows, according to Darwinian thinking, have a more recent common ancestor than either does to worms. When dealing with DNA sequences, the same logic is applied: when chimpanzees and humans are found to have more DNA in common than either does to other organisms, this is seen as powerful confirmation of Darwin’s ideas. But DNA has an extra panache to it in that it is the very genetic material that is passed from parents to offspring.

Viewed from a creationist perspective, DNA similarity between humans and chimpanzees is hardly surprising. Of all the animals, chimpanzees and gorillas are clearly the ones that most resemble humans. It would be startling to discover that the Creator went back to the drawing board and drew up a completely different code for chimpanzees. This would be illogical, something like noting that Toyota Camrys and Corollas look similar and then predicting that the engineering plans for them must be completely different. Apes look more like humans than cows do because, among other things, their DNA is more like humans. Thus, while DNA sequence similarities appear to be exactly what creationists and evolutionists would expect, some Darwinists act as if they are somehow confirmation of Darwinian thinking and thus disproof of creationism.

How differences between genomes came to be

A far more interesting question, one that creation readily explains and Darwinism claims to explain, is how differences between the human and chimpanzee genomes came to be. Understanding this requires knowledge of the various classes of differences that may exist between any two genomes. Figure 1 summarizes some of these differences. While analogies with language are not perfect, there are enough similarities between the way in which DNA encodes information and the way letters encode information in the English language that a general illustration is possible of the problems inherent in deciding how similar two sequences of DNA are can be made using English examples.

Remember that DNA is spelled out in molecular “letters” called bases. Unlike English, there are only four letters in the DNA “language,” abbreviated as A, T, G and C. Now, imagine two DNA sequences:



There are a total of six letters in each sequence, and sequence 1 and sequence 2 only differ by two bases, the first and the last bases in each sequence. If only the number of letters in common were being compared, then these sequences would be 2/3, or 67% identical. A similar example in the English language would be the words “dad” and “had”; they also are 67% identical if you only look at the letters, but their meanings are completely different. In the DNA example above, if these two sequences were part of a protein-coding gene, they would have completely different meanings. When coding for a protein, DNA uses words called “codons” that are all three bases in length. Each codon codes for one amino acid and proteins are simply specific sequences of amino acids that have been joined together. In this particular case, GAA in sequence 1 means the amino acid glutamic acid (glutamate), and TGC10 means a very different amino acid called cysteine. The codons in the second sequence, TAA and TGA, even though they differ by one base each from the codons in DNA sequence 1, have completely different meanings. In fact, neither codes for an amino acid at all. These codons are called stop codons, as they act like periods at the end of a sentence in the DNA language. They signal where the DNA coding for a protein ends.

The take-home lesson from this is that relatively small changes in DNA can make a very big difference. This is a common feature of both DNA sequences and words spelled out in English. Sometimes just moving a letter to a different position in a word can make a huge difference. In DNA, the codons GGU and UGG both code for amino acids, but the first one codes for the simplest amino acid, glycine, while the second codes for tryptophan, which is among the largest and most complex amino acids. An example in English would be simply moving the c in “creation” and making the completely different-meaning word “reaction.”

Let’s look at an example of two DNA sequences that differ by less than 1% but produce very different products. See figure 1.

There are 444 bases in each of these sequences, and they differ by only one base, the 20th one in the sequence (shown in bold).11 Thus, the sequence difference between these sequences is 0.225%; they are 99.775% identical, and yet the first sequence codes for one of the proteins found in normal hemoglobin, while the second sequence codes for an abnormal protein that causes sickle cell anemia, a devastating genetic disease.12 The 0.225% DNA sequence difference translates into a 0.676% protein sequence difference, and this tiny difference causes profound illness. Not all changes of this magnitude have such a big impact, but this illustration serves to show that small DNA sequence differences can, and in fact do, amount to very big differences in organisms.

Are two sequences the same or different?

How does one really determine whether two sequences are essentially the same or totally different? Obviously, simply looking at individual letters will not be useful in determining whether two documents are different or the same. The exact same letters of the alphabet are used to encode the information in the King James Bible and The Origin of Species. When looking at DNA, exactly the same bases are used to code the information in humans and the little E. coli bacteria that live in our guts. When comparing books, many if not all of the words used might be the same, but the books can be clearly different. When comparing organisms, the codons used to code for proteins may be the same, but the organisms are different. Clearly, one important factor to take into consideration when comparing DNA sequences is the length of the sequences that are being compared. This is illustrated by the exercise given at the end of this article.

Another important factor to consider when comparing DNA sequences is the way information encoding how DNA will be expressed as proteins appears to be quite different from the way we express things in the English language. While it is common to think of DNA as mainly coding for proteins, this is not really the case: only about 3% of human DNA actually codes for proteins. In the past, the remaining 97% was thought to be simply flotsam and jetsam of the evolutionary process and essentially functionless “junk DNA.” More recently, it has become evident that much of this noncoding DNA regulates the production of proteins from the protein-coding regions, while other parts are involved in additional vital activities.13

Within the human and chimp genomes, much of this noncoding DNA is in the form of repeated sequences. It is hard to gauge the importance of these repeated sequences, or even to evaluate them, as they present unique challenges to modern DNA-sequencing techniques. Thus, even though we talk of the human genome sequence as complete, it is not really 100% completed. Because repeated sequences have been assumed to be unimportant, they have been ignored in some sequence comparisons. For example, in the studies on which the figure of 98% similarity between human and chimpanzee DNA are based, repetitive DNA was first eliminated and then the comparison was made.14 This is loosely analogous to comparing the words used in two books after removing the most commonly-occurring words in English,15 something that could clearly skew the outcome of any statistical comparison.

A further complicating factor when looking at comparisons of different organisms’ genomes is that the differences seem to be concentrated in specific areas in their genomes, not distributed randomly. For example, the human and chimp genomes exhibit such variation in how much difference exists between analogous segments that it has been suggested that the two organisms evolved into separate species once, then separated for several million years before coming together again about 6.3 million years ago,16 and then separating again.17 This variation in the amount of difference evident in sequences is not just at the DNA level, but also in specific genes coding for specific proteins. For example, a number of genes known to play a role in development of the nervous system are, unsurprisingly, more different than the average difference between human and chimpanzee genes. Darwinists attribute this to “positive selection” on those genes,18 but why this selection would operate on those genes dealing with intelligence in human ancestors and not those of chimpanzee ancestors is not obvious. It is hard to imagine that intelligence is adaptive in only humans and their ancestors. But these variations in the degree of difference between different segments of DNA are not restricted to individual genes or parts of chromosomes. There is a strikingly small difference between chimp and human X chromosomes compared to differences between the other chromosomes. Exactly how natural selection would do this is not immediately obvious, and seems to require some type of contorted story to make the data fit with Darwinian assumptions.

Role of proteins in living things

There is one other profound difference between the ways in which the human and chimpanzee genomes work, and this may have the greatest impact on why they do not produce essentially identical organisms. To understand this requires a slightly different way of viewing the role of the proteins in living things. DNA codes for proteins in much the same way as a set of specifications might define the kind of screws or other parts to be used in a machine. Many parts can be combined in different ways to make different kinds of machines. For example, if the slotted truss-head screw that holds together a pair of scissors was lost, it may be possible to replace it with a socket cap screw. Conversely, it may be possible to take the same parts, or very similar parts to those found in one machine, and combine them to produce a very different device. For example, a leaf spring, some screws, cabling, and a few other parts from a car could be combined to make an excellent crossbow.

What is the point of all this when it comes to the human and chimpanzee genomes? While it is tempting to think of the differences between humans and chimpanzees to be the result of differences between their respective proteins, in reality the differences probably result more from differences in how the protein parts are put together. This seems to be exactly what is seen when individual proteins are produced from information found in the human and chimpanzee genomes, respectively. It turns out that the genes are expressed in very different ways in different primates, including humans and chimpanzees. These differences in gene expression appear to be the result of differences in a subset of proteins called “transcription factors.”19 It should not be surprising to discover that Darwinists also attribute these differences to “positive selection.”

It is not just that the proteins themselves are combined in different ways to make different kinds of creatures; when it comes to chimpanzees and humans, the genomes themselves are put together in interestingly different ways. For example, during sexual reproduction, the DNA from both parents is shuffled much like a deck of cards to create the unique chromosomes that will go into the sperm and eggs and ultimately into the offspring of a couple. When this happens, DNA has to be physically broken and then joined together again. This process is complex and does not happen in random locations. The locations at which cuts and new combinations (recombinations) occur in chimpanzee chromosomes are different from those in human chromosomes.20

So are humans and apes essentially identical? The answer to this question will depend heavily upon the philosophical assumptions one brings to the data. In this article, I have sought to show that the numbers given for percent differences between the human and chimpanzee genomes lack the precision implied in their use. In addition, where one looks in the respective genomes makes a very big difference in the conclusions that one might draw. Finally, the way in which information encoded in DNA is translated into proteins and ultimately into living creatures is clearly profoundly different between humans and apes. If one wishes to do so, a strong case could be made emphasizing the abundant differences between human and chimpanzee DNA. In addition, it is worth noting that as more information comparing the genomes is published, the differences appear to be more profound than was thought even a few years ago. But it would be ridiculous to suggest that chimpanzees are not more similar to humans than frogs, fish, flies, or finches. In any group of objects or creatures, some must have more in common than others. The big question is really one of what one should conclude from these similarities and differences.

There is one other thing that should serve as a caution to those who wish to draw sweeping conclusions, and that is the disturbing way in which proponents of both Darwinism and creationism have used data in the past as they advocate their various positions. In our own church, there are a number of published statements that were probably not helpful at the time and seem disturbing today. For example, Uriah Smith argued on the front page of the Review and Herald that “[N]aturalists affirm that the line of demarcation between the human and animal races is lost in confusion. It is impossible, as they affirm to tell just where the human ends and the animal begins.”21 This line of thinking can also be found in later statements like that of Dores Robinson, secretary to Ellen G. White, who wrote, “Anyone who observes the chimpanzee, the gorilla or the orang, would not find it difficult to believe that they have some common ancestry with the human race… It is far more reasonable to believe that apes descended from man…”22 On the other hand, at least one Darwinist, based on his understanding of 98% similarity between the human and chimpanzee genomes, has advocated the horrifying prospect of creating human-chimpanzee chimeras, “Because in these dark days of know-nothing anti-evolutionism, with religious fundamentalists occupying the White House, controlling Congress and attempting to distort the teaching of science in our schools, a powerful dose of biological reality would be healthy indeed. And this is precisely the message that chimeras, hybrids or mixed-species clones would drive home.”23

The Bible is explicit about the special place of humanity in creation: “God created man in his own image, in the image of God created he him; male and female created he them” (Genesis 1:27). Because of its very nature and because we now “see through a glass darkly” (1 Corinthians 13:12), science cannot give definitive answers about the nature of humanity; its conclusions are invariably tentative and subject to the philosophical filter through which data are viewed. Even with those limitations, it is interesting to note that a clear trend exists, one that is evident in some other cutting-edge areas of science, and that is that as understanding increases and data accumulate, the bold assertions of the past, which appeared to be inconsistent with traditional biblical views, are called into question, while views consistent with biblical claims appear more tenable.

Timothy G. Standish (Ph.D., George Mason University) is a scientist at the Geoscience Research Institute, Loma Linda, California, U.S.A. E-mail:


  1. This statistic is repeated in many places, including the San Diego Zoo’s website:
  2. For another example, see: J. Marks, What It Means to Be 98% Chimpanzee: Apes, People, and Their Genes (Berkeley: University of California Press, 2002), 325 pages.
  3. D.E. Wildman, M. Uddin, G. Liu, L.I. Grossman, M. Goodman, “Implications of natural selection in shaping 99.4% nonsynonymous DNA identity between humans and chimpanzees: Enlarging genus Homo,” Proceedings of the National Academy of Sciences 100 (2003): 7181-7188.
  4. A. Fujiyama, A. Watanabe, A. Toyoda, I.D. Taylor, T. Itoh , S.F. Tsai, H.S. Park, M.L. Yaspo, H. Lehrach, Z. Chen, G. Fu, N. Saitou, K. Osoegawa, P.J. de Jong, Y. Suto, M. Hattori, Y. Sakaki1, “Construction and Analysis of a Human-Chimpanzee Comparative Clone Map,” Science 295 (2000): 313-334.
  5. R.J. Britten, “Divergence between samples of chimpanzee and human DNA sequences is 5% counting indwells,” Proceedings National Academy Science 99 (2002): 13633-13635.
  6. The Chimpanzee Sequencing and Analysis Consortium, 2005, “Initial sequence of the chimpanzee genome and comparison with the human genome,” Nature, 437: 69-87.
  7. Frans de Waal is quoted on the National Geographic News website at:
  8. For example, see W. Allen, Editorial, National Geographic, November 2004.
  9. T.H. Huxley, Evidence as to Man’s Place in Nature, 1863.
  10. For consistency and to avoid confusion, DNA is being referred to here. Note, however, that the codons are only translated into proteins using RNA copies of DNA, and in RNA uracil (U) is used in place of thymine (T), thus as RNA copies, this codon would actually read UGC, not TGC. The codons in sequence 2 would read UAA and UGA as RNA, and not TAA and TGA.
  11. The mature beta globin protein begins with the amino acid valine; the altered amino acid in beta S-globin is the sixth amino acid which is converted from glutamic acid in normal beta globin to valine in the mutated protein. The first amino acid coded for in the sequences given is actually methionine, but this amino acid is removed in the mature form of the protein.
  12. This disease is sickle cell anemia, which occurs at higher rates among people living in equatorial Africa and their descendents. In individuals with sickle cell anemia, red blood cells become elongated due to polymerization of hemoglobin when it loses oxygen. These sickle-shaped cells clog blood vessels and are broken down rapidly, resulting in organ damage and chronic anemia.
  13. T.G. Standish, “Rushing to judgment: Functionality in noncoding or ‘junk’ DNA,” Origins 53:7-30.
  14. C.G. Sibley, J.E. Ahlquist, “The phylogeny of the hominoid primates, as indicated by DNA-DNA hybridization,” Journal of Molecular Evolution 20 (1984): 2-15. See also: Sibley and Ahlquist, “DNA hybridization evidence of hominoid phylogeny: Results from an expanded data set,” Journal of Molecular Evolution 26: (1987): 99-121. It is worth noting that the work of Sibley and Ahlquist, despite being widely cited and serving as a possible source for the 98% identical claim, is controversial due to accusations of alleged data manipulation. See
  15. To appreciate the impact of this, look at or some other source that gives the most common words used in English.
  16. These are the numbers used in the scenario outlined in the paper reporting these results and are provided to illustrate the point, not as an endorsement of the idea that life is millions of years old.
  17. N. Patterson, D.J. Richter, S. Gnerre, E.S. Lander, D. Reich, “Genetic evidence for complex speciation of humans and chimpanzees,” Nature 441 (2006):1103-1108.
  18. C. Ponting, A.P. Jackson, “Evolution of primary microcephaly genes and the enlargement of primate brains,” Current Opinion in Genetics & Development 15 (2005): 241-248.
  19. Y. Gilad, A. Oshlack, G.K. Smyth, T.P. Speed, K.P. White, “Expression profiling in primates reveals a rapid evolution of human transcription factors,” Nature 440 (2006): 242-245.
  20. W. Winckler, S.R. Myers, D.J. Richter, R.C. Onofrio, G.J. McDonald, R.E. Bontrop, G.A.T. McVean, S.B. Gabriel, D. Reich,
  21. P. Donnelly, D. Altshuler, “Comparison of Fine-Scale Recombination Rates in Humans and Chimpanzees” Science 308 (2005): 107-111.

  22. Uriah Smith, “The Visions – Objections Answered: Obj. 37,” Advent Review and Sabbath Herald 28(9) (July 31, 1866): 65, 66.
  23. D.E. Robinson, “Amalgamation Versus Evolution.” Elmshaven, St. Helena, California. White Document File 316, Heritage Room, Loma Linda University.
  24. By P. David, D.P. Barash, “When man mated monkey,” Los Angeles Times, July 17, 2006.,0,1775276.story?coll=la-opinion-rightrail.