Feature Article - January 2003
by Do-While Jones

98% Chimp

Is our DNA really more than 98% the same as chimpanzees? And, if so, what does that really mean?

You have probably heard an evolutionist claim that chimpanzees and humans are almost identical genetically. Statements like the one below are common.

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. This means that a very small portion of human DNA is responsible for the traits that make us human, and that a handful of genes somehow confer everything from an upright gait to the ability to recite poetry and compose music. 1

We need to know two things. First, are their figures accurate? Second, if they are accurate, what does it mean? Is genetic similarity really evidence for evolution?


We have always been skeptical of the 98% figure because we know that 82.3% of all statistics used in debates are simply pulled out of thin air. smiley face (For the benefit of other readers who didn’t get the joke--certainly not you--we will explain the joke to them. It is very unlikely that anyone has ever done a study of debates in which statistics were used to make a point, and then gone to the trouble to determine if the statistics are based on studies or not. So, the humor in the joke comes from the irony that someone is pulling a statistic out of the air to prove that statistics are often pulled out of the air to prove a point.)

For decades scientists have known that at least 98% of human DNA is identical to that of chimpanzees. 2

But the human DNA sequence was just recently decoded. (It was published in the 16 February, 2001, issue of the journal Science.) Work on decoding the DNA sequence of chimps is just beginning. (See Monkey Business, in the Evolution in the News column in this issue.) How could they have been able to calculate the similarity of two sequences “decades” ago when neither had been decoded? How can they calculate it now when only one of them has been decoded? Did they just pull 98% out of the air?

Perhaps they compared the 46 human chromosomes with the 48 chimp chromosomes. They could not possibly have done that and come up with a figure exceeding 97.8%. Here’s why:

Let’s compare the chromosomes of a boy and his mother. A boy gets 23 of his chromosomes from his mother and 23 from his father. Clearly, at least 23 of the chromosomes will be identical to his mother. Therefore, the similarity will be at least 50%.

But one of the chromosomes he gets from his father must be different because his mother has two X chromosomes (if she didn’t, she wouldn’t be female), and the son has one X chromosome and one Y chromosome (because he is male). Therefore, at most, 45 of the 46 (97.8%) chromosomes will be identical.

So, the boy’s Y chromosome is guaranteed to be different from his mother. What about the other 22 chromosomes he gets from his father? Societies generally try to discourage incestuous relationships, and scientists have discovered that there is a good reason for this. It reduces the chance that a baby will inherit the same defective gene from both mother and father. If the boy’s father and mother come from unrelated families, it is almost certain that most of those 22 chromosomes will have at least one different gene.

So, if you determine genetic similarity by counting identical chromosomes, the genetic similarity of a boy to his mother is likely to be closer to 50% than 100%. “Scientists” certainly could not have found that humans and chimpanzees are 98% alike by counting chromosomes.

Of course we know that they didn’t count chromosomes when making the comparison. We only mention it to make the point that what you count will affect the result you get. You can use a method of counting that gives close to 50%, or you can use a different method that gives a much higher number.

Let’s look at some of the most recently published data comparing chimps and humans.

In this report we present the construction and analysis of a first-generation human-chimpanzee comparative genomic map based on the alignments of 77,461 chimpanzee bacterial artificial chromosome (BAC) end sequences (BESs) to human genomic sequences obtained from the public databases. To prepare the BESs, we used two independently prepared BAC libraries, PTB1 and RPCI-43. Briefly, we sequenced 64,116 BAC clones (roughly 3.3 times coverage of the currently available human contiguous genomic sequence) that produced 114,421 valid BESs. The BESs were then aligned with the RefSeq human genome contigs [National Center for Biotechnology Information (NCBI)] through NCBI-BLAST. The number of BESs having an alignment longer than 50 base pairs (bp) with 90% identity was 77,461. Out of this number, 49,160 BESs from 24,580 clones formed paired ends where each pair was derived from the same clone. Only one end could be successfully aligned from the remaining 28,301 clones. The remaining 36,960 BESs that were not mapped to the human genome were categorized into three different classes: (i) those corresponding to repeat sequences (1168 BESs) or showing hits to human sequences not included in the NT contigs (20,376 BESs), (ii) those matched only with sequences from several species other than human (515 BESs), and (iii) the 14,901 BESs that did not match with human sequences, which either correspond to unsequenced human regions or are from chimpanzee regions that have diverged substantially from humans or did not match for other unknown reasons. 3

Creationists are often accused of “carefully choosing their data.” We have never understood why evolutionists thought this was worse than carelessly choosing data, but we sometimes have trouble understanding how evolutionists think. smiley face If you understood nothing else in the paragraph quoted above, you must certainly realize that they went into great detail to justify the way in which they chose the data they actually analyzed.

We aren’t criticizing them for doing that. Scientists have to choose what data they analyze. One of the services I perform at my day job is real-time data reduction. My computer programs present pertinent data to the customer in graphical form, suppressing the irrelevant data, so that the customer can tell how his test is working while the test is still in progress. This gives him the opportunity to modify the test while it is still in progress, if necessary. There is nothing fundamentally wrong with analyzing only part of the data. You usually have no choice. You can’t analyze it all.

Fujiyama and his associates chose the data they were going to analyze. What they were looking for affected what they chose to study. Their goal was clearly stated in the abstract of their paper.

The recently released human genome sequences provide us with reference data to conduct comparative genomic research on primates, which will be important to understand what genetic information makes us human. Here we present a first-generation human-chimpanzee comparative genome map and its initial analysis. The map was constructed through paired alignment of 77,461 chimpanzee bacterial artificial chromosome end sequences with publicly available human genome sequences. We detected candidate positions, including two clusters on human chromosome 21 that suggest large, nonrandom regions of difference between the two genomes. 4

They were trying “to understand what genetic information makes us human.” To do that, they looked carefully at two small parts of just one of the 46 human chromosomes. There is nothing wrong with that.

Furthermore, they picked areas “that suggest large, nonrandom regions of difference between the two genomes.” That was perhaps a poor choice of words. They probably meant “significant regions of difference”, as opposed to “irrelevant regions of difference”. Evolution is supposed to work through random changes. If the changes were “nonrandom”, that implies they were part of a conscious design. They certainly didn’t mean to imply that! smiley face

They must have used their judgment to distinguish “nonrandom regions of differences” from random differences. One might wonder how they did that. It implies that they might have some criteria for differentiating design from random processes. Too bad we don’t have space to explore that idea in this essay!

Let’s be perfectly clear on this point. Fujiyama et al. were perfectly justified in selecting what part of the genome to study. They were looking for differences in very similar sequences, so they picked very similar sequences that had some interesting differences. That is perfectly good science.

They were not trying to most accurately compute the similarity of chimpanzee and human DNA. But they did mention some interesting numbers in passing which do pertain to genetic similarity. If you refer back to the extremely technical paragraph we quoted earlier, you will see that they produced “114,421 valid BESs”. Of these, they found “14,901 BESs that did not match with human sequences”. That means 13% of the sequences were totally different. In other words, only 87% of the sequences showed enough similarity for them to even attempt to match them.

Looking at the most similar sequences, they said, “The number of BESs having an alignment longer than 50 base pairs (bp) with 90% identity was 77,461 [out of 114,421].” So, they found that only 67.7% of the sequences were at least 90% correlated. If that is true, where does the 98% similarity figure come from? Later in the report they say,

The BESs mapped with high confidence were used to calculate the difference between the chimpanzee and human genomes at the nucleotide level. The number of sites in valid alignments (nucleotide sites that have PHRED quality values q >= 30) was 19,813,086. Out of this number, 19,568,394 sites were identical to their human counterparts for a mean percent identity of 98.77. This value is consistent with previous observations; however, our calculation comes from a much larger random comparison of slightly less than 1% of the total genome. 5

That explains it. If you look at less than 1/100th of the total genome, you can find areas that are 98.77% similar! But this is not always true.

For almost 30 years, researchers have asserted that the DNA of humans and chimps is at least 98.5% identical. Now research reported here last week at the American Society for Human Genetics meeting suggests that the two primate genomes might not be quite so similar after all. … The researchers assessed the resemblance between the chimp’s chromosome 22 and the equivalent human chromosome, 21. They compared 27 million bases, and “much to our surprise, we found around 57 areas of rearrangement between the human and the chimp,” says Cox.

There seemed to be no rhyme or reason to the changes; they occurred just as frequently outside coding regions as within. The density of these differences is “a little higher than anyone would have predicted,” says Eichler. “The implications could be profound,” he adds …

Locke’s and Frazer’s groups didn’t commit to new estimates of the similarity between the species, but both agree that the previously accepted 98.5% mark is too high. [emphasis supplied] 6

How similar is human DNA to chimp DNA? We don’t know; but the 98% number certainly doesn’t seem to be born out by recently published data.

Significance of Similarity

Having said all that, we admit that there is a certain amount of genetic similarity between humans and other animals. What does that mean? Is genetic similarity necessarily the result of evolution?

evaporative cooler

mounting bracket

The answer might be found in an evaporative cooler.

Those readers who are not fortunate enough to live in the Mojave Desert probably aren’t familiar with evaporative coolers. Evaporative coolers have large fans which suck hot air (more than 100 degree F) through wet fiber pads. The hot air evaporates the water, resulting in a heat transfer which cools the air down to 80 degrees F (or lower, if you are lucky). The fan blows the cool, moist air into the house.

The lower picture is a close-up of the bracket that holds the electric motor on the evaporative cooler on the roof of my house. When both screws (and two other similar screws on the other side) are loosened, the bracket can be rotated so that the distance between the motor and the fan can be adjusted to produce the proper tension on the fan belt.

There is an almost identical bracket that holds the alternator in my truck with the proper tension against the fan belt! This bracket represents about 1% of the total mass of the cooler, but it is 98.5% similar to the bracket that holds the alternator in my truck. Not only that, the fan belts are virtually identical. (Both are cracked and liable to break at any moment.) The pulleys are identical too. There is less than 1.5% difference between an evaporative cooler and a truck!

To understand how evaporative coolers evolved into trucks, we have to study the electric motor in the cooler, and the alternator in the truck. Externally, both look very similar; but the motor is wound for a single phase, while the alternator has three phases. This is evidence of gene replication. Furthermore, the alternator has evolved a six-diode bridge, which originally had some unknown survival benefit, but was later adapted to converting alternating current to direct current.

Despite the obvious similarities, there are many differences between a truck and an evaporative cooler, which prove that it has been a very long time since trucks and coolers shared a common ancestor.

Some people might say that trucks and coolers were designed by engineers, and that the similarity in the brackets is evidence of design. After all, it is a simple and effective method for adjusting belt tension. But if trucks and coolers were consciously designed, it must be the case that the engineers conspired to make it appear that both trucks and coolers evolved from a common ancestor. Therefore, if engineers really do exist, they ought not to be trusted because they are sneaky and deceitful people. smiley face

Seriously, chimps and people really do have very similar genes. But that doesn’t argue in favor of a common ancestor any more than it argues in favor of a common designer.

P.S. See Chimps Are Like Us for a different calculation of similarity.

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1 Gibbons, Science, Vol. 281. 4 Sep 1998, “Which of Our Genes Make Us Human?” pp. 1432-1434, https://www.science.org/doi/10.1126/science.281.5382.1432 (Ev)
2 ibid.
3 Fujiyama, Science, Vol. 295, 4 Jan 2002, “Construction and Analysis of a Human-Chimpanzee Comparative Clone Map” pp. 131-134, https://www.science.org/doi/10.1126/science.1065199 (Ev)
4 ibid.
5 ibid.
6 Science, Vol. 298, 25 October 2002, “Jumbled DNA Separates Chimps and Humans”, pp. 719-720, https://www.science.org/doi/10.1126/science.298.5594.719b (Ev)