We’ve been discussing an important new paper in Nature, “Complete sequencing of ape genomes,” which reports data showing that the human and chimp genomes aren’t merely 1 percent different, as we’ve often been told, but are more like 14 to 15 percent genetically different. This 1 percent statistic has been an “icon of evolution” — a piece of evidence that is widely believed and used as an argument for evolution, even though it is false (and, in this case, actually says very little about evolutionary claims). 

Remember how I predicted that despite this new evidence, “Don’t expect the 1 percent statistic to go away anytime soon”? Well, we’re already seeing that prediction come true, as some folks are continuing to defend the now-refuted icon of evolution. The most ironic part is that many critics admit the new Nature paper shows humans and chimps are genetically 15 percent different, yet just can’t let go of the 1 percent statistic. 

This is remarkably similar to how evolution defenders responded to the refutation of another evolutionary icon, the old Haeckel’s embryos. Eugenie Scott admitted that Haeckel’s drawings were “fudged” and “not to be relied upon,” yet she defended their re-use in textbooks because she claimed they “illustrate a point” and “the basic point that’s being illustrated by the drawings is still accurate.” 

Authorities Support Our Calculations 

Before we dive into what critics are saying, I want to note that good authorities have come to similar numerical conclusions as I did. Richard Buggs, Professor of Evolutionary Genomics at Queen Mary University London, has written on the subject with posts on X and at his personal blog. He was not an author on the original Nature paper, but he is thanked there in the first line of acknowledgments. So clearly he knows something about the topic. 

Buggs wrote on X when the paper was first released back in April: “First complete sequencing of chimpanzee genome finds 12.5% difference with human genome (for non-sex chromosomes).”

He also posted an article on his blog stating:

When the latest human genome assembly was used as a target, and the latest chimpanzee assembly was aligned to it, the authors report gap divergence of 13.3% and single nucleotide variant divergence of 1.6% (these results can be found in Supplementary Figure III.11 and 12 respectively, for hg0002 vs PanTro3).

As I understand their methods, gap divergence was based on counting base (A, T, G or C) positions in the human genome that have no aligning base from the chimp genome in the whole genome alignment. Single nucleotide variant divergence was based on counting bases that align to a different base (e.g. an A aligning to a T). The authors calculated these divergences for each 1 million base segment[s] of the human genome then averaged them all to get a genome-wide figure.

Adding the average gap divergence and average single nucleotide variant divergence together gives a total difference of 14.9%.

Thus, as I understand it, for the latest assemblies, 85.1 % of the nucleotides in the human genome have one-to-one exact matches in the chimpanzee genome.

Note what Buggs did: he took the gap divergence of 13.3 percent and the single nucleotide variant divergence of 1.6 percent, and added them together to get “a total difference of 14.9%.” This is encouraging because it represents the exact number that I calculated in my own analysis, here! When a professor of evolutionary genomics, thanked in the acknowledgments of the technical paper, comes to the same result that I did using basically the same methods, it seems I can’t be completely off. 

What Are the Critics Saying?

In any case, Professor Buggs and I have received some pushback from folks who are apparently reluctant to relinquish the old 1 percent statistic. We’ve received a couple of critical inquiries as well. These responses can be boiled down to the following classes:

1. The alignment failures are due to “technical” problems rather than biological processes.
2. The vast majority of the divergent DNA between humans and chimps (e.g., repetitive DNA) is just junk so we can ignore it. 
3. We can’t trust the new ape genome assemblies.
4. Try to change the subject and talk about something else (specifically, human-human genetic differences).

Again, what’s ironic is that the critics generally acknowledge that the new data shows humans and chimps are 15 percent genetically different; they are just trying to find ways to dismiss that number as unimportant. 

The problem is that each of these objections is weak, and we have good rejoinders. Even if they have some relevance in some cases, they are no longer overriding considerations, and we have very strong reasons to think that the overall picture is that humans and chimps are far more genetically different than was previously thought. In a series of posts to follow, I will address each in turn.