Architect or ancestry?

Recent studies comparing primate DNA could disprove theoretical claims that only a 1% genetic difference separates humans and apes. The evidence could bolster the scientific case for intelligent design.

In April, Nature published the complete sequencing of the ape genome, the culmination of over two decades of work, with a side-by-side comparison to human DNA. Evan Eichler, professor of genome sciences at the University of Washington and a senior researcher on the project, joined the Human Genome Project in 2001.

Eichler later worked on the ape genome project, which he had wanted to finish since he was a student. He believes it holds the key to discovering what it means to be human. “In the case of chimpanzees and humans, we now know there are hundreds of genes that are unique to each of us, and those genes are important in terms of making us who we are,” he said. 

Earlier studies of ape genomes used human DNA to fill in the murky sections of ape DNA. “Think of it like a jigsaw puzzle, where we get all these big bits and pieces and then we’re trying to fit them against a map,” Eichler explained. “We used the human [DNA] to guide that. We aligned the parts that could be aligned and we did the calculations back then.”

Thanks to advances in computer programs capable of reading and sequencing long sections of DNA, a team of 123 National Institutes of Health–backed scientists and 60 research groups completed the ape genome “ab initio,” meaning “without any guidance to human reference,” Eichler said. New sequencing technologies mapped the genomes of the chimpanzee, gorilla, Sumatran orangutan, Bornean orangutan, siamang, and bonobo from scratch. Researchers discovered hot spots of genes in the apes that produce changes at rates 30 times higher than other areas and that don’t correlate to areas of rapid mutation in humans.

Humans have their own mutation hot spots. These regions “basically contribute to the building of a bigger brain in humans compared to other non-human apes,” Eichler said. “They lead to essentially an increase in synaptic connections. They lead to an increase in the number of neurons that are being produced … and so they make features of humans that are actually very unique.” Eichler said some of the same regions and genes that give humans an intellectual edge are involved in the genetic causes of autism, which motivates his research.

Darwinian evolutionary theory teaches that apes and humans evolved from a common ancestor, splitting off millions of years ago because of genetic mutations. Proponents of this theory use the study of the genome as proof because human genes align with the base pairs of chimpanzees more than any other ape. Earlier studies showed a 1.2% difference between human and chimpanzee DNA, but this calculation included human DNA, which was filling in the missing pieces of the ape genome.

This latest research provides the clearest comparison ever available, but Eichler doesn’t want to quantify the degree of difference. “It’s not a single number. It’s basically best thought of as two numbers. You know, 90% of the genome at 1%. And 10% of the genome at 12 to 15%. I don’t think those numbers are going to change.”

He says the way to think about it is that there are two parts to a genome: “a hot and a cold portion,” and “the rules and the mutation clocks are very different for these different areas.” Most of the genes are in the cold part, where the mutation rate is “clock-like.” The hot part is “the area that mutates 30 times faster,” where human and ape genes vary the most. “This is where we come up with these numbers of 12%, 13%, but these are estimates of gap divergence,” Eichler said.

Jeffrey Tomkins holds a doctorate in genetics and is a research scientist at the Institute for Creation Research. “I knew this day would come,” he said. “I didn’t know when. But at this point I don’t think I need to do any more research to prove that humans are radically different from chimps.”

Tomkins cited page 33 of the supplementary information that accompanied the April 9 study in Nature. It said that when the chimp and human genome were aligned, they were 84% identical.

“The initial paper was 17 pages long, and they never really gave the real data in the paper, in my opinion,” Tomkins said. “I think they were avoiding it. And so all the action really was in this 171-page, book-length supplemental material.”

Eichler said the researchers were being cautious, not avoidant. “You have this 10% of the genome where the clock mutates faster, and you have to be really careful about putting a number on it,” he said. “It isn’t that people are trying to obfuscate anything.”

In 2018, Tomkins and Richard Buggs, a professor of evolutionary genomics at the Queen Mary University of London, separately ran predictive computer comparisons of chimp and human DNA—long before the latest sequencing technology emerged. Both showed the similarity in chimp and human DNA right at 82-84%. The difference between the two was roughly 15-17 times greater than previous studies and right on target with the complete ape genome comparison.

Casey Luskin, a geologist and lawyer at Discovery Institute, says this disproves the theory of a 1% difference. He added that the gap between the human genome and the chimp genome is “basically representing sections of the genomes that are so different that you can’t align them together to figure out exactly what is the percent difference.” Now Luskin and Discovery Institute are demanding the Smithsonian National Museum of Natural History take down displays using outdated research arguing for common ancestry. The Smithsonian replied that, if it ever updates its numbers, it will take the study into account.

Luskin doesn’t see the similarities between human and ape DNA as proof of common ancestry. He explained how computer programmers borrow code and engineers use car wheels for planes—all to serve a specific purpose. “It’s a good design principle to reuse parts that work in different designs. The fact that we share a lot of similar DNA with the chimp could simply reflect the fact that we are built upon a common blueprint,” Luskin insists. “It shows common design, which could explain those similarities just as well as common descent.”

Eichler also sees “parts that are shared and used and reused in multiple ways” as he studies the primate genome. He looks at organisms as the “sum of the parts,” each functioning based on “the complete genetic blueprint it has in it.”

On April 23, Nature published another study by Eichler’s group, comparing human genomes. Eichler said they have identified the regions of rapid mutation and plan to “sequence probably thousands of more humans very soon,” along with hundreds of chimps. In the four-generation family being studied, “we can see the exact same changes at the same rates occurring in these regions,” he said. “If you want to use a single number, then you can’t say that humans are 99.9% identical anymore because then you have to change that number comparing your and my genome because we’re now comparing those very dynamic regions as well.”

For Tomkins, a Christian trained in evolution and now a creationist, the obvious structural differences between chimps and humans are evidence that there is more than a 1% difference in their DNA. “If you include these large regions they call structural variants, any two humans can be 4% to 5% different from one another,” he said. “So if we’re 4 to 5% different from one another, where’s this 1% difference from a chimp come into play?”

Tomkins doesn’t separate the blueprint from the Architect who drew it. He pointed to human capacity for communication through language due to specialized muscles in the voice box to make sound and dexterity in the hands to write. “We have highly specialized regions of our brains that chimps don’t have that allow us to communicate in language,” he said. “These studies are showing we are created in the image of God, completely unique.”

Eichler isn’t weighing in on the source of the blueprint. “Facts don’t change, right?” he said. “Interpretation can change, in terms of the theory of how things have gotten there. But I think that we’re laying the foundations for generations to do future research and to study. And I feel very blessed to be able to do that.”