How Intelligent Design Creationists try to deal with the similarity between human and chimp genomes

The initial measurement of the difference between the human and chimp genomes was based on aligning 2.4 billion base pairs in the two genomes. This gave a difference of 1.23% by counting base pair substitutions and small deletions and insertions (indels). However, if you look at larger indels, including genes, you can come up with bigger values because you can count the total number of base pairs in each indel; for example, a deletion of 1,000 bp will be equivalent to 1,000 SNPs.

Depending on how many of these large deletions and insertions you detect, the difference between the human and chimp genomes can be 4%, 10%, or even 20%. Intelligent Design Creationists seize upon these different ways of comparing the genomes as evidence that the case for common ancestry is weak. You can hear Casey Luskin try to argue against evolution in one of the latest podcasts from ID The Future [Chimp and Human Genomes: An Evolution Myth Unravels].

Luskin mentions a short paper published in Science in 2007 where Jon Cohen supposedly exposes the "myth of 1%" (Cohen, 2007). According to Cohen, the actual value is more than 6% and Luskin jumps all over this in order to make the point that "evolutionists" were wrong.

Luskin conveniently forgets to mention that even using these larger percentage differences allows us to infer that humans and chimps shared a common ancestor about 6-7 million years ago and to infer more distant relationships with other mammals that are consistent with the fossil record (see figure). The Twin Nested Hierarchy (sequence plus fossils) is the most powerful evidence supporting the common ancestry of humans and other species. Evolution explains the Twin Nested Hierarchy but I don't know of any other explanation that accounts for these observations—creationists certainly don't have one.

The main problem with debates over the exact percentage is that it obscures the real issue when it comes to inferring evolution. What we're concerned about is not the total number of nucleotide differences but the number of mutations that gave rise to those differences. In that sense, a single base pair substitution is the same as a single deletion of 1000 bp.

According to Luskin, "Your percent DNA similarity between two species really doesn't tell you anything about whether or not they are genetically related." He says that common design can explain the similarities. That's true up to a point, you could argue that the mystery designer used common features to design chimps and humans then tweaked the design to make them slightly different. That might work as an explanation for two species, such as humans and chimps, but it's much harder to explain the overall pattern of differences when you look at a lot of species. How do creationists explain that the number of differences between the genomes of multiple species just happen to correlate with their presumed evolutionary relationships based on the fossil record?

I suppose they could argue that what we're seeing is merely the handiwork of the designer who first built a mammal prototype then started experimenting with slight modifications to create working models of rodents, bats, and ungulates. Each of these other prototypes were then adjusted using small changes to make smaller groups (families, genera) and then species. Presumably this was done over several million years of experimenting and adjusting in order to account for transitional fossils and dating technology.

But in addition to being mere speculation based on the presumption of a designer, there's one other problem with this model. The differences between genomes aren't just due to specific modifications that create distinct species as the designer model predicts. Instead, the evidence shows that they are mostly concentrated in parts of the genome that are not under strong selection. What this means is that most of the mutations are effectively neutral and thus the affected DNA should be evolving at the neutral rate, which, according to population genetics, is equivalent to the mutation rate. This prediction turned out to be correct and changes at the neutral rate are what gives rise to the approximate molecular clock.¹ (See Calculating time of divergence using genome sequences and mutation rates (humans vs other apes).)

What this means is that our current understanding of evolution has enormous explanatory power. It satisfactorily accounts for the data on genome differences in a way that no competing model can. If Intelligent Design Creationists expect to be taken seriously as scientists then they have to do more than come up with hand-waving arguments about the possible motives of the designer. Instead, they have to explain why those differences just happen to fall in line with known mutation rates, which then give times of divergence from common ancestors that just happen to correlate with the fossil record.

---

1. It's important to keep in mind that the changes we see when we compare genomes are due to the combination of mutation and fixation of alleles by random genetic drift.

Cohen, J. (2007) Relative Differences: The Myth of 1%. Science 316:1836. [doi: 10.1126/science.316.5833.1836