Editor’s note: For the full “Chimps and Critics” series by Dr. Luskin, see here.

In a previous post I noted that critics are attempting to respond to the data in the new Nature paper showing that humans and chimps are about 15 percent genetically different. The irony is that most critics admit that the data shows this much greater degree of difference than the old “1 percent” myth; they’re just claiming that the differences can be ignored or dismissed. 

One response we’ve seen is that when human and chimp DNA could not be aligned, this was merely due to “technical failures.” The insinuation is that something went wrong in the lab during the attempted alignment process, and this is what prevented the DNA from aligning and being comparable. But such an interpretation of what the Nature paper means by “technical failures” is not supported by what the paper says. The main paper only uses the word “technical” once, as follows: 

Gap divergence showed a 5-fold to 15-fold difference in the number of affected megabases when compared to single-nucleotide variants, which was due to rapidly evolving and structurally variant regions of the genome as well as technical limitations of alignment in repetitive regions (Supplementary Figs. III.11 and III.12).

A Bit More Elaboration 

When we go to the paper’s Supplemental Data we find a bit more elaboration on what they mean by a “technical problem”:

Gap divergence is defined as the fraction of positions in the target haplotype that are not aligned to the other haplotype, which could be due to biological processes (e.g., gene loss/gain and insertions/deletions), missing data, or technical problems (e.g., alignment failure due to SVs, repetitive elements, etc.).

Read these quotes carefully. In the first one, a “technical limitation” pertains to the difficulty “of alignment in repetitive regions.” In the second quote, a “technical problem” is defined as “alignment failure due to SVs, repetitive elements, etc.”

In other words, a “technical problem” is equated with a failure to align the DNA. The standard reason for such a “technical failure” is simply that the DNA is so different that it can’t align. Thus, my understanding of the paper is that “technical failures” can and should be taken as prima facie evidence of real genetic “differences” — what they call “gap differences” between the species. 

To put it bluntly, under their definition “technical failure” does not equal some mistake that was made in the lab. Under their definition, technical failure = alignment failure = different DNA. Whatever label we use to describe them, there are real genetic differences between humans and chimps — about 15 percent of the genome in fact — and the differences  deserve to be recognized.