The 99% chimpanzee myth again - from an ailing magazine, no less

In Scientific American Magazine (April 20, 2009), Katherine S. Pollard asks, "What Makes Us Human?", explaining "Comparisons of the genomes of humans and chimpanzees are revealing those rare stretches of DNA that are ours alone." Interestingly, shse begins by repeating the myth that the human and chimpanzee genomes are 99% similar:

Six years ago I jumped at an opportunity to join the international team that was identifying the sequence of DNA bases, or “letters,” in the genome of the common chimpanzee (Pan troglodytes). As a biostatistician with a long-standing interest in human origins, I was eager to line up the human DNA sequence next to that of our closest living relative and take stock. A humbling truth emerged: our DNA blueprints are nearly 99 percent identical to theirs. That is, of the three billion letters that make up the human genome, only 15 million of them—less than 1 percent—have changed in the six million years or so since the human and chimp lineages diverged.

This is simply not a realistic picture.

If it were, it would only tell us that the genome is not as useful a source of information as we might have thought - because the actual differences between humans and chimpanzees are dramatic and obvious. Here's geneticist Richard Buggs on this point:

Looking closely at the chimpanzee-like 76% of the human genome, we find that to make an exact alignment, we often have to introduce artificial gaps in either the human or the chimp genome. These gaps give another 3% difference. So now we have a 73% similarity between the two genomes.

In the neatly aligned sequences we now find another form of difference, where a single 'letter' is different between the human and chimp genomes. These provide another 1.23% difference between the two genomes. Thus, the percentage difference is now at around 72%.

We also find places where two pieces of human genome align with only one piece of chimp genome, or two pieces of chimp genome align with one piece of human genome. This "copy number variation" causes another 2.7% difference between the two species. Therefore the total similarity of the genomes could be below 70%.

This figure does not take include differences in the organization of the two genomes. At present we cannot fully assess the difference in structure of the two genomes, because the human genome was used as a template (or ”scaffold”) when the chimpanzee draft genome was assembled.

One person who contested Buggs's theories put the similarity at 76%. But whether you like it or not, you are far more closely related to Ronald Reagan than to Bonzo.

So I am not exactly sure why some people are keeping the 99% story alive. It's not even plausible, and probably has more to do with ideology. Or to protect chimpanzees? A necessary cause - but one that is best addressed by recognizing the fundamental differences between them and us, not camouflaging them.

We are trying to protect them; they are not trying to protect us.

See also: Darwinism: Scientific American in trouble?