Hi Richard,
Well, I’m still waiting for you to propose a hypothesis for a sudden bottleneck to two hominins at ~700 KYA followed by explosive growth that is not miraculous, but as the song goes, you can’t always get what you want.
But I think you’re being a bit pedantic here. Your critique only really works if you press the word “entire” to mean “absolutely every nucleotide”. Maybe “genome-wide” would have been a better choice, but “entire” works just fine as well. And yes - 95% is the best estimate we have for the genome-wide identity of chimps and humans if you count indels on a per-nucleotide basis. That’s the published value based on the largest sample we have, and you’ve still given us no reason to suppose that the bits left over that haven’t been chased down to the nth degree are going to be significantly different than that value. Even if they are, it will most likely be due to indels of highly repetitive DNA, which is really hard to account for in any case.
But back to “entire”. If you google “entire” for dictionary definitions, you’ll see things like this:
The whole of, without missing any part. E.g. “I’ve traveled the entire world.” Not so! says the pedant. You may have travelled to every country, but have you visited every city? Every town? Every street in every town? Every house on every street? Every room in every house? Every square foot of every room?
Clearly this gets a bit silly.
Or take this recent headline:
“Pompeo: Iran will face ‘wrath of entire world’ if it pursues nuclear weapons.”
Not so! says the pedant. North Korea will probably approve, for that matter lots of Iranians will as well. There’s a guy in Albania who’s in favour as well. Clearly claiming the entire world will be wrathful is off base.
You also omitted my summary statement from your quote from Adam and the Genome:
“No matter how you slice it, the human and chimpanzee genomes are nearly identical to each other.”
That is what you have to deal with, even if you decide you want to slice it a little differently. That and all the other evidence for common ancestry. If you want to oppose common ancestry of humans and chimpanzees, it’s going to take a lot more than quibbling over the precise percent identity between the genomes.