Why not 6,000?

Disco. 'tute blogger Ann Gauger wants to make something clear:

There seems to be an idea on the part of some critics that my analysis in Science and Human Origins means that humans arose four million years ago. That is not the case.

The very idea that anyone would think Gauger agrees with the scientific evidence on any matter is clearly offensive, and her umbrage is duly noted.

Gauger doesn't ever specify who these critics are that maligned her so, or what they actually said.  She certainly doesn't link to the critics' work so that her readers can evaluate those criticisms themselves.  Links are the lifeblood of the internet, and by failing to link (or even name) these critics, Gauger shows just how little she respects her readers and even the basics of intellectual discourse.

As we discussed last week, the critic she's surely referring to is Paul McBride, who writes:

What Gauger…argues is that there are five major haplotypes [of a gene called HLA-DR] but only three of the haplotypes are "ancient". Because up to four haplotypes could be inherited from two people, the existence of only three leaves the door open for an Adam-and-Eve bottleneck. Unfortunately for Gauger, even if we accept all parts of her argument up to here, we are forced to conclude that this final step is wrong if the book is to be internally consistent.

The other two major haplotypes might not be "ancient", but they are still 4 to 6 million years old (Gauger agrees with this). While this does mean they originated in the hominoids, Gauger takes this as evidence they could have come from Adam and Eve. Why is this wrong? Well, if we recall Luskin's chapter [right before Gauger's], he argued that Homo habilis was seriously non-human. No self-contemplation for the habilines. Yet, H. habilis originated about 2.3 million years ago, and H. erectus did not arrive until about 1.8 million years ago, marking what Luskin accepts to be the start of humanness. Back at 4 million years ago when the last of the HLA-DR haplotypes originated, our closest relatives were Australopithecus. Anatomically modern humans were a long way away. So we can be sure that the five major haplotypes of HLA-DR all pre-date the genus Homo, and contradict the claim made by Gauger that:

The argument from population genetics has been that there is too much genetic diversity to pass through a bottleneck of two individuals, as would be the case for Adam and Eve. But that turns out not to be true.

Instead, the argument from population genetics still definitively rules out the possibility of Adam and Eve, if Adam and Eve were human.

Emphasis added.  McBride looks at the papers Gauger refers to, looks at the general literature on HLA genes, and concludes that the haplotypes in question are over 4 million years old, and infers that Gauger agrees with the papers she builds her whole case on.

But no!

Gauger insists that another paper could be read to indicate that these genes are younger (even though they weren't looking at the same three haplotypes; this bait and switch is part and parcel of the dishonesty and disrespect for their audience that pervades everything the 'tute does).  Therefore, she insists, the haplotypes may have arisen between 180,000 and 320,000 years ago.

Lop off a couple of zeros, and she might really advance the cause of creationism intelligent design.

A few things to note:

Gauger continues to focus on trying to find evidence of a two-person genetic bottleneck by looking at one gene, based on papers from the late '90s.  McBride notes that a genome-wide assessment of effective population sizes throughout human history from 2011 decisively rules out such a bottleneck.  Gauger is silent on that research.

Gauger is also trying to do a bait and switch, and executing it poorly.  She quotes her new favorite paper as finding:

The mean sequence difference among alleles within a lineage corresponds to an average age of 180,000-320,000 years (range based on the standard error). This implies that the vast majority (greater than 90%) of the more than 135 contemporary HLA-DRBl alleles have a very recent origin. 

She claims that this means:

over 90% of the allelic diversity within lineages arose within the last 180,000-320,000 years.

That isn't how averages work.  If the average age is 180,000-320,000 years, then something like 50% are younger, and something like 50% are older.  And her concern isn't with 90%, it's with 3 alleles.  Her new favorite paper is talking about 132 alleles, so even if 90% are quite young, that doesn't address the remaining 13 alleles.  You can't get 13 alleles from a two-person bottleneck.

Maybe that's the bottleneck from Noah's ark.