Pre-emptive Strike: Neanderthal Double-Think

Doing the science blogosphere rounds is a paper in PNAS – Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins, pdf available here – that claims that the observed differences in genetic similarity with Neanderthals between Eurasians and Africans can be explained entirely by the population structure of ancient Africa and without recourse to interbreeding between Neanderthals and humans leaving the continent. This has received a fair bit of flack from said blogs – first because the media were allowed to publish articles on the paper some time before it was actually released, but later on the grounds that the paper was “obsolete.”

What’s the reason for that dismissal? To quote from the Discover Magazine blog Gene Expression:

What did they do in the PNAS paper which claims that one can not reject the model that the Eurasian affinity to Neandertals is due to ancient African population structure (i.e., the African ancestors of Eurasians already had a closer affinity to Neandertals, perhaps due to continuous gene flow)? Basically they created an explicit spatial model with a temporal dimension. The authors simulated parameters of gene flow (and lack thereof) as well as bottlenecks, etc., and found that ancient structure easily generated the D-statistic which the original authors of the Neandertal admixture paper relied upon.

So why so dismissive from Reich & Patterson? Because the Yang et al. paper [Ancient Structure in Africa Unlikely to Explain Neanderthal and Non-African Genetic Similarity] admits this problem, and formulates a way to test alternative scenarios which generate just those D-statistics, but exhibit different demographic histories. What they found in Yang et al. is that a model where a population bottleneck occurs followed by admixture is the best fit to the site frequency spectrum that you see in real populations today. In other words, they also simulated situations where ancient structure generated equivalent D-statistics to admixture, and then furthermore explored scenarios where other population genetic statistics could further prune the alternatives. One could say that the appropriate follow up paper to the PNAS contribution was actually published before it.

(Emphasis in the original.)

That aside, the proposed ‘population structure’ system is, in other words, incomplete lineage sorting, which Todd C. Wood (who is that rarest thing: a young Earth creationist who may actually know what they’re talking about) explains in his own post on the subject:

For any population of critters, the gene pool (all the copies of genes in each organism in the population) is a mixture of genes that are very similar and some genes that aren’t all that similar.  When the population divides (as it does during speciation), the two new populations still have some genes that are very similar (implying a recent divergence) and some that aren’t so similar (implying a more ancient divergence).  If you want to reconstruct speciation events based on gene similarities, you have to be careful that you take into account this pattern of lineage (population) sorting, or you might come up with a really wrong answer.  Some genes will show a close relationship between the populations, and some will show a more distant relationship.

When the original Neandertal genome paper came out, all the attention went to interbreeding to explain the similarity of Neandertal and Eurasian genes, and I think that was well justified.  Since incomplete lineage sorting is a random process, I would not expect to see any modern human population significantly more similar to Neandertals than any other modern human population.  Modern human populations diverged well after the Neandertal divergence, so whatever genes were still very similar to Neandertals should have been evenly divided.  Even more interesting is the geography: the ancestors of the modern humans with Neandertal-like genes come from the same geographic region as the Neandertals.  If incomplete lineage sorting is to blame for Neandertal-like genes in modern humans, that geographic pattern would just be a weird coincidence.  That’s not to say that one couldn’t make a case for incomplete lineage sorting, but we would need some new evidence to really seal the deal (such as new samples of Eurasians that don’t have Neandertal-like genes or Africans that do).

The Institute for Creation Research has a bad history with ILS, which will make their article on this paper – should they publish one – quite interesting. But there’s no reason to wait as the author of the two previous ILS articles, Jeff Tomkins, has a blog of his own at designed-dna.org. His post, Neanderthal Myth and Orwellian Double-Think, is terrible.

Modern humans and Neanderthals are essentially genetically identical. Neanderthals are unequivocally fully human based on a number of actual genetic studies using ancient DNA extracted from Neanderthal remains. The DNA data fully confirms the numerous anatomical studies performed on a wide variety of skeletal remains found in diverse geographical regions across Europe and the Middle East. The anatomical data not only shows that Neanderthals had fully human bone structure, but larger brains and more robust features. In fact, to the uncritical observer, they appear superior to modern humans. Nevertheless, the Neanderthal issue, which is actually an evolutionary non-issue, continues to be debated to promote the failed Darwinian paradigm of human origins.

Designed DNA is not officially affiliated with the ICR, being Tomkins’ personal blog and website, so his independent masterpieces shall be honoured by becoming the second source (after the ICR itself) to get it’s own quote background-image thingy.

What’s Tomkins on about? He seems to be confusing the evidence for admixture for the actual genetic relatedness between humans and Neanderthals – we’ll get to that in a moment. It’s interesting to see that he does not attack the percentages given for the similarity between us and Neanderthals in the same way that he does with chimps, but that’s neither here nor there.

Tomkins does not really address the contents of this new paper:

Adding to this somewhat ridiculous scenario is a recent highly popularized journal report wherein computer models of demographics and interbreeding scenarios were simulated – all based on hypothetical data (1). The report claimed that modern humans and Neanderthals had a very low level of genetic relatedness. The popular media jumped all over the story as though it somehow represented real genetic data when in fact, it did not. It was just a bunch of computer simulations based on hypothetical ideas.

That this is just a model, and that getting more data of their own, is another avenue down which this paper has been attacked. Though that’s not to say that you can ignore models when you feel like it as creationists sometimes do.

The general idea surrounding Neanderthals is that only 2 to 4% of the modern human genome can be traced back to these mysterious creatures, yet they are fully human and essentially genetically identical to modern humans. Has the contradiction become apparent yet? And it gets even more absurd…even though we are essentially genetical [sic] identical to Neanderthals we are somehow not related, instead, we are related to chimps because (as they say) we are 98 to 99% identical to them.

This is a phenomenal misunderstanding. I’ll concede that it might not be completely obvious that the “2 to 4%” is talking about something completely different to the “98 to 99%,” but Tomkins has a PhD in genetics and really ought to know better.

The amount that a given ancestor of a person directly contributed to their genome decreases as we increase the generational difference, and you should all be perfectly familiar with the idea that ~25% of your genome will be from your paternal grandmother and so on. Similarly, it might be the case that – and I’m pulling my numbers out of thin air here – around 2% of the genome of people in a particular region comes from Genghis Khan, who was rather promiscuous. What’s more if everyone, and therefore both parents of a child, have 2% of their DNA coming from Khan, then the child with also have the same percentage and it will stay in the population unless diluted by gene-flow from outside.

What Tomkins is effectively saying is that this 2%-Khan idea is nonsense and “absurd” as Genghis Khan was clearly “fully human” and what’s more you would, should you do a genetic comparison between him and one of these descendants, find a match of something like 99%!

This reasoning is itself silly. You can still say that 25% of your genome came from your paternal grandmother even though almost all of it would be the same if it came from her husband, and the same goes for Khan. Tomkins’ objection makes no sense.

So what is really going on? Researchers look at “shared Neandertal derived SNP [single nucleotide polymorphism] alleles,” and can see that Africans have significantly less than Eurasians. In his post on the paper, John Hawks talks about his own research on this subject including that on Ozti the Iceman, who was apparently even more closely related to Neanderthals, probably due to being in the right time and place to be near the interbreeding:

He captioned this image:

I’d like to see the model of African population structure that could explain this result…

Giving a percentage is more difficult, and relies on assumptions including how much ancestry Africans have with Neanderthals as the baseline. Tomkins really should know all this, so his post is puzzling. Also of note is that he never mentions the most important part here – it’s not that Neanderthals have “a very low level of genetic relatedness” with humans, but that the relatedness varies. Why is this not mentioned?

And you thought Orwellian ‘double think’ or ‘news speak’ didn’t apply to science? In reality, evolutionary propaganda is full of it. If you ever read Orwell’s book “1984”, this deceptive fraudulent concept is where two completely contradictory ideas are maintained or merged in the same paradigm – to create imagined truth out of a lie.

No, this is not a case of “double think,” nor “news speak,” but instead a failure to think on the part of Tomkins when he evidently found a concept that he didn’t understand and ran with what he thought he knew without checking to see what was really up. There is no cognitive dissonance here, merely wilful ignorance.

He concludes:

The truth about Neanderthal DNA and anatomy, however, fits perfectly with the claims of the Bible which states “And hath [God] made of one blood all nations of men for to dwell on all the face of the earth” (Acts 17:26).

But where does the Bible mention Neanderthals? And how far does that verse stretch?

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The fact that Tomkins has written about this story on his blog before anything appears on the ICR’s website does suggest that there either won’t be an article there or it won’t be written by him. Alternatively, he might just be practising as this post would definitely be at home on the “Daily Science Updates” page with Thomas’ stuff. Hopefully there will be such an article because I’m sure, after this, it will be hilarious. Hilariously wrong, that is.