Millennials turn away from Creationism

When I was younger dealing with Creationists was something I had to do as a matter of course. Like many members of “Generation X” I haunted Usenet groups in the 1990s where the “evolution-creation” debate raged, always defending the consensus science from detractors. Even in the early years of this weblog, we tackled Creationists now and then. It was something you had to do.

But over the past decade or so there has been a change in the air. American society has become more secular, and religious conservatives do not wield as much power. Acceptance of evolution has been increasing, simply due to secularization. Books like The Creationists: From Scientific Creationism to Intelligent Design, seem to be artifacts of the 20th century, dealing with the concerns of a bygone age.

This is on my mind because recently I happened to read a positive review of Darwin’s Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design. I haven’t read a piece of apologia for Intelligent design since the 2000s, and it’s rather strange because we have so much data now due to genomics. Many of the old arguments that Intelligent Design advocates deploy ring hollow and theoretical because the data refute them. People like David Klinghoffer are beneath notice.

It is true that a minority of the population rejects evolution on cultural grounds. But as with the rejection of gay marriage, the broader society has moved on to other concerns. “Darwin’s enemies on the Left” are far more vocal and powerful than those on the Right. I can’t imagine an organ of mainstream secular conservatism such as The Weekly Standard publishing something like Evolutionary Psychology and Its True Believers today. At the time it struck me as a coalitional sop to evangelicals.

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Open Thread, 01/28/2019

If I haven’t made it clear, I highly recommend The First Farmers of Europe: An Evolutionary Perspective. A very readable book. One thing I haven’t emphasized is that the early European farmers seem to have been big consumers of cheese. This is curious as it doesn’t look like they have the modern European lactase persistence allele. Cheese is different from milk because the proportion of sugar is lower, as the fermenting process exhausts some of it. But cheese-base agro-pastoralism seems to have been common in many places before the arrival of Indo-Europeans.

David Reich is on giving talks in India. He has stated that the draft of the Indian ancient DNA paper is complete. This doesn’t speak to when it will be posted on bioRxiv, but we’re seeing the light at the end of the tunnel. Also, I assume the Iberian paper showing mass male-mediated migration ~2000 BC will arrive at some point this year.

A friend pointed me to a new book by Edward Dutton on J. Phillipe Rushton. After watching clips of Dutton speak about the contents of the book, it is not a flattering portrayal. Dutton depicts Rushton as a bit of a general sociopath (though he seems to couch it as part of Rushton’s individual “life history strategy” of being a “user”). More concerning than his personal life is that Rushton was clearly willing to fudge facts in regards to his science, which was of such a controversial nature regarding race and life history that ultimately he should have been much more careful than is the norm. Dutton documents some instances apparently in his book, but I can give another specific example.

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The diverse origins of the Bengali gentry

Satyendra Nath Bose, a Kayastha

I’ve been rather busy with other things and the South Asian Genotype Project has fallen a bit by the wayside. But, I plan on allocating a day on a weekend soon to getting through the backlog. But, before that, I thought I would submit something that might clarify or illuminate an aspect of South Asian history and culture that the data have shown.

The public data have a large number of Bangladeshis. Sampled in Dhaka. Unlike most South Asians they don’t exhibit much structure. But unfortunately, we don’t have too many samples from West Bengal. That being said, I do get some through this project. As you can see on the plot (round dark point) the Brahmins of Bengal are genetically very distinct from the Bangladesh samples (I have more samples, but this position is always the same for all of them). In fact, they are closer to Brahmin samples from Uttar Pradesh. Using modeled based clustering though I have become strongly convinced that the Bengali Brahmins do have a minor contribution from the non-Brahmin Bengali population because they have East Asian ancestry.

The triangles on the plot are from Kayastha individuals from West Bengal. I have seen a few Kayasthas from this region, and two trends about them:

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The European Neolithic, in fits and starts

On this week’s episode of The Insight I discussed the field of cultural evolution with Richard McElreath. The author of Mathematical Models of Social Evolution, he was in a good place to explain why the field is relatively formal. This is in contrast for example to modern American cultural anthropology. Basically, formality keeps you honest and allows you to be wrong. Verbal arguments are amenable to subtle and not so subtle updating so as to dodge the acceptance that a model is false nearly indefinitely. Words are just imprecise enough that miscommunication can creep into the discourse.

I thought of this while reading The First Farmers of Europe: An Evolutionary Perspective. This book outlines the latest results from a variety of fields and refutes once and for all one particular mathematical model of how agriculture spread to Europe. I am alluding here to the “wave of advance” model for the spread of agriculture in Europe (most forcefully pushed by Albert Ammerman and L. L. Cavalli-Sforza). The general idea here is that farming spread through demographic increase and the diffusion of the excess population as a particular region achieved its carrying capacity. Like R. A. Fisher’s ambition to make evolutionary genetics as regular as the laws of thermodynamics, the proponents of this viewpoint were attempting to reduce a complex cultural process down to a few parameters.

And certainly, it was a useful null model in its time.

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David Reich strikes back!

David Reich submits Five Corrections to The New York Times.

As you know, in the fact-checking process I was sent more than 100 statements of which a very high proportion (more than half) were incorrect. For example, as I mentioned to you in my letter of January 7, 20 of 49 statements presented to me for review on January 2 were incorrect, and 27 of the 36 statements presented to me for review on January 5 were incorrect. The high rate of errors was concerning as it suggested that the narrative based on them might not be supported by a solid set of facts. While a substantial number of these incorrect statements were removed through your fact-checking process, some errors got through, and I am therefore now requesting formal corrections of the following 5 errors that meaningfully affect the article, so it is important to set the record straight on them. (I have also identified additional errors, but those are for the most part smaller, so I am not requesting corrections in those cases.)

One of the frustrating aspects of The New York Magazine piece is that I have read probably read most of the Reich lab’s papers over the last 5 years or so (perhaps earlier), so I knew which factual points were false or exaggerations, but I didn’t want to highlight them incessantly because people would get lost in the muddle of detail. For example, in relation to this assertion:

About 5,000 years ago, a “relatively sudden” mass migration of nomadic herders from the east — the steppes of eastern Ukraine and southern Russia — swept in and almost entirely replaced the continent’s existing communities of hunter-gatherers and early farmers.

The figure from Haak et al. 2015 immediately came to mind. It literally rejects the characterization in a quick and simple figure (the population that purportedly “entirely replaced” is green). Obviously, the figure does not show what the piece claims Reich believes, and it is not credible that he would assert something that is refuted by the papers his own lab publishes. If you had read this area you would know all this, but even population geneticists who are not immersed in the human ancient DNA literature likely would not pick up on this. The sample size objection was in a similar class.

Here’s what I’m going to leave you if you are an outsider: if the author misrepresents so many details, how much should you trust them in broad strokes?

The piece was not reportage. It was rhetoric. Sophistry.

Open Thread, 01/20/2019

Peter Turchin recommended The First Farmers of Europe: An Evolutionary Perspective. It’s dry. But good. It is also one of those academic books where the cost of the Kindle version is $50 less than the hardcover version.

Two for Tea is a good podcast. One the most recent one they interviewed two anthropologists, both known to me. It was a nerdy but informative conversation and convinced me to not take up Sex at Dawn (it’s in my stack).

We’ve got 9 episodes now on the Brown Pundits podcast, the BrownCast. The latest is on Sanskrit. The current plan is to range over a lot of topics. If you have ideas, shoot them my way.

People have been asking about my other podcast, The Insight. It will be back soon!

The transferability of lipid-associated loci across African, Asian and European cohorts.

Genetic Nature or Genetic Nurture? Quantifying Bias in Analyses Using Polygenic Scores.

Nathan Glazer, Urban Sociologist and Outspoken Intellectual, Dies at 95. I read Ethnicity about 20 years ago. Glazer was a giant.

Tiny animal carcasses found in buried Antarctic lake.

The last two episodes of Tides of History on the War of the Roses have been some of the best. I really recommend them.

Justin Murphy is leaving academia. Murphy is way too much of an oddball to ever fit in. Probably for the best.

Genes lost during the transition from land to water in cetaceans highlight genomic changes involved in aquatic adaptations.

Estimating recent migration and population-size surfaces.

Approximate Bayesian computation with deep learning supports a third archaic introgression in Asia and Oceania.

Killer whale genomes reveal a complex history of recurrent admixture and vicariance.

Macroevolution of dimensionless life history metrics in tetrapods.

Sacklers Directed Efforts to Mislead Public About OxyContin, New Documents Indicate.

A Classic Genetic Model of Sexual Selection.

David Reich drops the mic

Update: David Reich asks for five corrections to the piece in The New York Times Magazine piece.

Didn’t mean to post so much about that crappy piece in The New York Tines Magazine. But there’s so much tendentious crap in it. That being said, I am probably not going to post much more on this, because David Reich’s response is up:

Letter in response to Jan. 17 article in The New York Times

January 19, 2019

To the Editor:

Gideon Lewis-Kraus (Jan. 17) profiles the nascent field of ancient DNA, which in the last few years has contributed to a transformation in our understanding of the deep human past. His article touches on important issues that we, as a field, have yet to deal with fully: including how to handle ancient remains ethically and in a way that preserves them for future generations; how geneticists and archaeologists can work in equal partnerships that reflect true respect for the insights of different disciplines; and how ancient DNA technology, which at present is applied efficiently only in large labs, can be made accessible to a wider group of scholars.

But Lewis-Kraus misunderstands several basic issues. First, he suggests that competition to publish is so extreme that standards become relaxed. As evidence, he cites a paper by my lab that was accepted on appeal after initial rejection, and another that was reviewed rapidly. In fact, mechanisms for appeal and expedited review when journals feel they are warranted are signs of healthy science, and both processes were carried out rigorously.

Second, he contends that ancient DNA specialists favor simplistic and sweeping claims. As evidence, he suggests that in 2015 I argued that the population of Europe was “almost entirely” replaced by people from the Eastern European Steppe. On the contrary, the paper he references and indeed my whole body of work argues for complex mixture, not simple replacement. Lewis-Kraus also suggests that I claimed that our first study of the people of the Pacific island chain of Vanuatu “conclusively demonstrated” no Papuan ancestry. But the paper in question was crystal-clear that these people could have had some Papuan ancestry – and indeed, to support his claim, Lewis-Kraus could only cite his own notes from an interview I gave him long after I had published a second paper proving that there was indeed a small proportion of Papuan ancestry.

Lewis-Kraus also suggests that I use small sample sizes to make unjustifiable sweeping claims. In fact, small sample sizes can be definitive when they yield results that are incompatible with prevailing theories, as when my colleagues and I described two samples that proved the existence of the Denisovans, a previously undocumented archaic human population. In my papers, I am careful to only make claims that can be supported by the data I have. In small-sample size studies, I emphasize that more samples are needed to flesh out the details of the initial findings. A major focus of my lab is generating the large data sets needed to do this.

Lewis-Kraus’s critiques are based on incomplete facts and largely anonymous sources whose motivations are impossible to assess. Curiously, he did not ask me about the great majority of his concerns. Had he done so, the evidence underlying his thesis that my work is “indistinguishable from the racialized notions of the swashbuckling imperial era” would have fallen apart. The truth, and the main theme of my 2018 book Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past, is exactly the opposite – namely, that ancient DNA findings have rendered racist and colonialist narratives untenable by showing that no human population is “pure” or unmixed. It is incumbent on scientists to avoid advocating for simplistic theories, and instead to pay attention to all available facts and come to nuanced conclusions. The same holds true for journalists reporting on science.

David Reich
Harvard Medical School and the Howard Hughes Medical Institute, Boston, Massachusetts

On “big science”, ancient DNA, and David Reich

A lot has happened in the last few days in backchannel conversations and social media in relation to the piece in The New York Times Magazine which put the spotlight on ancient DNA, and David Reich, for the general audience. Unlike Carl Zimmer’s ancient DNA column in the science section of the paper, the people reading Gideon Lewis-Kraus’ 12,000-word piece are not going to be familiar with the field and will miss omissions and the context.

To “bullet” some of the issues with the piece, in order of simplicity and straightforwardness to me:

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The ancient DNA oligopoly and the stories people tell about David Reich

There is a very long piece in The New York Times Magazine, Is Ancient DNA Research Revealing New Truths — or Falling Into Old Traps?. It’s the talk of DNA-Twitter for obvious reasons. The very fact that you have a long piece in The New York Times Magazine on this topic means that David Reich is almost certainly going to made into something of a villain. The reason I say this is that these sort of narratives pitched to a general audience have to exhibit novelistic drama and plot, and so there are “spots” preexistent for both antagonists and protagonists. If the writer doesn’t create that narrative, the piece would probably never see the light of day. Who would read it?

So before the first pixel loaded, I knew:

1) David Reich was going to be the antagonist
2) And indigenous people, along with supporting archaeologists were going to be protagonists

This does not speak to whether this is “true” or not. It is simply how it was going to work out if the piece was ever going to be published because those are the elements of a story that would appeal to readers of The New York Times. This is a product strongly shaped by consumer demand.

One thing I want to address is a critique, expressed by some academics in the piece, that researchers in ancient DNA do not have the number of samples to make the generalizations that they make. This seems reasonable on the face of it, but one thing you have to consider is that when you obtain an individual’s DNA you get a window onto their whole pedigree. A single individual is actually a pedigree if you have its genome. A genome provides an enormous amount of data. It is an endpoint of a historical process of sexual reproduction that extends back many generations. This is how you can use a single whole genome to infer whole population histories. One of the consequences of humans being “evolutionarily young” is that we all bear the stamp of some common processes and events.

From a naive perspective, you can say things like “how do you know this person is related to other people in the area?” And taken in the aggregate there are cases where unrepresentative individuals will yield results that mislead researchers. But on the whole over the last decade or so these groups have developed certain intuitions and guidelines, and have been rather good at making inferences based on a few data rich individuals. They make mistakes. But most objections about the nature of the data are really unfounded (albeit, widespread).

Many of the aspects of the piece do ring true. There are only a few huge laboratories in the ancient DNA space which tend to hoover up samples and collaborators. I have a suspicion I know who this is: ‘One geneticist compared competing with the big labs to battling an entire navy ‘with a little dinghy, armed with a small knife.”‘ For Holocene period analysis, the two big players are the Reich group and that of Eske Willerslev (Johannes Krause is going to make a splash with Late Antiquity). Though Eske’s group is mentioned offhand, it is curious that he himself is not mentioned at all.

Young Eske

In many ways, Eske is a much more colorful figure than Reich, and many of the issues applicable to the work of the latter and his relationships with indigenous peoples and archaeologists apply to the former. But in the United States David Reich is a brand name to the general public that Eske is not, and there can be only one devil in the underworld. But from a narrative perspective, Reich presents less raw material. He is a soft-spoken and delicately built vegetarian computational biologist. Eske Willerslev is the scion of Vikings whose background is in fieldwork as an anthropologist. His autobiography, written in Danish, is apparently very colorful!

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The state of Neanderthals in early 2019

PNAS has published a paper, Limits of long-term selection against Neandertal introgression. It’s from a preprint which I blogged this summer. What are the major takeaways here?

It’s been about 10 years since the draft Neanderthal genome was published. At around that time everyone realized that there was archaic introgression into the modern human genome. More precisely, reticulation in the human phylogeny was a major thing in the time scale of 50,000 years and earlier.

But there were a lot of details to clear up. For example:

  1. Did % Neanderthal admixture vary outside of Africa?
  2. Was there really only one single admixture?
  3. Has natural selection shaped the proportion of Neanderthal genetic material in our genomes?

The reason the new paper above is interesting is that they used differences between Neanderthal populations (of different relatedness to the source into moderns), as well as modeling different demographic scenarios through simulation, to show that:

  1. Neanderthal % is Europe is no different than Asia, rather, there is West Eurasian gene-flow into Africa
  2. Selection against Neanderthal genes seem to have occurred very early, and little later one
  3. Selection seems to be strong around regulatory elements
  4. The lack of variation due to basal Eurasian admixture indicates they may have been part of the admixture

This is not the final world. Rather, it illustrates that though the first pass result stands, a lot of details are being worked out, and that this dynamic field is sensitive to the samples available and theoretical frameworks that leverage those samples.