Saying crazy things makes you less credible

440px-Desembarque_de_Pedro_Álvares_Cabral_em_Porto_Seguro_em_1500I pay a subscription to The New York Times because it’s America’s premier middle-brow journal. Its science pages are decent, so my interest was piqued when I saw the the bold headline, Discoveries Challenge Beliefs on Humans’ Arrival in the Americas. But the article is a total mishmash, alternating between spotlighting paradigm challenging scholars, and crazy. Here’s the crazy:

Having their findings disputed is nothing new for the archaeologists working at Serra da Capivara. Dr. Guidon, the Brazilian archaeologist who pioneered the excavations, asserted more than two decades ago that her team had found evidence in the form of charcoal from hearth fires that humans had lived here about 48,000 years ago.

Dr. Guidon remains defiant about her findings. At her home on the grounds of a museum she founded to focus on the discoveries in Serra da Capivara, she said she believed that humans had reached these plateaus even earlier, around 100,000 years ago, and might have come not overland from Asia but by boat from Africa.

These are changing times in human evolutionary biology. But if humans couldn’t make it by boat to Madagascar until 1,000 to 2,000 years ago, there’s no way they made it to Brazil.

Not by cline alone

Citation: Moreno-Estrada, Andrés, et al. "Reconstructing the Population Genetic History of the Caribbean." PLoS genetics 9.11 (2013): e1003925.
Citation: Moreno-Estrada, Andrés, et al. “Reconstructing the Population Genetic History of the Caribbean.” PLoS genetics 9.11 (2013): e1003925.
The Chronicle of Higher Education has an article up on the intersection of genomics and sociology, In Research Involving Genome Analysis, Some See a ‘New Racism’. Most of the quotes are from sociologists, which is a problem, because whenever I try and delve into the topic it seems that sociologists don’t actually engage with the latest genomic research, but simply rehash older models which refute naive essentialism which biologists would never find plausible in the first place. But there was an intriguing quote in the piece from Jiannbin Shiao: …The social sciences should replace their biology-based rejection of race “with a version of the feminist distinction between biological sex and socially constructed gender,” he writes. With several co-authors, he has developed a concept called “clines,” adapted from how economists talk about social class, which reflects the continuous nature of human variation while allowing loose clusters to develop, depending on how you zoom into the data.

The paper is The Genomic Challenge to the Social Construction of Race. It is admirable in its attempt to engage in the recent literature. Unlike other sociologists the authors seem to have read publications from the 21st century. I do think it’s strange that they are talking about clines as if it is a new idea, seeing as they cite its long-standing usage in biology. But perhaps it is somehow a novel concept in sociology? That says something about sociology I suppose.

But in an area of research such as genomics citations that are six years old may be out of date. The authors published in the summer of 2012, and no doubt had been working on the paper for a few years before that. I’m pretty sure that Steve Hsu, a former colleague of the first author at the University of Oregon, actually told me about the genesis of this paper in the spring of 2011 when I had coffee with him at Berkeley. The authors state:

The primary tools for identifying population structure have been, in order of emergence, (1) comparisons of predefined populations, (2) the Bayesian clustering approach of the program STRUCTURE developed by Pritchard, Stephens, and Donnelly (2000), and (3) new variations on the classical technique of principal components analysis (Paschou et al. 2007). Although social studies of science continue to criticize the circular research design of the first method (Bolnick 2008; Duster 2006b; Marks 2006), the second and third methods have been preferred among academic researchers for over a decade (Risch et al. 2002; Rosenberg et al. 2002).

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A genetic map of fireworks in time

 Citation: Towards a new history and geography of human genes informed by ancient DNA, Joseph Pickrell, David Reich, doi: 10.1101/003517
Citation: Towards a new history and geography of human genes informed by ancient DNA, Joseph Pickrell, David Reich, doi: 10.1101/003517

And when the Lord thy God shall deliver them before thee; thou shalt smite them, and utterly destroy them; thou shalt make no covenant with them, nor show mercy unto them.

Neither shalt thou make marriages with them; thy daughter thou shalt not give unto his son, nor his daughter shalt thou take unto thy son.

– Deuteronomy 7:2, 7:3

In my post below I did not elaborate in detail my personal model for how the genetic variation we see around us in modern humans came about. Part of the reason is that what I have in mind is not necessarily parsimonious. Rather, it’s a conception that has developed organically over the years reading papers, looking at the data on humans myself, and finally feedback from people in the comments of this weblog. One thing that Joe Pickrell and David Reich have shown with simulations though is that elegant parsimonious models can fit data with low enough granularity. To be concrete the “serial founder bottleneck” framework wasn’t constructed out of thin air. Rather, it actually was rooted in empirical patterns which were evident in the genotypic data. But all models are approximations and miss details. For example, Sohini Ramachandran’s 2005 paper was anchored around Addis Ababa. But this was even at that time obviously a simplification, as the authors surely knew that there was plenty of circumstantial evidence that Ethiopia has been subject to recent admixture, so that particular population could not be the source of the Out of Africa expansion (see Pagani et al. for confirmation with dense marker data sets).

As another example, consider India. Between Western and Eastern Eurasia, this region is inhabited by populations which are at approximately symmetrical genetic distance in either direction, with perhaps a mild bias toward Western Eurasians (this may be an artifact of sampling too many high caste populations though). Taken at face value it is a perfect illustration of the maxim that geography predicts genetic variation. But what Moorjani et al. most recently have confirmed is that raw genetic distance measures which summarize allelic differences on the population wide level missed patterns of recent admixture evident on the genomic scale. That is, when you look across segments of the genome of South Eurasians it is obvious that they are the outcome of an admixture event between a West Eurasian population and another group which has closer affinities to Eastern Eurasians (and closest to Andaman Islanders). When you average these ancestral components out it does place South Asians between the two antipodes of Eurasia, but that elides an essential component of historical information about how that average came about.

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The Holocene lattice

Citation: Towards a new history and geography of human genes informed by ancient DNA, Joseph Pickrell, David Reich, doi: 10.1101/003517

440px-PazuzuDemonAssyria1stMilleniumBCEThere were giants in the earth in those days; and also after that, when the sons of God came in unto the daughters of men, and they bare children to them, the same became mighty men which were of old, men of renown.

– Genesis 6:4

Joe Pickrell and David Reich have put up a preprint at BioRxiv, Towards a new history and geography of human genes informed by ancient DNA. Since it’s a preprint at BioRxiv you can 1) read it for free 2) comment on it. It is a magesterial review of “where we are,” though close readers of this weblog may not find much that is new in their survey of the empirical results which are coming out of human population genomics and ancient DNA analysis. In regards to this let me highlight two sentences. First, it is now clear that long-range migration, admixture and population replacement have been the rule rather than the exception in human history. Second, the serial founder effect model is no longer a reasonable null hypothesis for modeling the ancient spread of anatomically modern humans around the globe. For the second I’m thinking in particular of Sohini Ramanchandran’s 2005 paper, Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa, though the model is older than that obviously, as is made clear in the acknowledgments. For the massive ground that the paper covers when it comes to the latest findings it is highly concise, and I commend it to anyone wishing to dive into this exploding literature. Pickrell & Reich show how the analysis of dense marker data sets with more powerful techniques has allowed for the teasing apart of the interlaced layers of the historical genetic palimpsest. But, the complement to this has been the development of the field of paleogenomics, which allows for the explicit analysis of ancient genomes. Another section of the preprint touches upon the technological changes which are allowing for more and more DNA analysis of ancient samples. In particular they point out that rather than focusing on sequencing very rare pristine remains the near future may be in looking at known SNPs on a larger number of samples, because the technical challenges for such typing are far lower.

Credit: Maulucioni
Credit: Maulucioni, Haplogroup R

The preprint is focused on the genomic aspects of this research because the authors are statistical geneticists, but it does not hesitate in offering up a host of historical and archaeological hypothesis which might be tested in the next few years. Also, they do not take a definitive position on the role of long distance migration and punctuated admixture events, as opposed to more continuous gene flow (though the methods which analyze contemporary populations seem to be better at detecting the former). So I will hazard a general model. It seems that root of what is driving these demographic changes are cultural changes. And cultural changes over the past ~30,000 years have been very fast and punctuated, and have accelerated. To given an example, the cultural chasm between a Egyptian in 500 AD as opposed to one in 500 BC would be far greater than that between two that lived in 500 BC and 1500 BC. Whether the word “revolution” is necessary for cultural adaptations such as the acquisition of agriculture, it seems clear that these were shifts in lifestyle which radically changed the local human demographics, as some populations entered into a phase of rapid population expansion in a condition of land surplus (e.g., farmers can extract many more calories per unit of land than hunter-gatherers, so the first farmers invariably encounter massive land surplus and  operate at the higher boundary of productivity). Basically Peter Bellwood’s model in First Farmers captures many of the broad features of what occurred in the Holocene to produce ubiquitous admixture we see in the map at the top of this post (the methods pick up the strongest signals, and so usually underestimate admixture). Small group of individuals acquired a cultural adaptations which resulted in a winner-take-all scenarios of demographic expansions until a new equilibrium was attained repeatedly over the past 20,000, and especially 10,000, years. These the primary layers in the palimpsests that geneticists are teasing apart. Additionally, I will add the proviso that I suspect these long distance leapfrogs often became strongly male-biased in the genetic signal. It would be totally unsurprising to me if haplogroup R has its origins in the North Eurasian population which has left a legacy in Native Americans and Europeans.

Archaeologists and historians are going to be reluctant to shift from a dominant position which is skeptical of migrationism. Part of this is due to an ideological bias which emerged after World War 2. It is also simply the fact that the statistical methods employed by the newest batch of researchers are abstruse and difficult for outsiders to decrypt (though I find the methods in Ancient Admixture in Human History comprehensible after a close reading, so it’s not impossible). But archaeologists and historians are essential in constructing plausible models which can explain the genetic patterns we see around us. The motive engine for these changes are cultural phenomena, and cultural researchers are the ones who can shed the most light on the possibilities.

National pride in Ukraine by region and home language

I dislike the tendency to have opinions on topics by recycling cliches and superficial data in circulation. After all there are free and useful resources such as the World Values Survey. There is a question within it that asks “How proud of nationality” one is. The results below are from a survey taken in 2006. The  home language and regional difference are obvious.

Demographic Category N Very Proud Quite Proud Not Very Proud Not Proud At All
Russian 484 0.224 0.43 0.235 0.112
Ukrainian 421 0.449 0.42 0.101 0.03
Western 212 0.536 0.352 0.085 0.027
Eastern 290 0.19 0.445 0.252 0.113
Central 278 0.353 0.475 0.136 0.036
Southern 137 0.26 0.41 0.2 0.13

But the 1999 survey had results by oblast, a finer grain. I mapped the results below, as well as the raw data. The darker the shade, the more patriotic. Note that Crimea is an outlier.

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Religion is important to understand

300px-Quan_Am_1656On Twitter and elsewhere (e.g., on this weblog, in real life) I often get into confusing arguments with people when it comes to religion because I approach the topic from a somewhat strange angle. Specifically, it is one which integrates cognitive science, evolutionary anthropology, intellectual history and sociology. My interest in this topic was more in evidence in the middle years of the last decade (yes, I’ve been blogging a long time!). One of the last long posts on the topic I published in 2007 was titled Levels of analysis of religion, Atran, Boyer & Wilson. The shorter version is that I believe it is important to understand religion from the ground up. Ergo,

– Religion as a cognitive phenomenon which emerges out of banal basic human intuitions

– Religion as a social phenomenon which emerges out of the interaction and cooperation of individuals within groups

– Religion as a social phenomenon which emerges out of the interaction and conflict across groups

– Religion as political phenomenon which emerges out of the interaction of different groups, constructing a ‘meta-ethnic’ identity (using Peter Turchin’s terminology)

– Religion as an intellectual phenomenon, which can be bracketed into two classes, the mystical and the philosophical-rational

The last is to a great extent what we moderns think of religion as. That is, religion qua religion. Some who are more aware of history and anthropology might acknowledge a phase of ‘primal religion,’ which is pre-philosophical. Animism and such. What my study of religion suggested to me is that the fixation upon religion as a intellectual system totally misses the primary reasons that religion exists, and why it has existed for all of human history and has had adherents across most of humanity. To see how this is relevant, analyses of individual religious believers of various world faiths has emphasized how incredibly similar their conceptualizations of the supernatural world is when stripped away of the exoteric terminology. By this, I mean that terms such as ‘monotheistic,’ ‘henotheistic’, and ‘polytheistic,’ do not really sink deep into the mental architecture of humans. They’re surface concepts with a logical coherency, such as non-euclidean geometry. But intuitively they’re as substantive as the colors upon a flag.

Obviously I’ve moved onto to other things, but perhaps the field has also updated. I checked out Justin Barrett’s Cognitive Science, Religion, and Theology: From Human Minds to Divine Minds to see if the scholarship has moved in this decade. I’ll read it when I have time. My personal experience is that most educated people are weak on understanding the lower levels of the organization of the religious phenomenon. The psychology and social structure. Pascal Boyer’s Religion Explained is a rather easy introduction. David Sloan Wilson’s Darwin’s Cathedral is probably the best treatment of a neo-functionalist understanding of religious organization. Scott Atran’s In God’s We Trust is a harder read, but worth it.

Austronesians out of the cauldron


Many years ago I mentioned offhand the idea of the Bantu Expansion on Jonathan Edelstein’s weblog Head Heeb. To this someone responded that the idea of the Bantu Expansion was contested. By who I asked? My interlocutor declined to say. The point of bringing up this old exchange is that on questions prehistorical the scholarly field is such that obfuscation and revisionism are the things of doctorates and controversial high cited papers. And yet the truth Is. The archaeological, linguistic, and now genetic, evidence for the Bantu Expansion is overwhelming. There can be no denying it, no matter how much one deconstructs the semantics or argues about the historical context in which the paradigm crystallized.

And so it is with the emergence of Austronesians. Linguistics and archaeology already were rather clear on the pattern of expansion, and when. But now an ancient DNA remain from off the coast of Fujian dated to ~8,000 years ago solidifies in totality the where and when. This is not an argument anymore. Early Austronesians: Into and Out Of Taiwan:

A Taiwan origin for the expansion of the Austronesian languages and their speakers is well supported by linguistic and archaeological evidence. However, human genetic evidence is more controversial. Until now, there had been no ancient skeletal evidence of a potential Austronesian-speaking ancestor prior to the Taiwan Neolithic ∼6,000 years ago, and genetic studies have largely ignored the role of genetic diversity within Taiwan as well as the origins of Formosans. We address these issues via analysis of a complete mitochondrial DNA genome sequence of an ∼8,000-year-old skeleton from Liang Island (located between China and Taiwan) and 550 mtDNA genome sequences from 8 aboriginal (highland) Formosan and 4 other Taiwanese groups. We show that the Liangdao Man mtDNA sequence is closest to Formosans, provides a link to southern China, and has the most ancestral haplogroup E sequence found among extant Austronesian speakers. Bayesian phylogenetic analysis allows us to reconstruct a history of early Austronesians arriving in Taiwan in the north ∼6,000 years ago, spreading rapidly to the south, and leaving Taiwan ∼4,000 years ago to spread throughout Island Southeast Asia, Madagascar, and Oceania.

It is done.