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A Collection of Interesting, Important, and Controversial Perspectives Largely Excluded from the American Mainstream Media
Gene Expression Blog

the-clan-of-the-cave-bear On Facebook Nathan Pearson challenged me to name 10 books that have stuck with me. Many of you have probably been tagged on this challenge. For what it’s worth, here’s the list:

Principles of Population Genetics* (Hartl & Clark)
From Dawn to Decadence* (Jacques Barzun)
The Language Instinct* (Steven Pinker)
History and Geography of Human Genes* (L. L. Cavalli-Sforza)
Prelude to Foundation* (Isaac Asimov)
In Gods We Trust (Scott Atran)
The First Man in Rome (Colleen McCullough)
Genome (Matt Ridley)
The Rise of Western Christendom (Peter Brown)
The Bible with Sources Revealed (Richard Elliott Friedman)

The challenge stipulated that you not think too long, and I came up with the list in less than two minutes. But the first five, which I’ve placed asterisks next to, came to mind within 10 seconds. I’m rather sure that these five would be on any list of 10 books of note from my own perspective. The History and Geography of Human Genes and Principles of Population Genetics probably explain to some extent why I’m where I am professionally. From Dawn to Decadence is a testament to the continuity of the life of mind of a sort which I aspire to attain (though I doubt I will). Steven Pinker’s The Language Instinct opened up for me a window to a world where disciplinary boundaries are violated for both fun and profit. The last five took me longer because there are many books which have stuck with me with at the next tier of salience. These might change from instance to instance, though the set isn’t that large.

Prelude_to_Foundation_cover Which brings me to Prelude to Foundation. Why is it in the top five? It’s not even the best of the Foundation novels (I would probably go with Foundation and Empire for that). As Nathan pointed out my list leaned toward non-fiction. Prelude to Foundation is on this list because it is the first fiction book I proactively selected at the library at the age of 13. The main reason I picked it is because I’d read some of the author’s non-fiction works for children when I was younger, and was curious that he’d written science fiction (only later did I find out that he was originally known as a science fiction author). But I have to be specific here. After responding to Nathan I realized that I’d read two works of fiction before Prelude to Foundation, Mrs Frisby and the Rats of NIMH, when I was 12, and Clan of the Cave Bear, when I was 9. My reading Clan of the Cave Bear was something of a mistake. I was sleeping over at a friend’s house, and he had a copy of the book, which I mistook for a work of paleontology. I began reading it sometime around 9-10 PM, and kept going until the sun came up, when I was done. Mrs Frisby and the Rats of NIMH I read over an extremely boring Christmas vacation where my parents visited old friends for a week, and I forgot to bring any books and had to find something to read in the house we were staying at.

This is autobiographical trivia, but I thought I’d submit it into the record because as you can tell by the precision of my recollections I had very little interest in fiction when I was younger. To some extent this remains true, when I have little marginal time I continue to read non-fiction and basically cut out fiction totally. From interacting with people as I grew older I began to realize this was a little strange. I wonder how many other children are the same as me? I’m also curious how my children will turn out.

Addendum: To be clear, I was a huge reader of non-fiction from about the age of 7 onward.

• Category: Miscellaneous • Tags: Reading 
Credit: Segal, Nancy L., Jamie L. Graham, and Ulrich Ettinger. "Unrelated look-alikes: Replicated study of personality similarity and qualitative findings on social relatedness." Personality and Individual Differences 55.2 (2013): 169-174.

Credit: Segal, Nancy L., Jamie L. Graham, and Ulrich Ettinger. “Unrelated look-alikes: Replicated study of personality similarity and qualitative findings on social relatedness.” Personality and Individual Differences 55.2 (2013): 169-174.

The New York Times summarizes some new research in behavior and personality, Holding a Mirror to Their Natures: Looking at Twin Personality Through Look-alikes:

As she expected, the unrelated look-alikes showed little similarity in either personality or self-esteem. By contrast, twins — especially identical twins — score similarly on both scales, suggesting that the likeness is largely because of genetics. Her results were published in the journal Personality and Individual Differences.

For a second study, she teamed with a skeptic, Ulrich Ettinger, a psychologist at the University of Bonn in Germany who had heard about the look-alike project during a postdoctorate at the University of Montreal.

“I thought that if two people looked alike, they would have similar personality traits because people would treat them the same,” he said. “For example, I thought men who looked alike and were tall and handsome would probably be extroverts.”

Their analysis was consistent with the findings of Dr. Segal’s first study: Personality traits do not appear to be influenced by the way people are treated because of appearance. Moreover, they found, there appears to be no special bond between look-alikes.

Segal, Nancy L., Jamie L. Graham, and Ulrich Ettinger. "Unrelated look-alikes: Replicated study of personality similarity and qualitative findings on social relatedness." Personality and Individual Differences 55.2 (2013): 169-174.

Segal, Nancy L., Jamie L. Graham, and Ulrich Ettinger. “Unrelated look-alikes: Replicated study of personality similarity and qualitative findings on social relatedness.” Personality and Individual Differences 55.2 (2013): 169-174.

The original study, Unrelated look-alikes: Replicated study of personality similarity and qualitative findings on social relatedness, is quite modest in scope. You can see the sample sizes are not large in the table to the left. With that said, I think this is adding to a growing body of results that validate the soundness of the original work on twins in behavior genetics. For many reasons this research program has come under sharp critiques over the past 50 years, but it seems to me that the big picture findings NoTwoAlike of modest heritabilities for most behavioral phenotypes is holding up. For a complementary tack I suggest Whole genome approaches to quantitative genetics, which uses different methods to explore some of the same class of
traits. Relying on the body of twin research alone as a foundation might be a shaky basis for conjecture, but now this area is going multi-disciplinary,
allowing for a stool with multiple legs. Of course all it is doing is confirming modest heritabilities for behavioral phenotypes. But one needs to remember that a lot of the environmental component is not amenable to control, whether by parents or society (i.e., it is “non-shared environment”).

God does play dice.

• Category: Science • Tags: Behavior Genetics 

Recently in Washington D.C. at the International Conference for Genetic Genealogy Spencer Wells ran through a survey of personal genomics, and asserted that over the past year we’ve nearly doubled the number of genotypes on dense marker arrays, from ~1 million to nearly ~2 million. Talking to people that seems about right, 23andMe is approaching the million mark itself alone. Combined with the databases of National Geographic, Ancestry and Family Tree DNA the 2 million mark is surely approaching us. But the presentation wasn’t simply about personal genomics today. He integrated the modern changes to events which occurred over the past generation to bring genetics to the people, and allow its widespread utilization among researchers to explore historical questions. Coming out of the Human Population Genetics Lab at Stanford in the 1990s Wells pointed out that the constituent populations of the HGDP were selected by L. L. Cavalli-Sforza consciously to be biased toward those which were more isolated and genetically less subject to globalization. The theory was to pick up stronger signals of ancient population structure which might be obscured by more recent movements of peoples across the earth.

MDS representation of Europeans, with a focus on Germans. Click to englage. Credit: Family Tree DNA

MDS representation of Europeans, with a focus on Germans. Click to englage. Credit: Family Tree DNA

By and large Cavalli-Sforza’s intuition has been validated. The HGDP data set has yielded enormous insight, first with classical markers (see History and Geography of Human Genes), then during the Y and mtDNA era around 2000, as well as microsatellites and dense SNP arrays in the aughts. I’ve heard that the Sardinian samples that Cavalli-Sforza selected were somewhat less cosmopolitan than other Sardinians that have been collected later, indicative of his personal knowledge of Italian genetic variation on a personal level. But he also had the area knowledge to sample both the western and eastern Pygmy populations of the Congo. The evolutionary history separating these two groups is likely on the order of that dividing inter-continental populations outside of Africa, and the eastern Pygmies in particular are an invaluable reservoir of human genetic variation. To answer a few big questions a data set of 1,000 specially selected humans from across the world turns out to have been sufficient.

But there is a flip side. The answers to the many small questions are going to require much more sample coverage. Wells himself illustrates this reality, as he recounted a story from his Geno 2.0 database where a few percent of ethnic Hungarians exhibit Central Asian uniparental haplotypes. He points out that standard analyses don’t show anything special about Hungarians, but then again you are likely to miss admixtures on the order of a few percent here and there if you are working with sample sizes of less than 100, which is still typical for European nations. Even a large data set, such as the POPRES, is dwarfed by those of commercial firms and National Geographic.

Germany population density

Germany population density

Last week I reported that Afrikaners do seem admixed using the Family Tree DNA database. But that’s not the first strange thing that I saw. When devising myOrigins I had to attempt to tackle the problem of German ancestry and assigning individuals to a particular cluster. I was skeptical for a simple reason: the historical literature was clear that substantial numbers of Germans from the eastern zones of habitation were acculturated Slavs. But I was met with a surprise. Yes, the genetic variation showed substantial amount of admixture with Slavs. Using MDS/PCA you can see that there is an admixture cline with a Polish reference population for individuals who state that both their parents were born in Germany. But there is a second distinct cluster among Germans which overlaps with that of northern France. I don’t have data on the scale of specific geographic points, but my suspicion is that the region around Cologne is genetically distinct because of long-term gene flow with northern France. The scale of Hugenot migration to Germany in the 18th century seems unlikely to explain this.

On the scale of the “big questions” this is trivial and of minor note. But, to answer this sort of question about genetically close populations you need dense geographic coverage and large population sizes. Currently only the personal genomics firms have this, to my knowledge. POPRES and Framingham Heart Study both have sample sizes in the ~5,000 range total. 1000 Genomes is an improvement, but even its sample sizes and coverage is not sufficient. Where are we going? Spencer Wells talks a lot about citizen science. Many of the enthusiasts for scientific genealogy have done very deep analyses of their own genotypes. They certainly have skills to analyze bigger datasets. If computing power is needed then an Amazon cloud server could provide that. The problem though is that customer data can’t just be shared by the big companies themselves. In the short term the ultimate solution is to scale up projects, like Harappa DNA, and formalize their structure so that those who submit their genotype data are protected in some fashion (e.g., exposure of identity). Academic scholars are going to be focusing on whole genomes, more subtle methods, as well as exotic and obscure populations which can get at the big questions. To really see my point, see what Google Scholar returns when you type “genetic population structure germany”.

• Category: Science • Tags: Germans 

Well, there was an earthquake in Northern California. Everyone’s OK here, though it wasn’t exactly a minor event across the region.

• Category: Miscellaneous • Tags: Open Thread 

Religion_Explained_by_Pascal_Boyer_book_cover My post The Islamic State Is Right About Some Things was a “success” as far these things go. It was noted in a column in The New York Times, and highlighted issues which you can see being emphasized in pieces in Slate and The Spectator. But obviously in a single post there is a lot of nuance which I had to elide for reasons of space. Though I may be a population genomicist by day, I do think that in certain domains outside of my bread & butter I bring insights which you can’t find elsewhere, so I try to inject it into the broader discussion. But I’m limited in what I can do in a single post. One of the things I noticed as my post was circulating is that many people asserted that I was suggesting you can understand the actions of the Islamic State by the nature of its theology. Long time readers (I’ve been writing for 12 years on these sorts of issues) might be surprised by this, as was I, because actually I think that is one of the major problems that people have when attempting to understand the nature of religious phenomena. Theology is an abstruse field which is the purview of religious professionals of a particular sort. The vast majority of humans today are marginally literate at best, and for most of human history have been illiterate. To put it succinctly and semi-accurately I think our interpretations of theology are actually effects of prior beliefs, which are due to non-theological parameters. For example, I suspect most Christians would assert that their theology is such that slavery is anathema to their moral system with a proper understanding of God (i.e., theology). Obviously this was not so for the whole of Christian history up until 1800. One conclusion I derive from these sorts of facts is that theology derives its content from the subjective preferences of its practitioners. It is not like mathematics, an objective sequence of inferences and derivations from axioms. Nor is it like the natural sciences, extending itself step by step along a scaffold defined by the world around us. Rather, it starts from a presupposition, that God, with particular semantically distinct characteristics, exists, and then proceeds to enter into complex and subtle interpretations of that fact.

0195149300 I have come to this state of affairs over time through reading. Though I was raised in a religious (Muslim) environment, it was not exceedingly devout or observant, and my personal beliefs were rather devoid of much interest or consideration of supernatural entities. For some people God is an intuitive and intoxicating concept, which draws them in a magnetic fashion. For me a lack of belief is, and was, the natural state. Atheism bubbled up naturally, unbidden, at the age of eight when I decided to look within. When I considered God’s existence seriously, I couldn’t help but reject it. This meant that my understanding of religion has always been as an outsider, and I tended to take religious people at their word when it came to what they believed and how they believed. Religious people of the sort I interacted with explained that their faith was revealed in a set of scriptures, and from those scriptures one could derive the nature of religion. Even religions, such as Roman Catholicism, where scripture is not emphasized generally accept that the foundational texts are necessary and essential in truly comprehending the faith in a deep way with mind (as opposed to just receiving sacraments through liturgy). This was congenial to my mind, as it rationalized religion, turning into a system of propositions from a set of axioms. My scientific bent meant that I naturally understood this sort of mentality.

Therefore, to understand something like Islamic violence, one only need to look at the foundational texts. But though this seems like a fruitful way to go I no longer believe it describes the structure of reality because on an individual level religious belief and practice does not seem rooted at all in texts. Though one can make broad correspondences and draw arrows of causality, with an understanding at a lower and more fine-grained scale this model has as much validity as Galenic medicine. It captures fragments of reality and presents it before us in a persuasive fashion, but at a deeper level of inspection it fails to explain the basic mechanics of religious belief. To understand how I came to this position one has to know that I have long been interested in evolutionary psychology, and therefore cognitive science. After 9/11 I decided to read books on religion besides the basic scriptures, and I stumbled upon the field of evolutionary cognitive anthropology, and in particular the scientific study of religion in the naturalistic paradigm. Two of the primary sources in this domain are Scott Atran’s In God’s We Trust and Pascal Boyer’s Religion Explained. In these dense works they illustrate the cognitive foundations of religious belief and practice, and exposed me to the reality that despite what many religious believers might tell you religious scripture is actually a sideshow to the richness of the phenomenon. Like the coffee table book that one proudly displays, the value of scriptures is that is a visible marker and a common point of reference, as opposed to an instruction manual. In Theological Incorrectness the author explores the reality that religious people don’t even seem to believe what they say they believe on a deep level. For example, monotheists and polytheists seem to have the same internal model of the supernatural world, despite their explicit verbal scripts being very different. To put this in another context, many people who espouse views which deny the existence of the supernatural still get “spooked” in a dark cemetery. Why? They are sincere in their belief that there are no ghosts and demons in the dark, but in the deep recesses of their minds reflexive intuitions honed over evolutionary time remain at the ready, alert for any sign of danger in the darkness. Similarly, most religious people may believe sincerely in a glorious afterlife, but when there is a gun to their head they may soil themselves nonetheless.

Belief matters, but it seems likely that it matters at the margins. For whatever reason we humans tend to believe that we have explicit control over our beliefs and actions, and our decisions are due to conscious reflection. This is just often not so, and it has been scientifically validated to my satisfaction. On a personal level I think it is possible that in a different social milieu I would have “rediscovered” my faith in God at some point because of constant feedback from my peers. Though the United States is often depicted, correctly, as a particularly pious developed nation, it is not difficult to seal oneself in a secular bubble. Very few of my friends are religious, despite most Americans being religious. So my atheism is nicely insulated from countervailing pressures. My beliefs, my understanding of reality, is the outcome of a complex interaction between my dispositions and my social-cultural environment. So it is for us all.

But I don’t want to imply from this that if you understand the cognitive science of religion you understand religion. Rather, it is the basic general chemistry of the understanding of the religious phenomenon. In Darwin’s Cathedral David Sloan Wilson outlines a theory of religion which explains the patterns around us in functional terms; i.e., religions as forms of cultural adaptations. Though I’m sceptical of religious models predicated on rational choice theory, that also has its utility in particular contexts. Religion in a socially corporate context such as India is far different from that in the United States, where religion is understood in more individual terms (e.g., defection from a mainstream religion to another mainstream religion does not necessarily entail a massive rupture in your social ties to friends and family in the United States, so churn is common).

So where does this leave us in relation to the Islamic State? Does genocide history and scriptures of Islamic explain its atavistic savagery? I think not. Unlike most Muslim spokespersons I don’t think the behaviour of the Islamic State is “un-Islamic.” Religion is to my mind a made-up affair, and people can remake it in its own image however they want. And, as a point of fact the early Wahabbi movement in the 18th century exhibited many of the same ticks as the Islamic State, down to genocide treatment of those who avowed wrong belief. What I found particularly interesting in a detached manner about the Islamic State is how well versed many of its proponents are in a particular streak of the history of Islam. Watching the Vice documentary of the Islamic State I can pick up terms and concepts from my rudimentary religious education, as well as references to “the Romans,” which in that case refers to the Byzantines under the Heraclian dynasty. Rather than theology I suspect history is a better guide as to what’s going on, and why, from the violent exclusive strain of Islam which periodically emerges from the Kharijites down to the Wahabbis, to early modern period and post-colonial conflicts, as well as the ethnography of political radicalism among small motivated groups such as the anarchists. Most proximately the Islamic State clearly draws energy and strength from Sunni resentment toward Alawite hegemony in Syria and Shia dominance in Iraq. Over time this may evolve into something else, as a generation grows up under the influence of the message of the Islamic State and its broader Weltanschauung. It is essential to keep in mind both the generalities (e.g., it is a Sunni movement) and particularities (e.g., it is global in its imagination and aspiration, at least notionally) when attempting to gauge the possible arcs of the future.

Addendum: And in the interest of frankness, I will also admit that though comments can be highly informative, I don’t listen closely when someone decides to lecture me on the nature of religion because it is rare than I encounter anyone with as much breadth of knowledge as me in this domain (i.e., I have read economic, sociobiological, cognitive, and historical models of religion). If I seem to dismiss your opinion, that’s probably because I don’t think much of your ideas because you likely know far less than I do.

• Category: Foreign Policy, History • Tags: Religion 

Woman_in_niqab,_Aleppo_(2010)USA Today is blasting a headline, More British Muslims fight for Islamic State than Britain, based on the fact that a conservative estimate suggests that 800 fighters for the Islamic State hold British Passports. It turns out that 600 Muslims serve in the British armed forces, which number 200,000. A separate article in The New York Times gives ballpark figures of 10 to 20 thousand as the number of fighters for the Islamic State overall. That means that 5 to 10 percent of the forces of the Islamic State are British.

There are about 2.7 million Muslims in the United Kingdom. There are 1.6 billion Muslims in the world. That means 0.17% of the world’s Muslims are British. About 1 out of 600. Let’s say that 5% of the fighters for the Islamic State are British. 1 out of 20. British Muslims are represented at a 30-fold greater rate in the Islamic State than their world-wide representation among Muslims. Overall about 2,000 Europeans are believed to be serving in the forces of the Islamic State. About 20 to 45 million Muslims live in Europe (this is dependent on whether you’re talking about the European Union only, or include Russia). So at most 3% of the world’s Muslims are European nationals. But they make up 10 to 20 percent of the fighting forces of the Islamic State, depending on how you gauge the figures.

I review these numbers because I believe they are a place where we can start to grapple with the facts that confront us. It is easy to say “Islam is the problem,” but that is as informative as saying that all phenomena can be reduced to physics. That is true on some level, but it is useless in a practical sense. The gross over-representation of European Muslims is of interest, because if it was simply Islam then there wouldn’t be an over-representation. On flip side it seems hard to deny that Left multiculturalism which presupposes that accommodation and acceptance will serve as a balm against all separatist inclinations among Muslims simply is hard to support. Britain arguably is the most accommodating of European nations to Islam and the Muslim community, but it is contributing far greater than its quota to the forces of the Islamic State. These issues are complex, but they need to be confronted without qualms. The chickens are going to come home to roost soon.

Addendum: “European Muslims” includes a diverse array of individuals and populations. There are European ethnic groups which are historically majority Muslim, such as Albanians and Bosnians. Then there are the immigrant communities. And finally there are the converts.

• Category: Foreign Policy • Tags: Islamic State 
Credit: Forbes

Credit: Forbes

Matt Herper’s piece in Forbes, Flatley’s Law: How One Company Is Creating Medicine’s Genetic Revolution, is a must read. Here’s the conclusion:

It’s hard to disagree with him. The cost of sequencing a human being’s DNA is less than one-hundred-thousandth of what it was when Flatley started running Illumina 14 years ago. Illumina is hoping to lower the price further. Ronaghi, the CTO, says the market has been disrupted every time the cost of sequencing has dropped by five to ten times. He foresees DNA sequencers that might cost $10,000, as compared with $250,000 for Illumina’s midline models, opening up whole new markets–and cures. Says Flatley: “The road maps that we have are pretty breathtaking as far as where the technology can move in the next three to five years.”

As narrated in the piece competiters have tried to take Illumina down a notch since 2008, and failed. So you don’t want to bet against them. That being said its dominance is having an effect on the famous chart of “cost per genome” decline. With the stabilization of the monopoly prices haven’t really dropped much since 2012. It might take a full frontal assault by a credible competiter like Oxford Nanopore to induce more than incremental change on the margins.

• Category: Science • Tags: Illumina 

In the post below I made an offhand comment that most Americans with colonial stock in their family could probably trace at least one genealogical line back to a Native American. To some extent this implies omniscience, as most people don’t have such a paper trail. But to give an example of what I’m talking about, a huge number of Americans can trace descent from Pocahontas, because her great-grandson John Bolling is an ancestor of the semi-endogamous gentry of Virginia, the First Families.

America before 1800 was one of the world’s highest fertility societies. The over 1 million people living in New England at the time of the American Revolution were almost totally descended from ~30,000 settlers who arrived in the 1630s from England. Because of this finite pool of ancestry the genealogies of people of Yankee stock often intersect, and the same individuals show up over and over. Just a few Native Americans in the genealogy of settler stock can quickly propogate, so that in the present day it is entirely likely that the majority of the population with settler ancestry would be able to trace a sequence of ancestors back to someone who was of Native American stock.

But, that doesn’t mean the vast majority of these individuals would exhibit evidence of ancestry on the genetic level. The reason is illustrated in the chart above, published in a blog post by Graham Coop’s lab, How much of your genome do you inherit from a particular ancestor? The answer is that for ancestors who lived in ~250 years ago, and don’t show up in your genealogy over and over (so they get more than one shot), you are unlikely to have inherited any distinctive genetic segments. That’s because aside from parent to child transmission there’s a random component around the expected value of how much ancestry you are going to inherit from an individual, due to segregation and recombination at the genomic level. The shuffling during meiosis usually skews the fraction transmitted from the maternal and paternal parents of the transmitter away from parity (50% each). As the expected fraction get’s smaller and smaller with each generation it is no surprise that there is a high probability that some segments of ancestry don’t get transmitted at all.

The above framework has interesting implications. One of the results of Afrikaner admixture is that it was relatively evenly distributed across the sample. Instead of one individual with 5-10% non-European ancestry, and the rest with ~0%, the range was closer to 3-7%. I’ve done some local ancestry inference with RFMix, and the segments are all over the genome, and not particularly long. Admixture on the order of 250 years ago seems plausible, in line with the historical evidence in regards to the ethnogenesis of the Boer/Afrikaner people. The people who moved into the Dutch settler population with large amounts of non-European ancestry were not isolated individuals, like Pocahontas. Almost certainly they were a substantial number in the original founding population of thousands. In contrast in a place like Canada a segment of Native American ancestry among Quebecois or old stock white Anglo-Canadians reflects the Pocahontas scenario. A few non-Europeans entered the genealogical tree of the compact and endogamous community, and so are direct ancestors of most or many, but their genetic segments are only found in a small fraction.

• Category: Race/Ethnicity, Science • Tags: IBD 

Simon van der Stel, first governor of the Dutch Cape Colony. His maternal grandmother was an Indian slave

Simon van der Stel, first governor of the Dutch Cape Colony. His maternal grandmother was an Indian slave.

In the comments below a question was asked about the non-European admixture in white Canadians, New Zealanders, and Australians. It was prompted by the fact that low levels of non-European admixture do seem to be found in most whites in the Family Tree DNA database where both parents were born in South Africa (granted, a small sample). My hunch is that these individuals must be Afrikaner, because I have a hard time understanding how else one would detect Khoisan and Southeast Asian ancestry (West African and South Asian ancestry would be easier to explain). So what about other “white dominions,” those realms of the British Empire united by being either dominated or ruled by white people. I actually just looked at the data for Australia, Canada and New Zealand. The sample size for New Zealand was small. But, in these cases those individuals of preponderant European ancestry have no non-European ancestry, by and large. A few Canadians do have some fractions of Native American ancestry. This seems in line with the data on American whites from 23andMe. Only a small minority have non-European ancestry. Afrikaners are somewhat like many Latin American whites, in being visibly white European, but usually carrying some recent non-European ancestry because of the history of their people.

Addendum: Please recall that lack of genetic signal from ancestors 200-300 years back is not uncommon. Most Americans with colonial stock for example can probably trace a line of genealogical descent back to a Native American. But, because of the small fraction most of these genealogical descendants will not exhibit any genomic segments identical by descent with these individuals.

• Category: Race/Ethnicity, Science • Tags: Admixture 

I teased this yesterday, and I don’t like to do that, so I’m going to put up a quick post. Something more thorough will go up on the Family Tree DNA blog at some point soon. Basically I have heard through the grapevine that something on the genomewide patterns of Afrikaners would be published “soon” in the fall of 2012, but that hasn’t happened. So a few weeks ago I went looking in the Family Tree DNA database, and extracted individuals who stated that both parents were born in South Africa. Twelve of those had more than 90 percent European ancestry. So it is likely that these individuals are either Afrikaner or non-Afrikaner South African whites. I’ll hold off on the admixture results until the Family Tree post, but visual inspection made it clear that most of them they had non-European ancestry. American whites and Europeans generally have no non-West Eurasian/North African ancestry, with the exception of some Spaniards, who have small Sub-Saharan segments, probably mediated through the Moors. Many of these individuals had affinities at low levels to Khoisan, South Asians, Southeast Asians, and West Africans. These are as it happens the non-European groups who contributed ancestry to the Cape Coloureds.

So as a preview, below are MDS plots of various populations. I filtered the SNPs down to ~150,000.

• Category: Race/Ethnicity, Science • Tags: Afrikaners 

Been busy. First, I’ll be posting about the genetic admixture of Afrikaners soon. What I can say is that using genome-wide data from hundreds of thousands of markers it’s pretty obvious that the genealogical studies were correct, and that the admixture into Afrikaners of non-European ancestry is on the order of 5 percent. The sources are Khoisan, Bantu, Southeast Asian an South Asian. Basically exactly what you see in Cape Coloureds, but obviously only a very small fraction. Also, this admixture is likely found to some level in most Afrikaners, probably because it dates to a very old period.

Second, there has been lots of reporting recently about the Islamic State kidnapping Yezidi women to convert them. This article in The Washington Post is interesting because it actually presents some nuance in this barbaric group. Because Yezidi women are not Muslim they are being encouraged to convert, but the militants are not molesting them. At least until they convert. A minor issue in the media coverage is that traditionally in Islam it is allowed to marry Christians and Jews. So this is a case where if they had kidnapped Christian women they could have married them without obtaining a conversion, at least by the standards of most Muslims. Also, note that in the Yezidi villages where massacres have occurred it is reported that it was prompted by the killing of several Yezidis who converted to Islam by the Yezidi elders of the village. This is the sort of thing I mean when I caution against rendering black and white judgments of good or evil in a world of gray.

• Category: Miscellaneous • Tags: Open Thread 

download I just want to mention that a friend is coming out with a book soon which many readers might find of great use (I’ve checked out some of the drafts), Bioinformatics Data Skills: Reproducible and Robust Research with Open Source Tools. Talking to some of my colleagues it’s obvious that 10-20 years from now so many of “best practices” will be established, and we’ll laugh at the ad hoc scripting which is so common today. There are some pipelines which are so difficult to implement that I’ve ended up writing my code own code, because I anticipate that it won’t take as much time.

In other news, my post on the Islamic State has been widely distributed, including being referenced in Ross Douthat’s column. I would have chosen a better title if I had known how it would blow up, but who knows such things. Most of the reaction has been positive, but a few have come up with this sort of feedback:

500px-Leonard_Nimoy_William_Shatner_Star_Trek_1968The post was long, so this individual may not have read it in full. Or, they may have some issues with reading comprehension, I’m not the clearest writer sometimes (though often it is by design because sometimes I don’t want to be explicit about secondary or sideline issues). But it’s not an uncommon response over the years when I talk about controversial or difficult things. There are several definitions of rationalize, but the key is that often I write in a somewhat bloodless and detached manner about topics which people are emotional about. The problem here is with people who are emotional and allow their emotions to cloud all ability to reason. To understand something you need to engage in Epoche, detach yourself from your conventional perspective and attempt to fly over the landscape. Those who lack emotional self control can’t comprehend that sort of self control in others, and so impute emotional motives. This is unfortunate, since it helps turn everything into screaming match. On the other hand, I do agree with David Hume that reason serves emotions. But that service of reason is rendered null if the two aspects are muddled.

• Category: Miscellaneous • Tags: Open Thread 

Above is part 1 of a VICE documentary on what it is like inside the Islamic State. Listening to what seem like the sincere voices from within the domains of the Islamic State I am struck by how detached from reality they are. And yet the fact is that a few months ago we would have thought the idea of a polity spanning eastern Syria and northwest Iraq, and leaning upon social-political paradigm notionally from the 7th century, was pure delusion. From the perspective of those who believe that they have the only access to truth, and whose victories defied the expectations of their opponents, it seems natural that dreams of grandiosity would ensue. They believe that they have the mandate of heaven.

It has been expectation that with the conquest of the northern part of Iraq the Islamic State would recapitulate the overreach by its predecessor organization, al Qaeda in Iraq. In short al Qaeda’s brutality toward those under its rule resulted in a rebellion of the people who it purportedly aimed to liberate. But the Islamic State has already forged a path which is different al Qaeda in Iraq. It has won victories on the field of battle, and created not just a shadow state, but the outlines of a true state. Social conformity is a powerful human instinct.

Update, part 2:

• Category: Foreign Policy • Tags: Islamic State 

So I guess you need to be a more successful actor to get full teeth work done? Also, in most cases Key of Awesome actors are better looking than who they are parodying (see the Ke$ha and Rihanna). Not in this case.

• Category: Humor 
Yezidi Peacock Angel

Yezidi Peacock Angel

I’ve talked about the Yezidis many times over the years. The main reason is that I find the obscure marginal sects of the Middle East interesting. This is a part of the world where religious pluralism existed under very precise and strict conditions, and these groups deviated from those conditions and lived to tell the tale. The Muslim rulers, and more specifically in historical memory the Ottomans, tolerated a specific set of enumerated dhimmi, generally traditional Christian and Jewish groups. Though subject to persecution and oppression, in principle these groups had rights to exist within the Islamic framework. Heretics and pagans on the other hand were not tolerated. For example, I have read the account from the 17th century of an Ottoman official who was making a progress from Baghdad to Istanbul, which turns out to be an excellent piece of ethnography. His entourage stopped in an isolated mountain valley in what is today Kurdistan. The local population were not Muslims, and when the official inquired as to their religion they told of how they worshiped the sun. Whatever the details of their origin this group obviously would be classed as pagans, and so the official was faced with what to do with these people. The choices were conversion to Islam or death, the implementation of which would have been difficult at that moment. As a solution the local Jacobite Orthodox Christian bishop agreed to accept them as his own, with nominal baptism. Presumably these people eventually became Christians in fact as well as name. But it goes to show that in the pre-modern world of the Middle East religious diversity persisted in the isolated places.

Groups such as the Druze offend Sunni Muslims because they are clearly derived from Islam itself, and Islam is the capstone religion in its own conception. Alawites seem to have emerged from the same milieu as the Druze, but they have retained a tenuous Muslim identity, which has accelerated under the Assad family. The Sunni Muslim stance toward these groups is that they are viewed as illegitimate heresies, not protected religions. The extent of Salafi* influence in one’s orientation also conditions how Sunnis view Shia (and there is variation within the Shia group, the Ismailis in particular viewed as heretical because their practice and theology differs more in obvious ways from Sunni orthodoxy; the Zaydi Shia are at the opposite extreme, being very similar to Sunni norms).

All this leads up to why the Islamic State, and Muslims generally to a lesser extent, tend to be extremely harsh in their attitude toward the Yezidi sect. The details of the Yezidi belief system are somewhat obscure, like that of the Druze, but they are clearly not Muslim. The media reports that the Yezidi are an ancient religion, with some relationship to Zoroastrianism. Many Kurds will also agree with this statement, assuming that something like Yezidism was the primal faith of their ethnic group. This may or may not be true. The origins of the Yezidi may actually be more like the Druze, if somewhat more ancient and obscure. Part of the lack of clarity I think goes back to the fact that there is some opaqueness overall in the first century or so of Islam. The social-religious world of the Middle East was a product of those years, but it is very different from them. For example Zoroastrianism and Zoroastrian-influenced syncretistic Muslim sects were powerful anti-establishment forces across the Iranian cultural zone down to the 9th century. Quite a few extremist Shia sects (ghulat) seem to have made the transition to post-Islam, often imbibing Zoroastrianism of a Mazdakite flavor. Such a transition though was usually a cultural death sentence. Survival depended upon attaching oneself to a Shia identity, however tenuous (the Alawite strategy), or, fleeing to a geographically isolated region (in some cases these sectarians fled to the Byzantine Empire, and converted to Orthodox Christianity rather than revert to normative Islam!). Flight from the world is what the Druze and Yezidi have done in their fastness.

Yezidi children killed by ISIS in Syria

Yezidi children killed by ISIS in Syria

The current capture of Sinjar has been a humanitarian catastrophe for the Yezidi because it has been one of their traditional redoubts. The kidnapping of women, and the summary beheading or crucifixion of men, can be comprehensible in light of the Salafi Muslim vision of groups such as the Yezidi, which literally should not exist. Their obliteration would bring balance back into the Salafi world. While Christians and Jews may persist with the barest of sufferance, the existence of the Yezidi is an abomination to Salafi Muslims. What is occurring is a ethnic cleansing and genocide in straightforward terms. In fact Salafi Muslims would probably agree with the appellation cleansing, because the Yezidi to them are an offence to Being itself. Their existence is a matter of ritual purity in a metaphysical sense. I am wary of ever making analogies to Nazi Germany and the way it viewed the Jews, but this one clearly is a close fit. There is no path toward accommodation of Yezidi existence for the Islamic State, it is now down to an animal battle of survival for them, as they flee into the mountains as they have done so many times in the past.

nationsbook The relationship of Kurdish Muslims to the Yezidi has often been fraught, but there has been a modus vivendi of late. The Yezidi looked to the Peshmerga to protect them, though in this case the Peshmerga failed. The Kurdish reaction overall seems to confirm much of the argument in Azar Gat’s Nations. It is not civic virtue which is drawing out their outrage, or adherence to the state, but ethnic-national honor as a whole, irrespective of boundary. Their identity as Kurds is motivating them to fight the Islamic State first and foremost (whether the Yezidi are Kurds is under debate, but they are of the same general group of Iranian speaking mountain people). See in The New York Times, Iraq Agrees to Help Kurds Battle Sunni Extremists:

On Monday, the Kurdistan Workers’ Party, a militant Kurdish separatist group in Turkey that for decades has waged an insurgency against the Turkish state, in a statement called for its fighters to go to Sinjar, one of three Iraqi towns where the Kurds were pushed out on Sunday.

“The treacherous ISIS attacks have been humiliating for the Kurds,” the statement said. “Until the Kurds develop a strong resistance, they will not be able to take back their honor.”

The soldiers of the Islamic State certainly seem to behave in a manner which we find ghoulish. But ghoulish behavior is not a monopoly of religious fundamentalists; Assad’s Syrian regime has sent militias to rape and murder children in front of their parents to sow fear into the opposition. The moderate Free Syrian Army has also committed war crimes. But the Islamic State is fighting for principles, a vision, with atrocity as the end and not the means. For the Assad regime atrocity is a tool to instill terror. For the Free Syrian Army atrocity is a reflex against the brutality of the Assad regime. An eye for an eye. In contrast, the vision of the Islamic State necessitates atrocity as the ends of their existence. In theory Yezidis could be given the option to convert to Islam, but the current pattern of killings indicates that pure elimination seems just as likely an end. From my perspective, and most people’s, it is an evil vision. But it is giving its fighters something to fight for. This vision has prompted four upper middle class Indian men to join them, to the shock of the Indian security establishment. The article waxes on about the privileged background of these men, but transnational jihadists have long had a more “up market” demographic. The Islamic State is fundamentally an abstraction, and so appeals to those who deal in abstractions. It is utopian in its fundamentals, just as the Khmer Rouge was utopian. They are attempting to go back to the “year zero” of Islam.

But even error sometimes speaks truth. The Islamic State is right that the Sykes-Pico Agreement is a shambles and ended. The delusion of a multi-ethnic and multi-religious Iraq and Syria has collapsed. What replaces it we do not know. Currently the American government continues to support policies which strengthen the unitary Iraqi state. The major weak point in this strategy is that even the superficial appearance of a unitary Iraqi state seems out of reach. That game is lost. We don’t want to admit it, but it is over. We don’t know what gambits with follow, but the local actors will be ultimate deciders.

Roman_Eagle_by_Wittman80What can be done? The Iraq invasion and occupation has made Americans wary of direct intervention. And rightly so. Unless we wish to take upon the mantle of a New Rome, sending our sons (and now daughters) to impose order and justice, and implicitly the American Way, in foreign lands we are better off not getting deeply involved. On the other hand there is no point in pretending that we are neutral in the clash between antinomian barbarians and ethno-religious autocrats. The latter are imperfect, but they have a vision of life which we recognize as life.** We must stand in some way with imperfect humans when they are battling against organic automata, motivated by an ideology which bears false witness to any traditional social order. People can disagree on the details, but there is a moderate position between total detachment and taking upon the burdens of the world upon one’s shoulders.

I do think that the rise of the Islamic State, and the past 10 years of chaos and violence, suggest that this is the end of the persistence of ethno-religious sects such as the Yezidi across most of the Fertile Crescent. The Jacobites Christians, Assyrians, and Yezidi, lack powerful patrons and protectors. Though most Sunni and Shia would not countenance genocide, they are focused more on the exigencies of their own internecine conflicts. Many minorities already have large Diaspora populations Europe. Tens of thousands of Yezidi live in Germany, and tens of thousands of Assyrians live in Sweden. The most practical short-term solution would be to extend refugee status selectively to ethno-religious minorities to prevent them from being eliminated by genocide. Certainly the dominant Muslim groups of the Fertile Crescent are dying in large numbers in the conflicts, but at the end of the day when peace comes the Syrian and Iraqi state(s) are going to be their making, their dominion. They will have something to build up from. In the long term it seems implausible that the Sunni majority can be excluded from the leading role in governance in Syria. When majoritarianism does come I doubt it will look keenly upon the rights of the minorities after the litany of horrors afflicted upon the Sunni populace by the Assad regime and its Alawite militias.

Of course a final irony is that the migration of the ancient Middle Eastern minorities to the West will likely result in their diminishing over the generations. The corporatist straight-jacket of the Middle Eastern milieu was constricting, but it allowed for a communal identity to maintain itself. In the individualist West these small communities are unlikely to be able to self-segregate in large enough ghettos where their cultural norms are dominant. This means that identity will become a choice, and over time intermarriage will likely result in a decrease in numbers. Though the Yezidi are rightly objects of sympathy, their cultural norms are quite retrograde in many ways. These folkways were adaptive in the circumstances of Kurdistan, a persecuted minority which had to maintain a high level of group cohesion. But in the West they are often impediments to full flourishing, and produce inter-generational conflicts.

Dancing-in-the-Glory-of-Monsters-Stearns-Jason-9781586489298 Finally, currently the world is paying attention to the dire humanitarian situation in northern Iraq because that is where the media spotlight is. And rightly so. But let us remember that these sorts of events have an old pedigree. Consider the Assyrian Genocide of the early 20th century. Many thousands died then, and many thousands are dying now. And what about the three-year-old children shot in front of their parents by the militia loyal to the Assad regime? The events in Gaza are quite raw and fresh, but read Dancing in the Glory of Monsters: The Collapse of the Congo and the Great War in Africa, and you gain perspective as to what atrocity truly is. It reminds me of the apocryphal quote attributed to Stalin, the “Death of one man is a tragedy. Death of a million is a statistic.” Right now infants are dying of thirst in northern Iraq. Horrible. But the Central African Republic still teeters on the edge of genocide. I am not saying that because we cannot do all things we should not do anything, but we should keep in mind that for all the positive trends in the world there is a vale of tears we must confront. The soldiers of the Islamic State fight under the banner of demons, but their enemies are no angels.

Assyrian demon Pazuzu

Assyrian demon Pazuzu

But not all distinctions can be erased. When enumerating the horrors meted out by the Assad regime, or noting the ubiquity of rape in the Congo, I can not help but think that these are the products of human venality. The thugs who murder children for Assad, or the soldiers who rape women in the Congo, may have their ad hoc justifications for what they do. But they do what they do not in a spirit of purpose, but on the orders of their paymasters or in a fit of amorality coming to the fore. Atrocity, even on a grand scale, can still be the marshaling of individual human weakness. The power of the Islamic State derives in part from the fact that it inverts the moral order of the world. Some of its soldiers are clear psychopaths, as the most violent and brutal of international jihadis have been drawn to the Islamic State (as opposed to Al Qaeda, which is more pragmatic!). But a substantial number believe in its utopian vision of an Islamic society constructed upon narrow lines. A positive vision of a few evil goals, rather than a grand quantity of small evil pleasures. The Islamic State ushers in an evil new order, it does not unleash unbridled chaos. Though its self-conception that it is resurrecting the first decades of Islam is self-delusion in my opinion, it is still a vision which can entice some in the Islamic international.

I do not think that the Islamic State is here to stay. I believe it will be gone within the next five years, torn apart by its own contradictions and its rebellion against normal human conventions, traditions, and instincts. But that does not mean it is not going to cause misery for many on its way down. The irony is that the iconoclastic Islamic State may as well be worshiping the idols conjured in the most fervid of Christian evangelical apocalyptic literature, because they shall tear the land end to end and leave it in a thousand pieces, a material sacrifice to their god. They live under the illusion that they are building utopia, but they are coming to destroy an imperfect world and leave hell in its wake.

* The modern Salafis are just the latest in a particular extreme of Sunni belief, which goes back to individuals such as Ibn Taymiyyah.

** My distinction here has some similarities to the typology outlined in the Kirkpatrick Doctrine.

• Category: Foreign Policy, History • Tags: ISIS, Islam, Yezidis 

Posting will be light in August. I probably won’t get to Nick Bostrom’s Superintelligence, but I wish I could. I often don’t agree with people who take transhumanism and its assorted topics seriously, but generally I find engaging them extremely though provoking. Usually people use “thought provoking” as a throwaway line, but I mean it literally.

• Category: Miscellaneous 
Citation: Skoglund, Pontus, et al. "Genomic Diversity and Admixture Differs for Stone-Age Scandinavian Foragers and Farmers." Science 344.6185 (2014): 747-750.

Citation: Skoglund, Pontus, et al. “Genomic Diversity and Admixture Differs for Stone-Age Scandinavian Foragers and Farmers.” Science 344.6185 (2014): 747-750.

We are Whigs, whether we want to be or not. History moves in one direction, and that direction is associated with progress. Progress being something we would recognize as associated with ourselves in some fashion. Ergo, the “mystery” of the evacuation of Greenland by Scandinavians in the 1400s. Today that mystery seems to be solved to the satisfaction of most. With the waning of the Medieval Warm Period the Scandinavian agro-pastoral economic system of production was not a viable form of subsistence at high latitudes. Greenland got less green. In contrast the Greenland Inuit’s ancestors, the Thule culture, were eminently well prepared for the shift in climatic regimes. In a previous more Eurocentric age the curiosity was that a European society which was advanced enough to receive bishops from Rome could be replaced by hunter-gatherers in sealskin canoes.

440px-Saami_Family_1900Of course many peoples would not have been shocked, the ancients were well aware of the concept of societies falling from states of greater complexity or social elaboration to ones of simplicity, as a matter of necessity (see: Dark Age Greece). It was in Europe where the Age of Discovery transformed into the industry & science driven era of European colonialism, that gave us the idea that the world was ascending up a ladder of development evermore, under the aegis of the white race. Cases where Europeans gave ground to non-Europeans, and ones in an earlier mode of production in a historical determinist sense (i.e., societies moving through modes of production in sequence), would certainly raise eyebrows in a culture where the Garden of Eden had been turned into a legend and Greek myths of ages of Gold giving way to Silver and Bronze were seen as anthropological curiosities.

Obviously things have changed a great deal, but the shadow of the Whig, and the vision of eternal progress haunts us. Scratch a Critical Race theorist, and you get James Mill. A Whiggish and Eurocentric perspective colors our own perceptions of the past, even if we live in an age of the critique of all things Western and white. Most especially thees sorts of biases are a problem when it comes to prehistory, when we don’t even have to bother to twist and interpret the past’s words to fit our preconceptions. We can simply impute upon it because it is mute. In this blog I have been talking about the impact ancient DNA has had upon our understanding, and the impact it will have. But the inferences we make are only as good as our interpretative framework. The researchers who are working at the cutting edge of the field understand they aren’t explaining everything. Rather, they are attempting to construct some broad sketches which can serve as a scaffold for more specific detailed understanding of events which transpired before history.

Citation: Cramp, Lucy JE, et al. "Neolithic dairy farming at the extreme of agriculture in northern Europe."

In Proceedings of the Royal Society B there is a paper which explores the dynamics of the transition from hunting & gathering to farming as the dominant way of life in Finland, Neolithic dairy farming at the extreme of agriculture in northern Europe. As you can see in the map to the left Finland spans the same latitudes as southern Greenland. Only its position along the western maritime fringe of Eurasia moderates the conditions so as to make agriculture marginally viable. The paper takes as a starting point what we know in general about the transition to farming in the far northeast of Europe. It came late. Around ~2500 BC. It was associated with the Corded Ware culture. Though such suppositions are fraught with uncertainty, believe that the Corded Ware were the first early Indo-Europeans in Northern Europe. The hunter-gatherers preceding the Corded Ware were of the Comb Cermic culture. The culture relatives of these people in Scandinavia were the Pitted Ware culture.

The basic results of the paper are easy to understand from a non-specialist perspective. Around ~2500 BC there was a very rapid shift to agro-pastoralism utilizing dairy from a predominantly marine diet. This correlates with the switch from Comb Ceramic hunter-gatherers, who were specifically reliant on marine animals in much of Finland, to the Corded Ware people. Later it seems that marine organisms made something of a comeback in the diet of the peoples of Finland, and a culturally more synthetic society emerged, with elements from the Comb Ceramic and the Corded Ware.

This should be somewhat familiar. Genetically it seems that in Northern Europe the arrival of agriculture was heralded by a demographic and culture eruption, which was eventually synthesized with the local substrate. If you read ancient DNA papers Scandinavians today are genetically an admixture of farmers and hunter-gatherers, with perhaps a modest bias toward the latter. The figure at the top of the post illustrates that the Pitted Ware populations seem to be genetically distinct from modern Northern Europeans, and in particular Finns. The same goes for the first farmer populations in the north. They were either emulsified in the still dominant hunter-gatherer demographic substrate, or, they experienced a major die off.

A simple model, implied in this paper, is that the modern Finns are a synthesis of the Corded Ware agro-pastoralists and indigenous hunter-gatherers populations. One can then envisage an admixture shock ~2500 BCE, and the past 5,000 years have been an equilibration. Obviously most people will immediately wonder though about the fact that Finns speak a Uralic language. And more specifically a Finno-Permian language. There have long been arguments about whether the Finns, in a cultural sense, are primal to Northern Europe. This plays out in the context of the fact that non-Indo-European languages in Europe always get special attention. What we do know from high density SNP data, as well as earlier Y chromosomal work, is that Finnic peoples seem to have a connection to populations in Siberia. By this, I do not mean the Ancestral North Eurasians. Rather, a population with affinities to modern Northeast Asians. If the Pitted Ware genetic results can be generalized to the Comb Ceramic people, and I do think they can be, then the Siberian admixture in Finns post dates 2500 BC. Since this element is not found in most populations descended from the Corded Ware (the ones where it is found, the Russians, have historical reasons for likely admixture from Asian populations, or, were Russified Finns), I doubt it is from the Corded Ware. Rather, the most likely scenario involves Finnic peoples moving into the population, and adding themselves as a dominant cultural element. The modern Indo-European language spoken in Finland by natives is Swedish, which arrived during the Common Era. With Swedish cultural hegemony and some colonization broad coastal zones of modern Finland are dominated by ethnic Swedes. But if the model I’m outlining above is corrected then Swedish is not the first dominant Indo-European language in Finland. Rather, an earlier Indo-European speaking population were absorbed by the Finns.

Swedish hegemony over Finland after 1200 was to a large extent a function of the fact that Swedes were a post-tribal population which were in the early states of constructing a nation-state. In Finland they encountered a tribal population which was easy to dominate, and integrated into a Swedish Baltic zone of rule. One ultimate basis of the Swedish superiority in domains of statecraft and social mobilization is probably economic, in that the ecology of Sweden was marginally more favorable to agriculture than that of Finland. The Finnish tribes were operating closer to the margins of subsistence, and at a lower limit of population density enforced by Malthusian strictures. But like the Thule conquest of Greenland I suspect the success of the Finnic tribes from the margins of Siberia is the very fact that they were masters of the cultural adaptations necessary for survival on the sub-arctic littoral of Eurasia. The Corded Ware people were like the Greenlanders of their era, agro-pastoralists who attempted to transfer a southern way of life in totality, but who ultimately were transformed and superseded.

• Category: Science • Tags: Finland 
Citation: Craniofacial Feminization, Social Tolerance, and the Origins of Behavioral Modernity Author(s): Robert L. Cieri, Steven E. Churchill, Robert G. Franciscus, Jingzhi Tan, and Brian

Citation: Craniofacial Feminization, Social Tolerance, and the Origins of Behavioral Modernity
Author(s): Robert L. Cieri, Steven E. Churchill, Robert G. Franciscus, Jingzhi Tan, and Brian

Increased brain size across Homo. Luke Jostins

Increased brain size across Homo. Luke Jostins

Humans are a pretty big deal. I’m human, you’re human. We’re a very successful large mammal. A substantial proportion of the earth’s biomass is us, or, is due to us. So the field of human paleoanthropology gets a lot of attention in comparison to something like materials science, even though materials science is far more practical, and a much bigger deal in our day to day life. Most people have heard the name Richard Leakey. They might not even know there’s a field called materials science.

Because people are interested in paleoanthropology there’s a demand for discoveries, and people promising understanding. The root of a lot of this is ontological. Why us? Necessarily us? But more prosaically many scholars have responded by generating models of the rise of humanity with silver bullet explanations. To give a few examples, fire, tools, gossip, and meat. One phenomenon that has interested scientists for years is the rise to dominance of an African lineage 50,000 years ago, and the subsequent manifestation of “behavioral modernity” in the archaeological record. To illustrate behavioral modernity researchers might present you with the image of ostrich shells which may have been painted, or the artistic caves of France and Spain. I think it is simply enough to contrast behavioral modernity with what came before. The Acheulean tool culture persisted for over 1 million years. Can you imagine a cultural tradition today persisting for 10,000 years? Obviously something changed.

One elegant model proposed by the paleoanthropologist Richard Klein is that human culture is a product of a punctuated evolutionary change, which resulted in a revolution in capacities, and a rapid marginalization of all other populations. The phenotypic manifestation of that neurological shift may have been the capacity for fully featured language. In this scenario the chasm between archaic and modern human populations is enormous. At the opposite extreme you have theories which posit a gradual shift across the Homo lineage over time, with behavioral modernity being only the latest manifestation of a trajectory which was initiated long ago. A possible implication in this framework is that something like us was inevitable at some point, or, the Homo lineage would just go extinct (yes, we are going to go extinct at some point in any case).

In 2005 or so I would probably have been close to the Klein model of relatively quick biological driven changes that gave rise to H. sapiens. Today I am much nearer the second scenario. One of the reasons is that a few years back the geneticist Luke Jostins produced the result that Homo as a whole was undergoing encephalization. To some extent this is obvious in hindsight. Neanderthals had larger brains than their ancestors. But Jostin’s plot suggested to me that the path which led to our big brained lineage had roots somehow early on in the emergence of our broader lineage, and not just in the recent past of H. sapiens sapiens. Only that could explain a world wide pattern across disparate lineages which were genetically isolated. I don’t have a specific outline of what I’m thinking of, but in the generality there are cases where evolutionary processes exhibit path dependence. One could argue then that Homo was going to get big brained, or go extinct. We do know that apes as a whole have been less successful in the evolutionary game if being speciose is a guide over the Cenozoic. Monkeys have taken over many of the niches which were previous held by the apes. There used to many more of us. Homo is then the exception to the rule, as it broke out of the niche which monkeys were taking over, and made lemonade from lemons.

So how might this inevitable process have played out? As implied in the title I suspect that early in the Pleistocene Homo got “trapped” in a unidirectional ratchet where biological changes allowed for the elaboration of complex culture, which then drove further biological changes, again resulting in culture transformations, and so forth. The evolutionary process did not explore the whole parameter space with equal frequency. H. floresiensis stumbled upon a unique, but rare, niche (you can speculate about what it was, but its small size and peculiar anatomy indicate sit differed from others of the lineage quite a bit in its circumstances). In contrast other groups of Homo were getting bigger brained. In fact the shift toward bigger brains leveled off at about ~100,000 years ago, before behavioral modernity. This is probably a consequence of the fact that there are various biological limits in terms of how disproportionate our brains and heads can be in relation to the rest of our bodies (e.g., we are born at a rather fetal stage because otherwise our heads would get too large to fit through the birth canal, whose widening is achieved at some cost to female locomotion). At yet changed continued.

A new paper in Current Anthropology attempts to bring various threads together to explain the rise of modern humans in a manner Charles Darwin would appreciate, Craniofacial feminization and the origin of behavioral modernity. Like most of you I can see that the figure above at the top of this post illustrates two individuals where one is more gracile or feminized than the other. But that’s about it. I don’t know skeletal anatomy well enough to comment with great force on the data within the paper, though it does seem that the results are somewhat confused, with data scarcity and combining agriculturalists and foragers in the Holocene confounding the signal. Nevertheless, they conjecture is that over the past 100,000 years humans have been subject to the domestication syndrome. Less aggressive social behavior at higher densities due to reduction in androgen levels produces the more feminine features in the fossil record. At least according to their model.

The major problems I have is that the signal in their data is not that clear to me. There is a lot of talk about why agriculturalists seem more masculinized than Holocene foragers. Obviously that sort of result is not as “neat” as they might like across the time period of interest. They acknowledge that limitations on their data set might explain this, but that makes me wonder what conclusions they can draw then in the first place from their data. Or, their model is just too simple. It’s a bit rich for me to say that, because compared to Richard Klein’s thesis that one mutation produced modern human behavior the argument outlined in exceedingly elaborate. But, if behavioral modernity arose via processes which were gradual, and often worked upon standing genetic variation, I don’t see why the selection should have been through the same processes across hundreds of thousands of years. It could be that in some epochs higher population density was due to biological changes in humans triggered by culture shifts, while in other phases the higher density itself was driving biological change. This is not congenial from a scientific perspective because it isn’t parsimonious. But it isn’t wrong on the face of it.

• Category: Science • Tags: Human Evolution 

220px-DNA-Sequencers_from_Flickr_57080968 (1)If I’m reading the headlines right the 100,000 Genomes Project in the UK is getting 500 million dollars to see it through its target date of 2017. From what I can tell they haven’t even hit 1,000 genomes, so they need to ramp up. But the way technology in this area is moving it doesn’t seem implausible that they could hit their target. The focus of the project is biomedical, so I hope that there is a good representation of the UK’s Asian and African descended populations. Even proportional representation will increase the number of whole genomes of some of these populations (e.g., the UK is ~5 percent South Asian, so that would be 5000 whole genomes), especially if the coverage is very high.

As is the case with most of these sorts of endeavors the payoff is probably much higher in the medium to long term than in the foreseeable future. Before 2025 for example. But someone’s going to have to make this sort of technology banal and boring first, and the Britain with a centralized National Health Service is probably a good candidate for that. Obviously the results are going to be somewhat top down, but the capital investment is too high in the short term to imagine that a firm like Personalis is going to be able to revolutionize the sector in a broad sense.

I’m skeptical this is vaporware. National pride is on the line, and you have major backers like Illumina. But I have to observe that the Faroes Genome Project hasn’t updated its website for a year. So there are instances of lack of follow through.

• Category: Science • Tags: 000 Genomes 

9780226520438 There’s a new paper in Science, A network framework of cultural history, which is interesting, and naturally a media splash (it is in Science). The paper illustrates the power of “Big Data” in a domain where most people have not thought to utilize big data. The authors state that “we have reconstructed aggregate intellectual mobility over two millennia through the birth and death locations of more than 150,000 notable individuals.” In the past historical judgments, especially those in the domain of culture, had to be conceded to those with a thick and dense personal database gained through a lifetime of erudition. I’m thinking for example the reduction of a lifetime of scholarship that you can literally feel as you work your way through Jacques Barzun’s magisterial From Dawn to Decadence. But there are serious shortcomings with this sort of intellectual endeavor when it comes to gaining a better grasp of reality. A personal example should suffice. I’ve been thinking of purchasing Alan Cameron’s The Last Pagans of Rome. We don’t need to get into the details, but Cameron basically argues for a major revision for our understanding of the Late Antique transition from paganism to Christianity. This argument is buttressed by the fact that Cameron is one of the world experts, a master of the literature without parallel. The problem is that how exactly do you judge the quality of argument from someone who has a better grasp of the topic than you, perhaps by orders of magnitude? Who are you to disagree if Peter Brown is impressed?

Origin_and_Evolution_dust_jacket_small Some of the same issues outlined by Noam Chomsky in his famous critique of fashionable “deconstructionism” actually applies to elements of humanistic scholarship in practice if not the ideal. In actuality I could learn Latin and Greek and wend my way through the scholarship which Cameron draws upon (I suspect that I would do so more slowly because I lack a strong natural adult fluency with languages, but it is feasible). But in reality very few people have the time to reproduce to the same magnitude the knowledge database of a specialist in a particular area. With the diversity within academia it may even be that a given topic has only a few individuals of parity in terms of expertise. Obviously this causes a problem, because at the end of the day many arguments have to be resolved by appeals to authority. There are some workarounds. For example, one may not have specialized knowledge about a particular area, but in many cases specific instances are likely part of a broader pattern. I’m more liable to give credence to a particular argument if I can check analogous cases in other contexts where I do have thick knowledge, and see that it checks out. If, on the other hand, the argument flies in the face of the general trend I am more skeptical.

downloadBut a better ultimate solution is to quantitize and formalize. This is why the above paper is exciting. The only schematic that I can recall from The Origin of Species is a tree of life, the precursor to the phylogenetic trees which are common today. But it was the cladistic revolution, and later the emergence of computational statistical methods, which have revolutioned phylogenetics and turned it into a reproducible science which does not rely upon specialized domain knowledge. Before World War II if you wanted to know about the systematic relationship of ant genera you would have to consult an expert or a work written by experts. Today you can actually pull some sequence data and construct the tree yourself! That is where we need to be when it comes to a scientific understanding of human culture and history.

Nevertheless there are downsides to this process. In National Geographic Peter Turchin says of this work: “This is a terrific data set, but they are not testing a scientific question here….” If you read the paper, and the press coverage, you see lots of neat visualizations which are representations of the patterns extracted from the data, but to a great extent they are representations of what we already know. Very few non-quantitative scholars would be surprised that eminent individuals tend to move from rural areas to urban ones. Or that Rome and Athens were prominent magnets in 300 AD while London was in 1800 AD. There is value to be gained in formalizing this, to establish an algebra of history if you will. But this is not revolutionary; the field of cliometrics has been around for two generations. What is different is that computational methods can be brought to analyze data far more effectively. But a major temptation of this sort of cutting edge analysis is data dredging, as well as the issues that come with ascertainment bias. For example in National Geographic the first author states:

The distance that people moved over their lifetimes has also changed “very little,” the study says, over the past eight centuries. It grew from a typical distance of 133 miles (214 kilometers) in the 14th century to 237 miles (382 kilometers) today, despite the advent of automobiles and airplanes. Schich expected that the opening of the 3,000-mile (4,828-kilometer) trip to the New World after 1492 would stretch the distance much farther.

“People in the past were not so different from us,” Schich says, noting the records include accounts of Jesuit priests who traveled to China in the 17th century. “It’s very strange to think my odds of moving a long distance are similar,” he says, with a laugh.

This is certainly a result that would surprise many, but please remember that the database is a selection of notable individuals. I would bet that the change would be far greater if you had a sampling of most of the world’s population, rather than ~150,000 extremely notable ones from the last few thousand years. Immanuel Kant aside, those people in the past who became famous often did so by migrating and getting involved in the events of the world, which entailed travel. They were atypical (consider also that every single Roman Emperor was probably functionally literate in a world where this was a minority capacity [the idea that Justin was illiterate is probably a slander]).

To make the best use of the data we need to be clear about our thinking. I do think it goes beyond just asserting that we need hypotheses, though that’s part of it. Genomics is the product of the age of big(ger) data, and it has had to deal with problems of false positives being confused for real signals because old statistical thresholds became out of date. Culturomics has a lot it could learn from the experience of biologists before 2010. With all that said, there is a body of formal theory which can move in and start to operate upon the data set. Boyd and Richersen’s The Origin and Evolution of Cultures and Cavalli-Sforza and Feldman’s Cultural Transmission and Evolution are good places to start. Recently I read Alex Mesoudi’s Cultural Evolution: How Darwinian Theory Can Explain Human Culture and Synthesize the Social Sciences, which is newer, and probably aimed at an audience that is a touch less specialist. I highly recommend it for those interested in this topic (if you have an evolutionary genetics background much of it goes fast because it is review of basic theory).

Let me finish with a quote from The Genetic Basis of Evolutionary Change by Richard Lewontin:

For many years population genetics was an immensely rich and powerful theory with virtually no suitable facts on which to operate. It was like a complex and exquisite machine, designed to process a raw material that one had succeeded in mining. Occasionally some unusually clever or lucky prospecter would come upon a natural outcrop of high-grade ore, and part of the machinery would be started up to prove to its backers that it really would work. But for the most part the machine was left to the engineers, forever tinkering, forever making improvements, in anticipation of the day when it would be called upon to carry out full production….

Apply your regular expression substitution where appropriate.

• Category: History, Science • Tags: Cultural Evolution 
Razib Khan
About Razib Khan

"I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. If you want to know more, see the links at http://www.razib.com"