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2016-10-23 08.40.37 Bought Marie Sharpe’s green habanero sauce at Granville Market. The spice level is nothing to sneeze at, and it’s got a nice flavor. But the salt is out of control.

danbo There is a lot of good Asian food in Vancouver. A pretty good meal at the downtown Kirin, but I want to highlight Ramen Danbo. The servers were all young women from Japan, so the ambience and food exhibited an authenticity that’s not typical.

Annexation_Bill_of_1866_mapAfter four days in Canada I really don’t see why at minimum we don’t have a customs union and open borders so we can dispense with these sorts of friction to travel. Canadians are easier to understand in terms of their English for most people who speak General American than some of our fellow citizens. Vancouver in particular reminds me a lot of Seattle, a city I know decently well since I’m from the Pacific Northwest originally and still go back to visit family.

Pandora was blocked in Canada for some reason. And I had to call to make special provisions to maintain data on my phone. Really is there a reason for this?

I am struck by the colonialism described by Colin Woodard in American Nations when it comes to Reconstruction. In his telling Yankees swarmed to the South believing that they could recreate New England in the post-war societies. Eerily familiar in light of what happened after the Iraq War.

51y9UBanyFL._SX386_BO1,204,203,200_ Someone in a comment below asked what population genetics they should read. Start with Principles of Population Genetics. It’s the gold standard. Some people would suggest starting with Population Genetics: A Concise Guide, but I didn’t start with that and I’m fine.

Joe Felsenstein and Graham Coop have some good notes online.

Spent some time with “reiver” online. He seemed curious as to my ability to read a lot and read fast. There’s nothing very impressive or amazing about it actually. I’ve been reading a lot in several areas since I was an early elementary school student, and so I can read and process new information fast because I already have a lot of preexistent structure.

416NQwBS-+L._SY344_BO1,204,203,200_ But you can lose things. For example I read books on cognitive neuroscience more slowly than I used to because I stopped reading in this topic when I went to grad school. I’m a big fan of Stanislas Dehaene’s work, but I get less out of it than I used to. That’s unfortunate.

Overall I do worry that I’ve focused too narrowly in my interests as my brain has aged and I’ve matured. My knowledge of specific areas is deeper, but I am not as broad in my curiosity as I used to be.

ASHG was good. I’ll say more later, but the popgen was a little thinner than in previous years.

It was interesting that many seemed to know about the company I work for. The fact is that our canine genomic test is the most comprehensive and robust out there. That’s not marketing fluff, and geneticists can discern bullshit from reality pretty easily. So the discussions were more brass-tacks about the value customers. I had a pretty good case for why a purchase is justified or feasible, so easy discussions.

417otmYuMcL._SX303_BO1,204,203,200_ Reading about Poststructuralism, and having a hard time understanding how people take this stuff seriously. That’s a problem, because people do. Perhaps a validation of its weirdly grand take on the power of language to shape the structure of reality.

It will be nice to read about something different. In particular, functional programming. Need to get my NumPy skills up, as I spend so much time struggling with data-types.

• Category: Miscellaneous • Tags: Open Thread

MacCulloch_Reformation_sm Since we’re on the topic of religion, I thought I would make a book recommendation. If there is one book I would read on the Reformation if there was one book, it is Diarmaid MacCulloch’s The Reformation. I read this magisterial work in 2004 over a week and it has stuck with me in a way no other work on this topic before or since, has (similarly, if you are going to read one book on Byzantine history, it would be A History of the Byzantine State and Society).

MacCulloch’s history of Christianity was relatively disappointing (thin gruel, stretching out a deep topic too far in a survey). But I see he’s come out with a new book on an old topic, All Things Made New: The Reformation and Its Legacy. I just got a copy and it seems interesting. More thematic than narrative in comparison to the earlier survey.

• Category: History • Tags: Reformation

41I42XDmNfL._SX335_BO1,204,203,200_ There are some topics which I have some interest in, such as prehistory illuminated by genetics, in which there is constant change and new discoveries every few months. If a new paper doesn’t drop in a six month interval, I think something is wrong.

There are other topics where I don’t perceive much change, and have stopped paying much attention. Psychometrics for example is one area where I basically just stopped paying much attention after reading The g factor. I understand that it’s a live field, but at this point to me the details are academic, as the broad sketch seems well established (this will change in some ways over the next decade due to genomics, but since I think genomics will confirm what we already know it won’t be very revelatory for me).

The scientific study of religion is another topic where I once had a lot of interest, but where I concluded that the basic insights have stabilized. Since I stopped reading much in this area I stopped writing much about it too. To get a sense of where I’m coming from, Scott Atran’s In Gods We Trust: The Evolutionary Landscape of Religion is probably the best place to start. It’s about 15 years old, but I don’t see that much has changed since then in the basics of the field.

9780195178036 And what are those basics? At its fundamental basics religious impulses must be understood as an outcome of our cognitive mental intuitions. All religion operates on top of this basic kernel of our mental OS. Religion may have functional utility as a social system of control, or channeling collective energies, as argued by David Sloan Wilson in Darwin’s Cathedral. Or, one might be able to fruitfully model “religious marketplaces” as argued in Marketplace of the Gods. But these are all basically simply applications installed into on top of the operating system.

Why does this matter? For me this is a personal issue, because I’m one of those people who has never really had a strong religious impulse. Since I didn’t have a religious impulse, my model of religion was as that of an outsider, which led to some confusions. For example, there was a point perhaps around the age of 18 where I thought perhaps if someone just read a book like Atheism: A Philosophical Justification they’d be convinced. Just as if I’d been a Roman Catholic I would have thought a reading of Summa Theologica would have convinced. This was all wrongheaded.

Very few are Roman Catholic because they have read Aquinas’ Five Ways. Rather, they are Roman Catholic, in order of necessity, because God aligns with their deep intuitions, basic cognitive needs in terms of cosmological coherency, and because the church serves as an avenue for socialization and repetitive ritual which binds individuals to the greater whole. People do not believe in Catholicism as often as they are born Catholics, and the Catholic religion is rather well fitted to a range of predispositions to the typical human.

One thing that the typical human does not have is intensive need for rationalization of our daily life, and the totality of their beliefs. There are a non-trivial subset of Catholics who have heard of the Five Ways, or might be conversant in the Ontological Argument. But this is a very small minority of Catholics, and for even these this philosophical element is a sidelight to most of their spiritual practice and orientation.

The reason I am posting this is in response to something Rod Dreher wrote, Mystery Of The Ages:

Here’s something I have never figured out. In theory, Catholics ought to be a lot more theologically conservative on such matters. They have a clear teaching proclaimed by a clear church authority, with a deep Biblical theology behind it. And yet, on the whole, it doesn’t seem to matter to lay Catholics. Evangelicals, on the other hand, have the Bible, but no binding interpretive authority to keep them from diverging. Yet, on these issues, they are more morally conservative than Catholics — even by Catholic standards.

Why is this? I’m asking in a serious way. Any of you have a theory? I’m not going to publish gratuitous Catholic bashing or Evangelical bashing in the comments.

The best book to fully address this paradox would be D. Jason Slone’s Theological Incorrectness: Why Religious People Believe What They Shouldn’t. But that’s the generality. If you want specifics, see Jay P. Dolan’s In Search of an American Catholicism: A History of Religion and Culture in Tension. Though American Catholics retain identity and affiliation with the Roman Catholic Church, it has operationally become Protestantized when it comes to how people view their relationship to the religion (in a similar way, American Reform Jews also transformed their religion to conform with American confessional Protestantism).

There are a subset of believers who are not well captured by the generalizations in books such as Slone’s, or in ethnographic descriptions which trace the assimilation of Catholicism into the American scene. They are usually highly intellectual and analytical in their orientation. Often, they seem to be converts. Rod Dreher was a convert to Catholicism from Methodism, before he became Orthodox. Leah Libresco and Eve Tushnet also seem to fall into this category. Highly intellectual. And, converts to Catholicism.

Because they are analytical and articulate, these sorts of religious people are highly prominent on the public stage, and, they also write the histories that come down to us through the centuries. These are also the type of people who are overrepresented in the clerical apparatus of any organized religion. This is a problem, because their prominence can obscure the reality that they are not as influential as you might think. As a metaphor, imagine mountainous islands scattering amidst a featureless ocean. The islands are salient. But it is the vast ocean which will ultimately be determinative. Similarly, the vast number of believers who move along a nexus of inscrutable social forces, and driven by powerful universal psychologies, may be hidden from our view.

51jUZQV3r1L._SX329_BO1,204,203,200_ And yet even for the “analytics” reason does not dictate. Both Dreher and Tushnet have made references to mystical and emotional occurrences and impulses which are beyond my ken. I have no need, no wish, no impulse, and no intuition as to what they are talking about in that dimension (Libresco seems a somewhat different case, but I haven’t read much of what she’s written; I suspect I’ve been in the same room with her since she worked for an organization which I have many personal connections with, but I’m not sure).

It isn’t a surprise that I think Hume was onto something when he asserted that “reason is a slave to the passions.” In many instances I suspect theological analysis is simply the analytic engine being applied to a domain whose ultimate rationale is driven by a passion.

Addendum: Leah Libresco seems to have been associated with the broad umbrella group of Bay Area rationalists. I’ve been associated in some fashion with these people as friends and acquaintances for nearly 10 years. I will admit that I’ve generally found the conceit of rationality as an ends, as opposed to a means, somewhat off-putting. Ultimately I’m more of a skeptic than a rationalist I suppose at the root.

• Category: Science • Tags: Religion

51I3Hux0TsL._SY344_BO1,204,203,200_ I reread Colin Woodward’s American Nations: A History of the Eleven Rival Regional Cultures of North America on the plane recently. It’s a less scholarly work than Albion’s Seed or The Cousins’ Wars: Religion, Politics, Civil Warfare, And The Triumph Of Anglo-America, but arguably more straightforwardly relevant to modern conditions and events. I’m rather sure that Woodward would be interested in a further edition which updated with the goings on of the 2016 election campaign, if he’s not working on it already (an important complement, Replenishing the Earth: The Settler Revolution and the Rise of the Angloworld, 1783-1939, which takes a broader Anglospheric view).

The important point here is that initially developed cultural folkways can be persistent and reinforcing. The author observes that Nordic immigrants seem to have almost invariably chosen the region of the American frontier dominated by a Yankee ethos, the Upper Midwest. Though they overwhelmed this region demographically, rather than changing the culture, they simply accentuated its longstanding features, which were established by Yankees (e.g., social progressivism and communitarianism).

What else is going on? Going to be at ASHG a lot this week.

• Category: Miscellaneous • Tags: Open Thread

12_01_2016_Alice_headshot The new Alice Roberts documentary is going viral. Or at least its spin is.

E.g., Western contact with China began long before Marco Polo, experts say:

However, Chinese historians recorded much earlier visits by people thought by some to have been emissaries from the Roman Empire during the Second and Third Centuries AD.

“We now have evidence that close contact existed between the First Emperor’s China and the West before the formal opening of the Silk Road. This is far earlier than we formerly thought,” said Senior Archaeologist Li Xiuzhen, from the Emperor Qin Shi Huang’s Mausoleum Site Museum.

A separate study shows European-specific mitochondrial DNA has been found at sites in China’s western-most Xinjiang Province, suggesting that Westerners may have settled, lived and died there before and during the time of the First Emperor.

Let’s go with the easy part first: there were no “Western” people when the Afanasevo culture was pushing into the fringes of what is today Xinjiang.

There are two extreme polarities of definition of what Western is. One is cultural.

516C6LMzGTL As outlined in David Gress’ From Plato To NATO: The Idea of the West and Its Opponents, the West did not emerge fully grown like Athena from the head of Zeus in the 6th century BCE along the Aegean. Rather, the West evolved organically as a synthesis over time of Classical Greco-Roman elements, Christianity, and later the post-Roman societies, often dominated by barbarian martial elites. By this definition it is clear that a blue-eyed Sogdian merchant who was resident in Xian in the 7th century was not Western. Their only affiliation with the West would be adherence to Christian Church derived from Persia, and even here this stream of Christianity was relatively marginal that of the Western variety (most Sogdians were probably Zoroastrians of course).

A second definition of being Western is racial, whether explicit or implicit. That is, there is an association with being Western and white. This is certainly true, but the problem with this formulation is that though Western people were invariably white, white people were not invariably Western. To give a concrete example, Buddhist Tocharians who had light hair and eyes, and flourished as late as 1000 A.D, were white people by any definition, but they were not Western in anything but the most reductive and biologistic sense. The cultural valence of what it means to be Western is clear on the southeastern fringes of Europe, where Muslim populations are often considered non-Western, even when they are genetically similar to their Christian neighbors.

The mtDNA they found is probably of haplogroup U, or perhaps H. Its presence in Eastern Asians is unsurprising, as skeins of migration seem to have laced themselves across the landscape of Eurasia across the whole Holocene, and earlier.

Finally, I think the media is misleading its depiction of Greek influence. Greco-Bactrians were culturally influential for several centuries in Asia. The Greek influence then did not come from the Mediterranean, but from the furthest outputs of Hellenistic society. Still noteworthy, but not so spectacularly surprising.

• Category: History • Tags: History

American Math Olympiad Team, 2015

For various ideological reasons there is an idea in some parts of the academy that Asian Americans are not a “model minority.” That that “model minority” designation is a myth. The mainstream media often repeats the idea that this is a myth which has been “debunked.”

Actually, it hasn’t been debunked. Rather, through a set of common talking points and empirical shell games Asian American achievement is masked, obfuscated, and explained away. This is not to say that Asian Americans have not, and do not, experience racism. But, it is to assert that the perceptions of Asian American success in particular domains is not an illusion. Your eyes and mind are perceiving real patterns (see here for a typical example of the “Asian American model minority myth”).

From PBS, These groups of Asian-Americans rarely attend college, but California is trying to change that:

Chang, a 22-year-old psychology student at California State University Fresno who grew up in this Central Valley city, chose to study close to home, and she’ll probably remain on campus for her master’s degree. But for someone from an ethnic group that contradicts the Asian-American “model minority” myth, even this is a rare achievement.

As one group of Asians who don’t go to college in large numbers, the Hmong help illustrate the complex changing demographics of students arriving at American universities and colleges: increasingly nonwhite, low-income, and first-generation.

Among the 281,000 Hmong in the United States, 38 percent have less than a high school degree, about 25 percentage points lower than both the Asian-American and U.S. averages, according to the Center for American Progress. Just 14 percent have at least a bachelor’s degree, less than half the national average.

Upending the stereotype that most Asian-American children go to college, the Hmong and other Southeast Asian immigrants including Cambodians, Laotians and Vietnamese have markedly low college-going rates — especially compared with Chinese, Japanese, and Korean Americans, who are actually more likely than other Americans to earn bachelor’s degrees.

This is the “Hmong gambit.” I’ve been hearing about this for 20 years from Asian American activist friends. The Hmong are genuinely marginalized. They were marginalized in Laos as well, where they were a hill tribe outside of the pale of Theravada Buddhist civilization. The fact that they have particular trouble integrating into the United States in comparison to other Asian Americans is not surprising. But the Hmong are not very representative of California Asian Americans.

UC Berkeley provides undergraduate (non-international) student data. And you can find various Asian American ethnic numbers from the Census and other sites.

Berkeley 2015 % California 2010 % Ratio
Chinese 20.5% 3.9% 5.26
Filipino 3.4% 3.9% 0.87
Japanese 2.1% 0.7% 2.82
Korean 5.3% 1.4% 3.94
South Asian 8.2% 1.8% 4.55
Vietnamese 3.6% 1.7% 2.1

One thing you can see immediately is that the reporting is sloppy and uninformed. Vietnamese shouldn’t be bracketed with other Southeast Asians. They are somewhat overrepresented at Berkeley. This is not surprising. Many of the Vietnamese are themselves Hoa, or from the Catholic middle class. The Filipinos are represented at about their proportion in the population. The Chinese, South Asians (mostly Indian), Koreans, and Japanese are all overrepresented.

At this point you might wonder about all the other groups such as Pacific Islanders, Cambodians, and Mongolians (?). But look up the numbers and you’ll see that the six groups above represent 80-90% of Asian Americans in California. These are representative communities, not the Hmong.

One aspect of the “model minority myth” myth is that the 1965 immigration system, which was highly selective for the first post-65 wave of Asians, shaped modern conceptions. More or less this is a lie, as the “model minority” thesis was formulated in the 1960s against the backdrop of black urban unrest, and when “Asian American” mean Chinese and Japanese, who were by and large descendants of very modest people. In the case of the Japanese in particular it is well known that those who left the home islands were often the most socially and economically marginalized.

• Category: Race/Ethnicity • Tags: Model minority


David_Hackett_Fischer_-_Albion's_Seed_Four_British_Folkways_in_America.jpeg There has been lots of comment on Mormons and politics recently. I think the key aspect which is underemphasized in these pieces are the deep differences within Anglo-American cultural streams (as opposed to the short-term reasons for Mormon disaffection from the conservative coalition, such as their internationalism). If you haven’t read Albion’s Seed, you should. If you have read Albion’s Seed, also read The Cousins’ Wars: Religion, Politics, Civil Warfare, And The Triumph Of Anglo-America, and American Nations: A History of the Eleven Rival Regional Cultures of North America. The Cousins’ Wars in particular frames Albion’s Seed into a global context.

51FGXEssAhL._SY344_BO1,204,203,200_ The major insight from these works of narrative history is that a model which incorporates the genealogical origin of Anglo-American subcultures hundreds, and even thousands, of years into the past can be quite fruitful. In David Hackett Fischer’s Albion’s Seed the biggest chasm is arguably between Yankees and the Scots-Irish. Geographically distinctive today, even their origins in the British Isles were disparate (mostly East Anglia toward London, and borders of England and Scotland, respectively).

The cultural elites of the Yankees ultimately gave rise to a large portion of the Northeastern WASP ascendancy (including the Bush family) in a direction fashion, or influenced immigrants who assimilated into that subculture (including the Kennedy family). The ~30,000 settlers who took root in New England in the 1630s ultimately became the ~750,000 colonials in the New England colonies at the cusp of the Revolutionary War. The Scots-Irish in contrast are identified not by their elite families, the ‘backcountry ascendancy,’ but their marginalized position as a subculture in comparison to the other Anglo-American streams. When they arrived in the mid-18th century from Ulster and the English-Scottish border region they were termed “crackers.” Here is the Wikipedia entry explaining the origin of the term:

A 1783 pejorative use of “crackers” specifies men who “are descended from convicts that were transported from Great Britain to Virginia at different times, and inherit so much profligacy from their ancestors, that they are the most abandoned set of men on earth.” [3] Benjamin Franklin, in his memoirs (1790), referred to “a race of runnagates and crackers, equally wild and savage as the Indians” who inhabit the “desert[ed] woods and mountains.” [4]

The differences between the Yankees and Scots-Irish redound down to the present. In 1850 Arkansas and Michigan were two states of roughly similar population settled at the same time, by Scots-Irish and Yankees respectively, in the main. While Arkansas hardly had any public schools, Michigan had hundreds. The differences between Yankees and Scots-Irish emerge over and over in the cultural fissures of “mixed” states such as Ohio, Illinois, and Kansas.

How does this tie in to Mormons? The early cultural history of Mormons is directly rooted in the Yankee Diaspora. The Yankees of New England were a fecund lot in the years around 1800, and they spilled over into upstate New York, and across a vast swath of the Midwest ringing around the Great Lakes. The original Mormons were by and large Yankees, and their migration west took them into the lands of the Scots-Irish, who descended upon them like wolves to the slaughter, as was often the case when Yankees faced Scots-Irish in an unorganized fashion.

Below the fold is a post from 2008 that I wrote which I think is now relevant again. So I am reposting it. The Mormon position within the Religious Right is one driven by sincere and genuine alignments of values, but on a deep level it will always be tactical individually, because this is an alliance of two very different groups in their mores and history. That means that one shouldn’t expect individuals from one group to die on the hopeless hill for the other.

Post from 2008:

A few friends have emailed me some objections to the four culture model of american history. In short, though New England Puritans, Highland South Scotch-Irish and Lowland South Cavaliers are reasonable cultural entities which are easy to put a finger on, the Mid-Atlantic is a hodge-podge which to a great extent is simply thrown in a bin together for simplicity. In 1750 Pennsylvania was the first American colony where people of British descent became a minority. This sort of diversity makes it rather peculiar to speak of a Mid-Atlantic cultural folkway in which Germans, Dutch, Quakers, Roman Catholics, Swedes and Long Island Yankees can be thrown together into one pot. It’s somewhat like assigning the term “environmental” to all the components of variance in quantitative genetics of a phenotype which can not be attributed to genetics. You know what it isn’t, but what is it?

But that’s just an aside. You might infer from the image above that the point of this post is not to explore what the term “Mid-Atlantic” can tell us in any model of social history. Instead, I want to focus on one aspect of American coalitional politics which might be of interest in the next four years: Mormon America is a representative of the New England Puritan cultural tradition in “Red America.” The map above is going to be more informative here than words. “English America” in the American West is really Mormon America.

When I say Mormons are “Puritan,” I’m not saying this as a figure of speech; Mormon America is to a great extent both a direct cultural and genetic descendant of New England Puritanism. The proportion of “English” ancestry in Mormon America is somewhat exaggerated by the fact that missions were sent to England and so you had direct migrants from Europe to Utah. But this can’t explain the whole of the phenomenon, American Mormonism began as a religion of Greater New England. First in upstate New York, and later in northern Ohio. Its relocation to the Midwest was problematic for a host of reasons, but the fact that they were often neighbors of people whose origins were in the South and they were quite clearly Yankees probably exacerbated tensions.

Mormonism is a very communitarian religion, not unexpected from a faith with Puritan origins. Mormon settlements in Utah were laid out like New England towns, as opposed to isolated yeoman farmsteads. Brigham Young socialized water usage to optimally allocate resources for irrigation. A tendency toward campaigns for temperance and high fertility were features of New England society. Mormons are famously fertile (relatively) and do not drink. In Wisconsin administrators preferred Yankee settlers because they were more likely to be willing to raise money for pubic goods such as schools than migrants from the South. Mormons may be low-tax Republicans, but those in good standing tithe a very large proportion of their income obligately in their private life (10% from what I recall), while the church runs itself like a corporation which has economies of scale.

Unlike evangelical Christians in the South, Mormons do not accept with resignation that many youth may “raise hell” before settling down. Mormons do not accept the Protestant contention that salvation is through faith alone. Behavior matters. Social pathologies and the personal disorder which has been a feature of Southern cultural life since its inception are not features of Mormon America, which reflects Puritan fixation on public order as a check on private liberty.

Over the past generation Mormons and Southern Protestants have entered into a de facto alliance because of their social traditionalism. The recent controversy over Proposition 8 in California will likely result in even more esteem for the Mormon church from structurally suspicious evangelicals (they do not believe Mormons are Christian, and resent that they claim that they are Christian). In other ways Mormons have come to identify themselves with conservative Protestant America, which to a great extent means Southern America. There are data which show that while 70% of Brigham Young University students rejected Creationism in 1930, 70% now accept it. I believe this is due to cultural influence from evangelical Protestantism, with whom Mormons are now politically allied.

But I believe that the differences between Puritan Mormon America and Southern evangelical America need to be kept in mind. Some of Mitt Romney’s supporters were irritated that some conservative kingmakers (e.g., Richard Land) were leaning to Fred Thompson because of cultural affinities. Culture matters. Mormons may be aligned with the South, but the alliance will always play out in the framework of differences in cultural priors. Mitt Romney is a social conservative, and likely was before he had to lie to become governor of Massachusetts. But he is not a Southern social conservative, and that matters, and when he pretended to be he seemed phony.

Addendum: One can encapsulate what I’m trying to get at by considering an even more extreme case: Jews & black Americans. These two groups are most Left-leaning and Democratic demographics in American society, but, they obviously aren’t equivalent and there are qualitative differences in their liberalism. This doesn’t mean that the position of both these groups on the American Left is in question, but there will always be a tension within the alliance.

• Category: History • Tags: American History

8412068Episode 728: The Wells Fargo Hustle. Elizabeth Warren is right, there won’t be any accountability at the top. Hope I’m wrong.

Started reading A New History of Western Philosophy last summer, but got bogged down in the medieval section. I started reading it last week and it’s going much faster now that I’m in the “modern” section.

Sensitivity of quantitative traits to mutational effects and number of loci.

Reference-based phasing using the Haplotype Reference Consortium panel.

The genetic history of Cochin Jews from India.

How the compact disc lost its shine.

Actually, Facebook’s New Craigslist Competitor Should Be a Little Debauched. How is it that CraigsList is still around?

Piece of carved wood suggests Persian taught maths in Japan 1,000 years ago.

Ages of Discord: My Third Independently Published Book (Peter Turchin’s).

A Review of Cognitive Abilities in Dogs, 1911 Through 2016: More Individual Differences, Please!.

• Category: Miscellaneous • Tags: Open Thread

Screenshot 2016-10-08 09.46.41
Screenshot 2016-10-08 10.06.17 Many people have skin problems. Though luckily I’ve never had an issue with acne, most people who know me personally are aware that I suffered from extreme eczema as a child. Most of the major issues occurred when I was under five years of age, and in my first few years, so I have only minimal first hand recollection. The problem runs in my family, though I was the most extreme sufferer. Eczema also correlates with asthma, something I also suffer from.

Naturally I was curious about this new paper in Genome Biology, Atopic Dermatitis Susceptibility Variants In Filaggrin Hitchhike Hornerin Selective Sweep:

Human skin has evolved rapidly, leaving evolutionary signatures in the genome. The filaggrin (FLG) gene is widely studied for its skin-barrier function in humans. The extensive genetic variation in this gene, especially common loss-of-function (LoF) mutations, has been established as primary risk factors for atopic dermatitis. To investigate the evolution of this gene, we analyzed 2,504 human genomes and genotyped the copy number variation of filaggrin repeats within FLG in 126 individuals from diverse ancestral backgrounds. We were unable to replicate a recent study claiming that LoF of FLG is adaptive in northern latitudes with lower ultraviolet light exposure. Instead, we present multiple lines of evidence suggesting that FLG genetic variation, including LoF variants, have little or no effect on fitness in modern humans. Haplotype-level scrutinization of the locus revealed signatures of a recent selective sweep in Asia, which increased the allele frequency of a haplotype group (Huxian haplogroup) in Asian populations. Functionally, we found that the Huxian haplogroup carries dozens of functional variants in FLG and hornerin (HRNR) genes, including those that are associated with atopic dermatitis susceptibility, HRNR expression levels and microbiome diversity on the skin. Our results suggest that the target of the adaptive sweep is HRNR gene function, and the functional FLG variants that involve susceptibility to atopic dermatitis, seem to hitchhike the selective sweep on HRNR. Our study presents a novel case of a locus that harbors clinically relevant common genetic variation with complex evolutionary trajectories.

This shows the importance of whole genomes, as the earlier result correlation variation to climate seems to be due to ascertainment bias in terms of SNP discovery. Additionally, it’s intriguing that the haplotype which eczema-like diseases are associated with is very ancient. It’s found in Africans, and ancient genomes. So it’s been segregating in human populations for a while. That indicates some sort of balancing selection going on, so that it’s never purified.

What they found is that in Chinese samples there has been a recent positive sweep. I don’t really buy their conclusion that the haplotype wasn’t found in European hunter-gatherers, they don’t have a large enough sample. But it does seem to be a case where there is balancing selection maintaining standing genetic variation, which purified may be selected for or purified in some populations.

This may be a more common dynamic than we might realize. Many complex diseases may exhibit risk profiles due to being dragged up in frequency because of associations with a nearby region, or, a genetic-correlation where the positive benefit is greater than the negative.

• Category: Science • Tags: Genetics

Migraciones_austronesiasGgas_human_soc One of the most incredible journeys that the human species has undergone is the Austronesian expansion of the past 4,000 years. These maritime peoples seem to have emerged from the islands of Taiwan, and pushed forward south, west, and east, so that their expansion pushed to East Africa, and the fringes of South America. There now also some circumstantial evidence that Polynesian contact with the Americas predates the Columbian Exchange. Looking at the map above in hindsight it seems natural to imagine such contacts.

Though where the Austronesians went is incredible, their origins are somewhat more opaque, but rather tantalizing. That is because their original expansion was likely just before the horizon of history. In Guns, Germs, and Steel Jared Diamond alluded to the “express train” vs. “slow boat” models of the expansion. Basically, whether the Lapita peoples rapidly pushed out from Taiwan, or whether there was a long period of coexistence with Melanesians in Near Oceania. Over the past few years genetics seems to have supported the “slow boat” model.

Here is a paper from 2012, Population Genetic Structure and Origins of Native Hawaiians in the Multiethnic Cohort Study:

The “Express Train” and the “Slow Boat” models of Polynesian migration are expected to have uniquely distinct genetic signatures on present day genomes of Native Hawaiians. Under the “Express Train” model, the proportion of admixture in Native Hawaiians of Melanesian and Asian ancestry is expected to be near zero, whereas under the “Slow Boat” model, the proportion of admixture is expected to be substantially greater than zero. To test these two models, we conducted a supervised ADMIXTURE analysis using Papuan and Melanesians as one source population of Polynesians and Han Chinese, She, Cambodian, Japanese, Yakut, and Yi as surrogates for the second source population of Taiwanese aborigines [18], [19]. Importantly, we did not fix ancestry for the Melanesians or Asians and therefore allowed for admixture within either ancestral groups–thus, mitigating bias by earlier admixture processes and allowing for accurate clusters of ancestry membership. We set K = 2 and estimated in 40 100% Native Hawaiians an average of 32% and 68% of their genomes to be derived from Melanesian and Asian origins, respectively (Figure 4). This notable proportion of Melanesian admixture (32%) among Native Hawaiians, substantially greater than zero, lends support of the “Slow Boat” model of ancestral origins.

This is not an isolated study. Y chromosomes indicate substantial Melanesian admixture, while the mtDNA does not. One inference then was a “slow boat” model predicated on matrifocality. That is, expanding Polynesian groups were centered around matrilineal lineages, and absorbed Melanesian men into their communities. The above research was from a Hawaiian data set, but the results are consistent across Polynesia in relation the proportion of Melanesian ancestry.

Case closed? No so fast! Ancient DNA has now been brought to the question, and fundamentally changed our perceptions. Genomic insights into the peopling of the Southwest Pacific:

The appearance of people associated with the Lapita culture in the South Pacific around 3,000 years ago1 marked the beginning of the last major human dispersal to unpopulated lands. However, the relationship of these pioneers to the long-established Papuan people of the New Guinea region is unclear. Here we present genome-wide ancient DNA data from three individuals from Vanuatu (about 3,100–2,700 years before present) and one from Tonga (about 2,700–2,300 years before present), and analyse them with data from 778 present-day East Asians and Oceanians. Today, indigenous people of the South Pacific harbour a mixture of ancestry from Papuans and a population of East Asian origin that no longer exists in unmixed form, but is a match to the ancient individuals. Most analyses have interpreted the minimum of twenty-five per cent Papuan ancestry in the region today as evidence that the first humans to reach Remote Oceania, including Polynesia, were derived from population mixtures near New Guinea, before their further expansion into Remote Oceanian…our finding that the ancient individuals had little to no Papuan ancestry implies that later human population movements spread Papuan ancestry through the South Pacific after the first peopling of the islands.

These results strong indicate that the original Lapita migration did not mix with Melanesians. And, the ancient samples share common ancestry with modern Polynesians, so that their heritage persists down to the present. Looking at the distribution of Melanesian ancestry they concluded this admixture occurred on the order of ~1,500 years before the present (their intervals were wide, but the ancient samples serve as a boundary). Additionally, in line with the Y and mtDNA the X chromosome indicated more of the ancient ancestry than the autosome. The authors conclude that “it is also possible that some of these patterns reflect a scenario in which the later movement of Papuan ancestry into Remote Oceania was largely mediated by males
who then mixed with resident females.”

The take home message than is that we need to be more modest with our models. Without ancient DNA it seems likely that we would not have stumbled onto this result; the ancestry deconvolution methods which date admixture have wide confidence intervals when you go back far in time.

• Category: Science • Tags: Genetics, Genomics


51qciM4cBhL._SX258_BO1,204,203,200_ A friend asked me about population structure, and methods to ferret it out and classify it. So here is a quick survey on the major methods I’m familiar with/utilize now and then. I’ll go roughly in chronological order.

First, you have trees. These are pretty popular from macroevolutionary relationships, but on the population genetic scale (intraspecific, microevolutionary) you’re mostly talking about representing distances between groups in a tree format. You saw this in History and Geography of Genes, where genetic distances in the form of Fst values (proportion of genetic variation unique to between two groups) were used as distance inputs.

A problem with trees is that they don’t model gene flow, a major dynamic on a microevolutionary scale. Also, complex relationships can get elided in tree frameworks, and as you add more and more populations you often end up with an incomprehensible fan-like topology.

journal.pgen.0020190.g005 Then you have principle component analyses (PCA) and related methods (e.g., multidimensional scaling, which is very different in the sausage-making but generates a similar output). Like trees, this is a visualization of the variation, in this case on a two dimensional plot (please don’t bring up three dimensional PCA, there’s no such thing until holograms show up).

The problem with PCA is that different types of dynamics can lead to the same result. For example, someone who is an F1 of two distinct groups occupies the same position as a population which happens to occupy a genetic position between two groups. Additionally, by constraining the variation into two dimensions, one can mislead in terms of relationships. There are many dimensions, but operationally you focus on on two at a time.

A paper of interest, Population Structure and Eigenanalysis.

Rosenberg4 Next you have model-based clustering introduced in Jonathan Pritchard’s Inference of Population Structure Using Multilocus Genotype Data. There are many flavors of this, but they operate under the same framework. You have a model of population dynamics, and see how the genotype data can be explained by parameters of the model. Of particular interest is assignment to one of K populations, which can be combined to explain the variation in the data.

Unlike PCA these model-based methods are rather good at identifying people who are first generation mixes, as opposed to those from stabilized groups along a cline. But, they also produce artifacts, because they are quite sensitive to the input data, and lend themselves to cherry-picking.

journal.pgen.1002967.g003 (1)Earlier I said that one problem with the tree methods is that they don’t model gene flow. Joe Pickrell’s TreeMix does so. Like the original tree methods, and unlike PCA or unsupervised model-based clustering, you specify a set of populations. Then you compare the populations in terms of their genetic distance, and fit them to a tree, but add migration parameters to that tree where the fit between the tree and the data is the most tenuous fit.

All visualizations are deformations of reality. TreeMix attempts to mitigate this somewhat by introducing another representation, that of migration.

Screenshot 2016-10-02 22.38.02Next we have local ancestry methods. By local ancestry, basically we mean methods which can assign ancestry to particular regions of the genome. While tree methods measure differences across pooled populations, PCA and model-based methods compare genotypes between individuals (this is a simplification, but bear with me). Local ancestry methods, like RFMix, compare regions of the genome with each other.

Related to, but not exactly the same, as local ancestry methods are haplotype based methods. In particular, I’m thinking of the FineStructure and its related methods. These leverage variation across the genome in terms of haplotypes, rather than just looking at genotypes. They also tend to benefit from phasing, for obvious methods. FineStructure and its relatives tend to need more marker density than model-based methods, which require more marker density than PCA, which requires more marker density that tree based methods. These haplotype based methods allow for correction of and accounting for forces such as genetic drift, which tend to skew results in other methods.

Finally, there is the AdmixTools framework which is good for testing very explicit hypotheses. While many of the above methods, such as TreeMix and unsupervised model-based clustering, explore an almost open-ended space of structure possibilities, the methods in AdmixTools exists in large part to test narrow delimited models. This goes to the fact that many of these methods are complementary, and you should use them together to arrive at a robust result. For example, if you are assigning populations for TreeMix, you should use PCA and model-based clustering to make sure that the populations are clear and distinct, and outliers are removed.

There’s a lot I left out, but many of the other methods are just twists on the ones above.

• Category: Science • Tags: Genomics

9780192805577Online Life Is Real Life, Aleph-Nought in a Series:

I thought of this while I was reading John Scalzi’s epic post about self-presentation, prompted by someone who complained that he behaved differently in person than that person had expected from Scalzi’s online persona. (Personally, having met John in person several times, I don’t see it, but whatever…) Scalzi rightly notes that there’s nothing at all wrong with this, and that much of the difference is (probably) just basic courtesy and politeness.

It’s a major pet peeve of mine that people deduce from what they see on this blog and Twitter to generate a full picture of whom I am. If the data you saw were representative, then that might be one thing, but they really aren’t. Rather, they’re strongly biased.

A long time reader (as in, back to the ScienceBlogs days) is someone who I now socialize with semi-frequently. One observation he makes is that I tend to engage in more unguarded bloviating in real life. That sounds about right. In real life everything I say is not recorded for posterity.

The basic insight thought is that there is much you don’t see when you consider just what you see.

When people engage in others, they use theories to fill in the background of their interlocutors. It’s pretty impossible not to do so. On the other hand, theories are always imperfect, and you shouldn’t get surprised when those who you theorize about are angry when your theories miss the mark.

One way that my “non-internet” and internet personas do align well is that I’m rather aggressive. If think you’ve mischaracterized me, I won’t be happy in person, or online.

I read Foucault: A Very Short Introduction on a plane last week. I have the “very short introductions” series a great deal (have also read Hegel). It strikes me they’re good to orient and refresh you before a deeper dive.

A commenter below dismissed the importance of the genealogy of intellectuals and their movements in comparison to mass culture. But reading Foucault: A Very Short Introduction you see clearly the lexical armamentarium on display decades before it would percolate to Facebook threads and MSNBC.

51k6n6ma-NL._SY344_BO1,204,203,200_ Reading about Postcolonialism, I’m really struck by the possibility its intellectual apogee was already attained by Edward Said in Orientalism. I read Said about 15 years ago, but dismissed the work. My objection? It was simply wrong on many facts. In hindsight, it strikes me that I was naive in regards to what people admired about Said’s work, and its significance. That is, it’s importance was not as a narrative about the historical past, but possibilities for narrative frameworks relevant for organizing the political present.

Campus debate on Black Lives Matter called racist, shut down by protesters (VIDEO). If state campuses are to be thought of as arms of the Left-progressive movement in America, I can’t see any reason for states where the majority of the population is not Left-progressive to continue funding them.

My friend David Bachinsky has a GoFundMe to help fight his brain cancer.

Next Big Tech Corridor? Between Seattle and Vancouver, Planners Hope. Next year in Jerusalem. There is only one. There shall be only one.

Pre-Industrial Societies Reward High Status Men With More Children.

ASHG in Vancouver in two weeks….

• Category: Miscellaneous • Tags: Open Thread

41mWHpXBYvL._SX370_BO1,204,203,200_ A few days ago I joked on Facebook that life isn’t about the score up on the board, but standing with your team. By this, I have come to the position that when it comes to arguments and debates the details of the models and facts, and who even wins in each round, is irrelevant (barring extinction) when set against the value and gains to group cohesion. In the middle 2000s a friend advised that I should be more explicitly partisan and ideological, because that is how I could gain friends and allies in my hour of need.

In my short jaunt through Theory writ large I have finally come that conclusion as well. I am a naive realist and a positivist. I work under the assumption that there is a world out there, that that world out there manifests itself in the order we see when we decompose it with analysis and empirical methods. As long as I kept my eyes on prize, the “score,” I felt at peace.

This was dangerously naive. Whereas before I had worked under the hypothesis that my interlocutors were falling prey to cognitive biases when they engaged in ad hominem or logical fallacy, I am now coming to suspect that one some level they are aware that they are engaging in the dialectics of ultimate victory. Every battle they lose is simply another opportunity to shore up their forces in future battles. Just like Rome against Hannibal, their contention that the structure of human society, rather than the world “out there,” is determinative, may very well be true in relation to all that matters.

9780195335613 Years ago I laughed at D. Jason Slone’s satirical tongue-in-cheek take on “discourse” and “Theory” in Theological Incorrectness: Why Religious People Believe What They Shouldn’t. Slone was working in a positivist and analytic tradition which attempted to understand religious phenomena on a rational level, to turn it into another phenomenon among phenomena. But with all due respect, Slone works in relative obscurity more than a decade later, while some of the people he mocked for being wrong walk hallowed halls. Who was truly right in all that matters in this world?

Slone knew the score. His side easily runs up the points. But while his side, my side, focuses on the banality of reality, their side, the other side, works to secure victory in the hearts of men. When you have gained master over human sentiment, you gain mastery over human action.

As an illustration of this, consider this piece in Vox, A new school year. A new fight against affirmative action. This time at Harvard. People make fun of Vox, but I believe that the people running it actually do think empirics matters. They attempt analysis. But at the end of the day, it all comes down to who and whom.

The Vox piece interviews a professor OiYan A. Poon, who expresses views typical of a certain segment of the professional Asian American intelligentsia. I say professional Asian American in the sense that these individuals are professionals at being Asian American, at being the Asian American voice among progressive cultural elites. Their Asianness is almost incidental to their identity, which steeped in what might be the termed the discourse of white supremacy, predicated on cross-identity alliances against Oppression.

At this point I might “fisk” Poon’s assertions, many of which don’t bear even superficial scrutiny, or her assertion that Asians who oppose her politics are basically stooges of white people without any independent agency. But that’s not the point of this piece at Vox. It’s not to explore facts, it’s to reinforce narratives. The author of the piece engages in no critical rationalism, no attempt to actually probe the assertions Poon makes, because Poon is on the right side, the right team. The interview is an exercise in team building, not an attempt to describe the real world that would hold up to any deep scrutiny. The people at Vox probably don’t see it this way, because the shape of reality has already been determined, the terms of have been set.

They believe because it is absurd. They make the leap of faith.

• Category: Ideology • Tags: Ideology

k8488 In The Horse, the Wheel, and Language: How Bronze-Age Riders from the Eurasian Steppes Shaped the Modern World the archaeologist David Anthony outlines the thesis that migrations from the west Eurasian steppe during the Bronze Age reshaped the culture of Northern Europe. When Anthony published the book, which you should really read if you are interested in this topic, it was a somewhat heterodox position. Though his intellectual pedigree is of long standing, arguably going back centuries, and extending down the present with J. P. Mallory’s In Search of the Indo-Europeans, in the past few decades diffusion of different sort has been paramount. In particular, the thesis that Indo-Europeans arrived with the first agriculturalists was of late ascendant, with some support being received from phylogenetic modeling of language evolution.

Anthony’s thesis in a way was a halfway house between early modern migrationism from the Eurasian steppe the newer theories. He proposes that the influence from the steppe via the Kurgan people was due to elite dominance and cultural emulation. An analogy here might be that of Hungary, where a Ugric speaking elite eventually imparted to the people a language, but very few distinct genes.

Eventually Anthony collaborated with some geneticists, and provided samples for DNA analysis. The results ended up resulting in a resurrection of migrationism, Massive migration from the steppe was a source for Indo-European languages in Europe. From what I have heard Anthony’s reaction was one of some shock as the magnitude of the genetic change.

5156rR+E2lL._SX326_BO1,204,203,200_ That’s the high level view. But what about the details? Over the past few years I’ve highlighted work that indicates that many Y chromosomal lineages are star-shaped. That is, they underwent recent demographic expansion. Recent as in on the order of ~5,000 years ago in the past. But the Y chromosome is just one locus. I’ve always been curious about results from the X because the X also gives you good sex specific dynamics; 2/3 of the time it is spent in females, and 1/3 of the time in males.

Amy Goldberg has done so, Familial migration of the Neolithic contrasts massive male migration during Bronze Age in Europe inferred from ancient X chromosomes:

Dramatic events in human prehistory, such as the spread of agriculture to Europe from Anatolia and the Late Neolithic/Bronze Age (LNBA) migration from the Pontic-Caspian steppe, can be investigated using patterns of genetic variation among the people that lived in those times. In particular, studies of differing female and male demographic histories on the basis of ancient genomes can provide information about complexities of social structures and cultural interactions in prehistoric populations. We use a mechanistic admixture model to compare the sex-specifically-inherited X chromosome to the autosomes in 20 early Neolithic and 16 LNBA human remains. Contrary to previous hypotheses suggested by the patrilocality of many agricultural populations, we find no evidence of sex-biased admixture during the migration that spread farming across Europe during the early Neolithic. For later migrations from the Pontic steppe during the LNBA, however, we estimate a dramatic male bias, with ~5-14 migrating males for every migrating female. We find evidence of ongoing, primarily male, migration from the steppe to central Europe over a period of multiple generations, with a level of sex bias that excludes a pulse migration during a single generation. The contrasting patterns of sex-specific migration during these two migrations suggest a view of differing cultural histories in which the Neolithic transition was driven by mass migration of both males and females in roughly equal numbers, perhaps whole families, whereas the later Bronze Age migration and cultural shift were instead driven by male migration, potentially connected to new technology and conquest.

Screenshot 2016-09-30 22.33.39 The figure to the left shows the inferences made in regards to the quantitative contribution of farmer males and females, and steppe males and females, to Bronze Age European populations. In short, it looks like the population of Northern Europe derives from a fusion of males from the steppe, and native females, who themselves arose out of a group of peoples which synthesized the ancestry of European hunter-gatherers and West Asian farmers.

But one of the more interesting things about this preprint is that the admixture can’t be modeled by a single pulse event. It seems that there were repeated migrations out of the steppe over multiple generations. But, these men did not bring women, at least in large numbers. The preprint lays out the common sense reason: these were mobile groups, probably bands of men with weapons. If your game is predation on other humans, having a baggage train of women and children is not optimal.

There is a historical analog to what might have happened. Argentina is a nation where mitochondrial lineages show a lot of Amerindian heritage. But the whole genome far less. This is because of male biased migration from Europe. One generation of this would result in a mixed population, but many generations would slowly replace the whole genome.

We will never know in concrete terms what social-political organizations the Indo-Europeans set up once they conquered the plains of Northern Europe, because we don’t have writing. But it seems unlikely that we’re talking about only band or clan level scales of organization. Rather, it was likely that a ‘Indo-European commonwealth’ of some sort existed initially, predicated on domination and extraction of value from the natives. In such a fashion one can imagine Europe being a draw for enterprising males from the steppe. This could also explain likely ‘back migration’ over time, leading to ‘European’ ancestry among later steppe cultures.

• Category: Science • Tags: Ancient DNA, Genomics

Screenshot 2016-09-30 08.23.21 As you may know in Britain there is a new direct to consumer genetic testing service, Living DNA. Debbie Kennett has a post up where she talks about how it works and why it’s different. For now it is British focused, and leverages haplotype-based methods with the PoBI database to give really fine-grained analysis to their customers on those sceptered isles.

Brought to you by the same people who brought you FineStructure, this is a major offering in this space.

But there’s a more general issue I want to comment on. In the video accompanying the website, one of the presenters states that people are “very surprised how admixed” humans are. This depends on scale.

Let’s start at a time, 0. In the short term you are not very admixed usually. Outside of the Americans and other settler societies admixture is not common on the scale of recent generations. But as you go further back, you become quite admixed. E.g., The Geography of Recent Genetic Ancestry across Europe showed lots of admixture on 1,000 year scales within Europe. David Reich’s lab has shown lots of admixture between very diverged populations on a 5,000 year scale. But as you go further back the ‘admixture’ gets lower and lower, and at some point you hit the species barrier, and you see the same genealogies coalescing again and again through the bottleneck.

Now, look at space. As distance is ~0 you’ll see lots of admixture. But as you push further and further away, the admixture drops. At some point the admixture is quite boring. Ergo, all the “you are 100% European” results from DTC companies.

The two dimensions look quite different. Admixture increases as you go further back in time…until it doesn’t. You’re hitting the “species” taxonomical barrier. In terms of space, admixture decreases the further you go away from your focal point of interest.

• Category: Science • Tags: Genetics

Will be back soon.

• Category: Miscellaneous

4197TkGD1DL._SY344_BO1,204,203,200_ At a readers’ suggestion I got Explaining Postmodernism: Skepticism and Socialism from Rousseau to Foucault. Unlike The Dialectical Imagination this is not necessarily a detached academic book. Rather, the author has a definite perspective. About 20 years ago I read George H. Smith’s Atheism: The Case Against God, and there are a lot of similarities between the two books. From that I suspected before doing some research that the author had some influence from Objectivism, and that seems correct. I don’t care too much, and I probably broadly share the authors’ libertarian/classical liberal politics, but the middle sections of the Explaining Postmodernism got a little preachy for my taste.

Nevertheless the first half especially is excellent, and it outlines a genealogy of the Postmodern movement very concisely and in an illuminating manner. There are some details where one might quibble (e.g., the relationship of Immanuel Kant to religion is much more in dispute than presented in Explaining Postmodernism, though that’s a minor objection). But the progression of Transcendental Realism down to the morass we see around us today is a familiar story told more crisply here then elsewhere.

The author does outline a sociological origin for Postmodernism which is very intriguing, as it explains why it is an overwhelmingly far Left movement, despite the implications toward extreme relativism and subjectivism one might infer from the worldview. But there is something that is omitted here, perhaps because the author was not aware of this fact: there is a relationship of Postmodernism to elite intellectual religious revival in the past few decades.

418lqzfRjwL._SY344_BO1,204,203,200_ Alister McGrath is a proponent of this school, and outlines his thesis in The Twilight of Atheism: The Rise and Fall of Disbelief in the Modern World. To condense McGrath’s argument, if everything is a superstition, then people will fall back on the tried and true superstitions. McGrath asserts the collapse of the authority of rationality and philosophical realism signal the end of the Enlightenment project, and undermines the secular world. As an empirical matter there is a lot one can quibble with here; in particular, though Postmodernism may be vigorous in the academy, science and technology are concrete witness to power of naive realism and rationalist presuppositions. But McGrath’s position is philosophically cogent. And, it is not well known, but the doyen of modern Intelligent Design, Phillip E. Johnson, has admitted that the he was strongly shaped by Critical Theory:

I used to refer jokingly to myself as the entire right wing of the Critical Legal Studies movement, which in their view was a contradiction in terms. Their critique was purely the instrument of a left-wing political program, which was chosen arbitrarily and presumed to be good. It was a faith commitment.

So I’m reading a lot of things on Postmodernism. I’m going back to Hegel. On the one hand this is a major opportunity cost. There’s a lot of science and programming stuff I want to read that I don’t have time to read. On other hand, much that I was suspecting becomes very clear. Ultimately I’m respecting Postmodernism more insofar as it is a reasonable tool from what I can see in destroying certainty and realism for those who are innumerate. If you have any understanding of statistics you’re pretty insulated from Postmodernism. But very few people think statistically. I also now believe it is ultimately far more dangerous than before, because it is a serious intellectual tool that can deconstruct much that is precious and rare in the world. In particular, the Enlightenment project, which in many ways goes against the world historical grain, or at least the grain of human intuitions and preferences. Postmodernism as an intellectual exercise is easy to dismiss. But as a tool of political battle it has to be taken seriously.

A Single Migration From Africa Populated the World, Studies Find. I will blog these papers. It’s a question of time. Please don’t pester me on non-open threads about this stuff.

Widespread allelic heterogeneity in complex traits.

14390818_10153997292567984_5603508903928344619_nGunman kills Jordanian Christian writer charged over anti-Islam cartoon. The title is misleading, as the cartoon was making fun of jihadists, not Islam. He posted the cartoon on Facebook.

Chinese Jews of Ancient Lineage Huddle Under Pressure. Most of the Kaifeng Jewish community was absorbed into the Han, though some became Muslim.

Academic Research in the 21st Century: Maintaining Scientific Integrity in a Climate of Perverse Incentives and Hypercompetition.

Please use the “open thread” for random stuff. The OT comments early in threads are pretty annoying.

Also, if you follow me on Twitter if you tweet at me a lot, and I don’t respond, but you keep tweeting at me demanding a response, I’m probably going to block you. Also, I get annoyed at readers and Twitter followers who presume they know my state of mind or aspects of my life from what they see on the interwebs. If you do that and tweet at me, I’m going to block you, just as if you do that in the comments here your chances of me publishing future comments goes way lower. If you have read me for a while you should be aware that I have a really long memory and recall commenters who have crossed me in some way for years, so even if I let you comment again please don’t think I’ve forgotten. The major problem is commenters who presume over-familiarity with me. Probably a function of the low social intelligence of many of my readers.

Finally, Sean don’t post anything on sexual selection on this thread. I won’t post the comments.

• Category: Miscellaneous • Tags: Open Thread


Airports are in interesting window into architecture and perceptions of the future. When I landed at Vienna International in 2010 it was as if I landed back in the 1970s. In contrast, Frankfurt Airport was the closest I’ve felt to really be pushed into the “gleaming future” you sometimes see in science-fiction films.

With that in mind, lately I’ve been thinking that for some reason the airport at Detroit reminds me of what the future was going to be like in my childhood of the 1980s.

• Category: Miscellaneous • Tags: Future


There was a time, five years ago or so, when we knew all the humans who had been sequenced. Or at least most of them. But now we’re coming into the period when the first sequenced animals of any given species are starting to die. Above is Cinnamon, the first sequenced cat is no longer with us. And some day the hour will come when Craig Venter, who was a major contributor to the first human genome, will no longer be with us.

Something to consider.

• Category: Science • Tags: Genomics

The Estonian Biocentre has been one of the best resources in human population genomics, because their policy under Mait Metspalu seems to be to release the data once it’s published. Today I went and checked the site, and noticed a vlog accompanying their Nature paper, Genomic analyses inform on migration events during the peopling of Eurasia.

Well done.

• Category: Science • Tags: Genomics
Razib Khan
About Razib Khan

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