Open Thread, 5/1/2016

51OftfuYlSL._SX316_BO1,204,203,200_I’ve been very busy the past month.

That being said, I made time to read The Monkey’s Voyage. My main interest was driven by the fact that macroevolution and biogeography aren’t scientific questions which I’ve focused much on lately. But, ultimately the book totally convinced me that vicariance doesn’t explain much in terms of geographic patterning of biological variation.

To make it more concrete: the flora and fauna of New Zealand are not relics of Gondwanaland, but relatively recent arrivals due to dispersal. This is in my opinion rather less romantic than the popular view, but the argument and evidence offered in the book are pretty convincing.

The New Yorker has fact-checkers, they should use them

darwin-as-an-old-man-337-450-17The New Yorker has a piece up, Same but Different: How epigenetics can blur the line between nature and nurture, which I think on the balance is pretty good. It introduces epigenetics to a broader audience in a manner that’s more than just a catch-phrase, and, cautions that people shouldn’t over-hype what is a legitimately interesting field of science.

But there’s a major factual problem which I mentioned when it came out, and, which some friends on Facebook have been griping about. I’ll quote the section where the error is clearest:

…Conceptually, a key element of classical Darwinian evolution is that genes do not retain an organism’s experiences in a permanently heritable manner. Jean-Baptiste Lamarck, in the early nineteenth century, had supposed that when an antelope strained its neck to reach a tree its efforts were somehow passed down and its progeny evolved into giraffes. Darwin discredited that model….

It is true that in Neo-Darwinian evolution, the modern synthesis, which crystallized in the second quarter of the 20th century, genes do not retain an organism’s experiences in a permanently heritable manner. But this is not true for Charles Darwin’s theories, which most people would term a “classical Darwinian” evolutionary theory. This is because first, Darwin worked in the pre-genetic era. He did not posit particulate inheritance, and had no genetic model. Second, though it is correct that Charles Darwin’s deemphasized the role of acquired characteristics, he himself was quite open to Lamarckianism in some cases. This openness persisted into the early 20th century, Ernst Mayr started his career as a Lamarckian!

In the least The New Yorker should have had someone with a background in evolutionary biology read the draft. The error is pretty obvious, and easy to fix.

Cladist fundamentalism takes on new meaning

51OftfuYlSL._SY344_BO1,204,203,200_One of the strangest things I’ve read in a while in The Monkey’s Voyage:

What Nelson and Platonic were saying was that, if the evolutionary and tectonic patterns matched, one could infer that the human lineage-meaning people as people, not as porto-humans or tree-living apes or any more distant ancestor-extended back to 66 million years and more to the Mesozoic, which was…the Age of Dinosaurs. Never mind that the intensively studied human fossil record indicates that the genius Homo is only a few million years old. Never mind that the genes of humans and chimps are so similar that they suggest that the common ancestor of these two lineages…existed only 7 million years or so ago. Never mind a whole host of fossils showing that a success of progressively deeper human ancestors-the first hominids, the first apes, the first monkeys-were not around in the Mesozoic. All that evidence is worthless. Molecular clocks don’t work. The fossil record is hopelessly incomplete. People might have lived with dinosaurs.

The author is referring to a portion of Systematics and Biogeography (free PDF at link), a text which was at the forefront of the cladistic revolution which was in full swing in the 1970s. Cladistics was an important development, in that the discipline introduced rigor in systematics and a more formal scaffold onto evolutionary phylogenetic methods. But many evolutionary biologists believe that the movement has lost its way and become ossified into a dogmatic philosophy at best, and a cult at worst.

Dinotopia_LAFT_coverSo as to not fall into the trap of woolly and ad hoc thinking which was common in evolutionary biological methods of systematics and taxonomy in the first half of the 20th century, the cladistic school tends to hew very strongly to a set of methods, and follow their implications to their logical, if weird, conclusions. Here you see it on display. Human phylogeographic variation does reflect continental scale structuring, and continents have emerged on the order of tens of millions of years. Ergo, a hypothesis that is being entertained above is that human differentiation is due to vicariance, where a panmictic population is separated by geographic barriers. So the author are seriously suggesting that humans have developed tens of millions of years ago, and modern differences emerged due to the separation enforced by Plate Tectonics! (the author of The Monkey’s Voyage emailed one of the author’s of the text that this section wasn’t a weird tongue-in-cheek thought experiment, and it seems it wasn’t)

Often science gives strange results. We mustn’t shy away from that. But we also need to be wary of the crazy. The punctilious to a fault adherence of cladists to a very precise and delimited set of methods can be commended on some level, and it was certainly useful in past decades. But more recently they’ve withdrawn into a weird intellectual ghetto as the world has moved on.

The invention of slavery

41ncnodwApL._SY344_BO1,204,203,200_My main gripe with Inventing the Individual: The Origins of Western Liberalism, is that I don’t think individualism is a sui generis invention of Western civilization (the author, Larry Siedentop, gives particular pride of place to Western Christianity as the mother and midwife of liberal individualism). It’s hard to generalize about human nature and history without portraying cut-outs, but I’ve contended for over ten years now that basal, constitutive, and modal, human nature is already quite individualistic. Western liberalism is a rediscovery or excavation, not a novel creation.

Yes, as per The Secret of Our Success humans are very social creatures. But ultimately that sociality redounds to individual success (e.g., positional games/status hierarchies take up more time and energy than coordinating to achieve group success). Western civilization’s individualistic ethos is to my mind a reversion to a more primal norm, as dense human living became less constrained by the eternal Malthusian traps of the agrarian civilizations which arose after the Neolithic. Individualism and wealth go hand and hand.

41ezBQHrx7L“Traditional” customs and values which were handed down to early moderns by their ancestors were cultural adaptations to novel ecologies that were the product of dense existence on the Malthusian limit. There may be limitations to the classical evolutionary psychological conception of the “Pleistocene mind,” but I suspect that the emotional importance of friendship and pairbonds between mates existed during that period, and were ubiquitous. I say this because platonic and romantic love don’t seem to be learned in any deep sense, but are naturally evoked out of our cognitive hardware. And yet norms, values, and rituals over the past 10,000 years have constrained the importance of love, because individual interests can sometimes be at cross-purposes with group/social interests. The friendship between Cú Chulainn and Ferdiad should naturally transcend divisions of honor, obligation, and nationality. Yet in early Iron Age Ireland they do not. The dramatic tension at the heart of Romeo and Juliet, or Tristan and Iseult, arises because of the reality that almost everyone can relate to the individuals whose preferences and needs are constrained and thwarted by considerations of family, religion, or ethnicity (the substitution of divine love for most is probably not an equal value substitute, with all due to respect to god).

The_10,000_Year_Explosion_(Cover)Complex societies are a big deal. They’ve changed the genetic makeup and characteristics of humans a fair amount. But cultural evolution is even more plastic, pliable, and adaptive. Human cultures are protean, and rearrange preexistent cognitive furniture in a manner which makes them functional for a particular time and place. Much of this comes together during the Axial Age with the evolution of “higher religion.” These cultural innovations fused multiple strands together into a very robust alloy. Philosophy compelling to the literate castes was deftly interleaved with devotionalist theism which appealed to the masses and proffered fictive kinship, hammered together by mass ritual, and scaffolded in the institutional frameworks of the despotisms and oligarchies of the age.

41YXHblIQEL._SY445_QL70_I doubt that humans are naturally egalitarian. We strive for excellence, and engage in individual and intergroup competition. But our penchant for rank and status exhibits constraint and moderation. Humans are social apes, and if an “alpha male” gets too big for his britches, then a coalition of subordinate males is likely to topple him. I presume this sort of equilibrating system operated for most of the Pleistocene…but things began to change during the Holocene. Big men became despots. Peter Turchin has argued in UltraSociety that the despotisms of the Bronze Age were unstable, with the consequences for toppling catastrophic. Universal religion, which allowed for constraint on autocrats by positing an ethical principle or supernatural agent above the king or emperor, was a cultural innovation that allowed for greater stability. Sometimes the adaptation was peculiar; both the Imperial Romans and early Muslims avoided the term “king” for rhetorical reasons, even though the princeps and caliphs were kings in all but name.

Evolutionary processes in complexes species generally involves an element of intraspecific competition. Some would even posit that in many cases this is the dominant dynamic driving evolutionary change. But the invention of a caste of slaves, and masses of servile peasants, to serve a small elite, was a feature of agricultural civilization. This was no natural consequence of natural competition.

We know all this happened. The current project has to be to understand how it happened. Why it happened.

A new paper in Nature Genetics sheds light on a critical piece of the puzzle, Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences. The figure below communicates the main results:

Screenshot 2016-04-25 21.40.08

In some ways this seems an incremental improvement over last year’s A recent bottleneck of Y chromosome diversity coincides with a global change in culture. Much of the detail of this current paper, and why it adds to earlier work, can be found in the supplements.

The major takeaway is again you see evidence in Y chromosomal male lineages of incredibly rapid and explosive demographic growth. This is the rise of patriarchy, the arrival on the scene of despotic lineages which monopolized access to a disproportionate amount of the goods and services of many societies, including women.

In the plot above three lineages jump out at you. E1b, R1a, and R1b. The first is associated with the Bantu expansion, that occurred over the last 4,000 years. The second two are likely associated with Indo-Europeans in both Asia and Europe, respectively. The timescale is on the order of 4 to 5,000 years in the past. The association between culture and genes, or the genetic lineages of males, is rather clear, in these cases. In other instances the growth was more gradual. For example, the lineages likely associated with the first Neolithic pulses, J and G. Interestingly, the authors of the paper notice that the same is true in East Asia. Here one sees a more gradual accumulation of genetic mutations as lineages branch out from each other at a stolid pace, a sharp contrast to the explosive “star phylogeny” that is the case for R1b and R1a. This is almost certainly due to the differences in the cultural revolutions, and the reproductive success that that allowed a given male.

Finally, the authors suggest that haplogroup E, which is today the dominant lineage within Africa, though it is found in the Middle East and Europe, is the product of a back migration ~50,000 years ago. The argument is from parsimony. E and D are clearly a clade, and D is found in Japan (and also Tibet and Southeast Asia). If E originated in Africa, and later spread to Europe, so did D. Rather, the authors favor the model that E is a basal Eurasian haplogroup which percolated back into Sub-Saharan Africa during the Pleistocene. It would not be surprising that Southwest Eurasian humans would maintain contact with nearby African populations, but this sort of phenomenon does seem to point to the possibility for a Levantine origin for modern humans!

This is all based on contemporary DNA, and contemporary distributions of populations. There may have been mass extinctions which hide from our perception other demographic revolutions. Additionally, if there is one thing that ancient DNA has taught us, it is that modern distributions may not reflect ancient ones. Nevertheless, this is a good step in understanding the cultural changes which have resulted in the world we see around us.


51OftfuYlSL._SX316_BO1,204,203,200_I don’t know where this recommendation occurred (on this blog, Twitter?), but The Monkey’s Voyage: How Improbable Journeys Shaped the History of Life, is a very interesting book. Haven’t had time to read much of it, but what I have read is fascinating. It seems to be one of those works which is taking a stand on a “big” evolutionary question, this one having to do with the geographic distribution of species across the globe. One school is the vicariance model, where the primary parameter seems to be geological scale forces (e.g., the separation of Gondwanaland into the southern continents). The other looks to stochastic long distance dispersal events. The author of The Monkey’s Voyage is of the second school.

Dinosaurs in decline tens of millions of years before their final extinction. I find clade-level decline rather curious. Additionally, many non-dinosaur lineages went extinct in the K-T event. I think they might be finding a real result, but not sure of the significance.

The end of the line for the Isle Royale wolves

700px-ISROTobinWhen I was 13 years old I had a deep interest in America’s national parks, so I have long been familiar with the ecology and conservation genetics work associated with Isle Royale. In particular, there has been a long-term study of the predator-prey dynamics on the island dating back decades. Before the recent resurgence of the wolf across the West, the Isle Royale pack was not an inconsequential proportion of the national headcount in the lower 48 states.

But these wolves were always on a knife’s edge. The island is small, and there were never more than a few dozen wolves. This is below the generally accepted minimum census size for a viable long-term population. And in fact, the Isle Royale wolves are newcomers, descending from a pair that arrived in the 1940s. Census size aside, this fact itself points to the likelihood that these wolves are going to be plagued by the downsides of inbreeding. Not only is there average population size rather small, but their genealogies coalesce back to a very small bottleneck, possibly an original mating pair.

Now the wolves of Isle Royale are back to where they began: with a single pair. And these two are not promising candidates for the perpetuation of the population. From Science:

A few years ago, eight to nine wolves roamed the island, but the population dwindled to three last year. The remaining two are the most closely related of the group. The inbreeding coefficient of their potential offspring—a measure that varies between zero for unrelated parents to approaching one after many generations of brother-sister mating—is 0.438. (By comparison, the inbreeding coefficient among some of the European Habsburgs was 0.25, according to a 2009 analysis.) Some captive and experimental animal populations approach this level of inbreeding, but such populations are prone to abnormalities—and extinction—and managers try to avoid it. Wolves themselves naturally avoid mating with such close kin, but the pair on Isle Royale have no other options….

The male is the father of the female. They are also half-siblings, as they share the same mother (so the male is the son of a female with whom he mated to produce the female who is his current mate). If mating with near relatives over generations could purge the genetic load of deleterious alleles in a mammalian population, these wolves would have done so. As it happens apparently the wolves of Isle Royale have suffered from typical ailments of inbreeding and reduced fertility for a while.

Family DNA Land

I loaded my children’s pedigree into DNA.LAND to get some better imputation (so taking hundreds of thousands of markers and “filling” with millions based on known associations). Below are the new ancestry inferences for:

-My son
-My daughter
-My wife
-Son/daughter’s paternal grandfather
-Son/daughter’s paternal grandmother
-Son/daughter’s maternal grandfather
-Son/daughter’s maternal grandmother

Screenshot 2016-04-19 22.00.36

Razib Son


Screenshot 2016-04-19 22.06.10

Razib daughter


Screenshot 2016-04-19 21.59.38



Screenshot 2016-04-19 21.57.57

Razib wife


Screenshot 2016-04-20 08.30.51

Razib father


Screenshot 2016-04-20 08.32.52

Razib mother


Screenshot 2016-04-20 08.35.29

Razib father-in-law


Screenshot 2016-04-20 08.38.37

Razib mother-in-law



51aEM-jiATL._SX323_BO1,204,203,200_In the 1960s W. D. Hamilton attempted to solve the “problem of altruism,” in the process developing a formalism that allowed for the elaboration of the concept of inclusive fitness. In concert with this Robert Trivers pushed forward the ideas which led to reciprocal altruism. Finally, John Maynard Smith developed evolutionary game theory. These are the dominant frameworks which biologists depend upon to model the evolution of sociality, as well as its persistence.

But, there is an alternative tradition, which offers up other possibilities besides the big three frameworks. Often this tradition attempts to explain altruistic behavior as a group level fitness optimization problem, rather than an individual level one, as is the case with inclusive fitness, game theory, and reciprocal altruism. David Sloan Wilson has presented this viewpoint in his books Unto Others: The Evolution and Psychology of Unselfish Behavior, and Does Altruism Exist. Wilson’s multi-level selection theory seems particularly apposite for humans, whose baroque social complexity seems to be difficult to derive from elegant individual level theories.

51sdHZvYfTL._SX334_BO1,204,203,200_The field of cultural evolution deals in these sorts of complex models of between group competition and interaction, and it serves as a critical aspect of Joe Henrich’s recent The Secret of Our Success: How Culture Is Driving Human Evolution, Domesticating Our Species, and Making Us Smarter. Meanwhile, in Ultrasociety and War, Peace, and War, Peter Turchin outlines how human group level cohesion, asabiyya, can be the driver for complex social institutions and polities. Another way to conceive of this is esprit de corps.

All this was on my mind as I read Scott Atran’s research groups report, On the Front Line Against ISIS: Who Fights, Who Doesn’t, and Why. I follow Atran’s Facebook, and many of his posts read like what you might expect if Dexter Filkins was a social scientist steeped in evolutionary theory.

This part in particular jumped out at me:

Kurds and Yazidis are fighting for their survival, or rather, as they say, the survival of “Kurdeity” and “Yazideity.” These are core cultural values, sacred and inalienable, which give a sense of “who I am” and “why we are” in a world of ever shifting sands. And the level of commitment to fight and, if necessary die or sacrifice their families in defense of these values, matches or surpasses that of the Islamic State fighters (and al Qaeda’s al Nusra fighters) that we have interviewed and tested with a variety of psychological measurements on “will to fight.”

The Yazidis faced extermination in their ancient homeland. They have no choice but to stand their ground even when faced with the suicidal attacks from ISIS’ North Caucasian fighters, who combine devotion to the cause with military effectiveness. Similarly, the Kurds are fighting for their nationhood, while groups affiliated with the PKK augment that with a utopian Left-wing ideology.

The Sunni Arabs lack such devotion. They have no nation, alienated from the Iraq in which they are an oppressed minority, rather than the ruling caste that they have been habituated to be. They fight for their families, perhaps for their tribe. A neoclassical model of rational actors where clans are “firms” may well model their behavior, which is selfish interested and situational. As Atran’s dispatch makes clear, these were people who were for ISIS before they were against ISIS.

There is some symmetry within ISIS itself, with portions of its collective exhibiting less asabiyya. Local recruits occupy a second class status, and some of them are clearly the marginal or self-interested. Rather, the foreigners, especially units from the Caucasus and the French-speaking West, seem to be the closest that the shiekhs of ISIS have to a praetorian guard. In this way the al-Baghdadi and his inner circle are recapitulating an ancient Muslim pattern, where the rulers rely upon ideologically aligned outsiders to control and prod the populace whom they rule and represent.

Ideology and asabiyya have limits. I believe Atran tends to underestimate the professionalism and cohesion of American fighting units, but even if his judgment was correct (that they lack as much spirit as ISIS), the material advantage would just be too great for ISIS to withstand them. Japan and Germany both were cohesive nation-states, but they were just ground down by the massive industrial power of the United States and the strategic depth of Russia.

Set this against the concerns of the American intellgensia. E.g., White Privilege Conference Attendees Complain Conference Is Too White. What is increasingly normative in elite American circles are positional games, where individuals jockey for money and professional status, as well as ideological infighting which turns on semantic leverage and privilege of identity (where lack of privilege is the privilege in the discourse!).

This way of thinking has bled into the mainstream media. Consider this asinine article on Hillary Clinton and Bill deBlasio, Racially Charged Joke by Hillary Clinton and Bill de Blasio Leaves Some Cringing. I’m not a big fan of Bill de Blasio, who I am fond of calling New York City’s Communist mayor. But, if there is one white person who is not racist, it’s probably de Blasio. The journalists reporting this story must know this, but they still go through with the article. And most of the readers know that de Blasio is married to a black woman and has black children, which is far more integration than most white people achieve in their lifetimes. The journalists know you know that Bill de Blasio is very not racist, but they still have to read about his comments being “racially charged”. It’s a game.

The artifice probably why I found old style economic Leftism of Bernie Sander’s sort much less annoying than new style cultural Leftism steeped in critical theory. I’m very opposed to socialism, and skeptical of big government, but I can see that the proponents of these views are trying to do something for the human race. In contrast, #TeamProblematic seems only to be concerned with tearing down other people through leveraging their accrued victories in the privilege olympics. Rather than sacred values, these are squalid values. It is the intellectual form of going on a shopping spree at a crappy second rate indoor mall.

I’ll leave you with this: Feminists mock Green Party young women’s group for invite to ‘non-men’.

Religious variation in South Korea by region

Religion in Korea by province

Religion in Korea by province

The map to the left is derived from 2005 census data from South Korea. You see religious affiliation by region. The blue bar represent Buddhists. The purple bar Protestants. And the orange bar are Catholics. The figures do not add up to 100% because a large number of South Koreans do not have a religious affiliation.

The Korean peninsula has witnessed a lot of religious change over the past three generations. Traditional beliefs and mores were stronger in the southern part of the peninsula, so Pyongyang was a major center of Christianity. The division between North and South was accompanied by a migration of Christians from the North to the South. On the order of 1% of the population around ~1950, today Christians form about 30% of the population, with 20% being Protestant, and 10% being Roman Catholic. Buddhists comprise 20% of the population. Most of the gains to Christianity occurred between 1950 and 1995.There has also been a more pronounced growth in Roman Catholicism, which is arguably more prominent than its numbers would warrant. Three of the eight listed potential presidential candidates in 2017 list Roman Catholicism as their religion.

Spatially the patterns make some sense and are not surprising to me. The southwest of the peninsula has traditionally been supporters of the more Left political party, while the southeast has been aligned with the Right. Seoul and its environs to the northeast is arguably the locus for the most Westernized segments of Korean society.

I’m curious what Korean readers, or people who have lived in Korea, have to say about this.

Sichuan and spice

14782272393_d2d91f4d35_bInteresting piece in Nautilus, Why Revolutionaries Love Spicy Food: How the chili pepper got to China. As you may know there isn’t any specific thing which is “Chinese food”, anymore there is “Indian food”, or “European food.”* The article focuses on the emergence of Sichuan cuisine, which unlike Cantonese food, took to the arrival of New World chili pepper in the past few hundred years and seamlessly integrated it into its armamentarium.

What was a total surprise for me is the fact that it seems possible that the population of modern Sichuan has only weak demographic connections to classical Sichuan, as instability in the 17th century resulted in a population crash to around ~1 million. Subsequent to this over 10 million Han Chinese from the regions directly to the east, Hunan and Hubei, migrated into the region, replenishing its population. This obviously has cultural and genetic implications…. (if this was common, as some have asserted, then the low between population differences between Han regions in terms of genetics makes a lot of sense)

* My mother thinks most Americans eat hamburgers and cookies.

The California problem

California Surfers Look to Courts for Relief Against ‘Bay Boys’:

…intimidation that has kept outsiders like Mr. Taloa away for generations, a group of surfers is fighting to open up the beach to all comers. A class-action lawsuit filed last month by the Coastal Protection Rangers and two surfers seeks to bar the Bay Boys from congregating at Lunada Bay — similar to the way injunctions have been used against members of criminal street gangs.

The alleged members hail from one of the most exclusive communities in Southern California; many of them are middle-aged; some live in multimillion-dollar homes so close to the coastline here that the morning fog rolling off the ocean leaves their lawns damp.

If you live in SoCal you know there is a problem where rich people basically strangle access to public beaches in some areas so as not to be bothered and annoyed by the populace. The story above is just of a piece with that tendency.

The article I linked to earlier, about pro-growth activists fighting established progressive factions in the Bay Area illustrate the same pattern: entrenched local interests trying to prevent development and growth. The California property tax system is also famously skewed toward incumbents who have been in the state for a long time.

There’s a paradox here. The culturally liberal ethos is now in favor of mass immigration, while the business class of all ideological stripes wants workers of various skill levels. That means more people, who need more housing (and transportation). But the regulatory regime and the social norms are still biased toward skepticism of growth derived from a combination of 1960s environmentalism (on the Left) and anti-tax (property) and classist sentiment (on the wealthy Right).

Open Thread, 4/17/2016

41yT8hhOZJL._SX339_BO1,204,203,200_A day may come when the courage of men fails, when we forsake our work and break all bonds of employment. But it is not this day. And yet it shall come to pass that I’ll make room for finishing The Shape of Ancient Thought. Say what you will about e-books, but that you can have someone’s magnum opus for $20 is a good thing.

My daughter improvised a song about me. It begins: “I’m a brown guy.” But there is a line where she says “I work a lot.” Obviously having issues with work-life balance. People always say that at the end of their life they wish they had spent more time with their loved ones.

Estimating Basal Eurasian. Remember, some of the devisors of “Basal Eurasian” admit it may just be a useful construct….

A lot of people are talking about The Green Room. I grew up in Oregon. And not Portland (rather, the eastern parts). I know that the Pacific Northwest makes for a good setting for these sorts of films because of the gloomy ambience and the real presence of white nationalists, but really their presence is all but invisible. Don’t get the wrong impression from these sorts of films.

This study 40 years ago could have reshaped the American diet. But it was never fully published.

Here is an intro video from the company I’m working for:

Still trying to get used to humidity again. There’s a reason people live in California. In Cramped and Costly Bay Area, Cries to Build, Baby, Build.

McDonald’s of the future coming to St. Joseph. The owner says that the high tech features won’t eliminate labor, but it’s pretty clear that this is where it’s going (and not a moment too soon in light of minimum wage hikes!).

I’m excited to be going to the Evolution Meeting in June in Austin. Should be a change-up from ASHG.

The Aerogram uses an illustration which depicts a woman in a niqab, presumably as a Muslim. I’ve noticed this pattern on other progressive websites. This strikes me as really strange because even many practicing and believing Muslims of a non-liberal religious persuasion (e.g., my parents) find the niqab to be extreme and somewhat disturbing. The difference from the hijab is simple: not being able to see someone’s face in a public situation is alarming, especially when they can see you. All part of the weirdness of the tight embrace between Islam and political liberalism/progressivism in the West. Sometimes my (liberal) friends are curious why I’m conservative. One answer is that I can’t align with people who align with people who would look the other way while I was killed. It’s pretty simple. I’d rather be #problematic than dead.

Mounting evidence suggests antibacterial soaps do more harm than good.

macbookpro-select-intheboxI’ve started to work on a Macbook Pro…now my friends can stop making fun of me. Kind of confusing going between Mac and Ubuntu at home, but perhaps I will finally get an iPhone instead of the next Edge.

Gene-edited CRISPR mushroom escapes US regulation.

Country Star Zac Brown Busted With Pot, Strippers, Cold Beer, Trucks, Freedom.

The Great Ordeal

611jQLzlbwL._SX338_BO1,204,203,200_I notice that R. Scott Bakker is finally coming out with a sort-of conclusion to his second trilogy, with The Great Ordeal. I say sort-of because it seems that his final book in the second trilogy of this planned three trilogy series is going to be one of two, as Bakker submitted a manuscript that was far too long.

Presumably there were issues in relation to the logistics of publishing, because it’s been nearly five years since The White Luck Warrior. That’s unfortunate, because Bakker’s series really has no parallel in the epic fantasy genre from what I can tell. It leverages standard genre tropes, but introduces a dark philosophic undertone set against the foreground of an incredibly rich and finely crafted world. Much of the brutality in The Prince of Nothing seems almost gratuitous, but if you want a more antiseptic narrative, there’s always Brandon Sanderson.

Bakker’s descriptions of the antagonists threaded throughout his series are chilling, and communicate both menace and mystery. The Inchoroi are like no other villains I’ve read of in fantasy….

DNA.Land and new ancestry inference

Screenshot 2016-04-16 22.56.14

DNA.Land has a new ancestry report. Above is my own. I’m pretty aware that designing these consumer-oriented services/applications isn’t easy. But I want to express a little skepticism that two of the three South Asian populations which they used for their “Dravidian” reference are not Dravidian speaking. In fact, geography and ethno-linguistic affinity in South Asia is only modestly correlated with genetic variation because of caste. Something more generic, such as “South Indian” is what I would have gone with.

Neanderthal Y chromosomes, a tale of loss?

445px-Neanderthal-2D-MJCThere’s a new paper in AJHG (open access), The Divergence of Neandertal and Modern Human Y Chromosomes. From the discussion:

The fact that the Neandertal Y-chromosome lineage we describe has never been observed in modern humans suggests that the lineage is most likely extinct. Although the Neandertal Y chromosome (and mtDNA) might have simply drifted out of the modern human gene pool…it is also possible that genetic incompatibilities contributed to their loss. In comparing the Neandertal lineage to those of modern humans, we identified four coding differences with predicted functional impacts, three missense and one nonsense….

For obvious reasons the media has found the argument of functional differences compelling. E.g., Anne Gibbons in Science, Modern human females and male Neandertals had trouble making babies. Here’s why. That’s fine. But I think it is important to note that for many people the loss of ancient Y chromosomes is actually a pretty strong null model. Basically, Y and mtDNA are tree phylogenetic trees (no reticulation), and as you traverse up the tree you note that there is consistent gene loss as surviving lineages coalesce together. Additionally, the rate of extinction will be higher because of higher drift in uniparental lineages (Y and mtDNA effective population sizes are constrained to one sex).

As far back the mid-2000s John Hawks was arguing that lack of high diverged mtDNA and Y lineages, which would suggest archaic admixture, was not evidence for lack of admixture, because of the high likelihood of extinction. In other words, lack of evidence in this case tells us far less than evidence itself.

Peak pr0n, the massive social experiment


The Washington Post posted an op-ed about a week ago with the title Is porn immoral? That doesn’t matter: It’s a public health crisis. The author is listed as follows: Gail Dines is a professor of sociology at Wheelock College in Boston and author of “Pornland: How Porn has Hijacked our Sexuality.” To not put too fine a point on it sociologists are generally full of shit. Sometimes they are correct. Oftentimes they are wrong. But they are always full of shit. The “reproducibility crisis” means we need to look at a lot of science with a skeptical eye, from the sexy findings of social psychology, to the medical studies which clinicians rely upon. Out of all these scholarly endeavors sociology may be the most insulated from concerns of reproducibility since it is such a brazen prostitute of a discipline, beholden to political considerations Über Alles.

41WL2k2+47L._SY344_BO1,204,203,200_Dines uses the words “association” and “correlation” several times. Here is the only reference to cause in the piece: “Pornography can cause lifelong problems if young people are not taught to distinguish between exploitative porn sex and healthy, safe sex.” They rest on associations and correlations.

If you’ve read Jim Manzi’s Uncontrolled you know that you need to be very wary of modest correlations in social science. I would not be surprised if Brazilian fart porn was associated with sexually deviant behavior. But my own supposition is that it is more likely that Brazilian fart porn is an indicator of serious underlying problems, rather than the cause of those problems.

But, we do have a massive social experiment going on today in relation to the impact of porn on society. Starting around 1995, and at various points of initialization over the next then years, the internet became ubiquitous enough in the developed world that the tight constraint on “supply” of porn was removed, so that it met “demand.” This is pushing porn in more perverse and kinky directions. It also means youth over the past generation have had incredibly easy access to very hardcore pornography for a generation.

As you can see above in the early 1990s the FBI began receiving fewer reports of rape, concomitant with the decline in violent crime generally. The decline in rape has continued through the age of porn. I doubt there is a causal relationship. But it goes to show that there is no macrosocial evidence that porn results in increased rapes in the aggregate.

Early and rapid settlement of the New World


The above model of the settlement of the Americas is from a new paper which utilized ancient mtDNA, Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas (open access):

The exact timing, route, and process of the initial peopling of the Americas remains uncertain despite much research. Archaeological evidence indicates the presence of humans as far as southern Chile by 14.6 thousand years ago (ka), shortly after the Pleistocene ice sheets blocking access from eastern Beringia began to retreat. Genetic estimates of the timing and route of entry have been constrained by the lack of suitable calibration points and low genetic diversity of Native Americans. We sequenced 92 whole mitochondrial genomes from pre-Columbian South American skeletons dating from 8.6 to 0.5 ka, allowing a detailed, temporally calibrated reconstruction of the peopling of the Americas in a Bayesian coalescent analysis. The data suggest that a small population entered the Americas via a coastal route around 16.0 ka, following previous isolation in eastern Beringia for ~2.4 to 9 thousand years after separation from eastern Siberian populations. Following a rapid movement throughout the Americas, limited gene flow in South America resulted in a marked phylogeographic structure of populations, which persisted through time. All of the ancient mitochondrial lineages detected in this study were absent from modern data sets, suggesting a high extinction rate. To investigate this further, we applied a novel principal components multiple logistic regression test to Bayesian serial coalescent simulations. The analysis supported a scenario in which European colonization caused a substantial loss of pre-Columbian lineages.

The key here is that looked at whole mitochondrial genomes, which gives them more information to work with. Earlier work often focused on a particular variable region of the mitochondrial genome. And, mtDNA is copious, so they got good quality data from all of their samples (really 5x is decent for population genomic work, and that was the worst). Combined with the fact that they had ancient genomes, which allow them to investigate the phylogeny in a more precise manner temporally, and have you the potential to make some really strong inferences.

F3.largeFigure 3 in the paper makes everything really clear. The last common ancestors between Native American mtDNA lineages and those of Siberians is >20,000 years before the present. That is, before the Last Glacial Maximum. The next major feature you see is an explosion of lineages aroun ~15-16 thousand years ago. This is the hallmark of a rapid population expansion. But after the initial period of diversification you see the persistence of a lot of deeply divergent lineages. Additionally, further population genomic modeling indicate that there was a major extinction event ~500 years ago, no doubt due to the Columbian Exchange and the arrival of Old World populations and their diseases.

This paper is fundamentally about Native American historical genetics. It is another nail in the coffin of the “Clovis first” model of Amerindian origins. Basically, that the Clovis group of megafaunal hunters were the First Americans. No, it does seem likely now that modern humans were present in portions of the New World thousands of years before Clovis. The Monte Verde site’s occupation on the Chilean coast less than two thousand years after the opening of a coastal route from Beringia indicates that perhaps there was a strong focus on marine environments for a significant period of time. Once the New World was settled there seems to have been a lot of persistent population structure, until the arrival of Europeans, at least in comparison to what ancient DNA has told us about Europe. Additionally, the long isolation of the Beringians is also significant in my opinion.

In a world of billions of humans it may be that we lack proper intuition for how little gene flow may have occurred between populations in a sparsely populated globe. The Beringians were separated from Siberians for on the order of ~5,000 years. It only takes ~1 migrant between two populations per generation to prevent them from drifting apart in allele frequencies, so the gene flow was very low (this is mtDNA, so not strictly applicable, but the same logic holds). But it is possible that in much of northern Eurasia during the Last Glacial Maximum humans retreated to zones of survival, and vast swaths of territory became empty. This would result in islands of human habitation diverging and become very different over several thousands of years. In sharp contrast, the world over the past 4,000 years or so has been characterized by the ability of humans to travel long distances over inclement territory, and settle amongst strangers, usually through conquest. Partially this is due to the domestication of the horse, but partially it is probably due to the emergence of high density complex societies which can incubate specialist castes whose role arose initially as defense, but who often engage in offense whenever the opportunity arises.

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