Celebrating what is, not what was

51VGBO04szL._SY344_BO1,204,203,200_In the year 2000 I watched the film The Patriot. Some British observers protested that the depiction of frankly Nazi-like behavior by the redcoats in the film was total fiction. There are scenes in the film where slave are promised freedom in the revolutionary cause. Even those with a cursory knowledge of history in this period know that that is a painfully ahistorical element of the plot. Finally, the historical individual upon whom the protagonist was based was a nasty fellow.

There is a tendency to compress the past, and turn it all into a blurry equivalent haze. Consider the American Civil War next to the Revolutionary War. Though I people of the North were no more angels than those of the South, it eventually came to be that the sectional chasms of the 1850s culminated in Dred Scott v. Sandford decision, as well as a war in the service of a peculiar institution (do note, I accept the proposition that the upstream causes were structural-economic, even if their cultural manifestations were ideological; see Clash of Extremes: The Economic Origins of the Civil War). As I have noted, as a child who came to consciousness in Greater New England there was never any doubt as to who was on the “right” side in the Civil War. Looking back with hindsight it does seem to me that by and large the armies in blue singing “John Brown’s Body” are more prophetic of a modern outlook than those who fought for the Southern way of life.

OrnamentalismTo be unequivocal about the American Revolution is more difficult for me. Unlike the Lost Cause, Britain did not disappear. Britain is still here. In fact, for a century Britain and the United States of America have been fast friends on the international stage. In the game of “what-if” it is natural that one look to the course of events in the British Empire and consider if that was perhaps the road not taken. At Vox offers 3 reasons the American Revolution was a mistake. They are, in order:

- Abolition would have come faster without independence

- Independence was bad for Native Americans

- America would have a better system of government if we’d stuck with Britain

One can agree or disagree with these assertions. The first two do seem more probable than not, though I am not entirely confident. The last is a matter of some complexity which I will set to the side. The key concern that immediately crops up in my mind is that the retention of the thirteen settler colonies would have irrevocably altered the course of British history. History is made up of contingent events, even if there are broad trends, and the addition of the massive dominion of the American colonies, and their likely demographic arc toward parity with the metropole just across the Atlantic, would have changed British culture. As Kevin Philips observed in The Cousins’ Wars the independence of the American colonies and the demographic collapse of Ireland in the wake of the famine resulted in a British population stripped of a large number of dissenting Protestant elements as well as a huge Catholic minority.

9780199604548There is a line of economic determinism that argues that American secession from union with the metropole was inevitable. That is because of the distinctiveness of the American Northern economy as it progressed in the early 19th century, the conditions of which were already in place by the 18th. While dominions such as Canada and Australia, and the erstwhile Southern colonies and the non-white possessions, were geared toward producing raw inputs for British manufacturing (one reason that the British elite were pro-Southern in their sympathies for much of the Civil War), the North was almost certainly bound to become an industrial rival (this explains the fixation on traffic policy in American politics up until the middle of the 20th century. It is hard to imagine the existence of a Dominion dominated by groups with dissenting Protestant sympathies and economically ascendant in a manner which competes with England not being a major question in the 19th century in lieu of the American Revolution. It may be that many of the things distinctive in British history as opposed to American, and preferred by the sort of people who write at Vox, may not have occurred in the same if American and Britain remained politically fused, due to greater cultural exchange.

51VLZmyVmRL._SY344_BO1,204,203,200_Second, there is the issue of British elite culture would influence the United States. Within the American experiment there was pregnant a panoply of radicalisms, some of which were resisted by broad swaths of the America itself. Britain has a hereditary aristocracy, and class has a particular valence in British culture which it does not in the United States of America. The economic realities of the frontier suggest to me that some of this is structural and not conditional. After all, Canada and Australia are less fixated on class than England. But, it seems that a tighter integration between British and American society could help by dampen down the populism of American culture in its orientation. Additionally, a quick survey of the population statistics for Canada and Australia show that they are much more British than that of the United States. The massive waves of German immigration to the United States may have been much more modest in an American under the Empire, and the Anglo-Saxon demographic character of much of the North would have been more thoroughly preserved (one can imagine knock-on effects, such as a larger wave of German migration to South America and Eastern Europe?)

Reflecting on history is important. And thought experiments, counter-intuitive, even shocking, are to be welcomed. But we live in the year 2015, and the past and the past. What has been done can not be undone. So tomorrow I’m going to celebrate the American Independence, because whether the omniscient scales of history judge the arc of utility positive or negative, without it we wouldn’t be who we are, and we can always make the future better no matter the substance of the past.

CRISPR and Confucianism

51UiMG9M0FL._SY344_BO1,204,203,200_A few days ago The New York Times published a piece with the headline, A Scientific Ethical Divide Between China and West. My instinct as to what the piece was going to be focusing on was totally off. Whereas my own assumption was that it would focus on perceptions of widespread corner cutting, and sometimes fraud, in Chinese science, it was mostly about CRISPR and genetically engineering humans. As you probably know I find some of this a bit much. I take those who are worried about misapplication of “gene drive” technologies more seriously than those worried about germline edits in humans, because the latter are likely to happen, but be few and far between. In the wide world of human rights concerns CRISPR edited fetuses are very low on my list. Though CRISPR is much better than most older genetic engineering techniques in terms of specificity, for the near term future it is unlikely to be good enough that you’d want to “perfect” your child.

Then there’s this post over at Quartz, Why China won’t listen to Western scientists about genetically modifying the human embryo, which focuses a lot on cultural differences. It concludes with this: “Inside China, there are people who are opposed to international standards, citing cultural differences. This force is actually quite powerful sometimes.” Actually, I have cultural differences with many people who are averse to genetic engineering. I agree with Alex Tabarrok, if the risk/reward proposition for CRISPR in the context of humans shifts enough, I don’t have any hesitation of allowing it on an individual basis (i.e., it shouldn’t be mandatory obviously!). In fact, for adults who want to take the risk the time table for elective genetic engineering is probably much closer.

But this section of the Quartz piece jumped out at me:

“Confucian thinking says that someone becomes a person after they are born. That is different from the United States or other countries with a Christian influence, where because of religion they may feel research on embryos is not ok,” Deng Rui, a medical ethicist at Shanxi Medical University, told the New York Times.

Two East Asian nations have large numbers of Catholics, Protestants, Buddhists, and those who are irreligious, in The World Values Survey. There is a question which asks, “is abortion ever justifiable?” The respondents are given a 1 t o 10 scale. 10 is “always justifiable,” and “1″ is “never justifiable.” Below are the results (Poland is a “control”).

Abortion is….
 
Singapore No Religion Buddhist Protestant Catholic
Never justifiable 19.4 20.0 33.3 24.6
2 5.0 10.4 10.4 13.8
3 9.0 12.0 16.6 11.0
4 11.7 13.5 8.4 9.7
5 28.5 26.2 20.9 25.5
6 10.6 6.9 4.5 4.6
7 7.0 6.9 3.9 7.6
8 5.7 3.1 0.8 2.5
9 0.9 0.6 0.9 0.7
Always justifiable 2.2 0.4 0.4 0
N 349 579 197 120
South Korea None Buddhist Protestant Catholic
Never justifiable 31.8 41.0 38.6 41.1
2 5.5 6.0 7.8 9.6
3 9.4 17.0 13.4 7.9
4 11.1 6.6 9.6 11.9
5 21.4 14.9 14.1 14.9
6 9.5 3.7 8.1 3.3
7 5.5 5.2 3.8 6.2
8 4.3 3.2 1.0 3.4
9 0.7 1.2 3.4 1.3
Always justifiable 0.8 1.1 0.2 0.4
N 493 244 252 188
Poland None Catholic
Never justifiable 13.2 48.4
2 4.0 10.1
3 8.3 8.0
4 4.1 3.8
5 27.2 14.0
6 14.7 5.0
7 5.9 3.9
8 9.3 3.0
9 2.1 1.3
Always justifiable 11.2 2.5
N 45 844

What’s this telling us? In South Korea there really isn’t much of a difference between the religions, and the gap between religious and irreligious is modest.  South Korea has historically been the most Confucian nation in the world. But there is a lot of ambivalence about abortion. The results for Poland show that the irreligious are very different from Catholics. Singapore shows that Buddhists and those with no religion cluster together, but Catholics are not particularly anti-abortion, but Protestants are.

For all the talk about culture, I think old fashioned Marxism and nationalism can explain the Chinese pushing the envelope. There are material rewards to scientists who publish high impact and notable findings. And, there are glories which accrue  to the nation as a whole. If China wants to “catch up” with the West in science, then it’s going to push into areas that the West is not focusing on.

Major in physics if you don’t want to be distressed

51teQS2zYBL._SY344_BO1,204,203,200_Before adolescence, when I discovered science fiction, I didn’t read much fiction (a bit of Charlotte’s Web and Clan of the Cave being exceptions). But I did read a fair amount of Greek mythology. I quickly outgrew the “childrens’ section” of the library, and spent a fair amount of time reading Greek mythology from the adult stacks. This meant that I encountered a lot of weird material, which I a was definitely not psychologically ready to process. Some of that stuff is seriously fucked up. It starts at the beginning, when Cronus eats his own children. And it ends with Orestes slaying his own mother, though perhaps more disturbing to me was the killing of Astyanax (though let’s be honest, you can pick your poison in The Iliad). Then there’s The Odyssey, which can be spun as an adventure tale. What’s not to like? But it definitely makes The Hobbit seem rated PG. For a pre-adolescent child the climax, where Odysseus kills all his suitors, was disturbing and confusing. Specifically, this seemed a major overreaction! But then at that point I didn’t understand the social context, nor did I really understand romantic feelings and jealousy in any concrete manner.

I bring this up because The Wall Street Journal has a piece out which is now a standard template form, School’s Out at Columbia, but a Debate Over Trigger Warnings Continues:

But students said the school is prioritizing an outdated, Eurocentric selection despite Columbia’s diverse student body, mandating works with overtones of racism and sexism and teaching them uncritically. Many of them have said that if the school insists on requiring works depicting rape then those books should come with a warning—either verbally from a professor or stated on the syllabus.

“Some people would prefer not to be blindsided by reminders of traumatic experiences,” said Charlotte Bullard Davies, a rising senior studying political science.

Some of the issue here is the standard demand for a canon that expands beyond “Dead White Males.” And some of the concern has to deal with people who have experienced genuine trauma. I’m not a psychologist, but there are two rejoinders that came to mind. First, there was a whole generation of Jews who survived the Holocaust and likely encountered disturbing literature. How exactly did they deal with being “triggered”? It strikes me that some of the premises of being triggered need be examined, in terms of the science. My mom was shot, “by mistake”, by the Pakistani army in the early 1970s, and nearly bled to death. But she’s never expressed being disturbed by the presence of guns and such in film or even on the racks of pick-up trucks. Perhaps there are individual differences.

A second response is that one way to avoid having classroom discussions which challenge and disturb you is to major in science. That way you can avoid all the social and political questions, and just be freaked out by quantum indeterminacy. Yes, it is true that there are aspects of the science curriculum which will challenge the beliefs of some students. Those who are Creationists, for example. But we all know that these sorts of students getting disturbed and overwrought with their beliefs being put under the microscope is not a major issue for academia (it’s a bug, not a feature). The sensitivities of religiously conservative students are irrelevant to most academics (well, unless it happens to be Islam).

51Q1mfRFtXL._SY344_BO1,204,203,200_Which gets to the heart of the subjectivity of all of this. How can one talk about the fact that “this canon represents a particular segment of the privileged population”, without acknowledging that Columbia University students are privileged and used to getting what they want? The average Ivy League undergraduate is from an upper middle class background. They’re achievers, they succeed, and they’ve been told they’re the best, and been validated all their life. Not only do they think they’re clever, but the university has told them they’re clever by admitting them. It is unfortunately likely that these issue will bloom indefinitely in a culture of quasi-egalitarianism, where the university maintains a pretense that student feedback is welcome. Not only do these upper middle class students think they are special snowflakes, but society has told them they are special snowflakes and the university has backed that up by admitting them out of all their applicants.

Finally, it is always ironic to me that those protesting the literature of ancient cultures offer up as an alternative contemporary authors of prominence (e.g., Toni Morrison in The Wall Street Journal Piece). The reality is that modern authors, no matter how “radical”, are of our time and place, and reflect our history and values. They are worth reading, obviously, but they don’t offer up a window into a startlingly alien Weltanschauung. Consider The Golden Ass. Though a broadly sympathetic portrait of the Roman lower orders, the narrative takes slavery for granted in a world where it was a relatively uncontroversial practice. Reading the The Golden Ass can be instructive in as an example of literature in shedding light on a our deep commonalities across millennia, along with radical divergence in values.

And it need not be “Dead White Males” or their ancestors. Recently I read with great interest the figures central to Bushmen mythology. When referring to marginalized authors outside of the mainstream of the Western canon it seems rare to me that the alternatives are as radically alien as this, though I would like to be corrected on that.

Less intelligent still oppose gay marriage (on average)

gaymarriage_htm_c47cf983

The WORDSUM variable in the General Social Survey has a correlation of 0.71 with general intelligence. That is, IQ. As you can see in the figure above the distribution isn’t quite normal, though those with at least a college degree are skewed toward having higher scores. A 10 out of 10 means getting the definition of all 10 vocabulary words on the test correct. A 0 out of 10 means the converse.

It’s often illuminating to see how WORDSUM tracks social views. My rule of thumb is that if an overwhelming skew of the intelligent is toward one particular opinion, that will determine social policy. To me that explains why Creationism has had only spotty traction in this country’s public schools despite relatively broad avowed support for “equal time” in the classrooms in the interests of fairness. While the liberal elites are uniformly opposed to this, the conservative elites are divided.

Looking at attitudes toward abortion by intelligence also sheds some light why this political debate seems to be an eternal feature of the American landscape since the 1970s. I took WORDSUM and combined 0 to 4, 5 to 7, and 8 to 10. You can think of these as the “dumb,” “average”, and “smart.” Then I compared them to the ABANY variable in the 1980s and 2000s. This asks whether respondents think a pregnant woman should be allowed to have an abortion for any reason. The results are below.

gaymarriage_htm_d567c5bf

As you can see, there is almost no change over the past generation.

Now what about gay marriage? You can probably guess where I’m going with this. No matter what intellectual Christians say I believe that this generation will come to pass such that the vast majority of Christians will accept gay marriage and their faith as compatible. More precisely, I believe that by the year 2100 the majority of the world’s Christian population is likely to be accepting of gay marriage.

Personally it has been interesting to see how attitudes have changed. In my own family individuals who were opposed to gay marriage ten years ago have now put a rainbow filter on their Facebook profile. More starkly, there are those I know from my adolescent years who are excited about gay marriage now. I grew up in a very conservative area (the county routinely votes 70 percent Republican), and remember debates in classrooms about ballot measures which we all termed “anti-gay”. Now some of those children who argued in favor of these measures are putting rainbow filters on their Facebook profiles!

So how have things changed? The GSS has a variable, MARHOMO, which asks if “Homosexual couples should have the right to marry one another.” It was asked in 1988, and then every few years from 2004 on. I combined those who strongly agree and agree that homosexual couples should have the right to marry. Below is a contrast between 1988, and the 2000s and 2010s, by WORDSUM.

gaymarriage_htm_65b56188

Screenshot - 06292015 - 09:48:18 AMSo what’s next? Some liberals are now opening the debate about polygamy in the interests of fairness and justice (and more broadly construed polyamory). But as you can see from the map to the left polygamy is already legal in much of the world. This experiment has been done. The satirical slogans write themselves: “In the 7th century love for old rich men for many young women won! Back to the future.” A few years ago I put up a post, Monogamous Societies Superior to Polygamous Societies. That’s obviously a judgment that varies by where you stand. If you are the median human, it seems reasonable to me. Polygamous societies have been around for thousands of years. Almost always polygamous means polygynous, not polyandrous or polyamorous. We know the score. Yes, if you take a narrow liberal and liberal hedonic perspective about individual human flourishing it does seem unjust that those who love more than one individual can’t enter into legally binding relationships with those individuals. But the big picture is not so pretty.

220px-Donald_Trump_announcing_latest_David_Blaine_feat_3-altPerhaps this time it will be different. But we have a track record of who enters into polygamous relationships, and who benefits. Polygamy allows extremely powerful and wealthy males to gain access to many women simultaneously. Of course serial monogamy and lack of fidelity show that this isn’t a very tight fix for the perceived problem. But the de jure laws which constrain elite individuals to one official marriage partner serves as a check on this phenomenon.

To put it more plainly, gay marriage has a huge impact on gays, and not much impact on straights (at least non-psychically). Gay marriage is basically an extension of a social-legal apparatus operative among straights to gays. Polygamy is different, in that it tinkers with major parameters of the machinery of the marriage, not simply who can partake. Polygamy does impact straight people, usually in situations where young males must scramble to accrue enough resources to be one of the fortunate men be able to have a wife, and perhaps a few to spare. From the perspective of women they have to consider the option of being a secondary wife of a rich man, as opposed to being the primary wife of a poor man. Enforced monogamy might be a behavioral strategy to dampen status competition and maintain social cohesion for both sexes (in the hunter-gatherer world a sort of serial monogamy was probably the norm). The basic thesis is that mass agricultural society allowed for the evolution of radical inequality, and the social norms of the ethical religions evolved precisely to bring the system back into balance.

Genome architecture in Caenorhabditis

450px-Adult_Caenorhabditis_elegansC. elegans is kind of a big deal, because it is a model organism. Model organisms are a big deal because they illuminate general principles in biological processes, and allow life science to become more than “stamp collecting.” As a practical matter it is also great be part of a model organism community because they are communities. And these scientific cultures have come a long way. It used to be that you had the “fly room.” Today you have the “fly meetings”, which boast ~1,500 scientists attending! (the fact that these meetings are sponsored by the Genetics Society of America should make it quite clear how central Drosophila are in the world of genetics)

51DX03NQH6L._SY344_BO1,204,203,200_For C. elegans Andrew Brown’s In the Beginning Was the Worm: Finding the Secrets of Life in a Tiny Hermaphrodite is the best treatment I know. It’s an organism whose every cell has been mapped, thanks to the sort of bench science labor that’s unlikely to be repeated in the near future. This pinpoint precision in the cytological and morphological structure is one reason my friend Armand Leroi can wax eloquently about elegans. He’s a developmental geneticist. But as Patrick Phillips admitted to me years ago a hermaphroditic selfing species exhibits some deficiencies from a population genetic perspective. C. elegans just doesn’t have that much genetic diversity. Not a big deal if you are exploring molecular genetic mechanisms, but kind of a problem for exploration population variation (unless you are studying H. sapiens, in which case all is forgiven). Luckily, there are “outcrossing” variants of Caenorhabditis out there. These outcrossing lineages are more amenable to traditional population genetic theory, which was developed in the context of sexually reproducing diploid organisms such as Drosophila and humans.

originsgenomearchitectureThis being 2015, to do cutting edge population genetics you need to also develop genomic resources for these exotic outcrossing species of worms. That seems to be exactly what’s happening, as highlighted in a new paper, Reproductive Mode and the Evolution of Genome Size and Structure in Caenorhabditis Nematodes. While elegans is very low in variation (many researchers like to work on isogenic lines which differ by a mutant here and there), some of the outcrossing lineages are very polymorphic. This makes assembly of the genome more difficult for various technical reasons (ergo, for de novo assembly you usually attempt to find an extremely homozygous individual of a given species). On Twitter Patrick offered that they “generated more than 2,000 inbred lines for sequencing and genetic map”, and that over “90% went extinct.” Obviously they got it done, but it was tedious.

Citation: Fierst JL, Willis JH, Thomas CG, Wang W, Reynolds RM, Ahearne TE, et al. (2015) Reproductive Mode and the Evolution of Genome Size and Structure in Caenorhabditis Nematodes. PLoS Genet 11(6): e1005323. doi:10.1371/journal.pgen.1005323

Citation: Fierst JL, Willis JH, Thomas CG, Wang W, Reynolds RM, Ahearne TE, et al. (2015) Reproductive Mode and the Evolution of Genome Size and Structure in Caenorhabditis Nematodes. PLoS Genet 11(6): e1005323. doi:10.1371/journal.pgen.1005323

The above wasn’t a population genomic paper. They didn’t have large sample sizes, nor were they focusing on questions that applied to the microevolutionary scale (within species level lineages). Rather, they were comparing the genomes of Caenorhabditis lineages which diverged on the order of ~30 million years ago. The effective population size difference between selfing and outcrossing lineages is huge, with the authors reporting Ne < 10,000 for C. elegans Ne > 1,000,000 for C. remanei. This is a big deal because variation in effective population size has been argued by many, foremost Mike Lynch, as one of the drivers of the phenomenon of huge genome size differences. Lynch is a fertile mind with many ideas, and if you are curious about them I’d recommend a purchase and read through of The Origins of Genome Architecture. But the upshot from this paper seems to be that the broader thesis of Lynch and his supporters is not favored by these specific results utilizing comparative genomics. Every few years I reread Lynch’s 2005 paper, The Origins of Eukaryotic Gene Structure, because genomics is a rapidly changing field, and many of the predictions and conjectures are now being tested.

Ideally genetics is a science which produces powerful general theories. Actually, it’s not an ideal. It’s the concrete aim. Genetics as a science was forged in the fires of Mendelism. It was a formal and abstract advance over intuitive models of blending inheritance. It worked for 50 years without any knowledge of its concrete biophysical mode of transmission, DNA. With the emergence of genomics, and the fusing of this field with classical genetics, it is expected that one would probe the bounds of generality. E.g., what population genetic parameters influence genome size, or the proportion of the genome that is intergenic, and the number of self genetic elements? The genomic is a rich multi-dimensional topography, and for many organisms we have poor singular drafts. That will change. The quest for the abstract frameworks from which we can deduce and predict will probably come with more data, and the computational power to analyze that data. Almost certainly this will start with the model organisms in the wake of the maturing of human genomics. I’m not sure that the reduction in genome size of selfing organisms says much generally about evolutionary processes, but it’s part of a broader puzzle which needs to be assembled so that genomics moves beyond its exploratory phase of description.

Citation: Fierst JL, Willis JH, Thomas CG, Wang W, Reynolds RM, Ahearne TE, et al. (2015) Reproductive Mode and the Evolution of Genome Size and Structure inCaenorhabditis Nematodes. PLoS Genet 11(6): e1005323. doi:10.1371/journal.pgen.1005323

Open Thread, 6/28/2015

What_Hath_God_Wrought_-_The_Transformation_of_AmericaSectionalism is derived from what I term the “Dark Matter” of American history. These are deep social-cultural norms and values which predate the American Founding, and differentiate disparate regions of our nation. In fact, some of the norms likely predate the discovery of the Americas, and are rooted in ways of life which differentiated British regions by the late medieval period (e.g., independent agro-pastoralists vs. serfs). The books Albion’s Seed: Four British Folkways in America, American Nations: A History of the Eleven Rival Regional Cultures of North America, and The Cousins’ Wars: Religion, Politics, Civil Warfare, And The Triumph Of Anglo-America, are good primers on the deep structure in an American context of what I’m referring to. I hadn’t totally realized how important these folkways were in determining one’s world view until I’d read Dianne Purkiss’ The English Civil War: Papists, Gentlewomen, Soldiers, and Witchfinders in the Birth of Modern Britain, as I had a very difficult time not seeing the Puritans in this long forgotten (in the United States) conflict as the “good” side. Why? I had to admit it had a lot to do with the fact that I was American, and in particular, grew up in my formative years in a part of America which was in the shadow of the Puritan legacy. Similarly, when we learned about the Civil War there was no doubt which side was the good side, not just because that’s what seems on the “right side of history” today, but because so many young men left the local area to fight battles far away from their family

903564But what about after the Founding? Two books which are really influential in my thinking about the antebellum republic are The Rise of American Democracy: Jefferson to Lincoln and What Hath God Wrought: The Transformation of America, 1815-1848. These works take slightly different perspectives. The author of the first, Sean Wilentz, seems to be broadly sympathetic to the transformation of the American republic, whose democratic pretensions were far more understated and disputed in 1800, to a full fledged democratic republic under Andrew Jackson (The Rise of American Democracy can be thought of as an homage to earlier The Age of Jackson). Daniel Walker Howe’s What God Hath Wrought is a more equivocal work, insofar as it seems to tell more the story of the era’s political losers and underdogs, the Whigs and the Northeast. The irony here is that ultimately the Whig views on American political economy arguably won after the Civil War, or were at least dominant. And culturally the industrious and technological society of the North, with roots in Greater New England, but eventually to wash over the Mid-Atlantic, emerged victorious by the end of the 19th century (the failure of the Populists confirms this).

It goes without saying that the Civil War was the great watershed of American history. After this event the idea of the United States as a singular and unitary nation, despite its federal structure, was ascendant. The older model of the United States as a loose federation of states, went into decline (I have heard it stated that the Civil War marked the period when the United States superseded the phrase these United States). To a great extent the arc of history before the Civil War is surprising and alien to moderns. Many college educated Americans are aware of the nadir of American race relations in the late 19th century. But despite the importance of Dred Scott, they are less cognizant of the fact that the 1850s was arguably the first nadir of race relations. Over at Scholars Gate there is a post, There Is No “Right Side” of History that highlights the fact that it was between the Founding and the Civil War that the “Slave Power,” and a fully elaborated formal system of white racial supremacy, emerged in these United States. It was not there at the Founding, though it was already present in chrysalis in many regions of the South with black demographic majorities.

Most educated Americans are aware that there was a hardening of attitudes toward racial slavery in the American South across this period. In the earlier decades the fact of white supremacy was clear and understood, but its implementation was rather fluid. In the 1830s Richard Mentor Johnson was the Vice President of the more avowedly white supremacist party of the time, the Democrats. He also happened to be a man who was well known to have had a common-law marriage with a mixed-race slave, whose daughters he acknowledged as his own. The point in illustrating this anecdote is that it seems likely a man with his biography could not get nominated for high office in the 1930s, but could in the 1830s! Second, along with the rise of white supremacism in the South, the rise of Democratic party populism across much of the North, especially outside Greater New England, produced the concurrent phenomena of dropping of property qualifications from white men along with the abolition or curtailment of voting rights from blacks who had earlier had suffrage (and in some cases women as well!).

Nonzero_-_The_Logic_of_Human_Destiny_coverThis is all relevant because it is rather common today to assert that “The arc of the moral universe is long, but it bends towards justice.” A cursory examination of American history tells us that this is often not true on the 100 year scale. I would agree with the broader thesis outlined by Robert Wright in Nonzero: The Logic of Human Destiny, that non-zero sum interactions result in increased human flourishing over the long term. But, that is on the scale of 1,000 years, not 100 years. You can ask the Romans of St. Augustine’s day, or those who watched Argentina’s decline in prosperity across the 20th century. A little history would help, because it keeps our “theory” in check. Unfortunately our social and political elites are history-poor, let alone the average person on the street.

Second, I have a piece in USA Today with Dolezal’s delusion, with Alex Berezow. It’s short & sweet, and I doubt regular readers will be illuminated by novel insights. Our basic contention is that race is both biological and social, and you can’t reduce it to either. This strikes me as common sense, but it does have to be restated in our day and age. Despite the fact that we are a young and relatively homogeneous species, genetic variation apportioned by geography and shaped by history is real, important, and non-arbitrary.

People keeping asking me if there is an update to History and Geography of Human Genes. I keep saying wait until next year, because there’s a prominent geneticist working on such a book. But, the “problem” is that there are so many results right now that it might be more advised to simply wait five years or so until the rate of change has leveled off.

Also, re: gay marriage. At the secular humanism conference a few years ago I made the case that rather than focus on gay marriage as a route purely to individual happiness and autonomy, it was important to focus on the issue of what we want a flourishing society to be. That is, evaluate utility as more than the sum of its parts. With less than ten percent of the population being gay, and legal monogamy being the aim, unlike many social conservatives I don’t see this as the End Times for Western civilization. Contra Pascal-Emmanuel Gobry, I also think Christians will quickly make peace with gay marriage.

Something which has cropped up on Facebook among some of my more culturally radical friends is the idea that the problem with gay marriage is that it is a victory for a particular vision of straight monogamous fidelity and the nuclear family. Anyone who is familiar with the most radical currents of sexual liberation of the 60s and 70s knows where this is coming from. Freddie deBoer elaborates a more straightforward liberal individualist argument in favor of polygamy, which is actually a traditional form of marriage in much of the world. The key point to emphasize is that love doesn’t, and shouldn’t, win always. To give a currently non-controversial example, sexual relations between people with differing levels of powers, or radically different ages, was more acceptable among cultural liberals than gay sex in the 1970s. Today gay sex between adults is not that controversial, but sex between minors and adults is even more controversial. Similarly, despite more toleration of premarital sex among younger generations, they have fewer partners than in the past. I suspect social conservatives are going to be happily disappointed with how little impact on cultural mores the legalization of gay marriage is going to have, while sexual radicals will also observe that the co-option of “queer culture” will proceed rapidly over the next generation.

Sorry I haven’t been very engaged in comments recently. I was traveling up the California coast, and was monitoring comments mostly through my phone. I haven’t been able to even fully digest some of the comments, so that’s why I haven’t responded.

Finally, I’ll be in Houston much of the summer. We’ll see if I can survive the humidity.

First Peoples: it’s complicated

"Sapiens neanderthal comparison" by hairymuseummatt - <a href=http://www.flickr.com/photos/hmnh/3033749380/ >http://www.flickr.com/photos/hmnh/3033749380/.</a> Licensed under CC BY-SA 2.0 via Wikimedia Commons - <a href=https://commons.wikimedia.org/wiki/File:Sapiens_neanderthal_comparison.jpg#/media/File:Sapiens_neanderthal_comparison.jpg >https://commons.wikimedia.org/wiki/File:Sapiens_neanderthal_comparison.jpg#/media/File:Sapiens_neanderthal_comparison.jpg</a>

First Peoples is PBS’ attempts to update the story of human evolution for 2015, particularly informed by the ancient DNA revolution of the past 5 years. It is worth watching, but not without its faults. The first two episodes on online, and I’ve watched them. Kristina Kilgrove at Forbes has a review of the whole series up. Below are some impressions of the first two episodes.

300px-Namibian_Bushmen_GirlsOne immediate problem is that modern actors have to play the “First Peoples” in reenactments. This imposes limitations. The Africa episode begins with Omo 1, one of the first anatomically modern humans in the fossil record. When dramatically depicting his life and death the actors used looked vaguely East African to me. This stands to reason because Omo 1 died in southwest Ethiopia. But this individual died between 100 and 200 thousand years ago! There’s been a lot of population movement, and evolutionary change, between then and now. There’s no reason to assume that modern Africans are a good representation of ancient hominins who were resident within Africa. The Khoisan people of southern Africa, whose ancestry diverged first from the rest of modern humanity 150 to 200 thousand years ago, look notably different from their Bantu speaking neighbors. The Nilotic Luo of Kenya look different from their Bantu speaking Kikuyu neighbors. And so forth.

To be fair, there is a vaguely similar phenotype among some non-African people in relationship African groups. Melanesians and Andaman Islanders come to mind. Remember, these “African-looking” Asian and Oceanian groups are genetically no closer to Africans than a Swede or Native American (Oceanians are actually somewhat further because of more Denisovan admixture). The best modern genetic data point to common descent for non-Africans from one ancestral population, so that their descendants are symmetrically distinct from all Africans without recent Eurasian admixture.

The important point to remember with these phenotypic racial categories is that these groups are only vaguely similar. Even a geneticist like me can tell that Papuan Highlanders look quite distinct from any African group. Phenotypic variation among Sub-Saharan Africans, Oceanians, and Negrito Asian peoples, should tell us that the human populations of African 100 to 200 thousand years ago were probably also somewhat diverse, even if their expected range of variation is not arbitrary (e.g., it is likely that their skin was on the dark side; loci for pigmentation are somewhat functionally constrained around the tropics). But the expectation should not be overwhelming that modern Africans more accurately reflect the ancestral phenotype of tropical adapted modern humans than, say, Bogainville Islanders.*

My nit with this issue is that it feeds into a larger narrative of “ancient people” and “living fossils.” In the Africa episode the narrator states that Pygmies are closer to the earliest anatomically modern humans. This is wrong. All modern human populations are about equal close to the earliest anatomically modern humans. The main qualification here is that likely all of us have different proportions of ancestry form distinct “archaic” lineages. That is, hominin groups which are outside of the main branch that contributed between 90 to 99 percent of our ancestry. It does seem that the ancestors of the Pygmy groups of Central Africa are the second most basal group of humans in comparison to non-Africans (the most basal being Khoisan). But the generations between early humans and modern Pygmies is about the same as that between early humans and Europeans or Asians or Oceanians. Though we aren’t totally sure from what I know, it also seems likely that the earliest modern humans were residents of the open woodland ecology, and not the deep forest. The presence of Pygmy-like groups across tropical forest biomes from Gabon to the Philippines suggests that in fact this is a derived phenotype. An evolutionary change from the ancestral state.

519gldjJoAL._SY344_BO1,204,203,200_In general First Peoples does a rather good job by the standards of the media not recycling older models which have embedded an implicit “Great Change of Being.” Though I would find some minor fault in their depiction of the phylogenetic relationship of Pygmies and the first humans and humans more generally, their treatment of hybridization was mixed as best, and misleading at worst. In particular, the attitude toward the idea of species was confused and incoherent. The biological species concept (BSC) comes closest to colloquial understandings of what species are, but First Peoples seems to crystallize this framework as if it was an indubitable iron law of nature. With that in mind, rather frequent instances of hybridization between divergent hominin lineages seem more startling, adding dramatic twists to the narrative. The problem I have with this is that most biologists I know view the BSC as just one of many species concepts. It’s not written in stone, but rather, an instrumental device in getting science done. Obviously the biological species concept, predicated on sexual reproduction, is irrelevant for asexual organisms. Additionally, there are wide swaths of the tree of life where hybridization is ubiquitous. In particular, plants. It is in mammals, with our peculiar system of reproduction which involves rather complex mechanisms of gestation, that hybridization barriers are particularly high. But even among mammals there is variation in obstacles to hybridization conditional on placenta type.

With all that in mind it’s pretty unsurprising, with hindsight, that there was gene flow across diverged hominin lineages. First Peoples itself acknowledges this likelihood by referencing research on baboon hybrid zones, and asserting that this phenomenon might be totally par for the course among primates. There’s nothing special about humans biological makeup then that would preclude hybridization.

Not only does hybridization play a role in the emergence of new human traits (one researcher seems to imply that human faces are subject to a liger-like effect), but John Hawks seems to posit a multi-regionalist like model for the origin of modern human within Africa, whereby hybridization between lineages eventually produced a complex suite of characters which define modern humans. More specifically Hawks points to the archaeological record that suggests contacts all across the continent, which would also likely mediate gene flow from different African hominin groups. This is set as a counterpoint to the classic “African Eve” narrative, informed by mtDNA, in the 1980s. This model is illustrated by an explosion from a small East Africa group 50 to 100 thousand years ago, as it swept across the continent, and then the world. Today, we know the reality was more complex, and Hawks presents a reasonable contrast in perspective.

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The most recent evidence, informed by genomics, indicates that the migration out of Africa was the major bottleneck. Within Africa the situation is less clear. Hawks thesis of a sort of multi-regionalist network of hominin lineages may be correct. In fact much of human evolutionary may be characterized by a series of alternating phases of multi-regional evolution mediated by gene flow and admixture, along with rapid demographic expansions whereby one lineage overwhelms the others (much of this may be due to cultural changes and inter-group dynamics). This is a complicated model, and hard to render in TV-friendly units of consumption. I feel for the producers of First Peoples.

Which brings me to a quibble about the America episode. Overall I really enjoyed how they framed the slow erosion of the Clovis overkill hypothesis. I’ll be honest that the “unveiling” of the Kennewick Man results, which suggest that he was the ancestor of modern groups in the region, was overly dramatic for me. But the biggest issue I had is that it oversimplifies the peopling of the Americas. It does seem that the New World was predominantly populated by the first wave out of Berengia, but there is also genetic evidence that later waves were significant, even in the Kennewick results themselves!

First Peoples is worth watching. Definitely a step forward, as they put a lot of new concepts in front of the general public. But everyone is still figuring things out, the science, and how to present it to people. I’d say that you just have to remember this is an alpha version, and if you want to know the whole story you had better do your follow up.

* Let me be clear here that I understand that some prejudice should be given to the African phenotypes as being more likely, as that continent was the ancestral home with particular environmental conditions which have not varied. And, Oceanians have admixture from other hominin lineages. But to me the priors are not such that the case is overwhelming. Ancient modern humans may have looked nothing like any extant population!

The False Dawn of modern humans in Eurasia

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A little over a month ago I asserted that “The Cro-Magnons Have No Descendants in Europe Today”. By “Cro-Magnon” I really meant the modern humans who spread the Aurignacian culture through the continent ~40,000 years ago (that is explicitly stated in the post). This was the first human culture across the continent associated with populations which had recently expanded, and are termed “anatomically modern.” A few weeks ago in The New York Times Carl Zimmer on recent ancient DNA results from the past 10,000 year clarifying ancient and modern population relationships had a line, “The first ["Western European hunter-gatherers, WHG, -Razib] were hunter-gatherers who arrived some 45,000 years ago in Europe. Then came farmers who arrived from the Near East about 8,000 years ago.” I responded on Twitter to Carl that it seemed very unlikely that the ancestry of European Mesolithic hunter-gatherers dated to the initial settlement of the continent 45,000 years ago. On Twitter I offered up that a proportion of ancestry on the order of 1% might be possible to Chris Stringer.

Why did I say this? Because ancient DNA over the past few years has indicated that across much of Eurasia population turnover has been very common on a 10,000 year time scale (see Joe Pickrell and David Reich’s review for details). With that in mind, why would one expect that European hunter-gatherers would exhibit population continuity across the more than 30 thousand years between the initial replacement of Neanderthals ~40 thousand years ago, to the first arrival of farmers? Not to mention the non-trivial fact that the Last Glacial Maximum was situated right in the middle of this period. The fact is that many of the ancient DNA results suggest that the populations which defined the range expansion of humans across Eurasia were characterized by very small breeding populations. Not only would these be subject to genetic risk of extinction via mutational meltdown, but small populations are more vulnerable to stochastic environmental events which result in range contractions. This also seems to apply to “archaic” hominins; Neanderthals and the Denisovan human seem to be either inbred or genetically homogeneous. The Neanderthal samples from the Altai all the way to Western Europe seem to be much more closely related than is plausible for a lineage whose regional geographic populations exhibit time depths of hundreds of thousands of years (at minimum Neanderthals flourished for ~100 thousand years, but to my knowledge the extant individuals do not seem to be that different at all).

Another reason I made that statement is that people have been leaving telltale clues for a while. Nothing explicit, but sometimes you can infer things from radio silence. In any case, here’s the Nature paper on the Romanian ancient sample dating from ~40,000 years before the present, An early modern human from Romania with a recent Neanderthal ancestor. From the last paragraph of the discussion:

The Oase 1 genome shows that mixture between modern humans and Neanderthals was not limited to the first ancestors of present-day people to leave Africa, or to people in the Near East; it occurred later as well and probably in Europe. The fact that the Oase 1 individual had a Neanderthal ancestor removed by only four to six generations allows this Neanderthal admixture to be dated to less than 200 years before the time he lived. However, the absence of a clear relationship of the Oase 1 individual to later modern humans in Europe suggests that he may have been a member of an initial early modern human population that interbred with Neanderthals but did not contribute much to later European populations….

Modern Europeans can be thought of as compounds. The first element are a set of populations which descend from, or are genetically very close in nature to, Mesolithic hunter-gatherers who likely descend from groups extant during the late Pleistocene on the fringes of the continent. The second element seems to be a population which is an outgroup to all other non-Africans. That is, this group diverged from the ancestors, jointly, of European Mesolithic hunter-gatherers, the people which gave rise of the Mal’ta boy, as well as Oceanians, East Asians and Andaman Islanders. Like the “Ancestral South Indians” my impression is that this group does not exist in “pure” form today, but rather must be inferred. As this 40 thousand year old individual from Peştera cu Oase, Romania, is no closer to Europeans than to East Asians, it seems implausible that it was ancestral in any substantial fraction to modern Europeans.

51yuNuckdiL._SY344_BO1,204,203,200_Influenced in part by Clive Finlayson’s The Humans Who Went Extinct, I think it seems likely that the earliest group in western Eurasia to contribute substantial ancestry to modern Europeans are the Gravettians. Though even they flourished prior to the Last Glacial Maximum, so this is not assured in my mind.

The main fly in the ointment of this narrative is the Kostenki 14 remains, which date to a few thousand years later than Oase 1, and is from its north and east (the Don river valley). Kostenki 14 seems to exhibit all the hallmarks of carrying the signatures of ancestry which define mother Europeans. That is, the hunter-gatherer heritage, the mysterious Eurasian element defined by the Mal’ta boy and found in Native Americans and brought to Europe by groups from the east ~4,000 years ago. So where does that leave us? My understanding is that people don’t have good clarity on Kostenki 14 right now. But the possibility that most ancient human populations left no descendants would be an easy explanation. It was an earlier admixture of the basic elements which came together again during the Holocene.

Addendum: A minor aspect is to note how Y and mtDNA may give different inferences. I suspect that that is a function of the fact that we don’t know about the ancient distribution of the Y and mtDNA well enough.

Why CGI will not eliminate porn actresses

4146cuHZENL._SY344_BO1,204,203,200_Strange as it may be to say this, but the film San Andreas made me reflect on the nature of particular service sector professions, and their future, recently. It was typical for its genre. Very little plot or characterization (less than a week out I’m still vague on these aspects), and a lot of CGI. A lot. Dwayne Johnson plays the father of Alexandra Daddario, with Carla Gugino plausibly cast as the mother. In fact, Daddario resembles Gugino enough that you might wonder about the possibility of genomic imprinting. But the real star was the CGI.

Alexandra_Daddario_April_2015And the effects overwhelmed the acting so much that it made wonder again when actors will become totally dispensable. The “comic book movie” genre is already known for being driven more by special effects and the characters than the actors who play them (with the notable exception of Robert Downey Jr.). Which brings me to porn. Recently a controversial documentary came out, Hot Girls Wanted, about a group of young women living a house and trying to break into the industry (the controversy is not the porn, but rather how the women and the industry were depicted). One event in the film is that one of the actresses quits because of family pressure. It has to be admitted that In relation to porn many men are quite happy for it to be around, but would be aghast if any women in their personal social network participated in the industry. So perhaps CGI the answer to this tension? Once you have CGI good enough to simulate real actors, it would be pretty easy to apply to pornography. And porn has some major downsides which would be obviated by CGI “performers.”

But it wouldn’t be so easy, and that is because demand for flesh & blood performers will always be there. In How Pleasure Works Paul Bloom teases out the implications of the latest cognitive psychology in this domain, making extensive recourse to concepts such as “aliefs.” The easiest way for me to illustrate what an alief is is to give an example. Imagine that you see someone use the raw ingredients of fudge brownies to construct the simulacrum of feces. You know for a fact that the faux-feces are not feces, and in fact are delicious fudge brownies…which happen to look like feces. Your beliefs about this are informed by copious facts at hand. But many individuals would nevertheless exhibit difficulty and aversion in consuming these faux-feces. Deep in your bones are concepts and ideas about entities which inform how you react to them. In simple “objective” hedonic units of sensory qualia a $200 dollar wine may not be superior to a $10 wine, but the knowledge that the $200 wine is expensive, rare, and from France (as opposed to California or Australia for the $10 wine), can actually impact how you experience the taste.

414IU4oOQnL._SY344_BO1,204,203,200_Paul Bloom asserts that we are all born essentialists (see Descartes’ Baby). And this fact about human nature is probably why we pay so much for “artisanal.” Artisanal isn’t necessarily better in a reductionist sense that Jeremy Bentham would recognize. But people appreciate the products better because of their history of production, and who made them. In short, a service isn’t just about what, it’s about who. Which brings me back to porn. At some point in the very near future software will get good enough to mass produce pornography where the performers are virtual. Likely these performers will be produced “on the fly” by consumer preferences (e.g., there almost certainly is someone out there who prefers blonde Asian females with small breasts and large buttocks). In terms of raw dimensions, and flawlessness of skin, they will blow real actresses out of the water. But one of the appeals of “amateur porn” for many consumers is who the performers are. That means there will be a demand for “real” porn by “real” women. Artisanally produced porn, not the faceless (in a metaphorical sense) output from a well tuned algorithm. Of course the CGI can simulate the more rough and natural “artisinal” look, so there will be authenticating agencies or firms so that consumers know that these girls are actually “real amateurs.”

This line of argument could apply to many service sector activities. In the near to medium term future it seems plausible that the bottom 90% of the population will be employed in occupations which serve the demand of the top 10% for “authentic” human servility and handcrafts.

Open Thread, 6/21/2015

CoverReadingInTheBrainThe experience of Stanislas Dehaene’s Reading in the Brain: The New Science of How We Read is strange. After all, you are reading about the science of reading. So as you read, you become more explicitly conscious of the cognitive processes which allow you to read in the first place. I encountered Dehaene first via the The Number Sense 13 years ago. Why the big gap between reading him again, despite my appreciation for this dense by accessible prose? It reflects the fact that my “book diet” has shifted away from cognitive neuroscience a lot since then. In particular, since I started on my journey toward becoming a professional geneticist I’ve been subject to a sort of tunnel vision . There’s something about academic science is sucks many people into hyper-specialization, and I’m not immune obviously. Other areas of biology outside of genetics, and in particular genomics, strike me as terra incognita now. The same problem doesn’t hit me when it comes to history, religion, philosophy, etc. Perhaps because these are less technical fields more open to generalists.

I’ve been away from the internet mostly this week, except my phone. Speaking of which, going to a child-friendly museum or park is somewhat difficult today because so many people are taking pictures with their phones. To be polite you have to stop a lot so as not to occlude the photo, but after a while it gets kind of ridiculous, as you are dodging so many lines of sight. I think “Google Contacts”, where individuals can snap photos sliced out of their day to day perception would be an improvement on this.

Finally, the Kennewick Man paper is out. It’s open access, so read it. The basic results were leaked by the press a while back. Kennewick Man seems to be ancestral to modern Native American stock. Intriguingly though he is not symmetrically related to all Native Americans, not even all “First Americans” (a la Reich lab terminology for the descendants of the first wave out of Berengia, who contributed most of the ancestry of Amerindians). Also, the morphology as reflected in skeletal features would not have resolved these issues definitively. On an individual level these phenotypes are too noisy to make robust population level inferences in many, though not all, cases.

The Aryan Invasion Was Not Fantasy

51IQSePVDRL._SY344_BO1,204,203,200_If there is one Peter Heather book you should read because it is timely, it is Empires and Barbarians: The Fall of Rome and the Birth of Europe. In it Heather makes an apologia for a revisionist view which resurrects some aspects of the old folk migration theories, and understandings of the arrival of barbarians into the the collapsing Roman order of the middle of the first millennium. This is in contrast to th conventional view of modern archaeologists and historians which posits that the barbarian invasion was more a change of power at the elites, with the emergence of ethnic identities and coalitions almost in an ad hoc fashion among groups of mercenaries who took control from their paymasters. Heather does not posit total replacement of the indigenous population. In fact, it turns out in the best case scenario for such an event, in what became Anglo-Saxon England, the genetic data does not support such a proposition. Rather, there was an amalgamation between a culturally dominant intrusive minority, and the indigenous majority. The evidence from the rest of Western Europe is much more equivocal, suggesting that the demographic impact of the barbarians was minor (this not the case in Eastern Europe, where the Slavic migrations are associated with signals of strong genetic correlations between recently settled populations in the weak of German and Roman declines on the eastern frontier).

Heather’s position is really one of moderation or the Golden Mean. It is rather like those who do not take a pure hereditarian or environmentalist position in behavior genetics. In Empires and Barbarians he marshals evidence which points to the reality that the barbarian groups entered the Empire as self-conscious tribal-ethnic entities, with whole families on the move, and that they were not created de novo within the Empire. This is not to deny the reality of cultural shifts in identity, with Roman elites in Gaul taking to trousers and referring to themselves as “Franks,” and German tribal leaders attempting to accrue to themselves the glamour and respectability of Romanitas. But the fundamental identities which are combined were distinct, and organic, not recently constructed and inchoate.

51sBGrYcIEL._SY344_BO1,204,203,200_The most recent work from ancient DNA, which I wrote about extensively this weekend, support Heather’s contentions broadly, if not specifically. The evidence from prehistory indicates far more demographic disruption than during the fall of the Roman Empire. That is, folk wanderings were much more significant in prehistory than in antiquity. That probably has to due with social-demographic changes that occurred in the first millennium before the Common Era, as ruling elites became decoupled from the population they ruled in many ways, though often bound together by a religious ethos. The fusion of the conquered and conquerors was a process made much more feasible by the emergence of “meta-ethnic”, to use Peter Tuchin’s terminology, religious ideologies which transcended folk boundaries.

The reality of new facts on the ground means that we need to reinterpret aspects of archaeology and myth in terms of the dynamics which are reflected by our new understanding. One side aspect of my writings on these topics is that many Indians are not very happy with the newest results, because they validate threads of a frankly colonialist model of an Indo-Aryan invasion. The model is that a European-like population invaded the Indian subcontinent, imposed the caste system, and imparted many aspects of high culture upon the natives. Despite racial mixture between the indigenous and intrusive elements, the higher castes and peoples of the Northwest had more Aryan ancestry.

This model wasn’t totally a figment of the British colonialist imagination, and had much to do with the discovery of the connection between Sanskrit and other Indo-European languages, such as ancient Greek and Latin. Yes, the theory was utilized for political ends, but the model itself reflects some factual realities on the ground. For reasons which I will not elaborate in detail, because I don’t know that much about it, and don’t care either, a dominant strand of Indian nationalism has turned against the Indo-Aryan model of intrusion. In fact this school has “flipped the script,” asserting that Indo-Aryans, and therefore Indo-European languages, are indigenous to the subcontinent.

Linguistic sanity indicated that this was always unlikely. But the idea that most of the ancestry of South Asians dates to the last Ice Age, that is, the Indo-Aryan invasion was demographically marginal, was a defensible position until recently. For example, in 2006 you have  a paper such as Polarity and Temporality of High-Resolution Y-Chromosome Distributions in India Identify Both Indigenous and Exogenous Expansions and Reveal Minor Genetic Influence of Central Asian Pastoralists. Additionally, as individuals have pointed out to me ad nauseam, archaeologists are skeptical of mass migration because of lack of remains.

R Graphics OutputFirst, a paper from 2006 is wildly out of date for this field. The methods used have been superseded. Instead of using one locus, the Y chromosome, and focusing on microsatellites (which have upsides and downsides), researchers now look at the whole genome. Probably the best paper to read on the latest results is Genetic Evidence for Recent Population Mixture in India. The authors date the admixture between two different lineages in the subcontinent to “1,900 to 4,200 years ago.” One of the lineages is rather like West Asians and Europeans genetically (ANI). The other is most closely related to Andaman Islanders (ASI), but diverged from this group on the order of 20 thousand years ago. It can be accurately stated the the ASI are part of a broader constellation of East Eurasian populations which diverged from West and North Eurasians 40 thousand years ago (and from Basal Eurasians even earlier). In other words, modern South Asians are a compound of two highly diverged lineages, which explains their ambiguous position in relation to West and East Eurasian “reference” groups. And, this fact means teasing apart the ancestry is relatively easy, though time elapsed means that for all practice purposes South Asians are now a cluster of their own in any analysis of human population structure (that is, though they can be decomposed into parental elements, that’s not practical or useful in most cases).

Screenshot - 06152015 - 01:39:27 PMAnd, not surprisingly, the ratio of the ANI/ASI ancestry varies as a function of caste and region. This is the hallmark of relatively recent admixture, maintained by social barriers in caste. Indian caste groups (really jati) exhibit runs of homozogosity in their genome which are signs of a low effective population. In other words, not too much gene flow across groups. The direction of admixture is exactly as predicted by the old theories, as if an intrusive population arrived via the Northwest, and imposed itself upon the indigenous groups.

Now, let me address the major objections:

1) What about the mtDNA, which shows that most of South Asian ancestry is indigenous, and not West Eurasian.

Answer: The migration may have been male-mediated. All this means is that gene flow from the northwest occurred mostly through males. Over multiple iterations this can replace much of the whole genome, while leaving the single mtDNA lineage intact. This is exactly what happened in Argentina.

2) What about Y chromosomal results, which imply that R1a1a is indigenous to South Asia

Answer: Much of that work has utilized a small number of SNPs or microsatellites. The issues of phylogeography and dating for Y chromosomes are such that we really have had low clarity until whole genome analysis era, which is occurring now. The fact is that the Y chromosomal phylogeny of R1a1a the world over exhibits the hallmarks of massive population expansion ~5,000 years ago. No one knows where the R1 lineages are truly from in a deep time sense, as it seems likely they were low frequency variants before their explosion.

3) What about various aspects of mythology and archaeology which don’t posit an invasion/migration?

Answer: First, the archaeologists have a big record now of being wrong in Europe. Though many archaeologists (and historians who drew upon their scholarship) were cautious, some were not, and stridently argued that demographic replacements were not seen or evident in the archaeological record. The ancient DNA has basically proven them wrong. So either their methods miss migration, or, their results are labile when ideology is applied. Second, in regards to the lack of Indo-Aryan memory of migration, the Greeks also had no memory of migration. Both Greeks and Indians (Indo-Europeans) can not simultaneously be indigenous. Clearly oral memory has an expiration date, and may not be reliable.

Perhaps the archaeologists are totally right. I can’t evaluate their scholarship. I can evaluate the genetics, and it is getting progressively more persuasive. Scientific disciplines often have conflicts, though they are ultimately resolved (see the age of the earth controversy between geologists and biologists vs. physicists in the late 19th century). The recent track record of archaeologists has not been the best in my opinion when it comes to broader theoretical implications.

Finally, I want to state that I am skeptical, or not convinced, that most of the ANI ancestry in South Asia is from the Indo-Europeans. The ANI ancestry might be a composite, and perhaps the dominant language of the first ANI people was Dravidian. The closest populations to the ANI seem to be the people of the Caucasus, though this may be a function of changes in West Asian genetics. The Indo-Aryans may have been one of the later peoples to arrive.

Additionally, the Indo-Aryans were not blonde Europeans. Blonde Europeans seem to have evolved in Europe in situ over the past 4,000 years due to the admixture of diverse threads, indigenous and exogenous. There are elements of European ancestry (particular EEF) which do not seem to be evident in West Asia or South Asia, suggesting that the origination of Indo-European was complex, and perhaps multi-faceted. The Indo-Aryans had an affinity to the peoples of Europe, but it is a rather circuitous connection. We haven’t unpacked all the details.

Where does this leave us? There are many Indians who are like Creationists, for whom the scholarship is simply a way to buttress their ideology. They may cite the scholarship, but it is to a great extent just a matter of dressing up their nationalistic preferences. For these the new results are not only threatening, they are irrelevant. They will continue to cite papers from ~2005, because at that time period the results were more congenial to them. There are others who will “update” their views. There is much updating and revision that will occur over the next few years, and ancient DNA may change our perceptions about South Asia again. So be it.

Addendum: Wendy Doniger’s The Hindus is a controversial book. Religious fanatics and nationalists have waged a campaign against it. It is a testament of their milder nature that Doniger wrote under her real name, something that might not have happened if she was writing about Islam. I read the book when it came out, and it wasn’t my cup of tea, but I didn’t see what the big deal was (of course, why would I? I’m an irreligious atheist). But today I now think back to the passages which refer to the contact between Aryans and non-Aryans. Within these folktales and mythological memories may actually be a record of interaction which we do not in general have from Europe of “first contact” between startlingly disparate worlds.

Open Thread, 6/14/2015

41hdiv6SmHL._SY344_BO1,204,203,200_If you haven’t read Prehistory of the Mind, it’s an interesting book, even if somewhat dated. The same author’s After the Ice: A Global Human History 20,000-5000 BC is also recommended. Obviously this sorts of works attempting to synthesize evolution, psychology, and archaeology, are a lot more relevant right now since ancient DNA is introducing a whole new landscape to us. There’s a lot that gets out of date fast. On Twitter I mentioned that Barry Cunliffe’s Britain Begins gets the archaeogenetics wrong because it was published a year or two early.

Obviously I spent a day writing the post below, Genetics Allows the Dead to Speak from the Grave. I don’t do research myself in ancient DNA and don’t plan to. But it’s a hot field producing a lot of results, and I know a fair amount of history, so I thought a “core dump” of some sort was useful, at least for Google. Unfortunately I don’t have that good of an intuition for prehistory, so perhaps I’ll have to read some archaeology books front to back. History is being made literally right now, so it is important make appropriate interdisciplinary connections. Even with nearly 10,000 words I left out a lot of important issues.

I’ll be spotty in terms of internet connection for a week.

Genetics allows the dead to speak from the grave

51qciM4cBhL._SX258_BO1,204,203,200_*The past after the word*

If science is hard, history is harder. Harder in that the goal is to understand what happened in ages which are fading away like evanescent ghosts of our imagination. But we must be cautious. We are a great storytelling species, seduced by narrative. The sort of empirically informed and rigorous analysis which is the hallmark of modern scholarship is a special and distinctive thing, even if it is usually packaged in turgid and impenetrable prose. It is too pat to state that history was born fully formed with the work of Thucydides (or Sima Qian). In fact Thucydides’ pretensions at historical objectivity despite obvious perspective and bias lend credence to the assertions of those who make the case that the past is fiction (in this way Herodotus may actually have been more honest). The temptation is always great to paint an edifying myth which gives succor to national pride or flatters our contemporary self-image. The fact that modern nation-states in the technological age have vigorous debates about details as to the nature of periods of history in the recent past, when the people who lived during those times are still here to bear witness, is telling in terms of the magnitude of the task before us. Fraught questions must be answered with far fewer resources.

Much of history we see only vaguely through chance and contingency, known through happenstance and the whims of our ancestors. In the West the documents which shed light upon antiquity come to us through tunnels of finite transmissions, a furious period of textual transcription in the last few centuries before 1000 A.D. The Carolingians, the Byzantines, and the Abbasids all engaged in sponsoring the capital intensive project of taking ancient texts and making copies for posterity. The vast majority of the works of antiquity we have today can be traced back to this period [1]. Biases and concerns of the elites who sponsored these projects were critical in determining the nature of the source material which serves as the foundation for our understanding of the deeper past which we take for granted today. We know how little was copied because the extant material make copious reference to a vast body of work which was circulating in the ancient world on assorted topics (and even many of the works we do have are only portions of multi-volume endeavours, such as that of Livy).

brotherhoodBut what about pushing beyond what the text can tell us, and transitioning from history to prehistory? Here is where matters become opaque and conditional upon the nature of the texts (or lack thereof). This is clear when you observe that there are very early periods of human history when our knowledge of individual actors and daily life is actually greater than later epochs due to regress of civilization, or, changes in technology which mitigated against preservation of texts [2]. The “Dark Ages” of Greece between the Mycenaeans and the Classical Greeks are the purview purely of archaeology (and even during the Mycenaean period most Linear B were of a bureaucratic nature; I do not know of narrative literature such as we have for Egypt or Babylon). For the Classical Greeks the rupture was traumatic enough that their Mycenaean past became the subject of legends. The citadels of the Bronze Age warlords were viewed as “cyclopean” works, as if only giants could have created them. Similarly, the period in Britain between the end of central Roman rule and the Christianization of the Anglo-Saxons, about two centuries, is perceived only faintly because of the paucity of written records (this also explains why this period is often utilized as the setting for historical fantasy).

9780192807281_p0_v1_s260x420Yet when text is silent one still has material remains. Their collection and analysis are the domain of archaeology, a historical science. The fact that history as we understand it deals in the written word, and so limits its focus to the period when we have texts, is itself a historical coincidence. Ideally traditional history and archaeology should work in concert, and critically, words have a way of deceiving and misleading. Most obviously we have a major ascertainment bias in our understanding of the past when we listen only to the perspectives of those who can speak through words, because they who were literate or had access to literate professionals were a very small subset of the broader human experience. Archaeology has less of this bias, because all classes leave behind their material evidence (though if one wants textual representations of a broader cross section of the Roman populace, the novel The Golden Ass is a good place to start). An excellent illustration of this for me, as readers know, is the extended argument in the book The Fall of Rome, which brings material evidence to buttress the position that the decline and fall of the unitary Roman state in the 5th century coincided with a genuine degradation of what we might term civilization. Revisionists looking purely at textual materials have long argued that the classical view was misleading, and to reduce their argument down toward its  essence, suggest that classical civilization evolved and transformed, channeling its energies into different activities (e.g., the rise of Christian theology as a successor to the classical liberal arts, see Peter Brown’s The Rise of Western Christendom). But what material remains tell us is that there was indeed an economic and demographic collapse, despite apologia that one can make as to the reshaping of high culture in texts. One may choose to weight these facts, or not, but the facts nevertheless remain, no matter how many glosses one wishes to upon them. The Rome of 600 may have had many more Christian theologians than the Rome of 400 (which was then a mainly non-Christian city), but the Rome of 400 probably had a population on the order of 10-20 times greater.

41hdiv6SmHL._SY344_BO1,204,203,200_In a world without text, which is almost all of human history, the material remains are all that we have to grasp upon. Though we can attempt to glean the minds of people long gone from paintings and scratches in stone, the reality is that what they hunted with, what they ate with, and the dwellings in which they lived, are going to give us concrete information where leaps of imagination are unnecessary. Moving beyond the text can allow us to truly illuminate the vast dark oceans of human history with more than our dreams, from the dawn of our species, down to even recent periods when literacy was the privilege of the few, and the experiences of the many were dead to us. Despite this, the paintings have only a few colors on the palette, because archaeology is filled with enormous gaps in perception. Pots not cloth. Caves not tents.

Which brings us to biology, and specifically genetics, as it turns out that DNA is actually one of the material remains that one can extract from archaeological field sites. It’s a robust macromolecule, and today researchers believe that it is feasible that some information can be drawn from remains as old as 1 to 2 million years, though that’s a best case scenario. When it comes to questions of demographic change genetic insights are key, and present data in a way that allows for more rigorous analysis. As has been the case in previous posts I must now give a nod here to L. L. Cavalli-Sforza and The History and Geography of Human Genes. Cavalli-Sforza’s magnum opus reopened the book in attempting to understand history through demographics. It was the first page, and the first chapter. Prior to this before World War II there was a cottage industry which attempted to do what Cavalli-Sforza achieved in the late 20th century. But these endeavors were hobbled by two problems. First, they was not scientific, often relying upon intuition derived from their erudition (they were not hypothetico-deductive, though that’s overrated if you have lots of data). Second, the reliance upon intuition meant that many of the conclusions dovetailed rather neatly with the ideological preferences of the day, National Socialism most horrifically, but much more widely than that was a shoddiness of nationalism inflected prehistory. Scientific romance without the genocide (see Pat Shipman’s The Evolution of Racism). After World War II archaeologists reversed course and decoupled cultural evolution and change from demographic variation. Works such as the Races of Europe became anachronistic when decades before they’d have been mainstream, and there was a strong bias toward a null hypothesis that pots, that is cultural traditions, migrate, but people do not.

k7442Into this intellectual climate stepped Cavalli-Sforza and his students, triggering a minefield in academic explosions (see The Human Genome Diversity Project: An Ethnography of Scientific Practice). Molecular anthropology in its earliest incarnations focused on deep time. In particular, there was a recalibration of time depth of the origin of apes and humans, where the molecular biologists clashed with paleontologists, and came out the victors (see The Monkey Puzzle for a history of these controversies). Then, there was the “Out of Africa” debate (see The African Exodus). Though these were somewhat fractious and personalized arguments, the emotions around the implications of these contests of ideas were often limited to scholars (though the scholars themselves may not have felt the fallout was limited; apparently at Stanford in the late 1990s a cultural anthropologist gave a presentation where he juxtaposed a photo of Cavalli-Sforza with Josef Mengele). What Cavalli-Sforza did was bring genetic science toward addressing more contemporary phenomena, to answer questions which come to the cusp of the present, tackling issues of relevance to living human people on the scale of nations and peoples. Over many decades his lab collected enough information from hundreds of genetic loci to arrive at the sum totality of inferences which were eventually presented in The History and Geography of Human Genes.


CosttoSequenceaGenome-e1409924136899Let’s take a step back here. Cavalli-Sforza and his colleagues had access to hundreds of markers at best. Note that ~2% of the human genomic codes for proteins, but there are 3 billion positions in terms of bases. Today anyone who wants to pay can get millions of positions through SNP-chip services. My son has billions of positions, because he’s been whole-genome sequenced. For phylogenetic purposes you don’t need billions, millions, or even thousands, depending on the nature of the questions you have in mind. But, it puts in perspective how far we’ve come in literally 20 years. Even 5 years.

As is the nature of science there was much that Cavalli-Sforza got wrong in  The History and Geography of Human Genes. But there was much that he got right, because the results were so clear and strong on particular points of contention. In short, very broad patterns on the continental level jumped out when analyzing even hundreds of neutral (that is, not subject to natural selection) markers. For example, the data confirm a gradient of genetic diversity which implies human origins from an African locus, as well as the relative homogeneity of Europe (aside from Finns, European populations have a surprisingly low between-population pairwise genetic distance in most cases). But, more subtle counterintuitive relationships were often not robust (e.g., North and South Chinese do not bifurcate in the manner that he reported in the 1990s). And, most critically for the purposes of this post inferring past demography from current phylogeographic patterns had serious limitations.

*The present as a window into the past*

downloadm511NSSGQNWL._SY344_BO1,204,203,200_The basic idea behind historical population genetics (archaeogenetics) which was pioneered by Cavalli-Sforza at the HPGL at Stanford was to look at patterns of diversity and relatedness among modern populations, and intersect that with what was and is known about history, as well as geography, and then allow those intersections to peal back the palimpsests of human history (see his The Great Human Diasporas). Though Cavalli-Sforza focused initially on autosomal markers scattered through the genome, in the period between 1995 and 2005 there was a great deal of work using uniparental data., the markers on the Y and mtDNA. The mtDNA is passed through women only, is copious in terms of quantity on a cellular level, and has a highly mutable region of utility for molecular phylogenetics. The Y chromosome exhibited some technical difficulties in comparison to mtDNA, but with the emergence of better extraction techniques as well as a focus on highly mutable microsatellite regions, it came to be set next mtDNA as a critical tool in the forensic reconstruction of human population history. In addition, both had the virtue of being nonrecombining, so that the generation of a phylogenetic tree was not an artificiality, but a reflection of the nature of the transmission of these two regions of the genome (congenial to a coalescent framework as well).

Human_migrationIn the end this line of research often resulted in a transposition of a phylogenetic tree upon a world map, outlining patterns of human migration. It also aligned well with another line of research which explicitly modeled the expansions of humans out of Africa as a “serial founder bottleneck” process. That is, each population which left Africa progressively branched out in a unidirectional manner, resulting in reduced genetic diversity as one progressed out of Africa.

Ramachandran, Sohini, et al. "Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa." Proceedings of the National Academy of Sciences of the United States of America 102.44 (2005): 15942-15947.

Ramachandran, Sohini, et al. “Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa.” Proceedings of the National Academy of Sciences of the United States of America 102.44 (2005): 15942-15947.

In its broadest strokes this model is not without validity. It does seem that most of the ancestry of modern humans can be traced to a population which flourished around or in Africa ~50-100 thousand years ago. Much of the inter-continental racial variation that we see in extant populations does nicely fit onto a bifurcating tree-like model (e.g., Non-Africans branch off from Africans, West Eurasians and East Eurasians diverge, Amerindians branch off from East Eurasians). The problem though is that the branches themselves turn out to be brambles which turn back in on themselves, and in some cases twist with other branches, creating lineages with very diverged ancestral roots. The yield of the earliest efforts by Cavalli-Sforza and his heirs was on a very coarse continental grain, where the effects of the dynamics were so striking that they would exhibit themselves across most neutral markers without much difficulty. But, when the questions were narrower, and the temporal and spatial scope more constrained, the earlier methods were not perceptive enough to smoke out the real dynamics.

Li, Jun Z., et al. "Worldwide human relationships inferred from genome-wide patterns of variation." science 319.5866 (2008): 1100-1104.

Li, Jun Z., et al. “Worldwide human relationships inferred from genome-wide patterns of variation.” science 319.5866 (2008): 1100-1104.

By the middle years of the 2000s researchers had gone back to a focus on recombining autosomal markers. But now they had a whole human genome to compare it to, as well as SNP-chips which quickly yielded large troves of data with little effort. In 2008 a paper was published which took the origin HGDP data set collected by Cavalli-Sforza and his colleagues, and utilized the new technologies to make deeper inferences. First, instead of hundreds of markers you had 650,000 SNPs. Second, the emergence of powerful new analytic and computational resources allowed for the complemention of tree-based and PCA visualizations of genetic relationship with model-based understandings of genetic variation and population structure. By “model-based,” I mean that the algorithm posits particular parameters (e.g., “3 ancestral populations”) and operates upon the data (e.g., “650,000 SNPs in 1000 individuals”) , to generate results which are the best representation of the fit of the data to the model.HGDPme This different from PCA, which has fewer assumptions, and represents genetic variation geometrically (each axis represents an independent dimension of variation within the data). Model-based clustering is very clear and aesthetically appealing. It gives precise results. But, the model itself is not necessarily right.

Anyone who uses these methods understands their limitations. If you use PCA to project variation of the data set, then the composition of the data you input is going to influence the largest principal components. Therefore, if you are asking questions on a broader spatial scale you should be careful about the possibility that you are overloading the sample set of interest with particular populations. More data in this case might result in less insight. Similar issues crop up with model-based clustering you don’t appropriately weight the populations. Another major problem is that the models are imposing limitations which might produce false inferences (false in that they do not accurately reflect demographic history). Most simply you might ask for many more population divisions than is realistic for the demographic and genetic history of the data. Consider a data set of Irish from Cork and Nigerians from a small village. PCA would no doubt show you two very tight and distinct clusters. With a model-based framework you could look for divisions and structure beyond K = 2 (two ancestral populations). The method is devised in such way that you would get results. But, they wouldn’t be very informative, and they’d be forced. They wouldn’t be robust. The model would be a poor fit to reality.

*From model to reality*

Obviously no model captures all elements of reality. But when the model deviates so much from reality that you get a false sense of what is true then that model is not nearly as useful. Being wrong is a definite bug. Aside from model-based admixture analysis, which posits a finite number of ancestral populations which come together to produce the genetic variation in the data set, you notice that the 2008 paper also had a tree representation of genetic variation. These two together give real and substantive results that can be useful. But, they mislead to the point of falsity in many specific cases.

nihms137159f3

Reich, David, et al. “Reconstructing Indian population history.” Nature 461.7263 (2009): 489-494.

This can be illustrated by the instance of South Asians, who are about 20% of the world’s population. A 2009 paper, Reconstructing Indian Population History, utilized both the higher autosomal marker density sets and new analytic frameworks to come to some specific conclusions which resolve many confusions about the nature of the genetic history of the peoples of the Indian subcontinent. So what did we know before? If you go back to the ideas of the old physical anthropologists they observed that many South Asian groups had an affinity to the peoples of West Eurasia (Europeans and West Asians). This varied as a function of geography and caste. In other words, there was a cline to the northwest, as well as up and down the caste system. You can see it in a PCA, where Indian groups vary in distance from Europeans, while Europeans form a very tight cluster. It also shows up in admixture based analyses. There is usually a K value where a South Asian modal cluster emerges, and it is near fixation in South Indian non-Brahmins, declining in frequency as one moves toward Pakistan, or, in North India up the caste hierarchy (the residual are West Asian and European clusters, except Bengalis, who have East Asian admixture). In The History and Geography of Human Genes South Asians form an outgroup to Europeans and Middle Eastern populations using older distance measures.

So far all good. One can imagine then a cline of genetic variation, with South Asians at one end, and West Eurasians at the other. On a PCA between East Asians and Europeans South Asians usually fall in the middle, but closer to Europeans. But there have long been major problems with this model when you drilldown into the details. The mtDNA and Y chromosomes of South Asians give very different results. The former classes them as distinct from West Eurasians, with distance affinities to East Eurasians. The latter on the other hand are quite a bit more like West Eurasians. Second, South Asians exhibit a lot of variation as a function of both geography and class in terms of their relatedness to word populations. If South Asians were deeply rooted in the subcontinent, as the migration maps above would imply, then we’re talking about massive barriers to gene flow which have persisted for tens of thousands of years. An alternative explanation is that South Asians are the product of recent admixture between two very different groups, which is what is often the norm when there is a lot of inter-individual variation in ancestral components and PCA position within a putative population group (e.g., African Americans). Finally, tests of natural selection geared toward detecting very recent sweeps have indicated a commonality between South Asians and Europeans and Middle Easterners on the haplotype of SLC24A5, which implies either extreme connectedness, or, recent admixture and migration (on the margin these two models are going to be hard to distinguish, since connections are mediated through migration).

I will sidestep the technical issues at this point, and just offer up that the work on South Asians has presaged much of what we’ve learned over the past decade when it comes to the genesis of modern population structure. The puzzles about South Asian genetic variation are resolved when you admit a model where a West Eurasian population mixed with a local indigenous group with distant affinities with other East Eurasians (see Genetic Evidence for Recent Population Mixture in India). The high level of between population variance within South Asia is due to the recent nature of the admixture event and the high genetic distance between the source populations. This may actually be the story of much of the world over the last 10,000 years. Instead of a regular branching process, imagine branches that periodically fuse back together, in a reticulated pattern. Another way to conceive of it is that the last 10,000 years have been a story of the destruction of population structure accrued over the past 100,000 years. A survey of this field can be found in the review Toward a new history and geography of human genes informed by ancient DNA.

*Inference made concrete, ancient DNA*

Up until now we have been talking about increasing the power of analysis of genetic variation in existent populations. Processes like bottlenecks and positive selection leave footprints in the genomes of modern peoples. But these methods of inference have limits. And, to a great extent they necessitate a simplicity of population dynamics to allow for them to have utility in painting a portrait of the past. Researchers had to assume that the past was simple, or the methods that they had wouldn’t be able to tell them as much as they claimed. The complexity of the demographic palimpsest could never race beyond ability of the genetic methods to peel it back, so there was a ceiling on the number of layers imposed upon the model.

41ePHetk1dL._SY344_BO1,204,203,200_Ancient DNA was a game changer, because it did not come with these limitations. Instead of just inferring the past from the present, the past could now be inferred from the past! That is, a temporal transect in time could be generated which explicitly explored the trajectory of genetic variation across time and space. As if to recapitulate history the earliest work was with mtDNA, just as it had been with “mtDNA Eve” in the 1980s. The sequence target here is small and mtDNA is copious. The immediate upshot though is that massive discontinuities were detected. Populations replaced each other repeatedly in many regions. Pulse admixture events being inferred with novel methodologies on extant populations now could be understood to have been the natural result of migration and population change over the past ~50,000 years. Thanks to the work of researchers such as Svante Paabo and Eske Willerslev the number of samples we have from ancient DNA for humans has grown to such an extent over the past 5 years that a bright line is shining into what had been a dark cavern of prehistory.

*European man, made and unveiled*

Because of both the concentration of researchers in Europe, as well as suitable preservation conditions in Northern Eurasia, ancient DNA has totally changed how we understand the genetic history of this continent most especially. Two new papers have expanded the sample set to 170 individuals, and many major questions have now been answered, and other new questions have been triggered by perplexing results. A few years ago I was talking to Spencer Wells about the age that we are privileged to live in. Spencer is a history and genetics buff (he was one of Richard Lewontin’s last grad students). So naturally as genetic science has emerged to shed light on history we’ve tracked its developments very closely. Spencer professionally, he’s a genetic anthropologist. Many questions which in the past would have been unanswerable are now answerable. Truth is coming at us so fast that it is hard to even respond to all of it (if you wait too long to publish, everything might have changed).

Carl Zimmer’s piece in The New York Times, DNA Deciphers the Roots of Modern Europeans, is accurate as to the current state of the accelerating research in this area. This is the equivalent of having a Rosetta Stone. The ancients are now coming back to life. They speak! Everything has changed. In Nature Ewen Callway quotes a scientist stating in plain language, “Christ, what does this mean?” I’ll try and flesh out further what it means, but the papers themselves do a good job. These are first steps, but they’re very big steps. There’s only so much more to go, and truth will be at hand.

First, the two papers, Massive migration from the steppe was a source for Indo-European languages in Europe, and Population genomics of Bronze Asia Eurasia. As might be suggested by the title the latter paper has coverage of populations outside of Europe, while the former focuses on Europe. The samples sizes are 69 and 101 respectively. The first paper uses a methodology which yields many SNPs, while the latter relied upon whole-genome sequencing (variation is variation, so really this is a minor detail for the results, though it matters a lot for the working scientists who are generating the data). Both agree broadly on the major results. Additionally, there is a third work, a preprint, Eight thousand years of natural selection in Europe, which has results in line with the second paper above (it has a section on selection as well as phylogenomics).

*European genetic structure is younger than the pyramids*

51IZQjMbVlL._SY344_BO1,204,203,200_

The old debate whether Europeans are descended from farmers or hunter-gatherers was always somewhat incoherent. All humans are descended from hunter-gatherers. Rather, the issue was whether modern Europeans descend primarily from people who were resident within the continent of Europe at the end of the last Pleistocene, or, whether they descend from peoples who developed agriculture in the Middle East ~10,000 years ago. That is, did farming spread through cultural diffusion or migration? Plants or people? The answer is actually not straightforward, but, the results are not controversial today.

First, migration seems to have been the dominant dynamic which defined the spread of farming, especially early on. These first farmers who arrived in Europe were genetically very different from the hunter-gatherers of Europe’s north and west. Some of their ancestry had been isolated by long distances for tens of thousands of years before contact. The people of the Iberian peninsula today have less genetically in common with the hunter-gatherers which were present in the region when the farmers arrived than do modern Northern Europeans, who harbor a greater fraction of ancestry which derives from the Pleistocene people. The main qualifier I’d put on this though is that the farmers themselves seem to have picked up European hunter-gatherer admixture on their way out of the Middle East. The fraction is on the order of ~50%. The other component has been termed “Basal Eurasian,” because this element is an outgroup to all other Eurasians, including the European hunter-gatherers. That is, the Basal Eurasians are an outgroup to a clade that includes such as diverse populations as Andaman Islanders, Australian Aborigines, Japanese, and European hunter-gatherers.

Lazaridis, Iosif, et al. "Ancient human genomes suggest three ancestral populations for present-day Europeans." Nature 513.7518 (2014): 409-413.

Lazaridis, Iosif, et al. “Ancient human genomes suggest three ancestral populations for present-day Europeans.” Nature 513.7518 (2014): 409-413.

The figure to the left is from the paper Ancient human genomes suggest three ancestral populations for present-day Europeans. WHG = “Western (European) Hunter-Gatherers.” EEF = “Early European Farmers.” You can see that EFF is a compound. I don’t think there’s too much clarity right now with where the EEF got its WHG-like ancestry. It could have been structure in the Middle East. Or it could have been in Southeast Europe. In the supplements of Haak et al. they test a Hungarian sample, and it does seem that the EEF individuals are closer to it than the Western European hunter-gatherer samples. So there might have been structure in the ancestral European population, but the confidence here is low. And from what I can tell Basal Eurasian is still something of a mystery, almost occupying the role of “Planet X” before the discovery of Nepture. To make the patterns make sense they have to exist, but much isn’t known about them in detail. And of course there seems to be a huge lacunae right now in terms of exploring the population genetics of the Middle East in a similar fashion as has occurred in Northern Eurasia (my understanding is that Carlos Bustamante was an important person in getting Latin American populations in the 1000 Genomes; unfortunate that there wasn’t someone else to advocate for including a Middle Eastern group, since this is such an important part of the world for human history).

With all that said, if one assumes that the West Eurasian admixture in EEF was from European hunter-gatherers, then it is clearly obvious that most of the ancestry of modern Europeans can date to the Pleistocene (i.e., EEF + Yamnaya likely means more than half the ancestry is WHG-like if you look back 10,000 years). But, this proportion obscures the fact that massive migrations and population turnovers have occurred, so that a simple model of expansion out of Ice Age refuges no longer holds. Cavalli-Sforza has long argued that pure proportions of ancestry are less important than the dynamic, as population growth driven “waves of advance” will over time dilute the initial genetic signal anyway (though the final proportion of non-WHG-like ancestry is actually higher in much of Europe than Cavalli-Sforza conceded in the early 2000s). Whether the ancestry of modern Europeans derives predominantly from those of European hunter-gatherers, the idea of dominant local continuity in a given region has been thoroughly refuted. The hunter-gatherer ancestry in the British Isles, for example, may be mostly from admixture into agricultural groups far to the south and east during the initial waves of advance, not from the people who initially recolonized Northern Europe in the early Holocene.

k8488The second demographic turnover event which has been highlighted by the papers cited so far is from the east. The migration from the steppes. This event had disproportionate, even dominant, impact across much of Northern Europe. Culturally it is often rooted in the Yamnaya complex, which gave rise to various disparate and wide ranging “daughter” societies. David Anthony’s The Horse, the Wheel, and Language surveys the archaeological terrain thoroughly. If you are interested in this topic, and haven’t read it, do read it. In this work Anthony outlines the spread of Indo-European languages via expansion of a mobile pastoralist elite. He was involved in the retrieval of some of the samples in these studies, and from what I am to understand he was personally surprised that the genetic data imply not just elite migration, but a folk wandering. Not just a band of brothers, but whole peoples on the move.

Haak, Wolfgang, et al. "Massive migration from the steppe was a source for Indo-European languages in Europe." Nature (2015).

Haak, Wolfgang, et al. “Massive migration from the steppe was a source for Indo-European languages in Europe.” Nature (2015).

Focusing on the genetics, these people seem to themselves be a compound of disparate elements. First, some of their ancestry derives from a population which Haak et al. term “Eastern Hunter-Gatherers” (EHG). And the other half derives from a population with affinities to those of the Near East, but different from that of the EEF. There is some disagreement between the two papers in Nature as to the details, but Allentoft et al. admit that they did not have EHG samples, which may have impacted their ability to detect admixture. Allentoft et al. also diverge from  Haak et al. in the emphasis they place on the ancestral component among the Yamnaya which some term “Ancient North Eurasian” (ANE) based on the location of the most ancient individual of this line (see Upper Paleolithic Siberian genome reveals dual ancestry of Native Americans). What does seem clear is that this element is deeply diverged from other West Eurasian populations, on the order of ~20 to 30 thousand years. And, they contribute about half the ancestry to the EHG (the rest is WHG-like). The descendants of the Yamnaya people brought this component all throughout Europe, with the exception of the Sardinians and Sicilians, likely isolated because of their position on the Mediterranean littoral (Sicilians have later Near Eastern admixture as well). But this is not limited to Europeans, as a substantial proportion of Native American and  West and South Asian ancestral heritage (at least the Kalash) also exhibit connections to this component.  Allentoft et al., like Haak et al., points out that there was likely structure in this broader group. That is, the ANE themselves were diversified, with the ancestors of the element in Native Americans and Europeans different from that which contributed to the Siberian component. In fact I have talked to researchers who believe that the term “Ancient North Eurasian” is misleading, as there is little clarity on the distribution of this group (the highest inferred fractions in Eurasia are in the North Caucasus). It is feasible that the Kalash have a different ANE source than Europeans.

A key issue to note, and that confuses some people, is that the ancestry of groups such as Yamnaya exhibited commonalities with other groups across Eurasia. Therefore, if you replaced similar groups then the change in admixture components utilizing model-based programs may not be as extreme as you would think. To illustrate what I’m getting at concrete, the population transfer between Greece and Turkey during the 1920s was far more impactful as a dynamic than simple before and after admixture estimates would suggest to you (since genetically the two groups were very similar). The figure from  Haak et al does not use admixture components that break out naturally, but their inferred demographic mixes taking into account the genetic character of the putative ancestral populations. The blue component refers to WHG, but WHG-like ancestry is also in both the green (Yamnaya) and orange (EEF) elements (this is why I’m saying it is likely that modern Europeans are mostly >50% WHG-like).

One temporal dimension that Haak et al emphasizes in particular, but seems clear in Allentoft et al. as well, is that non-Yamnaya ancestry slowly begins to rise again by the Bronze Age. Why? I will address that below. But, Allentoft et al. has broader Eurasian samples, including likely Indo-European populations in the trans-Ural and trans-Altai regions. In both of these areas the successor cultures had EEF-like ancestry. That is, like the Corded Ware population, and unlike the parent Yamnaya group. This strongly implies back-migration by this complex from Eastern Europe, as far east as western China, during the Bronze Age.

warbeforeIn The New York Times piece David Anthony states two things which puzzle me as an interested lay person without his expertise. First, he seems to think that the amalgamation of the Yamnaya and EEF-descended populations was not a warlike process. Specifically he says “It wasn’t Attila the Hun coming in and killing everybody,”. This is a useful image, but let’s be honest and note that the Huns were not primary producers, and did not aim just to increase pasturage by killing settled peoples as Genghis Khan had wanted to do (see The End of Empire: Attila the Hun & The Fall of Rome). Rather, they conquered and subordinated other barbarian groups, as well as extorted tribute from the East Roman Empire. The demographic impact of the Huns was not directly from them, but the fact that they and their successors (in particular the Avars) facilitated the migration of other groups, first, the Goths, and later the expansion of the Slavs. By the time of Attila barbarian leaders were well aware that the conquered were vital as economic producers whose capture and subjugation would allow them to engage in status competitions of conspicuous consumption. I do not believe that this was quite the case in the Copper and Bronze Ages beyond the limes of the civilized world, which was then an small archipelago of literacy in a sea of barbarism. Both the above papers indicate massive demographic disruption across Europ. Though war as we understand it is necessarily inevitable for our species, between the rise of agriculture and the modern period it seems to have been very common. It is not a coincidence that the Scandinavian Corded Ware culture are also called the Battle-Axe culture. Yes, many archaeologists believe that they were primarily a status symbols. I’m willing to bet many archaeologists are wrong. It’s been known to happen.

gokturk_empire_by_still_atesThe second issue which Anthony brings up is the connectedness of the various post-Yamnaya cultures, in particular that of the earliest Indo-Europeans on the fringes of western China, 4,000 miles from their likely point of origin. The genetic characteristics of these eastern groups is also such that it is likely that there was gene flow from Europe, mediated by a common steppe culture. Anthony states that “I myself have a hard time wrapping my head around explanations for that”. This totally confuses me, because he’s a professional archaeologist, so he must know that widespread gene flow and cultural ties cross the vast swath of the Eurasian heartland is not surprising at all! To Carl Zimmer I pointed out the example of the Goturk Empire of the mid 6th century A.D., which expanded rapidly from the core Altai zone, and prefigured the later distribution of the Turkic people, from the Nile to the fringes of the Arctic sea. Language and lifestyle mediate relationships and demographic contact. The peripatetic character of steppe peoples is well known and attested from the historical and semi-historical record. Groups such as the Huns, Avars, and Alans, had inchoate origins in the heart of Eurasia, and moved back and forth along lines of cultural affinity as needed. Alans were serving under the Mongols in China in the 13th century, but 800 years earlier they had accompanied the Vandal tribe to North Africa, and maintained a separate identity there until the conquest of Justinian. It seems entirely plausible that this pattern of hyper-mobility arose with agro-pastoralism along the whole range of continuous ecological appropriateness, only ending with the rise of gunpowder empires and the crushing of the Oirat by the Manchus (with the tacit approval of Russia).

*Northern European archetypical physical characteristics are younger than the pyramids*

Spencer Wells, a new look in the world

Spencer Wells, a new look in the world

Phylogenomics is tangled and complicated still, even with all these new results. I’ve only scratched the surface above. You really need to read the papers, and their supplements, to even get a sense of what’s going on (yes, ideally you’ll know what an f3 statistic is!). But, the population genomics which give us a sense of the character of natural selection and phenotype over time is much clearer. The suite of traits which we associate with white Europeans is quite possibly very recent, as late as post-Bronze Age. White supremacist scholars of the early 20th century who posited that ancient Egypt (in fact, all civilizations) were founded by blonde Nordic people turn out to likely be wrong because these civilizations probably predate the existence of blonde Nordic people, both in their genetic structure, and in their physical type (at least in any number).

nature14507-f4The genetic architecture of pigmentation is something geneticists know a fair amount about, because genome-wide association has been very fruitful in this area. Unlike traits such as height there is a large amount of between population variation in pigmentation. And, that variation is due in large part to a few genes of large effect.  At SLC24A5 there is a SNP which accounts for around 1/3 of the melanin index difference between Europeans and Africans, using an admixed African American population to test the effect. As I have observed before SLC24A5 in its derived form is as close to fixed as you can get in Europeans. In the 1000 Genomes data set of thousands of individuals I found a few samples with a heterozygote and the ancestral copy. In the Middle East this allele is also near fixation, though not quite. As you can see from the figure I adapted from Allentoft et al., among South Asians the derived allele is also at high frequency. My whole family is a homozygote for the “European” variant. There is some suggestive evidence that this haplotype derives from the Middle East. It was only at low frequency among European hunter-gatherers [3]. But, by the Bronze Age had it gone to fixation in Europe, as well as on the Eurasian steppe.

Of more interest to me is the trajectory of SLC45A2. The derived allele is nearly fixed in modern European populations, though not nearly to the same extent at SLC24A5. In Iberian and Sardinian populations the ancestral type is in the range of ~10%. During the Bronze Age in Europe it was only at ~50% frequencies, which is in the range of modern Middle Eastern populations. It was even at lower frequency in the steppe, from which the putative Indo-Europeans migrated.

Finally, in this panel for pigmentation they included a major SNP in OCA2-HERC2 region. This locus is famous for being involved in blue-brown eye color variation, explaining 75% of the variance, and also exhibiting the third longest haplotype in the European genome. Naively projecting from these SNPs one could credibly argue that the ancient hunter-gatherers of Europe at the beginning of the Holocene were dark-skinned and blue-eyed! The Bronze Age European samples, which in this case are biased toward Northern Europeans, had a range of genetic variation equivalent to modern Southern Europeans. The people of the steppe did not seem to have blue eyes at all.

skin2

These results align perfectly with those in Mathieson et al. One thing to observe is that the Paleolithic samples, which have a much deeper time depth, are “ancestral” at all these positions. Even if the sample size is small (N =4), they’re from diverse times and places. Does that mean that they were much darker than even the Holocene hunter-gatherers of Europe? As some have pointed out we can’t just straight-line extrapolate from the genetic architecture of today to the past. Remember that Neanderthals exhibited pigmentation polym]orphism, but of a different sort. A deeper functional analysis may yield the possibility that Paleolithic Europeans had alleles which also resulted in lighter skin, but they were different ones from the ones segregating as polymorphisms today. I have already stated that I doubt much of modern European ancestry derives form before the Last Glacial Maximum. The reason that modern genetic variation in terms of predicting phenotype gives these sorts of results is that they may have arrived at the same trait value via a different set of polymorphisms. Genotype-phenotype maps derived from modern populations may be a poor predictor of the relationship 30,000 years ago. Why would one think that selection upon variation in pigmentation began at the cusp of the Holocene?

But, I do think we can predict with more confidence the nature of phenotypes for populations which are genetically much closer to modern ones. Bronze Age Europeans fit that bill. And, I know something personally about what the appearance of individuals during this period might have been based on genetic architecture: both my children exhibit a genotype profile on pigmentation loci similar to many Bronze Age Europeans. That is, they’re fixed for the derived variant of SLC24A5, and are heterozygotes at SLC45A2 and OCA2-HERC2 (my son, but not my daughter, is a heterozygote at KITLG; it does seem to make a difference in hair color). In terms of just their complexion they could pass as indigenous Southern Europeans, but definitely not Northern European.

*Culture leads genes by the leash*

Another major finding of  Mathieson et al. and  Allentoft et al. is that the derived allele found across West Eurasians that allows them to digest lactose sugar as adults has been sweeping up in frequency over the last 4,000 years. This allele spans a diverse array of populations, from Basques to South Asians. With pigmentation it seems that we need to consider jointly the impact of ancestry and selection (in South Asia derived SLC24A5 frequencies are definitely a function of both selection and descent). But with LCT it seems likely that selection is paramount. The predominant genetic character of Eurasia was established by the Bronze Age, but the frequency of the lactase persistent allele was still far lower. Tests of natural selection which focus on patterns of haplotype variation long detected a huge hit from LCT so this is not surprising.

51r8Ph-vcaL._SY344_BO1,204,203,200_Intriguingly Allentoft et al. indicates that though the Bronze Age steppe populations had low frequencies of the derived allele, it seems that they did have a higher frequency than contemporary populations. This suggests that the origin of this haplotype, which spans the whole range of Indo-European speaking populations, and also into Finnic groups and the Basque, may still be attributed to the Yamnaya complex. In 10,000 Year Explosion Greg Cochran proposed the hypothesis that the favored mutation for LCT enabled the spread of Indo-European pastoralists. These results are not strong support for that direct causal relationship; rather, it strikes me that the ascendancy of the pastoralists drive the selection pressures for the allele in question. Biology did not drive culture, culture drove biology. The milk-drinking Celts and Germans encountered by Julius Caesar 2,000 years ago may still have been in the middle stages of adaptation to the agro-pastoralist lifestyle slowly being perfected by their ancestors.

*As the white man is, so shall we all be*

A new look as well

A new look as well

It is a running joke of mine on Twitter that the genetics of white people is one of those fertile areas of research that seems to never end. Is it a surprise that the ancient DNA field has first elucidated the nature of this obscure foggy continent, before rich histories of the untold billions of others? It’s funny, and yet these stories, true tales, do I think tell us a great deal about how modern human populations came to be in the last 10,000 years. The lessons of Europe can be generalized. We don’t have the rich stock of ancient DNA from China, the Middle East, or India. At least not enough to do population genomics, which requires larger sample sizes than a few. But, climate permitting, we may. And when that happens I am confident that very similar stories will be told. Using extant genetics we can already infer that modern populations in South Asia are a novel configuration of genotypes and phenotypes. The same in Southeast Asia, the Americas, and probably Africa. Probably the same in East Asia. Perhaps in Oceania. Even without admixture humans evolve in situ and changed, but with admixture the variation increases, and the parameter space of adaptation becomes richer and more flexible.

In Isaac Asimov’s later Foundation books he touched upon the existence of racial diversity in the future (from what I recall his earlier works from the pulp era were whites-only galaxies). At one point Hari Seldon encounters someone whose physical appearance seems to be East Asian, and they discuss the strangeness of people with East Asian ancestry being termed “Easterners” and those with European appearance being “Westerners.” With a loss of memory of the ancient distribution of these populations on the home planet only the shadow of a semantic recollection exists as a ghost in the galaxy-spanning Empire based out of Trantor. But of course tens of thousands of years in the future, even barring genetic and mechanical modification, it is unlikely that modern racial types will persist in any way we would recognize them.

But these results coming out of ancient DNA are telling us that what is likely to be true for the far future was also true for the recent past. White Europeans are a new type. But so are brown South Asians. Ethiopians have a recent ethnogenesis, as do most North African groups. The Bantu expansion has reshaped the face of Africa on the edge of the historical horizon. And so forth. In the big picture Young Earth Creationists are wrong, but in the specifics the idea that the sons of Noah populated the world ~5,000 years ago is not looking as crazy as it once did! Human genetic variation across Eurasia today may be mostly clinal, but in the recent past it was not. Rather, it was characteristic by sharp discontinuities and isolated local populations with diverged ancestry from their neighbors.

*And culture made man in its image*

51L3op-B8fL._SY344_BO1,204,203,200_About ten years ago it was common in paleoanthropology to assume that human beings emerged almost fully formed ~50,000 years ago, and wiped out all the others in a genocidal wave of advance. Richard Klein advanced this model in The Dawn of Human Culture. Klein’s thesis was that some stochastic event, a mutation, resulted in the punctuation of a new species, our own. This singular genetic process allowed for the emerged of fully formed linguistic faculties in our lineage, which allowed for the development of the cultural flexibility, which made the rest of the human lineages evolutionary dead ends. It was a single and elegant story. It appealed to the principle of parsimony. The reality of “archaic” admixture was a difficulty for Klein’s model, evidenced by the fact that he voiced his skepticism of genetic claims of admixture in The New York Times after most others had moved on. For Klein a biological change explained the rise and success of our species, not a cultural one.

At the time I found the thesis compelling. We were after all a very special species. Modern Homo made it to Oceania and the New World. Something must have happened. Something big. What else could explain our rapid expansion and marginalization of other lineages? I’m a biologist, and so biology is an appealing causal mechanism.

linear

*The luck of the English facing the ocean*

At about the same time the evidence for Neanderthal admixture came out, Luke Jostins posted results which showed that other human lineages were also undergoing encephalization, before their trajectory was cut short. That is, their brains were getting bigger before they went extinct. To me this suggested that the broader Homo lineage was undergoing a process of nearly inevitable change due to a series of evolutionary events very deep in our history, perhaps ancestral on the order of millions of years. Along with the evidence for admixture it made me reconsider my priors. Perhaps some Homo lineage was going to expand outward and do what we did, and perhaps it wasn’t inevitable that it was going to be us. Perhaps the Neanderthal Parallax scenario is not as fantastical as we might think?

41z97bDZvUL._SY344_BO1,204,203,200_Consider the case of Europe around 1600. In England and northern Germany (or what was to become northern Germany) you have two Protestant and genetically similar populations. But by 1850 it looked as if England was going to demographically overtake Germany in a broader genetic sense. James Belich’s Replenishing the Earth reviews the history of this period, when England spearheaded a demographic revolution far out of proportion to what one might have predicted in the year 1000. But by 2000 Germany, or Germans, had caught up somewhat. How? Millions of Germans migrated to the United States, starting in very large numbers in the mid-19th century, and were “picked up” by the demographic revolution which was the United States. The point is that contigencies of history, cultural and social, rather than biology, explain the trajectory of the gene pool over time. Much of the human past, and the sharp fluctuations in gene frequencies, might be driven by the long and forceful arm of culture.

In the treatment above I note that the EEF farmers who by and large replaced the indigenous hunter-gatherer groups in modern Southern Europe were themselves a compound. The hunter-gatherer ancestry within the EEF was far more successful than that of those they replaced, but the only reason that this was so was geographic coincidence. The WHG-like groups absorbed into the EEF were positioned further east, and so closer to the initial locus of expansion of Neolithic farmers. Similarly, the Neanderthal admixture into modern populations was almost certainly localized to particular groups. This is not to say that there are no biological differences between human populations which may explain a wide range of phenomena. Anyone looking at the skull of a Neanderthal and a modern human knows there are. There are also likely bio-behavioral differences between extent populations. Gene-culture coevolution is a real process, even if the details need to be worked out. But the interplay between biology and culture is complex, and in many cases cultural changes are driving the biological change, and then fixing differences which are advantageous to the “winners” (lactase persistence seems rather to be a perfect case of this). But just as in the individual case we must also remember that winning is often in part a function of being lucky. Naturally selection, generally thought of as a deterministic process, is also to some extent stochastic [4].

*From genetic islands to a roiling sea of humans*

One of the most shocking things for many of the geneticists working in the area of ancient DNA, and encountering the variation of the past, is the high level of population structure. That is, you have groups co-resident for many generations who nevertheless exhibit genetic distances of intercontinental scale. But as I stated above David Reich himself found the same results for India. And, in Africa you have long symbiotic populations, such as the pygmy groups of the Congo, and their agricultural neighbors, who are genetically very different, and have been for tens of thousands of years. Allentoft et al. dryly observe that “These results are indicative of significant temporal shifts in the gene pools and also reveal that the ancient groups of Eurasia were genetically more structured than contemporary populations.”

castesofmindAbout 10 years ago I read Nicholas Dirks’ Castes of Mind. Dirks is an eminent scholar who is now the chancellor of UC Berkeley. He emphasizes the power of European categories and systematization in creating the modern caste system. I don’t want to reduce his argument to a caricature. Obviously caste predates European colonialism. Dirks would admit this. But in Castes of Mind it is hard to shake the feeling that he believes that the British imposition of formalization made it what we truly understand it to be today. That caste has to be understood as a contemporary and early modern phenomenon, rather than an ancient one that was a structural feature of South Asian society.

The genetic evidence is clear now, and it paints a very different landscape. Many of the caste, even jati, boundaries we see today are thousands of years old. Endogamy long predates the British. It may predate the Aryans! Rather than the British, or Aryans, inventing caste, this form of ethnic segregation may date to the initial admixture event, to be reinvented and modified with each new population which arrives and imposes its hegemony on the subcontinent. In The New York Times David Reich states “You have groups which are as genetically distinct as Europeans and East Asians. And they’re living side by side for thousands of years.” He then he goes on to say “There’s a breakdown of these cultural barriers, and they mix,” alluding to the rise in WHG ancestry in farmer samples over time. Of course it is interesting to remember Reich’s work on India has highlighted exactly how persistent caste has been, and how it maintains genetic variation in a localized region that is often nearly inter-continental in magnitude.

We can never know if 6,000 years ago the LBK people, the first farming culture of Northern Europe, imposed a caste-like system of segregation when encountering the indigenous hunter-gatherers. Nor can we say with total confidence whether their relationship exhibited a symbiosis analogous to that between the Bantu agriculturalists and pygmies of the Congo (though do note that in these scenarios the Bantu communities are higher status, and the individual pygmies often have a semi-slave status). But, we need to look to what cultural evolutionary models and empirical results can tell us to make sense of these patterns. Ancient DNA can tell us very concretely the details of changes in allele frequencies. We can somewhat confidently reconstruct the faces and complexions of our ancestors. The questions population genomicists ask and answer in relation to animal models are relatively cleanly addressed by these data sets, assuming the sample sizes are large enough. But humans are the cultural animal par excellence, and that is the critical new variable which will require a new set of scholars to come together and create a truly multi-disciplinary understanding of the human past, present, and perhaps future. Powerful genomic techniques which produce results which have implications for the study of human history needs to leverage the full array of scholars who study human historical science.

1 – The three-fold copying is an important matter, because the different cultures had different preferences and goals. The Arab effort for example focused mostly on the philosophical production of the ancients. Without the Byzantines we would have far less of the humanistic production of Classical Greece, in particular the theatrical tradition.

2 – Much of what is known about the diplomatic history of the Bronze Age Near East has been preserved in cuneiform tablets. Though unwieldy, this form of writing on clay tablets is obviously more robust and less dependent upon copying than parchment and papyrus which came later.

3 – I would be curious to know if it is the same haplotype as is currently common in Eurasia.

4 – New mutations will usually go extinct, even if they are favored, in the initial generations. It is only when the frequency becomes high enough due to chance that selection will inevitably drive its frequency up, perhaps to fixation.

Only the glimpses of the shadows of history

41eAv4GeGqL._SY344_BO1,204,203,200_Sometimes what you infer about history is totally wrong. How often? Sometimes we find out. As I’ve outlined on this blog over the course of years inferences made in historical population genetics using extant variation have often turned out to be totally wrong. How do we know? Time machines. Ancient DNA.

Yesterday I received a copy of Sewall Wright and Evolutionary Biology. I read it about 10 years ago, but I didn’t know as much about evolutionary biology back then. So I wanted to get a copy of it (unlike R. A. Fisher: The Life of a Scientist there are actually affordable copies). I decided to get straight to the section which covered the general time period of the Wright-Fisher controversies, when two of the great eminences involved in the development of the field of population genetics were hashing out somewhat different perspectives.

41qS+5MyBmL._SY344_BO1,204,203,200_Rather than getting into that, what I want to recount is the passage the author, Will Provine, offers up from Sewall Wright’s personal correspondence which reproduced R. A. Fisher’s last letter to him. One interesting sidebar here is that R. A. Fisher, from all the biographical information I’ve been able to gain an impression from, was a much more flawed person than Sewall Wright. Fisher was the greater scientist (seeing that he made original contributions to statistics), but Wright was the greater human. After a period of somewhat frequent correspondence Fisher and Wright ceased their direct interaction, right at a time when their differences were being highlighted, leading to decades of ill feeling. In particular, there had been a mixed review of The Genetical Theory of Natural Selection which Wright had submitted to Genetics.

From everything Will Provine knew beforehand he was expecting a rather cold and unfriendly last letter from Fisher to Wright due to the nature of the review. His expectations were totally off base. R. A. Fisher was entirely gracious and good-natured, and seemed appreciate of the review despite its dissents. The lesson that Provine takes from this is that we don’t truly know what we don’t truly see, and we should have greater humility about the darkness outside of the bounds of our direct perception.

Mr. Martin, please acknowledge a “forking” of HBO’s show & the books

91-rbDuvMoL._SL1500_There are some of us who have waited years. It has even come to pass that we have grown into manhood, and one generation has waned and another waxed as George R. R. Martin has been weaving his series A Song of Ice and Fire. His “So Spake Martin” once had oracular aspect for the patient ones. Now we wait…we wait. Years pass.

And yet a new specter haunts the horizon, the specter of HBO. There are those of us who have not followed this show, which began at the beginning of the decade. We have watched with curiosity as the newcomers have reacted with horror at what we who have waited have known for all these years. But we harbor no ill will, we, the waiters. We know. We know the end will come, and a new creation will join the constellation of the volumes which have come before. We wait.

But now there is talk that the show is proceeding ahead of the books, and that our patience is for naught. George R. R. Martin needs to make this clear: are the shows “spoiling” the books, or, is the television series a “fork”? Obviously I’m hoping for the second.

Beyond printing with pixels: internet native science publishing

neveryone
german+flying+machine+paleo-futureThere is a season for everything. Last year my friend David Mittelman and I teamed up with GigaScience editor Laurie Goodman to write up a commentary in Genome Biology, Dragging scientific publishing into the 21st century. We’re obviously in the 21st century, but for science publishing we’re in the “long twentieth.” But wait, it’s worse! As we noted in the piece, to a great extent the internet is used as a PDF delivery device by many publishers, and the PDF is an electronic form of the classic paper journal article, whose basic outlines were established in the 17th and 18th centuries. In other words, in a qualitative sense we’re not that much beyond the Age of Newton and the heyday of the Royal Society. Scientific publishing today is analogous to “steampunk.” An anachronistic mix of elements somehow persisting deep into the 21st century. Its real purpose is to turn the norms of the past into cold hard cash for large corporations.

neveryone1Obviously I’m not the only one with this thought. To a great extent PLOS and the open access revolution arose to overturn the procrustean status quo. More recently preprint culture, and the transparency of “personal communication” via Twitter, have changed the terms of discussion. The metabolic pace has increased, and the transparency which breathes life into scientific discourse is on the march. It seems likely that the old order will die a death of a thousand cuts, as one practice after another fades into obscurity.

One of the main weak points of the current framework is that it does not serve the needs of the end user. For many, the goal of getting published is to add a line to the c.v., at least outside of the top-tier journals. This explains the emergence of vanity and fraudulent publishing houses. Many researchers of genuine eminence exist, but for some workaday scientists publishing somewhere will do well enough to keep the salary and perks coming. But science should be more than just a job. Science feeds the spirit of our society, it allows us to see with our mind’s eye how the world truly is. Scientific discussion has to flourish in a manner which is not simply an ends to careerism.

logo-v2.originalSo back to a specific weakness of the current system: how to engage with the end user? David has assembled a small team  to begin actualizing the “wish list” that we outlined in Dragging scientific publishing into the 21st century. That actualization takes the form of a new startup, N of Everyone, which exists to roll out technology to help folks better engage with and discuss science. Their first project is a reader which leverages the way people today actually read “papers.” That is, not simply a pixelization of paper, but a form of engagement with science which actually brings to the table the interactivity which is invited by the nature of electronic media. At many journal clubs people now read “papers” on tablets, notebook computers, and even phones. Why retrofit the print format of yore for the cutting-edge technology of today?

efbd8da242c257aadc4aa40c2383fb54_originalThis probably sound a bit vague and nebulous. To make this concrete N of Everyone is looking to the crowd for support and to raise initial funds. Funding to transform an idea into a reality. There’s already a prototype (I’ve seen it). Imagine leaving comments on specific sentences of papers. Basically, the sort of annotation you already do emailing files or sharing docs when it comes to collaborating to get a publication polished.

Here’s some more information from their Kickstarter page:

  • Share or comment on any sentence in the paper without having to leave the paper
  • Get in-line context for references as well as a map of where those references are discussed throughout the paper.
  • Get in-line context and discussion of figures in a paper as well as the entire discussion for a figure, even if it is distributed throughout the paper.

Get more information and lots of great screenshots at their their Kickstarter page, and consider contributing to the project (obviously). There’s a lot of ways one can imagine the communication of science going, and it will change. I’m confident of that. David and his partners are attempting to grab the bull by the horns and drive in a fruitful direction. I know they’re passionate about science, and for me that’s key. You can make money in a variety of ways. The reason they’re tackling this project is because this is an issue that’s close to their heart.

Note: comments are closed to this post. Since David & co. would appreciate feedback I’m sure, I’ll just point you to their Twitter, http://twitter.com/nofevery1.

Who’s afraid of a hybrid wolf?

Citation: Prüfer, Kay, et al. "The complete genome sequence of a Neanderthal from the Altai Mountains." Nature 505.7481 (2014): 43-49.

Citation: Prüfer, Kay, et al. “The complete genome sequence of a Neanderthal from the Altai Mountains.” Nature 505.7481 (2014): 43-49.

Quartz has a quizzical piece up, which is useful for fleshing out the incoherency of some tendencies within conservation biology. It turns out that the large coyotes which have been expanding across the eastern United States as the forests have taken over abandoned farmlands (due to the shift of agricultural activity to the Midwest in the 20th century from New England and Mid-Atlantic). To no one’s surprise these coyotes are filling the niche of the timber wolves of yore, predating upon the white-tailed deer whose numbers have increased with the rewilding of the landscape. But there’s a twist in this tale:

…scientists have since discovered these super-sized coyotes are only about two-thirds coyote. About 10% of their genes belong to domestic dogs and a quarter comes from wolves, with which they hybridized as they moved east north of the Great Lakes.

Monzón says hybridization enabled eastern coyotes to adapt quickly to fill the niche left by wolves. In fact, areas with the highest densities of deer had coyotes with the greatest proportion of wolf in their genomes. “There was a very rich resource that was waiting to be exploited,” says Monzón. “They’ve done very well here.”

So what’s the problem? As observed later in the piece our own species is to some extent a compound of diverged lineages. This pattern of reticulated ancestry is as old as evolutionary process itself. The “tree” metaphor was simply a stylized fact which elided detail so we could get to the heart of the matter in attempting to understand in our bones what common descent entailed. But supposedly there are rumblings:

Some scientists and conservationists see the coywolf as a nightmare of the Anthropocene—a poster child of mongrelization as plants and animals reshuffle in response to habitat loss, climate change and invasive species.

I am curious about any scientist that would use the term “mongrelization.” Name the scientists. It strikes me that a ghost-strawman is being set up here. But I’m willing to be proven wrong.

The reality is that many biologists have had issues with the biological species concept as an idealized and Platonic ideal, as opposed to an instrumental concept. Plant biologists have never had much truck with a strict form of the biological species concept, and how exactly does it to apply to asexual organisms? Our public policy has been built on a narrow conception of biological purity which only holds in a small slice of the tree of life, and even there it is violated constantly. Our own species is here as proof of that.

The end of the bookstore and the end of genre?

AmericanGods-ReprintThe new TNR seems to be a weird mismash of SJW-clickbait and interesting pieces on aspects of culture which the old TNR probably wouldn’t have thought to publish. I doubt that this version of TNR is long for this world, but I do appreciate pieces such as this conversation between Neil Gaiman and Kazuo Ishigoru, Breaking the Boundaries Between Fantasy and Literary Fiction. It’s rather self-indulgent, but what do you expect? The main question which they circle around is the nature of genre boundaries. This portion really jumped out at me:

NG: I loved the idea, because it seems to me that subject matter doesn’t determine genre. Genres only start existing when there’s enough of them to form a sort of critical mass in a bookshop, and even that can go away. A bookstore worker in America was telling me that he’d worked in Borders when they decided to get rid of their horror section, because people weren’t coming into it. So his job was to take the novels and decide which ones were going to go and live in Science Fiction and Fantasy and which ones were going to Thrillers.

KI: Does that mean horror has disappeared as a genre?

NG: It definitely faded away as a bookshop category, which then meant that a lot of people who had been making their living as horror writers had to decide what they were, because their sales were diminishing. In fact, a lot of novels that are currently being published as thrillers are books that probably would have been published as horror 20 years ago.

 

When I was an adolescent the way I would decide how to purchase a book, usually a paperback science fiction or fantasy, was to look for specific authors and covers. There wasn’t really that much planning or research ahead of time. There was a great deal of serendipity involved.

Things are different today. Usually before buying something in person I do some research online. Also, recommendation engines are pretty useful, and good at guiding you to a narrower set of choices attuned to your preferences. This obviates the need to some extent for genre categories as guides in the first place.

I’m thinking of this specifically because apparently Spotify Wants Listeners to Break Down Music Barriers (well, according to Farhad Manjoo). It makes sense for Spotify sense it has so much more data to work with than old style radio stations. Similarly, at some point Amazon will have enough reading and purchase information to get really good at pointing you to authors and works that are suited to your interests.

Open Thread, 6/7/2015

CoverReadingInTheBrainWhen you narrow in on a part of science it is easy to lose sight of the rest. That’s how I feel when it comes to Reading in the Brain: The New Science of How We Read. It’s been a while since I read much about cognitive neuroscience, so it’s a novel rediscovery. Though the most interesting point that I’ve internalized so far is that the irrationality of the English spelling system does result in a cost in terms of the amount of time that children must invest to become functionally literate. Apparently the Turkish transition from the Arabic script to Latin alphabet resulted in immediate yields in literacy gains, illustrating that writing systems are not arbitrarily useful.

Second, another comment about my comments policy:

I’ve been reading your blog for some time. It is always interesting. But one thing frequently puzzles me. The prose in your main posts is always so reasonable and persuasive that I am surprised by your surly, intemperate responses to some of the commenters. Often, as in your reply to Sean, you totally ignore the commenter’s remarks and simply “go postal.” Whether or not Sean has completed “post-doctoral research” really has nothing to do with the quality of his remarks.

First, I know more than you. You really should shut up sometimes. I know the post-doctoral researcher in question, and he’s done more thought on issues of reproduction than you or Sean have forgotten. So I don’t want people to waste his, mine, or, your, time. Don’t think I don’t keep track of commenters and what they’ve said. Comments can’t be evaluated in a singular fashion. If people have commented intelligently or informatively in the past, they get slack. If not, no.

Second, a recent poll suggests that 4 percent of Americans say they are less intelligent than average. It’s pretty obvious that people overestimate their intelligence and knowledgeability, and this includes readers of this weblog. I spend time, away from other activities, writing these posts. If you don’t like them, don’t read them. I don’t care. But if you make a comment don’t waste my time. If you tell me something I don’t know, I’m going to be happy. If you make errors in areas where I am more knowledgeable than you, I will not be happy. Unfortunately many readers of this weblog are used to being the “smartest person” in the room. That means that often they think I should be happy with their incredible comments, when they only usually pass muster because of their pathetic peer groups (this tends to be a major problem with older commenters who are never told that they’re not awesome).

My main posts are “reasonable and persuasive” because I do a lot of reading and thinking. If your comments are well informed and well thought out, I won’t be surly.

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