Demographic replacement in Southeast Asia during the Holocene

Well sometimes you feel silly, and it’s not your fault. Yesterday our podcast on Sundaland went live (we talked about Doggerland and Beringia too!). Though I expressed a fair amount of skepticism, I took the argument that Stephen Oppenheimer presented in Eden of the East, that modern Austronesians are long-term residents of Southeast Asia, seriously.

The alternative view, most forcefully put by Peter Bellwood in books such as First Farmers, is that Austro-Asiatic and Austronesian people were agriculturalists issuing out of southern China that transformed the region over the past 4,000 years (the Austronesians from Taiwan specifically, though during the Pleistocene Taiwan was connected to the mainland).

I lean toward Bellwood’s view, and today a preprint came out which basically confirms it in totality, Ancient Genomics Reveals Four Prehistoric Migration Waves into Southeast Asia. The abstract:

Two distinct population models have been put forward to explain present-day human diversity in Southeast Asia. The first model proposes long-term continuity (Regional Continuity model) while the other suggests two waves of dispersal (Two Layer model). Here, we use whole-genome capture in combination with shotgun sequencing to generate 25 ancient human genome sequences from mainland and island Southeast Asia, and directly test the two competing hypotheses. We find that early genomes from Hoabinhian hunter-gatherer contexts in Laos and Malaysia have genetic affinities with the Onge hunter-gatherers from the Andaman Islands, while Southeast Asian Neolithic farmers have a distinct East Asian genomic ancestry related to present-day Austroasiatic-speaking populations. We also identify two further migratory events, consistent with the expansion of speakers of Austronesian languages into Island Southeast Asia ca. 4 kya, and the expansion by East Asians into northern Vietnam ca. 2 kya. These findings support the Two Layer model for the early peopling of Southeast Asia and highlight the complexities of dispersal patterns from East Asia.

The transition to full-fledged rice agriculture occurred in Vietnam ~4,000 years ago. In First Farmers Bellwood reports on an archaeological site dating to that period where skeletal evidence has been adduced to record the presence of both Northeast Asian and Australo-Melanesian types. These results make clear though that these hunter-gatherers in Southeast Asia are more similar to the Onge of the Andaman Islands, as well as the Negritos of the interior of the Malay peninsula. They’re totally in alignment with the earlier morphological results (also, readers might be curious to know that one site of the Hoabinhian culture is in Yunnan, China). This shouldn’t be surprising, as the Andaman Islands were a peninsula which extended from southern Burma during the Pleistocene.

Already the most accepted model for the introduction of intensive agriculture into Southeast Asia is that it was brought by Austro-Asiatic peoples. These results confirm that. Additionally, it seems clear that Austro-Asiatic ancestry made it to island Southeast Asia, whether directly or through Austronesian admixture before arriving in island Southeast Asia. Java and Bali have some of the higher fractions ancestries most closely associated with Austro-Asiatic groups on the mainland.

Deeper digging into the admixture distributions has long made it pretty evident that some areas had much higher Austronesian fractions in Indonesia than others, and it wasn’t just a function of distance from the Phillippines. Why? My own hunch is that Austronesians brought social and cultural systems which were better adapted to island Southeast Asia, and were more fully able to exploit the local ecology. Meanwhile, aside from a few fringe areas such as the Malay peninsula and coastal Vietnam, they were not successful on the mainland.

The authors also detect migrations into Southeast Asia besides that of the Austro-Asiatics and Austronesians. One element seems correlated with the Tai migrations, and another with Sino-Tibetan peoples, most clearly represented in Southeast Asia by the Burmans. The excellent book, Strange Parallels: Volume 1, Integration on the Mainland: Southeast Asia in Global Context, c.800–1830, recounts the importance of the great migrations of the Tai people into Southeast Asia ~1000 A.D. Modern-day Thailand was once a flourishing center of Mon civilization, an Austro-Asiatic people related to the Khmers of Cambodia. The migrations out of the Tai highlands of southern China reshaped the ethnography of the central regions of mainland Southeast Asia. The Tai also attempted to take over the kingdoms of the Burmans. Though they failed in this, the Shan states of the highlands are the remnants of these attempts (tendrils of the Tai migrations made it to India, the Ahom people of Assam were Tai). Vietnam, shielded by the Annamese Cordillera, came through this period relatively intact. It is also well known that Cambodia’s persistence down to the present has much to do with the shielding it received from France in the 19th century in the wake of Thai expansion.

There are two bigger issues that this paper sheds light on. One is spatial, and the other is temporal.

They detect shared drift between Austro-Asiatic people and tribal populations in northeast India. This is not surprising. A 2011 paper found that Munda speaking peoples, whose variant of Austro-Asiatic is very different from that of Southeast Asia, are predominant carriers of Y chromosome O2a. This is very rare in Indo-European speaking populations, and nearly absent in Dravidian speaking groups. Additionally, their genome-wide patterns indicate some East Asian admixture, albeit a minority, while they carry the derived variant of EDAR, which peaks in Northeast Asia.

One debate in relation to the Munda people is whether they are primal and indigenous, or whether they are intrusive. The genetic data strongly point to the likelihood that they are intrusive. An earlier estimate of coalescence for O2a in South Asia suggested a deep history, but these dates have always been sensitive to assumptions, and more recent analysis of O2a diversity suggests that the locus is mainland Southeast Asia.

Now that archaeology and ancient DNA confirm Austro-Asiatic intrusion into northern Vietnam ~4,000 years ago, I think it also sheds light on when these peoples arrived in India. That is, they arrived < 4,000 years ago. As widespread intensive agriculture came to Burma ~3,500 years ago, I think that makes it likely that Munda peoples arrived in South Asia around this period.

I now believe it is likely that the presence of Austro-Asiatic, Dravidian, and Indo-Aryan languages in India proper was a feature of the period after ~4,000 years ago. None of the languages of the hunter-gatherer populations of the subcontinent remain, with the possible exception of isolates such as Nihali and Kusunda.

The temporal issue has to do with the affinities of these peoples, and how they relate to the settling of Eastern Eurasia. All the Southeast Asian groups after the original Australo-Melanesians share more of an affinity with the Tianyuan individual than Papuans. The implication here is that Tianyuan is closer to the ancestors of various agriculturalists in Southeast Asia than just some random basal Eastern Eurasian. But, since Tianyuan dates to 40,000 years ago, and, is from the Beijing region, it is hard to make strong inferences from comparisons with only it. The heartland of ancient Chinese culture in Henan was to the south of the Tianyuan, after all. More samples are needed before one can truly tease out the pattern of isolation-by-distance vs. admixture that led to the emergence of the proto-farmer populations which settled Southeast Asia.

In the podcast above one thing that came up is that a lot of genetic data indicate decreased diversity as one moves from the south to the north in East Asia. This has long been taken to mean that humans migrated north, and so were subject to bottleneck effects. I pointed out that this may simply be a consequence of admixture between two very different groups of people in Southeast Asia, elevating diversity statistics.

And yet as the map at the end of the preprint suggests it is highly plausible that Pleistocene Asia was marked by a south to north dynamic of migration. The Austro-Asiatic peoples who migrated south during the Holocene may simply have been backtracking the migration of their ancestors. What these results, and ancient DNA more generally, tell us is that humans were often on the move. The Pleistocene world of climate change probably meant that humans had to be on the move.

The Nation of Islam has an antisemitism problem, and that’s about it

Currently, there is a mini-controversy of sorts related to antisemitism, Louis Farrakhan, and some organizers of the 2017 Women’s March. The main problem seems to be that these three co-chairs of the Women’s March, Linda Sarsour, Carmen Perez, and Tamika Mallory, are balking at denouncing their association with and tacit tolerance of Farrakhan. In particular, the focus is on Tamika Mallory.

Personally, histrionic demands of denunciation usually leave me cold.

But in this case, there are strong grounds. Louis Farrakhan and his small splinter sect, the Nation of Islam, have a long history of very extreme perspectives on Jews, and whites more generally. The racism isn’t a minor idiosyncrasy with the Nation of Islam. It’s a constitutive part of their ideology. The Nation of Islam believes that white people are a race of mutants designed by a malevolent black scientist. There are some similarities fundamentally with white nationalist Christian Identity, which dehumanizes non-whites in a literal manner. And, both the Nation of Islam and Christian Identity operationally share very similar and stereotypical views of Jews as evil puppet-masters.

In reaction to this much of the media has taken to writing long analyses. This piece in The Atlantic, The Women’s March Has a Farrakhan Problem, meanders over an enormous amount of territory. Frankly, it seemed a bit much.

First, the co-chairs of the Women’s March are not the marchers themselves. The marchers are to the Left of center, but many of them are quite moderate and mainstream and conventional. I know some personally who aren’t even very liberal and self-identify as centrists. And many are Jewish. The point is that leaders and organizers can have very different politics and associations from the movement they lead. Tamika Mallory has a problem. The Women’s March, not so much.

Second, there was a theme in The Atlantic piece about the fraught and cooperative relationship between blacks and Jews in the United States. Impressionistically there’s something to this, especially considering the Crown Heights riot. But part of me wonders if there really is such that much antisemitism among American blacks that’s out of the ordinary.

The GSS has a variable, “JEWTEMP”, which measures respond attitudes toward Jews on a scale of 0 to 100 (0 being cooler and 100 being warmer). I binned the results into quartiles. You can see that black Americans are less warm toward Jews than white Americans, but the difference is very marginal.

Louis Farrakhan and the Nation of Islam are clearly antisemitic by any definition. But black Americans are not particularly antisemitic at all. Farrakhan is as representative of black American attitudes toward Jews as those on the “Alt-Right” who obsess over the “JQ”.

In fact, could it simply be that black Americans exhibit a demographic profile that is correlated with somewhat less positive feelings toward Jews, as opposed to something distinctive about black American culture? To check I played around with a multiple regression.

Changing variables around I found three traits that were robustly predictive of warmer feelings toward Jews:

1) The biggest effect was vocabulary score, which is correlated with general intelligence (r=0.7). If you don’t put this variable in, education matters. But once WORDSUM is in the equation the effect of education disappears.

2) Being a woman.

3) Being younger.

Being black as opposed to white is associated with being somewhat more antisemitic in many regressions, but it’s very weak as an association, and, it’s not statistically significant (this is probably due to sample size).

What’s the point of this post? Not to sound too much like Steven Pinker, but there isn’t a looming threat of antisemitism in the United States from any large demographic. Rather, there are small old groups like the Nation of Islam and white nationalists, which remain resolutely antisemitic. And, the Israel-Palestine issue does loom over campus politics in a way that blurs the line between being anti-Zionist and antisemitic. A small number of campus radicals and students from Muslim backgrounds do step pretty clearly from anti-Zionism to antisemitism in my opinion. In the latter case, it’s from personal knowledge, as when I was a graduate student a few kids approached me during controversies related to BDS from Islamic backgrounds expressing their strong reservations about Jews and taking courses from Jewish professors. These conversations were not welcome by me, but because of my physical appearance and name, they assumed I’d be sympathetic.

The problem here is simple, and it’s the indulgence that the black intelligentsia (that includes you President Obama) and some of the radical non-black Left, have given the Nation of Islam and Louis Farrakhan for decades. Remember, he was on Arsenio Hall‘s show in 1995. The issue isn’t the Women’s March (whose politics I somewhat disagree with), nor is it antisemitism in the black community. And most of the public doesn’t even know what BDS stands for.

Slack killed IRC? (sort of)

Interesting piece channeling some early internet nostalgia, Picking Up The Slack:
Internet Relay Chat beat Slack to real-time chat by decades and helped define much of our early online culture, yet way more people use Slack. Why is that?
. The article caught my attention because I use Slack at work, and have for a couple of years. In contrast, I probably check in to IRC once every few years now (I actually just installed an IRC client on my computer, it’s been so long).

And yet back during the summers between school years in college, I’d spend a fair amount of time haunting several IRC channels, mostly on UNDERNET. You met some weird people, some nice people, and some unpleasant people. Generally, my utilization of IRC was heavily cyclical, just like my reading and posting in USENET groups. If I had better thing to do, I’d go do them.

Perhaps one of the strangest things about IRC and USENET is a few people from those days actually ended up finding me on the web, with the rise of the paleoblogosphere. At least one long-time commenter knows me from a USENET group back in the late 1990s, while the RSS aggregator that pushes my total content feed was written by an anarcho-libertarian programmer and philosopher who I actually met first when he was a teen nerd in the Deep South.

That old internet culture is disappearing and becoming legend, just like the “homebrew computer” era of the 1970s was for my generation.

On the semiotics of “Judeo-Christian” as a misdirection

Recently on Twitter there emerged another flare-up of the debate as to whether the term “Judeo-Christian” was coherent, useful, and defensible. In general, I take a very skeptical view of the term, because I think it misleads the public as to the nature of some important facts and dynamics in the history of the West.

Perhaps intellectuals can agree amongst themselves that the term has utility for manipulating the masses, but oftentimes it seems even intellectuals don’t have enough of a grasp of religious history to understand why the usage is literally problematic (I’m not using problematic in a euphemistic catchall manner, I think it’s semantically confusing, not offensive).

First, traditionally Jews and Muslims have been much clearer in recognizing each other as non-idolatrous monotheists, as against Christians. The dominant non-Unitarian nature of Christianity, and the importance of divine representation in both medieval Eastern and Western traditions (with statuary in the latter), were the key issues for Muslims and Jews. This point is not dispositive, but it’s not irrelevant.

In the Western context, it seems American Christians in particular are attached to the term Judeo-Christian. I believe this is the outcome of a specific American history, where different European immigration streams were forged into a common people in the 20th century, especially in the post-World War II era. The general model is the one outlined by Will Herberg in Protestant, Catholic, Jew, the emergence of a white America united by shared values, with establishment mainline Protestantism at the center, and Roman Catholicism and Judaism as helpmates. Though the title of the book points to the real religious particularism still prevalent in that period, it was an early form of what Rod Dreher and his fellow travelers would term “morally therapeutic Deism.” The idea that it didn’t matter as to the details of the confession and practice of your faith, so long as you believed in God and were a good person.

Of course not all people who assert the utility of Judeo-Christian as a category are so religiously naive. But most Christians who adhere to the category seem to have a hard time not understanding Judaism as anything other an earlier form of their religion. In other words, Judaism as Christianity without the Christ.

I think this is very misleading. Rather, Judaism as it evolved after the rise of Christianity, and then Islam, was a distinct religion from the Judaism which Christians are familiar with from their Old Testament. Jewish religion in the first millennium A.D. became the religion of the Pharisees. That is, Talmudic Judaism, or Rabbinical Judaism. What we in the West often term Orthodox Judaism. Though there were schismatic sects, such as the Karaites, developments such as Hasidism, and isolated groups such as the Bene Israel of western India who seem to have practiced a more archaic form of the religion, over time Judaism qua Judaism became the religion which evolved out of the same milieu of Roman antiquity as Christianity. Though Christianity evolved out of the religion of the Hebrews, the Jews, the religion of the Jews evolved at the same time as well. It was not static, in chrysalis.

A whole Jewish Diaspora, what became the Ashkenazim, Sephardim, and Mizrahim (and Yemenite Jews and other assorted groups), developed a parallel cultural world to that of Western and Eastern Christianity, as well Islam.* Though Jews interacted with gentiles in a professional capacity, whether as physicians, merchants, or money-lenders, the intellectual exchange was relatively limited (Al-Andalus being an exception).

This may surprise many people, because Jews are extremely prominent intellectually in the West today. But this is a feature of the last few centuries, as they became absorbed by Western culture during the Jewish Enlightenment. Even a Jew who predates this period and influenced the course of early modern Western philosophy, Baruch Spinoza, did so after being expelled from the Jewish community, and occupying a sort of gray land of Deism. Neither Christian nor Jew.

What this gets to is that even if Judeo-Christian has some abstract ideal reality, there was no Judeo-Christian civilization before large numbers of Jews abandoned the civilization of Judaism as it had developed organically over the centuries. The civilization only became labeled Judeo-Christian in rhetoric after most Western Jews had abandoned their customary and traditional religion, whether for a congregational faith more recognizable to Christians in the form of the Reform movement, out and out secularism, and in a large number of cases, conversion to Christianity (to name three individuals of Jewish familial origin who were raised Christian no matter their adult faith, Ludwig Wittgenstein, Karl Popper, and Karl Marx).

The civilizational tension among Jews is evident today in the world’s only Jewish state, Israel. Many secular Jews are for all practical purposes members of Western civilization who happen to have a Jewish ethnic and nominal religious identity. In contrast, Haredi Jews are fully steeped in the mores and orientation of the classical Jewish civilization that matured in early modern Europe. The conflict between the Haredim and secular Jews is not just one of religious observance but of civilizational identity and affinity (with Masortim occupying the middle ground).

Western civilization as a project after Late Antiquity and before the modern period was never a partnership between the Jews and Western Christians. It was the project of Western Christian societies, which eventually fractured during the Reformation, and repaired themselves back into some sort of whole in the wake of the Peace of Westphalia. The transformations of the 18th century ushered in the revolutionary changes which allowed for Jews to become participants in Western civilization as something besides Christians.

In general, though I understand that for the public history is often a useful fiction, I prefer attempting to model the past with the greatest fidelity to the reality we can reconstruct among those with the will and ability to understand. The emergence of Western civilization as we understand it, post-Christian civilization, the nymph stage of the universal liberal democratic civilization which was to conquer the 21st century (but hasn’t, and may never!), is historically contingent on particular peoples, places, and cultural threads. Those threads properly constituted simply make the term Judeo-Christian seem peculiar and inappropriate. Therefore, amongst those who aim to know, the proper appellations must be applied so as to illuminate rather than obscure and obfuscate.**

* Some Jews also existed outside of the world of Christianity and Islam, such as the Cochin Jews of southern India, or the Jews of Kaifeng, who were probably originally an extension of Central Asian Jewry. These groups were part of the Diaspora intellectual and culturally, at least initially (the Jews of Kaifeng eventually lost their last rabbi, probably in the 19th century, and assimilated into the Han majority or converted to Islam).

** I have not written much about Islam in this post, but the term Judeo-Christian also misleads many people into thinking that traditional Christianity and traditional Judaism have more similarities of belief and practice than either do with Islam. In fact Islam and Judaism are arguably more similar than either is to Christianity due to the emphasis on prescribed ritual and law incumbent upon the laity guided by a non-priestly scholarly class, whether it be rabbis or the ulema.

The 23andMe BRCA test

In case you were sleeping under a rock, 23andMe got FDA approval for DTC testing of markers related to BRCA risk. Obviously, this is a pretty big step, in principle.

But the short-term implications are not that earth-shaking.

From the FDA release:

The three BRCA1/BRCA2 hereditary mutations detected by the test are present in about 2 percent of Ashkenazi Jewish women, according to a National Cancer Institute study, but rarely occur (0 percent to 0.1 percent) in other ethnic populations. All individuals, whether they are of Ashkenazi Jewish descent or not, may have other mutations in BRCA1 or BRCA2 genes, or other cancer-related gene mutations that are not detected by this test. For this reason, a negative test result could still mean that a person has an increased risk of cancer due to gene mutations….

Apparently, women with one of these variants have a 45-85% chance of developing breast cancer by age 70. So the penetrance is high.

It seems that you’ll know if this sort of test is going to have utility for you based on family history.

The big thing is the transition to DTC. This will increase availability and drive the price down. That’s probably going to mean more work for those engaged in interpretation and education. False positives are going to start being a major thing….

Open Thread, 3/6/2018

Eden in the East is a weird book. Written in the late 1990s before modern-day genomics, its central thesis about the origin of Southeast Asian people in Pleistocene Sundaland seems likely to be wrong (at least most of their ancestry). But the author, a polymath medical doctor, marshals an enormous amount of archaeological and textual data supporting old ideas of cultural diffusionism, much of it plausible.

Despite my skepticism of the general theses promoted, reading Eden in the East is useful insofar as you need data and interpretive sieve for the swell of ancient DNA.

The University of Wisconsin-Stevens Point is eliminating many majors and adding new ones. This is eliciting a lot of outrage on Twitter.

Public universities are funded by the public. If they aren’t fulfilling the public role then things will have to change. Unlike many people, I don’t shed too many tears about the elimination of some of these majors because most graduates of them are stupid and uninformed (some of them actually have a less accurate view of the world coming out than before they arrived at university).

Here’s the breakdown:

Expanding programs Change into majors Discontinuing the programs
Chemical Engineering Aquaculture/Aquaponics American Studies
Computer Information Systems Captive Wildlife Art – Graphic Design will continue as a distinct major
Conservation Law Enforcement Ecosystem Design and Remediation English – English for teacher certification will continue
Finance Environmental Engineering French
Fire Science Geographic Information Science Geography
Graphic Design Master of Business Administration Geoscience
Management Master of Natural Resources German
Marketing Doctor of Physical Therapy History – Social Science for teacher certification will continue
    Music Literature
    Political Science
    Sociology — Social Work major will continue


Let’s set aside the fact that some of these programs, such as sociology and American Studies, are often de facto political action outfits. As someone who has talked to people who have history degrees from universities of various prestige and stringency, institutions of higher learning are doing a really shitty job inculcating knowledge into these kids. Or love of the topic. Also, their critical faculties aren’t the best. Too much critical theory, not enough critical thinking. Recitation doesn’t cut it.

Aquaculture and aquaponics is a vocational program of study which isn’t sexy, but at least it aims to impart skills. That’s what a lot of these kids need.

So my buddies at DNA Geeks unveiled a new t-shirt, Pipe(tte) Dream.

I kind of thought it was funny, but it turns out there’s some demand for stuff like this. Is bench biology still a thing? I guess so…. Anyway, if you are interested, click on through!

Evolutionary inferences about quantitative traits are affected by underlying genealogical discordance. This is an important preprint. Read it.

The Silicon Valley elite’s latest status symbol: Chickens. Some of the people caught up in this are quite self-aware: Citroen’s 19-year-old son, Luca, who grew up around the family business, puts it this way: “Being able to say you have chickens says, ‘I have a back yard,’ and having a back yard says, ‘I have space.’ And having space means you have money, especially when it comes to Silicon Valley real estate.” Chickens are a “hard to fake” signal of wealth. Yeah (the Romans had sacred chickens).

My main hope is that some of these rich Silicon Valley hobby-farmers pick up a copy of Introduction to Quantitative Genetics. It would do them some good (and perhaps the world?).

Do any readers have a review copy of She Has Her Mother’s Laugh: The Powers, Perversions, and Potential of Heredity? It’s Carl Zimmer’s new book and the publisher is out of galleys.

Speaking of reviews, I’ll be writing one up for Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past for a publication most of you have heard of. Have to put the “writer hat” back on for a bit. Between my job, my intellectual interests, and family, I haven’t put much effort into that.

You probably know that Antifa went after Christina Sommers:

To be honest these forays by centrists (Sommers is a registered Democrat with libertarian leanings, similar to Steven Pinker) into the academy are starting to remind me of those ridiculous “debates” that Jews had to have with professional anti-Jews (mostly apostates) in the courts of medieval European monarchs. There were the outward forms of debate, but everyone knew what it was about (since Sommers and Pinker are from Jewish backgrounds perhaps that’s apposite).

Similarly, when the campus Left is against some speaker many people roll their eyes, and the administration makes the usual noises, but you know that the protestors are going to get a slap on the hands no matter how obnoxious or aggressive they are. For most academics, for various reasons, there are no enemies on the Left. Communists and Communist sympathizers like Angela Davis can be fulsomely praised with no worries about reputation, but those academics who think Sommers or Pinker are making reasonable points have to furtively communicate on secret direct message groups.

That’s where we are.

I now understand why Benedict Anderson’s Imagined Communities has been assigned to so many undergraduates: it’s a short and simple book. It’s depressing but unsurprising that it could be so influential. More on that later.

The criticisms that Enlightenment Now doesn’t really delve into the intellectual archaeology of the Enlightenment are spot on. But this seems a case where the title is a bit off, but the text itself is solid. I have seen on Twitter quotes about how Pinker has apologia for the Tuskegee experiment. My prior at this point about these sorts of invidious accusations is that they’re lies. For a variety of reasons, people lie about Steven Pinker. That’s sad, but we live in a world where liars prosper, so it shouldn’t be surprising.

My podcast with Spencer, The Insight, has been pretty successful so far. I just submitted it to a bunch of podcast directories this weekend to cover bases. Our goal is to get highlighted by iTunes, so if you haven’t, subscribe and leave a good review! (also, there are only three reviews on Stitcher so far)

We interviewed Chris Stringer a few weeks ago. This week we’re trying to get Milford Wolpoff recorded (to be posted next week). We have some ideas about guests we might have on. Currently, we want to mix personal genomics/biotech, genetics, and paleoanthropology. I think I want to mix in some straight history at some point, since so much ancient DNA is starting to percolate into that field.

Retweets Are Trash. Basically, the argument is that if you get rid of RTs some of the toxic effects of Twitter are dampened. Skeptical, but hopeful.

How Twitter Lost The Internet War. The most important part is the assertion that Twitter has a lot of tech-debt that it hasn’t retired or discharged, and that’s why it hasn’t been able to solve its troll problem in a non-manual manner. I have a hard time crediting this. But perhaps that’s how it is?

Turkey Is Turning Into the Next Pakistan. Being totally honest, it’s hard for me to believe that the media hasn’t been underplaying this story. Back when ISIS was a thing, Turkey was turning a blind eye to thousands of foreign fighters that were streaming into Syria. Even if Turkey isn’t pro-Islamist (and it kind of is), they are clearly backing Sunni Islamists who will impose a nasty majoritarianism if they ever win. Not that the anarcho-communist Kurds we’re backing would be any better in the long run.

Ultimately in Syria, I can’t begrudge ethnoreligious minorities for siding with the Assad regime against the rebels. And, I can’t begrudge the Sunni population their reliance on militants who are more fierce and principled in defending them and their interests against the government. But we’ve been through Iraq twice. Our Saudi ally has birthed monsters over the past generation. We turned a blind eye when our ally of convenience in the 1980s, Iraq, engaged in gas attacks against Iran and the Kurds.

We need to learn, and just stop. Stop!

On the lookout for Kindle deals in books. Here’s what I got recently:

* The Rise and Fall of Communism.
* Carthage Must Be Destroyed: The Rise and Fall of an Ancient Civilization
* The Sleepwalkers: How Europe Went to War in 1914.

I have a lot of books on Communism that I need to read!

Interesting paper, Understanding the factors that shape patterns of nucleotide diversity in the house mouse genome.

The 500 errors on this site are due to a plugin and some of the issues with porting this blog over a few months ago. I need to allocate a day to figure this out, but I’ll do it. The same issues with the South Asian Genotype Project. I will update it. But I need to have four or five uninterrupted hours, and that’s just hard to come by.

SXSW should be interesting this week. As per usual I’ll avoid most of the festivities.

Do the Amerindians descend from Southeast Asians?

Many people have recommended I read Johanna Nichols’ Linguistic Diversity in Space and Time over the years. I checked out the book in grad school once but didn’t get around to reading it. But today I see it being referenced in Stephen Oppenheimer’s very strange book about Lemuria-I mean Southeast Asia, Eden in the East.

Both of these books were written in the late 1990s, before the current swell of genome-wide and ancient DNA analysis. Oppenheimer reports Nichols’ comparative analysis of linguistics implies that the ancestors of the Amerindians were not interior Siberians, but coastal people who came up from Southeast Asia.

Today we know this is somewhat wrong. About 30 to 40 percent of the ancestry of modern Native Americans derives from Ancient North Eurasians, who seem to be most commonly found in the great Eurasian heartland, probably to the east of what we think of today as Europe, but west of the Pacific.

But there’s more. Most of the ancestry of Native American peoples seems to be more like that of East Asians. Today this component extends rather far north, into Korea, Japan, and such. But these are consequences of recent demographic movements. Nichols’ Southeast Asian hypothesis may actually not be off-base, in particular in light of other evidence suggesting admixture with an Australo-Melanesian population.

One of the major issues with the field of ancient DNA and the historical inferences people make is that the theories and models are often quite ad hoc, and emerge in response to the data. But these earlier ideas, informed by linguistics and archaeology, are actually a pretty good source of possible ideas. They may not be constrained by genetics, because we didn’t have that information (aside from mtDNA), but are richly informed by other disciplines.


Who We Are and How We Got Here, a book worth reading

Yesterday I talked to a friend who has a review copy of Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past. They gave me a preview (their overall assessment was positive).

I haven’t personally asked to get a copy because, to be honest, I thought there wouldn’t be anything new in it. If you “read the supplements” what more could there be in 368 pages? So I was waiting until the end of the month to buy the book and read it in my own sweet time as due diligence.

Well, this morning I asked a publicist to send me a copy. I will be getting it next week. The reason is that I’m told the latter portions of the book are quite challenging and candid as to what genetics may tell us in the 21st century. Who We Are and How We Got Here is a 21st-century revision and update of The History and Geography of Human Genes. But it’s apparently a lot more.

Also, I make a small cameo in the book, as does Eurogenes and Dienekes. I have always appreciated how the David Reich and Nick Patterson and their whole lab has taken people outside of the halls of the academy seriously. They didn’t need to as a matter of professional necessity but often engage as a matter of decency and seriousness.

Idle theories are the devil’s workshop

In the 1970s Richard C. Lewontin wrote about how the allozyme era finally allowed for the testing of theories which had long been perfected and refined but lay unused like elegant machines without a task. Almost immediately the empirical revolution that Lewontin began in the 1960s kickstarted debates about the nature of selection and neutrality on the molecular level, now that molecular variation was something they could actually explore.

This led to further debates between “neutralists” and “selectionists.” Sometimes the debates were quite acrimonious and personal. The most prominent neutralist, Motoo Kimura, took deep offense to the scientific criticisms of the theoretical population geneticist John Gillespie. The arguments around neutral theory in the 1970s eventually spilled over into other areas of evolutionary biology, and prominent public scientists such as Richard Dawkins and Stephen Jay Gould got pulled into it (neither of these two were population geneticists or molecular evolutionists, so one wonders what they truly added besides bluster and publicity).

Today we do not have these sorts of arguments from what I can tell. Why? I think it is the same reason that is the central thesis of Benjamin Friedman’s The Moral Consequences of Economic Growth. In it, the author argues that liberalism, broadly construed, flourishes in an environment of economic growth and prosperity. As the pie gets bigger zero-sum conflicts are attenuated.

What’s happened in empirical studies of evolutionary biology over the last decade or so is that in genetics a surfeit of genomic data has swamped the field. Some scholars have even suggested that in evolutionary genomics we have way more data than can be analyzed or understood (in contrast to medical genomics, where more data is still useful and necessary). Scientists still have disagreements, but instead of bickering or posturing, they’ve been trying to dig out from the under the mountain of data.

It’s easy to be gracious to your peers when you’re rich in data….

The tall and long tales that elephants tell (also, ancient DNA never forgets)

The new paper on ancient DNA from elephants, mammoths and mastodons, A comprehensive genomic history of extinct and living elephants, is pretty cool. It leverages next-generation sequencing and ancient DNA, to reconstruct the demographic history of several species of elephants, extant and extinct.

The major core finding is that ancient DNA along with better data from extant species suggests that straight-tusked elephant of Europe (P. antiquus), which went extinct 50,000 years ago, seems to have been an evolutionary synthesis of sorts. A substantial portion of its ancestry as from a deeply diverged lineage of elephant. But another fraction seems to derive from a branch of the African forest elephants, in particular, the West African variety. Finally, earlier on there was also admixture with an Asian pachyderm related to the woolly mammoth.

You can see from the figure at the top that the divergence between these lineages is on the order of hundreds of thousands to millions of years.

This section from the conclusion is a huge takeaway:

Our genomic analyses of present-day and extinct elephantids revealed a history of multiple major interspecies admixture events. Evidence for gene flow among closely related mammalian species is not unprecedented. Examples include cases of unidirectional gene flow [e.g., from polar bears into brown bears (47), similar to the Columbian mammoth gene flow into woolly mammoths observed in our study]; emergence of admixed species [e.g., North American wolves with ancestry from coyotes and gray wolves (48), similar to the straight-tusked elephants in our study]; different extents of gene flow [e.g., between gray wolves and Eurasian/African golden jackals (49), and between bonobos and central/eastern chimpanzees (50), as in the case of straight-tusked elephants and west African forest elephants/woolly mammoths in our study]; extended periods of gene flow during the initial diversification of species [e.g., between eastern and western gorillas (39), Sumatran and Bornean orangutans (39), and the ancestors of humans and chimpanzees (39, 51), like those inferred from most pairwise species comparisons in our study]; and adaptive introgression [e.g., in the great cats of the genus Panthera (52)], which could have played an important role in the evolution of elephantids as well. Our results in elephantids thus add to the growing weight of evidence in favor of the view that capacity for hybridization is the norm rather than the exception in many mammalian species over a time scale of millions of years.

Big speciose mammal lineages seem to have hybridzed a lot. Should this surprise us? Probably not.

Placental Invasiveness Mediates the Evolution of Hybrid Inviability in Mammals:

A central question in evolutionary biology is why animal lineages differ strikingly in rates and patterns of the evolution of reproductive isolation. Here, we show that the maximum genetic distance at which interspecific mammalian pregnancies yield viable neonates is significantly greater in clades with invasive (hemochorial) placentation than in clades with noninvasive (epitheliochorial or endotheliochorial) placentation. Moreover, sister species with invasive placentation exhibit higher allopatry in their geographic ranges, suggesting that formerly separated populations in mammals with this placental type fuse more readily on recontact. These differences are apparently driven by the stronger downregulation of maternal immune responses under invasive placentation, where fetal antigens directly contact the maternal bloodstream. Our results suggest that placental invasiveness mediates a major component of reproductive isolation in mammals.

Monkeys and apes (including humans), have very invasive placentas. Afrotheria, somewhat less so. Placental invasiveness isn’t the only criteria to predict or gauge the viability of hybridization, but it’s a major one.

I’ve stated before that genomics didn’t really change our understanding in a qualitative way in relation to evolutionary biology. Yes, stupid arguments about selectionism vs. neutralism really don’t happen anymore because there’s a mad scramble for data, as opposed to rhetorical tactics. But, perhaps in the area of understanding speciation with regards to mammals genomics has really changed things. That is, it’s a lot more about reticulation and a lot less about bifurcation.

To a great extent the “biological species concept” (BSC), which to the general public is the scientific species concept, is mammal focused. If plant geneticists had the catbird seat I think we’d have a different view of what species were. As it is, that’s not what happened. Species are human constructs and reify a certain Platonic sense of categories and kinds. What genomics is showing us here is even in the “best case” circumstances of the BSC, in mammalian lineages, when evaluated over reasonable time spans species barriers are highly porous.