Razib Khan One-stop-shopping for all of my content

August 31, 2017

Two thousand years of philosophy on the margin

Filed under: philosophical,philosophy — Razib Khan @ 9:50 pm

A little less than two years ago I began to read Anthony Kenny’s A New History of Western Philosophy. It’s a big book, on the order of ~1000 pages. But that’s not the reason I’m just now finishing it. The book is divided by chronologically and thematically. I read about the ancients in about a week, but struggled to get past the medieval section. I’ve mentioned this before.

And yet in my self-pity I did wonder: is this partly just a function of the fact that ancient philosophy provided most of the answers (or non-answers) in what we think of as philosophy over a few centuries? As they say, perhaps the rest is simply commentary and extension.

If society collapsed and we reverted to barbarism it seems it would be a loss if we didn’t have the Principia. But if we had philosophy up to Seneca, would we miss what came after?

August 30, 2017

People believe in evolution, just not for humans

Filed under: creationism — Razib Khan @ 7:58 pm

The term “liberal Creationism” refers to the fact that on the cultural Left there is a strong belief in the concept of evolution on the whole, but in the case of human beings biological evolutionary processes are seen as marginal in comparison to culture. In other words, natural selection and adaptation explain the diversity around us in the animal and plant world, but can tell us little about human beings.

This viewpoint exhibits various degrees of sophistication, but I think it gets at a real deeply held perspective (though not universal one, in Defenders of the Truth it is recounted that Noam Chomsky held his fire during the sociobiology controversy in part because he was quite open to the idea that behavior could have some biological basis).

Looking at the General Social Survey though, I believe now that the liberal Creationist viewpoint is actually just a spin on the normal American position. That is, Americans as a whole are quite open to the idea of descent with modification and common ancestry in the context of animals, but much more squeamish when it comes to humans. Some conservative religious Creationists admit that this rather frankly. Their objection to evolution is not about science, but about human dignity.

A new GSS variable, EVOLVED2, which complements an older variable, EVOLVED, allows us to explore this question.

Here is what they ask:

EVOLVED: Human beings, as we know them today, developed from earlier species of animals. (Is that true or false?)

EVOLVED2: Elephants evolved from earlier species. (Is that true or false?)

53 precent of respondents answered yes to true in the first case, but 86 percent in the second case. In other words, presenting evolution in a non-human context reduces resistance.

You can check the responses against attitudes toward the literality of the Bible:

I think this suggests to us that on a broader social scale resistance to evolution is culturally conditioned, and derives from deep intuitions about human dignity. The specific details of where that dignity comes from, whether it be Protestant Fundamentalist or Social Justice is incidental.

Heraclius was a great man, but a dirty old man

Filed under: Byzantium,History — Razib Khan @ 3:20 pm

The Emperor Heraclius is someone who more people should know. He saved the Byzantine Empire before it truly became the Byzantine Empire in a mature form. When he took power the Persians were on the march, and ruled vast swaths of the Asian and African possessions of the East Roman Empire. Theodore of Tarsus, one of the early Archbishops of Canterbury, grew up under Persian rule. Like Hannibal’s early victories Heraclius’ defeat of the Persians is a tour de force of strategic brilliance. I’ll leave it to the reader to find out why themselves (I recommend A History of the Byzantine State and Society to any reader).

But this post is inspired by pop-culture. People are talking about nephew-aunt relations right now. As it happens Heraclius’ second wife was his niece, Martina. Here is something I found on Wikipedia: “He had two children with Fabia and at least nine with Martina, most of whom were sickly children…Fabius (Flavius) had a paralyzed neck and Theodosios, who was a deaf-mute….” The history of this period can be patchy and unreliable. So I’m not sure there were nine children and most were sickly…but probably inbreeding was causing some serious issues.

August 29, 2017

Genetics books for the masses!

Filed under: Genetics — Razib Khan @ 10:49 pm

Since I’ve become professionally immersed in genetics I haven’t read many books on the topics. I read papers. And I do genetics. But back in the day I did enjoy a good book. The standard recommendation would be to read Matt Ridley’s Genome. It’s a bit dated now (it was published around when the Human Genome Project being completed), but I’d still recommend it.

But when in the mid-2000s I dabbled a little bit in the world of worm (C. elegans) genetics I read Andrew Brown’s In the Beginning Was the Worm: Finding the Secrets of Life in a Tiny Hermaphrodite. It’s pretty far from my current concerns and fixations, with more of a focus on developmental processes, but it is pretty cool to read about the race to “map” every cell in C. elegans.

The second book I’d recommend readers of this blog is the late Will Provine’s The Origins of Theoretical Population Genetics. Modern population genomics is a massive edifice built atop the foundations of the early 20th century fusion of Mendelism and the biometrical heirs of Darwin. Provine outlines how primitive genetics eventually seeded the birth of the Neo-Darwinian Synthesis.

Why do percentage estimates of “ancestry” vary so much?

Filed under: Genetics,Human Genetics — Razib Khan @ 10:36 pm

When looking at the results in Ancestry DNA, 23andMe, and Family Tree DNA my “East Asian” percentage is:

– 19%
– 13%
– 6%

What’s going on here? In science we often make a distinction between precision and accuracy. Precision is how much your results vary when you re-run an experiment or measurement. Basically, can you reproduce your result? Accuracy refers to how close your measurement is to the true value. A measurement can be quite precise, but consistently off. Similarly, a measurement may be imprecise, but it bounces around the true value…so it is reasonably accurate if you get enough measurements just cancel out the errors (which are random).

The values above are precise. That is, if you got re-tested on a different chip, the results aren’t going to be much different. The tests are using as input variation on 100,000 to 1 million markers, so a small proportion will give different calls than in the earlier test. But that’s not going to change the end result in most instances, even though these methods often have a stochastic element.

But what about accuracy? I am not sure that old chestnuts about accuracy apply in this case, because the percentages that these services provide are summaries and distillations of the underlying variation. The model of precision and accuracy that I learned would be more applicable to the DNA SNP array which returns calls on the variants; that is, how close are the calls of the variant to the true value (last I checked these are arrays are around 99.5% accurate in terms of matching the true state).

What you see when these services pop out a percentage for a given ancestry is the outcome of a series of conscious choices that designers of these tests made keeping in mind what they wanted to get out of these tests. At a high level here’s what’s going on:

  1. You have a model of human population history and dynamics with various parameters
  2. You have data that that varies that you put into that model
  3. You have results which come back with values which are the best fit of that data to the model you specificed

Basically you are asking the computational framework a question, and it is returning its best answer to the question posed. To ask whether the answer is accurate or not is almost not even wrong. The frameworks vary because they are constructed by humans with difference preferences and goals.

Almost, but not totally wrong. You can for example simulate populations whose histories you know, and then test the models on the data you generated. Since you already know the “truth” about the simulated data’s population structure and history, you can see how well your framework can infer what you already know from the patterns of variation in the generated data.

Going back to my results, why do my East Asian percentages vary so much? The short answer is that one of the major variables in the model alluded to above is the nature of the reference population set and the labels you give them.

Looking at Bengalis, the ethnic group I’m from, it is clear that in comparison to other South Asian populations they are East Asian shifted. That is, it seems clear I do have some East Asian ancestry. But how much?

The “simple” answer is to model my ancestry is a mix of two populations, an Indian one and an East Asian one, and then see what the values are for my ancestry across the two components. But here is where semantics becomes important: what is Indian and East Asian? Remember, these are just labels we give to groups of people who share genetic affinities. The labels aren’t “real”, the reality is in the raw read of the sequence. But humans are not capable of really getting anything from millions of raw SNPs assigned to individuals. We have to summarize and re-digest the data.

The simplest explanation for what’s going on here is that the different companies have different populations put into the boxes which are “Indian/South Asian” and “East Asian.” If you are using fundamentally different measuring sticks, then there are going to be problems with doing apples to apples comparisons.

My personal experience is that 23andMe tends to give very high percentages of South Asian ancestry for all South Asians. Because “South Asian” is a very diverse category when tests come back that someone is 95-99% South Asian…it’s not really telling you much. In contrast, some of the other services may be using a small subset of South Asians, who they define as “more typical”, and so giving lower percentages to people from Pakistan and Bengal, who have admixture from neighboring regions to the west and east respectively.*

Something similar can occur with East Asian ancestry. If the “donor” ancestral groups are South Asian and East Asian for me, then the proportions of each is going to vary by how close the donor groups selected by the company is to the true ancestral group. If, for example, Family Tree DNA chose a more Northeastern Asian population than Ancestry DNA, then my East Asian population would vary between the two services because I know my East Asian ancestry is more Southeast Asian.

The moral of the story is that the values you obtain are conditional on the choices you make, and those choices emerge from the process of reducing and distilling the raw genetic variation into a manner which is human interpretable. If the companies decided to use the same model, the would come out with the same results.

* I helped develop an earlier version of MyOrigins, and so can attest to this firsthand.

August 28, 2017

Popular songs in my household

Filed under: Culture,Music — Razib Khan @ 9:49 pm

When journalists get out of their depth on genetic genealogy

Filed under: DTC personal genomics,Genealogy,Genetics,Personal genomics — Razib Khan @ 7:39 pm

For some reason The New York Times tasked Gina Kolata to cover genetic genealogy and its societal ramifications, With a Simple DNA Test, Family Histories Are Rewritten. The problem here is that to my knowledge Kolata doesn’t cover this as part of her beat, and so isn’t well equipped to write an accurate and in depth piece on the topic in relation to the science.

This is a general problem in journalism. I notice it most often when it comes to genetics (a topic I know a lot about for professional reasons) and the Middle East and Islam (topics I know a lot about because I’m interested in them). It’s unfortunate, but it has also made me a lot more skeptical of journalists whose track record I’m unfamiliar with.* To give a contrasting example, Christine Kenneally is a journalist without a background in genetics who nevertheless is immersed in genetic genealogy, so that she could have written this sort of piece without objection from the likes of me (she did write a book on the topic, The Invisible History of the Human Race: How DNA and History Shape Our Identities and Our Futures, which I had a small role in fact-checking).

What are the problems with the Kolata piece? I think the biggest issue is that she didn’t go in to test any particular proposition, and leaned on the wrong person for the science. She quotes Joe Pickrell, who knows this stuff like the back of his hand. But a more space is given to Jonathan Marks, an anthropologist who is quite opinionated and voluble, and so probably a “good source” for any journalist.

Marks seems well respected in anthropology from what I can tell, but he’s also the person who put up a picture of L. L. Cavalli-Sforza juxtaposed with a photo of Josef Mengele in the late 1990s during a presentation at Stanford. Perhaps this is why anthropologists respect him, I don’t know, but I do not like him because of his nasty tactics (I wouldn’t be surprised if Marks had power he would make sure people like me were put in political prison camps, his rhetoric is often so unhinged).

Marks’ quotes wouldn’t be much of an issue if Kolata could figure out when he’s making sense, and when he’s just bullshitting. But she can’t. For example:

…“tells me I’m 95 percent Ashkenazi Jewish and 5 percent Korean, is that really different from 100 percent Ashkenazi Jewish and zero percent Korean?”

The precise numbers offered by some testing services raise eyebrows among genetics researchers. “It’s all privatized science, and the algorithms are not generally available for peer review,” Dr. Marks said.

The part about precise numbers is an issue, though a lot less of an issue with high density SNP-chips (the real issue is sensitivity to reference population and other such parameters). But if a modern test says you are 95 percent Ashkenazi Jewish and 5 percent Korean it really is different from 100% Ashkenazi. Someone who comes up as 5% Korean against an Ashkenazi Jewish background is most definitely of some East Asian heritage. In the early 2000s with ancestrally informative markers and microsatellite based tests you’d get somewhat weird results like this, but with the methods used by the major DTC companies (and in academia) today these sorts of proportions are just not reported as false positives. Marks may not know because this isn’t his area, but Pickrell would have. Kolata probably did not think to double-check with him, but that’s because she isn’t able to smell out tendentious assertions. She has no feel for the science, and is flying blind.

Second, Marks notes that the science is privatized, and it isn’t totally open. But it’s just false that the algorithms are not generally available for peer review. All the details of the pipeline are not downloadable on GitHub, but the core ancestry estimation methods are well known. Eric Durand, who wrote the originally 23andMe ancestry composition methodology presented on it at ASHG 2013. I know because I was there during his session.

You can find a white paper for 23andMe’s method and Ancestry‘s. Not everything is as transparent as open science would dictate (though there are scientific papers and publications which also mask or hide elements which make reproducibility difficult), but most geneticists with domain experience can figure out what’s going on and it if it is legitimate. It is. The people who work at the major DTC companies often come out of academia, and are known to academic scientists. This isn’t blackbox voodoo science like “soccer genomics.”

Then Marks says this really weird thing:

“That’s why their ads always specify that this is for recreational purposes only: lawyer-speak for, ‘These results have no scientific standing.’”

Actually, it’s lawyer-speak for “do not sue us, as we aren’t providing you actionable information.” Perhaps I’m ignorant, but lawyers don’t get to define “scientific standing”.

The problem, which is real, is that the public is sometimes not entirely clear on what the science is saying. This is a problem of communication from the companies to the public. I’ve even been in scientific sessions where geneticists who don’t work in population genomics have weak intuition on what the results mean!

Earlier Kolata states:

Scientists simply do not have good data on the genetic characteristics of particular countries in, say, East Africa or East Asia. Even in more developed regions, distinguishing between Polish and, for instance, Russian heritage is inexact at best.

This is not totally true. We have good data now on China and Japan. Korea also has some data. Using haplotype-based methods you can do a lot of interesting things, including distinguish someone who is Polish from Russian. But these methods are computationally expensive and require lots of information on the reference samples (Living DNA does this for British people). The point is that the science is there. Reading this sort of article is just going to confuse people.

On the other hand a lot of Kolata’s piece is more human interest. The standard stuff about finding long lost relatives, or discovering your father isn’t your father. These are fine and not objectionable factually, though they’ve been done extensively before and elsewhere. I actually enjoyed the material in the second half of the piece, which had only a tenuous connection to scientific detail. I just wish these sorts of articles represented the science correctly.

Addendum: Just so you know, three journalists who regularly cover topics I can make strong judgments on, and are always pretty accurate: Carl Zimmer, Antonio Regalado, and Ewen Callaway.

* I don’t follow Kolata very closely, but to be frank I’ve heard from scientist friends long ago that she parachutes into topics, and gets a lot of things wrong. Though I can only speak on this particular piece.

August 27, 2017

The Ghosts of the European Pleistocene

Filed under: European genetics,Ice Age — Razib Khan @ 9:19 pm

2011’s Cave of Forgotten Dreams was a strange film. I went to watch it in the theaters mostly to see the paintings of Pleistocene peoples in an immersive manner, but the director and narrator, Werner Herzog, used the film as an instrument to forward his thesis that humanity as we understand it emerged during this period in the European Ice Age.

Whether he knew it or not Herzog was channeling the “Great Leap Forward” model of the origin of our species. That in an almost punctuated manner the cultural proteanism which we take to be a defining hallmark of our species emerged at some point deep in what we call the Ice Age. In The Dawn of Human Culture Richard Klein localized this burst of humanity ~50,000 years ago in Africa, and hypothesized that it was triggered by a biological change which enabled language fluency. In The Humans Who Went Extinct Clive Finlayson posits that cultural changes associated with the Gravettian people in central Eurasia eventually defined what he meant to be human, and explained the marginalization of Neanderthals.

To a rough approximation I’m skeptical of both these models. I don’t think humanity emerged fully formed like Athena over the last 50,000 years. Rather, humanity we understand humanity is deeply primal, and a feature of the root of our lineage, millions of years in the past. If Homo erectus populations were still around they deserve all the rights of humans, despite their numerous differences.

I suspect that we’ll found out that ‘behavioral modernity’ is a cocktail of soft selection on standing variation and cumulative cultural change. But that doesn’t mean that the Pleistocene history of Europe is not important or interesting. And recently we’ve obtained enough ancient DNA to sketch out a general picture of demographic, if not cultural, change.

Everyone should read The genetic history of Ice Age Europe. But I suspect the impact is going to get deeper when more archaeologists are familiar with the implications. Here is the abstract:

Modern humans arrived in Europe ~45,000 years ago, but little is known about their genetic composition before the start of farming ~8,500 years ago. We analyze genome-wide data from 51 Eurasians from ~45,000-7,000 years ago. Over this time, the proportion of Neanderthal DNA decreased from 3–6% to around 2%, consistent with natural selection against Neanderthal variants in modern humans. Whereas the earliest modern humans in Europe did not contribute substantially to present-day Europeans, all individuals between ~37,000 and ~14,000 years ago descended from a single founder population which forms part of the ancestry of present-day Europeans. A ~35,000 year old individual from northwest Europe represents an early branch of this founder population which was then displaced across a broad region, before reappearing in southwest Europe during the Ice Age ~19,000 years ago. During the major warming period after ~14,000 years ago, a new genetic component related to present-day Near Easterners appears in Europe. These results document how population turnover and migration have been recurring themes of European pre-history.

I modified the model of demographic turnover to the left, adding labels for the primary paleoanthropological cultural groups. Instead of starting with the archaeology the authors let the genetic results guide them. What they discover is that there were roughly four turnovers in population defined by four “clusters”:

– the first Europeans who succeeded the Neanderthals, who seem to have left no descendents

– the Goyet cluster, associated with Aurignacians

– the Vestonice cluster is associated with the Gravettians

– the El Miron cluster with the Gravettians

– the Villabruna cluster with various late Pleistocene cultures, and is the direct ancestor of Mesolithic hunter-gatherers present in Europe when the first farmers arrived

A quick calculation suggests that very little of the ancestry of modern Europeans has deep roots across much of the continent going back to before the Last Glacial Maximum ~20,000 years ago. The “Pleistocene” ancestry of Europeans mostly derives from the last group, the Villabruna cluster. In the paper the authors note that this group is unique for several reasons:

– some individuals in this cluster have an affinity with East Asians (earlier Pleistocene groups do not)

– more universally, individuals in the Villabruna cluster have a notable affinity with Middle Eastern populations which was not evident in earlier Pleistocene clusters

Recall Middle Eastern populations can be modeled as a mix of a West Eurasian group similar to European hunter-gatherers, and, “Basal Eurasians,” who are an outgroup to all non-Africans (European hunter-gatherers to Oceanians to Amerindians!). The authors posit that the gene flow is more likely from the Middle East, because earlier European clusters have affinities with Villabruna, but they share nothing with the Middle East. The Villabruna cluster does not have Basal Eurasian ancestry though. So we might be looking at complex population structure.

Two general issues that crop up in this paper are sampling limitations and population expansions into Europe from the east. The disappearance of Goyet ancestry, only to reappear as part of the El Miron cluster, is curious. Perhaps the post-Goyet people occupied ecologies less likely to be fossilized? It reminds us of the resurgence of hunter-gatherer ancestry in Europe of the Middle Neolithic. As for why there seems to be an eastern bias into intrusive populations into Europe, these groups may simply have had a larger population, and so been more likely to avoid meta-population extinction events?

Finally, the authors point out that Gravettian culture in Siberia and Europe does not seem to be genetically related. This suggests that these people were very modern, because a hallmark of the modernity is that ideas can move between groups without too much genetic exchange.

Europe has the best coverage of ancient DNA. What we find here are repeated population turnovers and a lot of complexity and contingency. Is Europe peculiar? There is circumstantial evidence from modern DNA that Australians are descendants of first settlers. And to some extent this is also true in the case of East Asians if the work reported out of the Fu lab holds up. South Asians though are more likely to be like Europeans, and Middle Easterners show some of the same dynamics during the Holocene.

Open Thread, 08/27/2017

Filed under: Open Thread — Razib Khan @ 8:06 am
Razib & Dr. Ghulam Sarwar (1896-1996)

I showed my daughter a photo of my maternal grandfather yesterday. He was holding me in his lap. It’s probably about 1981, so he would have been about 85 years old then. I was his first grandchild, as he had a family late in life. He saw a lot of changes in his life. Born into the British Raj during the late Victorian period, he died when I was using the internet regularly to email friends and relatives.

In his home village they called him the “Goony Doctor”, as Ghani was part of his longer surname.

Restless Empire: China and the World Since 1750. Seems like an interesting and relevant book. On the other hand, we always have to keep in mind that China’s labor force peaked several years ago. The demographic pressures on China in the 21st century will probably always mean that it won’t exhibit the vigor of a nation like the United States of America during the baby boom.

Hurricane Harvey has been a big deal. In Central Texas we’ve been hunkering down, but it’s Houston that is in real danger. America’s 4th largest city.

Still soliciting sign ups for my newsletter. It’s more of a “hey Twitter has disappeared here is where I am on the web” notification system. Have only sent one mailing so far. Will increase frequency in future, but probably max once a month.

A lot of discussion on “science Twitter” about getting rid of GREs. Scientists are smart, but they don’t know everything. To understand ‘intelligence testing’ I recommend people read Intelligence: All That Matters or The Neuroscience of Intelligence. People throw around ideas like “GRE is culturally biased,” but cultural bias on testing is a whole topic with a specific meaning. That is, are the tests able to predict future performance on tasks to the same extent across groups?

I suspect that the GRE is on its way out though. Many scholars don’t support the shift, but they won’t say much in public lest they be attacked. Of course that will lead to greater emphasis on undergraduate school attended as well as the eminence of those giving recommendations.

August 26, 2017

The population genetic structure of Northeast Africa

The major frontier in the understanding of human population genetic structure in the next five years is going to be Africa. There are several reasons for this.

The ‘standard model’ of late has been that a group of humans left eastern Africa ~50,000 years ago, and swept across the world in one go. Though Africa itself was often an afterthought in that discussion, it now seems that there was a lot of demographic history that occurred after the “Out of Africa” event within Africa. Second, the whole picture outside of Africa and within Africa has been greatly complexified over the last decade.

The idea that modern humans, defined as the descendants of anatomically modern populations present in Africa ~100,000 years, only ventured out of the continent a bit before 50,000 years ago, is now rather shaky. There are several fossils from eastern Asia which seem older. But just as interestingly, there are Neanderthal genomic results from Altai populations which indicate an early admixture with an anatomically modern human population basal or almost basal to all extant groups. This means that this lineage is an outgroup to modern Africans and non-Africans, or, it was part of the original diversification of African lineages (one of which was the primary ancestor for non-Africans) ~200,000 years ago, give or take.

And that is the second major issue of complexification. Population structure within Africa, of both archaic and modern lineages, is going to be a major topic of interest. Just as non-Africans have admixture from highly diverged ‘archaic’ lineages (Neanderthals and Denisovans), some scholars have been arguing for years that Sub-Saharan Africans, especially those from “hunter-gatherer” lineages, have similar admixture. The most recent work seems to support the contention of very deep structure within Africa.

But much of this structure has been elided by the reality of the Bantu expansion. Starting 3,000 years ago a wave of agriculturalists from the environs of modern Cameroon pushed eastward and southward. Today the Bantu languages are dominant from the Gulf of Guinea to South Africa. This is a major problem in trying to understand the genetic variation which served as the context for the origin of modern humans, because the older structure has been overlain or replaced across much of its geographic extent. Though it is correct that modern Africans have the most genetic diversity one the whole, the between group diversity for Bantus is quite low, because they descend from a common population in the recent past.

But there are peoples within Africa who may preserve some of the ancestry of groups before the arrival of the Bantus. A new paper in PLOS GENETICS uses a very dense marker set to analyze Sudanese populations in particular. These groups are of interest because they seem reasonably distant from West Africans, but some of them do not have much Eurasian ancestry either. Like Mbuti Pygmies, or Kalahari Bushmen, they may therefore be one of the descendent groups from those which flourished within Africa when the ancestors of non-Africans left.

It’s called Northeast African genomic variation shaped by the continuity of indigenous groups and Eurasian migrations. It’s an uncorrected proof. Kind of like a preprint. So it may change. But here is the abstract:

…We investigate the population history of northeast Africa by genotyping ~3.9 million SNPs in 221 individuals from 18 populations sampled in Sudan and South Sudan and combine this data with published genome-wide data from surrounding areas. We find a strong genetic divide between the populations from the northeastern parts of the region (Nubians, central Arab populations, and the Beja) and populations towards the west and south (Nilotes, Darfur and Kordofan populations). This differentiation is mainly caused by a large Eurasian ancestry component of the northeast populations likely driven by migration of Middle Eastern groups followed by admixture that affected the local populations in a north-to-south succession of events. Genetic evidence points to an early admixture event in the Nubians, concurrent with historical contact between North Sudanese and Arab groups. We estimate the admixture in current-day Sudanese Arab populations to about 700 years ago, coinciding with the fall of Dongola in 1315/1316 AD, a wave of admixture that reached the Darfurian/Kordofanian populations some 400–200 years ago. In contrast to the northeastern populations, the current-day Nilotic populations from the south of the region display little or no admixture from Eurasian groups indicating long-term isolation and population continuity in these areas of northeast Africa.

The Eurasian admixture is well known. So not a big surprise. But I do think that this paper, like most, is somewhat biased toward detection of the most recent admixture event.

There are several Coptic samples in this data set. These individuals are descendants of recent migrants to the Sudan from Egypt. Because they are Christian, and resident in northern Sudan (I believe sampled in Khartoum), they are by necessity endogamous (marriage to a Muslim would have resulted in the result being raised as Muslim). It is no surprise that they are genetically similar to the Egyptian Muslim sample. But interestingly like the Egyptian Muslims they have a substantial minority of Nilotic Sub-Saharan African ancestry.

In much of the paper the admixture between Eurasian and Sudanic peoples is dated to after the rise of Islam. This is reasonable. For various reasons I am not totally clear on the emergence of Islam resulted in a far greater interconnectedness between Sub-Saharan Africa and North Africa & West Asia. But as non-Muslims Egyptian Christians, Copts, would not be part of the genetic admixture which slavery produced across the Middle East. Non-Muslim minorities tend to be rather less cosmopolitan than their Muslim neighbors. Perhaps the situation was different in Egypt, with Copts being a majority up until 1000 A.D. But, another factor may be that there were older pulses of admixture dating back to antiquity which the LD decay methods are missing (notice that Egyptians have West African ancestry which Copts lack).

The second major issue in this paper is that some groups, such as the Nuer, show no evidence of Eurasian admixture. This is not true of all Nilotic peoples. The Masai of Kenya for example have clear Eurasian admixture. But if indisputably Nilotic groups in southern Sudan lack it, it suggests that this occurred in East Africa due to mixing with Cushitic groups, some of whom, such as the Somalis, are also pastoralists.

Remember that Khoisan in southern Africa have Eurasian ancestry through the migration of Nilotic pastoralists. And yet somehow the Nilotic peoples of the Sudan, who have lived near to Cushitic and Semitic peoples with copious Eurasian admixture, lack that element. Similarly, the Bantus swept from Cameroon to the highlands of South African in 1,300 years, but were totally ineffectual at penetrating the Sudd. What this illustrates is that when it comes to human gene flow simple considerations of distance “as the crow flies” is not so important in many cases. Rather, cultures occupy territory in a geographically patchy manner, constrained by ecology and local human geography.

This reiterates the likely importance of ancient DNA in understanding African prehistory, and therefore, the prehistory of humankind as a whole.

Citation: Hollfelder N, Schlebusch CM, Günther T, Babiker H, Hassan HY, Jakobsson M (2017) Northeast African genomic variation shaped by the continuity of indigenous groups and Eurasian migrations. PLoS Genet 13(8): e1006976. https://doi.org/10.1371/journal.pgen.1006976


August 25, 2017

The less intelligent and uneducated really don’t tolerate unpopular views

Filed under: Free Speech,GSS — Razib Khan @ 7:10 am

When looking at the General Social Survey one of the most striking things is how much more the more educated and intelligent are in terms of accepting unpopular views. Since 2008 and the SPKMSLM variable has asked about anti-American hatred preached by Muslim clerics in the United States:

… consider a Muslim clergyman who preaches hatred of the United States.

If such a person wanted to make a speech in your community preaching hatred of the United States, should he be allowed to speak, or not?

The ideological breakdown is what you’d expect it to me, and tolerance for this sort of speech is low, at about 40% of Americans.


In case you are wondering, the impact of intelligence still matters after you correct for education. I ran a quick & dirty logistic regression, and you can see that below (in case you care, being a woman is associated with less tolerance for free speech here, and political ideology doesn’t matter much once you take into account religiosity):

Most liberals and smart people want racists to be allowed to speak

Filed under: GSS — Razib Khan @ 12:44 am

Over the past year or so there have been many worries that liberals are backing off from their support for free speech. Even mainstream figures such as Howard Dean have started to chant the mantra “hate speech is not free speech”. And then you have op-eds from professors such as When ‘free speech’ becomes a political weapon.

But whenever I look at the General Social Survey I see no great change in support for free speech in terms of the patterns. Perhaps something has changed in the year 2017, but I think what we are seeing are vocal and motivated minorities who are drowning out liberal (in the classical sense) majorities.

The GSS has a variable, SPKRAC, which asks:

…consider a person who believes that Blacks are genetically inferior. a. If such a person wanted to make a speech in your community claiming that Blacks are inferior, should he be allowed to speak, or not?

The plot at the top of this posts shows that the GSS sample respondents exhibit almost no change year to year on this question.

The GSS also has a variable, SPKMSLM, which asks:

Now consider a Muslim clergyman who preaches hatred of the United States.

If such a person wanted to make a speech in your community preaching hatred of the United States, should he be allowed to speak, or not?

This question has been asked since 2008, and only a minority would allow this person to speak, 41-43 percent.

Let’s break this down by ideology and intelligence from the year 2008 onward. The GSS has a variable, WORDSUM, which is a vocabulary test. Respondents receive a score from 0 to 10 (correct). I combined 0-4 as “not smart”, 5-6 as “average”, 7-8 as “above average,” and finally 9-10 as “smart.”

Also I limited the sample to non-Hispanic whites to compare “peaches to peaches.”

What the above plot shows is that liberals support free speech for both racists and Muslim radicals. Conservatives are more skeptical of free speech for both groups, but especially the Muslims. You might be curious why moderates seem so skeptical of free speech. That’s because on average moderates are less intelligent than people at the ideological poles, and the less intelligent are generally less supportive of heterodox speech (I suspect it’s because they are too dumb ever to come up with an original and transgressive idea).

But don’t take my word for it.


It’s a very robust pattern that the less intelligent are skeptical of deviant thought. I think it’s partly because they can’t empathize since they don’t have many thoughts.

Below is a table which does a cross-tab of views on speech for racists and Muslims (again, for non-Hispanic whites after the year 2008). You can see ideological and intelligence distribution for various positions. Conservative anti-Islamic and liberal philo-Muslim tendencies are on display. The less intelligent are overrepresented among the censorious.

  Extremely liberal Liberal Slightly liberal Moderate Slightly conserv Conserv Extremely conserv
Full sample 4 12 10 36 16 18 4
Allow both to speak 5 15 12 32 15 17 4
Allow Muslim to speak, not racist 7 18 15 32 15 12 2
Allow racist to speak, not Muslim 2 9 8 39 15 22 5
Ban both from speaking 2 9 9 42 13 21 5
  Not smart Average Above average Smart      
Full sample 13 40 33 13      
Allow both to speak 7 34 39 20      
Allow Muslim to speak, not racist 6 40 40 13      
Allow racist to speak, not Muslim 19 46 26 9      
Ban both from speaking 14 48 34 4    

August 24, 2017

Pain 100% hot sauce; 1000% pain!

Filed under: Hot Sauce — Razib Khan @ 8:53 pm

While I was up in Missouri chasing the eclipse I met up with a long-time reader of this weblog. He was kind enough to gift me with several hot sauces. So I took the Pain 100% Hot Sauce into the office, and the verdict is that this is a very spicy sauce indeed (grown men running to the fridge!).

It’s somewhat curious, because the label says that it has habanero pepper. Not some crazy scorpion or bhut jolokia. Going by the ingredient label list there’s no way that Pain 100% should be as hot as Rapture, but it is.

How can this be? I’d say it has to do with simplicity. The Rapture has a relatively subtle and complex flavor profile. It’s a ninja, silent and deadly. In contrast Pain 100% comes at you straight-up like a samurai; a strong kick of salt quickly fades, and the simple but potent spicy builds up within a minute and starts pounding at your palette..

Pain 100% is very spicy and simple. It’s the meat & potatoes of hot sauce. You know what you’re going to get, and you can describe the taste in a few sentences.

Give us your huddled scientists, yearning to innovate free

Filed under: Humanities — Razib Khan @ 8:21 pm

In regards to immigration policy I generally favor a shift toward the Anglo-Canadian solution: a points based system. From what I am to understand the immigration reforms proposed by Tom Cotton are dead on arrival in the Senate, but I think they are a step in the right direction. Representative democratic nation-states can adapt and evolve, but they are not stable with lots of demographic change.

A contrasting strategy would be to allow guest workers to arrive without extensive screening, but ban them from all the right (and duties) of citizenship. Imagine something like the ancient Athenian system with metics. Unfortunately for various psychological and cultural reasons this sort of system, with large number of second class individuals, doesn’t seem to be palatable today in the West (it is what you see in the Persian Gulf). A nation-state simply isn’t reducible to a system for mediating economic transactions between consenting adults.

If we are going to have a points system we need to think about what we prioritize in potential migrants. Recently on Twitter the prominent public intellectual and astrophysicist Sean Carroll expressed this opinion:

The idea that a science degree should count more than a humanities degree toward being allowed to immigrate is dopey. -Signed, a scientist.

As of this writing that tweet received 150+ retweets and 500+ likes. It’s a popular view. I also disagree with it. That is, I think those with legitimate STEM educational and professional backgrounds should definitely get preference over those with non-STEM backgrounds, and in particular those with humanities degrees. There are two primary reasons I will give for this.

First, STEM degrees confers upon the degree holder culture-neutral portable skills. My cousins who complete a degree in engineering often work abroad, usually in the Persian Gulf, in the occupational roles they were trained for. In contrast, those who studied Bengali literature have fewer options. Often they find menial work in the Persian Gulf, because their educational background is totally uninteresting to people doing the hiring outside of Bangladesh.

The example I used on Twitter made the contrast stark: a Saudi trained in chemical engineering has useful skills that transfer to the United States. A Saudi trained in Islamic studies, which is equivalent to humanities, has fewer transferrable skills. A non-Muslim analogy would be an Israeli with a technical degree from a secular institution, as opposed to a Haredi Jew who was steeped in Torah-learning from a prominent Yeshiva.

Second, in much of the developing world the stronger students pursue STEM as opposed to ‘softer’ disciplines. Therefore, having a degree in STEM is a good proxy for cognitive skills more generally. In Race And Culture: A World View Thomas Sowell points out that in Sri Lanka Tamils tended to be over-represented in STEM in comparison to the majority Sinhalese, resulting in resentment due to greater representation in professions such as medicine and engineering.

In the United States humanities graduates do relatively well, especially compared to some pre-professional majors. But a lot of this has to do with the fact that humanities degrees are emphasized at very selective and prestigious universities. Many of these institutions serve as finishing schools for the American elite, and these students are not focused on their immediate economic prospects because they intend to pursue post-graduate work (e.g., law school), or their social connections will probably suffice to land them good positions (also, affluent students can afford years of unpaid internships to position themselves).

Finally, an observation about the humanities. I think they are important. Knowing history and literature important. They are common touchstones that bind us, give richness and meaning to our lives. There is also variation in the humanities. People trained in analytic philosophy do learn genuinely portable skills in relation to analysis and decomposition of problems. In contrast, the majors influenced by Critical Theory produce ideological parrots.

When I was in college a religious studies graduate student once told me that having a background in the humanities was useful in the business world because you could talk to people about things and make yourself interesting. That is true, but I have a background in biochemistry and genetics and I have no problem in making myself interesting to talk to. All you need to do is read a lot, and I do do that.

Scientifically trained individuals would benefit from reading more widely in other disciplines. Scientists tend to be especially blind to the domain specificity of their ability to analyze and decompose problems, because their tools within-field are so powerful.

But that is neither here nor there when it comes to immigration. Ultimately it’s about values, and your vision for what your society should be. If we are going to limit immigration, and it seems like we will, then I believe that filtering for the “best and the brightest” is optimal, because these individuals, particular in STEM, will be innovators who generate positive externalities by ramping up productivity.

Addendum: Some people extoll the ability of the liberal arts to broaden your horizons and thinking critically about a wide variety of issues. My personal experience is that most people who study liberal arts are lazy, and the smart ones are pretty good at writing beautiful dense essays in short bursts. There are exceptions. People who go to “Great Books” schools, like St. John’s, for example, seem to exemplify what a liberal arts education should be about. But they are exceptions.

Android vs. iPhone

Filed under: Technology — Razib Khan @ 6:50 am

I’m thinking of updating the Samsung S8. But I’m getting some pressure at work to wait for an iPhone 8. In general I’m skeptical of the whole Apple ecosystem, but it isn’t as if good Android phones are cheap.

Any thoughts from readers who have switched back and forth?

Arab Islamic science was not Arab Islamic

Filed under: Islam — Razib Khan @ 6:43 am

Someone stupid who follows me on Twitter said “It seems @razibkhan forgot the Arabs gave us algebra and many other scientific/mathematical advances.” The history of algebra is actually somewhat more antique than the Arabs, as outlined in Unknown Quantity: A Real and Imaginary History of Algebra. But the origin of the word is Arabic. From Wikipedia:

The word algebra comes from the Arabic الجبر (al-jabr lit. “the reunion of broken parts”) from the title of the book Ilm al-jabr wa’l-muḳābala by Persian mathematician and astronomer al-Khwarizmi.

Though Wikipedia says that al-Khwarizmi is Persian, it is more accurate to say he was Iranian, because as his name attests his origins were in Khwarezm, which is in Central Asia. It is accurate to say that Arab Islamic civilization was intellectually productive in the centuries before 1000 A.D., but it is not accurate to say that Muslim Arab scholars were responsible for this.

A huge number of these scholars were not ethnic Arabs. In the early years a substantial number were not Muslim. Though it is often said that many were Persian, as recounted in Lost Enlightenment many of the “Persians” were not from Persia proper, but from Iranian regions of Central Asia which over the centuries have now become Turkified.

Why is this important? The multicultural nature of early Muslim (and later Ottoman) polities might inform us as to the future of this sort of diverse society. Second, it’s preferable that you don’t seem like an idiot if you want me to listen to anything you say.

August 22, 2017

Bringing back street kids

Filed under: Culture — Razib Khan @ 7:07 am

Just spent some time with a friend. He lives in a safe neighborhood, so I asked if there were any kids for his kids (they’re young) to play with. Apparently not really.

In this country today we have problems with racial and wealth inequality. There are huge debates about how we address these issues. And they don’t seem like they are going away any time soon.

But huge numbers of Americans adults grew up on the mean streets of the 1980s. We know there is a solution to childhood social isolation, because many of us grew up playing on streets, rather than being shepherded on ‘play dates.’ This is also an issue which most people agree on as a problem. We can solve this.

August 21, 2017

Totality, 2017

Filed under: Eclipse — Razib Khan @ 9:41 pm

We saw totality in Independence, Missouri. It was a pretty long car trip with the kids, all of whom are under school age (though just barely in the case of the eldest). We had a big fright because there was a massive thunderstorm in the morning…but it cleared out for a few hours. And that was when the total eclipse occurred.

Really words don’t do the experience justice.

Chase a total eclipse if you get a chance.

August 20, 2017

Open Thread, 08/20/27

Filed under: Open Thread — Razib Khan @ 4:46 pm

I’ve been off the map for a bit because I’m eclipse chasing. #TotalityOrBust as they say. The whole family has been converging on zone of totality, and now we’re there. Obviously I’m excited.

There are lots of things going on in the world. One thing though that I’m beginning to think is that people would benefit reading more cognition science. I know I certainly did years ago. The main issue is that we’re not rational in the way we think we’re rational, and that leads to a lot of confusions why other people behave the way they do. Check out Enigma of Reason (I came upon a lot of this literature through the study of the cognition of religion).

Complex Patterns of Admixture across the Indonesian Archipelago. Someone who knows archaeology should read this….

The genetic history of Ice Age Europe. This was published last year. But it should be re-read. Closely.

August 16, 2017

Blogging on an island as opposed to an archipelago

Filed under: Blog — Razib Khan @ 10:17 pm

On a Twitter conversation it came up yesterday that a lot of people know each other from blogging in the 2000s. It was a different world back then, and the pond was much smaller. To my knowledge Derek Lowe is the only continuously active science blogger who has been at this longer than me (there are some, such as Dave Appell, who began blogging before me, but stopped for a while before starting up again). I’ve seen a lot of changes. Some good. Some perhaps not so good.

One major aspect is that blogging is no longer a conversation with many nodes. Rather, it’s a platform for individuals or networks to speak to their particular audience. I’m obviously part of this. I don’t subscribe to many blogs in my RSS feed. Basically I use Twitter to find blog posts. There are a few blogs I subscribe to, like Why Evolution Is True, but mostly I just wait until content shows up in my timeline.

And I’m not the only one. I have Google Analytics that go back very far. Below are referrals by site for equivalent periods in 2007, 2012, and 2017. I’ve standardized the top referral source (in pageviews) to 100.

2017, June – Aug
1 twitter 100
2 mobile facebook 38
3 unz.com 36
4 facebook 33
5 feedly.com 20
6 slatestarcodex.com 19
7 razib.com 11
8 brownpundits.com 9
9 eurogenes.blogspot.com 9
10 vox.com 6
2012, June – Aug
1 reddit.com 100
2 stumbleupon.com 60
3 facebook.com 49
4 scienceblogs.com 34
5 gnxp.com 31
6 fark.com 31
7 pulsenews 21
8 twitter 13
9 digg.com 12
10 isteve.blogspot.com 10
2007, June – Aug
1 digg.com 100
2 reddit.com 38
3 slashdot.org 20
4 isteve.com 19
5 stumbleupon.com 17
6 scienceblogs.com 11
7 dilbertblog.typepad.com 6
8 instapundit.com 4
9 del.icio.us 4
10 buzzfeed.com 3

I removed stuff like organic Google search, which I get a fair amount of. Additionally, I bolded all the sites where I am somehow involved in driving the traffic. So in 2017 I bolded Twitter because I have a big Twitter footprint that drives a lot of the traffic. I did not bold Facebook because I don’t use Facebook much to promote this website. Other people are sharing my posts. I separated mobile and non-mobile Facebook to show you that in 2017 mobile really matters.

You can see that over the years I’ve had to drive more and more of the traffic. I never posted my posts to Reddit. But for Twitter I push all my own content.

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