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000e553e_medium In 2007 a friend told me of an encounter at a seminar where L. L. Cavalli-Sforza seem to offer agriculture almost reflexively as a solution to the conundrum of signals of positive selection in the genome of humans. Basically, all paths led to agriculture. I have to say that nearly ten years later Cavalli-Sforza’s deep intuition on these issues seems to be vindicated. Agriculture was an enormously big deal.

Carl Zimmer in The New York Times has a write up of Matheison et al. (it’s in Nature), Agriculture Linked to DNA Changes in Ancient Europe. There aren’t a whole lot of surprises, as the pre-print has been around for a year or so. But, having the work written up in a newspaper allows researchers to engage in some extemporaneous speculation. Ergo, you have:

Why? Scientists have long thought that light skin helped capture more vitamin D in sunlight at high latitudes. But early hunter-gatherers managed well with dark skin. Dr. Reich suggests that they got enough vitamin D in the meat they caught.

He hypothesizes that it was the shift to agriculture, which reduced the intake of vitamin D, that may have triggered a change in skin color.

This was to some extent Cavalli-Sforza’s idea, and I’ve proposed it as well. Then there is the model of sexual selection. These theories aren’t always exclusive, and pigmentation may have multi-causal underpinnings. It is very interesting that the best methods and ancient DNA seem to be suggesting lots of very recent change and likely adaptation. But ultimately, we still have no clear idea.

• Category: Science • Tags: Ancient DNA, Genetics

51DPT3AYDHL._SX321_BO1,204,203,200_ People like to quote Martin Luther King Jr., “The arc of the moral universe is long, but it bends towards justice.” This includes the president of the United States of America, arguably the most powerful non-plutocrat in the world. But after reading Frank McLynn’s biographies of Marcus Aurelius and Genghis Khan, I wonder if anyone actually bothers to read history when they say something that is so facile. Now, I agree that the trend does move toward one direction. Over the past 3,000 years the institution of slavery has gone from being a banal practice, to a necessary evil (e.g., as in Islam), to a taboo practice. But the phrase is often bandied about as if moral directionality is fine-grained on the scale of a generation or two, rather than on the scale of centuries or more. For all Marcus Aurelius’ strangeness in comparison to moderns, Genghis Khan was clearly more a figure who would fit in in a pre-Axial world.

In Genghis Khan: His Conquests, His Empire, His Legacy the author mentions legends that the “original” Mongols were a fair skinned and haired, eventually becoming more typically East Asian in appearance through admixture. There are some accounts where Temujin, who became Genghis Khan, had reddish hair. I note that Mongolian people seem to have a small proportion of West Eurasian admixture. My earlier assumption had been that this was recent (from Russians), but now I wonder if this is old. I note that if you look at the phylogeographic literature there is a lot of R1a1a in parts of East Asia. Among the Uyghurs, Altaic people, and to a lesser extent Mongolian groups. The Indo-Iranian modal R1a1a haplotype, Z93, is found among the Altaic people. My supposition at this point is that it may be that Christopher Beckwith’s argument in Empires of the Silk Road that Indo-Europeans were more influential on the eastern fringe of the Eurasian steppe than we may think.

Speaking of East Asia, and specifically China, a question came up on Twitter as to when it joined the rest of the World Island’s oikoumene. Though there were influences from the West at an early period (probably mediated by Indo-Europeans), I believe that the establishment of the Protectorate of the Western Regions around ~0 A.D. probably is a good early date. By the Tang dynasty China was clearly part of the “human web,” but by the first few centuries A.D. Buddhism and Roman merchants had already arrived through Central Asia.

The 2006 paper, Possible Ancestral Structure in Human Populations. Strange that it has only has 149 citations. I recently talked to Mike Hammer about the reception to these ideas in the mid-2000s, and he agrees with my recollection that they were totally marginalized and laugh out of the room back then.

Someone asked last week about a reader poll. I did one about a year ago. You can download and Excel file here of results.

galaxy-s6-edge_gallery_front_black In response to this question about writing, I don’t know if there is a most “complicated” writing system. I assume that Chinese is arguably more complicated since it takes longer for children to attain a high level of literacy. I don’t think it changes general fluid intelligence, though it probably has an effect on crystallized intelligence.

Response to this question, start here.

So I got a Samsung Galaxy S6 Edge. My previous phone decided that its sound was going to stop working while I was traveling on business. I don’t make regular phone calls often, but when I do, I like to be able to hear what the person on the other end says! This wasn’t a hardware issue, but a software problem, probably due to an app I downloaded. After wasting a few hours trying to get it working (it worked at one point, but then when I rebooted the problem cropped up again), I ended up just calling my provider to get a new phone for when I was back home.

As I’m a rebel from the hegemonic Apple ecosystem (now that I don’t use an iPod shuffle I don’t use any Apple products), I plunked down for the Edge. I have to say I’m pleased so far, though it does get annoying that some of these phones have so many features that I waste an hour or two just watching “tips & tricks” tutorials.

Recently I encountered the idea that the popularity of the “trans-Atlantic accent” in the 1930s and 1940s might have been due to the utility of this clipped and highly enunciated way of speaking when radio quality was low. Well, voice recognition today on these phones makes me wish I spoke with the trans-Atlantic accent….

Finally, Jerry Z Muller followed me on Twitter! It’s a personal “big deal” for me because his anthology, Conservatism: An Anthology of Social and Political Thought From David Hume to the Present, was very influential in my own thinking back in the late 1990s.

• Category: Miscellaneous • Tags: Open Thread

UltrasSoc_cover_epub A while back I promoted Joe Henrich’s The Secret of Our Success: How Culture Is Driving Human Evolution, Domesticating Our Species, and Making Us Smarter. I did finish Frank McLynn’s Genghis Khan book, and am re-reading his Marcus Aurelius biography. There will be a review of the first book coming out soon, but I will tease here that unlike Tyler Cowen I don’t think it would come close to being the best book of the year (in part, because unlike many readers I know a fair amount about the topic). I also have a copy of Mary Beard’s SPQR: A History of Rome, and someday really need to get to Dehaene’s Consciousness and the Brain: Deciphering How the Brain Codes Our Thoughts

But here’s another must read, Peter Turchin’s Ultrasociety: How 10,000 Years of War Made Humans the Greatest Cooperators on Earth. This seems like an excellent complement to Ian Morris’ War! What Is It Good For?: Conflict and the Progress of Civilization from Primates to Robots, which I have not managed to get to read, in part because I want to hit Foragers, Farmers, and Fossil Fuels: How Human Values Evolve. Yet I’ve read a fair number of Peter’s books (see my 10 questions for him), so I’ll probably be moving this up the stack.

Peter is a serious thinker, and human social complexity and cooperation is an important, and unresolved topic (I am not as sanguine or flip on this David Sloan Wilson). Currently only the Kindle edition is available, but Peter says that the “dead-tree” version should be available in the next few days.

(note, I have to read The Hive Mind!)

Addendum: Here’s Peter’s post on the book….



ncomms9912-f2 Over the past few years we have seen ancient DNA researchers “carve nature at its joints” when it comes to the paleohistory of Europe after the end of the last Ice Age. In relation to this historical reconstruction we aren’t at the end of the road, but I do think that the terminus is within sight. There are only so many populations one can sample, and so many statistical constructs one can posit, before one is on the plateau of diminishing marginal returns. For example, the model of Holocene Europe being a synthesis of two very distinctive populations which merged after the last Ice Age was too simple. A model with three populations is sufficient for the vast majority of European groups. Though in these sorts of situations more complex models may be consistent with the results, the bias is to go with parsimony, and attempt some alignment with linguistic and archaeological evidence.

A new paper in Nature Communications, Upper Palaeolithic genomes reveal deep roots of modern Eurasians, fills in some gaps in the broader picture. The figure at the top of this post illustrates the modification that these authors made to the schematic of Lazaridis et al. Iosif Lazaridis himself as weighed in on Twitter:

CHG = Caucasian hunter-gatherers. More specifically, the authors of this paper analyze two subfossils from Georgia dated to ~10 to ~13 thousand years, Kotias and Satsurblia. Kotias, at ~15x coverage (that is, each position is sampled ~15 times, so you have a good sense of variation at any given position), is particularly useful. What they found is as Lazaridis reports above: CHG seem one of the primordial groups to give rise to the extant variation of modern Europeans, and Western Eurasians writ large.

The rough stylized history of the non-African populations is as such: a “basal Eurasian” (bEu) population separates off first, and then west and east Eurasians diverge, and then in the west there is a divergence between the ancestors of western hunter-gatherers (WHG) and ancient north Eurasians (ANE). The early European farmers (EEF) are compounds between WHG and bEu, with a slight bias toward WHG. The Anatolian farmers were also admixed, though biased toward bEu. The eastern hunter-gatherers (EHG) are a balanced mix between WHG and ANE, and this group fused with the CHG to give rise to Yamnaya. This brings up the question: are CHG the basal Eurasians? I doubt it. The paleodemography of the ancient Near East has been barely elucidated. It seems likely that CHG, like the Anatolian farmers, are a compound of some sort. Basal Eurasians may manifest as an allele frequency spectrum across the Middle East during this period, the remnants of a back migration from west Eurasian groups mixing with the ur-Basal Eurasians, who were the first to split off from the Out of Africa migration. In the colder and drier world of the Last Glacial Maximum (LGM) it seems likely that some of the northern hunter-gatherer populations would move into territory occupied by basal Middle Eastern groups. In addition, the Sahara had periods of extreme dryness during the Ice Age, so the ur-basal Eurasians wouldn’t necessarily have been able to withdraw to Africa.

Using G-PhoCS they inferred separation dates between the various populations. I have two issues with this. First, their mutation rate seems likely, but there is still some debate about the exact value and whether it is constant across a lineage (for this level of phylogenetic distance the assumption of constancy seems valid). Second, the confidence intervals from these results are huge. The authors report the results, and tentatively attempt to relate separation to the LGM ~20 thousand years before the present, but know that they can’t assert anything robustly. It strikes me that we know the sequence of separations between the groups better than the period of separations.

ncomms9912-f4 But one definite result is the pattern of ancestry (or shared drift) which is derived from CHG. It is high in the Caucasus, as one would expect, but also in South Asia. This is not surprising. Several papers have suggested that the West Eurasian admixture into South Asians seems to have an affinity with northern West Asians. Agriculture in South Asia began at Mehrgarh with a traditional West Asian cultural toolkit, and likely the character of the ANI-ASI admixture took root here. In Europe many researchers believe that the replacement of the hunter-gather populations in most areas was rather complete after the initial admixture event that occurred when farmers initially entered the continent, and it seems possible that the same is true in South Asia as well. There are no “Ancestral South Indians” in pure form left, and the variation in ancestry between tribes and caste groups in many areas is not very large.

dstat When you into the supplements though it all becomes much clearer. To the left you see a table of D-statistics, where the left column are Indian populations, and in the right column are the top hits, X, for these groups in terms of inferred gene flow with the tree form (Yoruba, X; Onge, Indian population). The key thing to note is that while some Indian groups have the strongest hit from the Kotias CHG sample, others, and of note the North Indian Brahmin Tiwari community, the signal from the Afanasevo is strongest. The Afanasevo are genetically basically the eastern extension of the Yamnaya. In other words, the D-statistics are showing evidence of a migration from the steppe, and a migration from West Asia. This also makes sense of supplementary figure 3, which shows non-trivial shared drift among some South Asian groups with the Swiss Bichon WHG sample. The Afanasevo would have brought this via their EHG ancestry, which was about half similar to WGH.

The evidence from uniparental (Y and mtDNA) and functional genes is also interesting. CHG carry mtDNA haplogroups H13 and K3, and Y chromosomal groups J and J2. It seems likely that the prevalence of haplogroup in H is due to post-Neolithic population replacements. The CHG contribute about half the ancestry to Yamnaya, but these two did not have haplogroup R1a or R1b. Haplogroup J2 is particularly common among caste groups in South India. All this points to the likelihood that the Dravidian languages are probably derived from agriculturalists with West Asian roots, and gives a touch more plausibility to the idea that ancient Elamite in Khuzistan may have been a distant relative of Dravidian.

Additionally, the derived light-skin variant of SLC24A5 is found among the CHG, as it is among the Anatolian farmers. The haplotype is the common one found in West and South Eurasian populations. The variant for SLC45A2 in Kotias is definitely homozygous for the ancestral variant. On the whole most South Asians do not share European light-skin variants except for SLC24A5. The exceptions tend to be groups in the Northwest, and upper castes. Exactly the same groups which likely have the strongest Afanasevo stamp.

One thing the authors note is that the Caucasus themselves have been subject to great change. It is clear that a farmer group related to EEF has mixed with the CHG descended groups. And, today the Caucasus has very high fractions of ANE ancestry in some groups, but these samples did not at all. At ASHG a few years ago a prominent population geneticist offered to me that he thought ANE might not have been the best term, as there was no strong evidence that this group wasn’t more common elsewhere. But CHG did not have ANE ancestry, despite that being very salient in modern trans-Caucasian groups. This suggests a later expansion and mixing event. From what I know ANE drift is not evident in many Indian populations, pegging the arrival of ANE-bearing groups to a later period after agriculture. Gene flow into Amerindian groups, and high ANE fractions in Central Siberia and the Altai, do point to their locus of habitation in Northern Eurasia.

Finally, let’s remember that we’re constructing the past from the slim remains which we have on hand. Ten years ago we were using extant genetic variation, because that’s all we had, and that led us astray. In the broadest sketches the inferences were right, but in many details they were misleading. Similarly, we shouldn’t think that the ancient DNA yielding populations are necessarily the direct ancestors of any modern groups. We know, for example, that Ma’lta is actually not ancestral to the ANE population which contributed to both Europeans via the EHG and Native Americans. The ANE drift of these two groups has more in common than with Ma’lta. Like the ancient Ethiopian genome there are many interesting conclusions one can derive from novel results, but to the first carving of nature’s joints is not always the best.

• Category: History, Science • Tags: Ancient DNA, Genomics

I’ve been traveling on business this weekend.

• Category: Miscellaneous • Tags: Open Thread

51jFjmwJ3SL._SX317_BO1,204,203,200_ Several weeks ago I found out that the historian Lisa Jardine had died. This saddened me, as I have appreciated Jardine’s works. In particular two works stand out in my mind. Worldly Goods, which I read when I was 18, and which helped me to understand that there was a different sort of history from the standard one written by diplomats and taught in elementary schools, and Going Dutch: How England Plundered Holland’s Glory.

The subtitle for the second work is in my opinion somewhat misrepresentative of what the tone of the book is, from what I recall. That being said, Going Dutch does impart to one a sense of the menace which was threaded through the symbiotic and antagonistic relationship between these two similar Protestant North Sea nations. And, while the 17th century is recalled as the period when England rose and Holland fell as great imperial mercantile polities, Lisa Jardine’s narrative does highlight that the so called Glorious Revolution was implemented with more of a Dutch fist than is commonly recalled.

• Category: History • Tags: Lisa Jardine

Abdullah Öcalan

The Middle East is complex. I tried to get at that with my post The Islamic State Is Right About Some Things. Of late I have noticed the peculiar tendency toward soft-tinted reportage of the PKK-affiliated YPG and the nature of life in Rojava. Typical of what you see in the American media is this piece, On the Road in Syria, Struggle All Around (here is a more gritty take, Fried Chicken and Skulls of ISIS Fighters in The Daily Beast). Scott Atran, author of one of my favorite books, was actually in northern Iraq in Kurdish areas last year during an offensive against ISIS, and he reported (on his Facebook) first-hand the gratitude that the Yezidis in refugee camps felt toward the YPG militias, who saved them at great risk to their own lives when the Iraqi peshmerga fled and left them for dead. It’s not just propaganda, the YPG does care about Kurds and minorities to further their goals. They have Asabiyyah. So does ISIS. So does Hezbollah. The Alawites with their backs against the wall supporting the Assad regime probably have it as a matter of survival at this point. Most of our “allies” on the ground in Syria and Iraq, not so much.

Today we are reading that the coordinated push to retake the road supplying Mosul that goes through Sinjar seems to be a success, at least for now. But even this glowing report can’t suppress the reality that there are tensions between the various Kurdish factions. This will likely cause issues in the future, but it is also important to look back to the past. The PKK is basically an extension of the ideas of the imprisoned Kurdish nationalist, Abdullah Öcalan. In the context of the Middle East Öcalan is a genuinely heterodox figure. He began as a Marxist-Leninist, and to this day remains an atheist. But today his movement seems to promote some sort of Left-wing anarchism. The PKK has a long history in Turkey, and has been labelled as a terrorist group, not without some reason, though one can admit these designations are to a great extent political acts.

Though the YPG units are clearly on the side of justice, it is important to remind ourselves that the point of comparison here is ISIS. Even conservative Arab villagers with no sympathy toward Kurdish nationalism and suspicious of the aggressive secularism and gender-egalitarianism of the YPG units and seem to be welcoming them as liberators. For now. There is a history of Left-wing anarchist Utopian movements, and it does not terminate in an “end of history”, where all is sugar plums and good-fairies.

The Obama administration is catching a lot of flack for its handling of the crisis in the Middle East. There are liberal internationalists offering their critiques, and of course the whole American conservative establishment is chronicling every misstep. Some Europeans are even trying to point the finger at the American lack of intervention in the Syria war as the reason for their refugee crisis. Many of these criticisms have some validity. But they always seem to presuppose that their alternative solutions would be like magic fairy dust, and render the whole morass soluble. The fact is that this may be one of those scenarios where the world is going to muddle on for years, and there is no obvious solution. Fifteen years ago the George W. Bush administration decided to take an “all-in” approach, and go big. How did that exactly work out? I for one am not happy with the American policy in the Middle East. But I’m also terrified about the negative consequences for our nation, and the world, of too aggressive a stance which overplays our hand and explodes in our faces.

As a practical matter the Kurds in Syria and Iraq are our allies. The government of Turkey will never abide by that. I support Kurdish self-determination, but the idea that the YPG will enact a regime of of non-sectarian anarchistic amity when it is ascendant is a total fantasy. There are no good choices, and there are no angels. We are united by the devil before us, ISIS. That is all that is clear to me.

• Category: Foreign Policy • Tags: Middle East

onliberty At this point you have heard about the controversies at Yale and Missouri. If you haven’t, just Google it. Among liberals there has been some debate and soul searching about the value of free speech, and its diminishing status as inviolate among youth. Jon Chait has a pretty thorough take over at New York Magazine. You can follow links to the arguments of those who contextualize and apologize for the more Maoist of the protesters to “get the other side.”

Since I support free speech, offensive speech, and engage in a fair amount of offensive speech, obviously I have a reflex to side with Chait on principle. Additionally, I’m a conservative who finds intra-Left/liberal conflicts pretty interesting and delicious. Finally, I don’t think that America is horribly racist, nor do I think institutionalized racism is a huge problem on campus (and perhaps not so much outside of campus, at least insofar as policy can and should address it), and, I don’t think that much consideration should be given to “marginalized populations” in terms of being particularly sensitive or apologizing for them (there is a whole lexicon which has cropped upon the Left which has a lot of meaning within-group, but is useless when attempting to communicate out-group; I reject the legitimacy of the terms of the debate as it is presented by many on the Left and liberals).

711zuJb66HL In my more cynical moments I’ve stated that we need to stick a fork in John Stuart Mill, and the idea of a free exchange of ideas. The Left has started to go full Marcuse, to the point where even the language used by conservatives is deemed illegitimate. Yes, there are liberals who attempt to enforce the old rules of tolerance of vigorous dissent, but at the end of the day there’s not much broader policy daylight between the two campus, so will they stand up for unpopular views when push comes to shove? The best bet then would be to join in the animal-battle for the authoritarian state of yore as it comes back to life. Kill or be killed, while the libertarians keep shouting “can’t we just get along?!?!?!”

But my old standby is what do the data say? Back when “trigger warnings” were in the news I noticed that there was a question in the general social survey about the removal of library books. There is a variable LIBMSLM which asks about an “anti-American Muslim clergymen’s book”:

If some people in your community suggested that a book he wrote which preaches hatred of the United States should be taken out of your public library, would you favor removing this book, or not.

There are also similar questions about anti-religious books, militarist books, a book promoting homosexuality, and a book promoting racism. My question is simple: what demographic groups support the removal of these books? The detailed methods are at the end of this post (you should be able to replicate), but what I basically did is used a logistic regression to compare the effects of several variables at once in terms of predicting attitude toward book removal. The samples were limited to the year 2000 and later.

What did I find?

* Liberals support free speech more than conservatives. Even in cases, such as racist books, where ideologically you would suppose they would oppose it (and there is a modest trend if you look at the period between 1990 to 2014 for liberals to be more supportive of removing the racist book).

* The more educated and more intelligent support free speech more than the less educated and less intelligent (the effects hold independently of each other).

* Whites are more supportive of free speech than non-whites, except in the case of a book promoting homosexuality, where there is no difference.

* Atheists and agnostics are moderately more in favor of free speech than the very religious. They are not very differentiated when it comes to the anti-American Muslim clergymen, confirming secular discomfort with fundamentalist Islam.

If one follows Twitter of the elite media one might be surprised that liberals are more supportive of free speech than conservatives. A different set of similar variables support the same conclusion. So what’s going on here?

First, I do think that the hot-house of the campus environment results in distortion and extremism which has minimal support more broadly. My Twitter following is very diverse, and many liberals have been direct messaging me expressing worry and anger at the anti-free speech antics of the protesters. But please observe: the have been direct messaging, rather than putting up their objections in my public timeline. Though the majority of liberals still support free speech, the loudest and most organized element seem to be much more “nuanced” on the issue of freedom of thought.

Second, the modern Left is a coalition of very different groups. The majority of the non-white sample above was black, and it is clear that in regards to speech non-whites are less supportive of tolerance of taboo or unpopular ideas than whites. White liberals may be very strong supporters of free speech, but their political allies may not be. And, the reality is that in terms of intra-coalition dynamics white liberals have to be very careful in how they talk to non-whites, lest they be accused of racism (I’ve been told by my wife to curtail my trolling on Twitter, but pretending to be an SJW of color is pretty fun when engaging with white liberals, since they let you slice off their balls at will, and don’t even object when you’re totally incoherent in your argumentation). This probably explains some of the private expression of support for free speech, but the subdued public sentiments. Liberals who support free speech also still want to eliminate institutional racism and oppression toward marginalized groups, so they have to balance their values when they seem at tension, and don’t want to be supporting those who oppose their policies even if they support the right of those people to disagree.

Finally, the robust support for free speech by the intellectual and social elites is heartening, and suggests that the courts are going to consistently serve as a legal bulwark against attempts to curtail dangerous ideas and sentiments. But obviously that’s not going to always translate into social norms.

Ultimately the question comes down to will. The broad sentiment of liberals does remain in the corner of liberty of thought, right or wrong. But will they stand up for unpopular views, as they have in the past, because in this country you can? That’s an open question I guess.


The dependent variable names are below in the table.

The independent variables were: sex, age, realinc (income adjusted for inflation), god(r:1-2″atheist/agnostic”;6″very religious”), polviews(r:1-3″Liberal”;5-7″Conservative”), race(r:1″white”;2-*”non-white”), degree(r:0-2″No College”;3-4″College”), wordsum

Wordsum is a vocabulary test, with a 0.71 correlation with IQ.

Removing books was always coded as 1, and not removing as 2. Sex is 1 = male, 2 = female. For the god variable, 6 = those who “know god exists.” I did not look at moderates, but aggregated liberals and conservatives (extremely to slightly). For education I just divided between college and non-college.

To get an intuition for the direction of effect, for the anti-American preacher being a male, liberal, younger, more educated, more intelligent, and white, are statistically significantly contributing to greater odds of tolerating the book in the library.

B Exp(B) Probability B Exp(B) Probability B Exp(B) Probability
SEX -0.40 0.67 0.01 0.06 1.06 0.63 0.08 1.09 0.52
POLVIEWS(Recoded) -0.88 0.41 0.00 -0.50 0.61 0.00 -0.71 0.49 0.00
AGE -0.01 0.99 0.00 -0.03 0.97 0.00 -0.02 0.98 0.00
DEGREE(Recoded) 0.46 1.59 0.01 0.58 1.78 0.00 0.61 1.84 0.00
WORDSUM 0.32 1.37 0.00 0.18 1.20 0.00 0.20 1.23 0.00
REALINC 0.00 1.00 0.08 0.00 1.00 0.22 0.00 1.00 0.00
RACE(Recoded) -0.49 0.61 0.01 -0.77 0.46 0.00 -0.17 0.85 0.27
GOD(Recoded) -0.17 0.84 0.47 -0.57 0.57 0.01 -0.75 0.48 0.01
Constant 0.90 2.46 0.17 2.92 18.61 0.00 2.66 14.33 0.00
B Exp(B) Probability B Exp(B) Probability
SEX -0.21 0.81 0.09 -0.09 0.92 0.43
POLVIEWS(Recoded) -0.56 0.57 0.00 -0.29 0.75 0.02
AGE -0.02 0.98 0.00 -0.01 0.99 0.05
DEGREE(Recoded) 0.51 1.66 0.00 0.45 1.57 0.00
WORDSUM 0.22 1.25 0.00 0.15 1.17 0.00
REALINC 0.00 1.00 0.22 0.00 1.00 0.75
RACE(Recoded) -0.62 0.54 0.00 -0.55 0.58 0.00
GOD(Recoded) -0.75 0.47 0.00 -0.32 0.73 0.09
Constant 3.31 27.37 0.00 1.20 3.30 0.02
• Category: Ideology • Tags: Free Speech

512px-Bellcurve.svgThis year at ASHG one of the most fascinating talks was Po-Ru Loh’s, where he reviewed the BOLT-REML method. It’s introduced in the paper, Contrasting genetic architectures of schizophrenia and other complex diseases using fast variance-components analysis. As you likely know many diseases such as schizophrenia manifest as complex trait; that is, they’re basically quantitative in their genetic architecture. Lots of alleles in the population, at varied frequencies (e.g., it might be low frequency and large effect, or higher frequency and smaller effect). In the abstract they state that “We also observe significant enrichment of heritability in GC-rich regions and in higher-frequency SNPs for both schizophrenia and GERA diseases.” In other words, they’re getting toward the holy grail of these sorts of studies, actually fixing upon likely loci which explain the variation.

But the genesis of these methods goes back to the late 2000s, when some statistical geneticists began to synthesis the power of genomics with classical quantitative genetic frameworks and insights. Another paper which sums up this tradition is Genetic variance estimation with imputed variants finds negligible missing heritability for human height and body mass index. That is, the authors have confirmed the classical heritability estimates for height, using inferences such as twin studies, with genomic methods. Many geneticists operating just outside this field are totally unaware of the power, precision, and rapidity in advance of this set of techniques. If so, I suggest you read A Commentary on ‘Common SNPs Explain
a Large Proportion of the Heritability for Human Height’ by Yang et al. (2010)
(ungated). Here is the final paragraph:

Why have we encountered so much apparent misunderstanding of the methods and results in the human
genetics community? The core of our method is heavily steeped in the tradition of prediction of random effects and the estimation of variance due to random (latent) effects. While estimation and partitioning of variance has a long history in human genetics, in particular in twin research, the prediction of random effects is alien to many human geneticists and, surprisingly, also to statisticians (Robinson, 1991). Another reason could be the simultaneous use of population genetics and quantitative genetics concepts and theory in our paper, since these are usually applied in different applications, e.g., gene mapping or estimation of heritability. All concepts and methods that we used are extensively described in the textbooks by Falconer and Mackay (1996; chapters 1, 3, 4, 7–10) and Lynch and Walsh (1998; chapters 4, 7, 26, 27).

Please, if you read anything on this blog, read this.

• Category: Science • Tags: Genomics, Quantitative Genetics

440px-Daphnia_pulex Yesterday I read a paper which utilized Daphnia as a model to explore a very important theoretical question, which relates the role of effective population size to the genetic load (they’re inversely correlated). The theoretical aspect I am aware of, but I don’t know much about Daphnia. The paper is titled Genetic load, inbreeding depression and hybrid vigor covary with population size: an empirical evaluation of theoretical predictions, and it’s in Evolution. It’s not open access, and I can’t find a preprint around, for which I apologize (you could pester the first author on ResearchGate or something). But one reason I’m interested is that they assert this:

Our results are in clear support of theoretical models based on recurrent mutation to unconditionally deleterious alleles on the effects of population size on inbreeding depression, hybrid vigor, and genetic load. This study is the first to find such clear and unequivocal evidence for all of the predicted effects.

This makes me think of Richard Lewontin’s assertion back in the 1970s that theoretical population genetics was basically a machine designed to operating upon inputs which weren’t available (data). I don’t know this literature well, but it’s shocking that these ideas have only been robustly tested now! Or, perhaps these results are false positives of some sort, as it does note it’s the first to find clear and unequivocal evidence for a prediction.

The basic issue is that in small populations genetic drift has the potential to overwhelm the power of selection in purging deleterious alleles. How deleterious an allele is varies. Some alleles have very strong negative selection coefficients. For example, those with dominant lethal effects are going to be purged immediately for obvious reasons (if it’s dominant, it’s always expressed, and if it’s lethal, it isn’t passed on). The situation differs for those with recessive expression patterns. Even if it is lethal in homozygous form, an allele can persist at low frequency if the population is random mating, as the vast majority of copies will be in heterozygotes whose fitness is not impinged. But if the selection coefficient is low enough than even dominantly expressed alleles may not be purged. The variance in allele frequencies due to sampling is inversely proportional to the population size, so as that converges upon the selection coefficient in terms of magnitude, the efficacy of natural selection diminishes. This is at the heart of the nearly neutral theory, which suggests that a lot of variation is due to the input of very weakly deleterious alleles which can’t be purged in population sizes where drift is above a particular threshold.

originsgenomearchitecture Presumably, in large populations there will be many low frequency variants of weak deleterious effect and recessive expression. In contrast, in small populations the power of drift is such that even rather deleterious alleles can be fixed against the gradient of selection. At cross-purposes with this is the idea that because inbreeding populations tend to “expose” alleles which express recessively to selection they can “purge” the genetic load which drags on fitness. For example, with dog breeds there is some evidence that inbreeding needs to be conditional upon breed level variation, as some of the load may have been purged.

Apparently Daphnia are a species which exhibit a wide gradient of variation in genetic diversity (heterozygosity in this case), allowing one to test various hypotheses by crossing lineages sampled from wild populations in the laboratory. Their molecular assay of diversity were ~30 microsatellite loci. What they found is that in line with theoretical prediction those sampled from large populations had lots of segregating deleterious alleles, which manifested in strong inbreeding effect when individuals were purposely crossed with those genetically similar. In contrast, those from small populations did not exhibit so much inbreeding effect, indicating that a lot of the deleterious alleles were already fixed and so exposed. These individuals from small populations also exhibited lower fitness than those from large populations, reflecting in all likelihood their genetic load. Crossing individuals from different small populations resulted in immediately hybrid vigor, as the fixed variants differed across lineages.

There are a lot more details in the paper. If you have academic access, read the whole thing. If not, there’s always #icanhazpdf. I’m more interested in general conclusions. Two preprints just came out which addressed the reality that Neanderthals seem to have had a small effective population size. Meanwhile, the issue is very real and live in conservation genetics, and even in the understanding of mammalian lineages more broadly, many of which have gone through bottlenecks even human intervention aside. But how much can we generalize from the Daphnia, which has a small genome (<10% of the size of the human genome, which is around average for mammals), but ~1/3 more genes? I’d wager a lot. But I’m really going to be interested when there are whole-genome analyses of this sort of study done in Daphnia, and we can look at the site frequency spectrum, instead of just inferring from the fitness.

Finally, I do want to emphasize here a lot of the problems relating to inbreeding seem to be due to segregation load of partially recessive low frequency variants. This is an important foundational insight that allows us to properly conceptualize what’s happening in small populations, or in lineages that have gone through a bottleneck, and why that’s a problem.

• Category: Science • Tags: Inbreeding, Population Genetics

41L69h9XdRL._SX331_BO1,204,203,200_ At ASHG this year a friend and I were talking, and we noted in passing how much R. A. Fisher anticipated in The Genetical Theory of Natural Selection. In some ways it resembles Charles Darwin’s The Origin of Species. But while The Origin is an illustrious book, widely read, and even more widely owned, The Genetical Theory of Natural Selection remains somewhat obscure to the broader public, who are often under the illusion that Stephen Jay Gould is a grand evolutionary theorist, as opposed to a competent paleontologist who also became a master of self-aggrandizement. Any reader of this weblog interested in the science should think about getting a copy of The Genetical Theory and reading it, especially the more technical and abstruse first half.

41oVg-wh-1L._SX333_BO1,204,203,200_ Speaking of Gould, he again makes an appearance in Robert Trivers’ autobiography, Wild Life: Adventures of an Evolutionary Biologist. One chapter is basically the same as Vignettes of Famous Evolutionary Biologists, Large and Small, published on this website a few months back. But most of the book, which I’ve skimmed through, is more explicitly autobiographical. In response to a comment on an earlier thread, Trivers does get into detailed aspects of the mental illness that he has experienced. One of the stranger, but plausible, elements of the narrative to me is that during one episode he became convinced only he understood Wittgenstein. I think that’s rather funny, because from what I’ve read Wittgenstein himself went through phase when he thought he was crazy due to the nature of his own conclusions about the world (he apparently approached Bertrand Russell to inquire where he was insane or not).

885753 For me though, if you want an introduction to the classical Robert Trivers, Natural Selection and Social Theory: Selected Papers of Robert Trivers, is a definitely “must have.” I’ve read this book a few times cover to cover, and it’s very rewarding. It takes the same format as W. D. Hamilton’s Narrow Roads of Gene Land. Key scientific papers are presented, but interleaved with these are commentaries and introductions, rich with autobiographical context. I wish there were more books in this format.

I’ve been reading Frank McLynn’s Genghis Khan: His Conquests, His Empire, His Legacy, and switching back to his Marcus Aurelius: A Life. Two rulers who could not have been more different! Genghis Khan is a good book, but I’m not sure I’d recommend it for someone who hasn’t read other work on this topic, as McLynn’s scholarly judgement on what is, and isn’t, plausible from The Secret History of the Mongols isn’t something you want to rely too much on. In fact it has crossed my mind that people might be well served by reading Pamela Sargent’s historical novel, Ruler of the Sky: A Novel of Genghis Khan, as it presents the biography pretty faithfully, and more entertainingly than non-fiction (from what I recall Ruler of the Sky sugar-coats Temujin’s relationship to his brother Khasr a bit though).

In National Review Jonah Goldberg has a piece up, Fusionism, 60 Years Later. Recent events have made me convinced that really there’s no way American libertarianism can have an influence outside of the Right and the broad tent of conservatism. That means there will always be the sort of culture clash on a personal level, as the cultural preferences and mores of libertarians are more like that of liberals. But the Obama years seems to show that the Left really has no ability to put a stop to the warfare state (though I grant McCain really might have done some crazy things if he’d been elected!). Liberal internationalism is really the only game left in the Democratic party, just as a flavor of foreign policy neoconservatism is the only option in the Republican party. Additionally, I don’t really think of modern liberalism as “socially liberal.” With the rise of affirmative consent and a near maximalist idea of gender fluidity becoming normative, it sure doesn’t seem as if the cutting edge social movements on the Left want to “stay out of your bedroom,” and the events at Yale are a signal that freedom of thought in practice is something that isn’t even given the fig-leaf of protection from critique. There’s a specter haunting the American Left, and it’s Marcuse.

51VLZmyVmRL._SY344_BO1,204,203,200_ But I want to highlight one aspect of Goldberg’s piece which I want to dissent from somewhat: “The Founding Fathers were all classical liberals, but unlike many of their opposite numbers in the French Revolution, they were largely conservative in manners, morals, and faith. Their conservatism was not labeled as such because it suffused the culture and was simply taken for granted.” One needs to be careful about transposing modern categories back into the past. After all, to some extent modern Left-Right concepts come out of the maelstrom of the French Revolution itself, which post-dates the American Founding. But one of the most influential books in my own thought in attempting to understand the nature of the American Founding has been Jay Winik’s The Great Upheaval. It’s a broad work, but one thing it emphasizes is that the idea of a secular republic was rather strange when the United States was assembled out of the thirteen colonies. There were a range of arrangements. The medieval Christian model was one where one particular religious institution has a monopoly on the public life of the polity. The ancient Roman one was more pluralistic, though in practice state subsidies tended to flow toward established and favored cults. In the Chinese imperial system religious sects were controlled and managed by the state, so that they were much more explicitly subordinate to the powers that be than in the medieval Christian context. But, the imperial order was still rooted in a metaphysical understanding of the social and political structure as being reflective of something deep in the natural and spiritual world.

The American federal republic was revolutionary, and not conservative, in that it marginalized the role of specific sectarian commitments in the public sphere. Today we take it for granted, but at the time it was very strange and peculiar. Though the Founders were not atheists, a disproportionate number seem to have had sympathies toward a liberal religious world-view, with some veering toward private heterodoxy. This was not rare among the elite of the period, Frederick the Great being an exemplar of a ruler who was well known to be privately irreligious. But though his Prussia moved a bit toward relative liberality in matters of religion, it remained fundamentally a Protestant domain, where Catholics suffered discrimination, and Jews were marginally tolerated. The American republic did something radically different, a rupture with the norms not just of European civilization at the time, but the standard mode of operation of complex polities since the rise of civilization itself, privatizing the gods!

Of course the Founders would never have countenanced anything like the sectarian and anti-clerical atrocities that occurred in the War in the Vendee. In this way the period of the American Founding is going to always be difficult to interpret in a modern framework because everything changed after the French Revolution. The possibilities for social upheaval, for good or bad, were qualitatively different after emergence of a French republic, and Napoleon’s wars against the older aristocratic order.

• Category: Miscellaneous • Tags: Open Thread

At Reason, Watch Students Tell Yale to Fire a Staffer Who Upset Their Safe Space. The ‘staffer’ in question is Nicholas Christakis, a scientist whose work I’m mildly familiar with actually. The whole affair was kicked off by Christakis’ wife sending this email, where she said perhaps it was not the university’s job to patrol costume choices (for Halloween).

All this emerged in the context of the rumored white girls allowed only frat party at Yale. I say rumored because I don’t believe that it happened (which is pretty obvious from the link if you read it, despite trying to give accusations of racism the benefit of the doubt). The issue is that the sort of people who get accepted into Yale know exactly what to say in regards to issues relating to diversity to maintain appropriate optics. They would never be so crudely racist, even if the reality is that most men in that particular frat would prefer white girls attend their parties. As I noted on Twitter, all the of the men Taylor Swift dates are white (unless you count part-Native Americans Taylor Lautner and Joe Jonas as not), and that’s not a big deal. But if she said in public that she only dates white men, like her ex John Mayer admitted about women, she would become public enemy #1.

It strikes me that in our American culture right now what matters is less what you do, but what you say and signal. Erika Christakis dissented ever so slightly from the regnant norms in her elite university milieu, and now she’s paying for it. But the reality is that people like Erika Christakis live lives of cosseted privilege and insulation from the difficulties of the world, but that’s not worth comment. Rather, what matters is that she follow the appropriate norms and symbolic gesturing which we take for granted in our society.

This is not entirely unreasonable. Manners and decorum, even ritual that might not be heartfelt, tie societies together. By the public performance of words and actions, even if they are belied by revealed day to day preferences, we outline the moral fabric which we aspire to. But at some point it becomes a farce. By the end of the Communist period in the Soviet Union everyone was going through the motions, with no sincere belief. That explains partly why the system collapsed and reconfigured itself so rapidly; it was not robust, but brittle. Some level of hypocrisy is inevitable in any society which aspires to virtue, but when the chasm between words and deeds, between external signalling and internal sentiment, become too large then the system is ripe for overturning.

Though your guess is as good as mine about what might come next.

• Category: Ideology • Tags: Free Speech, Yale

41oVg-wh-1L._SX333_BO1,204,203,200_ The title says it all. It’s an e-book, Wild Life: Adventures of an Evolutionary Biologist. Obviously I just bought it. Not sure that there will be that much new material, but Trivers life and work is worth it if there is anything novel.

• Category: Science • Tags: Robert Trivers
Sharia should be law of land Muslims who believe sharia should be law who accept death penalty for apostasy % of Muslims who accept death penalty for apostasy
Afghanistan 99% 79% 78%
Pakistan 84% 76% 64%
Egypt 74% 86% 64%
Palestinian territories 89% 66% “59%
Jordan 71% 82% 58%
Malaysia 86% 62% 53%
Iraq 91% 42% 38%
Bangladesh 82% 44% 36%
Tunisia 56% 29% 16%
Lebanon 29% 46% 13%
Indonesia 72% 18% 13%
Tajikstan 27% 22% 6%
Kyrgyzstan 35% 14% 5%
Bosnia 15% 15% 2%
Kosovo 20% 11% 2%
Turkey 12% 17% 2%
Albania 12% 8% 1%
Kazakhstan 10% 4% 0%

41nsHqj5QIL._SY344_BO1,204,203,200_ The above data is from Pew. Questions were asked only of Muslims. In some nations, such as Turkey, “Muslims” include basically the whole population, at least nominally. In others, such as Malaysia it is somewhat over half the population. The first response column is the proportion of Muslims who wish to enact sharia as the law of the land in a given nation. The second set of responses are those Muslims who agree with the first question, and also agree with the traditional death penalty for apostates in Islam. Multiplying the two out, and you get the total proportion of Muslims in a given country who assent to the traditional death penalty for apostates in Islam. This is probably a floor, in that a minority of those Muslims who don’t want sharia enacted may agree with the death penalty for leaving Islam for a variety of reasons (Muhammad Ali Jinnah, who was neither personally religious or observant, nevertheless defended the killer of a “blasphemer” during the British period on the grounds of communal honor).

What you see above are a range of attitudes, and interesting conflicts with public practice. In Indonesia it is not illegal to convert from Islam to another religion, and this is done. But about ten percent of the population still accepts the death penalty for apostasy, at least nominally. In Malaysia it is very difficult for an ethnic Malay to convert to another religion, as the connection between that identity and Islam is quite close, though there is often more latitude for non-Malays. About half of Muslims accept the death penalty for leaving Islam. The difference between Indonesia and Malaysia probably is a reflection of divergent social norms which arose in different historical contexts (in Indonesia, the conflicts were as much between Muslim groups of various sects and ethnicities, while in Malaysia the cleavage was more between the non-Muslim Chinese and the Muslim Malay). Just because a given percentage agree with the death penalty for apostasy does not entail that they’d automatically kill an apostate personally, but it probably indicates a level of tolerance and acceptance of intimidation and violence directed toward the act of apostasy.

51+cUvOGl1L._SY344_BO1,204,203,200_ It is instructive to compare Bangladesh and Pakistan. About ~1/3 of Bangladesh’s Muslims (~90% of the population) agree with the death penalty for apostasy, while ~2/3 of Pakistan’s Muslims (>90% of the population) do so. The reason that there is no campaign against secular bloggers in Pakistan is that secular bloggers in Pakistan would be insane to be as public and vocal as their equivalents in Bangladesh. With the majority of the population accepting the legitimacy of capital violence against those who are more extreme in their defiance of religious orthodoxy, the equilibrium state is for that dissent to exist in an underground fashion. Bangladesh is somewhat different because of its peculiar history. As a multi-ethnic nation which was to serve as the state for the Muslims of the Indian subcontinent Pakistan’s attachment to religious identity is nearly necessary. In contrast, Bangladesh’s origins occurred through a rebellion by a left-wing nationalist movement grounded in the ethnic rights of Bengalis within the then Pakistan (and an Indian intervention!), and predicated on a common linguistic heritage. The national anthem of Bangladesh was written by the Hindu Bengali Tagore (compare the lyrics of the Bangladesh anthem with Pakistan’s).

There is a culture-war within Bangladesh, and it is conditioned on an understanding of the nation’s identity in religious terms. This is clear when you notice the official name of the nation: the People’s Republic of Bangladesh, a nod to the dominant party’s affinity with 20th century socialism. But, in 1988 Islam was also added as the “state religion,” a move that was rumored at the time to be motivated by potential aid largesse from Middle Eastern petrostates. In contrast, Pakistan is the Islamic Republic of Pakistan.

This is the context of the literal war within Bangladesh between those aligned with Islamism of various sorts and their critics, who range from non-Islamist Muslims to intellectuals from a Hindu background and outright atheists. Over the weekend there was another attack, prompting protests. Here are some relevant aspects:

Hundreds of people, including writers, publishers and bookshop owners, took to the streets of the capital, Dhaka, on Monday to protest against what they said was government inaction over a string of attacks, including the murder on Saturday of a publisher of secular books.

Rallies were also held in other cities and towns to demand more protection for publishers, bloggers and writers, some of whom have fled the country or gone into hiding.

The people who have so far fallen victim to the attacks are thinking people, those who believe in freedom of expression, and those who believe in secular values. A series of killings have taken place but now the focus is on publishers … I feel absolutely traumatised,” said Mohiuddin Ahmed, a publisher in Dhaka.

Fears of Islamic extremist violence have been rising in mainly moderate Muslim-majority Bangladesh after four atheist bloggers were murdered by machete-wielding attackers this year.

Two foreigners – an Italian aid worker and a Japanese farmer – have also been killed, while Dhaka’s main shrine for the small local Shia Muslim minority was bombed last month, killing two people and wounding dozens.

While it was believed to be the first attack on Shia Muslims in Bangladesh, in the past two years banned Islamic militant groups have killed more than a dozen Sufi Muslims and attacked Hindus and Christians.

The killing of foreigners has worried the country’s expatriate community and threatened its fragile economy, which is heavily reliant on foreign aid and a $25bn (£16bn) garment industry making clothing for international brands.

Points I want to note:

* Dhaka is a city of ~15 million, but “hundreds” of people show up at a protest. Lots of people are sitting this out, because they are scared. But, the terror is not such that some people won’t bravely stand up for freedom of expression, even for a group which is uniformly reviled within Muslim societies as traitors.

* Rallies outside of Dhaka suggest that the cultural division here is national, and not a function of metropolitan cosmopolitanism (it plays out a bit in my family, which divided down the middle between more religious and less religious).

* The attacks on intellectuals have a dark resonance for many Bangladeshis. During the war against Pakistan many creative intellectuals were killed in a targeted manner by the army because of their utility to the independence movement. And, it is known that some of the Islamist groups have roots which go back to pro-Pakistan elements during the 1971 war.

* The attacks on Shias indicates that these activists are adopting the norms of international Sunni Islamists, who target Shia. The attacks on foreigners also suggests that they want to move the needle on the climate in Bangladesh in terms of openness, trade, and general tolerance.

* Over the years Bangladesh, despite its corruption and political paralysis, has kept its head down in terms of international entanglements and domestic Islamic violence. This has allowed for the development of a non-aid based economy, and a flourishing NGO sector. The sort of institutional stability needed for this sort of development to proceed could easily be suborned by sectarian violence.

It strikes me that we’re at a precipice. The last time I went to Bangladesh was in 2004. If these killings continue, then I may not go back for decades. The government has a problem, in that it’s not very effective, and, there is probably some popular sympathy for this sort of violence, which the rival center-right Bangladesh National Party will want to tap into.

There are many people whose feelings on this issue are rather confused and inchoate. Here’s something from reddit (in response to someone posting one of my posts):

I feel like its one of those new ‘modern’ trends to declare oneself atheist in Bangladesh. Atheist muslims have always existed and will always continue to exist, its nothing new. As long as you arent shoving your views down other people’s throats or hating on other people’s beliefs (or lack of beliefs), there’s nothing wrong with it at all. Even in Islam, the only time capital punishment is applied to an atheist is when the atheist is going around giving hate speeches against the religion. Religious hate speech is punishable by law under Islam. But as far as your belief goes, how would anyone even know what’s in your heart?? Belief is a very personal thing, and no one can be certain of what’s in someone’s heart but the person and God himself.

I am very religious and very spiritual, but I was born and raised in Canada so I have friends of various faiths. We all share our beliefs and try to see things from each others’ points of views, but we never disrespect each other or put down each others’ beliefs even if something doesn’t make sense to us. The problem with these “modern” attention-seeking atheists is that they try to declare their views (atheism) by insulting the views of others (theism). Just because you have a difficult time comprehending the possibility of a universe outside our material universe, it doesn’t mean that other people can’t grasp this concept. Personally, I really dislike closed-minded, one-sided, ignorant people. Whether that’s an atheist or a theist is irrelevant. The ‘modern’ atheists in BD are all just closed-minded, arrogant, one-sided, ignorant attention-seekers. There’s nothing ‘educated’ or ‘enlightened’ about them at all.

To which one commenter responded: “Sure, but should they be chopped up with machetes in public?”

I can agree that many atheists are obnoxious, including myself on occasion. I find many religious people obnoxious too, but they should be free to practice and preach. Growing up in a Muslim milieu I can tell you that many Muslims were offensive and obnoxious when it came to generalizations about other religions, in particular Hindus. That’s their liberty in the United States of America, we don’t live in India where “hurt feelings” rule the day with an iron grip.

To me it is interesting that many liberals I see on the internet with whom I am on good terms otherwise with seem more focused on policing “Islamophobia” than in the genuine illiberalism which is so common among today’s 1.5 billion Muslims. So in response to the killings I put up a tweet which was self-consciously inflammatory:

The_God_Delusion_UK But, this is the United States, and you can say harsh things about religion. In particular, this religion has been sanctioning death to those who criticize it for a while now, so I take my American liberty to criticize when I can. Nevertheless, some were more curious about the jibe against Islam than the fact that people in Bangladesh are getting killed for criticizing Islam.

The data are what they are. I’ve pasted some of this at the top of the post to show how deep the animus goes against dissenters in Islam. And by Islam, I mean Muslims. Yes, Kosovo is tolerant. But there are fewer than 2 million people who live there. In contrast, Pakistan has nearly 180 million Muslims!

Several years ago the financial journalist Heidi Moore decided to “whitesplain” Islam to me. Her contention was that Richard Dawkins was racist and should not generalize about Islam. Similar barbs have been thrown at Sam Harris. As a point of fact I believe many of the things that Dawkins and Harris have said are not grounded in an empirical basis, nor are their analytic frameworks to my liking. But, I also think it is ludicrous to assume that their attitude toward Islam is rooted in racism, as opposed to a generalized distaste for monotheism, as well as a concern for the intolerance against atheists which is so common within the world of Islam and among Muslims.

The reality is that many liberals who are deeply worried about Islamophobia know as much about Islam as Ben Carson does. That’s a fact. I say this as someone who knows a fair amount about the religion, despite my obvious distaste for it. The arguments that American liberals and conservatives have about Islam are not about Islam, but about each other’s self-perceptions, and their cartoon of what Islam is.

That’s “problematic”, as they would say. There are 1.5 billion Muslims, and many of them are on the move. They’re going to be in your neighborhoods, assuming you aren’t part of the socioeconomic elite, which will no doubt insulate itself from the diversity that it welcomes rhetorically. We had better actually deal with reality of the world out there, rather than our own imaginings.

• Category: Foreign Policy, Race/Ethnicity • Tags: Islam


Nathan Taylor points out that sequencing costs are crashing again. Not very surprising from what I’ve been hearing about the direction that firms like Illumina are moving. The cost of sequencing isn’t going to be the rate limiting step in the near future. Here’s some raw data for the past year:

Cost per genome
Jul-14 $4,905
Oct-14 $5,731
Jan-15 $3,970
Apr-15 $4,211
Jul-15 $1,363
• Category: Science • Tags: Genomics

He under whose supreme control are horses, all chariots, and the villages, and cattle; he who gave being to the Sun and Morning, who leads the waters: He, O men, is Indra.

To whom two armies cry in close encounter, both enemies, the stronger and the weaker; whom two invoke upon one chariot mounted, each for himself: He, O ye men, is Indra.

- Rig Veda

Sons of Indra

Sons of Indra

Five years ago I found out that my friend Daniel MacArthur and I are members of the same Y chromosomal haplogroup, R1a. Both of us thought it was rather cool, that ~5,000 years ago there lived a man who was ancestral to us both on the direct paternal line. Five years on, and both Dan and I have sons who continue this lineage. True, surely Dan and I share more than one lineage of connection over the past ~5,000 years, the Y chromosomal one is simply the one that is genetically irrefutable since recombination does not break apart the sequence of variants, the haplotype, allowing the inference to be as simple as taking candy from a baby. The common ancestral information is transmitted as a whole block, excepting the mutations which separate us from our common forefather. Additionally, since he has attested South Asian ancestry (< 200 years), we probably share many lines of descent over the past ~3,000 years (one of Dan’s ancestors was stationed in Bengal in the 19th century, so I think our genealogies intersect a decent amount for non-related individuals).

Screenshot - 10272015 - 03:41:22 PM But there’s something special about R1a beyond the fact that it binds me paternally with a host of people who I know from all around the world. The figure to the right is from the supplements of a Genome Research paper, A recent bottleneck of Y chromosome diversity coincides with a global change in culture. You see that R1a1 diverges by very few mutational steps, and a rake-like pattern defines the phylogeny. That is in keeping with a history of relatively recent diversification, and rapid population expansion. The Genome Research paper found that R1a, along with a host of other Y chromosomal lineages, have undergone very rapid demographic expansion over the past when put through the sieve of phylogenomic inference. This is similar to what you see with the Genghis Khan haplotype. Remember, this is a very specific signature of direct male descent. It does not necessarily extrapolate well to the rest of the human genome. So, though Daniel MacArthur and I share a common Y chromosomal lineage, he is Northern European and I am South Asian, with all that implies for the set of genealogies which come together to contribute to the patterns of variation we see in our whole genomes.

Screenshot - 11012015 - 11:20:26 AM But recently we’ve been gaining even more understanding at the phylogeography of R1a, and its likely history. To the left is a figure from the supplements of Reconstructing Genetic History of Siberian and Northeastern European Populations. You see in this chart a few important things. First, the sister to the haplogroup R, which includes R1b and R1a, and therefore huge numbers of European, West, and South Asian men, is Q, an Amerindian one. The Mal’ta boy, who lived ~24,000 years ago, seems likely to have carried a basal R1 lineage. This is reasonable because most people peg the divergence of R1a and R1b ~20,000 years ago (or somewhat more recently). A major takeaway here is that the dominant lineages across much of western Eurasia today on the male side seem to derive from a group with central Eurasian affinities. The two R1 lineages are very rare in Europe before ~4,000 years ago, according to ancient DNA. This is also concomitant with the arrival of “Ancient North Eurasian” (ANE) ancestry, which is closer to that of Mesolithic European hunter-gatherers than East Eurasians, but still rather anciently diverged, on the order of ~30-40,000 years before the present. Amerindians also have substantial admixture from this group, as do many groups in the Caucasus, and South Asia.


The second major issue that is evident from this figure is that Western and most Eastern European R1a diverge from South Asian and Central Asian R1a. The Altay population in this paper are Turkic, but “trace approximately 37%…of their ancestry to another unknown population, which the model predicted to be related to modern Europeans.” And, its R1a looks basal to the South Indian sample, which because it is from Singapore, is likely to be Tamil. Nearly 15 years ago in The Eurasian Heartland: A continental perspective on Y-chromosome diversity, Spencer Wells reported R1a at reasonable frequencies even among non-Brahmin South Indians. More recent work using more markers suggests that R1a has two very common major lineages in Eurasia, with one very common in Eastern Europe, and decreasing in frequency west, and another common in South Asia, with appreciable fractions in regions of Central Asia such as the Altai mountains. Going back to the earlier work, and connecting the dots, it looks like these two “brotherhoods” of R1a diverged on the order of ~4,000 years ago, both undergoing rapid expansion in different regions of Eurasia.

Oh, but there’s more! Eight thousand years of natural selection in Europe has been updated with new ancient DNA results form Iosif Lazaridis’ work. As you might know by now it seems likely that the Indo-European languages were brought into Europe by peoples related to (descended from?) the Yamna culture of the trans-Caspian steppe. The Yamna were genetically a compound population, with about half their ancestry being derived form “eastern hunter-gatherers” (EHG), who themselves were a equal compound between “western hunter-gatherhers” (WHG), the latter presumably descendants of the Pleistocene populations which had retreated to the habitable fringes of the continent, and the previously mentioned ANE group, with Siberian affinities. The other half of the Yamna peoples’ ancestry derives from something similar to that of the early European farmers (EEF), but somewhat different. In particular, rather than western Anatolian affinities, this ancestry seems more trans-Caucasian or eastern Anatolian, with Armenians and Kartvelian groups either being source population, or related to the source populations.

Intriguingly, the Yamna carry the R1b haplogroup, today rather rare in Eastern Europe, but common, and modal, in Western Europe, with extremely high frequencies along the Atlantic fringe. The new version of the preprint now reports some ancient DNA results form the successor culture to the Yamna, the Srubna. There are two intriguing aspects to the new results. First, the Srubna have nearly ~20% ancestry from a population related to the EEF. There are two possible options here. One, that there was back-migration from Europe after the initial migration west. Second, that an EEF-like migration occurred directly from the Middle East to the steppe. But now, from the preprint:

Srubnaya possess exclusively (n=6) R1a Y-95 chromosomes (Extended Data Table 1), and four of them (and one Poltavka male) belonged to haplogroup R1a-Z93 which is common in central/south Asians…very rare in present-day Europeans…and absent in all ancient central Europeans studied to date.

First things first. There are some “Out of India” theorists who posit that R1a derives from South Asia. If you take a very deep time perspective this may be true; recall that much of Eurasia was not habitable during the Last Glacial Maximum (LGM), so the distribution of populations was very different from what we see today. But, on the scale of ~4,000 years ago it seems that one can say that the very common variant of R1a found in the eastern Iranian world and South Asia likely derives from the steppe. The reasoning here is that while peoples in South Asia have elements of ancestry across their genome with affinities to the steppe people (e.g., ANE), there is little evidence for South Asian distinctive ancestry (e.g., ASI) in the steppe people. Additionally, the majority of South Asia mtDNA does not have a West Eurasian profile, but is closer to the lineages of eastern Eurasia. This is strongly suggestive of mostly male migrants. What we can say definitively is that it looks as if male lineages overturned each other multiple times on the steppe. First, R1b was dominant. Then in the same region one lineage of R1a came to the fore, only to later be marginalized by another lineage of the same haplogroup. Finally, in Central Asia more generally the Turkic migrations reshaped the whole ethnographic landscape within historical memory.

F5.mediumThough I begin this post with Y chromosomes, I will not end with them. My belief though is that the Y chromosomal story gives us a deep insight into the nature of social relations over the past ~5,000 years. More on this later. But, the constant turnover of the Y chromosomal record should clue us in to the fact that human demographic history exhibits punctuated turnover events, which reshape the genetic landscape radically over a few centuries. This is a far cry from a model of a set of serial founder events from Africa, dispersing outward as a phylogenetic tree overlain upon a spatial map over a time-scale of tens of thousands of years in Fisher waves.

Specifically, I’m referring here to the 2005 paper, Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa. Currently, the best rejoinder to this model is probably Towards a new history and geography of human genes informed by ancient DNA, by Joe Pickrell and David Reich. In this review the authors show that though the serial founder bottleneck framework is consistent with the data at a certain level of granularity, it is not the only possibility. What ancient DNA in particular is telling is that local geographic continuity of lineage is often very rare. This result then should make us skeptical of taking contemporary genetic variation, inferring phylogenies, and then overlaying those phylogenies upon the spatial distribution of particular ethno-linguistic groups. Of course, on a coarser scale of granularity the “Out of Africa” model inferred from older genetic work from the pre-ancient DNA era is probably correct. That is, African populations tend to harbor lots of genetic variation, and are basal in relation to non-African lineages. Or, put another way, non-Africans are a derived lineage of Africans. ~100,000 years ago almost all of the ancestors of non-Africans would have been in Africa (or perhaps the biogeographic extension of Africa in the Middle East).

But the story beyond that scale is more complex. At least some of the first settlers of Europe have no modern descendants in Europe. In fact, these populations are nearly as close to East Asians as they are to modern Europeans, suggesting that the modern east-west and north-south axes in Eurasia are products of events of the last few tens of thousands of years at most. In fact, the synthetic origins of Europeans and South Asians is strongly suggestive of the likelihood that inferences from modern genetic variation only have time depths back ~4-5,000 years or so in much of Eurasia. A recent paper in Science, Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent, suggests widespread back-migration to Africa itself from Eurasia! Though I disagree with the interpretation in some details (I don’t believe that this occurred ~3,000 years ago), the circumstantial evidence from this and other studies is strong that there has been several waves of migration of Eurasian groups back to Africa. Excepting the northern fringe of the continent in no region is this preponderant, so that the status of Africa as the home of the original population of modern humans from which others derives, remains unshaken. For now.

Nevertheless, both ancient DNA and whole genome sequencing are fleshing out surprising and enigmatic details in relation to how human genetic variation came to distribute itself around the the world today. Here we can come back to Europe. Mostly because there has been a lot of genetic work on this continent, and the ancient DNA is probably thick enough that we won’t find any major new surprises. In short, the phylogenomic history of the continent over the past ~10,000 years has been “solved” more or less. What did we find out? What can it tell us about the more general human story?

nature14317-f3 We can start with the present. As noted in The History and Geography of Human Genes Europe is a very genetically homogeneous continent. The distances as inferred from allele frequency differences between two given populations is very low, and Northern Europe between the Atlantic fringe and the great Eurasian plain in particular is very uniform in terms of the total genome. Today, we know why. As outlined in Massive migration from the steppe was a source for Indo-European languages in Europe, Northern Europe was demographically shaken ~4,000-5,000 years ago by population movements triggered by peoples which left the steppe. It was not a total replacement. But the world of the first farmers, who had issued out of the Middle East ~8,000 years ago, was rocked in the north. The male Y haplogroups associated with these old farming groups, such as G2a, are found at low, though relatively even, proportions all across Northern Europe today.

One interesting aspect of the story is the huge genetic distance between some of these ancient groups. For example, that between the first farmers from the Middle East and their nearby hunter-gatherer neighbors ~8,000 years ago was of the same order as between Europeans and East Asians! This is more than ten times the larger genetic distances you can find in Europe today, but this persisted for thousands of years, though it seems that hunter-gatherer ancestry increased over time among the farming populations, likely through admixture with the local substrate. The reason for this high genetic distance is because the early European farmers carried ancestry which has been termed “Basal Eurasian” (BEu). This points to the fact that these people seem to have diverged first away from all other non-Africans when it comes to Out-of-Africa populations. In other words, ~40% of the ancestry of early European farmers is from a population which is more genetically distant from European hunter-gatherers than Andaman Islanders are. It was the arrival of the steppe people which resulted in the leveling of the genetic distances across much of Europe, overwhelmingly so in the north, and to a non-trivial extent in the south.

nihms132060f1 So if Europe went through a great homogenization and leveling ~4,000 years ago, why does the “genetic map of Europe” exist? That is, why does geography predict variation in genes so well? There are three things one might say about this. First, PC 1, the larger dimension of variation is north-south. This comports with the idea that the heritage of the early farmers persisted in the south to a far greater extent, and the Indo-European demographic impact was more modest, if not trivial. An earlier explanation I had seen floated around was that there was a north-south gradient due to expansion from the post-Pleistocene refugia, via the serial bottleneck effect. The real explanation for the north-south difference though seems more likely to be the differing proportions of Indo-European ancestry, overlain upon the early farmer and hunter-gatherer ancestry.

The second issue to consider is that the underlying genetic variation in Europe was absorbed into the expanding population. Even if the steppe invaders differed little from east to west, there were differing levels of absorption of the substrate, and after several thousand years there had likely been some divergence between the different early farmer groups, perhaps due to differing levels of admixture with hunter-gatherers. Basically, PC analysis could still pick up the signal of underlying variation even if that component was minor if the dominant element was not particularly structured (you can pick up indigenous structure in Mestizo populations in Mexico for this reason).

Finally, after the initial punctuated change, there was an equilibration as isolation by distance dynamics resulted in divergence across the North European plain. We have enough historical records to know that aside from the Slavic migrations there seems to have been little change in the population structure of Europe since the Roman period (the Saxon migrations were not trivial, but they were neither preponderant nor continent-wide in impact).

What general inferences can we glean from this specific European case? As Graham Coop’s group has noted, one must account both for continuous gene flow via isolation by distance dynamics, and pulse admixture events between very distant populations. Consider the metaphor of a forest expanding over the landscape. There will be local structure, accrued over generations, hundreds and thousands of years. But perhaps periodically a fire will sweep through the landscape and clear huge swaths of territory. Into this virgin landscape may expand forests which derive from isolated reservoirs which escape the flames. Over time geographic structuring will be evident again, and depending on the number of refuges the jigsaw puzzle of genetic islands expanding into the gaps will fade somewhat as migration smooths the edges.

The reference to fire here is conscious, insofar as fire can immolate structure which has taken generations to develop. Before the steppe people arrived in Northern Europe the first farmers had established a long-standing cultural commonwealth of sorts. Their legacy had persisted for thousands of years. Then, in a period of centuries, it all changed. Why? Culture.

Outright genocide with weapons is a dangerous business. Societies which engage in endemic long-term warfare as a primary male vocation, such as highland New Guinea, have high mortality rates. But in the context of the Malthusian world, where villages persist on the knife’s edge of subsistence, marginalization and disturbance of long-held patterns is all that might be needed for cultures to descend into famine and starvation. In 1493 Charles C. Mann notes that the mass death triggered by the arrival of Europeans and Africans to the New World had as much to do with the destabilization of society by illness as much as the illness itself. In a world where all hands were on deck to bring in the harvest, the loss of critical labor during those periods could result in starvation, and high death rates led to the rapid collapse of the institutions which served as scaffolds for the maintenance of everyday life.

The scenario then might be one where populations on the Eurasian steppe develop some of the basic elements which would lead to agro-pastoralism, and undergo population expansion. With numbers, and well fed on the agro-pastoralist diet, these tribes might have poured into the lands of the farmers as rapid mobile groups in their wagons. The pattern in antiquity down to the early modern period, from the Goths to the Mongols, was to extract rents and treat the farmers as cattle. There was no incentive for one to starve cattle, and so the demographic impact of conquests was relatively modest.

But what about a world with less institutional complexity? In a world where the basic levers of rent to extract from the conquered did not exist, the natural path would be to replace them. The story goes that Genghis Khan had hoped to turn North China into a vast pastureland by driving out the peasantry (and almost certainly killing most of them through starvation), but his sage Khitai adviser explained the wealth that could be gained by taxing humans rather than raising stock on land. But the Khitai themselves were a semi-civilized people with centuries of experience milking the Han peasantry, and were heirs to a tradition of pastoralist predation that went back to the Hsiung-Nu. And yet no doubt there was a time when the idea of collecting rents from a conquered people was an innovation in and itself. The genocidal antics of the Israelites in the Hebrew Bible strike us as dark and atavistic, but they reflect a cultural mindset which is nearly contemporaneous* with the arrival of Indo-Europeans to Europe.

This plausible sketch puts into better perspective Steven Pinker’s thesis in Better Angels of Our Nature as well as Peter Turchin’s War and Peace and War. The emergence of state institutions and pacific ideologies in the past ~3,000 years may be a sort of response to the high-stakes inter-group competitions which would level societies and turnover populations on a regular basis in the human past.

And yet not all was as sweetness and light. In terms of their total genome the differences between the Srubna and their predecessors were not very great. Conversely, the differences in the total genome between Slavic people and South Asians are legion. But interlaced more recently across the landscape of a more stable structuring of genetic variation, a great regrowth of the forest through isolation by distance equilibration if you will, has been the explosion of powerful patrilineages which trace out an intriguing skein across the landscape. The total genome signal of these men may quickly decay over the generations, as their female-line descendants lose the golden allure of their status, but their male-line descendants continue to accrue mating prowess by dint of their association with great kinship units which succeeded in a winner-take-all game with other such groups of men. On top of the story of migrations of whole peoples, and the extinction and absorption of others, is the story of bands of men operating as units, related either in truth or fictively, which extract rents across a thickly populated landscape of human cattle. Another way to state this is that the thuggish state which imposed a monopoly of violence on a chaotic world where small-scale conflict was becoming too expensive allowed for the emergence of patriarchy as we understand in its customary form. Like so many hirelings, the men charged with protecting the people, made the whole world their possession and left dreams of their people behind.

John Ross, Cherokee Chief

John Ross, Cherokee Chief

While the cultural and genetic affinities of folk wanderings were tightly coupled, I am not sure that the Y chromosomal lineages are so neat. The Hazara people of Afghanistan exhibit an Asiatic appearance in comparison to other Afghans, and their Y chromosomes suggest a close connection to the Khalkha Mongols, but they are Shia Muslims who speak Persian. It does seem that the R1 lineages ascendant in Europe and South Asia owe their success to the Indo-Europeans, but both R1b and R1a transcend a connection to Indo-European ethno-linguistic groups. In some cases, as in that of R1a in the Levant, one might see in that a submerged Indo-European element, from the Mitanni down to the later Persian and Kurdish peoples. But in other cases, such as R1b among the Basque and R1a among Dravidian-speaking tribal people in South India, what we are seeing is the long arm of the patriarchy reaching beyond bounds of cultural and genetic affinity. The great Cherokee chief John Ross was famously 7/8th Scottish in ancestry. But he was a voice for the Cherokee people nevertheless. In most places where the Mongol hordes washed over they assimilated to the cultural folkways of the people whom they conquered. Like modern corporations the patriarchies were only loosely associated with other units of human organization, even if they used them as their vehicles of choice.

And so the story ties back to the beginning. Many of us are the sons of Indra, Zeus, and Thor. The descendants of Herakles, and of Abraham who haggled with God himself. Of Ishmael, whose hand will be against everyone and everyone’s hand against him. Of Niall of the Nine Hostages, and Temujin. The interests of men like this know no nation, nations are but ends to their will. The tension we see in our modern world, between egocentric plutocratic elites jostling nation-states like playthings, might be simply the repetition of an old pattern. In the Bible Saul was rebuked for not destroying all the capital of the Amalekites, perhaps reflecting the tensions of interests which reflect the leader of a people who must act in the collective good, but have their own selfish needs and dreams of self aggrandizement for their own very particular posterity.

Addendum: Ancient DNA will expand in its ability to discern various patterns in the past. But the general disturbances will fall in line with what I have outlined above, I believe. Rather, the move will be from phylogenomics, to population genomics. Phylogenomics leverages genomic methods to attempt to infer phylogenetic patterns. Population genomics explores the classical parameters which shape the change in allele frequencies in lineages, and ultimately, deep evolutionary questions. We now know from ancient DNA that in all likelihood the phenotype which we associate with modern Europeans is a novel configuration. To some extent this is to be expected, as the basic elements which combine to form the European genome, fusing together lineages which diverged at least ~50,000 years before the present (BEu vs. everyone else outside of Africa) and ~35,000 years before the present (ANE vs. WHG), only came together around ~4,000 years ago. But there is more, as natural selection seems to have changed allele frequencies after these elements came together. That is, selection may have been operating across the European landscape when Hannibal was skirting the Alps!

And again, this is likely a general story. Physical anthropologists have long wondered why classical East Asian skeletal morphology seems to be scarce in the prehistoric past. But what if the classical East Asian appearance is relatively new? The Ainu, who have long been considered at “Lost White Race” turn out to be a basal Northeast Asian group. It may be that they retain more of the “ancestral” features of East Eurasians.

The first age of selection studies in the 2000s was fraught with confusion and false positives. To a great extent we still don’t know what to make many of the signals, which are deposited in the middle of obscure open reading frames. But the real golden age of selection will probably begin when we have more temporal transects with whole genome sequencing of ancient DNA, and with the phylogenomic context relatively robust as an interpretative framework.

* I am aware that the Hebrew Bible coalesced between thousands of the years after the arrival of Indo-Europeans to Europe, but it no doubt distills very ancient folkways. This seems obvious for example in the recollection of the Sumerian flood story.


k10543 Been too busy to read much, but Joe Henrich’s The Secret of Our Success: How Culture Is Driving Human Evolution, Domesticating Our Species, and Making Us Smarter, is out. I have read a little bit of Genghis Khan: His Conquests, His Empire, His Legacy. A touch too over-dramatic and credulous in regards to colorful legends for my taste so far to be frank.

Two Neandertal preprints you might want to check out, The Strength of Selection Against Neanderthal Introgression and The Genetic Cost of Neanderthal Introgression. If you haven’t checked out, you should. Though not totally clear how it’s much different from openSNP.

Nathan Taylor has a post up, Homo naledi and the braided stream of humanity. It’s miscegenation all the way down. I can agree with it in its broadest strokes. On Facebook I posted a link to some stuff about selection for height in Europe, and a reader asked “what does this mean for white people?” My simple response was nothing, because for much of this period people who we would recognize as white didn’t really exist. The ancestral genetic elements which combine to produce most of the population of Europe did not cohere together into one population until ~4,000 years ago, give or take. And, the most recent data suggest that the pigmentation loci which result in the typical light complexion of Northern Europeans did not arrive at their current allele frequencies until sometime after this period.

This isn’t to make Europeans special. I think this sort of reality probably holds for most of the major world populations. A recent paper on the Ainu seem to confirm that they’re relatively basal in relation to other East Asian populations. My own suspicion though is that this is simply because a lot of groups were absorbed or demographically marginalized by expanding groups of farmers from the region between the Yellow and Yangzi rivers.

Halloween was fun. But boy is it way more regimented than when I was a kid. Trick-or-treating at stores in the afternoon and very early evening downtown seems to be edging out the old traversing blocks at night.

• Category: Miscellaneous • Tags: Open Thread

Screenshot - 10262015 - 05:22:41 PM Iain Matheison, first author of Eight thousand years of natural selection in Europe, has a short note up at his website, Selection on height in Europe. He concludes:

More generally, it seems strange that height is the only trait for which a robust signal of polygenic selection has been observed. It’s hard to imagine that traits like diabetes risk and lipid levels were not also under selection in this period. I think it’s mostly down to lack of power in the predictors for other traits. Possibly larger GWAS and better predictors will reveal more. Finally, most of the work in this area has focussed on Europe, since that’s where the large cohorts are. But similar dynamics must also have happened in the rest of the world and it’s only by looking at other populations that we’ll be able to understand more generally the process of human adaptation.

North Chinese are also taller than South Chinese. And there are many quantitative traits in humans. We’re living in a golden age of phylogenomic analysis of humans in particular, but at some point in the near future the lens will begin to turn back onto classical population genetic questions of the parameters which shape the nature of variation. The initial wave of enthusiasm for selection scans ~2005 seems to have abated somewhat, but I think it’s only a slight pause, as polygenic selection and “soft sweeps” come onto the radar of genomicists….

• Category: Science • Tags: Evolution, Genomics

51ejzECZcAL._SX329_BO1,204,203,200_ Today I got on the internet after spending the morning with my kids and then lifting with a friend, to see Tyler Cowen say this: “this is one of the very best non-fiction books of the year,” in relation to Genghis Khan: His Conquests, His Empire, His Legacy. I’ve read a fair amount on the Mongols conquests and Central Asia in general (e.g., <Empires of the Silk Road: A History of Central Eurasia from the Bronze Age to the Present or Lost Enlightenment: Central Asia’s Golden Age from the Arab Conquest to Tamerlane). And, I’ve also read the author, Frank McLynn before. His Marcus Aurelius: A Life, could have been a bit more thoroughly edited. People ask me how I figure out which books to read. One of them is by strong recommendations from people whose judgement I don’t think is crazy. I don’t know Tyler Cowen that well, and he’s not a god in my universe, but he decided to type out “one of the very best non-fiction books of the year”, and it’s on a topic which I’m already somewhat interested in, then of course I’m going to read it (also, at 700+ pages, there is a high possibility of lots of information per unit of cost).

k10386 When people try to talk about cross-cultural comparisons I often tell them to shut up. For example, let me mention the reader (who I will not name though I know this person continues to read me) who could not think of any non-Western thought which expressed the sort of altruistic ethos reminiscent of the Christian Gospel (this reader was not at the time a Christian by the way). When I asked if they knew of the thinkers of ancient China they admitted they were only very familiar with Western works. Which immediately prompted me to ask how they could make a comparative judgement in the first place.

This is a reminder to readers that though any truly educated person does not need to know the works and thought of all societies across history, one does need to sample more than one. I have long thought one of the most important figures in fact, if not legend, in Chinese history was Xunzi, who influenced both later Confucianism as well as Legalism. And, as it happens, there is a recent affordable translation of his thought, striking the right balance between being overly academic and excessively abridged. Last week I promoted Meditations, so this week I thought I should balance it out.

Obviously still very busy with things since coming back from ASHG. My blogging productivity tends to be a bit punctuated…. You know how it goes.

• Category: Miscellaneous • Tags: Open Thread

Historic_cost_of_sequencing_a_human_genome.svg For several years there has been a nerdy debate in some labs about sequencing vs. genotyping (more precisely, doing genotyping-by-sequencing vs. going with an array). There are many pros and cons. If you are working on non-model organisms there may not be a good SNP array for you, so the decision is done. If you work on humans in contrast there are several options which are rather affordable. But at some point I assume that sequencing will get so cheap that that SNP array technology will be rendered obsolete, rather like what RNA-seq is doing to microarrays. Currently the cost of sequencing has not declined much for a few years, as Illumina basically squeezes de facto monopoly allowable price out of customers. At some point in the near future this monopoly will break, with the current bet being on a Nanopore driven disruption of the space. Then the collapse in cost by base genome will commence again, until the technology gets good enough that it’s not really the rate limiter in the pipeline.

With the announcement that 23andMe is increasing their price, from $99 to $199, it got me to thinking about comparing sequencing vs. genotyping. You see, 23andMe uses a SNP-chip. Last I checked just under one million markers, with a custom set of 30,000 added on to the standard Illumina set. They’ve got over one million people genotyped, so they’ve been at this for a long time. But is $199 worth it for a one million markers? As regular readers know I’ve been following the progress of the small start-up Full Genomes for a while. You can get WGS elsewhere, but this group has been very proactive about attempting to cultivate a retail presence (that is, direct-to-consumer). Their prices are on their website, but below is a comparison chart:

Company Service Cost Time User-friendly How much of genome?
Full Genomes 30x coverage $1,850 Months No Medical grade accuracy of whole genome
Full Genomes 10x coverage $745 Months No Not medical grade, but probably whole genome
Full Genomes 4x coverage $375 Months No Will have gaps in genome, but most
Full Genomes 2x coverage $250 Months No Lots of gaps in genome, but a lot of it
23andMe 1 million marker SNP $199 Weeks Yes Accurate genotype calls 1 million out of 5 million variants

Basically coverage is telling you how many times a marker is going to come back in the raw results. If there an error in one particular position you can figure that out pretty easily if you expect to have sampled it 30 times. In contrast, if you have only one read to look at for a position then if it’s not matching the reference it is highly like you’re seeing a false positive. For evolutionary genomics work low coverage is really not a major issue, because you’re curious about population wide dynamics. But if you want to make accurate calls which are medically actionable, then you need to be confident, and for that you need to have high depth on your coverage. With >30x you’re catching almost all the variants in your genome, and so can pick up things like mutations novel to you, which wouldn’t come back on a SNP-array in most cases, since they’re ascertained on common variants.

Since I knew Full Genomes‘ cost chart I knew that their 2x sequencing is now approaching the genotyping results provided by 23andMe in terms of apples-to-oranges cost comparisons. I say apples-to-oranges, because the truth is that Full Genomes is providing a different service. It’s very much of a “rough cut,” while 23andMe is delivering turn-key personal genomics. But, if you are comfortable with .bam and .vcf files, then now is the time to actually consider sequencing (though from what I know Full Genomes‘ turnaround time is on the order of three to six months, while 23andMe is closer to one month). For me the sweet spot right now would be 10x, as 30x is probably overkill, especially if you already have genotype data and are comfortable with imputation….

• Category: Science • Tags: Genomics
Razib Khan
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