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

June 30, 2017

Bret Weinstein talks about being hunted on campus

Filed under: Bret Weintsein — David Hume @ 8:37 pm

Does Tad Williams still have game?

Filed under: Fantasy,Tad Williams,The Witchwood Crown — Razib Khan @ 12:38 am

Like many people I was quite taken with Tad Williams Memory, Sorry, and Throne, when they came out in the years around 1990. George R. R. Martin has admitted that Williams’ trilogy helped awaken him to the possibilities of the fantasy genre.

I tried to read his Shadowmarch series, but I didn’t find it as original so gave up after one and a half books. So I was excited for Williams to go back to a world where he seemed to shine. The first reviews for The Witchwood Crown make it seem like it’s actually pretty good, and perhaps even might be better then the original series. Not sure frankly I’ll ever get to reading it, but who knows.

Addendum: In the fall Brandon Sanderson is coming out with Oathbringer, and R. Scott Bakker’s Unholy Consult will be out at the end of July. I preordered the latter because I thought Bakker’s second book in the tetralogy was actually better than the first two so I have hopes the fourth will be best of all.

Basal humans in our evolutionary closet

Filed under: Basal Humans,Neanderthal — Razib Khan @ 12:19 am

The ancient genome from South Africa was of not because it confirmed what many had long suspected: the deep structure of modern humans in Africa goes back quite a bit further than we had been assuming. A few years ago I co-wrote an op-ed for USA Today where I initially wrote that the Khoisan divergence from other humans was around ~200,000 years ago. For various reasons I let a “fact-checker” change that to ~150,000 years ago. But as I told my co-author Alex Berezow people had access to whole genomes just leaning toward an older date than in the current literature.

Now we know that the date of divergence may be closer to ~300,000 years. Both because of the ancient DNA, and the Moroccan fossils which make it obvious that morphology associated with our own lineage was already beyond incipient before 300,000 years ago.

The past was more complicated than we think. Ancient DNA has made us toss many of our preconceptions out. For example, several years ago researchers concluded that the Out of Africa populations exhibited a different structure than we had thought. Populations of the Near East and Europe had ancestry from a group that was basal to all other non-Africans. That is, if you have a family tree then Oceanians, East Asians, Amerindians, Siberians, and European hunter-gatherers would be on one branch. On the other branch would be “Basal Eurasians” (BEu), named due to their basal position on the tree in comparison to all other non-Africans. Ancient DNA has not uncovered any population which is mostly BEu. Early Holocene Near Eastern populations, the various first farmers, invariably seem to show mixture between BEu and a West Eurasian element similar to what gave rise to the Mesolithic hunter-gatherers of Europe.

It seems possible we may never find “pure” BEu samples. We know that 10,000-15,000 years ago in Europe there was a massive expansion of a population of hunter-gatherers with stronger affinities to modern Middle Easterners than in the past. Perhaps this was part of a broader expansion of this group of hunter-gatherers across vast swaths of Western Eurasia, and in the process they absorbed the BEu populations until there were no pure populations left?

These questions were triggered by novel results which couldn’t be accommodated by current accepted models. This reminds me of a paper from over a year ago which presented some puzzling results which make much more sense now, Ancient gene flow from early modern humans into Eastern Neanderthals. The authors compared the Altai Neanderthal genome, the Denisovan genome, and those of modern humans (as well as a European Neanderthal). The stylized phylogenetic tree is one which the Neanderthal-Denisovan clade spits off from African proto-modern humans ~600,000 years ago. Then around ~400,000 years ago you see the divergence between Neanderthals and Denisovans. This gives us rough expectations as to the nature of the genetic variation in these populations, as they shared quite distinct periods of evolutionary history together and apart.

What the authors found is that a small minority of the Altai Neanderthal genome exhibited much stronger affinities to modern African populations than to the Denisovan. On the order of ~5%. Looking at the length of the haplotypes they estimated that the admixture occurred ~100,000 year ago. Curiously, at least at the time, this modern human population was basal to all modern humans. The authors estimate that the divergence from modern lineages occurred about ~200,000 year ago based on what was understood about modern human differentiation at the time.

At the time that was pushing it, though not unreasonably so. Now that number is probably comfortably defensible. One important point to note is that the modern human admixture was from a group equally related to all Africans. This implied that this group separated before the division of the Bantu and the Yoruba. So if you accept the most recent genomics then this group may date to closer to 260,000 years before the present. And in fact if the fossil record is correct they might have separated as early 350,000 years before the present. Additionally, the group which published the South African genome study posited another group, Basal Africans (BA), who diverged far earlier than the Khoisan from most African (and also non-African) groups.

Maximal Neanderthal range

The Neanderthals are a well studied group. We know what their range was. One can spit all sorts of speculative scenarios, from wide range proto-modern humans pushing deep in Eurasia during the Eemian interglacial 130,000 years ago. Or, it may have been through contact in the Near East and expansion of a somewhat admixed Neanderthal population north and east over time. Who knows? At least until there’s more ancient DNA….

June 29, 2017

Desperately seeking the secret of FOXP2

Filed under: FOXP2,Human Evolution — Razib Khan @ 6:04 pm


Since the early 2000s FOXP2 has shown up again and again in the press and scientific literature. Dubbed the “language gene” it exhibits evidence of accelerated evolution in the human lineage after it split from other apes. Additionally, a homolog of the same gene shows evidence of evolutionary change distinctive to songbirds and whales. Obviously this locus is involved in vocalization. Mutated mice on FOXP2 can even sing.

It isn’t difficult to connect the dots here. From 2002:

Dr. Paabo says this date fits with the theory advanced by Dr. Klein to account for the sudden appearance of novel behaviors 50,000 years ago, including art, ornamentation and long distance trade. Human remains from this period are physically indistinguishable from those of 100,000 years ago, leading Dr. Klein to propose that some genetically based cognitive change must have prompted the new behaviors. The only change of sufficient magnitude, in his view, is acquisition of language.

Klein’s thesis, advanced in The Dawn of Human Culture, is that a singular genetic change resulted in some sort of developmental cascade that allowed for the emergence of syntactically rich recursive language. And from language comes culture, and from culture comes world domination.

It was a clean and powerful hegemony while it lasted, but genomic and archaeological findings of the last decade have put such a elegant and simple model under a harsh light. With genomic technology even FOXP2 turns out to be much more complex and rich than the earlier reports had suggested. Neanderthals exhibited all the same mutations as modern humans to make them distinctive from chimpanzees. In other words, the changes on FOXP2 by and large predate the emergence of modern humanity, and go back closer to the root of the hominin lineage (Neanderthals and modern humans diverged ~600,000 years ago).

But FOXP2 keeps coming back. Why? It is an important gene. But another issue is that researchers still perceive in it the key to the holy grail of finding out what makes us distinctively human.

A new preprint (which is somewhat peculiarly formatted), takes another look at FOXP2, Human-specific changes in two functional enhancers of FOXP2:

Two functional enhancers of FOXP2, a gene important for language development and evolution, exhibit several human-specific changes compared to extinct hominins that are located within the binding site for different transcription factors. Specifically, Neanderthals and Denisovans bear the ancestral allele in one position within the binding site for SMARCC1, involved in brain development and vitamin D metabolism. This change might have resulted in a different pattern of FOXP2 expression in our species compared to extinct hominins.

The big picture is now the authors are focusing on gene expression levels as what might allow for modern human traits to be distinctive. Basically the DNA does not magically turn into protein. Biological machinery has to transcribe the sequence, and to transcribe it it has to bind to a particular region, a transcription factor binding site.

Most of the analysis involves comparing genomes of Neanderthals, Denisovans, and the human reference. I would be curious if they looked across lots of whole genomes to check if there was polymorphism in modern human populations. If modern humans with Neanderthal and Denisovan mutations had perfectly fine speech, that would be interesting.

Also, they spend a lot of time talking about how other genes interact and express with FOXP2, and all the other functions that are implicated. This is important, because of course selection may have nothing to do with speech, though perhaps speech changes are a side effect? Remember to that the Altai Neanderthal had some modern human admixture, and that one of the introgressed regions turns out to be FOXP2.

This sort of comparative genomic style research is interesting and suggestive. But we need more population wide analysis.

But, the authors do allude other work using genetic engineering where cell lines did show radically difference gene expression based on the mutation above. I do believe that CRISPR/Cas9 technology is cheap enough and going to be widespread enough that someone’s going to play around with splicing in “human” variants into primate models. Meanwhile, bioethicists will furrowing their brows about sequencing humans….

June 27, 2017

Why you should learn some population genetics

Filed under: Population genetics — Razib Khan @ 10:03 pm

From reader surveys I know a substantial portion of the people who will see this post are financially well off (of those who aren’t, a large number are students). Therefore, you can invest in some books.

Often people ask me questions related to population genetics in the comments (sometimes I get emails). That is all well and good. But it is always better to be able to fish than have to ask for fish. Additionally, learning some population and quantitative genetics allows you to develop some tacit schemas through which you can process information coming at you, and through with you can develop some general intuition.

If you have a modest level of mathematical fluency and and the disposable income, here are three indispensable books which are like the keys to the kingdom:

* Elements of Evolutionary Genetics
* Principles of Population Genetics
* Introduction to Quantitative Genetics.

If you don’t have the cash to spare, there are online notes which are pretty good:

* Graham Coop’s Population Genetics notes
* Joe Felsenstein’s Theoretical Evolutionary Genetics

There are others online resources, but they are not as comprehensive. John Gillespie’s Population Genetics: A Concise Guide is good as very gentle introductions go, but if you are going to spend money, I think just plumping down for a more comprehensive textbook (which will have more genomics in it) is better over the long run.

The goal of getting these books isn’t to make you a population geneticist, but, if you are interested in evolutionary questions it gives you a powerful toolkit. Really nothing in evolutionary process makes sense except in the light of population genetics.

Genome sequencing for the people is near

Filed under: Genomics,Personal genomics — Razib Khan @ 7:22 am

When I first began writing on the internet genomics was an exciting field of science. Somewhat abstruse, but newly relevant and well known due to the completion of the draft of the human genome. Today it’s totally different. Genomics is ubiquitous. Instead of a novel field of science, it is transitioning into a personal technology.

But life comes at you fast. For all practical purposes the $1,000 genome is here.

And yet we haven’t seen a wholesale change in medicine. What happened? Obviously a major part of it is polygenicity of disease. Not to mention that a lot of illness will always have a random aspect. People who get back a “clean” genome and live a “healthy” life will still get cancer.

Another issue is a chicken & egg problem. When a large proportion of the population is sequenced and phenotyped we’ll probably discover actionable patterns. But until that moment the yield is going to not be too impressive.

Consider this piece in MIT Tech, DNA Testing Reveals the Chance of Bad News in Your Genes:

Out of 50 healthy adults [selected from a random 100] who had their genomes sequenced, 11—or 22 percent—discovered they had genetic variants in one of nearly 5,000 genes associated with rare inherited diseases. One surprise is that most of them had no symptoms at all. Two volunteers had genetic variants known to cause heart rhythm abnormalities, but their cardiology tests were normal.

There’s another possible consequence of people having their genome sequenced. For participants enrolled in the study, health-care costs rose an average of $350 per person compared with a control group in the six months after they received their test results. The authors don’t know whether those costs were directly related to the sequencing, but Vassy says it’s reasonable to think people might schedule follow-up appointments or get more testing on the basis of their results.

Researchers worry about this problem of increased costs. It’s not a trivial problem, and one that medicine doesn’t have a response to, as patients often find a way to follow up on likely false positives. But it seems that this is a phase we’ll have to go through. I see no chance that a substantial proportion of the American population in the 2020s will not be sequenced.

June 25, 2017

Over the long term civilization matters

Filed under: Culture — Razib Khan @ 9:09 pm

In Peter Turchin’s work modeling human historical dynamics he introduces the idea of a “meta-ethnic” identity. Quite often this is synonymous with a world religion. These identities emerged in the last few years as human polities scaled so large as to expand beyond tribal-national boundaries.

These sorts of dynamics are clear when we think about the Crusades, the defense against the Ottomans in the 17th century, or the Iberian “division” of the world between Castile and Portugal. Common ties of civilization and identity allow for ingroup cohesion, as well as heightening hostilities against outgroups.

Of course there many exceptions. When reading The Great Sea: A Human History of the Mediterranean I recall being struck by how southern Italian city-states like Amalfi opportunistically allied with Muslim pirates against other Christian powers. Similarly, during the Battle of Vienna Protestant Hungarians marched with the Ottomans against the broader Christian alliance which came to the aid of the Habsburgs.

These are two instances which show short term self-interest or necessity driving choices of group coalitions. Amalfi, like later Italian city-states, found it in their interest to do business with Muslims, even if it was to the detriment of their co-religionists. This did not mean they were no longer Christians. But in many instances they put that identity aside for their own gains. In the case of the Protestant Hungarians there’s was an alliance of necessity.

As recounted in Divided by the Faith the decades leading up to the Battle of Vienna the Hungarians experienced a concerted campaign of conversion and persecution of the part of the Habsburg monarchy in concert withe Roman Catholic Church. The Habsburg’s Austrian lands were brought back fully into Catholicism, as was most of Imperial Hungary. It is no coincidence that Hungarian Reformed Protestantism was strong in the east, which had been under Ottoman influence. The arrival of an expansive Austrian monarchy was an existential threat for them.

The flip side are cases where groups with the same civilizational identity engage in wars over resources or boundaries. The conflict between Ethiopia and Eritrea would certainly fit into this mold, and to some extent the Great War in the Congo which has flared for two decades now.

This sort of dynamic has been used to argue that Samuel P. Huntington’s The Clash of Civilizations and the Remaking of World Order is not a useful framework. But on the contrary what Turchin and colleagues have shown is that over the long run civilizational fissures tend to result in the most vicious and dehumanizing wars.

Open Thread, 6/25/2017

Filed under: Open Thread — Razib Khan @ 8:53 am

I’m beyond the “keto flu.” That was tough.

A few months ago I asked a Hindu nationalist friend of mine the best persons who promote the “Out of India Theory.” One name he forwarded to me was Koenraad Elst. Though Elst and I disagree on facts in relation to the issue at hand, a reader has pointed out that he’s taken a very strident and clear stand against the ad hominem attacks against me from those who would consider him a fellow traveler. This honorable stance frankly has shocked me to my core, as I’m just not used to it after engaging with SJWs and various ideologues for so long. The ad hominem is so easy that it takes some fiber and integrity to resist it.

One consequence of Elst’s clear stand is that I think I do need to revisit some of his work.

Read some of The Enigma of Reason yesterday. I would recommend it. I’ve read some of Dan Sperber’s previous stuff, like Explaining Culture: A Naturalistic Approach, and it’s familiar. Also, Sperber was a major influence on Scott Atran, so even though this book is new many of its ideas and orientation are prefigured in In Gods We Trust.

SMBE 2017 in about a week at the JW Marriott in Austin. I’m not going to be there the whole time, but when I’m there I’ll be tweeting.

Waking Up With Sam Harris #83 – The Politics of Emergency (with Fareed Zakaria). I agree with Fareed Zakaria more on Islam.

A left-wing journalist is attacking Richard Dawkins on the basis of his family having had African servants when they lived in Kenya. This person is some sort of Max Blumenthal clone from what I can see. A fringe element of far Left basically has a modus operandi: pick someone to destroy, and extract elements of their life to flog them as evil (call them racist, sexist, something -ist).

This is great on Twitter, but not optimal for movement building. I understand that there is a reasonable, moderate, liberal, Left. But this radical Left wants many of us out there on the street, our families dispossessed. When the lines are drawn, this is why some of us will keep voting Republican despite all our issues with the party: we don’t want to be personally destroyed.

Related to the chilling impact of this behavior, Liberals and Immigration, Kevin Drum says:

I have no idea what, if anything, we can do about this. But I will say this. I lurk on a number of message boards populated by liberals, and what they say privately is very often more nuanced than what they say publicly.¹ On immigration, there are probably lots of liberals willing to concede that there needs to be a limit to the flow of undocumented workers. There are cultural, economic, and nationalistic reasons for this. But there’s little benefit to saying so in public. It just invites massive, social media swarms insisting that you’re a closet racist.

White Cheese is white Supremacy

This is in response to Peter Beinart’s piece How the Democrats Lost Their Way on Immigration. I think Michael Brendan Dougherty has a pretty good response to this in National Review. Before he wrote this piece he observed on Twitter that Beinart wasn’t confronting something that had changed on the Left. I responded: “white supremacy.”

White supremacy has gone from being the KKK or Neo-Nazis, to basically all of American society. The term is used liberally and without much care. Just like the term racist or sexist. It’s both a cudgel in tactical debates, and, for many it’s a sincere belief. A Sister Souljah moment could never happen today for a white male Democratic politician because he would be accused of being a white supremacist for attacking a black woman (Obama himself was attacked for pandering to ‘respectability politics’).

On immigration, note that in the mid-2000s Republicans could have probably been able to muster the courage to ignore the base if the Democrats had agreed to a bill to flood this country with high skilled immigration (a proposal by some Republicans). But for political and policy reasons the Democrats wanted something comprehensive, which includes lower skilled workers who are both the Democrats’ future vote bank, and people who are important (often relatives) to Democratic voters.

Above Drum asks about conservatives and which views they keep quiet about in relation to policy. I think there is more variation on responses to climate change, foreign policy, and tax policy than you might think. The fear comes not from the social media mobs, but from the wealth people and interest groups funding fellowships.

About ten years ago Reiham Salam and Ross Douthat wrote Grand New Party in part to stake out a fiscally more moderate and socially conservat(ish) framework. There are obviously a lot of voters in that position, but the donor class was never a big fan. Trump seems to have taken that plank in a more populist direction and run with it, but there doesn’t seem to be the policy and personnel infrastructure to execute on this, so you see a more donor class friendly presidency (at least so far).

The Evolution meeting is happening right now in Portland. Check out the hashtag, #evol2017.

California just added four more ‘discriminatory’ states to its travel ban. This is going to impact academics in the UC system who may want to visit UT or UNC or Duke. As a friend pointed out the state of California is really punishing the blue areas of red states, since these are the places which interact the most with California. I think this is just BDS thinking spreading. It may trigger counter proposals, but as I said the people most impacted in red states are Democrats. Perhaps there won’t be any reaction? Like economic sanctions on authoritarian states this is going to hurt people you don’t want to hurt, without impacting the people you are targeting. But it makes you feel good.

Happy Eid.

In case you haven’t noticed I’ve been posting on Brown Pundits a fair amount.

The assumption of pulse admixtures is easy, but it’s often wrong. I really hope this gets more wide circulation because it might be leading us astray in many ways. Though this varies by taxa. Plants probably have less pulse admixture going on that social organisms.

In Turkey, No Teaching Of Evolution, But Banning Gays Is Fine. It’s hard to gauge Erdogan sometimes, because he made some liberal(ish) noises as late as the Arab Spring in 2011. No longer.

Translating Genesis. Alter’s translation and commentary is my favorite so far, but it’s been many years since I read Genesis. Any good recommendations? (please don’t say NIV)

New job.

Enrichment of low-frequency functional variants revealed by whole-genome sequencing of multiple isolated European populations.

Draft genome of the Reindeer (Rangifer tarandus). Huge on Sami Twitter.

Savarkar’s book Hindutva needs a new cover.

A former executive is accusing Infosys of racism that favours Indians #whiteSupremacy.

Genetic loci associated with coronary artery disease harbor evidence of selection and antagonistic pleiotropy. Not a huge surprise.

Did I mention SciReader is back?

Estimates of Introgression as a Function of Pairwise Distances.

Leaderless Uber Scrambles to Prevent Employee Exodus. I think if Netflix ever stumbles they’ll have enormous issues immediately, since their hiring and firing policy puts zero emphasis on loyalty.

US court grants Elsevier millions in damages from Sci-Hub. If you don’t know about Sci-Hub, read the article.

Robots That Make 400 Burgers an Hour May Soon Take over Fast Food Restaurants. Burger meat is usually the low quality stuff. I suspect a combination of lab grown meat and/or vegan meat-substitute is going to come to dominate the market in a generation. Combined with automated burger making a whole sector will be transformed (in contrast, steaks require a lot more work to imitate, so people will probably eat real meat steaks for a while).

Natural selection shaped the rise and fall of passenger pigeon genomic diversity.

Revenge of the scaly Tyrannosaurus.

June 24, 2017

We need more housing for the upper upper middle class

Filed under: Culture,Housing — Razib Khan @ 9:46 pm
$1.5 million dollar house in Palo Alto

When people talk about real estate affordability and gentrification often the focus is on housing for the poor. Myself, I don’t think this is the issue. People with means wouldn’t move into poor neighborhoods if there was housing they could afford elsewhere.

Most of the “multi-million dollar” houses in Palo Alto are not mansions. Many are not really worth that much because of the house; it’s just the land. These are modest homes which really are appropriate for middle class buyers. In fact they were often built with middle class buyers in mind.

But in places like Palo Alto they are now for two types of people: long-term residents (who also likely don’t pay much property tax), and those with very high incomes and/or wealth due to selling companies.

From an article published last year:

The average price of the Palo Alto homes that went on the market today is just over $3 million. With a 20 percent down payment and the state’s average 30-year fixed mortgage rate of 3.77 percent, the average monthly payment on those homes would be a little over $14,000, two-thirds of the monthly income for a quarter-million dollar household.

It’s hard to imagine that two married Google engineers in their twenties could afford a house in Palo Alto. It’s beyond their means. But these homes are not luxurious in and of themselves. They’re all that the upper upper middle class have access to nearby.

In Silicon Valley they love to reimagine stuff. But only some people like the demi-god Elon Musk are focusing on concrete things, like cars and rockets. They need to re-imagine housing. There’s no reason the people coding the future should live in post-war ranch homes.

The pork episode of Master of None

Filed under: Aziz Ansari,Religion — Razib Khan @ 7:14 pm


The Aerogram has a piece out, Bacon & (Un)Belief: Religion & American Secularism in Master of None, which reviews The Master of None episode about religion. I kind of agree that it was a little unbelievable in relation to his cousin, and how quickly he became a porkoholic.

That being said I think it is important to note a personal aspect of Aziz Ansari’s relationship to religion. Here’s a correction to an article in The New York Times profiling Aziz:

In an earlier version of this article, Michael Schur, the co-creator of “Parks and Recreation,” partly described Mr. Ansari as a Muslim. Mr. Ansari describes himself as an atheist.

Aziz Ansari does not define himself from what I can tell as a bad or liberal Muslim. He says he’s not religious. He happens to be a guy who is an atheist, a very negatively viewed group, who is from a Muslim background a very negatively viewed group. That is one way we have a lot in common.

Also, I had a bacon experience very similar to Aziz. Though in my case it was at a friend’s house where they were Hindus from West Bengal, and my friend was having bacon. My mom came over and I had a piece of bacon in my mouth. She was a little chagrined though she said I’m not supposed to eat pork products.

In general I still don’t eat much pork and ham. But I really love bacon, and have no problem with pork sausages.

Hasan Minhaj and Aziz Ansari: your race defines you and it doesn’t

Filed under: Aziz Ansari,Comedy,Film,Hasan Mihnaj — Razib Khan @ 4:31 pm

Today I watched Homecoming King, a comedy show by Hasan Minhaj. Honestly I wasn’t going to watch it, because Minhaj’s political schtick at The Daily Show was not geared toward someone like me. That is, it’s funny to laugh along with him, but it is much easier if you agree with him politically. To me this is a major contrast with Aziz Ansari, who probably shares most of the politics of Minhaj, but who does not seem to foreground it as much.

Some of this is happenstance. Minhaj blew up on The Daily Show, which focused on politics with a liberal slant. Ansari became more well known through episodic television. That’s going to impact the sort of comedy they put out there.

But after watching Minhaj outside of The Daily Show context, and comparing his routine to Aziz Ansari’s (I’ve also watched much of Master of None), I think it is notable how differently they come off despite the likelihood that on the fundamentals they probably agree about much in American society. In short, Minhaj’s experience and recollection of racism seems much more raw to me than Ansari, who seems to have taken it more in stride.

I was encouraged to watch Homecoming King  in part because Minhaj grew up in Davis, California. I lived there for five years and one of my closest friends during my undergraduate years is a Davis native. In fact I went to her wedding in Davis during Minhaj’s senior year in high school. The centerpiece of Homecoming King happens to be about an event before prom which involved racism of a subtle but hurtful form that traumatized him in a very deep fashion. He’s talked about this incident extensively so you can Google it. But it colors all of Homecoming King.

But there are some differences between Ansari and Minhaj which I think require highlighting. Ansari is 5’6 feet tall, while Minhaj is 6’0 feet tall. Ansari is also darker-skinned, and I think I can say he is less conventionally attractive than Minhaj (readers who are attracted to men can correct me here). Finally, Minhaj grew up in very liberal Davis, California, situated between the Bay Area and Sacramento. Ansari grew up in a small town in South Carolina. I suspect that Ansari probably faced more racism than Mihnaj when he was growing up if I had to bet.

And yet of the two Aziz Ansari seems to be less deeply impacted by the banal ubiquity of white American racism. He acknowledges that it exists, sometimes in a pointed fashion. But he does not seem to let it define him.

In  Homecoming King Minhaj’s trauma from his abortive relationship with a white girlfriend scars him so much that he says he could not date white girls after that. In contrast I’m sure Ansari has experienced some level of racism against him on the dating scene. Especially in the South where when he was growing up interracial relationships were probably more taboo than in Davis. It comes up a few times in Master of None, but it’s not defining in any way. He keeps on trying to find someone he can connect with no matter their race, even if “on paper” they should be out of reach for a short dark sinned guy.

Finally, this is a minor thing, but Ansari is more explicitly disconnected from his Muslim background. He has stated he is an atheist to the media. One episode of Master of None involves him eating pork in front of his parents. Minhaj in contrast seems to own his Muslim identity much more (albeit, of a very liberal cultural variety).

Rather than being exemplars of young brown men in the United States, the subtle differences between Ansari and Minhaj show that there isn’t one way to be brown, and that we aren’t impacted in the same way by how society views us. Like Minhaj I went to high school where I was the only brown kid. Also, like Minhaj I was called Saddam Hussein. Unlike Minhaj my town was overwhelmingly conservative, while his was overwhelmingly liberal. While my town was over 90 percent white (actually more than 95 percent when I went to high school since I’m about 10 years older than Minhaj), his was about 70 percent white. What was the difference between us? A lot of it comes down to personality.

Some liberals of a minority background feel besieged by the white majority. In contrast, many of us who are more conservative accept racism is part of life, but move on, and don’t believe it is as determinative as liberals assert. Much of this comes down to personality differences, rather than race differences. Minhaj and Ansari are both successful politically liberal Indian American comedians from a Muslim background. But how they experienced American society and present themselves still differences because they are still individuals with all the differences that entails.

Indian genetics, part n of many

Filed under: ancient india,History,Indo-Europeans — Razib Khan @ 2:59 pm

I put up close to definitive piece for me in relation to South Asian historical population genetics. At least until new research is published. I did leave out some stuff about my own vague thoughts…but I think the takeover of Hattian and Hurrian cultures by the Nesha (Hittites) and Haryannu (Mitanni) have something to teach us….

Indian genetic history: before the storm

Filed under: Genetics,History,India — Razib Khan @ 2:52 pm

Over at Brown Pundits I’ve mentioned the continuing simmer of controversy over a recent piece, How genetics is settling the Aryan migration debate. This has prompted responses in the Indian media from a Hindu nationalist perspective. One of these notes that the author of the piece above cites me, and then goes on to observe I was fired from The New York Times a few years ago due to accusations of racism (also, there is the implication that I’m just a blogger and we should trust researchers with credibility like Gyaneshwer Chaubey; well, perhaps he should know that Gyaneshwer Chaubey considers me “unbiased” according to an email exchange which I had with him last week [we all have biases, so I think he’s wrong in a literal sense]).

I was a little surprised that a right-wing magazine would lend legitimacy to the slanders of social justice warriors, but this is the world we live in. Those who believe that everything written about me in the media, I invite you to submit your name and background to me. I have contacts in the media and can get things written if I so choose. Watch me write something which is mostly fact, but can easily misinterpreted by those who Google you, and watch how much you value the objective “truth-telling” power of the press.

There’s a reason so many of us detest vast swaths of the media, though to be fair we the public give people who don’t make much money a great deal of power to engage in propaganda. Should we be surprised they sensationalize and misrepresent with no guilt or shame? I have seen most of those who snipe at me in the comments disappear once I tell them that I know what their real identity is. Most humans are cowards. I have put some evidence into the public record to suggest that I’m not.

Perhaps more strange for me is that the above piece was passed around favorably by Sanjeev Sanyal, who I was on friendly terms with (we had dinner & drinks in Brooklyn a few years back). I asked him about the slander in the piece and he unfollowed me on Twitter (a friend of Hindu nationalist bent asked Sanjeev on Facebook about the articles’ attack on me, but the comment was deleted). It shows how strongly people feel about these issues.

I’m in a weird position because I’m brown and have a deep interest in Indian history. But that interest in Indian history isn’t because I’m brown, I’m pretty interested in all the major zones of the Old World Oikoumene. Aside from some jocular R1a1a chauvinism I don’t have much investment personally (I just told said Hindu nationalist friend who turns out to be R2 to clean my latrine; joking of course, though I’m sure he resents that I’m descended on the direct paternal line from the All-Father & Lord of the Steppes and he is not!).

In the aughts I accepted the model outlined in 2006’s The Genetic Heritage of the Earliest Settlers Persists Both in Indian Tribal and Caste Populations. But to be frank it always struck me as a little confusing because the tentative autosomal data we had suggested that many South Asians were closer to West Eurasians than deep divergences dating to the Last Glacial Maximum would suggest. Since I’ve written something like 5 million words in 15 years, I actually can check if I’m remembering correctly. So here’s a post from 2008 where I express reservations of the idea of long term deep heritage of Indians separate from other West Eurasians. The reason I was so impressed by 2009’s Reconstructing Indian Population History is that it resolved the paradox of South Asian genetic relatedness.

To recap, Reich et al. proposed that modern Indians (South Asians) could be modeled as a two way mixture between two distinct populations with separate evolutionary genetic histories, Ancestral North Indians and Ancestral South Indians (ANI and ASI). How distinct? ANI were basically another West Eurasian population, while ASI was likely nested in the clade with Eastern Non-Africans. Additionally, there was a NW-to-SE and caste admixture cline. In other words, the higher you were on the caste ladder the more ANI you had, and the further your ancestors were from the north and west, and more ANI you had. The difference between Y and mtDNA, male and female, could be explained by sex-biased migration.

But there were still aspects of the paper which I had reservations about. After all, it was a model.

  • Models are imperfect fits onto reality. The idea of mass migration seemed ridiculous to me at the time, because even by the time of the Classical Greeks it was noted that Indian was reputedly the most populous land in the world (to their knowledge). But ancient DNA has convinced me of the reality of mass migrations.
  • I wasn’t sure about the nature of the closest modern populations to the ANI. The researchers themselves (in particular, Nick Patterson) told me that the relatedness of ANI to Europeans was very close (on the order of intra-European differences). But modern Indians do not look to be descended from a population that is half Northern European physically. Again, ancient DNA has shown that there was lots of population turnover, and it turns out that Europeans and ANI were likely both compounds and mixed daughter populations of common ancestors (also, typical European physical appearance seems to emerged in situ over the past 5,000 years).
  • The two way admixture modeled seemed too simple. I had run some data and it struck me that North Indian populations like Jats had something different than South Indian groups like Pulayars. In 2013 Priya Moorjani’s paper pretty much confirmed that it was more than a two way admixture along the ANI-ASI cline.

This March BMC Evolution Biology published Silva et al’s A genetic chronology for the Indian Subcontinent points to heavily sex-biased dispersals. It has made a huge splash in India, arguably triggering the write up in The Hindu. But for me it was a bit ho-hum. If you read my 2008 post it is pretty clear that I suspected the most general of the findings in this paper at least 10 years back. It is nice to get confirmation of what you suspect, but I’m more interested to be surprised by something novel.

Nevertheless A genetic chronology for the Indian Subcontinent points to heavily sex-biased dispersals has come in for lots of repeated attack in the right-wing Indian press. This is unfair, because it is a rather good paper. I suspect that it wasn’t published in a higher ranked journal because most scientists don’t consider the history of India to be that important, and they didn’t really apply new methods, as opposed to bringing a bunch of data and methods together (in contrast, the 2009 Reich et al. paper was one of the first publications which showed how to utilize “ghost populations” in explicit phylogenetic models with relevance to human demographic history).

As it happens I will be writing up my thoughts in detail in an article for a major Indian publication (similar circulation numbers as The Hindu). This has been in talks for over six months, but I’ve been busy. But a month or so ago I thought it was time that I put something into print for the Indian audience, because I felt there was some misrepresentation going on (i.e., the Aryan invasion theory has been been refuted by genetics, but this is what many Indians assert).

For any years people have told me there are certain topics that shouldn’t be talked about. I have offended people greatly. There are many things people do not want to know. I have come to the conclusion this is not an entirely indefensible viewpoint (though if you accept this viewpoint, I think acceptance of authoritarianism is inevitable, so I hope people will toe the line when the new order arrives; knowing their personalities I think they will conform fine). But my nature is such that I continue to have nothing but contempt for the duplicitous and craven manner in which people go about these sorts of private conversations. I assume that as someone with the name “Razib Khan” I will be attacked vociferously by Hindu nationalists, who will no doubt make recourse to the Left-wing hit pieces against me to undermine my credibility. The fact that these groups are fellow travelers should tell us something, though I will leave that as an exercise for the reader.

I will write my piece that reflects the science as I believe it is, without much consideration of the attacks. That is rather easy for me to do in part because I live in the United States, where denigrating the deeply held views and self-esteem of Hindu nationalists is not sensitive or politically protected (unlike say, Muslims). And Hindu nationalists are less likely to kill me by orders of magnitude than Muslim radicals, and they have far less purchase in this nation then the latter (though you may be interested to know that very conservative Muslims follow me on Twitter; they’re actually more open-minded than many SJWs to be entirely honest).

Let me go over some general points that I see coming up over and over on the relationship between Indian (pre)history and genetics in the critiques .

One of the major critiques has to do with the nature of R1a-Z93 and its subclades. Basically this Y chromosomal haplogroup, the greatest that has ever been known, exhibits a strong signature of very rapid expansion over the past 4,000 years or so. It is divided from Z282. While Z93 is found in South Asia, Central Asia, and Siberia, Z282 is European, with its dominant subclade the one associated with Eastern Europeans. Both of these clades of R1a have gone through massive expansion. In the Altai region R1a is 40% of the heritage of peoples who are now predominantly East Eurasian today. But they are Z93. Additionally, ancient DNA from the Pontic Steppe dated ~4,000 years ago from Srubna remains is Z93, as are Scythian remains from the Iron Age.

Much of the argument comes down to dating, and citing papers that give deep coalescence numbers between difference branches of R1a1a. Hindu nationalists and their fellow travelers point to recent papers which give dates >10,000 years ago, and so place the origin of Z93 plausibly in the Pleistocene. The problem is that Y chromosomal coalescence dating is something of a mug’s game. Often they use microsatellite data whose mutational rates are highly uncertain. In contrast, using SNP data, which has a slower mutation rate but requires a lot more data, you get TRMCA (common ancestry) between Z93 and Z282 around ~5,800 years ago. But coalescence estimates often have wide confidence intervals of thousands of years. And even with these intervals, the assumptions you make (e.g., mutation rate) strongly influence your midpoint estimate.

The Y chromosomal data is powerful, but its interpretation is still buttressed upon other assumptions. The really big picture framework is the nature of ancient genome-wide variation across Eurasia. Lazaridis et al. 2016 condition us to a prior where much of Eurasia was subject to massive population-wide genetic changes since the Holocene. Therefore, I am much less surprised if there was massive genetic change in India relatively recently. The methods in Priya Moorjani’s paper and in other publications make it obvious that mixture was extensive in South Asia between very distinct groups until about ~2,000 years ago. In fact, Moorjani et al. using patterns of variation across the genome to come at a number of two to four thousand years ago as the period of massive admixture.

Though we don’t have relevant ancient DNA from India proper to answer any questions yet, we do have ancient DNA from across much of Europe, Central Asia, and the Near East. What they show is that Indian populations share ancestry from both Neolithic Iranians and peoples of the Pontic steppe, who flourished ~5 to ~10,000 years ago. To some extent the latter population is a daughter population of the former…which makes things complicated. Conversely, no West Eurasian population seems to harbor ancient signals of ASI ancestry.

One scientist who holds to the position that most South Asian ancestry dates to the Pleistocene argued to me that we don’t know if ancient Indian samples from the northwest won’t share even more ancestry than the Iranian Neolithic and Pontic steppe samples. In other words, ANI was part of some genetic continuum that extended to the west and north. This is possible, but I do not find it plausible.

The reasons are threefold. First, it doesn’t seem that continuous isolation-by-distance works across huge and rugged regions of Central Eurasia. Rather, there are demographic revolutions, and then relative stasis as the new social-cultural environment crystallizes. This inference I’m making from ancient DNA and extrapolating. This may be wrong, but I would bet I’m not off base here.

Second, it strikes me as implausible that there was literally apartheid between ASI and ANI populations for the whole Holocene right up until ~4,000 years before the present. That is, if Northwest India was involved in reciprocal gene flow with the rest of Eurasia over thousands of years I expect there should have been some distinctive South Asian ASI-like ancestry in the ancient DNA we have. We do not see it.

Third, one of the populations with strong affinities to some Indian populations are those of the Pontic steppe. But we know that this group itself is a compound of admixture that arose 5,000-6,000 years ago. Because of the complexity of the likely population model of ANI this is not definitive, but it seems strange to imagine that ANI could have predated one of the populations with which it was in genetic continuum as part of a quasi-panmictic deme.

Finally, many of the critiques involve evaluation of the scientific literature in this field. Unfortunately this is hard to do from the outside. Citing papers from the aughts, for example, is not wrong, but evolutionary human population genomics is such a fast moving field that even papers published a few years ago are often out of date.

Many are citing a 2012 paper by a respected group which argues for the dominant model of the aughts (marginal population movement into South Asia). One of their arguments, that Central Asian migrant should have East Asian ancestry, is a red herring since it is well known that this dates to the last ~2,000 years or so (we know more now with ancient DNA). But the second point that is more persuasive in the paper is that when they look at local ancestry of ANI vs. ASI in modern Indians, the ANI haplotypes are more diverse than West Eurasians, indicating that they are  not descendants but rather antecedents (usually the direction of ancestry is from more divers to less due to subsampling).

There are two points that I have make here. First, local ancestry analysis is difficult, so I would not be surprised if they integrated ASI regions into ANI and so elevated the diversity in that way (though they think they’ve taken care of it in the paper). Second, if the ANI are a compound of several West Eurasian groups then we expect them to be more diverse than their parents. In other words, the paper is refuting a model which is almost certainly incorrect, but the alternative hypothesis is not necessarily the one they are supporting within the paper.

But there are many things we do not know still. Many free variables which we haven’t nailed down. Here are some major points:

  • Y chromosomal lineages have a correlation with ethno-linguistic groups, but the correlation is imperfect. R1b and R1a seems correlated with Indo-European groups, but both these are found in high proportions in groups which are putatively most “pre-Indo-European” in origin (e.g., Basques, Sardinians, and South Indian tribals and non-Brahmin Dravidian speaking groups). Also, haplogroups like I1 in Europe expands with Indo-Europeans locally, suggesting there was lots of heterogeneity in Indo-Europeans as they expanded. In other words, Indo-European expansion in relation to powerful paternal lineages did not always correlate with ethno-linguistic change.
  • There are probably at minimum two Holocene intrusions from the northwest into South Asia, but this is a floor. The models that are constructed always lack power to detect more complexity. E.g., it is not impossible that there were several migrations of Indo-Europeans into South Asia which we can not distinguish genetically over a period of a few thousand years.
  • If one looks over all of South Asia it may be that ASI ancestry in totality is >50% of the total genome ancestry. I haven’t have a good guess of the numbers. If this is correct, perhaps most South Asian ancestors 10,000 years ago were living in South Asia (though the fertility rate are such in Pakistan that ANI ancestry is increasing right now in relative rates).
  • But, this presupposes that ASI were present in South Asia in totality 10,000 years ago, rather than being migrants themselves. If ancient DNA confirms that ANI were long present in Northwest India, I hold then it is entirely likely that ASI was intrusive to South Asia! The BMC Evolutionary Biology Paper does a lot of interpretation of deep structure in haplogroup M in South Asia. I’m moderately skeptical of this. Europe may not be a good model for South Asia, but there we see lots of Pleistocene turnover.

So where does this leave us? Ancient DNA will answer a lot of questions. Pretty much all scientists I’ve talked to agree on this. My predictions, some of which I’ve made before:

  1. The first period of admixture is old, and dates to the founding of Mehrgarh as an agricultural settlement. The dominant ANI component dates to this period and mixture event, all across South Asia. The presence in South India is due to expansion of these farming populations.
  2. A second admixture event occurred with the arrival of steppe people. Those who argue for the Aryan invasion model posit 1500 BCE as the date. But these people probably were expanding in some form before this date.
  3. We still don’t know who the antecedents for the Indo-Aryans were. Probably they were a compound of different steppe groups, and also other populations which were mixed in (by analogy, in Europe it is obvious now that there was some mixture with the local European farmers and hunter-gatherers as Europeans expanded their frontier westward; the same probably applies for Indo-Aryans are the BMAC).

June 22, 2017

Nearly 20% of McDonald’s will have electronic kiosks by the end of 2017

Filed under: Economics — Razib Khan @ 9:56 pm


McDonald’s hits all-time high as Wall Street cheers replacement of cashiers with kiosks:

Andrew Charles from Cowen cited plans for the restaurant chain to roll out mobile ordering across 14,000 U.S. locations by the end of 2017. The technology upgrades, part of what McDonald’s calls “Experience of the Future,” includes digital ordering kiosks that will be offered in 2,500 restaurants by the end of the year and table delivery.

There are 14,500 locations. Right now 500 stores have kiosks.

June 21, 2017

American cities need to grow up to solve the housing crisis

Filed under: Culture,Housing Crisis — Razib Khan @ 7:51 pm

Martin Jacques observes in When China Rules the World that East Asian cities don’t have the organically evolved feel of European urban areas. He chalks this up to the rapid economic development of the “Asian Tigers” and Japan over the past few decades. Buildings were built, buildings were torn down. The rate of change didn’t allow for the accumulation of historical authenticity. There’s also another reason: many East Asian societies have built buildings out of perishable materials like wood and so not prized historicity of structures.

The oldest free standing timber building in China dates to 782. The Songyue Pagoda dates to 523, but it’s made of brick. In contrast great public buildings made of marble still exist in the Western world that date back to antiquity. The Pantheon became a church and so is preserved in nearly its full glory. Public buildings and historical architecture are great. But the valorization of the principle can come at a price.

Willamette Week has an article up on the attempt to “maintain historic character,” and how it prevents the emergence of affordable housing. Portland’s Laurelhurst Neighborhood Fights to Keep the Housing Crisis Out:

At the end of last month, residents of Laurelhurst turned out in record numbers to vote in their neighborhood association election for one reason: to get protection from developers.

The winning candidates pledged to bypass City Hall and ask the National Park Service to declare much of the 425-acre eastside neighborhood a historic site.

By being labeled “historic” the residents can block development, and preserve the state of their neighborhood the way they like it. They are very explicit about what they want to do:

By seeking to make the neighborhood a historic district, Laurelhurst residents are taking aim at what they see as the neighborhood’s greatest enemy: a real estate developer with a backhoe, bent on tearing down 100-year-old houses to replace them with apartments, a duplex or a huge new house.

“The whole street—it will look like Beaverton by the time they’re done,” says John Deodato, a longtime Laurelhurst homeowner who says he gets 20 letters a month from developers seeking to buy his home. “The city won’t do anything about it unless we do.”

Beaverton is a suburb of Portland. Though the analogy is imperfect, if Portland is West LA, Beaverton is Irvine. The connotation of this insult is clear to any Oregonian. It’s a sneer at those without refined sophistication and breeding.

Laurelhurst has a 14 to 1 Democrat to Repubican ratio, and median home value is $750,000. The median household income for the greater Portland area is $65,000. The median home value in Beaverton is about $360,000. I looked at Zillow and found an $800,000 home in Laurelhurst. You can see that it has appreciated nicely over the last 10 years.

The recent neighborhood association seats were contested. The outcomes were clear:

More than 800 people voted in the election—a record for the neighborhood, and more than 10 times the number of voters in the previous election. The vote went overwhelmingly for the historic district candidates. Pratt, the pro-historic district candidate for president, won just under 80 percent of the vote.

It is no surprise that the people who live in Laurelhurst are voting to protect their interests. Their implicit gated community, with its high property values. They may be progressive in their avowed values, but when their self-interest is at state, they make sure to take care of their self-interest and conserve what they have the way they like it.

There are of opponents to this trend of gentrified Portland neighborhoods. They profile an alliance between a developer and the head of 1000 Friends of Oregon, a nonprofit which favors density over sprawl. Below is some of their rationale, along with what someone in Laurelhurst has to say about these men:

“The reasons we are involved with this bill has nothing to do with whether the home builders are involved with it,” says McCurdy. “The bill increases housing opportunities—diverse housing opportunities and affordable housing opportunities—all of those inside our towns and cities, which is part of the land-use deal that we as Oregonians have had in place for 40 years.”

McCurdy believes what’s happening in Laurelhurst is a “misuse of historic district designation to prevent change.”

Critics of the bill call 1000 Friends’ and the home builders’ support an unholy alliance.

“Gov. McCall would be spinning in his grave to see his beloved 1000 Friends of Oregon organization working side-by-side with the Home Builders Association, buying into the alt-right, fake-news theory of demolition as the cure for affordability,” wrote Tracy Prince, vice president of the Goose Hollow Foothills League, in a May 17 letter to legislators.

In the early 2000s anything and anyone that self-styled progressives did not like was “neocon.” Today it is “alt-right.” Somehow this woman believes that allowing for development which would allow for an increase in the local housing supply and destroy some of the quaint town-like character of East Portland streets is “alt-right.” If she lived in the 1950s I wonder if she would accuse her enemies of being “Communists.”

The article has a definite slant against the Laurelhurst neighborhood association. The author of the piece lives in Northeast Portland, so she’s able to see through the pleading for the “special character” of Laurelhurst (in fact, records indicate that she is a recent transplant to the city from New York City, so her sympathies are likely not with the old-timers). At one point the author interviews a man who is living out of his pickup truck in Laurelhurst. He’s making $12 an hour, and couldn’t afford a place elsewhere in Portland, let alone Laurelhurst. She notes that “A Craigslist ad posted last week shows a restored attic in this neighborhood renting for $1,000 a month” in the neighborhood.

The piece concludes:

Pratt, the neighborhood association president, knows plenty about homelessness. A couple years ago, he served on the board of social services agency JOIN, which coordinates shelter beds.

Pratt acknowledges Portland needs to build more housing. But not too much of it in Laurelhurst.

“Everybody says the solution to homelessness is housing,” he says. “I don’t think the solution is that every neighborhood looks the same, and every neighborhood has everything, and your neighborhood [has] no uniqueness anymore.”

People have interests. But they don’t want to admit those interests in public. The Laurelhurst neighborhood association’s attempt to gain historic designation is regulatory arbitrage. They want to preserve their neighborhood and property values, and not let in the riff-raff have any space. Earlier in the piece there is a quote from the association president: “Pratt warns that if Laurelhurst isn’t allowed to decide what gets developed within its boundaries, the neighborhood will indeed become cheaper eventually—because it will become hideous.

Beauty is important. It has value. But if we need to sacrifice beauty for affordability, at some point the latter does have to overrule the former.

The political Left on the national level is at least waking up to the problem. Recently Mother Jones wrote Berkeley Says It’s Standing Up to Trump, But It’s Actually Busy Arguing About Zucchini. The title comes from this passage:

At Tuesday night’s city council meeting, which touched on a number of housing issues, this dissonance was on display in a resident’s complaint about a proposed new building that would cast shadows on her zucchini plants. The project was returned to the city’s Zoning Adjustments Board. The zukes live another day.

“Delaying or denying housing approvals suggests to Berkeley neighbors that their stalling tactics will work, and invites more of them in the future,” web developer Kevin Burke wrote in a letter to the council after the meeting, expressing his disappointment with the decision. “I would also much rather have a zucchini garden crisis than a housing crisis.”

The gut-punch is that an anti-development mayor has been elected in Berkeley. How “radical.” In San Francisco and San Mateo counties $105,000 a year for a household of four is low income. The average household income in San Francisco happens to be $105,000 per year.

Yesterday and today on Twitter there was a discussion about post-doc salaries. To a great extent this is a stage in academic life when the salary range is compressed because there are broad national guidelines and expectations. The median post-doc makes $46,000. The 10th percentile is $37,000, and the 90th percentile is $65,000.

So let’s compare some universities and their locales. In US News Stanford has the #2 genetics graduate program and Washington University in St. Louis the #5 program.

According to a cost of living calculator a “salary of $50,000 in St. Louis, Missouri should increase to $304,167 in Palo Alto, California.” This is because housing is 24 times more expensive in Palo Alto. So a hypothetical post-doc at Stanford that is paid $100,000 is equivalent to $16,000 in St. Louis. You might object that Palo Alto to St. Louis is apples to oranges, but the housing expense in the greater Bay Area means that you can’t just escape Palo Alto for relief. A Zillow check of Washington University vs. Stanford shows that houses within walking distance of the latter university are about 15 times more expensive than the former. The average assistant professor at Washington University has a salary in the low $100,000 range. At Stanford it is in the mid-$100,000 range. Basically a Stanford assistant professor makes about 1.5 times more in salary than a Washington University assistant professor, even though cost of living is going to be 6 times greater in Palo Alto.

At this point I could go into tangents about university housing for post-docs and faculty in the Bay Area (one of my friends is doing a post-doc at UCSF and had to have a subsidized apartment for obvious reasons). And obviously opportunities for consulting are more available in the Bay Area. But the point is not about academics and their careers. Rather, I’m using an illustration of the circumstances in which “winners” in American society, people with lot of higher education, can find themselves in financial stress.

There are genuine benefits of starting a career in the Bay Area. For an academic you have access to world-class institutions, with the Stanford, UCSF and Berkeley triangle, and UC Davis and UC Santa Cruz just beyond the horizon, and other institutions like San Francisco State to fill out the landscape. For a techie you know where the “action” is. If you are a single person, a $125,000 salary at Google won’t allow to you live luxuriously, but you can survive. Hopefully you’ll be able to make connections that help you later on, when you inevitably have to ask for a transfer because you want a house and a family.

This is the cycle of life now. But not for everyone. I lived in California for almost ten years, and there are those to the Golden State born whose families bought homes decades ago. The property tax regulations California are Byzantine, but there are plenty of cases where individuals are “grandfathered in” and pay very little tax on a very valuable property. And, these benefits can pass on to children. In other words you may have millennials paying tax rates on million dollar homes that date back to assessments in the 1970s, when their parents owned the house.

We can debate the merits of this system. One can make a case for giving those with deep lineage in an area privileges over newcomers. I lived in a house in Berkeley where the property owner told me once that he paid on the order of 15 times less tax than his neighbor, because the house had been in the family for 60 years. It was purchased by his grandparents, and owned by his mother, and it had passed on to him. His profession was as a part-time photographer and musician. Because his tax bills were so modest he could rent out rooms in the house and and survive in Berkeley even though his non-property income was irregular and not particularly high (when I lived in his house he would complain that he didn’t want to purchase health insurance due to the cost).

For those of us without those privileges if we want to live in the urban areas where our specialized skills return the greatest income and also where we can network and grow our career the best, we need to make sacrifices. For many people that means putting off getting married, putting off having children. Anyone who makes less than $100,000 a year will probably have to hustle in Silicon Valley. There are flophouses from San Francisco down to San Jose where young people of more modest means live together in a communal fashion in dormitories.

How did we get here? I think I’ve outlined a major part of how we got here. Many places people want to live are extremely expensive because supply of housing is constrained.

Houston has a great food scene, but quaint and charming is not something anyone would say about it. But it is very affordable. And, the fourth largest city in this country. It lacks zoning. In contrast San Francisco is beautiful. There is something special about it, from the feces on the sidewalks in the Tenderloin to the beauty of the Golden Gate bridge. Something would be lost if one allowed it to develop vertically. But do we want the city to become a playground for the wealthy and those born into old families of the city? Because that’s what’s happening with the choices we’re making in this country.

Our vision for the future used to be optimistic. We would live better. We would be space age humans. Much of it has come to pass. Our “phones” are amazing things. Electric driverless cars will transform our cities within the next generation. But the way we do housing in this country has not moved much beyond the middle of the 20th century. We need changes in culture, changes in technology, to make things better for future generations, rather than constraining them with the paltry opportunities of the present.

June 20, 2017

Liberals will never disappear (neither will atheists)

Filed under: Behavior Genetcs,Behavior Genetics — Razib Khan @ 1:33 am

In Quillette Hrishikesh Joshi and Jonny Anomaly* ask Are Liberals Dying Out? Since the piece has been shared a fair amount (judging by my Twitter timeline), I thought I should respond to why I don’t think that is a major concern. Let me jump to their last paragraph:

Nevertheless, despite cultural trends, the best available evidence suggests that political ideology is heritable, and that people with liberal personality traits currently have far fewer children than conservatives. If this trend continues, it is possible that the reproductive choices people are making today will influence the political climate of future generations. Over the long run, conservatives could end up winning the ideological contest with fertility rather than arguments.

First, I don’t think the title reflects the modest contentions of the piece. I beseech the editors of Quillette to not engage in the titular hyperbole so common in the mainstream media!

I agree that political orientation seems heritable. That is clear in books like Born That Way. But heritability expresses itself in an environmental context. If you had a totalitarian government most of the phenotypic variation would disappear. Yes, there would be dissidents, but they’d be freaks. Most humans would conform (no, I don’t think the citizens of Soviet Russia were genetic freaks unable to grasp freedom like Howard Roark). The correlation between religiosity and fertility varies by society as well. The more secular the society, the bigger the gap (though last I checked this was not true in China). In a totally conservative future heritable variation for liberalism could just reemerge.

Second, political orientation exists on a relative plane. If one imagines it as some specific thing, or disposition, one can imagine that in the future the liberal-conservative spectrum would exist, but just be shifted. Quantitative genetics has shown that selection can move the mean many standard deviations. I don’t think this is a strong objection to their overall point, but it gets at the fact that we view liberal-conservative tendencies along a distribution (1980s liberal commentator Jeff Greenfield was widely known for making disparaging comments about gays i the prime of his career; that did not destroy his career as a liberal pundit at that time). Perhaps liberal have already won in an age when most conservatives understand and accept that gay marriage is here to stay.

Third, some of the variation is not heritable. It’s random. In fact around half of it within the population. Some people may just be liberal for stochastic reasons. You aren’t going to get rid of this with selection.

Perhaps most essential in terms of theory: frequency dependence. The dynamics of human interaction and decision making are such that the frequency of liberals declining might have an impact on their fitness. To give a weird example, perhaps an economically post-Malthusian society needs a certain number of sub-replacement liberals who engage in particularly productive work to maintain itself. If society slouched rapidly back toward Malthusianism perhaps everyone would just trudge along at replacement.

The big picture problem is assuming constant directional selection and exhaustion of heritable variation is all well and good when you are selecting for wax-seed oil, but human societies are non-linear systems which are subject to big shocks. They aren’t controlled agricultural genetic experiments.

Finally, let me use an analogous case to make an empirical objection. Many people tell me that the future will be religious due to the same dynamics above. This despite the century long trend toward secularization (parenthetical, God is Back was an ill-timed books, as the United States was shifting toward secularization at that time).

But I want to go back further. France was the first nation to start the demographic transition. In the early 19th century the secular elite was worried about the fertility of devout Roman Catholics, in particular the Poles who were arriving. The secular future they envisioned was threatened. It’s been nearly 200 years since these worries, and in those 200 years France has become more and more secular.

My point with this illustration is that if your theory can not predict the past, it can’t predict the future. At least not robustly. Liberal people will always be with us. So will shy people. And atheists too. They may wax and wane, but human variation persists. On the evolutionary genetic level I think frequency dependent dynamics are such that the fait, in the medium term, of low fitness traits is generally to become oddballs, not extinct. And once they are odd they may become fortunes favorites….

* For real, is that his real name?

Democracy leads to Islamism

Filed under: Illiberalism,International Affairs,Islam — Razib Khan @ 12:36 am

The New York Times has a piece up on the rise in Islamic extremism in the Maldives, Maldives, Tourist Haven,
Casts Wary Eye on Growing Islamic Radicalism
. I want to highlight one section:

It was governed as a moderate Islamic nation for three decades under the autocratic rule of the former president, Maumoon Abdul Gayoom. But after the country made a transition to democracy in 2008, space opened up for greater religious expression, and conservative ideologies like Salafism cropped up.

Years ago in graduate school I told a friend that democracy and even economic prosperity did not monotonically lead to greater liberalism. In the long run perhaps, but in the short run it doesn’t necessarily do that at all.

Today we generally focus on the Islamic world, but there are plenty of examples in the past and in other places which suggest to us democratic populist passions can be quite illiberal. The Gordon Riots in England in the 18th century are a case where a pragmatic shift toward liberalism in regards to religious freedom for Roman Catholics triggered a Protestant populist riot. In the United States the emergence of universal white man’s suffrage during the Age of Jackson signaled the rise of a much more muscular and exclusive white supremacy in this country. In Iron Kingdom: The Rise and Downfall of Prussia, 1600-1947 you see the arc of democratization tethering itself to conservative rural vote-banks which reinforce aristocratic privilege. Finally, democratic developments in Burma have seen an associated increase in Buddhist radicalism.

Eric Kauffman argues in Shall the Religious Inherit the Earth? that modernization, economic development, and the expansion of political representation, integrates conservative rural populations and uplifts them all the while transforming the norms of urban areas. In other words, the rural bazar melds with the urban shopping mall, and both are changed. The 1979 revolution in Iran and its aftermath has been argued to be a victory of the bazar over the Western oriented gentry. In India the rise of Hindu nationalism is an assertion of the self-confidence of sub-elites from the “cow belt” who arose to challenge the Western oriented ruling class that had dominated since the early 20th century.

When the Arab Spring was in full swing in 2011 I wrote An Illiberal People:

In newly democratic nations which are pushed toward universal suffrage and the full panoply of democratic institutions the organic process of developing some safeguards for minorities and liberal norms has never evolved, because there was no evolution. Rather, these democracies are being created out of a box. Instead of a gradual shift toward more cultural conservatism with broader franchise, in these contexts it is a foundational aspect of the democratic system. I suspect this may have long term repercussions, as in other contexts liberal elites often institutionalized or established norms which served to check majoritarian populist impulses as they ceded much of their power over time.

The modern Left has a very anodyne view of Islam. It denies that there is something structurally within many Islamic societies which enables their illiberalism, the religion of Islam. In Islamic Exceptionalism Shadi Hamid argues that the religion itself may in some fundamental manner be inimical to the sort of secular liberal democratic society we perceive to be the terminal state of all cultures. I disagree with this view. Rather, I see in contemporary Islam the torture that Reformation era Christianity experienced attempting to navigate between an ideal of a universal church and the nascent emergence of nation-states. But in the short term both Shadi and I have the same prediction: greater democracy may lead to greater illiberalism and more repression of minorities. This an inconvenient truth for many Americans. But it may be true nonetheless.

June 19, 2017

Indian genetics, the never-ending argument

Filed under: Genetics,India,Indian Genetics,Indo-Europeans,science — Razib Khan @ 10:44 pm

I am at this point somewhat fatigued by Indian population genetics. The real results are going to be ancient DNA, and I’m waiting on that. But people keep asking me about an article in Swarajya, Genetics Might Be Settling The Aryan Migration Debate, But Not How Left-Liberals Believe.

First, the article attacks me as being racist. This is not true. The reality is that the people who attack me on the Left would probably attack magazines like Swarajya as highly “problematic” and “Islamophobic.” They would label Hindu nationalism as a Nazi derivative ideology. People should be careful the sort of allies they make, if you dance with snakes they will bite you in the end. Much of the media lies about me, and the Left constantly attacks me. I’m OK with that because I do believe that the day will come with all the ledgers will be balanced. The Far Left is an enemy of civilization of all stripes. I welcome being labeled an enemy of barbarians. My small readership, which is of diverse ideologies and professions, is aware of who I am and what I am, and that is sufficient. Either truth or power will be the ultimate arbiter of justice.

With that out of the way, there this one thing about the piece that I think is important to highlight:

To my surprise, it turned out that that Joseph had contacted Chaubey and sought his opinion for his article. Chaubey further told me he was shocked by the drift of the article that appeared eventually, and was extremely disappointed at the spin Joseph had placed on his work, and that his opinions seemed to have been selectively omitted by Joseph – a fact he let Joseph know immediately after the article was published, but to no avail.

Indeed, this itself would suggest there are very eminent geneticists who do not regard it as settled that the R1a may have entered the subcontinent from outside. Chaubey himself is one such, and is not very pleased that Joseph has not accurately presented the divergent views of scholars on the question, choosing, instead to present it as done and dusted.

I do wish Tony Joseph had quoted Gyaneshwer Chaubey’s response, and I’d like to know his opinions. Science benefits from skepticism. Unfortunately though the equivocation of science is not optimal for journalism, so oftentimes things are presented in a more stark and clear manner than perhaps is warranted. I’ve been in this position myself, when journalists are just looking for a quote that aligns with their own views. It’s frustrating.

There are many aspects of the Swarajya piece I could point out as somewhat weak. For example:

The genetic data at present resolution shows that the R1a branch present in India is a cousin clade of branches present in Europe, Central Asia, Middle East and the Caucasus; it had a common ancestry with these regions which is more than 6000 years old, but to argue that the Indian R1a branch has resulted from a migration from Central Asia, it should be derived from the Central Asian branch, which is not the case, as Chaubey pointed out.

The Srubna culture, the Scythians, and the people of the Altai today, all bear the “Indian” branch of R1a. First, these substantially post-date 6000 years ago. I think that that is likely due to the fact that South Asian R1a1a-Z93 and that of the Sbruna descend from a common ancestor. But in any case, the nature of the phylogeny of Z93 indicates rapid expansion and very little phylogenetic distance between the branches. Something happened 4-5,000 years ago. One could imagine simultaneous expansions in India and Central Asia/Eastern Europe. Or, one could imagine an expansion from a common ancestor around that time. The latter seems more parsimonious.

Additionally, while South Asians share ancestry with people in West Asia and Eastern Europe, these groups do not have distinctive South Asian (Ancestral South Indian) ancestry. This should weight out probabilities as to the direction of migration.

Second, I read some of the papers linked to in the article, such as Shared and Unique Components of Human Population Structure and Genome-Wide Signals of Positive Selection in South Asia and Y-chromosomal sequences of diverse Indian populations and the ancestry of the Andamanese. The first paper has good data, but I’ve always been confused by the interpretations. For example:

A few studies on mtDNA and Y-chromosome variation have interpreted their results in favor of the hypothesis,70–72 whereas others have found no genetic evidence to support it.3,6,73,74 However, any nonmarginal migration from Central Asia to South Asia should have also introduced readily apparent signals of East Asian ancestry into India (see Figure 2B). Because this ancestry component is absent from the region, we have to conclude that if such a dispersal event nevertheless took place, it occurred before the East Asian ancestry component reached Central Asia. The demographic history of Central Asia is, however, complex, and although it has been shown that demic diffusion coupled with influx of Turkic speakers during historical times has shaped the genetic makeup of Uzbeks75 (see also the double share of k7 yellow component in Uzbeks as compared to Turkmens and Tajiks in Figure 2B), it is not clear what was the extent of East Asian ancestry in Central Asian populations prior to these events.

Actually the historical and ancient DNA evidence both point to the fact that East Asian ancestry arrived in the last two thousand years. The spread of the first Gokturk Empire, and then the documented shift in the centuries around 1000 A.D. from Iranian to Turkic in what was Turan, signals the shift toward an East Asian genetic influx. Alexander the Great and other Greeks ventured into Central Asia. The people were described as Iranian looking (when Europeans encountered Turkic people like Khazars they did note their distinctive physical appearance).

We have ancient DNA from the Altai, and those individuals initially seemed overwhelmingly West Eurasian. Now that we have Scythian ancient DNA we see that they mixed with East Asians only on the far east of their range.

The second paper is very confused (or confusing):

The time divergence between Indian and European Y-chromosomes, based on the closest neighbour analysis, shows two different distinctive divergence times for J2 and R1a, suggesting that the European ancestry in India is much older (>10 kya) than what would be expected from a recent migration of Indo-European populations into India (~4 to 5 kya). Also the proportions suggest the effect might be less strong than generally assumed for the Indo-European migration. Interestingly, the ANI ancestry was recently suggested to be a mix of ancestries from early farmers of western Iran and people of the Bronze Age Eurasian steppe (Lazaridis et al. 2016). Our results agree with this suggestion. In addition, we also show that the divergence time of this ancestry is different, suggesting a different time to enter India.

Lazaridis et al. accept a mass migration from the steppe. In fact, the migration is to such a magnitude that I’m even skeptical. Also, there couldn’t have been a European migration to South Asia during the Pleistocene because Europeans as we understand them genetically did not exist then!!!

I assume that many of the dates of coalescence are sensitive to parameter conditions. Additionally, they admit limitations to their sampling.

Ultimately the final story will be more complex than we can imagine. R1a is too widespread to be explained by a simple Indo-Aryan migration in my opinion. But we can’t get to these genuine conundrums if we keep having to rebut ideologically motivated salvos.

Related: Ancient herders from the Pontic-Caspian steppe crashed into India: no ifs or buts. I wish David would be a touch more equivocal. But I have to admit, if the model fits, at some point you have to quit.

June 18, 2017

Open Thread, 06/18/2017

Filed under: Open Thread — Razib Khan @ 9:38 pm

In the centuries around and before 1000 A.D. there was a “Viking international” of sorts. Harald Hardrada may have died in England trying to become king of that nation, but he served for a time in the Varangian Guards in Constantinople. His connections to Kievan Rus were such that priests in the Eastern Christian tradition were brought in to aid in the conversion of Norway. The book The Vikings talks about much of this.

Speaking of Kievan Rus, as I noted in the comments below the Y chromosomal lineage of the Rurikids is clearly one of Finns, not Scandinavians. But the Primary Chronicle indicates that the recent ancestors of Vladimir the Great were Scandinavian, so the cultural assimilation must have occurred earlier.

And Kievan Rus itself was more connected to other parts of Europe than Russia itself later would be. Anne of Kiev was the mother of a future king of France

An Expanded View of Complex Traits: From Polygenic to Omnigenic. Everyone is talking about this. Have not read it. A lot of the discussion is going on on Twitter. Jonathan Pritchard has been very active in the discussions.

Punctuated evolution shaped modern vertebrate diversity. This paper is about morphology, but still cool.

How genetics is settling the Aryan migration debate. The author follows me on Twitter and quotes me in the piece (from one of my blog posts in 2009). He clearly knows his stuff and seems to have read my posts, so nothing new. But he does get some scientists to put into the record that they don’t believe things they believed in the late 2000s. One problem is that Indian “Out of India” proponents keep citing papers from the late 2000s which the authors themselves likely don’t stand by anymore.

Reading a bit of A Cooperative Species: Human Reciprocity and Its Evolution. I feel the field of human behavioral ecology gets short shrift, though to be fair before Joe Heinrich started writing books there really weren’t any popularizers (both David Sloan Wilson and E. O. Wilson do do some on the side in this area).

Berkeley Says It’s Standing Up to Trump, But It’s Actually Busy Arguing About Zucchini. Median home price in Berkeley is now $1,100,000.

Over the past year for various reasons I’ve gained 10 pounds. My waste has gone from 29-30 inches to 31-32. They did a measurement at the gym and my body fat is now 17%.

So I’m going on a ketogenic diet to cut some of the fat. Any advice is welcome.

The Finnic peoples emerged in Baltic after the Bronze Age

Filed under: Finland,History — Razib Khan @ 10:07 am


A reader in the comments reminds me there has been a preprint which is relevant to the population structure of Baltic Europe which came out a few months ago, Extensive farming in Estonia started through a sex-biased migration from the Steppe:

…Here we present the analyses of low coverage whole genome sequence data from five hunter-gatherers and five farmers of Estonia dated to 4,500 to 6,300 years before present. We find evidence of significant differences between the two groups in the composition of autosomal as well as mtDNA, X and Y chromosome ancestries. We find that Estonian hunter-gatherers of Comb Ceramic Culture are closest to Eastern hunter-gatherers. The Estonian first farmers of Corded Ware Culture show high similarity in their autosomes with Steppe Belt Late Neolithic/Bronze Age individuals, Caucasus hunter-gatherers and Iranian farmers while their X chromosomes are most closely related with the European Early Farmers of Anatolian descent…

As you can see in the PCA plot above the Comb Ceramic Culture and the Corded Ware culture in Estonia are modeled well by the three ancestral populations hypothesis for Europe. The problem with this is that Finns and Russians with Finnic background do not fit with this model. There has been clear later gene flow.

From the text:

Interestingly, modern Estonians showed a bigger proportion of the blue component [associated with European hunter-gatherers] than CWC individuals. Comparing to CCC individuals, modern Estonians lack the red component [Eastern Siberian]. This, together with the absence of Y chromosome hg N in CCC and CWC, points to further influx and change of genetic material after the arrival of CWC.

The sample sizes are small. Additionally these are from Estonia, not Finland. But the Comb Ceramic Culture was widespread throughout the region.

Also, from a 2015 paper (supplements):

Among the northern Europeans, the Finnish (finni3) show evidence of an admixture event involving a minority source most similar to contemporary North Siberians (469CE (213BCE-1011CE)). Finns are thought to have originated from the northward migration, and subsequent contact, between Central Europeans and indigenous Scandinavian hunter-gatherers closely related to the Saami [S33]. The Saami are closely related to the individuals that make up the North Siberian world region, and whilst our confidence in this admixture date is low because of the small size of the cluster, the event we see is likely to represent this key period in Finnish history.

The “North Siberia” cluster are: Selkup, Chukchi, Dolgan, Ket, Koryak, Nganassan, Yakut and Yukagir. The admixture is very recent. I suspect too recent. But it gets us to the qualitative point that the Siberian admixture into Finns is probably not that old.

Related: The Origin of the Finnic Peoples.

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