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


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.

American cities need to grow up to solve the housing crisis

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.

Liberals will never disappear (neither will atheists)

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

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.

Open Thread, 06/18/2017

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


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.

The origin of the Finnic peoples

 

Update: Please see related post.

One of the very first things I wrote about in relation to historical population genetics was in on the origins of the Finnic peoples. The reasons are two fold:

– first, the Finns and Estonians speak language is rather peculiar in a Europe dominated by Indo-European tongues (I suspect one reason that Tolkien based Quenya, the high elvish language, on Finnish is that it is so otherworldy to the Germanic ear. The Sindarin language, which was the common tongue of elves in Middle Earth, was based on Welsh). Rather, the distribution to the Uralic languages extends to the east, as far as Siberia. Even the closest affinities to Finnish and Estonian extend eastward, as there are Karelians who live deep in northwest Russia.

– second, there were peculiarities in the genetics of the Finns which date back to the 20th century that have always been notable.

Some of the distinctiveness of the Finns clearly has to do with the demographic isolation of the recent past, and the range expansion into the north and east. I will ignore this aspect of recent drift, and focus on their deep history and phylogenetic relationships.

New molecular genetic techniques in the 1980s and 1990s which enabled the genotyping of Y and mtDNA lineages immediately yielded the fact that the paternal heritage of the Finns is very unique in comparison to their neighbors, and erstwhile hegemons, the Scandinavians. While Swedes tend to be haplogroup I (indigenous to Western Europe dating to the late Pleistocene) or one of the two R1 lineages (intrusive from the Eurasian steppe during the Bronze Age), Finns tend to be haplogroup N3, with a substantial minority of I. While 63 percent of Finns are N3, only 3 percent of Swedens are. Due through the reality of migration of Finns to Sweden, as well as the prevalence of Saami all across Northern Sweden until the early modern period, Swedish N3 may be due to gene flow in the last thousand years. The two R1 lineages are ~10% of the Finnish paternal gene pool, they’re strongly skewed toward R1a, while the ~40% of Swedish R1 lineages are balanced.

In contrast the mtDNA profiles of Finns are very similar to their neighbors. Like Sweden the dominant haplogroup is a branch of H, with the reduced fraction accountable for the fact that Finns have a higher percentage of U5, which has been associated with European hunter-gatherers. The various haplogroups (e.g., T) associated with Early European Farmers are at somewhat lower frequency in Finland than Sweden.

A simple explanation then presents itself to us: the Finns have been subjected to male mediated admixture into a “conventional” European substrate. But there has been long been controversy as to whether the Finnish N3 haplogroup was indigenous to Europe, or its presence in Northeast Europe was due to migration. If it was indigenous than the admixture model does not make as much sense. But as with many things we’ve moved very far in comparison to where we were when I first began to look at this issue in 2002.

If you read Human Y Chromosome Haplogroup N: A Non-trivial Time-Resolved Phylogeography that Cuts across Language Families the likelihood than the Y chromsomal structure of Finland is old seems low. First, Finnish N3 lineages are very young and underwent rapid expansion beginning 4 to 6 thousand years ago (this is evident in their whole genome variation pattern). Second, the most diversity of N seems to be in Western Siberia. Third, N exists in higher frequencies in parts of Siberia than even in Finland. Fourth, the range of N pushes it all the way to the Pacific Ocean. It is not implausible that it expanded from one rim of Eurasia to the other, but the most likely scenario is that it came from somewhere in the middle.

Also, it is likely that there has been admixture into Finns from an East Eurasian population. To give some examples, a derived SNP at EDAR is at very high frequency in Northeast Asians. The ancestral variant is dominant outside of East Asia and the New World. In Europe among modern Europeans the derived variant of EDAR is not present in indigenous populations. A quick check in the 10000 Genomes data shows that it’s at ~6% in Finns (in contrast, the ancestral variant of SLC24A5 is present at frequencies of ~1; this could be random, but I suspect in situ selection….). You can see that the derived variant is absent in a rather large sampling of other Europeans.

Running ADMIXTURE unsupervised it’s immediately obvious that Finnic peoples have a minority component of East Eurasian admixture. This dark blue element is absent in most of the Swedes. Not surprisingly the Russians exhibit structure depending on where you sample. Some Russian populations are clearly Slavicized relatively recently, and exhibit a genetic profile rather like Finnic peoples (this northern Russian regions also have high frequencies of haplogroup N, which is much rarer in the south or among Ukrainians).

There’s a cline that runs east to west in relation to this component. The Finn’s neighbors immediately to the east, Karelians and Veps, have a higher fraction than the Finns proper. Additionally, some Finns in the data seem to lack it totally. One might speculate that these are people of Swedish origin who eventually assimilated to the Finnish identity. This is not impossible. In the 19th century Finnish nationalism was sparked in large part by middle class activists, many of whom were Swedish ethno-linguistically due to the connections between class and language at that time. But these individuals may be evidence of older structure in Finland. More on that later.

I also ran some Treemix on a subset of the data. You see there is gene flow coming into the Finns from a Siberian group. I used Nenets (a group of Samoyeds) and Yakut because the former have more linguistically in common with the Finns, while the latter are used by companies like 23andMe (Yakuts are the most northeasterly Turkic people). Strangely the Karelians and Veps get gene flow from Nenets, while the Finns get it from Yakuts (I pruned with PCA and ADMIXTURE to remove individuals with recent European ancestry).

But the model of a single pulse admixture is probably wrong anyhow. Rather, the spread of Finnic hunters and gatherers may have gradual, and/or occurred in several pulses. On the fringe of Northern Eurasia local extinctions were probably common. The landscape of Northern Eurasia, from the Baltic to Siberia, may long have been rather dynamic, with interactions between Uralic, Indo-European and Altaic peoples.

At this point I am at a loss. The archaeology of Finland is not something I know well, and the academic literature is hard for me to track down. Some scholars believe that the Comb Ceramic Culture plays a major role in the ethnogenesis of the people we call Finns. During the Bronze Age the Corded Ware zone spread into southern Finland, bringing agriculture. The fusion between the Comb Ceramic and Corded Ware led up to the societies which are first mentioned by Classical authors.

Finland was always liminal to early agriculture, and the Corded Ware Indo-Europeans may eventually have given away to the forest Finns as the climate turned more difficult. The predominance of N3 haplogroups may be a function of the nature of patriarchal societies, where certain lineages maintain powerful long term advantages.

Amazon purchases whole foods and the distribution channel comes to you

The purchase of Whole Foods by Amazon has sent grocery store stocks into tailspin. Could Amazon do to Safeway and Korger what it did to Borders and Barnes & Noble?

Some people have observed that the purchase impacts the nascent grocery delivery sector more than the established supermarkets. That was my first thought. For me Saturday used to involve a trip to Whole Foods. But not anymore. Basically I use Instacart. (I can’t use Amazon Fresh because it doesn’t delivery to where I live. For now….)

Because Amazon is such a monster of a company people are talking about grocery stores as the underdog in this new war. But the reality is that what we think of “grocery store” is something far different from what someone in 1900 would have imagined. Americans today assume that the supermarket is synonymous with groceries. But supermarkets as institutions are economic innovations which date to the 20th century. The rise of the sector by showcasing its pioneering firm is detailed in The Great A&P and the Struggle for Small Business in America. As the title makes clear the rise of supermarkets resulted in a massive creative destruction in the American economy and culture.

Before A&P reimagined the profession being a grocer was a way for working class men to have a job that could support a family and give them some independence. But as the supermarkets cannibalized small grocers, men who had run their own businesses became employees in large corporations. Entrepreneurs became clerks. Creative destruction also worked so that eventually A&P was marginalized by new-model supermarkets that catered to suburban families. Today Walmart and Whole Foods have been attacking the low and top ends of the market and squeezing out smaller players.

Walmart’s battle from the bottom-up seems to have beaten Whole Foods’ premium strategy. Amazon’s purchase makes sense since Whole Foods has some assets major it can bring to the battle, but Walmart scale just too much for them to tackle.

As we all know the retail sector is changing. Half of millennials now buy groceries online at least some of the time. Malls are closing as their anchor department stores struggle. Where would a modern day Tiffany do her tour? Obviously it’s YouTube.

But that doesn’t mean that people won’t venture out. Upscale retail plazas are replacing the role of malls. Independent bookstores are still around, while Borders is gone and Barnes & Noble is a shadow of what it was. The positive aspect of the death of bricks and mortar retail is that we spend less time out and about on errands. Rather, we go out to eat at a restaurant, or meet friends in the park or at a bar. The downside is a smaller and smaller set of firms are dominating the supply chains between producers and consumers. I think Amazon will be targeted by antitrust considerations in the 2020s.

The cultural revolution that will happen in China

If you’ve been hiding under a rock, please see Baby Genome Sequencing for Sale in China:

A Boston-based DNA sequencing company is offering to decode the complete genomes of newborns in China, leading some to ask how much parents should know about their children’s genes at birth.

Veritas Genetics says the test, ordered by a doctor, will report back on 950 serious early- and later-life disease risks, 200 genes connected to drug reactions, and more than 100 physical traits a child is likely to have.

Called myBabyGenome, the service costs $1,500 and could help identify serious hidden problems in newborns, the company says.

Obviously a $1,500 price point is beyond most Chinese. But the total fertility rate in China today is 1.56, and almost certainly lower among urban elites who could actually afford this service. Considering that genome is with you for life, more or less, $1,500 isn’t really that much.

For years there have been many fly by night genetics companies who have some presence in East Asia. They come and go. The combination of a lax regulatory environment and the allure of “genes” means that there is some money to be made. Veritas in contrast is a serious company. This is heralding the reality that widespread sequencing is going to go primetime.

Of course there is skepticism. Fortunately the piece doesn’t talk much to people who express Leon Kass style FUD. The objections are scientific:

But some doctors say the plan is a huge overstep. “I think it’s vastly premature to peddle a completely unproven set of data, especially to a vulnerable population like neonates,” says Jim Evans, a professor of genetics at the University of North Carolina Chapel Hill.

The problem is that the risk posed by many disease genes remains uncertain. Even if a child has a mutation in a gene, he or she may never be affected, prompting debate among doctors about whether it’s useful to inform parents.

These are real points, but I don’t see why sequencing should not be allowed as a choice by parents nevertheless. And widespread adoption of sequencing would actually allow us to start obtaining more data that we could use to make better decisions in the future. The genomics space for a while has had a bit of a chicken & egg problem. The sequencing is starting to get there, but we still need to get phenotypes. And this seems like one way to get the public involved and feel like they have a stake.

Like in vitro fertilization I see neonatal sequencing as inevitable in regards to whether it will be ubiquitous. It will be common. And “ethical problems” won’t really come up in the future because people will be comfortable with it. Right now there’s a fear factor.

This is in sharp contrast with CRISPR. That’s a technology that will have real consequences, and like male circumcision may be difficult to reverse for someone who as an adult was modified in infancy. In contrast a genome sequence is just more information.

For years may people have speculated that genetic testing technology will really begin to take off in Asia because for various reasons Americans and Europeans are wary. To me this is a signal that that might be occurring, depending on how successful Veritas’ venture is.

This is perhaps the most important point:

But Veritas will not reveal everything, in recognition that not all the information in the genome is appropriate to give parents right away. For instance, it won’t tell them about a gene that can strongly predispose people to Alzheimer’s in old age.

Instead, Veritas says, it will retain the rest of a newborn’s genome data and let parents purchase further information at a later date.

I think this may be more common than we think. Most people don’t want to deal with a ~3 GB text file. That being said, I think they should in the future have an option for people to buy their data outright.

Addendum: I met Robert Green at SxSW. Nice fellow. One thing that he mentioned was widespread opposition among physicians. I suspect one dynamic that MDs won’t like in the near future is decentralization of the distribution of medical services away from their own profession. This is part of it.

The system of the world by William H. McNeill

In the post below on book recommendations I forgot to mention William H. McNeill and John Robert McNeill’s The Human Web: A Bird’s-Eye View of World History. It’s arguably been one of the most influential works that has percolated in my mind throughout the years. It’s less than 400 pages, and illustrates in broad sketches that history has been through many random shocks, but that there are broad patterns that one can discern.

The elder McNeill is most famous for The Rise of the West and Plagues and Peoples. To a great extent he was Jared Diamond before there ever was Jared Diamond.

Unfortunately I did not notice that McNeill died last summer. From his obituary:

Refuting Francis Fukuyama’s premise in “The End of History and the Last Man” in 1992 that the American model of a liberal, capitalist democracy had become the paradigm for governance, Professor McNeill wrote in The New York Times Book Review: “I do not believe that human nature is uniform and unchanging. Rather, whatever penchants and capabilities we inherit with our genes are so malleable that their expression takes infinitely diverse forms.”

“When Asian models of social and economic efficiency seem to be gaining ground every day, and when millions of Muslims are at pains to sustain the differences, great and small, that distinguish them from Americans,” he continued, “it is hard to believe that all the world is destined to imitate us.”