The great rollback

Derek Thompson in The Atlantic has a piece up, How to Survive the Media Apocalypse, which gets at something I’ve come to believe:

Advertising has been critical to the affordable distribution of news for a century and a half in the U.S. Today’s media companies don’t have to reach all the way back to the early 1800s for a business plan, to when newspapers were an elite product, selling at the prohibitive price of six pennies per bundle. But they are going back in time, in a way, and excavating a dusty business model that relies more on readers, and less on advertisers, than the typical online publisher….

There are two groups of people who as readers truly value the truth in anything but the workaday (e.g., weather, traffic reports, etc.): nerds and those with money on the line.

The idea that news is about giving people the Truth is a conceit that was never attainable, but the American media had aspirations. Really most people want to be entertained, amused and vindicated. Conservatives complaining about the perceived Leftward drift of The New York Times who cancel their subscriptions are accelerating an inevitable process (as the readership gets more and more liberal). The fat profits generated by both advertising, in particular classifieds, and subscriptions, allowed the 20th-century media to not be beholden to one master. This is a new world, though a generation that grew up in the old world has not internalized the now.

Outfits which are geared toward the wealthy or business, such as Bloomberg, will retain a more straightforward positivist orientation. Facts will basically be a luxury consumption good, as well an input necessary for greater productivity on the margins for efficient allocation of capital. Those journals with mass audiences will fragment and develop sharper viewpoints and pay less attention to facts if they impede sensationalism and audience preferences. Basically, we’re going to become Britain!

Thompson’s reference back to the early 1800s made me think of Carl Friedrich Gauss. Like Gottfried Wilhelm Leibniz Gauss did not have absolute leisure to pursue intellectual activities. At some point, he was employed as a surveyor in Hanover. To the modern mind, this was a terrible waste of incredible talent. It is for this sort of reason that institutions of higher education with some independence arose to give scholars leisure and freedom to pursue their interests.

But will it always be so? The science fiction genre of steampunk obtains its novelty from injecting advanced technology into a Victorian world on its own terms. Perhaps in a few decades, many of our social and cultural arrangements will seem very quaint and antiquated to those of us who came into maturity in the fin de siècle of the 20th century, with all culture was mass culture.

Crescent over the North Sea

Pew has a nice new report up, Europe’s Growing Muslim Population. Though it is important to read the whole thing, including the methods.

I laugh when people take projections of the year 2100 seriously. That’s because we don’t have a good sense of what might occur over 70+ years (read social and demographic projections from the 1940s and you’ll understand what I mean). Thirty years though is different. In the year 2050 children born today, such as my youngest son, will be entering the peak of their powers.

First, one has to note that these statistics include a lot of people who are what some would term “Muslimish”. That is, they are not religious believers, but have some identification with Muslim culture. That’s explicitly noted in the methods.

The problem with this is that there is a wide range of religious commitment and identification across Europe’s Muslim communities. On the whole, they are more religiously observant than non-Muslims in their nations of residence,  but, for example, British Muslims are consistently more religious than French Muslims on surveys (or express views constant with greater religious conservatism).

Here are the results of a 2006 survey:

  France Britain Germany
Yes, Westerners are respectful of women 77 49 73
Yes, there is a conflict between being devout Muslim and living in modern society 28 47 36
Yes, sometimes violence against civilian targets in order to defend Islam can be justified 16 15 7
Did Arabs carry out 9/11? (yes) 48 17 35
People in Western countries are selfish (yes) 51 67 57
People in Western countries are arrogant (yes) 45 64 48
People in Western countries are violent (yes) 29 52 34
Do you consider yourself Muslim first? (yes) 46 81 66
In my country Muslims are perceived to adopt customs of nation 78 41 30
     

Numbers such as those above indicate even if France and the United Kingdom both have Muslim minorities on the order of 17% of the population, the nature of those populations differs to such an extent that that similarity in value may mislead.

In God’s Continent Philip Jenkins observes that public statistics of Christians often work to exclude cultural Christians, but those of Muslims include cultural Muslims. What many estimates of “Muslims” in the European context do is give a sense of the proportion of the population which is of Muslim background. This is especially true in a nation like France where religious survey data is not collected by government agencies.

Overall I think this data is important to consider, but there’s nothing really new in a qualitative sense. And, it is important to keep in mind the details. It is highly probable that the idea of a European superstate will have faltered by 2050, and each nation will its own Muslim minority, and engage with them differently depending on local values and context. Though Muslims, broadly construed, will form about the same proportion of the French and British general population, I suspect that in Britain the distinction between Muslim and non-Muslim will be much more obvious and strict than in France.

The Elephant, dragon and eagle


The relationship between China and India is clearly one-sided: India is obsessed with a China which is approaching lift-off toward becoming on the verge of a developed nation within a generation (certain urban areas are already basically developed, albeit not particularly wealthy in comparison to Hong Kong or Singapore).

Often when I see interviews with regular Chinese about their opinions of the other country the fixation is upon the manifest Third World nature of India, which seems to be changing much more slowly than their own nation. For me GDP is less important that vital statistics like child mortality or life expectancy. And it is in these sorts of statistics where you see the gap opening up between the two nations. India is developing…. but China is leading, and converging faster with developed nations.

It is in this context that this piece in The New York Times jumped out at me, Amazon, in Hunt for Lower Prices, Recruits Indian Merchants:

While Amazon.com has sellers hailing from many countries, Mr. Cheris said that India and China are the two most important places for Amazon to recruit new merchants since both nations are sources of cheap manufactured goods.

Unlike China, where local companies dominate e-commerce, India is also a huge domestic market for Amazon. Although most of India’s commerce is conducted offline, Indians are coming onto the internet at a rapid clip through their smartphones. Amazon’s chief executive, Jeff Bezos, views India and its 1.3 billion residents as vital to his company’s future, and he has vowed to spend at least $5 billion building up his India operations.

a, I was aware that Amazon really hadn’t gotten any traction in the Chinese market. I did not know that Amazon was so competitive in India, though Flipkart is still dominant there.

The story outlined seems to be part of a bigger trend whereby India is on a very different path from China in its relationship to the rest of the world. China’s economy is big enough and insular enough that it sees the world as either an export market or a source of commodities. It is quickly taking back its place of old as a lumbering hegemon. India, in contrast, seems to be developing a more integrative relationship with large economies such as the United States, despite its command and regulatory economy legacy.

Of course, the India-USA relationship is nothing like “Chimerica” in terms of magnitude, but the Sino-American relationship strikes me as very transactional. Despite the recent tendency of Indian society to espouse a stronger Hindu nationalist line, which is at odds with the West, it seems that there is more cultural exchange between elite Indians and Western societies in the deep sense of values, than has occurred with the Chinese and the West. And, yoga and aspects of spirituality notwithstanding, most of the cultural exchange seems to be toward cosmopolitan elites Indians assimilating to global values which draw from the mode of the West.

Ultimately all of this seems to have geopolitical implications. I’m assuming smarter people than me are keeping track of these trends….

Razib Khan’s raw genotype data on 23andMe, Family Tree DNA, Geno 2.0 and Ancestry

It has been a while since I posted an update on my genotype. Since then I’ve been tested on most of the major platforms. I don’t see any harm in releasing this to the public or researchers who want to look at it (though I don’t know why anyone would).

You can download all the files here.

Having my genotypes public is pretty useful for me. If I inquire about someone’s genetics oftentimes people get weirdly defense and ask “what about you?” I Just invite them to look at my raw data and analyze it for themselves! I’m not a hypocrite about this.

Over the years I’ve had researchers inquire about my ethnicity when they stumble upon my genotype on platforms such as openSNP. So in full disclosure, most of my ancestry is pretty standard eastern Bengali. I’m more East Asian shifted than most Bangladeshi samples in the 1000 Genomes project, but then my family is from Comilla, in the far east of eastern Bengal (anyone who cares, my Y is of course R1a1a-Z93 and my mtDNA U2b).

As before I’ll put the genotype under a Creative Commons license:Creative Commons License

Understanding prehistory through genetic inference and ancient DNA

Before David Reich’s book, Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past, I highly recommend a new preprint from Pontus Skoglund and Iain Mathieson*, Ancient genomics: a new view into human prehistory and evolution.

It’s basically at the sweet spot for a lot of readers: doesn’t overemphasize methods or archaeological minutiae that’s hard to follow. That being said I do think you would benefit if you read two things which would complement in those directions, First Farmers: The Origins of Agricultural Societies, and Ancient Admixture in Human History.

* I have to say, I consider Iain a friend, but am I the only one a bit perplexed by how a British person can have such a difficult to spell version of his name? I always have to look it up!

Most popular GNXP post of all time?

Was talking to a friend and mentioned offhand that the most popular GNXP post of all time was written in 2010 very casually and because of a question on Twitter posed by Jason Goldman. At 700,000 Google Analytics sessions it periodically still gets bumped up by places like Reddit.

The book to the right is a pretty big clue. Can you guess the post? I’m posting the link in the comments below….

Neanderthal vs us: for wont of a SNP?

Recently at a human evolution conference in England Svante Paabo (or someone in his group) was alluding to discovering how modern humans and Neanderthals differed by looking at the ~30,000 genetic positions (bases) where modern humans and Neanderthals exhibit fixed differences. That is, Neanderthals and modern humans exhibit totally disjoint frequencies.

I’ve been saying this for years, but I’ll say it again: this is probably a fool’s errand. I do think there are major differences at loci which we know about, such as at FOXP2. But, it isn’t clear that even at FOX2 Neanderthals and modern humans exhibited complete lineage sorting. That is, there’s evidence that the Altai Neanderthal had introgression from modern (or modern-related) human populations, and that those variants were sweeping. And there is still variation in modern human populations at FOXP2.

All Homo exhibit encephalization, credit Luke Jostins

It looks like Soft Sweeps Are the Dominant Mode of Adaptation in the Human Genome (also see Detecting polygenic adaptation in admixture graphs). But it may be that soft selections and recurring gene flow are common features of the broader Homo lineage for several million years.

In other words, looking for silver bullet variants which can explain why we are so special may always fail, because there are no silver bullets (for several years at ASHG I note that there were presentations which attempted to determine the locus of humanity by looking at the loci of functional interest where Neanderthals and modern humans differed). Rather, human exceptionalism is no exceptionalism, and human populations explore a wide space of phenotypes defined by a huge range of allelic variance which spans many of our extant lineages.

Open Thread, 11/26/2017

A few days ago there was a Twitter thing about top five books that have influenced you. It’s hard for me to name five, but I put three books down for three different reasons:

  • Principles of Population Genetics, because it gives you a model for how to analyze and understand evolutionary processes. There are other books out there besides Principles of Population Genetics. But if you buy this book you don’t need to buy another (at SMBE this year I confused Andy Clark with Mike Lynch for a second when introducing myself. #awkward)
  • The Fall of Rome. A lot of historical writing can be tendentious. I’ve also noticed an unfortunate tendency of historians dropping into contemporary arguments and pretty much lying through omission or elision to support their political side (it usually goes “actually, I’m a specialist in this topic and my side is 100% correct because of obscure-stuff where I’m shading the facts”). The Fall of Rome illustrates the solidity that an archaeological and materialist take can give the field. This sort of materialism isn’t the final word, but it needs to be the start of the conversation.
  • From Dawn to Decadence: 1500 to the Present: 500 Years of Western Cultural Life. To know things is important in and of itself. My own personal experience is that the returns to knowing things in a particular domain or area do not exhibit a linear return. Rather, it exhibits a logistic curve. Initially, it’s hard to make sense of anything from the facts, but at some point comprehension and insight increase rapidly, until you reach the plateau of diminishing marginal returns.

If you haven’t, I recommend you subscribe to Patrick Wyman’s Tides of History podcast. I pretty much wait now for every new episode.

The big Washington food fight. GMO labeling is coming.

In Our Time has two very good episodes recently I recommend on the Picts and Thebes.

The Unexamined Brutality of the Male Libido. When I read the title I assumed that the piece was somehow informed by evolutionary psychology. No. It’s larded with Freudianism.

Evolutionary psychology has taken its hits over the last 15 years, and rightly so when it’s basically re-warmed social psychology, but the stuff informed by primatology is 21st century science (you can agree to disagree, but there’s something to grab onto there). Freudianism sometimes gets a bad rap even though its origins were not nearly as woolly as we might think, but cutting-edge early 20th century psychology is really beyond its sell-by date today.

This is the stuff that makes me pessimistic that the “replication crisis” is going to have any impact on the media or the public. For example, At Yale, we conducted an experiment to turn conservatives into liberals. The results say a lot about our political divisions in The Washington Post. The author of the op-ed is a major person in the center of the controversy around replication. In particular, “ego depletion.” This op-ed is based on studies with p-values of 0.034 and such.

That being said, Radiolab has an episode on Stereotype Threat which acknowledges worries about its replication. Really all that matters to me is the funnel plot.

Detecting past and ongoing natural selection among ethnically Tibetan women at high altitude in Nepal. It’s polygenic and we don’t understand the architecture of the trait that well it seems. Basically, early selection sweep analysis detected some major loci, but it’s not the whole story. Reminds me of pigmentation.

An endogenous retroviral envelope syncytin and its cognate receptor identified in the viviparous placental Mabuya lizard. This is pretty cool, the same process seems to be occurring over and over.

Rethinking phylogenetic comparative methods. I think this is will be an impactful paper once it gets published.

Meanwhile, this looks interesting: The role of chromosomal inversions in speciation.

I posted some Taylor Swift memes to Twitter as a joke. They seem quite popular, especially the ones related to string theory and evolution, though the one related to Arminian and orthodox Calvinist soteriology took off in a different sector of Twitter.

The funny thing is several people were angry because they thought I was putting down Taylor Swift. I was just making fun of the media fixation on famous people and their stupid thoughts.

My friend D. Allan Drummond has gone “full artiste.” He’s now selling some of his incredible biologically-themed 3-D printing. You can read about his work in this profile at Nerdist (by day he’s a biochemist who used to be an evolutionary geneticist who used to be an engineer).

One month of DNAGeeks & Cyber Monday sale

For a while, one of the weird things about DNAGeeks sales in quantities has been that people who look at haplogroup I1‘s page have not been buying the shirts. This is in contrast to haplogroup R1b. The geographically the two groups overlap a fair amount. It’s not totally implausible to guess that 75% of the humans who have stepped foot on the moon have been paternal haplogroup’s R1b and I1. And the two have had about the same number of page-views.

I began to make gross generalizations about the type of man who carries I1. Well, the joke’s on us: turns out that the previous font made it look like “I1” was lowercase L, as in “l1.” Well we’ve fixed that problem, so let’s see how that works out!

When my friends and I started DNAGeeks over a weekend we didn’t have a precise idea where it was going to go and what was going to be popular. People keep asking “so what it’s about about?” Well DNA obviously, but the journey is just starting.

We knew genetics and genomics and have a wide diversity of other skills (I can write, others handle the code and business sides), but “DNA-themed products” was not something which I saw a lot of market testing on. So as they say in the start-up world we’re trying to iterate and figure out what works and doesn’t. The goal is make more people passionate about genetics, and also target people who are already passionate about genetics.

One thing we have learned is that the DNA helix symbol is very popular (thanks Joel!). We’re putting it on shirts, mugs, and now cellphone cases (iPhone only, since only iPhone owners spend money). Also, I’m happy to report a fair number of Gene Expression t-shirts have sold.

Until tomorrow if you used DNAEXPLAINED17 as a coupon code on checkout you get 15% off. Viva la consumerism!

The question should be “Who Are Salafi Muslims and Why Are Many So Extreme?”

Because of the horrible massacre at a mosque with Sufi tendencies in Egypt, there are a lot of “explainers” out there about sectarian divisions in Islam. The one in The New York Times, Who Are Sufi Muslims and Why Do Some Extremists Hate Them? could be worse. This portion especially gets at the major issue:

For a time, beginning in the 12th century, Sufism was a mainstay of the social order for Islamic civilization, and since that time it has spread throughout the Muslim world, and to China, West Africa and the United States. As Sufism spread, it adapted elements of local culture and belief, making it a popular practice.

Alexander D. Knysh, a professor of Islamic studies at the University of Michigan and expert in modern Sufism, describes it as a “very wide, amorphous movement” practiced within both the Sunni and Shiite traditions.

Specific claims about Sufism beyond the most general fail because vast swaths of Islamic history and Muslim peoples and practice are Sufi. In the modern western media, there is an unfortunate tendency to dichotomize Islam into a harsh and fundamentalist form and a moderate and mystical Sufi variety. Though a small minority of Sufis have drifted toward very heterodox beliefs, the vast majority are orthodox Muslims who also adhere to a school of Islamic law.

And Sufis are not all pacific saints. In the 19th century Libya the Sensussi Sufi movement was critical in the continuation of the trans-Saharan slave trade, and later served as a major focal point for violent resistance against the Italian colonial project. The great anti-philosopher of the medieval period, Al-Ghazali, who is generally agreed to have ushered in the decline of philosophical thinking within orthodox Sunni Islam, was a Sufi.

The question should not be about Sufis. Sufis are not moderate or mystical Muslims, they are simply Muslims. That is, they’re the mainstream. Rather, the crux of the issue is that violent radicals have emerged from the soil of Salafism. Not all Salafis are violent. But violent Salafis are the ones who regularly target other Muslims and their holiest of sites.

Salafism is a modern movement of the past few centuries. Like Protestant Fundamentalism, it is a product of the engagement of traditional religion with the modern world. Self-consciously Salafist Muslims have never known a world where the West was not dominant. Therefore it is no surprise that they look to the accrued tradition of Islamic civilization and see in it failure and decay.

Like some Radical Protestants, the Salafists imagine that they are creating a community of Muslims who are true to the path of the religion in its earliest years before it became tainted with monarchy. Basically, Salafists wish to transform Islam from a religion of history to one of pure axiomatic abstractions.

Why do Salafi radicals attack Sufis? Their tendency to engage in takfir against other Muslims goes back to the proto-Salafi Wahhabists. And Sufi Islam, with a venerable history going back more than 1,000 years, is naturally going to be the target of Salafi rage because it was the Islam that failed to stem the tide of Western ascendancy, the Islam that witnessed the slow and gradual decline from the greatness of the 8th and 9th centuries. The children shall eat their own parents.