Month: September 2017

The survivorship bias in book ratings

Posted on by Razib Khan

Just finished The Fortunes of Africa: A 5000-Year History of Wealth, Greed, and Endeavor by Martin Meredith, and gave it 4 out of 5 stars on GoodReads. At nearly 700 pages of narrative text The Fortunes of Africa is not a small book, but it’s pretty dense with fact and a “quick read”. The author is good at balancing narrative flow with packing a lot of information into any given page.

But as I rated the book I realized that the vast majority of my ratings are 4 out of 5. I reserve 5’s for really good books. But why so few ratings less than 4? Obviously, this is due to survivorship bias: in general, I’m not going to finish a book that I don’t like, and I won’t rate books that I don’t finish.

Additionally, the longer a book is, the better it probably has to be for me to finish it. If it is a short book (less than 200 pages) I may just push all the way through, but in general anything longer and I won’t read “cover-to-cover.” When I was younger I would sample chapters and such, but for whatever reason as I’ve gotten older I generally adhere to the sequential structure as envisioned by the author.

Of course there are exceptions. Stephen Jay Gould’s The Structure of Evolutionary Theory is very long. In general I did not really enjoy reading it (though it has its moments, in particular when it comes to history of science), but finish it I did. I read The Structure of Evolutionary Theory in full because it was Gould’s magnum opus, and the best place to get a sense of his thought without ploughing through his whole oeuvre. Though I did not think much of Gould’s ideas personally (few people with an evolutionary genetics orientation do), he was objectively an intellectual of some standing and influence, so it is useful to understand his thought. He mattered, for better or worse.

The Structure of Evolutionary Theory was Stephen Jay Gould’s last book (he died two months after it was published). He had become such an enormous public intellectual that he was clearly beyond the power of any editors to control his prose flourishes. It’s a prolix repetitious work (I read Wonderful Life more recently, and it benefited from being more tightly written).

In contrast when I read The Twilight of Atheism Alister McGrath I thought it was a decently well written book, but totally unpersuasive on the merits of the substance. But after ten years I think descriptively McGrath was right in some deep ways. So I’d probably change my rating of this book between then and now.

So categories of books I read all the way through:

  • Books I enjoy. I’ve read The Fall of Rome three times. I’ve only read The Genetical Theory of Natural Selection front to back a few times, but some chapters (especially the earlier ones) I’ve read many times.
  • Books which are important. I’ve read probably two dozen translations of Genesis in my life (it’s a short book when standalone, so not a big achievement). A lot of the religious stuff I read is because religion is so important to people, even if it isn’t important to me. Honestly, the same with a lot of philosophy.
  • Books which challenge my viewpoints in a substantive sense. The Structure of Evolutionary Theory and The Twilight of Atheism fall into these categories. I was a much more doctrinaire libertarian when I read Michael Parenti’s Blackshirts and Reds, which engaged some apologia for Marxist-Leninism.

After agriculture, before bronze

Posted on by Razib Khan

 

The above plot shows genetic distance/variation between highland and lowland populations in Papa New Guinea (PNG). It is from a paper in Science that I have been anticipating for a few months (I talked to the first author at SMBE), A Neolithic expansion, but strong genetic structure, in the independent history of New Guinea.

What does “strong genetic structure” mean? Basically Fst is showing the proportion of genetic variation which is partitioned between groups. Intuitively it is easy to understand, in that if ~1% of the genetic variation is partitioned between groups in one case, and ~10% in another, then it is reasonable to suppose that the genetic distance between groups in the second case is larger than in the first case. On a continental scale Fst between populations is often on the order of ~0.10. That is the value for example when you pool the variation amongst Northern Europeans and Chinese, and assess how much of it can be apportioned in a manner which differentiates populations (so it’s about ~10% of the variation).

This is why ancient DNA results which reported that Mesolithic hunter-gatherers and Neolithic farmers in Central Europe who coexisted in rough proximity for thousands of years exhibited differences on the order of ~0.10 elicited surprise. These are values we are now expecting from continental-scale comparisons. Perhaps an appropriate analogy might be the coexistence of Pygmy groups and Bantu agriculturalists? Though there is some gene flow, the two populations exist in symbiosis and exhibit local ecological segregation.

In PNG continental scale Fst values are also seen among indigenous people. The differences between the peoples who live in the highlands and lowlands of PNG are equivalent to those between huge regions of Eurasia. This is not entirely surprising because there has been non-trivial gene flow into lowland populations from Austronesian groups, such as the Lapita culture. Many lowland groups even speak Austronesian languages today.

Using standard ADMIXTURE analysis the paper shows that many lowland groups have significant East Asian ancestry (red), while none of the highland groups do (some individuals with East Asian admixture seem to be due to very recent gene flow). But even within the highlands the genetic differences are striking. The  Fst values between Finns and Southern European groups such as Spaniards are very high in a European context (due to Finnish Siberian ancestry as well as drift through a bottleneck), but most comparisons within the highland groups in PNG still exceeds this.

The paper also argues that genetic differences between Papuans and the natives of Australia pre-date the rising sea levels at the beginning of the Holocene, when Sahul divided between its various constituents. This is not entirely surprising considering that the ecology of the highlands during the Pleistocene would have been considerably different from Australia to the south, resulting in sharp differences in the hunter-gatherer lifestyles. Additionally, there does not seem to have been a genetic cline. Papuans are symmetrically related to all Australian groups they had samples from.

Using coalescence-based genomic methods they inferred that separation between highlands and some lowland groups occurred ~10-20,000 years ago. That is, after the Last Glacial Maximum. For the highlands, the differences seem to date to within the last 10,000 years. The Holocene. Additionally, they see population increases in the highlands, correlating with the shift to agriculture (cultivation of taro).

None of the above is entirely surprising, though I would take the date inferences with a grain of salt. The key is to observe that large genetic differences, as well as cultural differences, accrued in the highlands of PNG during the Holocene. In the paper they have a social and cultural explanation for what’s going on:

  Fst values in PNG fall between those of hunter-gatherers and present-day populations of west Eurasia, suggesting that a transition to cultivation alone does not necessarily lead to genetic homogenization.

A key difference might be that PNG had no Bronze Age, which in west Eurasia was driven by an expansion of herders and led to massive population replacement, admixture, and cultural and linguistic change (7, 8), or Iron Age such as that linked to the expansion of Bantu-speaking
farmers in Africa (24). Such cultural events have resulted in rapid Y-chromosome lineage expansions due to increased male reproductive variance (25), but we consistently find no evidence for this in PNG (fig. S13). Thus, in PNG, wemay be seeing the genetic, linguistic, and cultural diversity that sedentary human societies can achieve in the absence of massive technology-driven expansions.

Peter Turchin in books like Ultrasociety has aruged that one of the theses in Steven Pinker’s The Better Angels of Our Nature is incorrect: that violence has not decreased monotonically, but peaked in less complex agricultural societies. PNG is clearly a case of this, as endemic warfare was a feature of highland societies when they encountered Europeans. Lawrence Keeley’s War Before Civilization: The Myth of the Peaceful Savage gives so much attention to highland PNG because it is a contemporary illustration of a Neolithic society which until recently had not developed state-level institutions.

What papers like these are showing is that cultural and anthropological dynamics strongly shape the nature of genetic variation among humans. Simple models which assume as a null hypothesis that gene flow occurs through diffusion processes across a landscape where only geographic obstacles are relevant simply do not capture enough of the dynamic. Human cultures strongly shape the nature of interactions, and therefore the genetic variation we see around us.

America’s age of animated emojis

Posted on by Razib Khan

A few days ago I watched the unveiling of Apple’s new iPhone(s). Honestly, I was a bit underwhelmed…and I probably will stick with a Samsung. Of course, I know that the original iPhone was panned, and it created a whole sector and a lifestyle. We’re a bit jaded.

But this focus on lifestyle in the technology sector made me reflect on Peter Thiel’s techno-pessimism in the late 2000s, which prompted him to write Zero to One. I’m glad that the best and brightest are going to Silicon Valley in the 2010s, and not Wall Street as in the 2000s. They don’t do positive harm in my opinion, while they did in the 2000s by increasing risk and volatility. But Apple and Facebook seem to be about consumption rather than production. They don’t make us more efficient, effective, they don’t change our civilization in its bones.

There are worse places to be, but then I read that China is setting targets and goals in relation to moving from fossil fuels to electric cars. The Chinese make a lot of goals, and execution is often an issue. But they have aspirations. Do we?

Until then, animated emojis….

More “orthodox” Islam in Indonesia is inevitable

Posted on by Razib Khan


Curfews, Obligatory Prayers, Whippings: Hard-Line Islam Emerges in Indonesia:

In the Indonesian market town of Cianjur, new rules require government workers to clock in with their thumb prints at a downtown mosque to confirm attendance at morning prayers. That’s on the order of district chief Irvan Rivano Muchtar, who also wants a 10 p.m. curfew for the town and is sending police to stop teenage girls and boys hanging out without parental supervision.

One one of the first things I wrote on the internet in 2002 was about Indonesian Islam (on a blog platform which is now gone). The reason for me writing on that topic was that the media representations of Southeast Asian Islam in the wake of 9/11 seemed excessively simple and reductive. For the West Indonesian Islam is often asserted to be moderate, and a counterpoint to the intolerance and exclusion which is the norm in the Middle East. In other words, Indonesia as the world’s most populous Muslim majority name plays a specific role in a broader narrative. A bit part in the grand narrative of moderation and radicalism. In the process, the textured uniqueness of Indonesia itself often gets lost.

First, let’s take a step back and frame the history of maritime Southeast Asia, what eventually became Malaysia, Indonesia, and the Philippines. It is often stated that in Indonesia Islam spread peacefully through trade. This is supposedly in contrast to what occurred in the Middle East or South Asia, where military force was the dominant theme of Islamization. Superficially this is true.

But the reality is that forced conversion was likely a marginal phenomenon at any given time, and especially during the early centuries of Islam. The prominence of men such as Timothy, Patriarch of the Church of the East, under the Abbasids attests to the power of the non-Muslim majority (there was a similar eminence for the Zoroastrian community). But the conversion of Malays around Malacca in the early 15th century after the conversion of the king is not quite as different from what occurred in Persia after the Arabs arrived as one might think. The rapid shift of the Iranian nobility to Islam in provinces under Arab control seems to have triggered a gradual change among the masses (those regions, such as Tabaristan, where local elites maintained the old religion resisted Islamization until they were conquered and converted). It was not a matter of the sword or conversion.

Of course, religious wars were a necessary part of the expansion of Islam in the Middle East and South Asia, even if they did not effect much of the religious change which occurred later. But this is not a qualitative contrast with the Middle East and South Asia in comparison to Indonesia, though it is a quantitative one. Some polities, such as Malacca and Aceh, came to Islam through their integration into the maritime mercantile network of Muslims from Arabia to China. Centuries later the collapse of the Javanese kingdom of Majapahit, whose earlier hegemony served as some of the basis of broader Javanese-Indonesian claims to the whole archipelago, occurred due to attacks from Muslim sultanates who organized in part on the basis of religion. Majapahit fell because of jihad. It was not converted peacefully.

In sum, the history of what became Indonesia and its relationship to Islam is different from that of South Asia, or the Middle East, but that difference is one of degree, not kind. Second, one must also distinguish between Java and the rest of the archipelago. In the article above there is an reference to Aceh, a province where the practice of Islam aligns very strongly with that found in the Middle East. But Aceh is also culturally and historically very different from Java, Islam came to Aceh a the dominant religion at least two centuries before it did in Java, and probably earlier. On the map above Aceh is also geographically rather distant from the central islands, at the far northwest tip of Sumatra.

To a first approximation, orthodox Islam is a much more salient and central aspect of the identities of people from outlying islands than it is to Javanese. The complex indigenous-Hindu-Buddhist-Islamic synthesis which is said to characterize traditional Indonesian Islamic culture is actually a feature most evidently of Javanese culture. Parts of far western Indonesia came to Islam earlier, and integrated into the Muslim cultures of the Indian Ocean more thoroughly, so that earlier Buddhist affinities faded over time (Aceh at one point was aided by the Ottomans in fighting the Portuguese). In contrast, parts of eastern Indonesia, such as Sulawesi, were Islamicized after the fall of Majapahit, but the impact of Indic culture had been relatively superficial (though not trivial, as Indic influence is evidence as far east and north as the islands which became the Philippines).

At nearly 40% of the population of all of Indonesia the Javanese loom large in the identity of the nation-state. Most of the presidents of Indonesia have been Javanese (B. J. Habibie was raised in Sulawesi, where his father was from, but his mother was Javanese; Sukarno’s mother was Balinese, while his daughter’s mother was Sumatran, though both seem to have identified culturally as Javanese). Many of the things people say about Indonesian Islam are really about Javanese Islam, with the model implicitly derived clearly from Clifford Geertz’s tripartite division between santri, abangan and priyayi.

The santri are basically what we define as world normative orthodox Muslims. The priyayi are the Javanese aristocracy, who self-consciously explored mystical concepts and practices with an extra-Islamic origin. But the vast majority of Javanese are the abangan, rural peasants who practice an Islam which emphasizes custom and tradition as much as sharia. Because custom and tradition have deep organic roots within Java they naturally include many elements which are ‘pre-Islamic.’ In Java both the Mahabharata and Ramayana are still part of the living culture, for example.

It strikes me that the attitude of the Javanese may have analogs with that of the Persians in relation to their cultural history. By and large like the Persians the Javanese are Muslims without apology.* But like the Persians the Javanese take pride in a history before Islam, in particular Majapahit, whose writ tentatively spanned most of contemporary Indonesia. And Majapahit can not be separated from a Hindu-Buddhist synthesis which left massive cultural artifacts such as the Borbobudur temple complex (and the modern Balinese also serve as continuous cultural links with the Hinduism of Majapahit).

But the economic and social development of Java will naturally lead to a waxing in the santri tendency. Orthodox Muslims among the Javanese have not been part of the underclass, but rather outward facing portions of the traditional mercantile class or middle class urbanites. Santri Islam is portable, and commensurable with international Islam. Abangan Islam is rooted in the rural landscape of Java, and urbanization will inevitably erode its hold on future generations. Meanwhile, priyayi practices are structurally limited to a narrow class of elites.

Overall then the rise of ‘conservative Islam’ in Indonesia is a complex story with two primary threads. One is regionalism. The regulations introduced in the story above are in Cianjur, in western Java. This area is more Islamic than central or eastern Java, and the native people are not Javanese, but Sundanese.

As local identities were given more freedom of play after the New Order in the late 1990s it was reasonable to expect that more strikingly Islamic practices would become more public, as they were dampened earlier by the dominant Javanese orientation of the Suharto regime. Second, modernization within Javanese culture itself will likely lead to the emergence of a more numerous group of sharia compliant and world Islam oriented group of Muslims, as they can not rely upon community and adat in an urban landscape remote from their backgrounds of origin.

This is not to say that the standard chestnuts about Saudi funding are not important. But it is important to note that portions of Indonesian Islam have long been deeply connected to the Muslims of the Arabian Sea; this is not a function simply of the rise of petro-states, though their wealth has certainly allowed them to put their thumbs on the scale. Maritime Southeast Asia is the eastern segment of what is operationally a Shafi international of Sunni Muslims who ring much of the Indian Ocean. As Indonesia becomes globalized, it will gravitate to other nodes within the international network which it already has long-standing connections. This is probably inevitable in some ways, and the working out of the reality of contemporary Indonesian pluralism has to face the inevitable tensions that modernization will bring. A more universal and non-local Islam will probably also be more exclusive and culturally muscular.

* A minority are Christian or Hindu. A Hindu Javanese kingdom persisted in the east of the island until the 18th century.

Freedom of thought as a perpetual revolution

Posted on by Razib Khan

I mentioned offhand on Twitter today that I am skeptical of the tendency to brand the classically liberal emphasis on freedom of thought and speech as “centrist.” The implicit idea is that those on the Right and Left for whom liberalism is conditional, and a means at best, are radical and outside the mainstream.

This misleads us in relation to the fact that classical liberalism is the aberration both historically and culturally. Liberty of thought and speech have existed for time immemorial, but they were the luxury goods of the elite salons. Frederick the Great of Prussia had no use for religion personally, and famously patronized heretical philosophers, but he did not disturb the conservative social order of the polity which he inherited. For the masses, the discourse was delimited and regulated to maintain order and reinforce social norms.

The attempt to position the liberal stance as a centrist one is clearly historically and culturally contingent. It reflects the ascendancy of a particular strand of Anglo-American elite culture worldwide. But it is not universal. In the Islamic world and South Asia free expression of skepticism of religious ideas in public are subject to limits explicitly to maintain public order. The Islamic punishments for apostasy have less to do with the sin of individual disbelief and more to do with disruption to public norms and sedition against the state. Similarly, both China and Russia tap deeply into cultural preferences for state and elite paternalism in regards to public freedom of thought.

In fact, the classical liberal perspective on prioritizing freedom of conscience and the ability to explore the full range of ideas is probably counter to the “lowest energy state” of human cognitive intuitions. It reflects only a slice of the “moral foundations” which Jonathan Haidt explores in The Righteous Mind.

To explore some of the demographic correlates of classical liberalism I utilized the General Social Survey. As instruments to assess liberal attitudes toward free speech and thought I focused on two variables, SPKMSLM and SPKLRAC. For the first variable respondents were asked:

Now consider a Muslim clergyman who preaches hatred of the United States. If such a person wanted to make a speech in your community preaching hatred of the United States, should he be allowed to speak, or not?

For the second:

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

I assess the pro-free speech position by inspecting the subset who accept that both groups should be allowed to speak, and those who reject that either group should be allowed to speak. That is, these are people consistent in their attitudes when it comes to speech which conflicts with community norms.

For demographic variables, I looked at educational attainment (DEGREE), verbal intelligence (WORDSUM), and political ideology (POLVIEWS). For verbal intelligence scoring 0-4 out of 10 was below average, 5-7 was average, and 8-10 above average.

What is clear above is that those with more education and those who are more intelligent tend to support free speech more than those who lack education or are less intelligent. But it is also notable that moderates, in particular, are overrepresented among those who reject freedom of speech. Though tThe proportion of liberals goes up appreciably, the proportion of conservatives also goes up a bit!.

I ran a quick logistic regression model which attempts to predict the odds of two outcomes (support or reject free speech here) across a range of variables simultaneously. Statistically significant B coefficients are bolded. You can see that the demographics which support speech across the two are consistent:

B – Allow Muslim B – Allow racist Who supports free speech?
AGE 0.01 0.006 Younger people
SEI -0.008 -0.007 Higher SES people
POLVIEWS 0.061 0.072 Liberals
WORDSUM -0.306 -0.145 Smart people
DEGREE -0.274 -0.153 More education
INCOME -0.026 -0.026 Richer
SEX 0.45 0.24 Men
GOD 0.151 0.159 Less religious

From looking at the GSS data moderates are the less interested in politics overall, and also less educated and intelligent. In general, when they respond to a political issue they’re going with their gut. Humans are social animals and tend to not look favorably upon public disruption. The rationales for why one should discourage offensive and taboo speech are rather coherent. The liberal instrumental argument for freedom of thought as a social good tends to take a longer view that the proliferation of ideas will lead to greater prosperity and moral advancement.

This is a very Whig model of history. Whether the model is correct or not, it captures a particular moment in the Zeitgeist of the early modern West. The reason that classical liberalism is classical is that it in minimal terms it has never gone beyond its roots in the late 18th and early 19th century in relation to its preoccupations. Within the West many conservatives and reactionaries have argued against the presuppositions of classical liberal thought, which have tacitly been ascendant for the past two centuries (the fascists being the inchoate apotheosis of these reactive strands). Marxists and other radicals have gone beyond the liberal fixation on liberty narrowly defined, while modern Left-liberals tend to put as much emphasis on economic liberty through redistribution as upon civil liberty.

But I also want to suggest here that perhaps the classical liberal fixation on freedom of thought reflects the interests and preoccupations of a particular segment of society: those for whom ideas are fascinating and give sustenance and meaning to life. The Enlightenment can be thought of as the revolt of the middle class, broadly construed, from the mercantile high bourgeoisie down to the broad professional class. These are people for whom “post-materialist” considerations loom large because material considerations have faded into the background. For the poor and those in material want freedom of thought is less important by necessity. Similarly, the large segment of the population which is not interested in novel ideas may not care much about the importance of intellectual novelty. Finally, there are those with post-materialist values which may emphasize the importance of taboos and social conformity of the collective.

Though the majority of the population (at least in the West) seems inclined to go along with liberalism as part of the broader suite of post-Enlightenment Western culture, there is no guarantee that they will always hew to such a position. Classical liberalism understood to be fundamentally radical would be useful insofar as the elites for whom it is an ends, and not a means, would be less complacent and more motivated toward maintaining the primacy of the values which give meaning to their lives.

Inbreeding causing issues in Osama bin Laden’s family

Posted on by Razib Khan

I didn’t figure I would have to say much about 9/11 really that others could not say (aside from perhaps you should read Marc Sageman’s Understanding Terror Networks if you want an ethnography of the Salafi jihadist movement which lead to al-Qaeda). But The Daily Best has a profile of one of Osama bin Laden’s sons:

Moreover, by this time, bin Laden already had two wives. But Najwa, the first of them, encouraged him to pursue Khairia, believing that having someone with her training permanently on hand would help her son Saad and his brothers and sisters, some of whom also suffered from developmental disorders.

Osama bin Laden had two dozen some children (approximately). But it was strange to me to see mention of several children with developmental disorders. Inbreeding is a major burden for Arab Muslim societies. And sure enough, Osama bin Laden’s first wife was his first cousin. She gave birth to around 10 children. Her father was Osama bin Laden’s mother’s brother. With the possibility of several generations of cousin marriage their relatedness may have been closer than normal half-siblings.

Note: Osama bin Laden’s father was from Yemen and his mother from Syria. So he was most certainly not inbred.

Amazon will go to Denver

Posted on by Razib Khan

Lots of discussions last week in the office about where Amazon will locate its second headquarters. After looking at the criteria the consensus converged on Denver. The Upshot did a similar analysis…and settled on Denver as well.

The huge downside of Austin is its deficits in transportation. Its airport is relatively modest. The mass transit is minimal. And traffic congestion is horrible.

Open Thread, 09/10/2017

Posted on by Razib Khan

Read The Mormon People: The Making of an American Faith this weekend. It’s a quick read, and a pretty good concise survey of the religion and its history. Recommended.

Next up I think I’ll tackle Martin Meredith’s The Fortunes of Africa.

Genomic evidence for population specific selection in Nilo-Saharan and Niger-Congo linguistic groups in Africa. The title gets at the interesting parts (though unsurprising). Not sure about the phylogenomic/population history aspect…for example, contends that Sub-Saharan ancestry mostly derives from Nuba mountains. I don’t think that’s true.

“Open Threads” seem to have a huge variance in number of comments. Perhaps what I prime has a big impact?

Why I am not blogging anymore. I am one of a dying breed.

In relation to why Twitter is getting dumber, there are five times as many users as in 2010. Can the platform really keep quality up? What I like to think of as “dumb Twitter” is getting to be a bigger and bigger proportion, and the bigger it gets the more people go silent who are of high quality.

Posting on the Rohingya controversy the last few days has convinced me that most people who express opinions are mostly interested in posturing. People of conscience can agree that killing of civilians is wrong. But the details of action from that premise vary wildly. Also, my attempt to get at the facts of contextual elements apparently make me suspicious to many people!

In relation to foreign policy, I think that distrusting “elites” is probably for the best. The primary thing they know is their own interests.

The Last Days of ISIS’ Capital: Airstrikes if You Stay, Land Mines if You Flee.

PETA versus the postdoc: Animal rights group targets young researcher for first time. I think this sort of behavior is more acceptable in the world of ‘social media shaming.’

Americans Losing Faith in College Degrees, Poll Finds. Not all Americans:

Today, Democrats, urban residents and Americans who consider themselves middle- and upper-class generally believe college is worth it; Republicans, rural residents and people who identify themselves as poor or working-class Americans don’t.

Also, colleges don’t get it:

Schools such as Michigan State, the University of Wisconsin system and the University of Florida are trying to improve their public standing with marketing efforts. In Wisconsin, the university system has taken out billboards across the state highlighting the impact alumni have had on the local economy.

The problem isn’t in marketing, it’s in the product.

On a related vein, over at Oberlin, Enrollment Drop Creates Financial Shortfall. In the Pacific Northwest, After a turbulent spring, Evergreen faces enrollment decline, budget woes. Finally, Long After Protests, Students Shun the University of Missouri. Hyper-politicization does not seem good for the product.

Finally, interested readers should consider getting a copy of Introduction to Quantitative Genetics. The next five years or so will be saturated with results coming out of massive genomic studies which will make much more sense if one has a theoretical framework with which to interpret the them.

Quantitative genomics, adaptation, and cognitive phenotypes

Posted on by Razib Khan

The human brain utilizes about ~20% of the calories you take in per day. It’s a large and metabolically expensive organ. Because of this fact there are lots of evolutionary models which focus on the brain. In Catching Fire: How Cooking Made Us Human Richard Wrangham suggests that our need for calories to feed our brain is one reason we started to use fire to pre-digest our food. In The Mating Mind Geoffrey Miller seems to suggest that all the things our big complex brain does allows for a signaling of mutational load. And in Grooming, Gossip, and the Evolution of Language Robin Dunbar suggests that it’s social complexity which is driving our encephalization.

These are all theories. Interesting hypotheses and models. But how do we test them? A new preprint on bioRxiv is useful because it shows how cutting-edge methods from evolutionary genomics can be used to explore questions relating to cognitive neuroscience and pyschopathology, Polygenic selection underlies evolution of human brain structure and behavioral traits:

…Leveraging publicly available data of unprecedented sample size, we studied twenty-five traits (i.e., ten neuropsychiatric disorders, three personality traits, total intracranial volume, seven subcortical brain structure volume traits, and four complex traits without neuropsychiatric associations) for evidence of several different signatures of selection over a range of evolutionary time scales. Consistent with the largely polygenic architecture of neuropsychiatric traits, we found no enrichment of trait-associated single-nucleotide polymorphisms (SNPs) in regions of the genome that underwent classical selective sweeps (i.e., events which would have driven selected alleles to near fixation). However, we discovered that SNPs associated with some, but not all, behaviors and brain structure volumes are enriched in genomic regions under selection since divergence from Neanderthals ~600,000 years ago, and show further evidence for signatures of ancient and recent polygenic adaptation. Individual subcortical brain structure volumes demonstrate genome-wide evidence in support of a mosaic theory of brain evolution while total intracranial volume and height appear to share evolutionary constraints consistent with concerted evolution…our results suggest that alleles associated with neuropsychiatric, behavioral, and brain volume phenotypes have experienced both ancient and recent polygenic adaptation in human evolution, acting through neurodevelopmental and immune-mediated pathways.

The preprint takes a kitchen-sink approach, throwing a lot of methods of selection at the phenotype of interest. Also, there is always the issue of cryptic population structure generating false positive associations, but they try to address it in the preprint. I am somewhat confused by this passage though:

Paleobiological evidence indicates that the size of the human skull has expanded massively over the last 200,000 years, likely mirroring increases in brain size.

From what I know human cranial sizes leveled off in growth ~200,000 years ago, peaked ~30,000 years ago, and have declined ever since then. That being said, they find signatures of selection around genes associated with ‘intracranial volume.’

There are loads of results using different methods in the paper, but I was curious note that schizophrenia had hits for ancient and recent adaptation. A friend who is a psychologist pointed out to me that when you look within families “unaffected” siblings of schizophrenics often exhibit deviation from the norm in various ways too; so even if they are not impacted by the disease, they are somewhere along a spectrum of ‘wild type’ to schizophrenic. In any case in this paper they found recent selection for alleles ‘protective’ of schizophrenia.

There are lots of theories one could spin out of that singular result. But I’ll just leave you with the fact that when you have a quantitative trait with lots of heritable variation it seems unlikely it’s been subject to a long period of unidirecitional selection. Various forms of balancing selection seem to be at work here, and we’re only in the early stages of understanding what’s going on. Genuine comprehension will require:

– attention to population genetic theory
– large genomic data sets from a wide array of populations
– novel methods developed by population genomicists
– and funcitonal insights which neuroscientists can bring to the table

As many Americans think the Bible is a book of fables as that it is the literal word of God

Posted on by Razib Khan


America, that is, the United States of America, has long been a huge exception for the secularization model. Basically as a society develops and modernizes it becomes more secular. At least that’s the model.

In the 1980s Rodney Stark and William Sims Bainbridge wrote The Future of Religion: Secularization, Revival and Cult Formation. Stark and Bainbridge’s work was predominantly empirical; they looked at survey data to present a model of the American religious landscape. But they also had a theoretical framework, whereby religion was modeled with a rational choice framework on the individual religion, and denominations and sects were viewed as “firms” providing “goods and services” to “customers.”

A whole field emerged over time which attempted to use the methods and models of economics to explain religious phenomena. Larry Witham’s Marketplace of the Gods: How Economics Explains Religion surveys the various scholars in this discipline. I’ve read the book, and what I will say is that like many imperial ventures, this one failed. The predictions of the “supply-side” model of religion haven’t panned out.

In 2004 Samuel Huntington wrote in Who Are We? that the United States likely had a more Christian future than the present. He was actually writing this as a massive wave of secularization was going on in the United States; the second since that of the 1960s had abated.

For a long time, people were in denial about this. After all the United States had been the great exception to the secularization trend in the developed world. Their priors were strong. And the market also provided what consumers wanted; books such as God is Back and Jesus in Beijing catered to the demand. Writing in the early 2000s the author of Jesus in Beijing suggested that 20 to 30 percent of China would be Christian two to three decades, so between 2023 and 2033 (from the publication of the book). Credible statistics in 2017 put the current number of Christians in China at 2 to 5 percent.

In 2009 I took John Tierney of The New York Times to task for dismissing the secularization hypothesis in a column. I emailed him my blog post, and he denied that it showed what it showed. Today I suspect he’d admit that I was more right than he was.

Today everyone is talking about the Pew survey which shows the marginalization of the Anglo-Protestant America which I grew up in. This marginalization is due to secularization broadly, and non-Hispanic whites in particular. You don’t need Pew to tell you this.

At the top of this post you see the response to the GSS query BIBLE, which asks respondents how they view the Bible in relation to whether it is God’s literal word, inspired word, or a book of fables. I limited the data to non-Hispanic whites. In 2016 as many people viewed the Bible as a book of fables as the word of God. In 2000 twice as many people viewed it as the word of God as a book of fables. That is a huge change.

Note: Robert Putnam’s American Grace is probably the best book which highlights the complex cultural forces which ushered in the second wave of secularization. The short answer is that the culture wars diminished Christianity in the eyes of liberals.