Open Thread, 1/14/2018

Steven Pinker is one of my favorite public intellectuals. The Language Instinct is probably my favorite book from Pinker.

Last week I started seeing scientists who I respect(ed) starting to tweet that Steven Pinker, a moderately liberal academic of Jewish background, is a fan of Neo-Nazis. This stuff started to litter my timeline since I follow many scientists on Twitter. To find all the links and commentary, start with Jerry Coyne, who is a friend of Steve’s. All I have to say is that a substantial portion of the science Twittersphere is OK with bracketing Steven Pinker with Neo-Nazis. True fact.

I read Consciousness and the Brain: Deciphering How the Brain Codes Our Thoughts two years ago. I don’t remember much about that book though.

CBC under fire for documentary that says first humans to colonize New World sailed from Europe. There is less evidence for the Solutrean Hypothesis now than there was 20 years ago (in a relative sense). We also now know from ancient DNA that almost no Solutrean ancestry is present in modern Europeans.

If you don’t believe me, read this paper, The genetic history of Ice Age Europe.

At least most of my Twitter followers don’t seem to be anti-Pinker.

Having a hard time saying anything about Anhui of note. Perhaps that says something?

Genomweb story that mentions both my day-job and side-hustle.

Turning cheesecake into a weapon of war



Steven Pinker and many other evolutionary psychologists believe that music is cognitive cheesecake. That is, we have a lot of cognitive faculties working in concert, and musical appreciation and ability emerge out of the synthesis. But there wasn’t direct selection for music, as such. Musical appreciation then may not be adaptive.

And yet like reading and writing music clearly co-opts part of the human brain in terms of functional localization. There are people with brain injuries who can not speak well who nevertheless can sing well, and can communicate through song.

But perhaps most important, just because a trait did not emerge due to natural selection, does not entail that it might not be subject to later selection. One can make arguments that musical ability was adaptive at some point in human existence on the individual scale. But I have something else in mind: music is functionally important in war. Military marching bands did not arise coincidentally, music as an accompaniment to the march and a way to communicate and rouse the troops to action have been part and parcel of winning and executing battle. Music triggered social change in the 1960s.

I think much the same is probably true of religion.  My own position is that the shamanic/primal form of religious belief bubbles up out of our cognitive architecture as a side effect of other processes. But this byproduct can be co-opted by cultural evolutionary selection, and reshaped into something with functional utility.

The genetics of the St. Thomas Christians

First, I have to say I appreciate everyone who keeps sending data to the South Asian Genotype Project. Basically, I’m automating the pipeline, finding ways to merge data from a host of sources, but also figuring out how to refine the analysis.

But until then, today I decided to do some more manual analysis of three St. Thomas Christian samples I have (also called Nasranis). The reason is that there were some questions on Twitter in relation to the genetics of this group, and though three is not a great sample size, it’s better than nothing.

The St. Thomas Christians are a diverse group of people of various denominations in the southern state of Kerala who have diverse origin stories. Today the St. Thomas Christians have a range of denominational and sectarian affinities, but their origins probably have something to the Church of the East.

These Christians claim roots among the local Brahmin community, Jews, and West Asian settlers. To be honest, whenever people tell me about the Brahmin ancestors unless they were recent converts I discount this because there are about ten times as many St. Thomas Christians in Kerala as there are Brahmins. There is a small Jewish community in the area, and this region of India was long part of the Indian Ocean trade network of the Arabs.

I merged the three Nasrani samples with a lot of other populations. Zooming in on the South Asians, if you look at the PCA plot to the left (click it), you’ll see that they are not in the same cluster as the South Indian Brahmins (Brahmins from the four South Indian states are very similar to each). But, in comparison to non-Brahmin South Indians, they do seem Brahmin shifted.

As I have observed before these South Indian Brahmins can be thought of as more than 50% North Indian Brahmin, but the remainder being South Indian non-Brahmin. Aside from exotic exceptions (Parsis, Bengalis), most South Asians exist on an ANI-ASI “cline,” with lower caste South Indians being at one end of the cline (more ASI), and populations in the far northwest, such as the Kalash, being at the other end (more ANI). The PCA would suggest that the Nasrani are more ANI-shifted than a generic South Indian group, but less so than South Indian Brahmins.

Using Treemix to detect gene flow events, what I found is that the Nasranis look like a generic South Indian group. There’s no evidence of gene flow from Middle Eastern populations (Jews, Persians).

I did some f-3 tests and there isn’t anything conclusive I see to suggest Middle Eastern gene flow into the Nasranis.

Finally, I ran ADMIXTURE in supervised mode. Here are the average results for a set of South Asian populations (mean values):

Group Druze Georgian Han Iranian Telugu Yemenite Jew
Bangladeshi 1% 2% 12% 1% 83% 1%
Chamar 0% 0% 3% 0% 97% 0%
Gujurati_Patel 0% 1% 0% 10% 89% 0%
UP Kshatriya 0% 3% 1% 21% 76% 0%
Nasrani 0% 4% 1% 12% 83% 0%
Pathan 0% 4% 1% 55% 40% 0%
Piramalai_Kallar 0% 0% 2% 0% 97% 0%
SI_Brahmin 0% 4% 1% 16% 78% 0%
Telugu_Reddy 0% 3% 0% 0% 94% 3%
UP_Brahmin 0% 4% 1% 26% 69% 0%
UP_Kayastha 0% 0% 1% 20% 79% 0%
Velama 1% 1% 0% 2% 96% 0%
West_Bengal_Kayastha 0% 0% 7% 8% 85% 0%

In these results, the Nasrani do look shifted in the same direction as South Indian Brahmins, though less so. Observe that there is no clear Middle Eastern signal in the Nasrani above and beyond what you see in South Asians. This, despite the fact that Indian Jews show a very strong signal of admixture from the Middle East. At this point, I am confident in rejecting Nasrani St. Thomas Christian origins in a converted Jewish community, or one with a large degree of West Asian admixture.

Though the genetic profile of these three individuals does not support clear descent from South Indian Brahmins, I can not reject the model of Brahmin admixture into this community. On the contrary, a plausible model would see to be that various South Indian groups, including Brahmins, contributed to the Nasrani community over the centuries.

To be continued….

From the content to the creator

The science fiction writer S. M. Stirling has a problem with his series centered around the Domination alternative history because readers often confuse the narrative of the alternative history for the author’s endorsement of its arc and philosophy. You see, the novels and stories depict a world where a quasi-Nazi ghoulishly Nietzschean race termed the Draka eventually rise to conquer the whole world. Similarly, the fantasy writer Brandon Sanderson has had problems with readers who are curious why he has sympathetic atheist characters, despite he himself being a devout Mormon.

Obviously, some writers focus on what they know and have experienced. Jhumpa Lahiri comes to mind. She has said that she has no plans to delve beyond the purview of her West Bengali story arcs. But other writers like to explore viewpoints which are startlingly novel and at variance with those of themselves. This is probably particularly true of speculative fiction. Part of being human is the ability to do this with varying levels of fluency.

It is important in any case not to confuse the writer with what they are writing about.

Some of the same applies to what I talk about on this blog. This is clear and obvious when I’m considering the selection coefficient of a novel allele. But what about the Iranian regime?

  1. I am not personally a fan of the regime.
  2. I also believe it is important to describe it accurately and in its own terms.

Some of the latter is for instrumental reasons: if you are to defeat the enemy you must understand it. Even in the early 9/11 years, this was clear, but many people resisted this attempt, as emotions were quite raw. Islamist radicals were viewed in almost metaphysical terms, as forces of nature, evil essences of the universe. The reality though is that they are embodied creatures with needs, wants, and delusions, just like any other.

Ultimately I’m generally pretty frank with my views on a topic if I have them and want to express them. I’m not being cryptic. In some cases, I don’t want to interject my own personal views (which most can infer or know in any case). In other cases, I don’t have a strong opinion.

What religion is

It’s been about 10 years since I addressed this topic. Largely because I have no new thoughts. But probably after 10 years, it’s useful to revisit/clarify on this topic to clarify confusions, since people have a lot of opinions on this topic.

People mean different things when they mean “religion,” and the different meanings are not contradictory, nor in conflict.

At the lowest level in terms of individual cognition religion emerges from deep intuitions about the nature of the universe. Colloquially one might say that religion bubbles out of our unconscious.

In relation to social units, say the clan or tribe, religion consists of these intuitions about the nature of the universe and the world around us, bound together with rituals and verbal descriptions and narratives. These rituals and communal narratives help forge some sort of group Weltanschauung that has a functional utility in terms of inter-group competition and relations. Here religion steps out of the individual and becomes an expression of collective consensus.

As human societies became more complex the role of religious professionals became more elaborated. The common role of a shaman can be thought of as a magician, one who manipulates and operates in the domain of the supernatural. Shamans are common and ubiquitous in pre-state societies (even if a tribe does not have a “professional” shaman, someone takes on the role when needed). The priest adds on top of this institutional authority, often supra-clan or tribal. No king, no priest. Eventually, though the shaman-priest took on the role of the metaphysician. The metaphysician generates abstract principles and rationales, which can transcend the tribe or ethnicity, and allows religion to generate meta-ethnic civilizational identities in the service of priestly functions.

So in the post-Axial Age, the religious professional is often shaman, priest, and philosopher.

In relation to my post about why I am not a New Atheist, New Atheists, and the hyper-verbal expositors of modern organized religion, often tend to reduce religion to a branch of philosophy with some textual revelatory buttress. By refuting the philosophy of religion, they think that they refute religion in toto.  But what they refute is only the latest and most elaborated structural expression of the religious phenomenon.

What about the priest? Though I am wary of the term “political religion,” due to semantic confusion, it seems clear that the function of the priest can be stripped of its supernatural valence. Many of the most objectionable characteristics of religion for people of liberal orientations derives from the institutionalized priestly functions. Unfortunately, the persistence of the priest in the absence of gods, shamanic powers and metaphysical justification opens the doors to secular totalitarianism.

Finally, it seems almost impossible to stamp out the shaman. Shamanism is like music. You can banish it through institutional sanctions, but once those sanctions disappear, shamanism reappears.

These different aspects of religiosity exist and persist simultaneously in most contexts, but sometimes in tension. Philosophers and priests often take a dim view of shamanic religiosity. In organized religion of the modern sort shamanism is marginalized, or highly constrained and regulated in sacraments. But the recession of state-sponsored Christianity across much of the West has arguably resulted in a resurgence of shamanism, and the proliferation of diverse supernatural beliefs which had previously been suppressed (much of East Asia is characterized by relative weakness of philosophical religion but the strength of shamanism).

Jade Eggs anyone?

The relevance of all this in relation to New Atheism is that New Atheism seems to posit a religious “Blank Slate.” That is, children are indoctrinated in religion at a small age, previous to which they had been atheists. Part of this is due to the fact that the philosophical-metaphysical aspect of religion is quite clearly indoctrination, and often of a superficial sort at that (judging by how weak most believer’s grasp of theology is). But the communal and psychological aspects are not indoctrination, as much as specific instantiations of general human sentiments, dispositions, and intuitions. The erasure of a Christian, Buddhist or Islamic religious orientation will not necessarily leave in its wake a mind primed for scientific naturalism. Rather, it will simply be one shorn of Axial-Age accretions, reverted back to the shamanic age…

As someone who is an atheist, I have never had strong intuitions that lead me to find shamanism plausible. Additionally, the philosophical arguments are wanting for me in relation to God, though they are interesting (thanks to reader Thursday I’m reading Edward Feser’s work). Finally, obviously, I take a dim view of the conformity and structure which the priests attempt to impose upon us.  But I do not presume I am not typical.

Personal genomics question: am I related to my 5th cousins?

There are some personal genomics questions I get over and over via email. I thought I would post an answer so that Google could pick it up.

One of them usually has do with if someone is “really” related to someone who comes up as a 5th cousin on a DTC service. What does “really” mean?

Graham Coop has done the formal work to show that it’s highly likely all our genealogies intersect some point in the recent past. Several years ago in his paper with Peter Ralph, The Geography of Recent Genetic Ancestry across Europe, they used genetic data to infer just how closely European lineages coalesced with each other over the past few thousand years.

So yes, you are related (though that doesn’t mean you have matching genetic segments).

But that’s not the question people are really asking about. They are asking, does this DNA match increase the probability that I’m somehow related to this person?

In general, I think not. For example, I regularly get queries from South Asians about distant matches with Europeans. Does this mean they are European? No. I think what it means is:

1) There are lots of Europeans in the database, so a false positive match is likely to be European, even if you are non-European.

2) At short genetic distances, the segments are really mostly some sort of false positive.

Why I am not a New Atheist

Since this comes up now and then I thought I’d put up a quick and short post why I am not a “New Atheist.”

I am an atheist. But I have two major disagreements with the New Atheist tendency. One of them is descriptive and the other is prescriptive.

For the past fifteen years or so I have been strongly convinced that the cognitive anthropology of religion has a lot to say in explaining why most people have historically been religious. The thesis, outlined in books such as In Gods We Trust and Religion Explained, is that humans have strong innate cognitive dispositions which often synthesize together to produce intuitions that dispose them toward belief in the supernatural.

In contrast, a caricature of the New Atheist position would be that religion was written down in a book, and is a meme copied into human brains. As such, it is a meme which can be undone with enough social and cultural suasion. New Atheists, like the village atheists of yore, seem to think one can argue others out of their religiosity.

Fundamentally I do not think this is correct. Nor do I think that religious beliefs have much to do with logic or reason. Religion is a complex phenomenon which is rooted in supernatural intuitions and then evolves further in a cultural context, with some possible functional utility as a group-marker.

Second, I do not think religion is the “root of all evil”, and so see no need to convert the world to atheism. Obviously, the horror of Communism illustrates that removing supernatural religion does not remove the human impulse to atrocity.

More recently, I have been convinced that truth and knowledge is a minor value to most humans, including elites. Lying is pretty ubiquitous, and most people are rather satisfied with big lies girding social norms and conventions. One may try to avoid “living by lies” in private, but actually promoting this viewpoint in public is ridiculously self-destructive. Most people could care less about the truth,* while elites simply manipulate facts to buttress their social positions and engage in control.

In other words, the New Atheists seem to think that it’s a worthy to aim to enlighten humanity toward views which they believe align with reality.

At this point, I care about converting the common man to a true understanding of reality as much as I care about a cow grokking trigonometry. I don’t.

Note: I am not anti-New Atheist either! I think they play a role in the ecology of ideas. Also, I don’t really care if people get their feelings hurt. I hurt feelings all the time. To paraphrase George Constantza, you get a few New Atheists running around, and I’m not looking so bad.

* This includes journalists and scientists. And by “care,” I mean in revealed preferences. Not what people claim privately.

Zhejiang, on the margins of Jiangnan

Zhejiang is the province to the south of Jiangsu, and the heart of Jiangnan, the lower Yangzi river area. As noted in my previous post this region is notable for its economic productivity and wealth, which dates back more than 1,000 years, and persists down the present. Like Jiangsu, Zhejiang is outside of the core area of the rise of Han civilization, but by the 1st millennium A.D. became a redoubt of Chinese civilization in the face of non-Chinese incursions into the north.

Zhejiang is also the location for one of the major centers of Christianity in China, Wenzhou. On the order of ten percent of this city’s population is Christian.

Out of Africa-Out of Asia-Out of Africa

Roberta Estes recenty posted about the fact that Spencer & I will be revisiting The Journey of Man, fifteen years after he wrote the book and made the documentary.

As part of the preparation, I’m revisiting some uniparental results, in particular, recent ones. This preprint in bioRxiv Carriers of mitochondrial DNA macrohaplogroup L3 basic lineages migrated back to Africa from Asia around 70,000 years ago., caught my attention:

Background: After three decades of mtDNA studies on human evolution the only incontrovertible main result is the African origin of all extant modern humans. In addition, a southern coastal route has been relentlessly imposed to explain the Eurasian colonization of these African pioneers. Based on the age of macrohaplogroup L3, from which all maternal Eurasian and the majority of African lineages originated, that out-of-Africa event has been dated around 60-70 kya. On the opposite side, we have proposed a northern route through Central Asia across the Levant for that expansion. Consistent with the fossil record, we have dated it around 125 kya. To help bridge differences between the molecular and fossil record ages, in this article we assess the possibility that mtDNA macrohaplogroup L3 matured in Eurasia and returned to Africa as basic L3 lineages around 70 kya. Results: The coalescence ages of all Eurasian (M,N) and African L3 lineages, both around 71 kya, are not significantly different. The oldest M and N Eurasian clades are found in southeastern Asia instead near of Africa as expected by the southern route hypothesis. The split of the Y-chromosome composite DE haplogroup is very similar to the age of mtDNA L3. A Eurasian origin and back migration to Africa has been proposed for the African Y-chromosome haplogroup E. Inside Africa, frequency distributions of maternal L3 and paternal E lineages are positively correlated. This correlation is not fully explained by geographic or ethnic affinities. It seems better to be the result of a joint and global replacement of the old autochthonous male and female African lineages by the new Eurasian incomers. Conclusions: These results are congruent with a model proposing an out-of-Africa of early anatomically modern humans around 125 kya. A return to Africa of Eurasian fully modern humans around 70 kya, and a second Eurasian global expansion by 60 kya. Climatic conditions and the presence of Neanderthals played key roles in these human movements.

It was really hard for me to parse all the coalescene and phylogenies here. I know some readers are pretty well versed in this area so I’m curious about critiques and reactions to the above.

Why Confucianism matters

Human nature has not changed, within some broad parameters, across history. When I first became interested in topics such as ancient philosophy twenty years ago I recall being struck by the contemporary relevance of thinkers such as Aristotle. Previously my focus has been on the natural sciences, where the dead were just names, whose ideas had often been superseded and extended.

And yet when it came to ethics and moral living the philosophers and religious thinkers who flourished 2,000 years ago seem to have arrived at the primary issues at the general level, though progress and change occurred on the details (and continues to occur).

Why look to China? After all, there were ethical systems in the West. First, I’m not sure that the supernaturalistic religions work to bind elites together anymore due to lack of credibility. Christianity is getting weaker. My own personal hunch is that the current wave of Islamic assertiveness and violence is the paroxysm of a civilization confronting its irrelevance.

Second, Classical Antiquity had plenty of ethical systems, especially during the Hellenistic and Roman period. But Rome collapsed. There was a great rupture between antiquity and the medieval period. In contrast, the Confucian and Neo-Confucian system persisted down to the early 20th century in classical form and casts a strong shadow over East Asia even today. While Stoicism had personal relevance, Confucianism was designed to scale from the individual all the way to the imperial state.

The 1960s saw a radical transition to notional social egalitarianism in the West. This is the world I grew up and matured in. Arguably, I believed in its rightness, inevitability, and eternal dominance, until very recently. But I think that today that model is fraying and people are looking to find some mooring. In particular, I think we are in need of a rectification of names. From Wikipedia:

Confucius was asked what he would do if he was a governor. He said he would “rectify the names” to make words correspond to reality. The phrase has now become known as a doctrine of feudal Confucian designations and relationships, behaving accordingly to ensure social harmony. Without such accordance society would essentially crumble and “undertakings would not be completed.”

How are we supposed to behave with each given person? A lot of this is free-form and improvisational today, and it turns out that many people are not comfortable with this. Humans need scripts.

Finally, the world that Confucianism developed was highly stratified, though there was some chance of advancement. It was not a calcified caste system, but it was a hierarchical one. I believe that is the system that we are moving toward in the West, and it seems that a system that takes for granted non-egalitarianism, such as Confucianism, may benefit us.