Tuesday, April 17, 2018

Balu: Comparative Anthropology and Moral Domains

PDF

The knife appears to cut both ways: against the background of the western conception of’ethics’, Indian traditions ’chill the blood’.  Against the background of Indian traditions, the West appears totally immoral: Why does it appear so?  What causes this perception?

Saturday, April 14, 2018

Where's the Beef?

Worldwide Patterns of Ancestry, Divergence, and Admixture in Domesticated Cattle
http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004254

Bos taurus taurus was domesticated in the Middle East while Bos taurus indicus was domesticated in India. 

It is likely is that a hypothetical Punjab_N population from even before agriculture would have been related to the Iran_N people, somewhere along a cline between Iran_N in Iran (whose aDNA has been found) and peoples in India's interior. 

If Iran_N(eolithic) ingressed into India with a demic diffusion of agriculture, they didn't bring their cattle along. 

Tuesday, April 10, 2018

Ancestry Models

In Lazarides et. al. 2016, https://www.biorxiv.org/content/biorxiv/early/2016/06/16/059311.full.pdf,  modeling ANI (Ancestral North Indian)
While the Early/Middle Bronze Age ‘Yamnaya’-related group (Steppe_EMBA) is a good genetic match (together with Neolithic Iran) for ANI, the later Middle/Late Bronze Age steppe population (Steppe_MLBA) is not.
However, in Narasimhan et. al. 2018, Steppe_MLBA is seen to be a better match, and Steppe_EMBA is ruled out.  Underlying it are different other components of ancestry that are used.

In Lazarides,  the other components of ancestry are Iran_N(eolithic), Onge, and Han.
In Narasimhan, the other components of ancestry are Iran agriculturist (same as Iran_N?) , AASI (another name for Onge), and a composite of "Indus_Periphery" and Swat SGPT and early historic individuals.  

Why is it important? Because if these genetic findings are correlated with language (a big if!) and  because if the Rg Veda is taken seriously, e.g., its mentions of the Saraswati River, then a post-IVC arrival of I.E. is untenable.  Likewise with the Vedic Indra-Varuna-Mitra- Nasatyas in the Mitanni documents.  Steppe_EMBA doesn't rule out a pre-IVC-collapse arrival; but Steppe_MLBA pretty much does.

One should note that Steppe_EMBA itself lies on the cline between Iran_Chalcolithic and European Hunter Gatherer, and Steppe_MLBA is largely Steppe_EMBA but on the Steppe_EMBA - European_MidNeolithic_Chalcolithic cline.  (see Lazarides 2016 for this, excerpted diagrams here).
But in contemplating the difference between Lazarides and Narasimhan, it seems the Siberian Hunter Gather component is what makes the difference. 

A question would be - do Steppe_EMBA and Steppe_MLBA have "similar ancestry profiles"? Apparently in the context of the Narasimhan et. al. model, for the purpose of modeling ANI they do not.  Yet, for the purpose of modeling ANI,  Indus_Periphery and Swat individuals have a similar ancestry profile.  




Thursday, April 05, 2018

Some history of astronomy links

Wednesday, April 04, 2018

Comment: Re: confused

Looks like my IntenseDebate comments system is hosed. At least it doesn't work consistently.

So, to reply to a comment until I figure out how to make things work:

Suppose you said that X and Y had a similar ancestry profile of a Norwegian and Italian mix, except that Y also had 22% Japanese ancestry. It makes one wonder, what does a "similar ancestry profile" mean?

How about "X is half tin and half copper" vs. "Y consists of equal parts of tin and copper with 22% arsenic"? Seems like the obvious analogy to me.

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This analogy doesn't work for me for several reasons:

First of all, X and Y are different alloys, some variety of bronze versus arsenical bronze.

Next: the X itself consists of 14-42% AASI (and the rest Iranian farmer and Siberian Hunter Gatherer)

So this is like saying X is 14% tin and 86% copper or 42% tin and 58% copper and Y is various proportions of tin, copper and arsenic (arsenic averaging 22%).

Next: What does "similar ancestry profile" mean of X and Y when X and Y don't share at least 22% of their ancestors?

Next: since when is 78% of a genome similar to 100% of another? 

Next: A majority of Indians are somewhere on the ANI/ASI cline with little other admixture.  Would you say they "share the same ancestry profile"?

Next: Out of 246 groups of Indians that this pre-print had genetic profiles for, they excluded 106. Some for paucity of data; but others for having something more than just ANI/ASI.  i.e., for that part of the analysis, these 106 groups did not have "similar ancestry profiles".

Next: just as a practical thing - if someone said, I have the same ancestry profile as European Americans but also 22% African - well, unless they are "passing" this someone has gone from being white to being black.  Trump supporters (well, some of them) would likely riot over a statement that they share an ancestry profile.

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IMO, on an entirely different tack, I get a suspicion that some of the genetics people don't really understand the algorithms that underlie their computational analytic apparatus; it is largely black-boxes to them.

---
 PS: Let's get to some amusing applications of "similarity".

These two geometric figures are similar though one is triangle and the other is a quadrilateral.

"I'll offer you a similar deal as I offered him, except you'll pay 22% more."

Confused: The Genomic Formation of South and Central Asia

The recent preprint under discussion: The Genomic Formation of South and Central Asia, has the passages below.

Suppose you said that X and Y had a similar ancestry profile of a Norwegian and Italian mix, except that Y also had 22% Japanese ancestry.  It makes one wonder, what does a "similar ancestry profile" mean? 
 

276 Third, between 3100-2200 BCE we observe an outlier at the BMAC site of Gonur, as well as two
277 outliers from the eastern Iranian site of Shahr-i-Sokhta, all with an ancestry profile similar to 41
278 ancient individuals from northern Pakistan who lived approximately a millennium later in the
279 isolated Swat region of the northern Indus Valley (1200-800 BCE). These individuals had
280 between 14-42% of their ancestry related to the AASI and the rest related to early Iranian
281 agriculturalists and West_Siberian_HG. Like contemporary and earlier samples from Iran/Turan
282 we find no evidence of Steppe-pastoralist-related ancestry in these samples. In contrast to all
283 other Iran/Turan samples, we find that these individuals also had negligible Anatolian
284 agriculturalist-related admixture, suggesting that they might be migrants from a population
285 further east along the cline of decreasing Anatolian agriculturalist ancestry. While we do not
286 have access to any DNA directly sampled from the Indus Valley Civilization (IVC), based on (a)
287 archaeological evidence of material culture exchange between the IVC and both BMAC to its
288 north and Shahr-i-Sokhta to its east (27), (b) the similarity of these outlier individuals to post-
289 IVC Swat Valley individuals described in the next section (27), (c) the presence of substantial
290 AASI admixture in these samples suggesting that they are migrants from South Asia, and (d) the
291 fact that these individuals fit as ancestral populations for present-day Indian groups in qpAdm
292 modeling, we hypothesize that these outliers were recent migrants from the IVC.

449 Finally, we examined our Swat Valley time transect from 1200 BCE to 1 CE. While the earliest
450 group of samples (SPGT) is genetically very similar to the Indus_Periphery samples from the
451 sites of Gonur and Shahr-i-Sokhta, they also differ significantly in harboring Steppe_MLBA
452 ancestry (~22%). This provides direct evidence for Steppe_MLBA ancestry being integrated into
453 South Asian groups in the 2nd millennium BCE, and is also consistent with the evidence of
454 southward expansions of Steppe_MLBA groups through Turan at this time via outliers from the
455 main BMAC cluster from 2000-1500 BCE. Later samples from the Swat time transect from the
456 1st millennium BCE had higher proportions of Steppe and AASI derived ancestry more similar to
457 that found on the Indian Cline, showing that there was an increasing percolation of Steppe
458 derived ancestry into the region and additional admixture with the ASI through time.

Tuesday, April 03, 2018

The Mosaic Distinction


Jaideep Prabhu in firstpost.com:

Theo Sundermeier, professor of theology at Heidelberg University, makes an insightful distinction in his Was ist Religion? Religionswissenschaft im theologischen Kontext between primary and secondary religions. The former, Sundermeier explains, developed over hundreds, if not thousands, of years, usually within a single culture, society and language with which the religion is inextricably intertwined. These would include the Greek, Roman, and Egyptian religions as easily as Hinduism. The latter category of religions are those that originate from an act of revelation or foundation and are monotheistic, universal, and of the Book. Secondary religions denounce primary religions as paganism, a collection of superstitions, and idolatry. The three Abrahamic faiths fit this description well.
Note the Primary and Secondary Religions.
This seemingly obvious categorisation holds an evolution of great import. From primary to secondary, religion changes from being a system that is irrevocably embedded in the institutional, linguistic, and cultural conditions of a society to become an autonomous system that can transcend political, ethnic, and other boundaries and transplant itself into any alien culture. As Jan Assmann, an Egyptologist at the University of Konstanz, describes in his Die Mosaische Unterscheidung: oder der Preis des Monotheismus, this change, which he calls the Mosaic distinction, is hardly about whether there is one god or there are many gods, but about truth and falsehood, knowledge and ignorance.
Note Jan Assmann (thanks to a friend!)
Assmann argues that the Mosaic distinction created an entirely new category of truth - faith - and draws an interesting parallel with a scientific development that Werner Jäger, a 20th century classicist at Harvard University, described as the Parmenidian distinction in Paideia: The Ideals of Greek Culture.
 .....
Before the Mosaic distinction, there were four kinds of fundamental truths: experiential (water is wet), mathematical (two plus two is four), historical (the life of Mokshagundam Visveswaraya), and truths conducive to life (ethics). The Mosaic distinction cleaved faith from knowledge and installed the former as a fifth truth that claimed knowledge of the highest authority even if it could not be verified on scientific grounds.
Read the whole essay, please. Here's another key passage.

For the first time in history, justice, law, and freedom are declared to be the central themes of religion and the sole prerogative of god. Though technically true, this is a misleading statement. The monotheistic point of view is that since god is the true authority, only he can be the final arbiter of justice; the temporal laws of man are inferior to the divine. The story of the exodus from Egypt ties in well with ideas of liberation of the Jewish people from slavery. Furthermore, their escape, divinely sanctioned, also took the power to sit in judgment over them away from the pharaoh and invested it in god. The Shemot, or the Book of Exodus, is thus more concerned with political theology than with idolatry (the story of the golden calf). Thus, in monotheism, the political role of justice was given to religion. The authority of the king was superseded by that of the high clergy, god's representatives on earth, as papal power well into the Early Modern era demonstrated. This fusion of the political with the religious in secondary religions, but not primary belief systems, is exactly what makes secularism a requirement solely of the former in the modern era.
In pagan religions, justice was of this world for even the gods were of this world. A Roman or an Egyptian who had been wronged could appeal to the local magistrate for justice for its own sake without reference to the gods. Indeed, in Hinduism, dharma is not only properly a function of kaala, desha, and paristhiti but the chaturanga purusharthas mention it along with artha and kama as one of the three goals of mortal life. The ultimate goal, moksha, is beyond short-term earthly consideration. As Hindi novelist Gurudutt explains in Dharma tatha samajwad and Dharma, sanskriti, aur rajya, the individual is free to interact with the divine in a manner of his choosing but wherever he must interact with another, their conduct must be guided by the precepts of dharma, artha, and kama. Ethics and the law were intrinsically this-worldy and had no business to be under divine purview. Thus, justice, or ethics at least, existed much before secondary religions came on the scene but were not truly a part of the religious system.
 kaala = era;  desha = country, place,  paristhiti = circumstances (e.g., historical/social/political circumstances); chaturanga = four-fold; purushartha = object of human pursuit, goal of life;  artha = material prosperity; kama = pleasure; dharma = right way of living, human behaviors considered to be necessary to maintain right order in the universe,  duty, etc. (difficult to translate); samajwad = socialism; sanskriti = civilization, rajya ~= politics.

If you've come this far, here's a bonus for you:
(PDF file) Jan Assman, The Mosaic Distinction, Israel, Egypt and the Invention of Paganism.
The space "severed or cloven" by the Mosaic distinction was not simply the space of religion in general then, but that of a very specific kind of religion. We may call this a "counterreligion" because it not only constructed but rejected and repudiated everything that went before and everything outside itself as "paganism".  It no longer functioned as a means of intercultural translation; on the contrary, it functioned as a means of intercultural estrangement.  Whereas polytheism or rather, "cosmotheism" rendered different cultures mutually transparent and compatible, the new counterreligion blocked intercultural translatability.  False gods cannot be translated.
Primary and secondary religion; religion and counterreligion!  Where does it end?  

A comment from @bennedose

From here (copied in full):

This paper has some of the following issues which I find interesting. I believe that geneticists are mistaken when any good work that they do is mixed with the unscientific hypotheses about language spread that linguists have established for the last 150 years. Genes do not code for language. Genetic fact should not be mixed up with tenuous linguistic hypotheses.

1.The linguistics dates of IE spread are taken from David Anthony (ref no 46) whose assumptions linking the archaeology of Andronvo grave pits and Sintashta culture with grossly erroneous translations of the Rig Veda are untenable. In particular Anthony’s linking of Rig Veda 10:18 with Kurgans is based on an incorrect translation, apart from other assumptions.

2. This paper reinforces what was earlier suggested by Reich et al and Priya Moorjani (refs 44 and 45) that ASI-ANI mix occurred in the last 2000-4000 years ago. Both this paper and the earlier Reich paper suggest that there was lack of mixing of ASI and ANI before that. In fact this paper says that ASI and ANI were "largely unformed) 4000 years ago (page 14).

Now here is what is odd. If ANI and ASI ancestry represent IE speakers and Dravidian language speakers (respectively) and if they started mixing as recently as in the last 4000 years when the migrations are said to have occurred, but the admixture had NOT occurred before that date - it tears down all assumptions of a "Caste system" having been created by the migration of ANI/IE speakers displacing ASI/Dravidian language speakers. If they were mixing, there were not remaining separate. It is as simple as that.

If one assumes (probably wrongly) that IE languages came to India about 1500-2000 BCE then it appears that the real mixing of ASI and ANI started AFTER those people came contrary to all assertions by linguists that endogamy commenced in India with the arrival of IE speakers in India.

3. Of course all this ignores and fails to explain how the oldest IE language Sanskrit has references to hydronyms and the riverine geography of IVC area from 3000 BCE and the start of aridity in 2000 BCE - adding to the growing body of evidence that linguistic hypotheses have depended upon dubious assumptions.

It is notable that German and Greek have perhaps 25-40 % Indo-European language content, the rest of the words having a non Indo-European or pre- IE origin. However Sanskrit, the oldest known IE language has 97% Indo-European word content. This anomaly cannot be explained by saying that no language was spoken in India before the arrival of IE languages in 1500 BCE.

4. This paper makes statistical predictions about the entire Indian subcontinent with zero samples from IVC or anything east or south of that (as clearly admitted in the paper). The closest "south Asia" samples are from Swat in Pakistan. Swat is closer to "Turan" (Iran, Uzbekistan, Turkmenistan) than to major IE speaking areas of India like Bengal, south Gujarat, Maharashtra and the Eastern Gangetic plain. So linguistic conclusions connected to genetics need to be viewed with caution.

A Musing

Very roughly the story goes like this (don't use any dates or figures from here):

Let's look at 7000 years before present. What do we have?
- attested in Iran by aDNA "Iranian farmer".
- in India, unattested by aDNA, but reasonably safe theoretical assumption, the AASI profile.

What else in India? What would the ancestry of someone in Punjab 7000 years before present be? In the absence of anything other information we'd have to say, it is some combo of Iranian farmer + AASI.

Suppose we found in Punjab aDNA from 7000 years ago. Then whatever it was, it would not be explainable in terms of some contemporary Iranian farmer; at best it would trace to some common ancestor with the contemporary Iranian farmer aDNA, with the theoretical AASI thrown in. The finding in BMAC of 3 persons with AASI but no steppe ancestry suggests that this Punjab aDNA would also show no recent common ancestor with steppe.

The other peoples in India of 7000 years ago would presumably be better modeled via this Punjabi aDNA + AASI rather than Iranian farmer + AASI. But we don't have aDNA from Punjab from 7000 years ago, and so the only choice is to model people in India in terms of Iranian farmer (ostensibly an outsider) and AASI. And of course, in the absence of aDNA there is nothing really to model. A principle of parsimony says that the people of north India of this time had (Iranian farmer + AASI) ancestry. Nothing more can be said.

The same goes for Indians from 6000 years ago, 5000 years ago, 4000 years ago. 3000 years ago, we get the first aDNA in the Indian subcontinent, that from Swat. It can only be modeled in terms of aDNA found so far - Iranian farmer, Siberian and Central Asian Hunter Gatherer, Steppe MLBA, EMBA)  and theoretical populations like AASI. If we had aDNA from Punjab from 7000 years ago, for example, the best model of Swat aDNA might be rather different; just like the discovery of the aDNA of three Indus_Periphery persons turned the theoretical constructs ANI and ASI from being quite ancient (from more than 14000 years ago) to arising only post-Saraswati-Sindhu civilization.

One revelation of this paper (assuming that it is correct) is that genetic models seem to be not stable against small perturbations. Three samples of aDNA turned the origins of ANI and ASI upside down.

Similarly on the Eurogenes blog there is a post from about an year ago, that Indian populations are better modeled with Steppe EMBA than Steppe MLBA.  The recent pre-print finds Steppe MLBA to be more relevant. That is, with "Indus_Periphery" aDNA thrown into the mix, now Steppe MLBA provides a better fit for Indian populations than Steppe EMBA.  This is counter-intuitive to me, and IMO, is another indication of the instability of genetic models.

It may be a fair inference that further discoveries could destabilize the model that this pre-print proposes. Unfortunately it seems likely that little if any aDNA in the main part of India will ever be found.

Monday, April 02, 2018

Human generation times

1. The paper discussed in my previous two blog posts, "The Genomic Formation of South and Central Asia" uses a time per human generation of 28 years.

2. This time is derived from a paper by one of the authors, "A genetic method for dating ancient genomes provides a direct estimate of human generation interval in the last 45,000 years", P. Moorjani et. al. That paper comes up with an estimate of 26-30 years, from which the mid-value is used.

3. "The Genomic Formation...." uses this human generation time of 28 years in two places.
...we estimate that the time of admixture between Iranian agriculturalist-related ancestry and AASI ancestry in the three Indus_Periphery samples was 53 ± 15 generations ago on average, corresponding to a 95% confidence interval of about 4700-3000 BCE assuming 28 years per generation
....Using admixture linkage disequilibrium, we estimate a date of 107 ± 11 generations ago for Iranian agriculturalist and AASI-related admixture in the Palliyar, corresponding to a 95% confidence interval of 1700-400 BCE assuming 28 years per generation.
4.  Here we notice something.  (107 + 11) generations * 28 years =  3304 years.  The Iranian agriculturalist and AASI admixture in the (modern) Palliyar  dates to 1300 BCE to 700 BCE.

5. Moreover, if we go with the generation time measured with the !Kung, 25.5 years - the lower end of P. Moorjani's estimation, it only makes it worse for the idea that all this admixture happened around the collapse of the Indus Valley Civilization.

6. The ancestry of the Indus_Periphery samples may likewise become too late for the archaeological  record of agriculture.

PS: Note that for the Indus_Periphery, the date is 53 ± 15 generations prior to the date of the Indus_Periphery samples, i.e., prior to 3100-2200 BCE.

PPS: The life expectancy at birth in the Paleolithic is estimated to be 33 years per Wiki.  The per generation time of 28 years means that the average age of a woman relative to the birth of her children is 28 years.  E.g., if women uniformly bore children at ages 20, 24, 28, 32 the generation time would be (20 + 24 + 28 + 32)/4 = 26.  You can see that women would be bumping up into the life expectancy.  On the other hand, what is important is actually the conditional life expectancy, which is the life expectancy of women who survived up to at least one live birth, which may be better than that 33 years.  Still, one would think that in the Paleolithic, women in the 18-28 age group would have more children than the women 28-38 age group, if only for the reason that there's more of them.

PPPS: The Wiki that gives the Paleolithic life expectancy at birth also says "Based on the data from modern hunter-gatherer populations, it is estimated that at 15, life expectancy was an additional 39 years (total 54)"" Supposedly after surviving birth the probability of reach age 15 was 0.6.

A paper linked at the Wiki gives (figure 10) the yearly mortality rate ("Proportion that die") of the Aché people of Paraguay.  The yearly mortality rate starts at 0.10 around birth, and rapidly falls to 0.02 between five and ten years of age (the curves are different for males and females).  It then remains steady between 0.01 and 0.02 until age 40, after which it starts rising fairly rapidly.  A cohort of 100 women aged 20 years would reduce to 86 by age 30, and 74 by age 40 if the annual mortality rate ("proportion that die") was 0.015.

In comparison, in 2013, per WHO data, globally,  the adult mortality rate - the probability of dying between ages 15 and 60 - was for men 0.182 and for women 0.121.

Also note that if women were having a lot of babies, and if the population was growing very slowly if at all, then there must have been a corresponding number of deaths.