Out-of-India - From Theory to Truth: Part 2

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Re: Out-of-India - From Theory to Truth: Part 2

Postby peter » 18 Apr 2018 20:11

A_Gupta wrote:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5702378/
World-wide distributions of lactase persistence alleles and the complex effects of recombination and selection
Anke Liebert,1,3 Saioa López,1 Bryony Leigh Jones,1 Nicolas Montalva,1,2,4 Pascale Gerbault,1,5 Winston Lau,1 Mark G. Thomas,1 Neil Bradman,6 Nikolas Maniatis,1 and Dallas M. Swallow

Either Indians have major lactose intolerance or else there are more alleles to be discovered regarding lactose tolerance.
Image

PS: lactase is the enzyme; lactose is the sugar in milk that is not digestable if you lack lactase. Typos above corrected.

https://academic.oup.com/mbe/article/29/1/249/1749245

This says it is the exact same mutation in indians and europeans and it happened in last 10000 years. So it should be "easy" to find this in every ancient DNA unearthed in europe and anywhere else and correlate it with archaeological dating?
Last edited by peter on 18 Apr 2018 20:14, edited 1 time in total.

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Re: Out-of-India - From Theory to Truth: Part 2

Postby peter » 18 Apr 2018 20:12

Prem Kumar wrote:Let me ask a dumb question:

Modern Indian population is being modeled as a cocktail of Steppe_MLBA, Iran_N, AASI, Onge etc. Presumably because:

1) Common mutations can be found
2) They fit a statistical curve
3) aDNA from Steppe, Iran are available, thereby positioning them as a possible source

Point (3) is critical because that's what helps them postulate a directionality of gene flow. However, we know that Indian aDNA is missing. If Indian aDNA is available and carries the same mutations at a sufficient enough antiquity, the directionality is reversed. This is why Vagheesh is so keen to claim that Indian aDNA does not have Steppe DNA, even though he and others have never seen Indian aDNA! Because it can completely reverse the story.

However, even without Indian aDNA, why can't a statistical curve be drawn, which models Steppe_MLBA as a combination of say modern-Indian-DNA, Iran_N etc? We can see which curve fits best. By modern-Indian-DNA, I don't mean "modern DNA". Its ancient DNA but present in modern day Indians.

To me, this sounds like a vector algebra problem. I can pick any set of x, y, z co-ordinates as my basis vectors and represent any point in the 3-dimensional space in terms of these basis vectors. The question is what vectors are chosen & why

For Point 3 the word "available" is important. Absence of evidence is not the evidence for absence.

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Re: Out-of-India - From Theory to Truth: Part 2

Postby A_Gupta » 18 Apr 2018 21:50

Peter, there are now five different variants -as of 2017 - involved in lactase persistence. The European/Steppe variant is not sufficient to explain the lactase persistence in India described in the medical literature. Of course the medical literature which says that 40% of Indians are lactase persistent may be wrong.

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Re: Out-of-India - From Theory to Truth: Part 2

Postby shiv » 18 Apr 2018 22:13

A_Gupta wrote:Peter, there are now five different variants -as of 2017 - involved in lactase persistence. The European/Steppe variant is not sufficient to explain the lactase persistence in India described in the medical literature. Of course the medical literature which says that 40% of Indians are lactase persistent may be wrong.

The medical literature may be right in terms of clinical impact but may not indicate the genetic picture. This is my guess because a lot of people with problems related to this come to me. Clinically lack of lactase persistence is hardly a problem. It exists but is not crippling. Most lactose intolerants can have some milk and most end up being tolerant to Yoghurt which is big in India. Milk is expensive so humongous amounts of milk are never the norm for most Indians anyway

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Re: Out-of-India - From Theory to Truth: Part 2

Postby A_Gupta » 18 Apr 2018 22:43

^^^
https://academic.oup.com/mbe/article/29/1/249/1749245
Yet, despite being host to over 1 billion people and having a well-documented history of consumption of dairy products (Simoons 1970b), little is known about the distribution of lactase persistence beyond a flurry of studies conducted in the 1970s (Desai et al. 1970; Swaminathan et al. 1970; Gupta et al. 1971; Reddy and Pershad 1972; Tandon et al. 1981). These data suggest that phenotypic lactase persistence could be as high as 0.73 in some north Indian populations and rare or absent from some groups in the south of the country, predicting an overall north–south phenotypic frequency gradient, as well as a moderately high countrywide frequency of the phenotype.


the derived -13910*T allele has the highest frequency among the observed mutations as well as the widest distribution throughout the Indian subcontinent (table 1, supplementary table 1, Supplementary Material online). Its frequency ranges from 0.8% among the Tibeto-Burman speakers to 18.4% among Indo-European speakers, with west India showing the highest frequency of the derived allele; it has an average countrywide frequency of 10.3%. Seven other segregating polymorphic sites were also observed, one of which (-13779 G>C) has an overall frequency of 2.4% in India (supplementary table 3, Supplementary Material online), whereas the remaining six mutations combined have an overall frequency of roughly 1%.


i.e., 13910 is inadequate to explain the studies mentioned in the first quote.

On the basis of previously collected lactase persistence phenotype data (Desai et al. 1970; Swaminathan et al. 1970; Gupta et al. 1971; Reddy and Pershad 1972; Tandon et al. 1981), the average observed frequency of lactase persistence in India appears to be roughly 0.40 (supplementary fig. 1, Supplementary Material online). However, based on our -13910*T allele frequency data, the predicted countrywide phenotype frequency in our sample is only 0.196. The same is true when we calculate the mean predicted phenotypic frequency at the population group level, 0.158 (SD ± 0.191)—the median population value is likewise low, 0.089. In our data, point estimates of phenotype frequency explained by -13910*T allele frequency only reach or exceed 0.40 in 11 of the 81 sampled groups and are less than 0.1 in 45 of the 81 groups. Given that we observe an absence of -13910*T alleles in many of these samples, phenotype frequencies could in many cases be close to zero; 95% confidence intervals for all populations are given in supplementary table 1 (Supplementary Material online). Even when we assume that all observed mutations in the genetic region under study are causative and dominant, our predicted countrywide phenotype frequency only increases to 0.24, again substantially lower than 0.40 (supplementary table 5, Supplementary Material online). These results suggest either that there are other major genetic variants outside our sequencing range that are causative of the lactase persistence phenotype or that previous studies have overestimated the actual phenotype frequency in India

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Re: Out-of-India - From Theory to Truth: Part 2

Postby A_Gupta » 18 Apr 2018 22:45

https://www.researchgate.net/profile/Va ... ndians.pdf
Lactose intolerance in North and South Indians

Rakesh K. Tandon,3 Y K. Joshi,4 D. S. Singh,5 M. Narendranathan,6 V. Balakrishnan,7 and
K Lal
ABSTRACT A multicenter study was carried out in India to determine the incidence of lactose
intolerance in healthy volunteers from different parts of the country. The incidence was found to
be 66.6% in the subjects from two South Indian centers at Trivandrum and Pondicherry. In
contrast, the incidence in the subjects from a North Indian center in New Dethi was much lower,
i.e., 27.4% (p < 0.001). The lower incidence in the North Indian subjects may perhaps be due to the
fact that they are descendants of the Aryans who have been dairying for long and are known to be
lactose tolerant. Am. J. Clin. Nutr. 34: 943-946, 1981.

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Re: Out-of-India - From Theory to Truth: Part 2

Postby hanumadu » 19 Apr 2018 05:33

What do they mean by lactose intolerance? When they say lactose intolerance is 66.6%, do they mean 66.6% cannot have milk. Surely, there are more than 44% of people in those cities that have been drinking milk.

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Re: Out-of-India - From Theory to Truth: Part 2

Postby gandharva » 19 Apr 2018 06:04

Another front AIT walas have opened is Quantitative comparative linguistics ( https://en.wikipedia.org/wiki/Quantitat ... inguistics ). Vagheesh used the word "Computational Linguitics" which I confused with the engineering topic natural language analysis and modelling for man-machine intercation. But this is basically old Indologist philology stuff wrapped in a mathamatical language.

A sample
A Bayesian phylogenetic study of the Dravidian language family

"Our results indicate that the Dravidian language family is approximately 4500 years old, a finding that corresponds well with earlier linguistic and archaeological studies."

http://rsos.royalsocietypublishing.org/ ... 5/3/171504

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Re: Out-of-India - From Theory to Truth: Part 2

Postby gandharva » 19 Apr 2018 06:06

hanumadu wrote:What do they mean by lactose intolerance? When they say lactose intolerance is 66.6%, do they mean 66.6% cannot have milk. Surely, there are more than 44% of people in those cities that have been drinking milk.


I know one blck guy who is lactose intolerant. If he drinks milk, he starts farting like crazy and sometimes lose motions as wells.

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Re: Out-of-India - From Theory to Truth: Part 2

Postby sudarshan » 19 Apr 2018 06:15

hanumadu wrote:What do they mean by lactose intolerance? When they say lactose intolerance is 66.6%, do they mean 66.6% cannot have milk. Surely, there are more than 44% of people in those cities that have been drinking milk.


Nikhilam navatascharam dashathah (all from nine and the last from ten :)). It's a principle in Vedic mathematics, when subtracting a number from a power of 10. So the complement of 66% from 100 would be 34%, not 44% (sorry, couldn't resist, just nitpicking). But yes, a claim of 66% lactose intolerance in N. India is very suspicious. I doubt it's that high even in the western world.

I second the humble request by somebody else earlier in this thread - can we please have a layman's perspective (just a line or two) of the summary of the genetic findings, and the case for/against AIT, based on the genetics? I am of course doing my own research, but I am a neophyte in genetics, and my head swims listening to the technical terms. I will get to speed eventually even on the genetics aspects, but in the meantime, there's this desi guy in our company, who keeps gleefully peddling the AIT line to adoring goras. (He also peddles some other expected lines, such as "upper caste" Modi govt. out to destroy all the poor suffering dalits, etc.). I was about to counter him, when this Vagheesh paper came up, and I desisted, knowing that the first few links in any google search would point to that, and that the goras would only get that perspective. In any case, my strategy is more to let the guy come to the point of destroying his own credibility, with some blatantly false line, at which point I go for the jugular - but a little lay-terms summary and perspective of the genetic findings would go a long way at that point.

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Re: Out-of-India - From Theory to Truth: Part 2

Postby A_Gupta » 19 Apr 2018 07:38

Let's start with this:
https://ghr.nlm.nih.gov/primer/genomicresearch/snp
What are single nucleotide polymorphisms (SNPs)?

Single nucleotide polymorphisms, frequently called SNPs (pronounced “snips”), are the most common type of genetic variation among people. Each SNP represents a difference in a single DNA building block, called a nucleotide. For example, a SNP may replace the nucleotide cytosine (C) with the nucleotide thymine (T) in a certain stretch of DNA.

SNPs occur normally throughout a person’s DNA. They occur once in every 300 nucleotides on average, which means there are roughly 10 million SNPs in the human genome. Most commonly, these variations are found in the DNA between genes. They can act as biological markers, helping scientists locate genes that are associated with disease. When SNPs occur within a gene or in a regulatory region near a gene, they may play a more direct role in disease by affecting the gene’s function.

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Re: Out-of-India - From Theory to Truth: Part 2

Postby shiv » 19 Apr 2018 07:42

A_Gupta wrote:https://www.researchgate.net/profile/Vallath_Balakrishnan/publication/15963819_Lactose_intolerance_in_North_and_South_Indians/links/5458736e0cf26d5090ab6368/Lactose-intolerance-in-North-and-South-Indians.pdf
Lactose intolerance in North and South Indians

Rakesh K. Tandon,3 Y K. Joshi,4 D. S. Singh,5 M. Narendranathan,6 V. Balakrishnan,7 and
K Lal
ABSTRACT A multicenter study was carried out in India to determine the incidence of lactose
intolerance in healthy volunteers from different parts of the country. The incidence was found to
be 66.6% in the subjects from two South Indian centers at Trivandrum and Pondicherry. In
contrast, the incidence in the subjects from a North Indian center in New Dethi was much lower,
i.e., 27.4% (p < 0.001). The lower incidence in the North Indian subjects may perhaps be due to the
fact that they are descendants of the Aryans who have been dairying for long and are known to be
lactose tolerant. Am. J. Clin. Nutr. 34: 943-946, 1981.

:rotfl: This paper was apparently published shortly before I left JIPMER. I think Singh was there - I think this Singh was the same man we surgeons had to contend with for certain items of equipment. There was a life-saving item (in that era, no longer true) called a "Sengstaken tube" and when we wanted one we were informed that Singh had taken custody of it - so it was then called "Singh's Taken tube"

I love the way they have internalized the "Aryan invasion" business. But a lot less was known back then about what happens in the gut. We now know a lot more about what we don't know yet.

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Re: Out-of-India - From Theory to Truth: Part 2

Postby A_Gupta » 19 Apr 2018 07:52

Let's continue with this:
An allele is a viable DNA coding that occupies a given locus (position) on a chromosome.
Remember that chromosomes are paired.
An organism in which the two copies of the gene are identical — that is, have the same allele — is called homozygous for that gene.
An organism which has two different alleles of the gene is called heterozygous.

https://www.nature.com/scitable/topicpa ... otypic-706

The fixation index is a measure of how populations differ genetically. One derivation of the fixation index is FST = (HT – HS)/HT, in which HT and HS represent heterozygosity of the total population and of the subpopulation, respectively. This derivation measures the extent of genetic differentiation among subpopulations. The value of FST can theoretically range from 0.0 (no differentiation) to 1.0 (complete differentiation, in which subpopulations are fixed for different alleles).

A simple visualization of this idea is that of two squirrel subpopulations that are physically separated by a canyon and therefore cannot interbreed. Each subpopulation is homozygous for one allele of a SNP (in other words, each individual of one subpopulation might have a C at that position, while individuals from the other subpopulation have a T). The heterozygosity of the total population (HT) would therefore be 0.5. The heterozygosity of each subpopulation (HS) would be 0.0 (because every member of the subpopulation is homozygous). The calculation of FST in this oversimplified case would be (0.5 – 0.0)/0.5 = 1.0. In other words, 100% of the genetic variation of this population is between subpopulations, with zero variation within subpopulations.

While a value of 1.0 for the fixation index is theoretically possible, such value in reality is usually much smaller. In general, high FST values reflect a low level of shared alleles between individuals in the sampled population and the total population. Conversely, low FST values indicate that members of the subpopulation share alleles with the total population. The proportion of individuals in a population that carry a certain allele varies over time and is influenced by the forces of migration, genetic drift, and natural selection.


"There are variations between human populations, so a SNP allele that is common in one geographical or ethnic group may be much rarer in another. "

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Re: Out-of-India - From Theory to Truth: Part 2

Postby shiv » 19 Apr 2018 08:20

sudarshan wrote:I second the humble request by somebody else earlier in this thread - can we please have a layman's perspective (just a line or two) of the summary of the genetic findings, and the case for/against AIT, based on the genetics?

Please pardon me while I repeat what I have said in the past.

There is a tacit assumption embedded within your question that genetics can prove or disprove the idea that a people called "Aryans" (or someone) came to India bringing a particular language . The language part is critical here. That is the part that was used to rewrite our history. The migration part is irrelevant. Many migrations have occurred into India both within the historic period and no doubt before. Detecting a migration does not prove movement of language.

Unless we can get this straight we are not going to get anywhere. Unfortunately it seems that 80+% of people are yet to digest this issue.

Genetics can show migrations but it cannot prove the movement of language. A lesson in genetics is fine but do not expect genetic knowledge to either prove or disprove the "AIT"

That said, very briefly, DNA is a long string of a molecule that looks like a ladder. Each step of the ladder consists of a pair of two molecules called "nucleotides". A string of nucleotides in a particular order can be a gene. Or it can be a nonsense code that does nothing. These strings are faithfully replicated from generation to generation. If you have hair growing out of your ears it is because your father also had that and those genes were replicated in your body. If the gene code is damaged - you can get some genetic defect - like no head - so a child will not survive. Milder defects (lactose intolerance" will not cause death.

There are 4 types of nucleotide molecules - let us call them A,T, C and G

DNA consists of strings that look like A-A-A-C-G-G-T-C-G-G- etc. the strings are millions of nucleotides long.

Sometimes a string that looks like A-A-C-T-G may get mutated to A-C-C-T-G - the second A has become a C. This is s mutation of a "single nucleotide" It is a single nucleotide polymorphism. (poly= many, 'morph=shape/structure')

If that causes an absent head that person will not survive, But if that happens on a nonsense string it is like a scratch on your new car.

The older your car the greater the number of scratches
The older the string of DNA the greater the number of mutations where A, C, T or G have been replaced in one's DNA.

Genes are long looong strings of nucleotides in a fixed sequence. Changing the sequence might damage a gene and cause a genetic defect. But then again it might not if it is an inactive sequence in the gene. A given gene from a 5000 year old grave will have a certain sequence of nucleotides. That sequence will show some changes in modern humans. If that gene has spread from steppe to India, Indians will show some changes or SNPs(scratches on paint). the same gene in Europe will show a different bunch of "scratches"/SNPs. If Europe and Indian gene are almost the same that would require some explanation - tourist/invader/refugee/Paki

I hope I have thrown some light.

Remember none of this will help with language movement theories

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Re: Out-of-India - From Theory to Truth: Part 2

Postby Murugan » 19 Apr 2018 09:53

Thus the Behistun inscription mentions four divisions of Scythians,

the Sakā paradraya "Saka beyond the sea" of Sarmatia,
the Sakā tigraxaudā "Saka with pointy hats/caps",
the Sakā haumavargā "haoma-drinking Saka"(Amyrgians, the Saka tribe in closest proximity to Bactria and Sogdiana),
the Sakā para Sugdam "Saka beyond Sugda (Sogdiana)" at the Jaxartes.

note para, haoma (soma), varga

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Re: Out-of-India - From Theory to Truth: Part 2

Postby A_Gupta » 19 Apr 2018 18:19

https://www.biorxiv.org/content/biorxiv ... 8.full.pdf
The genetics of an early Neolithic pastoralist from the Zagros,Iran.

Another "Indus periphery individual"?

Fig. 1. GD13a appears to be related to Caucasus Hunter Gatherers and to modern South Asian populations. A) PCA loaded on modern populations (represented by open symbols). Ancient individuals (solid symbols) are projected onto these axes.
Image

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Re: Out-of-India - From Theory to Truth: Part 2

Postby shiv » 19 Apr 2018 22:06

Arun you were on full afterburner on Twitter..

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Re: Out-of-India - From Theory to Truth: Part 2

Postby A_Gupta » 20 Apr 2018 00:42

shiv wrote:Arun you were on full afterburner on Twitter..

:)
As long as I made sense :)

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Re: Out-of-India - From Theory to Truth: Part 2

Postby A_Gupta » 20 Apr 2018 07:54

“Corded Ware culture horseman...is a theoretical construct”
http://briai.ku.lt/downloads/AB/11/11_0 ... skaite.pdf

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Re: Out-of-India - From Theory to Truth: Part 2

Postby shiv » 20 Apr 2018 09:33

You're on a roll Arun. Let me digress. That blog mentioning David Anthony about whom I have been ranting gave new meaning to the statement "Jo Lahore mein gandu woh Peshawar mein bhi gandu"

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Re: Out-of-India - From Theory to Truth: Part 2

Postby Primus » 20 Apr 2018 16:33

shiv wrote:
A_Gupta wrote:https://www.researchgate.net/profile/Vallath_Balakrishnan/publication/15963819_Lactose_intolerance_in_North_and_South_Indians/links/5458736e0cf26d5090ab6368/Lactose-intolerance-in-North-and-South-Indians.pdf
Lactose intolerance in North and South Indians

Rakesh K. Tandon,3 Y K. Joshi,4 D. S. Singh,5 M. Narendranathan,6 V. Balakrishnan,7 and
K Lal
ABSTRACT A multicenter study was carried out in India to determine the incidence of lactose
intolerance in healthy volunteers from different parts of the country. The incidence was found to
be 66.6% in the subjects from two South Indian centers at Trivandrum and Pondicherry. In
contrast, the incidence in the subjects from a North Indian center in New Dethi was much lower,
i.e., 27.4% (p < 0.001). The lower incidence in the North Indian subjects may perhaps be due to the
fact that they are descendants of the Aryans who have been dairying for long and are known to be
lactose tolerant. Am. J. Clin. Nutr. 34: 943-946, 1981.

:rotfl: This paper was apparently published shortly before I left JIPMER. I think Singh was there - I think this Singh was the same man we surgeons had to contend with for certain items of equipment. There was a life-saving item (in that era, no longer true) called a "Sengstaken tube" and when we wanted one we were informed that Singh had taken custody of it - so it was then called "Singh's Taken tube"

.............


:rotfl: :rotfl: :rotfl:

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Re: Out-of-India - From Theory to Truth: Part 2

Postby Primus » 20 Apr 2018 16:37

Mean-e-while, the Priya Moorjani paper has now landed on the 'news' page of the latest issue of 'Science' with the expected 'Higher Caste' and 'Hindi, Urdu' speakers vs 'Lower Caste' and 'Dravidian language speakers' conclusions.

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Re: Out-of-India - From Theory to Truth: Part 2

Postby shiv » 20 Apr 2018 16:48

Link Primus - or is it offline?

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Re: Out-of-India - From Theory to Truth: Part 2

Postby shiv » 20 Apr 2018 17:02

Arun, Vagheesh has asked for everyone on Twitter to join hands and send him a document explaining how languages are related from Delhi to Dublin. This is a tall order on many counts, especially considering that we were discussing a genetics paper until he made linguistics conclusions and some of us questioned that while others have been disputing his genetics methods.

I have not dug deeper into the genetics side but I think Rudradev pointed out some things. I was looking at his assumptions today and I note that he claims that there are 7 populations that he has used to reconstruct the origins of all the others.

Among these - the last one is "AASI" a hypothetical ancestral southAsian hunter gatherer. He has linked ref no 19 to that. Ref no 19 is an easily accessible paper called the Simons genome Project by one Mullick and a thousand other authors. This paper speaks only of Onge and no one else related to India.

The 2009 Reich paper reported that ASI was on a cline that included Onge, but ASI is not Onge. So I have not managed to figure out how Vagheesh makes what seems to be Onge as a crucial original inhabitant, leaving out the rest of ASI which actually falls on an out of Africa cline that includes ANI ancestry: see image:Image

That apart Reich clearly states that the admixture dates of ASI-ANI go back 200 generations (5600 years)
Image

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Re: Out-of-India - From Theory to Truth: Part 2

Postby vsunder » 20 Apr 2018 19:08

Some years ago I recall a news article about a yogi buried in padmasana pose from Balathal 2700 BC a Harappan site.

https://www.indiadivine.org/2700-year-o ... ical-site/

The custom of burying enlightened individuals in padmasana pose is very, very old. Article above ^^ also talks about the Ahar people and how they predate IVC and how they worshipped bulls and cows. The distinguished Berkeley anthropologist Frits Staal who filmed the Agnicyana yajna in Kerala (its on youtube)and arranged for one after a gap of 80 years asked a pertinent question: If the "steppe" people were indeed those who brought Vedas and fire altars into India, how did they as nomadic people, carry bricks (to make the fire altars) around and also make them while on the move? After all one needs Agni as the messenger to the Gods. Agnicyana is found in the deep South and the Nambudri's to perform it utter mantras in a form that is very ancient so much so that Staal found a close correlation with the way they repeat Vedic mantras and Indian bird calls. He has a paper/s on it. The construction of the Agnicyana fire altar is very elaborate and Staal has a paper on it. It needs geometry and a knowledge of the Pythagoras theorem to square a rectangle, as the dimensions are created by the height of the yajamaan and a certain standard dimension. The youtube video shows the yajamaan being measured, his height, distance from knee to the ground etc. The construction of the Vedic fire altar is the beginning of Geometry in India. It culminates in the beautiful works of Brahmagupta on Rationality problems which lead to the famous works of Axel Thue (1908)and Gerd Faltings (1984) on the Mordell conjecture which he resolved in the positive and for which he was awarded the Fields medal.

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Re: Out-of-India - From Theory to Truth: Part 2

Postby Rudradev » 20 Apr 2018 19:54

A_Gupta wrote:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5702378/
World-wide distributions of lactase persistence alleles and the complex effects of recombination and selection
Anke Liebert,1,3 Saioa López,1 Bryony Leigh Jones,1 Nicolas Montalva,1,2,4 Pascale Gerbault,1,5 Winston Lau,1 Mark G. Thomas,1 Neil Bradman,6 Nikolas Maniatis,1 and Dallas M. Swallow

Either Indians have major lactose intolerance or else there are more alleles to be discovered regarding lactose tolerance.
Image

PS: lactase is the enzyme; lactose is the sugar in milk that is not digestable if you lack lactase. Typos above corrected.


Arun, what these figures are showing are "heat maps" for particular SNPs that govern lactase persistence.

The LACK of hotspots in Indian subcontinent (it is almost uniformly dark blue while other areas flare yellow and red for specific SNPs) itself tells a compelling story.

Basically the PHENOTYPE of lactase persistence: the fact that the vast majority of Indians have lactase that lasts past childhood and consequently, can and do consume dairy products, is not in any dispute. Meaning, nearly all Indians have SOME SNP OR THE OTHER that enables them to keep producing lactase past childhood, and hence to consume dairy products.

However the heatmaps show that there is NO ONE GENOTYPE that is responsible for all, or even a majority of the lactase persistence phenotype in India. Different people in India are able to produce lactase into adulthood for different reasons, i.e. because they have different SNPs that help them do so, OR possibly because of different epigenetic mechanisms of regulation operating that have nothing to do with SNPs. NO ONE SNP is the predominant cause of the lactase persistence that is almost universally seen in India.

This argues vehemently against lactase persistence in India being the result of one particular SNP (shared with the Steppe or Europe or anywhere else) that was introduced to India at one particular time and then inherited by all or most Indians.

This is also in stark contrast to various regions of Africa, Europe and the ME where the heatmap shows that lactase persistence IS often highly attributable to the predominance of a specific SNP.

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Re: Out-of-India - From Theory to Truth: Part 2

Postby sudarshan » 20 Apr 2018 20:23

shiv wrote:
sudarshan wrote:I second the humble request by somebody else earlier in this thread - can we please have a layman's perspective (just a line or two) of the summary of the genetic findings, and the case for/against AIT, based on the genetics?

Please pardon me while I repeat what I have said in the past.

There is a tacit assumption embedded within your question that genetics can prove or disprove the idea that a people called "Aryans" (or someone) came to India bringing a particular language . The language part is critical here. That is the part that was used to rewrite our history. The migration part is irrelevant. Many migrations have occurred into India both within the historic period and no doubt before. Detecting a migration does not prove movement of language.

Unless we can get this straight we are not going to get anywhere. Unfortunately it seems that 80+% of people are yet to digest this issue.

....

I hope I have thrown some light.

Remember none of this will help with language movement theories


Thank you saar. I do know the nucleotide part (A, C, T, G). You are right, genetics does not correlate with language movement, but if gene studies were to show that there was no sudden influx of "alien" genes into the Indian population, that's an argument against AIT, right? I know that Vagheesh's paper supposedly shows the opposite.

IOW, I agree that genetics-derived evidence of migration does not correlate with language movement, but absence of genetics-derived evidence of migration or invasion (if it can be shown) should serve to disprove the "violent invasion" component of AIT (though, again, there is no correlation with language movement).

That genetics does not correlate with language movement is a surprisingly difficult concept for lay-people to grasp. If somebody like Vagheesh shows some kind of "migration" or "invasion" from genetics, and then does some hand-waving to correlate that with language (which is actually what he's doing), then aam junta do get mesmerized by that and start believing it. The adoring goras that I mentioned would also be vulnerable to that kind of tomfoolery, and countering that is no mean task. Logic is a poor contender against these kinds of mesmerizing notions, unfortunately.

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Re: Out-of-India - From Theory to Truth: Part 2

Postby Rudradev » 20 Apr 2018 20:49

shiv wrote:Interesting Tweet from Vagheesh:

https://twitter.com/vagheesh/status/986303801173991424
In the next phase of the paper, I am specifically looking at lactose persistence alleles. This will show directly, that prior to steppe ancestry arrival, people within the subcontinent could not lacked the enzyme to process milk.


He already knows what the next phase will show?

Rudradev?


If you do Vagheesh-style "science" you always already know what your findings will show. Your bosses give you the required results and p-values and you deliver the appropriately pruned data distributions to fit. "Bayesian" genetics :rotfl:

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Re: Out-of-India - From Theory to Truth: Part 2

Postby Prem Kumar » 20 Apr 2018 23:39

In the loooong running tweet chain with Vagheesh, Shiv and others, I saw a comment of interest.

It asked "How are all Indian groups a combo of Steppe, Iran etc DNA?". Basically, if India was already heavily populated, how do you explain a handful of Nomadic pastoralists to pass their genes onto enough people that practically all modern Indians carry it?

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Re: Out-of-India - From Theory to Truth: Part 2

Postby Primus » 21 Apr 2018 02:19

shiv wrote:Link Primus - or is it offline?


I am a subscriber, so I get it every week, but hope this works:

Ancient DNA Untangles South Asian Roots

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Re: Out-of-India - From Theory to Truth: Part 2

Postby Gus » 21 Apr 2018 02:54

So, the key takeaway for me is - all these genetics papers are doing a trick with taking PIE as established truth whereas it is nothing but a circular argument as shiv said in that loooooong tweet chain.

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Re: Out-of-India - From Theory to Truth: Part 2

Postby A_Gupta » 21 Apr 2018 06:55

shiv wrote:Arun, Vagheesh has asked for everyone on Twitter to join hands and send him a document explaining how languages are related from Delhi to Dublin. This is a tall order on many counts, especially considering that we were discussing a genetics paper until he made linguistics conclusions and some of us questioned that while others have been disputing his genetics methods.


I'd propose:

1. Explain the antiquity of Sanskrit - the evidence for its antiquity via the Vedas, evidence for it being an Indian language (i.e., they didn't compose the Shatapatha Brahmana on the steppe).

2. The paucity of actual linguistic evidence. The fact that they're trying to deduce something rather complicated from limited data.

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Re: Out-of-India - From Theory to Truth: Part 2

Postby A_Gupta » 21 Apr 2018 07:02

Prem Kumar wrote:In the loooong running tweet chain with Vagheesh, Shiv and others, I saw a comment of interest.

It asked "How are all Indian groups a combo of Steppe, Iran etc DNA?". Basically, if India was already heavily populated, how do you explain a handful of Nomadic pastoralists to pass their genes onto enough people that practically all modern Indians carry it?


Only way I can think is if, e.g., steppe people brought some gene for malaria resistance (or some other such advantageous gene).

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Re: Out-of-India - From Theory to Truth: Part 2

Postby shiv » 21 Apr 2018 07:15

Vagheesh has asked for comments at length on biorxv. I will draft a comment here and then post it on there. Arun - would you like to take a shot? If I get inspiration in the next few minutes my draft comment will appear here first.

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Re: Out-of-India - From Theory to Truth: Part 2

Postby shiv » 21 Apr 2018 07:17

Prem Kumar wrote:
It asked "How are all Indian groups a combo of Steppe, Iran etc DNA?". Basically, if India was already heavily populated, how do you explain a handful of Nomadic pastoralists to pass their genes onto enough people that practically all modern Indians carry it?

As far as I am concerned - if that is their finding, that is their finding. As in all science this will either be reinforced or questioned by future papers.

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Re: Out-of-India - From Theory to Truth: Part 2

Postby shiv » 21 Apr 2018 07:45

sudarshan wrote: You are right, genetics does not correlate with language movement, but if gene studies were to show that there was no sudden influx of "alien" genes into the Indian population, that's an argument against AIT, right?


There have always been migrations into India. India is too attractive a land - warm with two crops a year. There is an ancient eastern European meme of an "Indija Koromandija" a sunny land in the south where crops grow twice a year. In the past I have actually found some Russian authored papers that reject the steppe-language hypothesis but they are ignored. The only question is did one or more of these migrations bring language to India. I doubt if Vahheeshs specific findings will work and my responsebelow will list what I think

Let me post some personal views. It appears to me that movement of IE language into Europe has occurred. If it occurred around Vagheesh's timeline - that is fine - but similar movement of language into India is unlikely because IE was present in India before the steppe people of Vagheesh paper came.

One of the possibilities that comes to my mind is a vast swathe of "pre-Sanskrit" speaking people from IVC to Steppe and all the areas in between. IE may have gone from more than one area to Europe. But this is just a hypothesis and I am not going to try and prove it or make it come true the way linguists have tried to make their hypothesis come true.

It occurs to me that linguists have (rightly) recognized relationships between all IE languages - to use Vagheesh's rhetoric "Delhi to Dublin". But after that the linguistic community have decided that there was one common ancestor and have proceeded to reconstruct that ancestor from multiple daughter languages. Let me use a tree analogy here. Leaves (modern languages) do not grow off tree trunks (single source). Leaves grow off branches and branches grow off trunks. A reconstruction of trunk from leaves should attempt branch reconstruction first and then trunk reconstruction. That means construct the branches like proto-Romance, proto-Germanic, Proto-Indo-Iranian before the mother PIE. It appears that this is happening only now - I found a 21st century proto-Germanic work and I will link, below a "proto-Romance" short paper that makes an important point.

I have also stated that in order for linguistics to become anything like science, research of the following type can be done. Get 5 students of linguistics who have some grounding in phonetics and sound change to "reconstruct" a proto language from Hindi, Bengali and Gujarati and see how close they get to Sanskrit. This would be a test of the level of accuracy that can be reached by linguistic methods. That aside all the collected up muck of 200 years of racist or religion tainted linguistic texts need to be weeded out. Not an easy task because there are thousands of texts in French, German, Russian, Romanian etc - each incestuously having fed off the other more than a century ago

Unfortunately Indians with our colonized sepoy minds are not going to do this. We will swallow anything thrown at us from the west.

Rant over - let me post that link about "proto-Romance" and a quote
https://apps.atilf.fr/homepages/buchi/w ... stract.pdf
As a written language per definitionem cannot attest directly a spoken language, this method goes against the principles of the reconstruction of proto-languages in historical linguistics.

If this statement is true all sound reconstructions of archaic Greek, Hittite, Tocharian and Middle Persian (Behistun) cannot by definition be "sound" (pun unintended)

More on PIE later. Need to write that draft..

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Re: Out-of-India - From Theory to Truth: Part 2

Postby A_Gupta » 21 Apr 2018 08:23

1. Language tree is more like a banyan tree than a pipal tree?

2. Roundtripping has happened. That is, a geography that had an I.E. language has had incursions of other I.E. languages. This has happened time and again.

Twitter is bad for the writing habit.

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Re: Out-of-India - From Theory to Truth: Part 2

Postby shiv » 21 Apr 2018 08:49

A_Gupta wrote:1. Language tree is more like a banyan tree than a pipal tree?

Then PIE is like Orchid. No roots.

Orchid also means balls. It's all balls.

See the number of US Americans who are now learning Spanish? Not because Spaniards colonized the US.

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Re: Out-of-India - From Theory to Truth: Part 2

Postby shiv » 21 Apr 2018 11:10

I do not intend to question the genetics findings of the Vagheesh et al paper because I am not a genetics researcher and I have myself not gone through all the details of the paper to critique its methodology. Obviously as in all science, the paper will get validated or rebutted via future papers from other researchers.

So I start with tacit acceptance of the finding of steppe genes as a marker for Indians.

My only point of contention is whether the steppe migrants implied in the paper carried Indo-European languages with them to India. I am in no way questioning the migration-language connection between steppe and Europe as made in the paper. But similarity between steppe migration to Europe and to India does not mean that IE languages first arrived in India with this wave of migrants. I believe that it is not sufficient to claim this particular migration to India as a source of IE in India

There are two important preconditions to make a claim that people from place A took their language to place B and introduced that language for the first time in place B. First there must be incontrovertible evidence that the migrants from place A actually used to speak the language that they took to place B in the pre-historic era that they migrated. Second, there must be evidence that the language they carried with them did not already exist in the "place B" to which they migrated. Anything less is conjecture. Not science. I will take these two points in reverse order.

Any migration carrying IE language to India for the first time has to be shown to have occurred before 2500 BCE because there is powerful evidence of IE language having been in India by 2500 BCE and most likely for millennia prior to that. I will try and be as brief as possible about the evidence which in detail is enough to fill a book chapter.

The evidence for IE in India prior to 2500 BCE falls under 2 main heads
1. Archaeoastronomy
2. Records of hydronyms, toponyms and climate related events

I am only going to deal with the latter

The presence of Vedic Sanskrit in India was attested in text form as recently as 150 AD or so and if attestation is the metric then all talk of Sanskrit as an ancient language is moot. However it was dubbed as ancient by Max Muller who surmised that the post Vedic texts were contemporaneous with the Buddha who was thought to have lived around 600 BC. Muller then worked backwards, assuming about 200 years for the composition of each class of post Vedic and Vedic texts and arrived at a date of 1200 to 1000 BC for the Rig Veda. However many factors have called these "guesstimated" dates into question.

1. Rig Veda 7.95.2 speaks of a mighty river called the Saraswati flowing from mountains to the sea (RL Kashyap, Rig Veda Samhita, Mandala 10, Sakshi trust 2012)
2. More information about the location of the "Saraswati" comes from Macdonell & Keith "Vedic Index of names and Subjects" 1912: In the enumeration of rivers (evidently from east to west) in Rv. x. 75, 5, Ganga, Yamuna, Sarasvati, Sutudri, the Sarasvati comes between the Jumna and the Sutlej, the position of the modern Sarsuti (SaraswatI). which, flowing to the west of Thanesar, is joined in Patiala territory "

These passages give a rough idea of some ancient river, real or imagined, called the Saraswati that was situated between the Yamuna river (that passes through Delhi) in the east and the Sutlej river in the west

3.Still more geographical information comes from Macdonell and Keith:
a. Madhya­desa, the ‘Middle Country,' is, according to the Manava Dharma Sastra, the land between the Himalaya in the north, the Vindhya in the south, Vinasana in the west, and Prayaga (now Allahabad) in the east that is, between the place where the Sarasvati disappears in the desert, and the point of the confluence of the Yamuna (Jumna) and the Ganga (Ganges)

b. The Baudhayana Dharma Sutra defines Aryavarta as the land east of Vinasana ; west of the Kalaka­vana, ‘ Black Forest,' or rather Kanakhala, near Hardvar; south of the Himalaya; and north of the Pariyatra or the Paripatra Mountains.

c. Vinasana, 'disappearance,' is the name of the place where the Sarasvati is lost in the sands of the desert.

Here we have references to "Vinasana" a place where a "Saraswati river" disappears in the desert. This information comes from post-Vedic texts - most likely composed centuries after the Vedas. The Himalayas in the north are mentioned. In the south are the Vindhya mountains, the traditional barrier between north and south India. The Paripatra mountains are the westernmost reaches of the Vindhyas. To the east is the Yamuna river which corresponds to what the Vedas record as being to the east of the Saraswati. West of that is the place where the Saraswati "disappears in the desert"

So here we have mention of a river that does not exist today but located in a recognizable geographic location. The Vedas call it a mighty river that reaches the sea and later texts claim that the river dries up in the desert

4.Now we come to more recent events and discoveries. To a man called RD Oldham must go the credit for identifying the site in the Rajasthan desert that was apparently the ancient Saraswati river. However it was his compatriot - a similarly named CF Oldham who wrote:

“..local legends assert ( that Sarasvati ) once flowed through the desert to the sea . In confirmation of these traditions , the channel referred to , which is called Hakra or Sotra , can be traced through the Bikanir and Bhawulpur states into Sind , and thence onwards to the Rann of Kach . . . attested by the ruins everywhere overspread what is now an arid sandy waste . Throughout this tract are scattered mounds , marking the sites of cities and towns . And there are strongholds still remaining... Amongst these ruins are found, not only the huge bricks used by the Hindus in the remote past , but others of a much later make..”

5. Next it was a British geologist called Aurel Stein who wrote, in 1942, a monograph entitled “​A survey of ancient sites along the`lost' Sarasvati River” in which he identified the Ghaggar river in north India as the remnant of the Saraswati, and said that for over a distance of 100 miles (160 km) the river bed of the Ghaggar is more than 2 miles (3.2 km) wide and in many places over 4 miles (6.4 km) wide. He noted the scanty flow in the modern Ghaggar and wide ancient river bed meant that there had been a much mightier river in the remote past. Aurel Stein also noted findings of ancient settlements by the sides of this old Saraswati river bed that he connected up with the Indus Valley civilization.

6. There is no doubt that a river existed in the site of the Saraswati as noted in old texts. But was it a mighty river that reached the sea? For that I refer you to a 2017 paper that has done isotopic analyses of cores from the Rann of Kutch.
Tracing the Vedic Saraswati River in the Great Rann of Kachchh, Nitesh Khonde, Sunil Kumar Singh , D. M. Maurya , Vinai K. Rai , L. S. Chamyal &
Liviu Giosan
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5511136/
This study shows that until 10,000 ybp (8000 BCE) there was a great river in that area that drained into the sea. Progressive drying started after that but the paper states that their method would not be able to detect how long the river flowed all the way to the sea after that

7. Another paper: Adaptation and human migration, and evidence of agriculture coincident with changes in the Indian summer monsoon during the Holocene Anil K. Gupta , David M. Anderson , Deep N. Pandey and Ashok K. Singhvi.
http://repository.ias.ac.in/21932/
This paper documents a massive in crease in rainfall over the entire Indian subcontinent from 10000 ypb to 7000 ybp (8000 - 5000 BCE) and mentions the effect this had on crops in Mehrgarh. Aridity started increasing after 5000 ybp.

So what are the facts we have? The Vedas mention a mighty Saraswati river that reached the sea. Later texts clarify its location but observe that it dries up in the desert. That location correlates perfectly with the finding of a massive river bed with IVC settlements alongside. Modern isotopic studies, palaeoclimatology and palynological studies indicate a mighty river in that location, which flowed into the sea up to 8000 BCE and possibly for a little longer. Heavy monsoons swelled subcontinental rivers from 8000 BCE to 5000 BCE. Aridification started after that. These facts correspond well with the ancient records that survived in the Vedas and post-Veda texts.

All the ancient records of events and geography, ostensibly from 8000 BCE are preserved in an "Indo-European language". That language, by the estimate of Indologist-Philologists has 96% IE words with minimal substrate of any other language. No other IE language to my knowledge has such a large proportion of IE derived words.

The pointers towards a very ancient presence of IE language in India, long before influx of the steppe people described in this paper is strong. In a separate post I will deal with the alleged area of origin of IE language coming to India, the steppe region.
Last edited by shiv on 21 Apr 2018 18:45, edited 1 time in total.

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Re: Out-of-India - From Theory to Truth: Part 2

Postby shiv » 21 Apr 2018 14:44

I pointed out in my earlier post that there are two important preconditions to make a claim that people from place A took their language to place B and introduced that language for the first time in place B. First there must be incontrovertible evidence that the migrants from place A actually used to speak the language that they took to place B in the pre-historic era that they migrated. Second, there must be evidence that the language they carried with them did not already exist in the "place B" to which they migrated.

I have already written about the destination area in India and will now comment on the steppe area from which people are stated to have carried their Indo-European language to India.

There is no record of what language the steppe people spoke. If the identity of the language those ancient people spoke was known that language should have been mentioned as the language they carried to India and elsewhere. However it is stated that the people of the steppe spoke "Proto-Indo-European" or PIE.

PIE is not a real language. It is a hypothetical construct created by linguists. PIE has been constructed out of known daughter languages and naturally owes its entire lexicon and grammar to the daughter languages that it was constructed from. Placing that hypothetical language in the steppe at some ancient time is only feasible because the original spoken language of the area is unknown. Claiming that PIE was a real spoken language in the steppe in an ancient era is obviously not true. It is a hypothesis based on a modelled hypothetical language. Nobody knows the real language that was spoken by the steppe people who migrated out. Unfortunately this point is missed in a series of genetics papers that all assume that PIE was a real language that was carried somewhere and that explains the IE origin of the language in the destination that the steppe people reached. If the source language is unknown it cannot serve as evidence of how the language at the destination appeared.

In the case of the paper under discussion, the link between steppe and IE language in India is not helped in any way by the creative addition of non-existent words to translations of the Rig Veda 10:62 by David Anthony (Ref No 46 in the paper). A reference to a grave in the Rig Veda is compared to steppe graves by the addition of words like "chamber", and "walls" that do not appear in any original translations of the corresponding sukta of the Rig Veda.

The point I wish to make is that the origin language in the steppe is unknown. The link made with the language in the destination is inaccurate and unacceptable. These deficiencies make the case for a steppe origin of IE in India conjectural. Not factual.


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