Tuesday, January 16, 2018

QOTD

Quote of the day, actually from January 13th.  This is the National Public Radio game show "Wait, Wait, Don't Tell Me".   In the Bluff the Listener segment, three bizarre stories are read out, only one of which is true, and the listener is supposed to guess which one that is.

Transcript here, or audio here.

The quote? Ah, yes!
See, this is the Silicon Valley, where everybody's got Asperger's syndrome or has to act like they do.

Monday, January 15, 2018

IBM's predictions from December 2013

http://venturebeat.com/2013/12/16/ibm-reveals-its-top-five-predictions-for-the-next-five-years/

In a nutshell, IBM says:
  • The classroom will learn you.
  • Buying local will beat online.
  • Doctors will use your DNA to keep you well.
  • A digital guardian will protect you online.
  • The city will help you live in it.

Monday, January 08, 2018

Lemuria and the Aryan-Dravidian "debate" in India

Please read this.

To understand the Dravidianists of today, it is absolutely essential to understand the history and mythology of the ancient Tamil country.

According to this history and mythology, in really really really ancient times (nobody has told us how ancient), the eastern, western and southern parts of today’s Kanyakumari were attached to a really really really vast tract of land known as Lemuria or Kumari Nadu or Kumari Kandam. This really really really vast tract of land was subsequently submerged in the sea. The Tamils who survived this catastrophe migrated northwards.

And then in a short period, these Tamils migrated further northwards and occupied all of Bharata, and also made as their home today’s Pakistan and Afghanistan. The language they spoke in those days has today transformed into what is known as Brahui.

Today’s Dravidianists claim that because the Aryans invaded from outside, the ancient Tamils were exterminated from the northern parts of India, and also that because the invasion was unsuccessful south of the Vindhyas, the Tamils lived in peace and prosperity in these areas.
 And this:
It was 10 at night when this happened. The Tamil Professor directly went to the Vice Chancellor’s house and gave him an adverse report of what had occurred at the dinner. “You have filled the [History Endowment] Committee with only Aryans! The Aryan members have naturally selected another Aryan as the speaker. And you endorsed their selection. Now look what has happened—a direct humiliation of Tamil itself! A massive, utter humiliation!”

I later learned that the Vice Chancellor had erupted in fury, twirled his moustache and patted his biceps.

Saturday, January 06, 2018

David Frum: who and what Trump is

David Frum in The Atlantic:

Who and what Donald Trump is has been known to everyone and anyone who cared to know for years and decades. Before he was president, he was the country’s leading racist conspiracy theorist. Before he was the country’s leading racist conspiracy theorist, he was a celebrity gameshow host. Before he was a celebrity gameshow host, he was the multi-bankrupt least trusted name in real estate. Before he was the multi-bankrupt least trusted name in real estate, he was the protege of Roy Cohn’s repeatedly accused of ties to organized crime. From the start, Donald Trump was a man of many secrets, but no mysteries. Inscribed indelibly on the public record were the reasons for responsible people to do everything in their power to bar him from the presidency.

Instead, since he announced his candidacy in mid-2015, Donald Trump has been enabled and protected.

The enabling and protecting not only continues. It accelerates.
 and

In 2016, there were voters who genuinely, in good faith, believed that Donald Trump was a capable business leader, moderate on social issues, who cared about the troubles of working class white America—and would do something to help. There may well still be some people who believe this—but nowhere near enough to sustain a presidency.

What sustains Trump now is the support of people who know what he is, but back him anyway. Republican political elites who know him for what he is, but who back him because they believe they can control and use him; conservative media elites who sense what he is, but who delight in the cultural wars he provokes; rank-and-file conservatives who care more about their grievances and hatreds than the governance of the country.

Friday, January 05, 2018

Some.Rakhigarhi news from April 2016

An Amar Ujala photo-story from April 14, 2016 says that a total of 18 skeletons have been recovered from Rakhigarhi.

The Tribune of Chandigarh reported that 15 skeletons were recovered in the recent round of excavation.
The sources said excavators had opened 20 graves and skeletons had been found in 15 of them. They said DNA samples were being sent to the laboratories for bio-molecular scientific analysis.
The archeologists said the DNA samples would be analysed at the Centre for Cellular and Molecular Biology (CCMB), Hyderabad; Howard University, USA; and the Seoul National University, South Korea.
This I had missed.  I had thought that they were still trying to get aDNA from the skeletons excavated in 2014, and apparently, so did Tony Joseph, in his article in the Hindu.



Metspalu v Laziridis: trying to understand

Am trying to square Metspalu, et. al.'s 2011 paper and Laziridis et. al.'s 2016 paper.

Here's what's bugging me.  The diagram below is a crop from a diagram in the Metspalu paper, a graphical representation of the genetic make-up of various populations.


You can see South Asia is mainly k5 and k6.  k6 is mostly confined to South Asia, while k5 extends into Central Asia, the Caucasus, the Middle East and into Western Europe.

They write:
We found no regional diversity differences associated with k5 at K = 8. Thus, regardless of where this component was from (the Caucasus, Near East, Indus Valley, or Central Asia), its spread to other regions must have occurred well before our detection limits at 12,500 years. Accordingly, the introduction of k5 to South Asia cannot be explained by recent gene flow, such as the hypothetical Indo-Aryan migration. The admixture of the k5 and k6 components within India, however, could have happened more recently—our haplotype diversity estimates are not informative about the timing of local admixture.
___________
PS: thanks to guest's comment below, I know clarification is needed: Metspalu et. al. run  ADMIXTURE, which estimates how much a modern sample of unrelated individuals derives their ancestry from a set of postulated ancestral populations.
 The typical dataset consists of genotypes at a large number J of single nucleotide poly- morphisms (SNPs) from a large number I of unrelated individuals. These individuals are drawn from an admixed population with contributions from K postulated ancestral populations. Population k contributes a fraction qik of individual i’s genome.
You try various Ks and ADMIXTURE also estimates the standard errors on the results.  Reich 2009 used a Principal Components Analysis (PCA) to come up with ANI/ASI.  ADMIXTURE was created in 2009 apparently. 

We are told:

Choice of an appropriate value for K is a notoriously difficult statistical problem. It seems to us that this choice should be guided by knowledge of a population’s history. Be- cause experimentation with different values of K is advisable, admixture prints values of the familiar AIC (Akaike Information Criterion) and BIC (Bayesian Information Criterion) statistics, widely applied in model selection. 
_______________ 

 Strictly speaking, their detection limit is 500 generations, and they use 25 years per generation. The point is that k5 in South Asia dates to more than 500 generations or 12,500 years ago.

The next is a little leap of mine - is it justified? In the Ancestral North Indian/Ancestral South Indian (ANI/ASI) model,  ANI corresponds to k5 and ASI corresponds to k6.  That this is so is not entirely clear to me.

We now come to Laziridis et. al.  They do an ancient DNA (aDNA) analysis of Near Eastern samples (Near Eastern with respect to Europe)  dating from 12000 to 1400 years ago, and they refer to aDNA analyses of Steppe inhabitants; as far as I know, the Steppe aDNA does not go back before 12000 years.  Now, the Laziridis paper says:
We show that it is impossible to model the ANI as being derived from any single ancient population in our dataset. However, it can be modelled as a mix of ancestry related to both early farmers of western Iran and to people of the Bronze Age Eurasian steppe...
 But if ANI == k5, and k5 spread before 12500 years ago (strictly speaking, 500 generations, while the aDNA dates are presumably radiocarbon dates) why would one expect to explain ANI in terms of contemporary peoples or peoples younger than ANI?

Perhaps one can say that Near Eastern aDNA,  Steppe aDNA and ANI (k5) all arose from the mixture of two ancestral populations X and Y (ancestors of the 12000-year-ago-people) and the Near Eastern aDNA and the Steppe aDNA represent relatively unmixed descendants of X and Y respectively, while ANI is a descendant mixture of X and Y.   I don't think this is what the Laziridis paper does.

My guess is Laziridis et. al. instead of sticking to just to genetics, also buy into the predominant theory of the spread of Indo-European languages, and hence attempt to explain ANI in this illogical way, or else Laziridis thinks the Metspalu paper is wrong and ANI(k5) is younger than 12500 years; or else I have misunderstood Laziridis or else ANI != k5.

PS: the most probable of the above alternatives is that I misunderstand Lazirides, the second most probable is that Laziridis et. al. don't think Metspalu is correct, and ANI is (much) younger than 12500 years.

_____
PS: Jan 6: This larger excerpt of a diagram in Metspalu shows ADMIXTURE with K=8 and K=12 (K is the number of hypothetical ancestral populations) and you can see that it does not really change the story that most of Indian ancestry traces to two components.  One would hope that one can come up with an objective definition of k5, k6 that is the same when computed with different but adequate samples.




Thursday, January 04, 2018

New Rakhigarhi gossip

The Hindi newspaper Dainik Jagaran has a story out today that purports to leak out the Rakhigarhi aDNA results.   The article goes into the current theory of how Indo-European languages entered India, and then the article says it is quoting Dr Neeraj Rai of the Birbal Sahni Institute (mentioned in a previous blog post) about the findings.

The key sentences:

लेकिन डॉ. नीरज राय के नेतृत्व में हरियाणा के हिसार, राखीगढ़ी आदि इलाकों में लगी अंतरराष्ट्रीय वैज्ञानिकों की टीम ने आनुवंशिक शोधों के आधार पर इस तथ्य को झुठला दिया है। अंतरराष्ट्रीय जर्नलों में प्रकाशित होने वाला शोध सामने आते ही पूरे विश्व में चर्चा, बहस और मंथन का नया दौर तो शुरू होगा ही मानव सभ्यता के वैश्विक इतिहास में बहुत बड़ा परिवर्तन हो जाएगा।

डॉ. राय बताते हैं कि डेक्कन कॉलेज, पुणे के कुलपति प्रोफेसर वसंत शिंदे ने हड़प्पा और अन्य स्थलों पर खुदाई का नेतृत्व किया है। इस दिशा में चल रहे शोधों के क्रम में उनकी अगुआई में पुरातत्वविदों की एक टीम ने सिंधु घाटी की सभ्यता में मिले सबसे महत्वपूर्ण शहर हरियाणा के हिसार में पड़ने वाले राखीगढ़ी साइट की खुदाई की। वर्ष 2014 की शुरुआत में उन्हें चार कंकाल मिले। इन कंकालों के डीएनए परीक्षण के लिए उन्होंने तब सीसीएमबी हैदराबाद और अब बीरबल साहनी इंस्टीट्यूट लखनऊ के युवा वैज्ञानिक डॉ. नीरज राय की टीम को लगाया।

डॉ. राय की टीम में देश-विदेश के अन्य वैज्ञानिकों ने मिलकर जो शोध हासिल किया, उससे पता चला कि राखीगढ़ी में मिले ये कंकाल उन प्रजातियों के पूर्वजों के हैं जो इंडो-यूरोपियन भाषा परिवार की भाषाओं के वक्ता हैं और दुनिया में स्वयं को सर्वश्रेष्ठ प्रजाति के रूप में घोषित करने का दावा करते रहे हैं। इन कंकालों के डीएनए उत्तर भारतीय ब्राह्मणों के डीएनए से काफी मैच करते हैं। 61 वर्षीय शिंदे के लिए, यह परियोजना पुरातत्व के एक लंबे और प्रतिष्ठित कैरियर की परिणति है। इस शोध के लगभग सारे परिणाम सामने आ चुके हैं। शीघ्र ही उनके प्रकाशन के बाद आर्य जातियों के आगमन, आक्रमण और प्रसार संबंधी विवादों पर भी विराम मिलने की संभावना है। 

The key point is that we are told that the Rakhigarhi aDNA matches significantly that of North Indian Brahmins.   This is interpreted in the article that the Rakhigarhi skeletons were of Indo-European language speakers. 

Of course, I'd advise waiting for the scientific publication.



Wednesday, January 03, 2018

New Yorker: Making China Great Again

A long article but should be read.

Yan Xuetong is the dean of Tsinghua University’s Institute of Modern International Relations. At sixty-five, Yan is bouncy and trim, with short silver hair and a roaring laugh. When I arrived at his office one evening, he donned a black wool cap and coat, and we set off into the cold. Before I could ask a question, he said, “I think Trump is America’s Gorbachev.” In China, Mikhail Gorbachev is known as the leader who led an empire to collapse. “The United States will suffer,” he warned.

Over a dinner of dumplings, tofu, and stir-fried pork, Yan said that America’s strength must be measured partly by its ability to persuade: “American leadership has already dramatically declined in the past ten months. In 1991, when Bush, Sr., launched the war against Iraq, it got thirty-four countries to join the war effort. This time, if Trump launched a war against anyone, I doubt he would get support from even five countries. Even the U.S. Congress is trying to block his ability to start a nuclear war against North Korea.” For Chinese leaders, Yan said, “Trump is the biggest strategic opportunity.” I asked Yan how long he thought the opportunity would last. “As long as Trump stays in power,” he replied.