Thursday, September 29, 2016

PCA, Neighbor-joining

This is from the 2016 Reich paper:

 The pink dots at the top of the PCA diagram are "West Eurasia".  The green dots down the side are "South Asia".  The blue dots further below are East Asia/C.A.S., clustered along with the dots for Amerindians.

The PCA diagram would lead you to believe that the green and pink are more closely related than the green and blue.   But the first two principal eigenvectors account for only 7.8% and 4.0% of the variance.   The remaining 88% of the variance is in dimensions not shown in the diagram.  It is a very high dimensional space, and perhaps the normal intuitions of distance do not apply, and that is why we see the counter-intuitive result that the group of green dots is closer connected to each other by neighbor-joining rather than some green dots being put close to some pink dots, and other green dots being put close to some blue dots.  The spread of green dots along PC2 does not preclude them from being closer to each other than to any other pink dot (the Tajik being the exception). Likewise the wide spread of the blue dots along PC2 does not preclude them from joining in one group; and finally, the green and blue join together before the green joins with the pink. 

The PCA in the 2009 Reich paper does not present how much of the variance is captured in their first two principal eigenvectors, as far as I can tell.

Tuesday, September 27, 2016

ANI, ASI, etc.

CIP wrote in the comments to the previous post about the 2016 Reich paper:
This is in accord with the conventional view that Europeans and Asians probably separated after leaving Africa in the Middle East. East Asians then separated from South Asians in India and Amerindians and related groups separated from East Asians much later.
Guest wrote in the comments about the 2009 Reich paper:
One, the ‘Ancestral North Indians’ (ANI), is genetically close to Middle Easterners, Central Asians, and Europeans, whereas the other, the ‘Ancestral South Indians’ (ASI), is as distinct from ANI and East Asians as they are from each other. By introducing methods that can estimate ancestry without accurate ancestral populations, we show that ANI ancestry ranges from 39–71% in most Indian groups, and is higher in traditionally upper caste and Indo-European speakers. Groups with only ASI ancestry may no longer exist in mainland India. However, the indigenous Andaman Islanders are unique in being ASI-related groups without ANI ancestry.
Guest wrote this in another comment:
You are confusing the ANI and Indians who currently live in the North. All Indians studied in the Reich paper (except Andamese) are mixtures of ANI and ASI, and consequently more related to each other than to outside groups like West Eurasians. The two papers are quite consistent, and David Reich is an author on both papers.

My response:

Sunday, September 25, 2016

New indications on the peopling of India

The NYT reports:
In the journal Nature, three separate teams of geneticists survey DNA collected from cultures around the globe, many for the first time, and conclude that all non-Africans today trace their ancestry to a single population emerging from Africa between 50,000 and 80,000 years ago.
The three teams are led by Eske Willersley of the University of Copenhagen (A genomic history of aboriginal Australia), David Reich of Harvard University (The Simons Genetic Diversity Project: 300 genomes from 142 diverse populations), and Mait Metspalu of the Estonian Biocentre (Genomic analyses inform on migration events during the peopling of Eurasia).

Unfortunately all the articles are behind a paywall, and a visit to the nearby university library is not in the plan for now.  The article with the most to do about anything Indian is the Reich article.

Some observations follow.

Thursday, September 22, 2016

Towards a sustainable economy

It should be fairly obvious that fisheries and timber industries cannot grow indefinitely.  They have a natural limit which is the renewal rate of the underling resources.  

It may be somewhat less obvious, but manufacturing on the planet as a whole also similarly has a natural limit.  About the only thing you can do here is replace lower value manufactures with higher value ones.  But the planet's ecosystem can sustain only so much manufacturing.   One could have manufacturing in space, and thus keep growing.   But that won't generate a lot of employment for humans on earth.

The obsession with manufacturing jobs is misplaced. Services - what humans do for each other - however are sustainable, can employ any number of people.  If the human touch is of value, then these can only be assisted but not replaced by artificial intelligence and robots.   The question then is - how to make human services more valuable?

Tuesday, September 20, 2016

Purna Swadeshi?

Our chromosomes are mostly shuffled versions of both of our parents' chromosomes. The two exceptions of unshuffled genes are those from the mitochondria, which are inherited from the mother only, and for men, the Y chromosome, that is from the father only.   Therefore, these two enable some tracing of deep ancestry, of my mother's mother's mother's ... and father's father's father's father's.... sometimes back to when homo sapiens first left Africa.

Note that my mother's father could have been from Mars, and my father's mother could have been from Venus, it won't show up in this particular set of DNA markers.

Per, a genetic testing company:
Paternal haplogroups are families of Y chromosomes that all trace back to a single mutation at a specific place and time. By looking at the geographic distribution of these related lineages, we learn how our ancient male ancestors migrated throughout the world.
My paternal haplogroup is H1a*.  Its estimated modern distribution is shown in the map below.
Origin: Haplogroup H arose in India between 30,000 and 40,000 years ago, likely in the eastern part of the subcontinent. Today it reaches levels of up to 90% among some isolated tribal populations on the subcontinent. H is also found in regions that have historical ties to India, such as Bali and Cambodia, and the Roma, or Gypsies.

Highlight: Today, haplogroup H is most common in the Indian state of Andhra Pradesh.

My maternal haplogroup is M37e.
Origin: Haplogroup M is one of two branches on the mitochondrial DNA tree that arose about 60,000 years ago, soon after humans first expanded out of Africa. Because of its deep roots it is widespread in southern and eastern Asia, and its branches extend into North America as well.

Highlight: Haplogroup M spread from Africa to southeastern Asia in a few millennia.

The estimated modern distribution of haplogroup M is shown in the map below.

This map from the National Geographic,  shows roughly the route humans took out of Africa, of the order of 100,000 years ago.

This map, from Wiki, places haplogroup M in perspective.

I surmise from all this that my ultimate maternal grandmother as far as it can be traced, was in India some 60,000 years ago.

Keeping in mind what I wrote about possible ancestors from Venus and Mars above, do I qualify as purna swadeshi? If recombination analysis of the rest of my genes show an Indian origin in the deep past, does that qualify me as an Adivasi? Or does alleged Sanskritization in my deep past disqualify me?

(Wiki): Adivasi (Hindi: आदिवासी, IPA: [aːd̪ɪˈʋaːsi]) is an umbrella term for a heterogeneous set of ethnic and tribal groups considered the aboriginal population of South Asia.


To fly-everywhere vacationers that worry about climate change

To the type of tourist who flies all over the world, and then laments climate change, you had better have a lot of carbon offsets. Know this, to keep the carbon dioxide in the atmosphere from increasing, there is a per capita per year carbon allowance, it is somewhere between 1 and 2 tons per person per year.   Just one long distance plane flight for a person already exceeds that allowance. 

It is ironic that to save the world we will need to avoid long distance visits (or else, find carbon offsets).

Monday, September 19, 2016

Photography: DSLR versus smartphone

As someone upgrading from Canon's 5D2 DSLR to its latest and greatest 5D4, it behooves me to think about whether I'm spending my money wisely.

The truth is that smartphone cameras are indeed very good. Arstechnica has a good recent shootout.  Their conclusion:
Ultimately, the winner here is the smartphone, not the DSLR. The DSLR triumphs technically, and it will produce better images under almost any circumstance, but it’s just hella hard to stack it against the iPhone’s portability and "good enough"-ness.

Is the smartphone better? No. The DSLR and its lenses, even in my unskilled hands, produce higher-quality images, period. They’re higher resolution, and they contain more detail. It’s impossible for the iPhone’s little 8.5mm-ish sensor to grab as many photons as the DSLR’s big 35mm full-frame sensor. The DSLR wins every time, and the iPhone’s output, while good, isn’t as good.

But that’s the thing: the smartphone may not produce the same massive, high-detail 22MP images as the full-frame DSLR, but the smartphone does manage to be good enough.
Remember also that it matters on what medium you are going to display your photographs.  The difference in quality between DSLR and smartphone cameras is less perceptible in typical web-sized photograph or on a tiny screen,  but will be visible on a large screen or in a large print.

From my perspective, it is not an "either-or" situation, the smartphone camera and DSLR are two different tools and my purposes are best met by having both.  There are pictures a DSLR will never take because it wasn't possible to carry it to the scene; and there are pictures a smartphone is simply incapable of taking.

Tuesday, September 13, 2016

Cixin Liu: The Dark Forest and The Three Body Problem

The first two books of Cixin Liu's trilogy, translated from the Chinese: The Three Body Problem and The Dark Forest are excellent science fiction, and I look forward to the final book Death's End that is due for release in a couple of weeks.

Reviews likely contain spoilers, so avoid them if you plan on reading the books. After reading the pair of books, I've read a few of the reviews that show up in the first page of Google search, and generally agree with them, so I won't burden the world with yet another review.  What to expect from the books, though?  The general portrayal of characters is weak, like in Asimov's early fiction, but the science fiction imagination on display is absolutely top-notch.  The author has to bend a little some well-known physics to make his plot work, but unless you are an insufferable purist, it shouldn't matter.   The Dark Forest sufficiently closes out the story that I don't feel compelled to read the third book to get closure, but rather to see what further worlds of imagination the author creates.

Monday, September 12, 2016

How to interpret the weather forecast

Someone wrote: "When a weather forecaster tells me the probability of rain tomorrow is 50%, I translate it as “I don’t know.”"

I translate the weather forecaster as saying "Out of a 100 days where the forecast is 50% probability of rain, it rains on 50 of them".

Is this the same as "I don't know"?

Some possibly relevant information:  where I live it rains on the average on 117 days of the year.   In Arizona, it rains on the average on 36 days of the year.  Honolulu, Hawaii has rain on 154 days of the year.

With the above examples, I think the forecast of "the probability of rain tomorrow is 50%" is the closest to "I don't know" in Honolulu, and the furthest away from "I don't know" in Arizona.   I haven't done any Bayesian calculations or anything, just working from intuition.

What do you think?

Sunday, September 11, 2016

Vedic Deities are indwelling.

The idea that Indra, Agni, etc.,  the thirty-three crore (1 crore = 10 million) devatas are indwelling powers I first heard from Dadaji Pandurang Shastri Athavale.  Dr. Nicolas Kazanas now writes on the same theme:

However, there is a vast difference between the Vedic conception of deities and other traditions including Buddhist, Christian etc, and even Hindu. This difference is hardly ever mentioned and when it is mentioned, as by Edgerton, it is hardly given much value. Vedic deities are forces within man. Yes, of course they are deities outside, all around, natural forces on earth, in the atmosphere and the sky, (the earth itself with its fecundity, waters, rain, air, sun, moon etc); there are also gods of morality like Varuṇa, Mitra and Bṛhaspati. But, as the Atharvavedic hymn 11.8.32 says, Man is the brahman and all devatā (deities, gods) reside in him as cattle in a pen!


But the internalisation of the deities had already appeared in the RV. Agni, the Firegod, is said to be set within man’s heart hṛ́daya āhitá and, so, is the constant light of all inspiration, in the early hymn 6.9.6 of the Bharadvāja clan. This luminous power is perceived through mind mánasā nicay – (3.26.1) and itself as mental force manas is the fastest of all entities that fly (6.9.5). Indra too is internalised identifying himself with sages Manu, Kakṣivan and Uśanās (4.26.1) and his state may be attained by men, though not by deeds or sacrificial rites (8.70.3). Then, human functions like foresight and vigour are deified in 1.53.5 as devī prámati and devī táviṣī respectively.


However, I do acknowledge that probably most people in the Vedic age regarded deities as external, imperceptible superhuman Powers that should be worshipped, placated and invoked for favours. Thus, from the very earliest hymns (Maṇḍalas 3, 6, 7) some people or clans, and certainly some rishis, knew that “deities” were not mere Powers of natural phenomena but also forces-functions within man. 

Friday, September 09, 2016


India was the "America" of the first thousand years of the common era.  India was prosperous for its time; more than 30% of world output was in India.  Indian goods were valued highly even in far-away Europe.  People fleeing religious persecution, Zoroastrians, Jews, "heretic" sects of Islam, all found a friendly refuge in India with the freedom to follow their religious traditions.   People from Southeast Asia, China, Japan came to India to study; and carried Indian influence back with them, so that the Buddha, the Vedic Indra,  Saraswati, and Ganesha all still have living traces in these lands.

But around 1000 AD, the invasions of Mahmud of Ghazni inaugurated a dreadful period of Indian history, where more was destroyed than created.  Mahmud himself reveled in the demolition of Mathura, which by his own estimate, would have taken two hundred years of labor to build.  And worse was to follow.

When one asks why a vibrant civilization fell prey to savage destructive warriors, it was because the people of that era could not bury their parochial differences and rivalries even in the face of that which would annihilate them.  So instead, they were picked off one by one and India became "a wounded civilization".  

Observing the American political scene today, it seems pretty much the same.  The political divisions are not anymore debatable policy differences on how to deal with ISIS, climate change, unsafe financial institutions,  economic growth,  mass incarceration, the crisis of drug addiction and such.  Policy debates, however heated, tend to produce solutions.   Instead today politics seems more like petty grudge matches.  NJ Governor Chris Christie's BridgeGate, where his officials created artificial traffic jams to punish a mayor who didn't endorse him, is an archetype.   In such circumstances, this Republic won't endure.