Friday, July 29, 2011

Absence of Heroism and the Road Inward

The debt crisis, largely artificial because it is not that the US government is unable to pay its dues but that it is not allowed to pay, is a failure of the political leadership to be rational.

This emerging trend of irrational governance is apparent in the US, Japan, and in Europe (see “Turning Japanese” The Economist July 30, 2011).

In the US at least, this is partly the result of electing into office a vocal minority of fiscal extremists, the Tea Party representatives. But it would be overly simplistic to stop there. One needs to probe the reason as to why the extremists got elected in the first place.

In a psychological sense, all extremists appear to suffer from various degrees of delusion of grandeur, a narcissistic view that the ills of the society can be bettered by making heroic demonstrations.

We in the US have had little occasion to be heroic lately. We fight a war for which no sacrifice has been required for the vocal middle class, because we have let the poor and the minority to die in it; we get a tax rebate instead. The face of the war does not leave much room for heroism either, because we fight an enemy that is not afraid of death as the ultimate sacrifice—a supposedly Western prerogative that has received much mythological support in our culture. What is worse, we are now led by a black intellectual, who is often identified as a half-Moslem. Racial inferiority and religious antagonism are the most difficult cultural instincts to overcome. If the media are to be believed, our businesses are increasingly run over by the Chinese and the Indians; Latinos are on the rise; we don’t even have a rocket science any longer. Where should we now vent our delusions of being a hero?

The answer presented to us is simple: dismantle the status quo. This Samson-like act of narcissism appears preferable even at the risk of collapsing the institutional dome of legitimacy above us.

Monday, July 11, 2011

My DNA: The Rashomon Factor

So here I am, having both paternal and maternal ancestries traced to the central Asian mountains and valleys, to the Hunzas and the Persians. How did I get here?

The 64 : 36 admixture of European and Asian polymorphic markers in my genome has evidently been preserved over many generations, because there is no European history known in either of my lineage within at least 10 generations. Were it the case that there was a single homozygous European who married a homozygous Asian, then their child would have both markers. Since there are many more Asians than Europeans in Bengal, and if all were homozygous Asians, then in every subsequent generation there is an overwhelming probability that the descendent of that lineage will breed with a homozygous Asian, thus at every subsequent generation the proportion of European markers will be halved (if the markers are all unlinked). This is akin to successive back-crosses with the Asian stock. Thus, after 10 generations, 2^(-10) or only 1 in approximately 1,000 or 0.1% of the European markers, if all are unlinked, will still exist.

The actual proportion might be somewhat more, because of linkage and linkage disequilibrium, which can be calculated, which will lead to loss of heterozygosity at the rate of (1 – r)^t, where t is the number of generations and r is the recombination frequency between marker pairs. But the frequency of retention under the above simplifying assumption will be far below 64%. This is because r for most marker pairs (~700,000 markers if randomly distributed over 23 chromosome pairs) would be approximately 0.04 for human chromosomes (~1 centiMorgan per megabase pairs). Therefore, the erosion will be approximately at a rate of (1 – 0.04)^t, which translates to 0.96^t. For 10 generations, we need to divide 0.1% by approximately 66%, which leads to a retention of 0.15% of the heterozygous markers on average. Although I arbitrarily chose 10 generations (i.e., t = 10), it is probably true that anyone in my ancestry mating with a person homozygous for European markers goes far deeper into the past because the very first Europeans in historical times came to Bengal only about 20 generations ago. The overwhelming conclusion is that my assumptions are incorrect. Where are they incorrect?

The main assumptions were that there was one rare mating between a European and an Asian, and that most people in Bengal are homozygous for Asian markers. Both are nearly certainly incorrect.

The heterozygosity of markers over many generations, in the absence of direct natural selection due to selective advantage (unlikely because it would predict an enormous selective advantage to rare heterozygous markers), is probably the result of selective breeding or kin-selection—the inevitable result of the caste system in India. It is because of this selective breeding and kin-selection that the heterozygous markers were conserved over many generations. Therefore in a moment of somewhat dampened literary inspiration, I am compelled to moderate my romantic scenarios of a Hunza couple eloping together and settling in Bengal, or a wayward Yemeni sailor marrying an Asian woman.

The reality is likely to be quite different. The most likely scenario is that my ancestors descended from individuals in south central Asia, the inhabitants of Afghanistan, Persia, and central Asian plateaus at some remote Vedic or pre-Vedic time, through selective marriages among a small number of communities who rarely married into the indigenous Asian stock. This ensured that the members of these communities are all highly heterozygous. If nearly all of these people are heterozygous at most markers, then the chance that any individual will be heterozygous at any marker is nearly 50%. The observed 64 : 36 distribution of markers is close enough to this expectation, if one assumes a slight bias towards marrying into families with more European (i.e., Brahmin) than Asian markers. Thus, for my ancestors, intermarriages largely restricted within the community in most generations with only rare breeding with non-Brahmins (having somewhat higher frequency of Asian markers) is a good explanation for my lineage.

This scenario is well attuned to an oral myth of the Vaidya or Baidya communities of Bengal. Tradition has it that the ancestor of the Vaidya caste was the result of an illegitimate union between a Vaishya woman by the name of Birabhadra and a Brahmin Galava Muni. The latter was reputed to be a Vedic Brahmin, apparently from the area currently known as northern Pakistan/Afghanistan (but see also: this). The child born became known as Dhanavantri. Since the child had no legal father, (s)he belonged to the family of his/her mother. Of course that is only one of the narratives, and there are several competing narratives. One fact is clear: the Vaidyas generally intermarried among their own communities, thus maintaining their genetic heterogeneity.

This is all a remarkable congruence of oral tradition and science, perhaps even more interesting than my romantic story of the eloping Hunza couple.

Sunday, July 3, 2011

My DNA: My Ancestry

My DNA result is out. I have 64% European and 36% Asian markers, which put me squarely in the Indian subcontinent, somewhat more heterogeneous than the upper caste Brahmins who have roughly 80% or more European and ~20% or less Asian markers on average. This is not surprising, because I am not a Brahmin, but am supposed to be a Vaidya, or, historically a class of Brahmins who were shunned from wed locks with other Brahmins for either reasons of envy, for accepting fees for medical treatment (you see, the Brahmins are supposed only to receive the gifts of gratitude and never a fee for labor) or, more likely, because a wayward Brahmin in my remote ancestry fell for a lower caste boy or girl…

I seem not to have any known marker for any debilitating disease, or even a carrier of any known disease markers. I might be more than average sensitive to Warfarin, a blood thinner given in cases of blood clot diseases or stroke, too much of which could cause bleeding, and knowing this the doctors would be cautious in case they catch me on a stretcher one of these days.

I seem to be a slow metabolizer of caffeine, which explains why I spend so much time in caf├ęs.

So far that is almost all I know that is of significance to my health…the rest are all typical.

The real fun begins when I look at my maternal and paternal ancestries.

Maternal ancestry is provided by the mitochondrial DNA sequence, which rarely changes, and is always contributed by the mother (never the father). Thus my mitochondrial DNA ancestry forms a continuous chain up the line of my mother’s mother’s mother’s mother’s…..mother the Eve in Africa. The same with yours.

The funny thing is that the mitochondrial DNA does change sometimes, but very very rarely. When it does, and the mitochondrion still functions, then the mutated (changed) mitochondrial DNA “diverges” in sequence a little bit from the previous generation, and this changed sequence is then inherited down the line, until all females in that line have all male children, in which case the mitochondrial DNA chain is annihilated. This provides a way to sleuth out the maternal ancestry of the current population on the earth because if my mitochondrial DNA is related to yours then we must have shared the same maternal lineage, and by checking this we can actually chart the migration patterns of groups of people across the globe.

My mitochondrial DNA belongs to the so called haplogroup R6, which is a minor part of a very ancient lineage R that arose in Southeast Asia not long after the first human migrations out of Africa into Asia, who then migrated to Europe, Australia, and the Americas. The haplogroup R arose some 60,000 years ago in Asia, before migration to Europe, Australia and the America; therefore it is found in all these places except in Africa. R6 is a variant of the the original R. R6 is quite rare, and is now found most frequently among some tribes in the mountainous regions of Afghanistan-Pakistan-India border and also in small pockets near Tamil Nadu of southern India and in northern Sri Lanka (source: Metspalu et al. BMC Genetics 2004, 5:26 doi:10.1186/1471-2156-5-26).

Therefore, a woman in my distant ancestry from either the mountains of Kashmir or Afghanistan region, or from Southern India, or one of their common ancestors, must have migrated to the plains of north-eastern Bengal, perhaps over many generations through bearing daughters who migrated slowly, or perhaps it was a single romantic affair that led to one couple eloping together and settling in Bengal, producing a daughter who bore another daughter, and so on. While eye and skin colors are not at all known to be inherited through the mitochondrial DNA—the mitochondrial DNA merely asserts the maternal inheritance line—other genes that do might also have descended from this couple. My maternal grand mother (who was born in north-eastern India in current Assam, in the Dibrugarh area, so far as I recall), from whom I must have inherited my mitochondrial DNA, had bluish green eyes and fair skin, something like what is seen among the tribes of Kashmir region of India, Afghanistan and Pakistan. But the couple might also have come equally likely from southern India, where the incidence of bluish-green eyes is rarer though.

How about my paternal line? This is even more interesting. My paternal line, derived from my Y chromosome, which was given to me by my father (by his father, and so on up to some Adam in Africa), who were all from the Chittagong region of current Bangladesh, belongs to a very rare group H1a*. The haplogroup H, from which H1a* is derived, is mainly restricted to the Indian subcontinent, mostly among the tribes of India and is rarely (~10%) found among the Brahmins, but also its variants are found among the Central Asians including the Afghanis, the Romani gypsies of the Balkans, some central Asians and Iranians, among the Saudis (including their royal families), and in Yemen, and a somewhat distant line in Cambodia/Vietnam. But if one looks more closely at the specific rare variant H1a*, then one finds the closest similarity to a group of "Balkarians" (a Turkish people of the Caucasus mountains), southern Iranians, and Serbians, all of whom contain the mutation M82 in H1a subgroup that is the closest ancestor of H1a* which is mine. Further derivatives of H1a, such as H1a1, H1a2, and H1a3 are found in Nepal, and Southeast Asian countries including Bali, Indonesia and Cambodia, but these are in parallel lineages to that of H1a*, all derived from the common H1a, which likely originated in Northern India or Central Asia.

Whatever I know of my immediate paternal ancestry, my great great grandfather was childless, and adopted a child who was my great grandfather. The only surviving photograph of my great grandfather shows him to be a man of about 50, who was reputed to have had greenish brown eyes, as did my father and as does my daughter.

Was there a lost sailor from Yemen who married a village girl in southern Bengal during his oceanic voyages along the spice route? Or was there a Balkarian soldier in the army of Babur who descended on the Bengal delta and married a woman who produced a son who provided the Y chromosome that ultimately gave rise to my great grandfather?

When I download the entire DNA marker set of my genome (some 700,000 of them) and do principal component analysis (PCA) against all known DNA markers of the world, my DNA markers appear to cluster on the first and second eigen vector spaces right near where the DNA of the indigenous people of central Asia (north of Afghanistan), closest to the Burushos of the Hunza valley of Pakistan-Afghanistan, appear to originate.

These are the stuff of which epic novels are made!

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*The above account, as might be expected after a reading, is colored with quite a flight of fancy. To get a slightly more nuanced scientific perspective, read the next entry, My DNA: The Rashomon Factor.