Razib Khan One-stop-shopping for all of my content

December 29, 2012

Brown Pundits is 2 years old!

Filed under: Uncategorized — Razib Khan @ 5:03 pm

For real. How time flies

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December 26, 2012

Shaheed Rani; Remembering Benazir Bhutto

Filed under: Benazir Bhutto — Razib Khan @ 6:11 am

I am reposting last year’s post on Benazir. Dont miss Hasan Mujtaba’s poem at the end.

Benazir Bhutto was murdered on December 27th 2007.  She and her father made many mistakes and had many weaknesses and flaws, perhaps fatal ones. But they mobilized the common people of Pakistan like no one before or since, and they did so using a left-liberal vocabulary that always seemed to get on the nerves of Pakistan’s deep state. And of course, whatever their flaws, no one could accuse either father or daughter of lacking courage.  Benazir knew the risks when she came back to Pakistan. She survived one assassination attempt in Karachi in which nearly 200 of her most ardent supporters were killed. But she continued to hold public meetings and she continued to speak out and paid the ultimate penalty…

Look at the crowds who danced for her (and who will mourn her in Garhi Khuda Baksh) and you will see why, in spite of all disappointments and mistakes, she is now “Shaheed Rani” (the martyr queen); she represents something larger than her actual political achievements. In her death she has become a potent symbol of people’s rights and democracy and a permanent thorn in the side of Pakistan’s establishment.

Incidentally, those too young to remember and getting extremely excited at the crowds who gather at Imran Khan’s public meetings may wish to see some clips in this video of Benazir’s arrival in Lahore in 1986. That was, bar none, the largest crowd ever seen in the history of Pakistan… and they were not sitting on chairs..

Some clips in her own voice.

A very nice photo and video montage in her memory, set to a famous ghazal by Shad Azeem Abadi : http://www.youtube.com/watch?v=EmzN7Z_GgIc

btw, the ghazal lyrics are quite appropriate and can be seen alongside a somewhat pedestrian translation here.

another montage here. Beena Sarwar’s collection of photographs from her arrival in Karachi, and a really good video and photo montage to round it off.

PPP tarana (anthem), arrangement by Stewart Copeland of The Police, vocals Bakhtawar Bhutto Zardari (her daughter) and Azra Malik. Original composition by Zahoor Khan Zeibi

Hasan Dars poem on her death, sung by Mazhar Hussain

Raza Rumi’s poem and his own translation: http://razarumi.com/2008/02/13/people-of-this-murderous-city/

Sidelined leader Aitazaz Ahsan in fine form at her anniversary, skip to minute 20 for his recitation of yet another poem with karbala references (lashkar e yazeed main, ik kaneez e karbala…in the midst of Yazeed’s army, one maid of Karbala…where would protest literature in the Islamicate world be without karbala?): http://tribune.com.pk/multimedia/videos/312770/

Bilawal Bhutto’s tribute today. And one by Suleman Akhtar on the progressive PPP website. 

In a media dominated by anti-PPP forces, Hamid Mir of Capital Talk presented a very good program on her death anniversary.

Mohammed Hanif, author of “a case of exploding mangoes” and “our lady of Alice Bhatti” has a piece.

The well planned assassination can be seen in this video

Hasan Mujtaba’s famous poem on the occasion is an absolute classic. I have translated it with his approval (I have taken some poetic license at places, and I am not a poet..so beware):

How many Bhuttos will you kill?

A Bhutto will emerge from every home!

This lament is heard in every house

These tears seen in every dwelling place

These eyes stare in the endless desert

This slogan echoes in every field of death

These stars scatter like a million stones

Flung by the moon that rises so bright tonight

How many Bhuttos will you kill?

A Bhutto will emerge from every home!

 

The one you killed is now fragrance in the air

How will you ever block its path?

The one you killed is now a spell

That is cast upon your evil head

Every prison and every lock

Will now be opened with this key

She has become the howling wind

That haunts the courtyards of this land

She has come to eternal life by dying

You are dead even while being alive

How many Bhuttos will you kill?

A Bhutto will emerge from every home!

 

You men in Khaki uniforms

You dark and long bearded souls

You may be blue or green or red

You may be white, you may be black

You are thieves and criminals, every one

You national bullies, you evil ones

Driven by self or owned by others

Nurtured by darkness in blackest night

While she has become the beauty that lives

In twilights last glimmers and the break of dawn

How many Bhuttos will you kill?

A Bhutto will emerge from every home!
She was the nightingale who sang for those who suffered

She was the scent of rain in the land of Thar

She was the laughter of happy children

She was the season of dancing with joy

She was a colorful peacock’s tail

While you, the dark night of robbers and thieves

How many Bhuttos will you kill?

A Bhutto will emerge from every home!

 

She was the sister of those who toil in the fields

The daughter of workers who work the mills

A prisoner of those with too much wealth

Of clever swindlers and hideous crooks

Of swaggering generals and vile betrayers

She was one solitary unarmed girl

Facing the court of evil kings

How many Bhuttos will you kill?

A Bhutto will emerge from every home!

 

She was the daughter of Punjab

Of Khyber and Bolan

She was the daughter of Sindh

Karbala of our time

She lay drenched in blood in Rawalpindi

Surrounded by guns and bullets and bombs

She was one solitary defenseless gazelle

Surrounded by packs of ruthless killers

O Time, tell the long lived trees of Chinar

This tyrant’s worse nightmare will come true one day

She shall return, she will be back

That dream will one day come alive

And rule again. And rule again.

How many Bhuttos will you kill?

A Bhutto will emerge from every home!

 

 

 

 

 

 

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December 23, 2012

Merry Christmas!

Filed under: Administration — Razib Khan @ 1:52 am

Because of the nature of modern American ‘work-life balance’ the next week or so is going to be my longest period of being the ‘primary caregiver’ for my daughter in her short life. Needless to say I’m quite excited! Especially because this will be her first Christmas.

I spent most of my childhood in a region on the margins of lake-effect, so I am familiar with a white Christmas in a classical fashion. More recently I’ve been resident on the maritime fringes of the western United States, and snow is rare in the lower elevations of this region. But I persevere!

Over the next week I will likely be blogging a great deal from my daughter’s playroom, where I’ll have a makeshift encampment. But rest assured this will be a great leisure for me. I hope readers of this weblog can find time to relax as well. Hopefully the comments will come back to a civilized state after the New Year….

History as intellectual hydrography

Filed under: History — Razib Khan @ 1:26 am

One of the great aspects of owning a Kindle has been that I have been able to load it with cheap copies of “classics.”* As it happens I had physical copies of many of these works, but often it became difficult to keep track of various books in even my modest personal library. Generally scientific references were placed prominently, and I made use of them often, and so always was able to mark exactly where they were. But when it came to Nicomachean Ethics or The Critique of Pure Reason, I would proactively seek them on only rare occasions. Now with a compact and well organized personal digital library I find that I revisit the ancients much more often to engage with them in dialogue. Here I recall what Niccolò Machiavelli once asserted:

When evening comes, I return home and go into my study. On the threshold I strip off my muddy, sweaty, workday clothes, and put on the robes of court and palace, and in this graver dress I enter the antique courts of the ancients and am welcomed by them, and there I taste the food that alone is mine, and for which I was born. And there I make bold to speak to them and ask the motives of their actions, and they, in their humanity, reply to me. And for the space of four hours I forget the world, remember no vexation, fear poverty no more, tremble no more at death: I pass indeed into their world.


Meghna River

I am far too much a Whig in instinct to agree with this sentiment without reservation. When I trudge through the extended diatribe that is City of God I cannot help but scoff at St. Augustine’s screed, 1,600 years on. And yet this contempt instills in me a sense of deep humility, for surely generations future will look toward our own orthodoxies and sneer and laugh. We are all embedded in our own presuppositions, and the ecology of ideas which nourish our prejudices, for good or ill.

It is as if we are an element of a broad and powerful river, flowing through familiar territory. If you asked a stream of the river to describe its place in the context of the whole, it would be at a loss, because the river is one, and as a category is indivisible. But step back, rise up, and you can see the topography and the overall course of the flow, from headwaters down to the floodplain. Similarly, ideas have history, and people have history, even if they are not aware of that history as it flows past them.

Human cognition is such that there is a strong bias to imagine that we are idealized rationality machines, who derive our own positions by force of our free will. But the reality is that much of our cognition is socially and historically contingent. This does not mean that beliefs are arbitrary, but, they are flexible and strongly shaded by context. The folly of the most brilliant of ancients brings home to us the reality that pure force of mental acuity can not break free of the shackles of history. What follies do we adhere to? What positions are we “evolving” toward at this very moment?

During a typical day my own interactions are with young people of a very precise and specific technical bent. There is no lack of cognitive processing power, but when conversation drifts away from areas of deep technical fluency, then St. Augustine begins to strike me as a man of objective ahistorical clarity. The technics of the modern age are humans who sustain our civilization, but they often lack background or interest in the human past, or a more expansive view of the present. There is a very definite poverty of imagination in regards to the range of human opinion, and a conceit that the shape of the world is as precisely defined as the arc of planetary motions.

Whereas before I had held to the position that a minimal level of liberal classical education was critical in tying together the higher orders of a social system through a common set of narratives and frames, today I believe that a canon is essential to allow people at any given moment to see that human experience is broad, and that we are all creatures in a specific time and place. I cannot help but wonder if the occasional outbursts of extreme relativism which issue out of the academy may simply be a function of the inability of narrowly trained moderns to comprehend that one can hold onto one’s values and views, while at the same time appreciating differences of perspective. It may be to difficult to withhold ill will across the chasms of contemporary partisanship, but surely one must acknowledge Aristotle’s brilliance and his folly!

* You may wonder why I would pay even a nominal fee when these are public domain. My personal experience is that a minimal amount of commentary and attention to formatting is worth a few dollars.

December 22, 2012

The “Asian quota” and implicit cultural knowledge

Filed under: Education — Razib Khan @ 6:31 pm

The Myth of American Meritocracy, Ron Unz

A recent conversation I had with a friend whose parents are immigrants from Germany made me reconsider and reflect on the power of implicit information in shaping one’s life; that information being culturally mediated. Though my friend was raised in the United States, because of her parents’ immersion in the German expatriate community her upbringing was very bicultural. In fact, she is much more German than I am Bangladeshi. Despite the fact that to anyone who is a Baby Boomer or older she looks American, and I do not, there are many similarities in outlook due to our 1.5 generation background. Both of us are from families where graduate educations in the sciences are the norm. We succeeded in academics and pursued higher education without much effort or obstacles. This is not a story of overcoming the odds in a conventional  sense. In explicit terms we are entirely American, but there are nevertheless implicit aspects of being American of a particular social class which we had to experience after leaving home at 18.

This brings me back to the issues which were highlighted in Ron Unz’s recent piece in The American Conservative, The Myth of American Meritocracy (note: I was an Unz Foundation Junior Fellow between February 2007 and February 2012). You can see further discussion of the topic at The New York Times, as well as Unz’s weblog. Steve Hsu has also been discussing the results as well. My primary focus here is not going to be on the article itself. I broadly accept many of the empirical findings. The chart above shows to me that it is clear there has been implicit collusion between Ivy League universities in regards to the proportion of people of Asian ancestry who attend these institutions. In hindsight it should not be too surprising. I commend you to read Austin Bramwell’s perspective in the Top of the Class, where he outlines exactly how elite prep schools cooperate with the admissions offices of Ivy League universities to perpetuate the pipeline which maintains the generations of the customary American gentry (of which he is a member).

Institutions like Harvard exist to shape the nature of the American ruling class. It makes sense that they would be keen toward particular demographic considerations. I am personally not particularly pleased as the prospect of racial quotas, but then again my image of an “elite university” is that it should be elite in scholarly terms, rather than as a finishing school for the next generation of America’s rulers (and I have no interest in the types of demographic diversity which are of concern for most). But I am not the dictator of this world, and I am rather confident that no matter what the Supreme Court rules in the near future, a de facto quota system will continue, with some marginal modifications, at private universities for the indefinite future. The American ruling class, whether it be intellectuals, politicians, or corporate executives, favors some form of affirmative action and diversity, and I am convinced that they will get their way, no matter legal obstacles or populist sentiments.

Reality is what it is, and it is on the matter of transparency, and explicit comprehension, where I think we need to make our stand. There are many people who have long been aware of the “Asian quota,” or the fact that “holistic admissions” serve to allow particular universities to modulate their demographic outcomes appropriately. But not everyone is aware of this. I am thinking, for example, of a friend who was raised by a single mother. He happens to be 1/4 Asian in ancestry, and when applying to elite private universities he made sure to put “Asian” as his race, under the false assumption that being a minority would aid his chances of admission. Raised by a white single mother he was not in a milieu where the “real rules” on what counts, and doesn’t count, as a minority, were understood. We live in a system where the child of Korean shopkeepers is not an underrepresented minority, while the child of a Venezuelan doctor most certainly is. Similarly, when elites talk about “diversity,” it is implicitly clear that this alludes to very particular and specific demographic diversities. Race, sex, and the reality of some ancestry derived from Latin America most certainly. Our modern elites may give a rhetorical nod to socioeconomic diversity, but there will never be any substantive action in this direction which might jeopardize the chances of their own children ascending the ladders of power. The extant scholarship on elite university admissions suggests that non-Hispanic whites who are below the middle class are extremely underrepresented at elite private institutions, but there is no prospect to my knowledge that this deficit in the texture of the future ruling classes will be addressed. This is just understood by all who count, and requires no great public discussion.

Success in life in the United States today demands that you understand the implicit and subtextual filaments which thread their way through the American cultural landscape. My daughter is an Asian American because her father is an Asian American (thanks to the reclassification of South Asians as Asian Americans in 1980). But the reality is that her physical appearance strongly favors her Northern European heritage. With that in mind we quite consciously gave her a series of names which allowed her own ethnic identity to be optional and situational. As I have no great emotional interest or preoccupation with collective identities I feel no pang of guilt or regret about this. The world is a bureaucratic machine, and there are those born who understand that the machine must be manipulated, and those who allow themselves to be tossed about by its machinations. If you don’t have a cynicism and mercenary attitude toward the machine, you will be consumed by it. The children of the American elite take the machinery for granted by dint of the implicit cultural wisdom they receive with their mother’s milk. The machine will always load the die so as to favor then. Those who are outside can only even the odds through information, and being better than those who are to the American manor born.

Of course there are many serious issues to address in regards’ to Unz’s piece. Many point out that perhaps there are rational reasons to discount the academic successes of Asian Americans (i.e., are these tests truly representative of intellectual vigor and curiosity?). But these honest discussions can only be had once honesty and transparency is the foundation and starting point. Until then we will continue to muddle on, trying to make sense of a complex world.

Cultural differences in film

Filed under: Multiculturalism — Razib Khan @ 1:18 pm

One of the issues which I occasionally bring up on this weblog is that despite all the talk about diversity and multiculturalism which most people air rhetorically, I live with diversity and multiculturalism because of my family background everyday (more honestly, whenever I have to engage with my parents). Though aspects such as food and religion are visible and obvious, sometimes it is the small things which are striking. Just today my mother-in-law stumbled upon some old photographs of her mother and uncle as infants. They were fraternal twins, born right at the end of World War I to Norwegian immigrants. Interestingly, my daughter bears a notable resemblance to her great-uncle, more so than to her own great-grandmother!

11438_190710812983_5574912_nThe peculiar aspect of this is that there are no photographs of me at an equivalent age to serve as a ‘control’ on this comparison. Despite their parents being working-class immigrants (my daughter’s great-great-grandfather was a longshoreman from Norway) my mother-in-law still has nearly century old photographs of her mother and aunts and uncles. In contrast, my father was a college professor in 1970s Bangladesh, whose wife was the daughter of a medical doctor, and yet my parents and their relatives couldn’t be bothered to take and preserve photographs of me. The image on the left, from when I was three years old, is the earliest that is preserved. I can count on one hand the number of photographs of me before the age of five.

I’d be curious about the experiences of readers.

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December 21, 2012

The causes of evolutionary genetics

A few days ago I was browsing Haldane’s Sieve,when I stumbled upon an amusing discussion which arose on it’s “About” page. This “inside baseball” banter got me to thinking about my own intellectual evolution. Over the past few years I’ve been delving more deeply into phylogenetics and phylogeography, enabled by the rise of genomics, the proliferation of ‘big data,’ and accessible software packages. This entailed an opportunity cost. I did not spend much time focusing so much on classical population and evolutionary genetic questions. Strewn about my room are various textbooks and monographs I’ve collected over the years, and which have fed my intellectual growth. But I must admit that it is a rare day now that I browse Hartl and Clark or The Genetical Theory of Natural Selection without specific aim or mercenary intent.

R. A. Fisher

Like a river inexorably coursing over a floodplain, with the turning of the new year it is now time to take a great bend, and double-back to my roots, such as they are. This is one reason that I am now reading The Founders of Evolutionary Genetics. Fisher, Wright, and Haldane, are like old friends, faded, but not forgotten, while Muller was always but a passing acquaintance. But ideas 100 years old still have power to drive us to explore deep questions which remain unresolved, but where new methods and techniques may shed greater light. A study of the past does not allow us to make wise choices which can determine the future with any certitude, but it may at least increase the luminosity of the tools which we have iluminate the depths of the darkness. The shape of nature may become just a bit less opaque through our various endeavors.

Figure from “Directional Positive Selection on an Allele of Arbitrary Dominance”, Teshima KM, Przeworski M

So what of this sieve of Haldane? As noted at  Haldane’s Sieve the concept is simple. Imagine two mutations, one which expresses a trait in a recessive fashion, and another in a dominant one. The sieve operates by favoring the emergence out of the low frequency zone where stochastic forces predominate of dominantly expressing variants (i.e., even if an allele confers a large fitness benefit, at low frequencies the power of random chance may still imply that it is highly likely to go extinct). An example of this would be lactase persistence, which in the modal  Eurasian variant seems to exhibit dominance. The converse case, where beneficial mutations are recessive in expression suffer from a structural problem where their benefit is more theoretical than realized.

The mathematics of this is exceedingly simple, a consequence of the Hardy-Weinberg dynamics of diploid random mating organisms. Let’s use the gene which is implicated in variation in lactase persistence as an example, LCT. Consider two alleles, LP and LNP, where the former confers persistence (one can digest lactose sugar as an adult), and the latter manifests the conventional mammalian ‘wild type’ (the production of lactase ceases as one leaves the life stage when nursing is feasible). LP is clearly the novel mutant. In a small population it is not unimaginable that by random chance the frequency of LP rises to ~10%. What now? At HWE you have:

p2 + 2pq + q2 = 1, where q = LP allele. At ~10% the numbers substituted would be:

(0.90)2 + 2(0.90)(0.10) + (0.10)2

This is where dominance or recessive expression is highly relevant. The reality is that LP is a dominant trait. So in this population the frequency of LP as a trait would be:

(0.10)2 + 2(0.90)(0.10) = 19%

Now imagine a model where LP is favored, but it expresses in a recessive fashion. Then the frequency of the trait would equal q2, the homozygote LP-allele proportion. That is, 1%. Though population genetics is often constructed on an algebraic foundation, the results lend themselves to intuition. A structural parameter endogenous to the genetic system, dominant or recessive expression, can have longstanding consequences in terms of the likely trajectory of the alleles. Selection only “sees” the trait, so a recessive trait with sterling qualities may as well be a trait with no qualities. In contrast, a dominantly expressed allele can cut like a scythe through a population, because every copy “counts.”

In preparation for this post I revisited the selection on Haldane’s Sieve in the encyclopediac Elements of Evolutionary Genetics. The authors note that this phenomenon, though of vintage character as these things can be reckoned is a field as young as evolutionary genetics, is still a live one. The dominance of favored mutations in wild populations, or the recessive character of deleterious ones in laboratory stock, may reflect the different regimes which these two genes pools are subject to. The nature of things is such that is easier to generate recessive mutations than dominant ones (i.e., loss is easier than gain), so the preponderance of dominant variants in wild stocks subject to positive selective pressure lends credence to the idea that evolutionary rather than development forces and constraints shape the genetic character of many species.

And yet things are not quite so tidy. Haldane’s Sieve, and the framework of dominant versus recessive alleles, operates differently in the area of sex chromosomes. In many lineages there is a ‘heterogametic sex’ which carries only one functional chromosome for most of the genome. In mammals this is the male (XY), while in birds this is the female (ZW). As males have only one functional copy of most genes on the sex chromosome, the masking effect of recessive expression does not apply to them in mammals. This may imply that because of the exposure of many deleterious recessive variants to natural selection within the heterogametic sex one would see different allelic distributions and genetic landscapes on these chromosomes (e.g., more rapid adaptation because of the exposure of nominally recessive alleles in the heterogametic sex, as well as more purifying selection on deleterious variants). But the reality is more complex, and the literature in this area is somewhat muddled. More precisely, it seems phylogenetically sensitive. Validation of the theory in mammals founders once one moves to Drosphila.

And that is why research in evolutionary genetics continues. The theory stimulates empirical exploration, and is tested against it. Much of the formal theory of classical evolutionary genetics, which crystallized in the years before World War II, is now gaining renewed relevance because of empirical testability in the era of big data and big computation. This is an domain where the past is not simply of interest to historians. Scientists themselves, chasing the next grant, and producing the expected stream of publications, may benefit from a little historical perspective by standing upon the shoulders of giants.

Holiday reading

Filed under: Books — Razib Khan @ 11:49 am

Christmas is a time when I accelerate my reading, and catch-up for lost time. Here’s my three books I plan to get through:

The Fall of Rome: And the End of Civilization. I’ve read this twice already. This short book has been one of the most influential works in my own personal thinking. Even if you don’t agree with the thrust of Bryan Ward-Perkins’ thesis, it will clarify your own position.

Through the Eye of a Needle: Wealth, the Fall of Rome, and the Making of Christianity in the West, 350-550 AD. The author, Peter Brown, is the modern day eminence on ‘Late Antiquity’. I’ve read many of his earlier works, and always found his exposition enjoyable. But I’m re-reading The Fall of Rome in part to have a good counterpoint in my head to Brown’s arguments, which are subtle and difficult to box in (for what it’s worth, I think Brown makes a bit too much of Late Antiquity, but to some extent this is a normative judgement).

The Founders of Evolutionary Genetics: A Centenary Reappraisal. This is an exciting time to be interested in evolution and genetics (see Haldane’s Sieve and prepare to be overwhelmed!). But I also think it is useful to have some historical perspective. Science is a human enterprise, and it is critical to step outside of the flowing river, and observe the parameters which shaped its past course and trajectory, and therefore where it may be going.

With that, an “open thread” for what you are reading, and why.

Note: The comments systems should be improved in the near future. Or so I’m told.

December 18, 2012

Buddy, can you spare some ascertainment?

The above map shows the population coverage for the Geno 2.0 SNP-chip, put out by the Genographic Project. Their paper outlining the utility and rationale by the chip is now out on arXiv. I saw this map last summer, when Spencer Wells hosted a webinar on the launch of Geno 2.0, and it was the aspect which really jumped out at me. The number of markers that they have on this chip is modest, only >100,000 on the autosome, with a few tens of thousands more on the X, Y, and mtDNA. In contrast, the Axiom® Genome-Wide Human Origins 1 Array Plate being used by Patterson et al. has ~600,000 SNPs. But as is clear by the map above Geno 2.0 is ascertained in many more populations that the other comparable chips (Human Origins 1 Array uses 12 populations). It’s obvious that if you are only catching variation on a few populations, all the extra million markers may not give you much bang for the buck (not to mention the biases that that may introduce in your population genetic and phylogenetic inferences).


To the left are the list of populations against which the Human Origins 1 Array was ascertained, and they look rather comprehensive to me. In contrast, for Geno 2.0 ‘ancestrally informative markers’ were ascertained on 450 populations. The ultimate question for me is this: is all the extra ascertainment on diverse and obscure groups worth it? On first inspection Geno 2.0′s number of SNPs looks modest as I stated, but in my experience when you quality control and merge different panels together you are often left with only a few hundred thousand SNPs in any case. 100-200,000 SNPs is also sufficient to elucidate relationships even in genetically homogeneous regions such as Europe in my experience (it’s more than enough for model-based clustering, and seems to be overkill for MDS or PCA). One issue that jumps out at me about the Affymetrix chip is that it is ascertained toward the antipodes. In contrast, Geno 2.0 takes into account the Eurasian heartland. I suspect, for example, that Geno 2.0 would be better for population or ancestry assignment for South Asians because it would have more informative markers for those populations.

Ultimately I can’t really say much more until I use both marker sets in different and similar contexts. Since Geno 2.0 consciously excludes many functional and medically relevant SNPs its utility is primarily in the domain of demographics and history. If the populations in question are well covered by the Human Origins 1 Array, I see no reason why one shouldn’t go with it. Not only does it have more information about biological function, but the number of markers are many fold greater. On the other hand, Geno 2.0 may be more useful on the “blank zones” of the Affy chip. Hopefully the Genographic Project results paper for Geno 2.0 will come out soon and I can pull down their data set and play with it.

Cite: arXiv:1212.4116

Gene surfing with David Dobbs

Filed under: Behavior Genetics — Razib Khan @ 2:04 am

Over at National Geographic David Dobbs of Neuron Culture has an eminently readable and engrossing piece up, Restless Genes. I have never really read about ‘allele surfing’ on the wave of demographic expansion in the way that Dobbs’ rendered it. I certainly wouldn’t have been able to produce that sort of spare but informative prose.

On Twitter there was some concern about the focus on DRD4. The issue is a general one in much of behavioral genomics, and I’m not too interested in rehashing the point. But the broader question of heritability of behavior remains. It seems to me that we have some ‘natural experiments’ now. For the past 50 years there have been a series of cross-cultural adoptions from Asia to North America and Europe. If human behavior variation across and within populations is substantially heritable than this might be a good place to start. Rather than focusing on genes, we need to focus on heritability first.

Unveiling the genealogical lattice

To understand nature in all its complexity we have to cut down the riotous variety down to size. For ease of comprehension we formalize with math, verbalize with analogies, and visualize with representations. These approximations of reality are not reality, but when we look through the glass darkly they give us filaments of essential insight. Dalton’s model of the atom is false in important details (e.g., fundamental particles turn out to be divisible into quarks), but it still has conceptual utility.

Likewise, the phylogenetic trees popularized by L. L. Cavalli-Sforza in The History and Geography of Human Genes are still useful in understanding the shape of the human demographic past. But it seems that the bifurcating model of the tree must now be strongly tinted by the shades of reticulation. In a stylized sense inter-specific phylogenies, which assume the approximate truth of the biological species concept (i.e., little gene flow across lineages), mislead us when we think of the phylogeny of species on the microevolutionary scale of population genetics. On an intra-specific scale gene flow is not just a nuisance parameter in the model, it is an essential phenomenon which must be accommodated into the framework.


This is on my mind because of the emergence of packages such as TreeMix and AdmixTools. Using software such as these on the numerous public data sets allows one to perceive the reality of admixture, and overlay lateral gene flow upon the tree as a natural expectation. But perhaps a deeper result is the character of the tree itself is torn asunder. The figure above is from a new paper, Efficient moment-based inference of admixture parameters and sources of gene flow, which debuts MixMapper. The authors bring a lot of mathematical heft to their exposition, and I can’t say I follow all of it (though some of the details are very similar to Pickrell et al.’s). But in short it seems that in comparison to TreeMix MixMapper allows for more powerful inference of a narrower set of populations, selected for exploring very specific questions. In contrast, TreeMix explores the whole landscape with minimal supervision. Having used the latter I can testify that that is true.

The big result from MixMapper is that it extends the result of Patterson et al., and confirms that modern Europeans seem to be an admixture between a “north Eurasian” population, and a vague “west Eurasian” population. Importantly, they find evidence of admixture in Sardinians, which implies that Patterson et al.’s original were not sensitive to admixture in putative reference populations (note that Patterson is a coauthor on this paper as well). The rub, as noted in the paper, is that it is difficult to estimate admixture when you don’t have “pure” ancestral reference populations. And yet here the takeaway for me is that we may need to rethink our whole conception of pure ancestral populations, and imagine a human phylogenetic tree as a series of lattices in eternal flux, with admixed nodes periodically expanding so as to generate the artifice of a diversifying tree. The closer we look, the more likely that it seems that most of the populations which have undergone demographic expansion in the past 10,000 years are also the products of admixture. Any story of the past 10,000 years, and likely the past 100,000 years, must give space at the center of the narrative arc lateral gene flow across populations.

Cite: arXiv:1212.2555 [q-bio.PE]

December 17, 2012

Conservative atheists not rare in South Korea?

Filed under: Politics,Religion,South Korea — Razib Khan @ 11:30 pm

In a few days South Korea will have a new president, and this is very important because of how large North Korea looms in geopolitics. An interesting aspect of this race for Americans is that the candidate of the conservative party, Park Geun-Hye, may be an atheist, running against a Roman Catholic liberal. I say may be because there are some confusions over Park Geun-Hye’s religious identity. Her parents were Buddhist, she was baptized as a young woman as a Roman Catholic, and seems to have drawn without much discrimination from a variety of religious teachings to inform her world-view. It wouldn’t be shocking if Park Geun-Hye was an atheist. According to the World Values Survey ~25% of South Koreans are convinced atheists.

I was curious if atheists in South Korea leaned to the Left or the Right, and from what I can tell there’s no strong correlation. This may surprise Americans, but the historical experience of the two nations is very different. Until recently South Korea has had weak institutional religions, and a substantial portion of what we might term “progressives” were Christians, in particular Roman Catholics. Below are the results for the USA, Great Britain, Sweden, and South Korea for the World Values Survey using religious identification and political self positioning. Percentages and sample sizes are included.

 

N Religious person Not religious person Convinced atheist
Great Britain 854 49.90% 39.10% 11.10%
Left 30 40.00% 36.80% 23.20%
2 24 39.60% 36.40% 23.90%
3 70 40.30% 34.60% 25.10%
4 78 41.20% 48.70% 10.10%
5 340 50.20% 42.20% 7.60%
6 129 56.30% 38.30% 5.40%
7 80 48.40% 43.90% 7.60%
8 56 55.50% 28.40% 16.10%
9 23 59.70% 18.60% 21.70%
Right 24 70.80% 15.80% 13.30%
United States 1175 71.80% 24.70% 3.50%
Left 21 51.10% 33.70% 15.20%
2 18 67.90% 27.10% 5.00%
3 70 50.80% 41.00% 8.20%
4 96 62.80% 31.20% 6.00%
5 418 72.30% 26.60% 1.10%
6 233 71.10% 25.80% 3.10%
7 130 77.00% 16.90% 6.10%
8 104 82.90% 11.70% 5.40%
9 43 97.50% 2.50% -
Right 43 69.00% 31.00% -
Sweden 953 33.10% 49.70% 17.20%
Left 26 25.70% 49.20% 25.10%
2 36 26.80% 36.40% 36.70%
3 137 28.40% 54.10% 17.60%
4 132 27.30% 51.80% 20.90%
5 139 32.70% 51.20% 16.00%
6 109 42.50% 47.80% 9.60%
7 156 32.70% 49.00% 18.30%
8 149 32.50% 53.20% 14.30%
9 41 48.70% 39.50% 11.80%
Right 29 45.90% 37.50% 16.60%
South Korea 1195 30.10% 41.40% 28.60%
Left 18 17.00% 56.30% 26.70%
2 32 28.00% 31.70% 40.30%
3 148 41.70% 30.00% 28.30%
4 145 34.60% 37.20% 28.20%
5 245 22.10% 50.10% 27.90%
6 142 30.20% 40.20% 29.60%
7 169 26.00% 38.20% 35.80%
8 182 36.80% 39.80% 23.40%
9 62 27.20% 51.90% 20.90%
Right 54 20.40% 51.20% 28.30%



Buyer beware in ancestry testing!

Filed under: Personal genomics — Razib Khan @ 10:20 pm

Over at Genomes Unzipped Vincent Plagnol has put up a post, Exaggerations and errors in the promotion of genetic ancestry testing, which to my mind is an understated and soft-touch old-fashioned “fisking” of the pronouncements of a spokesperson for an outfit termed Britain’s DNA. The whole post is worth reading, but this is a very grave aspect of the response of the company:

…The main reason is that listening to this radio interview prompted my UCL colleagues David Balding and Mark Thomas to ask questions to the Britain’s DNA scientific team; the questions have not been satisfactorily answered. Instead, a threat of legal action was issued by solicitors for Mr Moffat. Any type of legal threat is an ominous sign for an academic debate. This motivated me to point out some of the incorrect, or at the very least exaggerated, statements made in this interview. Importantly, while I received comments from several people for this post, the opinion presented here is entirely mine and does not involve any of my colleagues at Genomes Unzipped.

From what I can gather this firm is charging two to three times more than 23andMe for state-of-the-art scientific genealogy, circa 2002. So if you can’t be bothered to read the piece, it looks like Britain’s DNA is threatening litigation for researchers having the temerity to point out that the firm is providing substandard services at above-market costs. Plagnol’s critique lays out point-by-point refutation of assertions, but the interpretation services on offer seem to resemble nothing more than genetically rooted epic fantasy. A triumph of marketing over science.


In other scientific genealogy news, a friend recent sent me results for his family from Ancestry.com’s AncestryDNA service. Looking at the pie-charts, I can say one thing: they were whack! But the question then is are they truly just whack, or does their peculiarity indicate real genetic insight? I have no way to judge, because they still aren’t providing raw data downloads, though they promise to soon. I actually talked to a scientist from Ancestry.com for a little while at ASHG 2012, and he claimed that they were tweaking the algorithms as as we were speaking. Nevertheless, bizarre results still seem to abound. It would be nie to figure out the method to this madness.

Finally, the genomic angle to the Dan MacArthur → Dan MacCurry saga is approaching closure. My friend Zack Ajmal promises to put up his analysis before he goes on vacation. I asked Zack to look into the matter because he has a very large database of South Asians, and I want to see if he could find the best match to Dan’s chromosome 10. If it does turn out that it is highly probable that Dan’s South Asian ancestry is Bengali, then I’ll have to make sure he’s introduced to the aloo bhorta which his ancestors no doubt relished (and which is unpalatable to people of other South Asian ethnic groups because of the mustard oil).

December 15, 2012

The Hobbit, part 1

Filed under: Culture,Hobbit — Razib Khan @ 2:48 pm

I went and saw The Hobbit: An Unexpected Journey yesterday with some friends. It’s been 20 years since I last read The Hobbit, and even longer since I watched the television film from the late 1970s. So I really didn’t notice all the differences between the three hour film and the original novel. Two quick comments:

1) I didn’t pick up on all the big technological changes. I suspect this is something movie reviewers are going to focus on, because they have such a good grasp of the technical element. But for the average person it’s not as obvious. Some of the 3D was well done, but much of it was a little excessive for me.

2) I wasn’t too bored, but a two hour film would have been more than sufficient. Someone behind me literally fell asleep, judging by the persistent snoring.

I’d give the film a B-. This wasn’t in Jar Jar Binks territory.

Merry Christmas, hold the Hanukkah?

Filed under: Religion — Razib Khan @ 2:02 pm

It’s that time of the year, and I quite like “the Holidays.” I am, of course, looking forward to my daughter’s first Christmas. Though no one in our family believes in the religious justification for the holiday, it is still an important time of the year, for reasons I have outlined before. But for the first time in 16 years I am going to a “Hanukkah party,” and my feelings about this are a little mixed. The reasons is that the more I heave learned about Hanukkah, the more I’ve become irritated by the fact that this minor Jewish holiday just happens to align well chronologically with Christmas. Most people are aware that as a religious matter for Jews Hanukkah bears no equivalence to what Christmas does for some Christians. But most non-Jews, and even many Jews, know little about the festival aside from the miracle of olive oil.


In The National Post David Frum highlights the salient aspects which concern many Jews. In short, Hanukkah is a  celebration of rebellion, violence, and realpolitik. There is no gain in reducing these ancient events into simple truisms, but a Jewish friend of mine expressed the heart of the matter when she stated that “in antiquity the Jews were al-Qaeda.” In relation to the Maccabee revolt one only needs to follow up on the broad outline of the Wikipedia entry. In a positive light one might frame the Maccabees as religious nationalists, but in a negative light they were reactionary chauvinists.

The story of the Maccabees is the first chapter in the ancient conflict between Jews who were ambivalent toward Hellenization,* and those who were unabashed synthesizers. The Maccabee response to those factions who wished to debase what they viewed as Judaism qua Judaism was to decapitate and disembowel them. The savagery and cultural intolerance of the Seclucid tyrant in this case seems to be easily explained by the rhetoric and behavior of the anti-Hellenists. When it comes to the old dichotomy between Athens or Jerusalem, I clearly sympathize with Athens. More broadly I think most modern Westerners would see their own world view much more in the Hellenists than their enemies, whose victory Hanukkah celebrates.

Ultimately this isn’t going to make me a grinch about Hanukkah. We don’t celebrate the real Hanukkah, we celebrate a Jewish holiday which happens to be near Christmas in timing, and so accommodate what we perceive to be legitimate sensitivities while a good time is had by all. And in an ironic twist the particular party I am attending is dominated by gentiles, with the only Jews present being those who are in relationships with gentiles. So I suppose in the end we make our reasons for this particular season.

* Though some Reform Jews claim to be heirs of Hellenistic Judaism, ultimately only the Pharisees who opposed the Hellenists maintained cultural continuity from that time down to the present. I say ambivalent because traditional Judaism itself has been influenced by Greek thought.

The G.O.P. as the white Christian party

Filed under: Politics — Razib Khan @ 1:13 pm

A few weeks ago I reiterated that the most parsimonious explanation for why Asian Americans have been shifting to the Democratic party over the past generation (George H. W. Bush won Asian Americans according to the 1992 exit polls) is a matter of identity politics (reiterated, because I noticed this years ago in the survey data). In short, since the 1950s a normative expectation that America was defined by its historic white Protestant majority has receded. The proportion of “Others,” non-whites, non-Christians, etc., has grown to the point that for all practical purposes these groups have found a secure home in the Democratic party, and the Democratic party has been able to benefit electorally from this support (this would not be the case in 1950, because not enough Americans were non-white or non-Christian). Naturally then the Republican party has become the locus of organization for white Christians, and more specifically white Protestants.

My rough argument is that identity is multifaceted and complex. In relation to the Republican party an evangelical Protestant Korean American Christian sees part of “themselves” in the party. A secular white New York banker from the Midwest who went to Northwestern University may also see themselves in the Republican party. The problem is that a Indian American Hindu cardiologist may have a difficult time emotionally connecting to the party, despite the clear economic rationale for such an affinity. The political scientist Andrew Gelman has argued that in fact it is the economic elites who vote on cultural issues, so it is not surprising that non-Christian Asian American business and professional elites feel alienated from a Republican party whose appeal is purely material and economic.

There may be  other more complex explanations, but the data seem sufficient to warrant this being a working hypothesis. I am now rather pleased to see that this viewpoint is gaining traction among some conservative movement types. Over at TownHall Jonah Golberg has a column up, The GOP — Not a Club For Christians. In the column he relates his own personal experience (as an identified Jew), and the opinions of two conservative Indian Americans (one a convert to Catholicism, and another now a well known Christian apologist and polemicist).

The aspect that needs to emphasized here is the matter of style. In my original posts I did not outline a prescription (contrary to what some who don’t bother to read posts that they characterize may think). Rather, I described the situation. As a matter of politics the broad outlines of the Republican and Democratic party seem inevitable, and it would be bizarre for the Republicans to try to reinvent themselves as something they are not. Rather, my suggestion is simply that the Republican party needs to soften the edges and be less sectarian. For better or worse the Republicans are not viewed as the white Christian party, but as the party of white evangelical Southern Protestants. Though this segment of the electorate is the core of the base, it is not sufficient for victory.

In the 1970s and 1980s the Democratic party for all practical purposes became defined by its McGovernite core; the secular liberals, ethnic minorities, and grab-bag of special interests. Bill Clinton and Al Gore, as white Southern Baptist males, were not sufficient to redefine the party, but they began a process of reinvention, and the perfection of a stylistic affect which manages to embrace just enough of the white suburban and moderate vote to produce a winning coalition. The irony here for the Republicans is that the party is notorious for giving the social conservative white evangelical wing nothing but rhetoric, all the while placating economic conservatives. But it is the symbolism of the former which is coming to define party, and narrow its base. A perhaps audacious ‘solution’ to this problem would be for the Republican party to actually follow through on the promises made to social conservatives, while shedding their explicit sectarian coloring.

Addendum: In response to the thesis above Steve Sailer has pointed out that the nominees were neither white Protestants in 2012. A quick response to that is that despite white male Southern Baptists being nominated in 1992 and 1996, everyone knew clearly who and what the Democratic party was. And it wasn’t the party of white Southern Protestants.

December 13, 2012

The spread of ‘white people problems’

Filed under: Culture,Future,Futurism — Razib Khan @ 10:21 am

Life Expectancy Rises Around the World, Study Finds:

A sharp decline in deaths from malnutrition and diseases like measles and tuberculosis has caused a shift in global mortality patterns over the past 20 years, according to a new report, with far more of the world’s population now living into old age and dying from diseases more associated with rich countries, like cancer and heart disease.

In the West declinism has set in, for legitimate reasons. But that doesn’t mean that things aren’t getting better in the rest of the world. They are. What irritates me is that some of my acquaintances who fancy themselves cosmopolitan internationalists nevertheless engage in declinism, despite their avowed concern for the well-being of humans as a whole. Yet their fixation on the decline in the relative status of their own societies, and their own status, reveals the transparent false signalling nature of their cosmopolitan internationalism.

Mind you, I think it is legitimate to worry about your own, and your society’s, position the relative order of things. But to constructively address this issue you need to not confuse your own station with that of the aggregate whole.

Population projections 50 years into the future are fantasy

Filed under: Demographics — Razib Khan @ 8:17 am

There’s another Census Projection out. Yes, I understand that the character of the children born today is going to have obvious impacts on the nature of the population 50 years from now, but we really need to heed the stupidity of past projections. Here’s a piece from 1930, A Nation of Elders in the Making:

To explain convincingly why we believe that we shall certainly not have more than 185,000,000 people here in 2000 A.D. and why we further believe that our population may cease to grow before that time, it is only necessary to make a rapid survey of our national trend of births and deaths….

For what it’s worth, the population of the USA in 2000 A.D. was ~280 million. The Baby Boom + massive immigration = revisions to projections.

We are Nature

Filed under: Genetics,Genomics,Human Genetics,Human Genomics — Razib Khan @ 8:03 am

There’s an interesting piece in Slate, The Great Schism in the Environmental Movement, which seems to be a distillation of trends which have been bubbling within the modern environmentalist movement for a generation now (I’ve read earlier manifestos in a similar vein). I can’t assess the magnitude of the shift, but here’s the top-line:

But that is a false construct that scientists and scholars have been demolishing the past few decades. Besides, there’s a growing scientific consensus that the contemporary human footprint—our cities, suburban sprawl, dams, agriculture, greenhouse gases, etc.—has so massively transformed the planet as to usher in a new geological epoch. It’s called the Anthropocene.

Modernist greens don’t dispute the ecological tumult associated with the Anthropocene. But this is the world as it is, they say, so we might as well reconcile the needs of people with the needs of nature. To this end, Kareiva advises conservationists to craft “a new vision of a planet in which nature—forests, wetlands, diverse species, and other ancient ecosystems—exists amid a wide variety of modern, human landscapes.”


Let’s take this debate as a given. It is fundamentally normative. That is, it is about values. We we need to tread carefully before projecting values across disputants. Far too often in this domain people seem to presume normative alignments, and therefore confuse ideological disagreement for rejection of factual truths. But, one thing to consider is that it is probable that human beings have already radically reshaped the ecological character of the world over the past 100,000 years. The implicit model that many older environmental activists seem to present is a framework pitting man & the machine vs. nature (the Shire vs. Mordor). But it is just not a useful dichotomy for many.

It is possible that there was, and is, no “pristine” nature. These disparate perspectives come to the fore in particular in post-colonial landscapes settled by Europeans. There is a long tradition in these areas of transforming ‘natives’ into ‘Noble Savages,’ who have attained some idealized harmony with Nature. The reality is that it is not harmony that was attained, but equilibrium. The arrival of anatomically modern humans to Australia and the New World resulted in a ‘shock’ to the ecological system, as megafauna went extinct due to the new variable of human predation. Even if H. sapiens were not the sufficient condition for these extinctions (populations naturally go through cycles), it is likely they were necessary (i.e., humans might extirpate species during times of low census size). But it is not just the initial impact in terms of species turnover. Australian and Amerindian populations seem to have reshaped the long term character of the landscape through fireCharles C. Mann argues in 1491 that  the vast forests which colonial and early American settlers cleared were in fact second growth, which emerged in the wake of massive die-offs of indigenous peoples due to Old World disease.

All of this is fundamentally complicated. Instead of a decision tree with two options, ‘Civilization’ vs. ‘Nature,’ there is actually a space populated with a multitude of positions. As someone touched by a moderate amount of biophilia my vision for the future is one of arcology based urbanism, massively scaled up algaculture, and megafaunal rewilding through genetic engineering and ancient DNA. Rather than idealize a mythic past we should endeavor to forge a new future. So it was, and so shall it ever be.

December 12, 2012

A lighter shade of brown: Dan MacArthur, look east or south!

Filed under: Genetics,Genomics,Human Genetics,Human Genomics — Razib Khan @ 2:58 pm

South Indian Udupi cuisine

In the post below I offered up my supposition that Dan MacArthur’s ancestry is unlikely to be Northwest Indian, which precludes a Romani origin for his South Asian ancestry. Indeed this is almost certainly so, Dienekes Pontikos followed up my crude analyses with IBD-sharing calculations (IBD = ‘identity by descent,’ which is basically what you would think it is). The South Asian population which MacArthur has the closest affinity to is from Karnataka, which is one of the Dravidian speaking states of the South. This does not necessarily refute my earlier contention, as aside from Brahmins most Bengalis seem to have broad South Indian affinities, except for the fact that they often have more East Asian ancestry.


Now, I may seem a touch obsessive on this issue at this point. There are several things motivating me. First, this was laying around in plain sight, but we missed it for years! Second, I’ve known Dan for a while, so this is very amusing on a personal level. Third, Dienekes’ has been pushing me to continue my exploration in a friendly competition. None of this is very difficult, and I’ve been going at it in the early hours of the day before work, or right before I go to sleep. In short, I’m doing this in part to show that you don’t need to just talk genomics, you too can do genomics. Ironically the age of “Big Data” is also the age of distributed data.

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