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

June 30, 2011

Pakistani genome

Filed under: Genetics — Razib Khan @ 9:28 am

Scientists map genome of first Pakistani man:

“Our nation is a mix of a lot of races,” said Prof. Dr M Iqbal Choudhary, who heads the project. “Pakistanis are like a “melting pot” ie a mix of Mughals, Turks, Pashtuns, Afghans, Arabs, etcetera.”

When will the first Jehovah’s Witness be sequenced?

Filed under: Anthroplogy,Genomics,Personal genomics — Razib Khan @ 9:13 am

An amusing article, Dr Atta-ur-Rehman, first Pakistani to have genome mapped:

Prof Dr M Iqbal Choudhary, Director International Centre for Chemical and Biological Sciences (ICCBS), Karachi University (KU), disclosed on Thursday that former Chairman, Higher Education Commission (HEC) Prof Dr Atta-ur-Rehman is the first Pakistani whose genome has been mapped by Pakistani scientists at a cost of $40,000 in just 10 months.

China has contributed $20,000 in the total cost of the genome project. Pakistani and Indian genomes have similarities compared to others, he said, while speaking at a press conference, held on Thursday at Dr Panjwani Center for Molecular Medicine & Drug Research (PCMD), Karachi University (KU).

“Dr Atta has become the first Muslim man with this distinction, while he is the third one among a list of renowned people in the world whose genomes have been mapped by scientists. The names of the first two persons are Prof Watson and Dr Ventor (2007), while others are unnamed.

First, yes, it’s not accurate that Dr. Choudhary is the third person with a full sequence done. In fact poking around it looks like that the total is high enough, > 100, that it isn’t easy to find a nearly-comprehensive list anymore. ...

June 29, 2011

Why hominin fossils matter

Filed under: Homo erectus,Human Evolution,paleontology — Razib Khan @ 11:57 pm

Yesterday Dienekes had a post up, Homo erectus soloensis fades into the past…. In it he states:

Every year or so there seems to be a redating of a key fossil in human evolution. It’s nice to see scientific self-correction in action, and soon after Neandertals got a little older, casting doubt on their supposedly long co-existence with modern humans, we now have a redating of Homo erectus soloensis from Java to about 150-550 thousand years ago, but certainly long before there were any anatomically modern humans in the area.

I think Dienekes is jumping the gun a bit in terms of the solidity of any given finding in knocking down prior consensus. That being said, the very young ages for Southeast Asian H. erectus, on the order of ~30-50,000 years B.P., always seemed strange to me. The paper Dienekes is referring to, The Age of the 20 Meter Solo River Terrace, Java, Indonesia and the Survival of Homo erectus in Asia, is rather technical in the earth science, as it involves dating and interpreting confounds in the stratigraphy. But this section of the discussion gets to the gist of the matter if you can’t follow the ...

Google+, not Wave or Buzz

Filed under: Facebook,Google,Technology — Razib Khan @ 10:33 pm

I’ve been playing around with Google+ a little today. Farhad Manjoo no like, More Like Google Minus:

… First, I don’t know whom the company thinks it’s kidding; Google+ is obviously a direct competitor to Facebook. Given the large overlap in functionality, I can’t imagine that many people will use Google+ and Facebook simultaneously. For most of us, it will be one or the other. Google+’s success, then, will rest in large part on Google’s ability to convince people to ditch Facebook for the new site. For that, Google+ will have to offer some compelling view of social networking that’s substantially different from what’s available on Facebook. And that’s where Google+ baffles me. What is so compelling about Google+ that I can’t currently get on Facebook or Twitter? Or Gmail, for that matter? At the moment, I can’t tell….

But circles are nothing new. Facebook has offered several ways to break your network into smaller chunks for many years now, and it has worked constantly to refine them. And you know what? Almost no one uses those features. Only 5 percent of Facebookers keep “Lists,” Facebook’s first attempt for people to categorize their friends. Recognizing that “Lists” weren’t great, last ...

No bookstores in Nashville?

Filed under: Books — Razib Khan @ 3:19 pm

That’s what Ann Patchett is claiming. More specifically, there are no bricks & mortar institutions which specialize in selling new books. There are places you can get used books in the city of Nashville. To remedy the situation Patchett is opening up a bookstore herself. She asserts that “…we’ve got to get back to a 3000-square-foot store and not 30,000. Amazon is always going to have everything – you can’t compete with that. But there is, I believe, still a place for a store where people read books.”

I recall going to a Barnes & Noble when I was in Nashville in the summer of 2004. Here’s some demographic data: “As of the 2010 census, the balance population was 601,222. The 2000 population was 545,524.” The details here are a bit muddy because parts of Davidson county are included with the Nashville total, but you get a general sense of how substantial the population of this city is. As a point of comparison Eugene, OR, has a population of 156,185, and 29 Yelp hits for bookstores. Nashville has 46 results.

Back to Patchett’s claim, I think there is something there. I don’t know how it’s ...

June 28, 2011

The punctuated equilibrium of culture

Filed under: Cultural Evolution,Culture,Punctuated Equilibrium — Razib Khan @ 11:32 pm

John Winthrop, ~1600. Mitt Romney, 2008 – image credit, Jessica Rinaldi

Recently Megan Mcardle had a post up where she expressed curiosity as to why “futurists” circa 1900 had a tendency not to imagine revolutions in clothing style which might have been anticipated to occur over the next few decades. You also see see this in Star Trek in the 1960s, where faux-future fashion was clearly based on the trends of the day, from the beehive hair to miniskirts. So I thought this comment was of interest:

I don’t know the answer, but I don’t know that they were wrong to do it. Keeping fashions exactly the same as the present generally winds up with more in common with the actual future than deliberate “future” fashions. A fair number of men still wear ties, and on rare occasions a few even wear tailcoats; rather fewer wear silver jumpsuits.

There have been a few counters to extreme fashions in media SF: “Blade Runner”‘s lead wore the same trenchcoat as his noir forebears; “Babylon 5″ went for modified business suits and moderate variations on military uniforms; the “Battlestar Galactica” ...

“What if you’re wrong” – haplogroup J

Back when this sort of thing was cutting edge mtDNA haplogroup J was a pretty big deal. This was the haplogroup often associated with the demic diffusion of Middle Eastern farmers into Europe. This was the “Jasmine” clade in Seven Daughters of Eve. A new paper in PLoS ONE makes an audacious claim: that J is not a lineage which underwent recent demographic expansion, but rather one which has been subject to a specific set of evolutionary dynamics which have skewed the interpretations due to a false “molecular clock” assumption. By this assumption, I mean that mtDNA, which is passed down in an unbroken chain from mother to daughter, is by and large neutral to forces like natural selection and subject to a constant mutational rate which can serve as a calibration clock to the last common ancestor between two different lineages. Additionally, mtDNA has a high mutational rate, so it accumulates lots of variation to sample, and, it is copious, so easy to extract. What’s not to like?

First, the paper, Mutation Rate Switch inside Eurasian Mitochondrial Haplogroups: Impact of Selection and Consequences for Dating Settlement in Europe:

R-lineage mitochondrial DNA represents over 90% of the European ...

South Asian genetics would be nowhere without Pakistan

Filed under: Genetics — Razib Khan @ 12:24 pm

It looks like there have been some changes in the South Asian samples in the 1000 Genomes Project. Earlier there had been a notification that they were trying to get obtain samples of Kayasthas from West Bengal, Marathas from Maharashtra, and Ahom from Assom. No more. Now you have Sri Lankan and Bangladesh populations. What went on? Judging by its past history the Indian biomedical bureaucracy probably made those projects unfeasible. So instead of those samples we have Bengalis from Bangladesh and Sri Lankan Sinhalese and Tamils in the UK. The Punjabis from Lahore are now out for collecting, so that we are probably guaranteed, even if the others fall through too.

What’s going on with Pakistan? You might notice that the Human Genome Diversity Project has Pakistani groups, but not Indian ones. That wasn’t because they didn’t want to get Indian populations, it just wasn’t ever doable, so that they had to settle for Pakistanis, who aren’t quite South Asian representative. But thank god for Pakistan when it comes to human genetics! And thank god for the Diaspora. At the current rate HAP might be the best we have for a while!

India shining & ignorant everyone!

Reify my genes!


In the comments below Antonio pointed me to this working paper, What Do DNA Ancestry Tests Reveal About Americans’ Identity? Examining Public Opinion on Race and Genomics. I am perhaps being a bit dull but I can’t figure where its latest version is found online (I stumbled upon what looks like another working paper version on one of the authors’ websites). Here’s the abstract:

Genomics research will soon have a deep impact on many aspects of our lives, but its political implications and associations remain undeveloped. Our broad goal in this research project is to analyze what Americans are learning about genomic science, and how they are responding to this new and potentially fraught technology.

We pursue that goal here by focusing on one arena of the genomics revolution — its relationship to racial and ethnic identity. Genomic ancestry testing may either blur racial boundaries by showing them to be indistinct or mixed, or reify racial boundaries by revealing ancestral homogeneity or pointing toward a particular geographic area or group as likely forebears. Some tests, or some contexts, may permit both outcomes. In parallel fashion, genomic information about race ...

June 27, 2011

‘Indianization’ in the first 1,000 years after Christ

Filed under: History — Razib Khan @ 10:16 pm

I am in the ‘Indian’ section of Strange Parallels and the author contends that Southeast Asian and South India were ‘Indianized’ at about the same time. By Indianized he means the suite of cultural characteristics which issued out of the Gangetic plain during the first millennium, after the Sangam period but before Mahmud of Ghanzi. Please note that the author is Burma specialist, but though I can’t discount this assertion at first blush, I have an urge to find it to be implausible. That is, I presume that there must be a deeper cultural connection between North and South India which predates the expansion of the Indic cultural zone to Southeast Asia, dating back to the Maurya Empire. What say you? I suspect my urge is rooted emotionally in the fact that India obvious coheres as a cultural whole today, and has since the rise of the Indo-Islamic societies, as well as my knowledge of the deep time genetic connections. But the latter doesn’t speak to connections and distinction which characterize Indic thought during the Axial Age.

First Farmers Facing the Ocean

The image above is adapted from the 2010 paper A Predominantly Neolithic Origin for European Paternal Lineages, and it shows the frequencies of Y chromosomal haplogroup R1b1b2 across Europe. As you can see as you approach the Atlantic the frequency converges upon ~100%. Interestingly the fraction of R1b1b2 is highest among populations such as the Basque and the Welsh. This was taken by some researchers in the late 1990s and early 2000s as evidence that the Welsh adopted a Celtic language, prior to which they spoke a dialect distantly related to Basque. Additionally, the assumption was that the Basques were the ur-Europeans. Descendants of the Paleolithic populations of the continent both biologically and culturally, so that the peculiar aspects of the Basque language were attributed by some to its ancient Stone Age origins.

As indicated by the title the above paper overturned such assumptions, and rather implied that the origin of R1b1b2 haplogroup was in the Near East, and associated with the expansion of Middle Eastern farmers from the eastern Mediterranean toward western Europe ~10,000 years ago. Instead of the high frequency of R1b1b2 being a confident peg for the ...

Changes to 1000 Genomes South Asians

Filed under: 1000 Genomes,Dataset — Razib Khan @ 11:53 am

Looks like there have been some changes to the populations in the 1000 Genomes:

At least we'll be able to answer questions about the origin of the Sinhalese soon enough. I'm a little bummed that the Indian populations in Maharashtra and West Bengal disappeared. Did the Permit Raj strike again?

Muslim Britons & the gays

Filed under: Culture,homosexuality — Razib Khan @ 10:57 am

Sunny Hundal states:

The poll marks a sharp contrast to findings by Gallup in 2009 that 0% of British Muslims were tolerant towards homosexuality. But the two results are not contradictory: Muslims can agree that Islam does not tolerate homosexuality, while celebrating gay rights enshrined in the law.

This is possible. But honestly it just doesn’t pass the smell test. This is a tenable position for very religious people, and the norm among inward looking sects derived from Anabaptism, in part because they believe that they are islands of virtue in a fallen world. But this is a minority position usually. Passionate religious views generally entail passionate espousal of policy prescriptions, whether you think it is good or ill. And Muslims as a whole have not been keen on the extreme church-state separationism which radical Protestant sects have advocated. I double checked in the World Values Survey, and 28 out of the 41 Muslims, 68%, agreed that homosexuality was “never justifiable,” as opposed to 25% of the general British population.

So what’s going on? I suspect that the poll is aggregating a host of divergent views and reactions. How many dollars/pounds are you will bet that non-religions Britons are more tepid toward gay rights as than the median British Muslim? I’m willing to be $250 dollars that this is not so. Rather, I suspect that some of the lukewarm responses are probably to those who on the far cultural Left who want much more radical sexual orientation anti-discrimination legislation passed, in particular in regards to marriage rights.

Via thabet’s twitter.

The impact of genetic ancestry testing

Filed under: Genome Blogging,Genomics — Razib Khan @ 12:07 am

Attitudes on DNA ancestry tests:

The DNA ancestry testing industry is more than a decade old, yet details about it remain a mystery: there remain no reliable, empirical data on the number, motivations, and attitudes of customers to date, the number of products available and their characteristics, or the industry customs and standard practices that have emerged in the absence of specific governmental regulations. Here, we provide preliminary data collected in 2009 through indirect and direct participant observation, namely blog post analysis, generalized survey analysis, and targeted survey analysis. The attitudes include the first available data on attitudes of those of individuals who have and have not had their own DNA ancestry tested as well as individuals who are members of DNA ancestry-related social networking groups. In a new and fluid landscape, the results highlight the need for empirical data to guide policy discussions and should be interpreted collectively as an invitation for additional investigation of (1) the opinions of individuals purchasing these tests, individuals obtaining these tests through research participation, and individuals not obtaining these tests; (2) the psychosocial and behavioral reactions of individuals obtaining their DNA ancestry information with attention given both to expectations prior to testing and ...

June 26, 2011

Heritability and genomics of facial characteristics

Filed under: Face genetics,Genetics,Genomics,Heritability,Human Genetics,Morphology — Razib Khan @ 11:49 pm

On several occasions I’ve gotten into discussions with geneticists about the possibility of reconstructing someone’s facial structure by genes alone. Combined with advances in pigmentation prediction by genetics, this could put the sketch artist out of business! But all that begs the question: how heritable are facial features anyhow? Impressionistically we know that feature are broadly heritable. This isn’t a tenuous supposition, you see the resemblance over and over across families. All that being said, what are the specific quantitative heritability estimates? How do they relate to other traits we’re interested in? This review from the early 1990s seems to have what I’m looking for, The Role of Genetics in Craniofacial Morphology and Growth. Below is a table which shows averaged heritabilities for a range of facial quantitative traits from a large number of studies:

h2 is the narrow-sense heritability. Also, in care you are curious cephalometry seems to be utilizing imaging of some sort. Anthropmetry refers to the more conventional measuring techniques (get out the calipers!). These results suggest that facial features are typically more heritable than behavioral traits (usually < 0.50), but less heritable than ...

The collapse of Myspace and its legacy

Filed under: Facebook,Myspace,Technology,Web 2.0 — Razib Khan @ 10:06 pm

BusinessWeek‘s The Rise and Inglorious Fall of Myspace is a compelling read. But a huge piece of the puzzle which I thought was omitted was that Myspace was incubated in the short term bottom-feeder world to begin with, so the later fixation on revenue now rather than a long term vision may simply have been part of its original DNA. See this Planet Money podcast, MySpace Was Born Of Total Ignorance. Also Porn And Spyware, for what I’m talking about. As it is in the BusinessWeek piece Chris DeWolfe just tries to blame News Corp. Remember that DeWolfe and Tom Anderson sold out to Rupert Murdoch, while Mark Zuckerberg was uninterested in an immediate cash windfall. As far as the long term impact of Myspace I notice that the Urban Dictionary entry for ‘myspace angle’ is still more fleshed out than ‘facebook angle’, so the word “myspace” might still get preserved in this manner. In this way Myspace may resemble the audio cassette, which is still haunting our culture as the “mixtape”. Not surprisingly some young people are totally unaware that the tape portion actually refers to ...

The different dynamics of memes vs. genes

Filed under: Anglo-Saxons,Celts,Culture,Demographics,Genetics,History — Razib Khan @ 9:28 pm

In my long post below, Celts to Anglo-Saxons, in light of updated assumptions, I had a “cartoon” demographic model in mind which I attempted to sketch out in words. But sometimes prose isn’t the best in terms of precision, and almost always lacks in economy.

In particular I wanted to emphasize how genes and memes may transmit differently, and, the importance of the steps of going between A to Z in determining the shape of things in the end state. To illustrate more clearly what I have in mind I thought it might be useful to put up a post with my cartoon model in charts and figures.

First, you start out with a large “source” population and a smaller “target” population. Genetically only the migration from the source to the target really has an effect, because the source is so huge that migration from the target is irrelevant. So we’ll be focusing on the impact upon the target of migration both genetically and culturally.

To simplify the model we’ll imagine a character, whether genetic or memetic, where the source and target are absolutely different at t = 0, or generation 1. ...

On the Raju affair

Filed under: Hermon Kaur Raju — Razib Khan @ 1:26 pm

Anna John has an interesting post up on Hermon K. Raju. One thing I would like to add: the transparent society is probably inevitable.

Geert Wilders and banning lying

Filed under: Culture,Europe,Multiculturalism — Razib Khan @ 12:55 pm

A few people have asked me about the Geert Wilders’ affair. If you don’t know Geert Wilders’ is a right-wing Dutch politician prone to making inflammatory remarks about Islam. He’s been brought to court on the grounds of whether his comments violated the speech laws in much of Europe, which sanction inciting or hateful speech.

The main issue as an American that one always has about these sort of things is that because of the First Amendment and the way it has been interpreted our social norms are such that in regards to speech we are exceedingly liberal. Prosecuting Wilders would not be an issue in the United States. Rather, it is much more likely that he’d be marginalized and ignored as a kook.

From my perspective the main problem with prosecutions for hate speech in relation to Islam and immigrants in Europe is that these attempts seem like banning lying; it’s a nominal and symbolic salve on the underlying diseases. Additionally, one must note that the attacks are focused on Muslim immigrants in particular, who from what I can tell have shown (in part) the greatest concerted collective resistance to becoming absorbed into the “European consensus,” as it has evolved.

Some of Wilders’ statements are so extreme and strange that I can’t but help believe that he’s working the Overton window. And from what I’ve read his strategy has worked, the whole center of gravity of public discourse has shifted in the Netherlands and much of Europe. The very fact that Wilders was acquitted is probably a reflection of this, as the enforcement of these laws often is a signal of public mood.

Overall I think there are several issues in Europe which must be addressed in the near future which are relevant to the rise of the right-wing sentiment:

- The likely unworkability of the European “super-state” because of cultural incompabilities

- The nature of employment regulation in Europe which discourages labor market mobility and fluidity

- The welfare state predicated on a common set of values affinity across lines of class and age not always compatible with a multicultural order

- The cultural insularity of many minority ethnic groups in Europe, especially Muslims, vis-a-vis the mainstream

And that’s the tip of the iceberg. The main problem is that because of the nature of politics many of these issues are neatly reduced into catchphrases. Muslim populations in Europe complaining of racism neatly neglect that black Africans who are not Muslim probably experience as much racism, but are not the locus of social unrest or panic, in part because they don’t pose a coherent challenge to Europe as it is. Anti-immigrant voices neglect the fact that even if all immigrants left tomorrow Europe would still be facing massive structural problems because of the reality of their demographics, as fewer and fewer young people are supporting large populations of economically inactive older pensioners.


Islam as perversion

Filed under: Culture — Razib Khan @ 12:28 pm

There are some actions which are alien, and frankly repugnant, in other societies. But there are other some actions which are simply obscene on the face of it, and the utilitarian or casuistical logic which justifies them are perverse and simply brook no comprehension beyond the fact that they take humans to their logical ends as a means to some greater purpose.

If this is true, this seems like a case in point, Afghan Girl Tricked Into Carrying Bomb, Officials Say:

Insurgents tricked an 8-year-old girl in a remote area of central Afghanistan into carrying a bomb wrapped in a cloth and then detonated the bomb remotely when she was close to a police vehicle, the Afghan authorities said Sunday.

Only the girl was killed in the blast, which occurred in Uwshi Village of Charchino District, said Fazal Ahmad Shirzad, the police chief of Uruzguan Province.

Mr. Shirzad said he believed that the girl was completely unaware that the bag that she had been given by Taliban insurgents held a bomb. The girl’s body was later “taken to a nearby security check post and the police called her relatives, “ he said.

Even if the authorities are lying and the girl knew what she was doing, if she was 8 years old I think it is reasonable to assert that she couldn’t truly consent to becoming a suicide bomber. She was too young.

In any case, I’m really sick of hearing conservative Muslims talk about how decadent and perverted the West is. This is decadence and perversion. Meanwhile, people are killing themselves for god knows what in Iraq.

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