When will the first Jehovah’s Witness be sequenced?

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. …

Why hominin fossils matter

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

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?

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 …

The punctuated equilibrium of culture

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

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 …

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

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.