Archive for March, 2012

We are all…Sardinians?

By Razib Khan | March 18, 2012 2:54 pm

The title is tongue in cheek. But I have been noting with interest Dienekes’ trial runs with TreeMix. With it he has discovered a very peculiar admixture event, at least as determined by the software. The results are below, with my clarifying labels:

Basically the software seems to be implying that there has been gene flow into the Yoruba of West Africa from from populations related to the Basque & Sardinians. The most plausible explanation for this would be that this migration event was ancient, so that later admixtures of European populations are not reflected. Whether you believe that the Basque/Sardinians are Neolithic or pre-Neolithic (i.e., that they derive from Holocene settlers, or derive from Paleolithic European substrate), it is probably true that they have a relatively long period of residence in Western Europe.

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MORE ABOUT: Human Evolution

Who is the decider of the good life?

By Razib Khan | March 18, 2012 2:21 pm

‘Ashley treatment’ on the rise amid concerns from disability rights groups:

A controversial procedure to limit the growth of severely disabled children to keep them forever small – which ignited a fiery debate about the limits of medical intervention when it was first revealed five years ago – has begun to spread among families in America, Europe and beyond.

Five years ago details first emerged of Ashley, a nine-year-old girl living near Seattle. She was born with developmental disabilities that meant she was unable to talk or walk, and continues to have the cognitive ability of an infant.

The core of the treatment was hormone therapy: high estrogen doses to bring forward the closure of the growth plates in her bones, which would in turn stop her growing. In addition, surgical interventions included removal of her nascent breast buds to avoid the discomfort of fully-formed breasts later in life, and a hysterectomy to avoid menstruation.


Silvia Yee, a lawyer with the Disability Rights Education & Defense Fund that is run jointly by disabled people themselves and parents of children with disabilities, said: “This is what we were fearing. It is becoming just one more choice on the menu of possibilities – a medical operation that will change a person’s life. Who has the right to decide to change an individual into a different entity?

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Mike Snyder profile in Science

By Razib Khan | March 17, 2012 11:27 pm

Examining His Own Body, Stanford Geneticist Stops Diabetes in Its Tracks:

Over a 14-month period, the molecular geneticist at Stanford University in Palo Alto, California, analyzed his blood 20 different times to pluck out a wide variety of biochemical data depicting the status of his body’s immune system, metabolism, and gene activity. In today’s issue ofCell, Snyder and a team of 40 other researchers present the results of this extraordinarily detailed look at his body, which they call an integrative personal omics profile (iPOP) because it combines cutting-edge scientific fields such as genomics (study of one’s DNA), metabolomics (study of metabolism), and proteomics (study of proteins). Instead of seeing a snapshot of the body taken during the typical visit to a doctor’s office, iPOP effectively offers an IMAX movie, which in Snyder’s case had the added drama of charting his response to two viral infections and the emergence of type 2 diabetes.

Hopefully in about 10 years this will be the norm, not cutting edge science.

CATEGORIZED UNDER: Personal Genomics
MORE ABOUT: Mike Snyder, Science

Cloning the mentat

By Razib Khan | March 17, 2012 10:28 pm

There’s news about the Woolly Mammoth cloning attempts again. This gets floated every few years, and nothing has come of it…yet. I assume with enough money and time invested it will come to fruition. And whoever invests their time and energy and gets a successful return will probably get really famous, really quickly. But I’ve recently been thinking of a more practical application of cloning: reproducing enormous numbers of individuals who are mostly replicates of John von Neumann.*

To get a sense of why, see this Steve Hsu post. You can read about how much of a genius von Neumann (he was a source for Dr. Strangelove), but his legend is even larger in the oral history of mathematical science. There are still individuals alive who knew von Neumann personally, and they continue to maintain the memory of his preternatural mind.

My argument for cloning von Neumann in large numbers has a practical rationale: the world needs genius to maintain complex human civilization. John von Neumann certainly qualifies as a genius. And we need more than one, as it is likely that there is a random element to the expression of his particular brilliance.

* von Neumann is buried in Princeton, so partially degraded DNA would have to be extracted from his grave. One can also utilize DNA from his daughter, who is still alive.


The Indonesian cline

By Razib Khan | March 11, 2012 2:34 pm

Dienekes has touched upon it in detail, so I don’t have much to add. Except for two points:

1) The ancestry cline here is not due to isolation-by-distance, but the expansion of the Austronesian population rather precipitously ~4,000 years ago. As Dienekes observed this was rather clear by non-genetic means; this is just icing on the cake.

2) There is evidence of an Austro-Asiatic substrate across maritime Southeast Asia. For whatever reason it seems that Austro-Asiatic speaking agriculturalists ceased their push east at the Wallace Line.

MORE ABOUT: Southeast Asia

Health insurance remains (and will remain) relevant

By Razib Khan | March 9, 2012 11:39 pm

How a $1,000 test could destroy the health-insurance industry:

As we sequence more genomes, mine more data, and conduct more studies, we’ll find a lot more of these connections. Eventually, genomic testing will be a powerful predictor of future illness. And it raises the potential that young people will get themselves tested and then purchase insurance based off the result. So those with a clean genomic result might go for a cheap catastrophic plan, while those with a high risk of developing pricey illnesses will opt for more comprehensive insurance.

The result would be, in insurance terms, an “adverse-selection death spiral,” as the healthy opt out of expensive insurance, the sick opt into it, and premiums spin out of control.

“For all of human history, humans have not had the readout of the software that makes them alive,” Larry Smarr, a member of the Complete Genomics scientific advisory board, told The New York Times. “Once you make the transition from a data poor to data rich environment, everything changes.”

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Barack Hussein Obama: Yankee & Cavalier

By Razib Khan | March 9, 2012 12:46 pm

I’ve mentioned before that though Barack H. Obama’s most salient ethnic identity is that of a black American, in many ways he far more resembles his “Yankee” maternal family (who raised him). By Yankee, I mean that I presumed that they were from the Yankee component of the Kansas population, with names like Emerson in the family lineage. Later the family settled in parts of Greater New England, the Pacific Northwest and Hawaii. Religiously they seem to have veered into conventional New England liberal denominations such as Unitarianism. And interestingly as an adult Barack H. Obama chose a black nationalist church which had an explicit connection with a liberal Protestant denomination with dominant roots in New England, the United Church of Christ. All this is not to say that there is a “Yankee conspiracy” on Obama’s maternal side. Rather, people have “folkways,” and are often unconsciously attracted to cultural forms and locales which have an air of familiarity.

But interestingly a regularly correspondent has uncovered that Obama’s maternal lineage, or more specifically his maternal grandfather’s paternal lineage, is more Yankee in cultural identity than genetics:

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MORE ABOUT: Barack Obama

Natural selection and dopamine receptor genes

By Razib Khan | March 9, 2012 6:50 am

Long time readers will be familiar with the large literature in behavior genetics/genomics and dopamine receptor genes. So with that, I point you to a paper exploring the patterns of variation and their relationship to possible natural selection, No Evidence for Strong Recent Positive Selection Favoring the 7 Repeat Allele of VNTR in the DRD4 Gene:

The human dopamine receptor D4 (DRD4) gene contains a 48-bp variable number of tandem repeat (VNTR) in exon 3, encoding the third intracellular loop of this dopamine receptor. The DRD4 7R allele, which seems to have a single origin, is commonly observed in various human populations and the nucleotide diversity of the DRD4 7R haplotype at the DRD4 locus is reduced compared to the most common DRD4 4R haplotype. Based on these observations, previous studies have hypothesized that positive selection has acted on the DRD4 7R allele. However, the degrees of linkage disequilibrium (LD) of the DRD4 7R allele with single nucleotide polymorphisms (SNPs) outside the DRD4 locus have not been evaluated. In this study, to re-examine the possibility of recent positive selection favoring the DRD4 7R allele, we genotyped HapMap subjects for DRD4 VNTR, and conducted several neutrality tests including long range haplotype test and iHS test based on the extended haplotype homozygosity. Our results indicated that LD of the DRD4 7R allele was not extended compared to SNP alleles with the similar frequency. Thus, we conclude that the DRD4 7R allele has not been subjected to strong recent positive selection.

In that vein, I also stumbled upon this paper recently, Contrasting signals of positive selection in genes involved in human skin-color variation from tests based on SNP scans and resequencing:

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CATEGORIZED UNDER: Genetics, Genomics
MORE ABOUT: Selection

Seeing Ötzi through our eyes

By Razib Khan | March 8, 2012 11:29 pm

Dienekes got his hands on Otzi’s genome finally, and decided to confirm some suspicions. In general no great surprise, though I think the number of SNPs he used (44,000) is a little on the low side for the questions he was asking. But the details here aren’t too relevant because all the available evidence points to the “Iceman” being affiliated with modern day Sardinians, of whom we know much more with many more markers.

In any case, he points out that if you run ADMIXTURE you tend to see that Sardinians, and to a lesser extent Basques, are lacking in some ancestral components. One phenomenon which is implied by this is that these populations which are less “cosmopolitan” may reflect more ancient patterns, when there was less admixture. I’ve indicated this myself when it comes to non-Muslim minorities in the Middle East. But one caution I would immediately make is that we are judging the variation of smaller populations by the yardstick of larger populations. Distinct and less numerous groups, such as Sardinians, may show less ancestral cosmopolitanism in part because the reference populations which could be used to adduce such a state no longer exist.

To give an extreme example the Onge of the Andaman Islanders often pop up as a very distinctive genetic component. But what if there were many more related populations in the data sets generating patterns of variation? We might see that the Onge themselves are composites! The idea I’m trying to get across is that we imagine the past was demographically pristine. But if it wasn’t, then our attempts to make inferences become all the more difficult.


Not just genomics: the creeping future

By Razib Khan | March 8, 2012 8:44 am

In 2007 Reihan Salam asked me when the $1,000 genome was going arrive. On paper, probably around this year, or early next. But as I’ve been suggesting it really isn’t that big of a deal (the sticker price isn’t real in any case, someone will want the publicity). Over at The Crux I try and do my own impersonation of Peter Diamandis. But I wanted to emphasize that genomics alone, ubiquitous as it will be, is not going to be the “real deal.” Rather, it has to be integrated into a much thicker and richer information environment plugged into more efficient analytic tools. Personal genomics is a visible manifestation of the likely revolution in the health information ecology which is possible just around the corner. As an example, Mike Snyder starts out with his genome in his presentations on the outlines of this nascent revolution, but probably the more important aspects have to do with fine-grained tracking of his biomarkers (which resulted in actionable information for him personally). Imagine a daily check-up instead of a six month check-up (or a minute by minute tracking system for the hypochondriacs out there).

With all that said, keep in mind the dynamic that Christina Agapakis highlights in The Crux. The hype around some technologies always results in them being 10-20 years into the future.* Artificial intelligence is probably a case of this, but less commented upon is the similar phenomenon in humanoid robotics. And yet it is easy to “problematize” the contention that robotics hasn’t yielded anything; I put the qualifier humanoid there precisely because my understanding is that robotics is more pervasive away from prying eyes than we might think. Genetic engineering probably hasn’t hit people as being a revolutionary technology, but it is, in the form of GMOs. There are many ways that we don’t live in the world of the Jetsons, but there are many ways that the Jetsons could not imagine our own world. We see the visions of the future through a dark mirror.

* Shiny unitards are always in the future it seems.

CATEGORIZED UNDER: Genetics, Genomics
MORE ABOUT: Futurism

Tigons, ligers, leguars, and jagupards, oh my!

By Razib Khan | March 7, 2012 11:39 pm

The recent publicity around the gorilla genome highlighted to me that eastern and western gorilla lineages seem to have diverged ~1 million years ago. In the process of trying to figure out hybridity I stumbled upon this matrix from Wikipedia on panthera hybrids:

Lion ♀ Tiger ♀ Jaguar ♀ Leopard ♀
Lion Mars symbol.svg Lion Liger Liguar Lipard
Tiger Mars symbol.svg Tigon Tiger Tiguar Tigard
Jaguar Mars symbol.svg Jaglion Jagger Jaguar Jagupard
Leopard Mars symbol.svg Leopon Dogla Leguar Leopard

The links will take you where you need to go. Unleash the 10 year old within!

Image credit: Wikipedia

CATEGORIZED UNDER: Genetics, Genomics
MORE ABOUT: Genetics, Genomics

Where the wild clines aren't

By Razib Khan | March 7, 2012 7:38 pm

In the recent ‘do human races’ exist controversy Nick Matzke’s post Continuous geographic structure is real, “discrete races” aren’t has become something of a touchstone (perhaps a post like Cosma Shalizi’s on I.Q. and heritability).* In the post Matzke emphasized the idea of clines, roughly a continuous gradient of genetic change over space. Fair enough. But in the map above I traced two linear transects. I would suggest that anyone who has a general understanding of the demographics of South-Central Eurasia would immediately anticipate that these transects would reveal a relatively sharp break in allele frequencies. True, there are intermediate populations between the two end points, in Nepal, and on the fringes of India’s northeastern states. But clearly about halfway through the southwest-northeast transect you’ll see a rapid shift in allele frequencies. The blue transect is different, insofar as the change occurs very near its eastern pole. In Bengal, 85% of the length of the transect from its western terminus, the populations will still be far closer genetically to those on the western pole than those just to the east!


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Beyond trees and European trees

By Razib Khan | March 7, 2012 6:59 pm

Submitted for your approval, a very important post and preprint from Dr. Joseph Pickrell, Identifying targets of natural selection in human and dog evolution. If you read the preprint there’s a lot of good stuff. Dienekes highlighted the most relevant aspect: representation of genetic relationships with phylogenetic trees mask the likely reality of gene flow and admixture. In the guts of the paper though Pickrell et al. use their framework to identify some novel patterns. For example, that Cambodians may be descended in small part from some basal Eurasian lineage (~15 percent), perhaps their equivalent of “Ancient South Indians”? Using ADMIXTURE and such it has long been evident that there’s something funny there. My own working assumption was that the relatives of “Ancient South Indians” could be found in Southeast Asia, though these results (preliminary as they are) might imply something even more interesting. Second, there is a tidbit which might lend support to the fans of the Solutrean model, or can be interpreted in that way (I suspect that it does not, but it could be spun in such a fashion).

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MORE ABOUT: Human Genetics

Google+ bombs

By Razib Khan | March 6, 2012 7:57 am

Google+ Lags Far Behind Facebook, Twitter and MySpace in Latest Study:

Google+ became the fastest growing social network within months of its debut last June, but a recent study casts doubt on whether most of its users are spending much time on the site.

According to ComScore, users spent an average of just 3.3 minutes on Google+ in the month of January, a decline from its recent figures and a tiny sliver of Facebook’s total.

I accept the argument of friends that G+ and Facebook are fundamentally different, and that Google’s aim here is not to replicate Facebook. But I also think that this is well short of what Google was intending for G+ at this stage; otherwise they would surely have quashed the media bubble and hyperbole which crested last summer. G+ is obviously much better than Buzz. But that’s a low bar.


Half of white liberals want less immigration

By Razib Khan | March 6, 2012 6:00 am

As I have mentioned elsewhere my espousal of conservatism at Moving Secularism Forward went well. Interestingly several people came up to me afterward and admitted a sympathy for the “conservative” position on immigration (i.e., restrictionism). The rationales were both environmentalist (population control types) and law & order. Just out of curiosity I wanted to see any possible changes in attitudes toward immigration for non-Hispanic whites by ideology and education since 2004, when the issue has become more polarized.

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CATEGORIZED UNDER: Politics, Uncategorized
MORE ABOUT: Immigration

Extraordinary claims require a lot of evidence

By Razib Khan | March 5, 2012 8:23 pm

Several people have emailed me about the Solutrean hypothesis. The trigger is the publication of Across Atlantic Ice: The Origin of America’s Clovis Culture. To my surprise this has received a lot of media attention. The Washington Post, io9, and The New Scientist. Granted, the coverage has been appropriately skeptical. But it still gets to the truth of it that all publicity is good publicity, and here I am talking about a model which I believe is pretty much bunk.

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Dream of the 1890s

By Razib Khan | March 5, 2012 2:49 pm

Reminds me of Greg Cochran’s idea of a Minoan themed restaurant. Eat as King Minos, served by hostesses in authentic dress.


Race: maybe it's agriculture

By Razib Khan | March 2, 2012 3:23 pm

I’m too busy to really blog today, but I thought of putting up a post, the gist of which was actually expressed in Ian’s comment below:

When I was younger, I thought of human races as archetypes, and the variation between them a product of mixing. I blame it on the fact that I read Coon when I was about 14. Still, as a (half)Indian, it’s hard to see reconcile the reality of a billion people in the subcontinent with models that try to classify people into 3-5 races. As I learned more biology, I came to the conclusion that human variation was clinal, and race was really an artefact of where you chose to sample along the continuum…as a plant ecologist, I think about things like that a lot. (I’m also somewhat skeptical of ecozones.)

Thanks to a number of convergent strands (of which Razib’s blogging has been a key element), I have come to a rather different conclusion. Race, in my opinion, is more a feature of agriculture than evolution.

Consider two possible models of race: Model 1, in which sharp distinctions existed before the Neolithic, and have been maintained and enhanced as certain groups adopted agriculture and displaced their hunter-gatherer neighbours; and Model 2, in which variation was clinal prior to the Neolithic, but that the immense demographic expansion of certain groups expanded THEIR specific points on the continuum, and brought them into contact (or nearly into contact) with other expansionist agriculturalists.

To me, the Model 2 seems more plausible than Model 1. Is that an argument against race? No, but it does suggest that races shouldn’t really be seen as “locally adapted optima” and rather, should be seen more as transient phenomena produced by historic contingency. Whether this means that race is “real” or not is, to me, a little beside the point. But I’m not convinced by Coyne’s argument that these differences represent the “accumulation of genetic differences between isolated populations”.

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