Archive for February, 2010

We are still the world's workshop

By Razib Khan | February 28, 2010 4:32 pm

And more productive. FiveThirtyEight has a nice meme-buster post, US Manufacturing Is Not Dead. This was known to me, but Tom Schaller has all the charts put together nice.
Here’s industrial output:
Industrial Production.JPG
The labor force engaged in producing durable goods:

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Singularity Institute Research Challenge

By Razib Khan | February 28, 2010 4:40 am

Ends today. Last Chance to Contribute to 2010 Singularity Research Challenge!:

Thanks to generous contributions by our donors, we are only $11,840 away from fulfilling our $100,000 goal for the 2010 Singularity Research Challenge. For every dollar you contribute to SIAI, another dollar is contributed by our matching donors, who have pledged to match all contributions made before February 28th up to $100,000. That means that this Sunday is your final chance to donate for maximum impact.

Since ~1/3 of readers of GNXP are sympathetic to transhumanism I thought it might be worthwhile to post this….


Pacific Biosciences: is the hype for real?

By Razib Khan | February 28, 2010 2:57 am

Check out Dr. Dan MacArthur’s assessment of the Pacific Biosciences presentation at the Advances in Genome Biology and Technology conference. Also check out Genetic Inferences take on AGBT (yes, they’re really original with catchy blog names at the Sanger Institute!). In any case, a friend of mine was raving about Pacific Biosciences a few months ago, so I assumed it would blow up soon.


Quantitative genetics strikes back! (?)

By Razib Khan | February 27, 2010 10:26 pm

The Genetics of Human Adaptation: Hard Sweeps, Soft Sweeps, and Polygenic Adaptation:

There has long been interest in understanding the genetic basis of human adaptation. To what extent are phenotypic differences among human populations driven by natural selection? With the recent arrival of large genome-wide data sets on human variation, there is now unprecedented opportunity for progress on this type of question. Several lines of evidence argue for an important role of positive selection in shaping human variation and differences among populations. These include studies of comparative morphology and physiology, as well as population genetic studies of candidate loci and genome-wide data. However, the data also suggest that it is unusual for strong selection to drive new mutations rapidly to fixation in particular populations (the ‘hard sweep’ model). We argue, instead, for alternatives to the hard sweep model: in particular, polygenic adaptation could allow rapid adaptation while not producing classical signatures of selective sweeps. We close by discussing some of the likely opportunities for progress in the field.

The whole review is well written & open access, so I would recommend just reading the whole thing. I would though add that obviously population and quantitative genetics complement each other because they approach the same phenomenon from opposite ends. Additionally, one of the major criticisms of Charles Darwin’s original work was its heavy reliance on domesticated lineages which had been subject to artificial selection on quantitative traits. I suspect in many ways humans are themselves “self-domesticated,” and the protean nature of the selection regimes shaped by rapidly changing culture makes it more likely than not that we adapt through tweaking standing genetic variation.
Citation: The Genetics of Human Adaptation: Hard Sweeps, Soft Sweeps, and Polygenic Adaptation, Pritchard, Jonathan K.; Pickrell, Joseph K.; Coop, Graham, doi:10.1016/j.cub.2009.11.055

CATEGORIZED UNDER: Evolution, Genetics

Canada vs. USA

By Razib Khan | February 27, 2010 7:28 pm

It’s on.


Blacks aren't that much more pro-life

By Razib Khan | February 26, 2010 10:46 pm

For a hot-button issue which is arguably the social lodestar for American culture-wars people make a lot of unfounded assertions and assumptions about abortion. For example, poking around the GSS data set it’s pretty evident that there isn’t a sex difference in regards to the legal status of abortion. What I have found is that there may be an intensity difference between men an women among the educated pro-choice segment of the population, which might give pro-choice women the impression that there is a general difference (as people tend to extrapolate inordinately from their social milieu).
What about race? One of the occasionally resurrected talking points from conservative Republicans is that black Americans should be targeted because their social values are more aligned with the Republican party. You do see some of this when it comes to gay marriage, though I judge the difference to be relatively modest. But a new story in The New York Times made me wonder about abortion, To Court Blacks, Foes of Abortion Make Racial Case:

For years the largely white staff of Georgia Right to Life, the state’s largest anti-abortion group, tried to tackle the disproportionately high number of black women who undergo abortions. But, staff members said, they found it difficult to make inroads with black audiences.
So in 2009, the group took money that it normally used for advertising a pregnancy hot line and hired a black woman, Catherine Davis, to be its minority outreach coordinator.
Ms. Davis traveled to black churches and colleges around the state, delivering the message that abortion is the primary tool in a decades-old conspiracy to kill off blacks.

The black abortion rate is eye-popping:

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USA beats Finland

By Razib Khan | February 26, 2010 8:27 pm

US routs Finland 6-1, will play for hockey gold. It’s really not even fair; this is a nation which was oppressed by Swedes for nearly a thousand years. I really hope those losers beat Slovakia so we can face them for the gold. Most of the time we don’t have to think about them, except in the areas of humor and hockey.



By Razib Khan | February 26, 2010 1:39 am

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Anthropology as a dog side-effect skill

By Razib Khan | February 25, 2010 4:36 pm

Social Cognition in Dogs, or How did Fido get so smart?. This you know:

Domesticated dogs seem to have an uncanny ability to understand human communicative gestures. If you point to something the dog zeroes in on the object or location you’re pointing to (whether it’s a toy, or food, or to get his in-need-of-a-bath butt off your damn bed and back onto his damn bed). Put another way, if your attention is on something, or if your attention is directed to somewhere, dogs seem to be able to turn their attention onto that thing or location as well.
Amazingly, dogs seem to be better at this than primates (including our nearest cousins, the chimpanzees) and better than their nearest cousins, wild wolves.

But there are two explanations for how/why dogs are better than primates at this task:

And so it was that biological anthropologist Brian Hare, director of the of Duke University Canine Cognition Center wondered: did dogs get so smart because of direct selection for this ability during the domestication of dogs, or did this apparent intelligence evolve, in a sense, by accident, because of selection against fear and aggression?

I didn’t even consider that it would be anything except for direct selection. In any case, read the whole post for a run-down of the paper, but here’s the blogger’s conclusion:

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CATEGORIZED UNDER: Cognitive Science

Madoff to Morgan

By Razib Khan | February 25, 2010 4:29 pm

Citing shame, danger, one Madoff seeks name change:

Stephanie Madoff, who is married to Madoff’s son Mark, has asked New York Supreme Court for permission to change her last name to Morgan and also, according to local media reports, made similar requests for her two young children.


Too many doctors!

By Razib Khan | February 25, 2010 12:37 pm

Mike the Mad Biologist has a post up, Yes, We Have a PhD Glut… Which is interesting, because it isn’t has if getting a doctorate is financially lucrative. Though getting a medical doctorate is financially lucrative. Perhaps the medical profession has the right idea, control labor supply?* Right idea for medical doctors at least….
* At least the medical profession hasn’t opened the floodgate and enabled the overproduction of those with MDs who will never practice the profession and so be saddled with a lot of debt, which is the case with the legal profession (and for those who do pass the bar and enter into the legal profession, there’s a two-tiered pay scale).


Why we need to avoid Middle Eastern entanglements: too complicated!

By Razib Khan | February 25, 2010 6:02 am

The New York Times has an article attempting to clarify complex political tensions cross-linked with religious identity (or not), In an Iraqi City, the Real Ballot Contest Is for Shiite Leadership. The author, Anthony Shadid, states:

The contest bears down on one of the unanswered questions in Iraq’s tortured narrative of invasion, occupation, war and recovery. The country today stands as the only Arab state in which Shiite Muslims rule. Nasiriya is a stage, rendered small, where several Shiite currents, from street movements to venerable parties, are now vying for ascendancy.

That’s not really true. The Alawites of Syria dominate that Sunni-majority nation arguably with as tight a fist as the Sunni Arabs dominated Baath-era Iraq, or the Sunni royal family of Bahrain dominates that island nation. The Alawites are Shia, or at least identify as such. They’ve long had a tacit alliance with Iran, and the Iranian regime’s lack of support for the Sunni Islamists of Hama, who were massacred by Hafez Assad’s army in 1982, reputedly had a lot to do with Sunni rejection of Iran as a leader for worldwide Islamic revivalism. Throughout the 1980s Baathist Syria was aligned against Baathist Iraq during the Iran-Iraq War, in keeping with Syria’s traditional pro-Iranian tilt (Syria also is a secondary patron of Hezbollah).
In any case, this is all relatively academic, except for the fact that Syria borders on Iraq, has millions of Iraqi refugees, and likely served as a base for Iraqi insurgents. How does the fact that Syria is dominated by a heterdox Shia sect which rules a Sunni majority influence its relationship to Iraq? That’s for you to explore. I just think it is worth pointing out this error, because if The New York Times can get basic facts retrievable from Wikipedia wrong how much should you trust it when it comes to the political dynamics of an obscure Iraqi city?*
* Vali Nasr’s The Shia Revival: How Conflicts within Islam Will Shape the Future is worth reading, as he outlines the network of Shia religious movements which span Iran to Lebanon, and now have come into stark relief with the emergence of a “Shia arc” of Iran, Iraq, Syria (Shia dominated) and Lebanon (Hezbollah becoming operational king-makers).


Liberals & atheists are smarter than conservatives & very religious, but why?

By Razib Khan | February 25, 2010 3:20 am

Why Liberals and Atheists Are More Intelligent:

The origin of values and preferences is an unresolved theoretical question in behavioral and social sciences. The Savanna-IQ Interaction Hypothesis, derived from the Savanna Principle and a theory of the evolution of general intelligence, suggests that more intelligent individuals may be more likely to acquire and espouse evolutionarily novel values and preferences (such as liberalism and atheism and, for men, sexual exclusivity) than less intelligent individuals, but that general intelligence may have no effect on the acquisition and espousal of evolutionarily familiar values (for children, marriage, family, and friends). The analyses of the National Longitudinal Study of Adolescent Health (Study 1) and the General Social Surveys (Study 2) show that adolescent and adult intelligence significantly increases adult liberalism, atheism, and men’s (but not women’s) value on sexual exclusivity.

I don’t have access to the paper, but ScienceDaily reports the values. For the NLSY, which surveys teens:
Very liberal IQ = 106
Very conservative IQ = 95
Atheist IQ = 103
Very religious IQ = 97

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CATEGORIZED UNDER: Culture, Psychology

Be safe and live long

By Razib Khan | February 25, 2010 1:57 am

Arboreality has allowed for the evolution of increased longevity in mammals:

The evolutionary theory of aging predicts that species will experience delayed senescence and increased longevity when rates of extrinsic mortality are reduced. It has long been recognized that birds and bats are characterized by lower rates of extrinsic mortality and greater longevities than nonvolant endotherms, presumably because flight reduces exposure to terrestrial predators, disease, and environmental hazards. Like flight, arboreality may act to reduce extrinsic mortality, delay senescence, and increase longevity and has been suggested as an explanation for the long lifespans of primates. However, this hypothesis has yet to be tested in mammals in general. We analyze a large dataset of mammalian longevity records to test whether arboreal mammals are characterized by greater longevities than terrestrial mammals. Here, we show that arboreal mammals are longer lived than terrestrial mammals at common body sizes, independent of phylogeny. Subclade analyses demonstrate that this trend holds true in nearly every mammalian subgroup, with two notable exceptions–metatherians (marsupials) and euarchontans (primates and their close relatives). These subgroups are unique in that each has experienced a long and persistent arboreal evolutionary history, with subsequent transitions to terrestriality occurring multiple times within each group. In all other clades examined, terrestriality appears to be the primitive condition, and species that become arboreal tend to experience increased longevity, often independently in multiple lineages within each clade. Adoption of an arboreal lifestyle may have allowed for increased longevity in these lineages and in primates in general. Overall, these results confirm the fundamental predictions of the evolutionary theory of aging.

The same logic probably explains the long lifespans of tortises. Until humans showed up their shells were pretty good at insulating them from the risks of predation.
Citation: Milena R. Shattuck and Scott A. Williams, Arboreality has allowed for the evolution of increased longevity in mammals, doi:10.1073/pnas.0911439107

CATEGORIZED UNDER: Environment, Evolution

Face recognition is highly heritable

By Razib Khan | February 24, 2010 7:42 pm

Human face recognition ability is specific and highly heritable:

Compared with notable successes in the genetics of basic sensory transduction, progress on the genetics of higher level perception and cognition has been limited. We propose that investigating specific cognitive abilities with well-defined neural substrates, such as face recognition, may yield additional insights. In a twin study of face recognition, we found that the correlation of scores between monozygotic twins (0.70) was more than double the dizygotic twin correlation (0.29), evidence for a high genetic contribution to face recognition ability. Low correlations between face recognition scores and visual and verbal recognition scores indicate that both face recognition ability itself and its genetic basis are largely attributable to face-specific mechanisms. The present results therefore identify an unusual phenomenon: a highly specific cognitive ability that is highly heritable. Our results establish a clear genetic basis for face recognition, opening this intensively studied and socially advantageous cognitive trait to genetic investigation.

In other words, the strength of face recognition does not seem to track other intelligence test results much at all (including tests which measure verbal and visual memory). Rather, it seems to be a domain-specific competency, rather than emerging out of general intelligence. And, the variation in face recognition ability is highly heritable.
What’s going on here? A reasonable guess for me is that the ability to recognize many, many, different faces isn’t something that came up for most of human history. Even in a pre-modern village you’d see the same people over and over. By contrast, if you work in sales you probably need to juggle a lot of faces & names to be successful.
Remember that if a quantitative trait is highly heritable then by definition that means that directional selection wasn’t operating to drive genes to fixation so that the population was monomorphic in trait value. In English that means if there was a huge benefit to being able to recognize hundreds of faces very well in the past, then we would be able to recognize hundreds of faces very well to the same extent. As it is the strongly for face recognition has to be more complex, with the direct selection applicable being some sort of balancing selection.
Citation: Jeremy B. Wilmer, Laura Germine, Christopher F. Chabris, Garga Chatterjee, Mark Williams, Eric Loken, Ken Nakayama, and Bradley Duchaine, Human face recognition ability is specific and highly heritable, doi:10.1073/pnas.0913053107

CATEGORIZED UNDER: Cognitive Science

They really do hate us: "small dog" haplotype from the Middle East

By Razib Khan | February 24, 2010 7:08 pm

pekingese_burgess.pngThe IGF1 small dog haplotype is derived from Middle Eastern gray wolves:

A selective sweep containing the insulin-like growth factor 1 (IGF1) gene is associated with size variation in domestic dogs. Intron 2 of IGF1 contains a SINE element and single nucleotide polymorphism (SNP) found in all small dog breeds that is almost entirely absent from large breeds. In this study, we surveyed a large sample of grey wolf populations to better understand the ancestral pattern of variation at IGF1 with a particular focus on the distribution of the small dog haplotype and its relationship to the origin of the dog.
We present DNA sequence data that confirms the absence of the derived small SNP allele in the intron 2 region of IGF1 in a large sample of grey wolves and further establishes the absence of a small dog associated SINE element in all wild canids and most large dog breeds. Grey wolf haplotypes from the Middle East have higher nucleotide diversity suggesting an origin there. Additionally, PCA and phylogenetic analyses suggests a closer kinship of the small domestic dog IGF1 haplotype with those from Middle Eastern grey wolves.
The absence of both the SINE element and SNP allele in grey wolves suggests that the mutation for small body size post-dates the domestication of dogs. However, because all small dogs possess these diagnostic mutations, the mutations likely arose early in the history of domestic dogs. Our results show that the small dog haplotype is closely related to those in Middle Eastern wolves and is consistent with an ancient origin of the small dog haplotype there. Thus, in concordance with past archeological studies, our molecular analysis is consistent with the early evolution of small size in dogs from the Middle East.

If you read The Origin of Species you know that the origin of the domestic dog has long been of interest to biologists. Charles Darwin leaned toward the proposition that modern dog breeds derive from a wide range of canids, but the more recent genetic work seems to imply one domestication from gray wolves, though the details are still to be worked out. Interest in the evolutionary history of dogs is not just academic, as a medium-sized mammal with a wide phenotypic range and a likely recent radiation, dogs are looked to as a possibly fruitful animal model in exploring the relationships of human diseases and genes.
This paper notes that though recent genomic work utilizing mtDNA pinpoints the origin of domestic dogs to East Asia, this does not comport with the archaeological evidence. Though the preponderance of evidence seems to lean toward a single-origin model, there may be detailed nuances due to the interfertility of domestic dogs and gray wolves which will always complicate the picture (it is a matter of debate whether dogs are really just a morph of wolves, or a separate species altogether). In this paper the authors focused on a major phenotypic difference among dogs, size, and its localization in terms of genetic control to a QTL which overlaps with the IGF1 locus (insulin-like growth factor). It doesn’t look like they know exactly what’s going on here around IGF1 (e.g., what exact SNP is doing exactly what in a molecular genetic sense to produce variation in dog size), but, they do conclude that:

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CATEGORIZED UNDER: Evolution, Genetics

Lars von Trier wants you to visit Denmark

By Razib Khan | February 24, 2010 4:49 am

Denmark Introduces Harrowing New Tourism Ads Directed By Lars Von Trier
I think “Karen the single mom” ad does a better job of selling Denmark:

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The other half of the Inner Asian pendulum

By Razib Khan | February 24, 2010 4:33 am

A few months ago I read Empires of the Silk Road, where the author makes the argument that contrary to the common perception of Inner Asians as uncouth barbarians who were inimical to civilization as we understand it, in fact these populations were critical to the emergence of particular civilized values, as well as their role as facilitators of the spread of particular ideas and technologies. The latter is addressed in a somewhat overly enthusiastic fashion in Genghis Khan and the Making of the Modern World, but the point seems to be robust. The transmission of chariots and horse culture to China and the civilizations of the ancient Near East seems to have been a function of mobile populations expanding out of the western margins of the Inner Asian plain. Religions such as Buddhism, Christianity and Islam were spread by the cultural networks of Inner Asians. This explains how a substantial number of Mongol tribesmen in Genghis Khan’s armies were Nestorian Christians, while Buddhism’s arrival in China nearly 2,000 years ago almost certainly was facilitated by Inner Asian traders and warriors.
But in the historical era there is a peculiar bias in our perceptions. The Huns, and later the Avars, Magyars and Bulgars are all instances of populations which emigrated from the zone between the lower Volga and Mongola into the heart of Europe. The Turks made an impact on a huge swath of the Ecumene, from India through the world of Islam, to southeastern Europe, and all the way into the heart of what is now European Russia! The Mongols exploded out from their heartlands and came near to conquering all of Eurasia, while only the farthest reaches of western Europe and southern India escaping their threats.
Notice a pattern? These are east-to-west movements. Until the expansion of the Russians into Siberia there was no historical record of an intrusion of west Eurasian populations analogous to what occurred in Hungary, Bulgaria or Anatolia. The Arabs and the Persians never made it beyond Transoxiana. In contrast there were multiple leap-frogs from east to west. One explanation is that over the past 2,000 years China has been a robust political entity. The rise of barbarian confederacies led by populations with roots in eastern Inner Asia, the Huns and Avars, in central Europe, date to the period of the decline of Roman hegemony.
But this is not the only story. There is the other half of the swing of the historical pendulum, when western barbarians pushed to the east. That movement is obscured because it occurred on the margins of, and prior to, history. In The Horse, the Wheel, and Language: How Bronze-Age Riders from the Eurasian Steppes Shaped the Modern World much of the argument rests on archaeology, in contrast to Empires of the Silk Road, which utilizes philology and conventional historical records. The former book focuses on the west-to-east swing, which the author asserts is correlated with the expansion of Indo-European speaking populations.
That there needs something to be explained is evident when one glances at a map of the distribution of Indo-European langauges. We don’t have a historical record of what was going on here; unlike in the case of the spread of Turkic or Arabic. But that’s unfortunate because the expansion had a bigger linguistic impact. Something big happened, but we don’t really know much about it. And we don’t think about it. This is why the fact that the Tarim mummies seem to be of west Eurasian provenance is always of interest, it goes against our expectations. But those expectations sample only the historical record, one half of the swing of the pendulum.

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Amy Bishop's husband, creepy dude

By Razib Khan | February 24, 2010 3:56 am

Papers Link Husband of Professor to ’93 Threat:

The husband of the neuroscientist accused of killing three colleagues at the University of Alabama in Huntsville told a witness he wanted to harm a Harvard professor who was later mailed a pipe bomb in 1993, according to newly released federal documents.
James Anderson Jr., the husband of Amy Bishop, wanted to “shoot,” “stab” or “strangle” the professor, Paul Rosenberg, according to documents released Tuesday by the Bureau of Alcohol, Tobacco, Firearms and Explosives.
Dr. Bishop had worked for Dr. Rosenberg in the neurobiology lab of Children’s Hospital in Boston, but resigned because Dr. Rosenberg felt that she “could not meet the standards required for the work,” according to the documents, first reported by The Boston Globe. Dr. Bishop was “reportedly upset” and “on the verge of a nervous breakdown,” according to the documents, which cited interviews with witnesses.


Evolution, genetics & behavior

By Razib Khan | February 23, 2010 7:17 am

Two posts for your consideration.
On the Less Wrong weblog, Babies and Bunnies: A Caution About Evo-Psych. I am not one to make blanket dismissals of “evolutionary psychology.” But, there are structural problems with the strong incentives toward generating hypotheses at the equipoise of novelty and intuitive plausibility. In other words, much of the evo-psych which penetrates the broader public mindspace is driven by demand-side forces.
Over at EconLog Bryan Caplan has a post, Born Gay, where the newly famous Ryan Sorba is shown to be pretty close to a total behavior genetics denialist. Until they find the “gay gene” Sorba & company will reject the behavior genetics findings. Unfortunately, if the “gay gene” hasn’t been found yet, we might have to a wait a while (i.e., probably not a common variant of large effect). It would be nice to do a survey of the rejection of specific behavior genetic results as a function of ideological differences. The is-ought problem doesn’t seem to be a problem for most people; it seems a background assumption, so that what is is actually back-derived from what ought to be.


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