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

February 28, 2010

We are still the world’s workshop

Filed under: Economics — Gene Expression @ 1:32 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

Filed under: Transhumanism — Razib @ 1:43 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….

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Singularity Institute Research Challenge

Filed under: Transhumanism — Gene Expression @ 1:40 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....

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Graphs lack mass appeal?

Filed under: Graphs,Humans are Stupid,Rational Misanthropy — Razib @ 12:41 am

Andrew Gelman, Red State, Blue State sales are a factor of 2^100 lower than they should’ve been:

In his forthcoming book, Albert-László Barabási writes, “There is a theorem in publishing that each graph halves a book’s audience.” If only someone had told me this two years ago!

More seriously, this tongue-in-cheek theorem, if true, defines an upsetting paradox. As we discussed at the beginning of the Notes section of Red State, Blue State, we structured the book around graphs because that seemed to be the best way to communicate our findings. Tables are not a serious way of conveying numerical information on the scale that we’re interested in, and, sure, we could’ve done it all in words (even saying things like “We ran a regression and it was statistically significant”), but we felt that this would not fully involve readers in our reasoning. The paradox–or maybe it’s not such a paradox at all–is that graphs are grabby, they engage the reader, but this makes reading the book a slower, more intense, and more difficult endeavor.

I recall hearing about the lack of appeal of equations, and their negative impact on book sales, but not graphs. Then again, I remember that the author of Calculated Exuberance was a bit perplexed when I enthused about his chart & graph heavy posts.

Here’s a chart from from a paper in Current Biology, The Evolution of Human Genetic and Phenotypic Variation in Africa:

All that information in prose would take up more time, and be way less precise.

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February 27, 2010

Pacific Biosciences: is the hype for real?

Filed under: Genetics — Gene Expression @ 11:57 pm

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.

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Quantitative genetics strikes back! (?)

Filed under: Evolution — Gene Expression @ 7:26 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

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Canada vs. USA

Filed under: Culture — Gene Expression @ 4:28 pm

It's on.

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February 26, 2010

Blacks aren’t that much more pro-life

Filed under: Politics — Gene Expression @ 7:46 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

Filed under: Culture — Gene Expression @ 5:27 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.

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February 25, 2010

Katz

Filed under: Blog — Gene Expression @ 10:39 pm
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Anthropology as a dog side-effect skill

Filed under: Cognitive Science — Gene Expression @ 1:36 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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Madoff to Morgan

Filed under: Culture — Gene Expression @ 1:29 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.

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Too many doctors!

Filed under: Culture — Gene Expression @ 9:37 am

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).

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

Filed under: Culture — Gene Expression @ 3:02 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).

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

Filed under: Culture — Gene Expression @ 12:20 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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February 24, 2010

The Hobbits Six Years On

Filed under: Flores,Hobbits,Human Evolution — Razib @ 11:36 pm

The Guardian has a long piece about the hobbits of Flores, and how they may have split from from the lineage which led to H. sapiens further back in time than had previously been assumed. In other words, where the hobbits had been theorized to have been a local adaptation of H. erectus, now the model is that they are the descendants of habilis or some other earlier hominin. In classic British style the article seems somewhat sensationalized to me, not to mention using terms that seem quaintly archaic, like “apemen.” I stopped paying attention to the hobbit stories after it seemed obvious that paleoanthropologists couldn’t agree on what they were. In other words, I’ve put it into a class similar to ALH 84001. What do readers think?

Note: Wasn’t too impressed with Mike Morwood’s book A New Human.

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Be safe and live long

Filed under: Environment — Gene Expression @ 10:57 pm

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

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Face recognition is highly heritable

Filed under: Cognitive Science — Gene Expression @ 4:42 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

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

Filed under: Genetics — Gene Expression @ 4:08 pm

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

Background
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.

Results
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.

Conclusions
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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Methodists are still Baptists who can read

Filed under: Denominations,Religion — Razib @ 2:50 pm

Income by Religions:

Good has a rather unwieldy graph showing religion by income. No surprises, with Jews first and Hindus second in percent with six figure incomes, and Jehovah’s Witnesses and black Protestant churches last. It would be interesting to know whether there are still affluence distinctions mainline white Protestants, such as Episcopalian v. Methodist.

On a national level, there are. Pew’s Religious Landscape Survey has detailed tables on educations, income, etc., broken down by denomination. Here’s a table I created (I left out historically black denominations). The values are percentages in each category, though the last column is a ratio:

Denomination < $30 K $30 – $49 K $50 – $74 K $75 – $99 K $100 K + Post-grad Liberal ($100 K income)/(Post-grad)
Episcopal 16 19 11 18 35 27 26 1.3
Presbyterian Church USA 16 19 19 18 28 24 16 1.17
United Methodist 23 21 19 16 22 14 14 1.57
Disciplines of Christ 31 14 21 14 20 17 12 1.18
Presbyterian Church in America (Evangelical) 34 20 16 12 18 13 14 1.38
United Church of Christ 27 20 21 14 18 21 21 0.86
Evangelical Lutheran 24 24 21 15 17 11 15 1.55
Lutheran, Missouri Synod (Evangelical) 24 20 20 18 17 9 12 1.89
Southern Baptist 30 25 19 11 15 7 10 2.14
Church of Christ 37 24 17 11 11 6 12 1.83
Independent Baptist 37 25 17 11 11 5 9 2.2
Seventh-Day Adventist 46 26 10 7 11 5 16 2.2
American Baptist 46 22 16 9 8 5 16 1.6
Assemblies of God 41 26 15 11 8 4 6 2
Total Population 31 22 17 13 18 11 20 1.64

I ordered by % with more than $100,000 per year income, except for the total American population, which is at the bottom. The relationship between education and income is pretty strong on a denominational level:

I was curious if there was a relationship between liberalism and being relatively poor in relation to educational attainment. The United Church of Christ stands out here. So here’s a plot:

This probably needs to be looked at in more detail, this was just a “quick & dirty.” Though it is striking to me how the 19th century truism of a social rank order of Episcopal > Presbyterian > Methodist > Baptists, seems to obtain in the early 21st century. Sensitivity to initial conditions.

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