Archive for January, 2010

Bonus Katz

By Razib Khan | January 31, 2010 11:09 am

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The business cycle, then and now

By Razib Khan | January 30, 2010 4:31 pm

Two interesting graphs from Calculated Risk. The first shows that the changes in GDP seem during the last recessive are on a par with those of the early 1980s and before (though we don’t know if we’re in a U or V shaped recession yet, though the odds are probably more U than V right now). But the second shows that in terms of employment we may be in uncharted territory, the worst of both worlds in terms of the jobless recoveries of the shallow recessions of the 1990s and early 2000s as well as the deep declines in employment of earlier recessions.
I’ve been hearing about the soon-to-come structural realignments in the economy resulting in a higher basal rate of unemployment for nearly 20 years. Economists will of course scoff at this sort of fatalism, pointing out such prognostications have always been falsified in the past. We’ll see….

CATEGORIZED UNDER: Culture, Economics

Asia, land of the godless & godly

By Razib Khan | January 30, 2010 5:57 am

A comment below prompted me to slap together a post quickly displaying some data which illustrates just how religious South Asians are compared to East Asians. Anyone with an interest in world history will not be surprised by this assertion. When reading surveys of East Asian history I would occasionally reach a chapter titled “Religion,” and the author would offer a quick explanation and apologia for why the topic was not given pride of place. By contrast, some have argued to a first approximation South Asian history is a history of South Asian religion. (Though I do not focus on that issue in this post, the “Islamic world” is strongly defined by religious identity as well)
But how about the Diaspora communities? Where I have seen data the patterns seem to recapitulate themselves, more or less. Singapore, Canada and the United Kingdom collect data broken down both by religion and ethnicity. The United States has surveys performed by academic institutions, but unlike a national census the sample sizes are modest enough that I would not trust them much when it comes to very small minorities. Finally, I can use the World Values Survey to look at religious attitudes in the “homelands.”
First, Canada:

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Financial stress correlated within families

By Razib Khan | January 29, 2010 8:26 pm

Jobless Turn to Family for Help, Often With Complications:

More than half of the respondents to a recent New York Times/CBS News poll of 708 unemployed adults nationwide said they had borrowed money from friends or relatives. In most cases, their financial pictures were bleak. Nearly 80 percent of those who reported borrowing money said their family’s financial situation was “fairly bad” or “very bad,” a significantly greater proportion than among those who had not had to borrow.

The numbers here might exaggerate the effect some, as an individual who is going through financial turmoil may assess the world more darkly than one who isn’t. That being said, it is pretty obvious that income is not randomly distributed across familial networks, and those with resources who are less likely to require aid are actually the ones who will have family in a position to offer it if needful. By contrast, those on the margins are the most likely to have family on the margins.
In pre-modern societies this likely explains how inequality across lineages becomes amplified. Families with more buffer on the margin are less likely to become dispossessed through inclement shocks, and can use their surplus to acquire the property of those lineages which have become impoverished.
This is why economic growth and gains in productivity are essential. In a Malthusian world the way that a high tension state of high inequality eventually “corrected” itself was for massive institutional collapse and general chaos to level the playing field. Of course, the playing field was far more barbarous than it had been previously, so there was probably a trade off between cultural creativity and equality.

CATEGORIZED UNDER: Culture, Economics


By Razib Khan | January 29, 2010 4:42 pm

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Reflections on The Jihadist Next Door

By Razib Khan | January 28, 2010 4:41 pm

The New York Times Magazine has a long profile of an American from Alabama, Omar Hammami, who is now fighting for the Islamists in Somalia, The Jihadist Next Door. The optics of his family background seem tailor-made for a compelling narrative (or a TV-movie). A father who is a Syrian immigrant, a standard-issue American Muslim and professional. A mother who is a Southern Baptist and native Alabaman. The childhood is framed as “torn-between-two-worlds.” Both his parents were members of exclusive religious traditions. Apparently Omar’s was raised in both his parents’ religions, and both sides of the family held views whereby unbelievers would be consigned to hell. This is what you might term an unstable equilibrium.

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Review of the Hobbit paper

By Razib Khan | January 28, 2010 3:41 pm

Excellent one at A Primate of Modern Aspect:

Okay, so we’ve got lots of increases in brain size, and a few decreases. In the cases where we have decreases, we usually have body size decreases as well. More often than not, we have body size decreases which result in a disproportionately large brain size, but occasionally we have a body size increase which results in a disproportionately small brain size. And all of that brings us to the Hobbit.
The authors looked at Homo floresiensis in relation to the Dmanisi hominids, Homo habilis, and a Homo erectus from Ngangdong and found that if we use Dmanisi or habilis as an ancestor, the decrease in brain size and body size isn’t exceptionally weird when compared to other primate groups. The mouse lemur decreased in both to a greater degree, for example.
But if you use the Ngangdong erectus as the ancestor, it is a really weird decrease.
So, I guess the question is, is it reasonable to use Dmanisi or Homo habilis as the ancestor and not Homo erectus? And of course, we don’t know that yet!


Question about Google Chrome Extensions

By Razib Khan | January 28, 2010 4:43 am

I’ve got a few installed now. Has anyone had any issues with performance yet? I recall back when I used Firefox that was the main downside of having extensions.
If you don’t know what I’m talking about, see TechCrunch. Or just update your browser and Google will start telling you all about it, in Settings -> About Google Chrome.


The thorium revival

By Razib Khan | January 28, 2010 3:37 am

Mike the Mad Biologist points me to an interesting article in Wired, Uranium Is So Last Century — Enter Thorium, the New Green Nuke. Of course Wired is a booster of many things which never take off, but in general I think it’s probably safe to bet on nuclear power becoming more prominent in the near-to-medium-future. I recently have been reading a bit about oil, stuff that’s not written by Daniel Yergen, and was fascinated by this chart of long term crude prices:
The inflation adjusted values are of interest. But look at the lack of volatility before 1974! My whole life has been characterized by volatility of crude oil prices, so I simply assumed that that was the nature of the beast….

CATEGORIZED UNDER: Culture, Economics, Technology

The World Space Agency a comin'?

By Razib Khan | January 27, 2010 3:58 pm

NASA to Review Human Spaceflight:

The National Aeronautics and Space Administration is preparing for a major evaluation of its human spaceflight program, even as many who will conduct the survey have yet to be informed of the agency’s revised mission.

The administration might also enlist the help and financing of other nations to handle parts of space exploration — perhaps giving the European Space Agency the job of building a lunar lander, for example.

Perhaps China vs. the world? Fodder for near-future science fiction.

CATEGORIZED UNDER: Space, Technology

Hobbits small brains not so anomolous

By Razib Khan | January 27, 2010 2:35 am

Is the Hobbit’s Brain Unfeasibly Small?:

Brain expansion began early in primate evolution and has occurred in all major groups, suggesting a strong selective advantage to increased brainpower in most primate lineages. Despite this overall trend, however, Mundy and his colleagues have identified several branches/lineages within each major group that have shown decreasing brain and body mass as they evolve, for example in marmosets and mouse lemurs.
According to Mundy, “We find that, under reasonable assumptions, the reduction in brain size during the evolution of Homo floresiensis is not unusual in comparison to these other primates. Along with other recent studies on the effects of ‘island dwarfism’ in other mammals, these results support the hypothesis that the small brain of Homo floresiensis was adapted to local ecological conditions on Flores.”

The paper will show up in BMC Biology at some point. The main question I have is in regards to the purported tool use of the Hobbits. I can believe that a local adaptation toward small brains, Idiocracy-writ large, occurred. Brains are metabolically expensive, and it isn’t as if the history of life on earth has shown the massive long-term benefits of being highly encephalized (though I think one can make a case that there has been a modest trend, with primates, and especially H. sapiens as extreme outliers above the trend). But could small brained creatures maintain the relatively advanced toolkit which the Hobbit finds have been associated with? Seems to me that there’s a high probability here of some sort of contamination, but I’ll be happy to be put in my place by anthropologists in-the-know….

CATEGORIZED UNDER: Ecology, Evolution

The last Iberian Neandertal

By Razib Khan | January 27, 2010 1:00 am

spanishneandertal.pngThe debates about the timing of the extinction of the last Neandertals in Iberia seem to one of those interminable disagreements around which paleoanthropologists can’t ever reach a resolution. Another offering from PLoS ONE, Pego do Diabo (Loures, Portugal): Dating the Emergence of Anatomical Modernity in Westernmost Eurasia:

Methodology/Principal Findings
Using AMS radiocarbon and advanced pretreatment techniques, we dated a set of stratigraphically associated faunal samples from an Aurignacian III-IV context excavated at the Portuguese cave site of Pego do Diabo. Our results establish a secure terminus ante quem of ca.34,500 calendar years ago for the assimilation/replacement process in westernmost Eurasia. Combined with the chronology of the regional Late Mousterian and with less precise dating evidence for the Aurignacian II, they place the denouement of that process in the 37th millennium before present.
These findings have implications for the understanding of the emergence of anatomical modernity in the Old World as a whole, support explanations of the archaic features of the Lagar Velho child’s anatomy that invoke evolutionarily significant Neandertal/modern admixture at the time of contact, and counter suggestions that Neandertals could have survived in southwest Iberia until as late as the Last Glacial Maximum.

The paper is pretty long, and probably as opaque to most readers who are as unfamiliar as I with the nuts & bolts of physical anthropology, so ScienceDaily is worth reading:

These findings have important implications for the understanding of the archaic features found in the anatomy of a 30,000 year old child unearthed at Lagar Velho, Portugal. With the last of the Iberian Neanderthals dating to many millennia before the child was born, ‘freak’ crossbreeding between immediate ancestors drawn from distinct ‘modern’ and ‘Neanderthal’ gene pools cannot be a viable explanation. The skeleton’s archaic features must therefore represent evolutionarily significant admixture at the time of contact, as suggested by the team who excavated and studied the fossil.

Those of you in the “know” could probably guess the relevance, as the Lagar Velho 1 skeleton has an entry in TalkOrigins.
Citation: Zilhão J, Davis SJM, Duarte C, Soares AMM, Steier P, et al. (2010) Pego do Diabo (Loures, Portugal): Dating the Emergence of Anatomical Modernity in Westernmost Eurasia. PLoS ONE 5(1): e8880. doi:10.1371/journal.pone.0008880


Show me the data

By Razib Khan | January 26, 2010 4:16 pm

Update: Also see p-ter at Gene Expression Classic.
Follow up on
yesterday’s post on the new Dickson et al. paper from David Goldstein’s lab, A New Way to Look for Diseases’ Genetic Roots:

The Icelandic gene-hunting firm deCODE genetics, which emerged last week from bankruptcy, has long led in detecting SNPs associated with common disease. Dr. Kari Stefansson, the company’s founder and research director, agreed that whole genome sequencing would “give us a lot of extremely exciting data.” But he disputed Dr. Goldstein’s view that rare variants carried most of the missing heritability. Both deCODE genetics and scientists at the Broad Institute in Cambridge, Mass., have sequenced regions of the genome surrounding SNPs in search of rare variants, but have found very few, Dr. Stefansson said.
“We can speculate till we are blue in our faces,” he said, “but the fact of the matter is that there is no substitute for data.”

It would have been nice to get a quote from someone whose recent career hasn’t been as checkered as Stefansson. The issue of missing heritability is going to be interesting in the near future….


The origins of the Yakuts

By Razib Khan | January 26, 2010 9:48 am

One of the more substantive consequences of the powerful new genomic techniques has been in the area of ancient DNA extraction and analysis. The Neandertal genome story is arguably the sexiest, but closer to the present day there’ve been plenty of results which have changed the way we look at the past. The input of genetics has basically demanded a revision of the contemporary consensus of the origins of the Etruscans which emerged from archaeology. Though certainly ancestry and genetic relationship are informative, ancient DNA has also given us windows into the change of function and a record of adaptation which rests less on inference. I’m thinking here of the fact that ancient inhabitants of Central Europe 7,000 years ago do not seem to have been able to process milk in the manner which is the norm in that region today; some we know about because we know that they lacked the mutation which confers lactase persistence in Europeans. There are other examples, and I assume that in the near future we’ll still see a steep exponential increase in the generation of new results as techniques get better and cheaper.
A new paper explores the demographic history of an obscure Siberian population using DNA extraction and phylogenetic analysis. The questions are historical, and relatively easy to resolve. Who are the Yakuts, where did they come from? Those of you who have played Risk know that Yakutsk is a region of Siberia, and the Yakuts are residents of that region. Interestingly the Yakuts speaking a Turkic language. Here is a map which shows the modern distribution of Turkic languages (I have shaded in what is presumed to be the Turkic Urheimat):
Within the last 2,000 years the Turkic languages have rapidly spread across Eurasia. Most of the expansion was to the south and west, but as you can see, some pushed their way into Siberia. These are the Yakuts. I have discussed the genetics of Anatolian Turks before. These Turks sit at one end of the domains of the language family, and how Anatolia came to be Turkic-speaking can tell us something about the dynamics of language change and ethnic reorientation more generally. The Yakuts may tell us something more.
Human evolution in Siberia: from frozen bodies to ancient DNA:

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CATEGORIZED UNDER: Genetics, History

Common disease-common variant hypothesis taken down a notch (again)

By Razib Khan | January 25, 2010 10:03 pm

David Goldstein, a geneticist at Duke, has critiqued the current focus on large-scale genomwide associations before. Now he is taking to the next step, as his group has a paper out which suggests that the reason that association studies have been relatively unfruitful in terms of bang-for-buck is due to the fact that they’re picking up “synthetic associations.” Rare Variants Create Synthetic Genome-Wide Associations:

It has long been assumed that common genetic variants of modest effect make an important contribution to common human diseases, such as most forms of cardiovascular disease, asthma, and neuropsychiatric disease. Genome-wide scans evaluating the role of common variation have now been completed for all common disease using technology that claims to capture greater than 90% of common variants in major human populations. Surprisingly, the proportion of variation explained by common variation appears to be very modest, and moreover, there are very few examples of the actual variant being identified. At the same time, rare variants have been found with very large effects. Now it is demonstrated in a simulation study that even those signals that have been detected for common variants could, in principle, come from the effect of rare ones. This has important implications for our understanding of the genetic architecture of human disease and in the design of future studies to detect causal genetic variants.

The conclusion in the discussion elaborates on the relevance:

… Under our model, the causal sites are both rare and relatively high-penetrant contributors to disease, and will therefore be unlikely to be detected in a small number of control samples. Finally, the focus of attention on genes that are near GWAS signals may be incomplete or misleading in that the actual causal sites may occur in many different genes surrounding the implicated common variant. It is also worth emphasizing that as few as one or two rare variants, at much lower frequency than the associated common SNP, can create a significant synthetic association. In such a case, sequencing a small number of cases that carry the “at risk” common variant might miss entirely the causal rare variants even if the correct genome region is resequenced. These considerations argue for caution in efforts to resequence around genome-wide associations and argue instead that genome-wide sequencing in carefully phenotyped cohorts might be a better use of resources.

PLoS thought that this paper was important enough to commission and accompanying article, Common Disease, Multiple Rare (and Distant) Variants:

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Bat & whale echolocation genetic convergence

By Razib Khan | January 25, 2010 5:48 pm

In Bats and Whales, Convergence in Echolocation Ability Runs Deep:

…”However, it is generally assumed that most of these so-called convergent traits have arisen by different genes or different mutations. Our study shows that a complex trait — echolocation — has in fact evolved by identical genetic changes in bats and dolphins.”
A hearing gene known as prestin in both bats and dolphins (a toothed whale) has picked up many of the same mutations over time, the studies show. As a result, if you draw a phylogenetic tree of bats, whales, and a few other mammals based on similarities in the prestin sequence alone, the echolocating bats and whales come out together rather than with their rightful evolutionary cousins.
Both research teams also have evidence showing that those changes to prestin were selected for, suggesting that they must be critical for the animals’ echolocation for reasons the researchers don’t yet fully understand.
“The results imply that there are very limited ways, if not only one way, for a mammal to hear high-frequency sounds,” said Jianzhi Zhang of the University of Michigan, who led the other study. “The sequence convergence occurred because the amino acid changes in prestin that result in high-frequency selection and sensitivity were strongly favored in echolocating mammals and because there are [apparently] very limited ways in which prestin can acquire this ability.” Prestin is found in outer hair cells that serve as an amplifier in the inner ear, refining the sensitivity and frequency selectivity of the mechanical vibrations of the cochlea, Zhang explained.

This obviously plays into the arguments about contingency and inevitability. On the one hand the convergence across these two taxa suggest that this trait seems to result in an inevitable genetic architecture. But perhaps only for mammals. So inevitability might be a contingent aspect of evolution here. Reminds me a bit of opsins and vision.


  1. Yang Liu, James A. Cotton, Bin Shen, Xiuqun Han, Stephen J. Rossiter, Shuyi Zhang. Convergent sequence evolution between echolocating bats and dolphins. Current Biology, 2010; DOI: 10.1016/j.cub.2009.11.058
  2. Ying Li, Zhen Liu, Peng Shi, Jianzhi Zhang. The hearing gene Prestin unites echolocating bats and whales. Current Biology, 2010; DOI: 10.1016/j.cub.2009.11.042
CATEGORIZED UNDER: Evolution, Genetics

Rice, alcohol and genes

By Razib Khan | January 25, 2010 5:59 am

Changes in human diet driven by cultural evolution seem to be at the root of many relatively recently emerged patterns of genetic variation. In particular, lactase persistence and varied production of amylase are two well known cases. Both of these new evolutionary genetic developments are responses to the shift toward carbohydrates over the last 10,000 years as mainstays of caloric intake. Rice and wheat serve as the foundations of much of human civilization. It is notable that both China and India are divided into rice and wheat (or millet) belts, so essential are modes of agriculture in our categorizations of societies. Even nomad societies are dependent on carbohydrates in the form of “simple sugars,” as much of the nutritive value of milk is from its lactose sugar.
Carbohydrates are convenient because they can be grown and controlled by humans, but also because they can be stored, and finally, reprocessed. Some of that reprocessing is straightforward, such as with breads, but for this post alcohol is what we are concerned with. Tom Standage’s A History of the World in 6 Glasses documents the importance of beer & wine in ancient human societies (and hard liquor in modern ones), and also argues from both empirics and theory that fermented beverages are almost an inevitability in an agricultural society. Alcohol is rich in energy, portable, keeps, and, has a far lower pathogenic load than water in a pre-modern environment. Not to mention the pleasant “buzz” it provides. But like milk, those “without tolerance” often suffer negative physiological consequences. It turns out that like LCT, the locus critical in controlling the levels of the enzyme lactase, the alcohol metabolization loci exhibit variation across populations.
A new paper is out which argues for the causal connection between the spread of rice agriculture, and a derived variant of ADH1B, The ADH1B Arg47His polymorphism in East Asian populations and expansion of rice domestication in history:

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CATEGORIZED UNDER: Anthroplogy, Evolution, Genetics

Religious change in the United States by state, 1990 to 2008

By Razib Khan | January 24, 2010 10:25 pm

As a follow up to the previous post, here’s some of the raw data for the ARIS. I sorted by “Nones” for 2008.

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The rise of the irreligious Left

By Razib Khan | January 24, 2010 6:36 pm

Barry Kosmin at CUNY has published the results of three surveys of American religion since 1990. These “American Religious Identification Surveys” (ARIS) were done in 1990, another in 2001, and finally in 2008. One of the major findings of the ARIS has been the rise of those who avow “No Religion”. Looking through the data it is also clear that aggregating nationally understates some of the local changes. In 1990 47% Vermonters were non-Catholic Christians (i.e., Protestants). In 2008 29% were. In 1990 13% of Vermonters had No Religion. In 2008 34% of Vermonters had No Religion! In fact, No Religion has a plural majority in Vermont, with 26% of the population being Catholic. This is a much bigger shift than nationally. In Kosmin’s book One Nation Under God, which drew upon the 1990 survey results, he noted that though the Northeast has a reputation for being relatively secular, it is in fact highly confessionalized in comparison to other regions, such as the Pacific Northwest. This isn’t true anymore; much of New England has experienced a wave of rapid secularization and disaffiliation. If current rates of secularization continue Vermont may become the first minority non-Christian state. It was only 55% Christian in 2008.
I am going to explore these data with scatterplots and maps. All the plots have 1990 data on the X-axis and 2008 data on the Y-axis. I also look at the 1988 vs. 2008 presidential race, and attempt to see if there is any connection between secularization and political change.

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CATEGORIZED UNDER: Culture, Politics, Religion

Doberman Pinscher with OCD

By Razib Khan | January 23, 2010 7:45 pm

doberman.pngIn the wake of my post on selection and variation in dog skull shape, I thought it would be useful to point to this short paper, A canine chromosome 7 locus confers compulsive disorder susceptibility. Here’s the conclusion:

The highly significant association of CCD with the CDH2 region on chromosome 7 is the first genetic locus identified for any animal compulsive disorder, and raises the intriguing possibility that CDH2 and other neuronal adhesion proteins are involved in human compulsive behaviors. A genetic association of cadherins with autism spectrum disorder, which often includes repetitive and compulsive behaviors, has also recently been reported…As little is known about the underlying molecular mechanisms for compulsive behaviors, this discovery could provide a better understanding of disease biology and facilitate development of genetic tests, enabling earlier interventions and even treatment or prevention of compulsive disorders in at-risk canines and humans.

The New York Times has much more.
Citation: Molecular Psychiatry (2010) 15, 8-10; doi:10.1038/mp.2009.111

CATEGORIZED UNDER: Biology, Genetics

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