Archive for November, 2009

Diary of an ex-Muslim

By Razib Khan | November 30, 2009 5:51 pm

A friend of mine pointed me to an interesting weblog, Here in Glitner. From the “About” page:

Reflections from my life as a Muslim, perspectives on Islam in my true life as a non-Muslim. I was a Muslim woman, a Muslim wife, a Muslim mother, a Muslim sister. I wore hijab, abstained from pork, obeyed my husband, studied quran and sunnah, and avoided all forbidden and doubtful things as much as I could. And then, slowly, from the blip of one thought to a full-blown realization more than five years later, I emerged into my true life, into reality, and realized my atheism. As you will read, if you go back to the start, it took a long time – roughly two years, to sort out my lifestyle, the life I was living, my family, and my beliefs. This blog mixes in old journal entries from those times with my thoughts on Islam from the perspective of a kafir – an infidel.

The friend is an ex-Muslim as well, though they keep that information to themselves because of negative experiences. By some definitions I’m an “ex-Muslim,” insofar as I identified as a Muslim before the age of eight, at which point I realized I was basically what would be termed an “atheist” (I didn’t know that word at that point). But I never had a coherent supernatural world view. Though before the age of eight I could parrot the general cosmology imparted from Islam, my genuine understanding of the world was totally naturalistic. I had always had a deep interest in evolution and astronomy, and even when I wasn’t a self-conscious atheist God had no place in my model of the cosmos. Nor am I culturally Muslim, as my social network is almost exclusively non-Muslim (and mostly irreligious to boot). Though I can repeat suras I was taught as a child, I never grew up in a world where Islamic material civilization was prominent in any way. In other words, my lack of connection with my “ancestral religion” has had almost no psychic or social cost, and I do not have any personal history of rupture with a tradition which accompanies apostasy. My shedding of a Muslim identity as a child was plainly superficial, as I had never evinced a deep interest in religion, and generally dreaded the boredom of Islamic holidays.
That is why I am fascinated by the weblogs of both converts and apostates, though naturally I have more affinity with the latter. The psychological experiences are in a sense deeply alien to what I am familiar with. I suspect it is analogous to never having been drunk. The mental shock of going from a world filled with supernatural agents to one without, or vice versa, must be jarring. But from what I can tell most religious people take great solace in their personal beliefs, so losing such an anchor might be analogous to a hangover.


Coywolves; hybrid wolf-coyotes in New England?

By Razib Khan | November 30, 2009 1:24 pm

This article pointed me to this interesting paper, Rapid adaptive evolution of northeastern coyotes via hybridization with wolves:

The dramatic expansion of the geographical range of coyotes over the last 90 years is partly explained by changes to the landscape and local extinctions of wolves, but hybridization may also have facilitated their movement. We present mtDNA sequence data from 686 eastern coyotes and measurements of 196 skulls related to their two-front colonization pattern. We find evidence for hybridization with Great Lakes wolves only along the northern front, which is correlated with larger skull size, increased sexual dimorphism and a five times faster colonization rate than the southern front. Northeastern haplotype diversity is low, suggesting that this population was founded by very few females moving across the Saint Lawrence River. This northern front then spread south and west, eventually coming in contact with an expanding front of non-hybrid coyotes in western New York and Pennsylvania. We suggest that hybridization with wolves in Canada introduced adaptive variation that contributed to larger size, which in turn allowed eastern coyotes to better hunt deer, allowing a more rapid colonization of new areas than coyotes without introgressed wolf genes. Thus, hybridization is a conduit by which genetic variation from an extirpated species has been reintroduced into northeastern USA, enabling northeastern coyotes to occupy a portion of the niche left vacant by wolves.

Here is a figure which shows the distribution of mtDNA lineages geographically:

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Climate & the Out of Africa migration(s)

By Razib Khan | November 30, 2009 1:07 pm

Wet phases in the Sahara/Sahel region and human migration patterns in North Africa:

The carbon isotopic composition of individual plant leaf waxes (a proxy for C3 vs. C4 vegetation) in a marine sediment core collected from beneath the plume of Sahara-derived dust in northwest Africa reveals three periods during the past 192,000 years when the central Sahara/Sahel contained C3 plants (likely trees), indicating substantially wetter conditions than at present. Our data suggest that variability in the strength of Atlantic meridional overturning circulation (AMOC) is a main control on vegetation distribution in central North Africa, and we note expansions of C3 vegetation during the African Humid Period (early Holocene) and within Marine Isotope Stage (MIS) 3 (≈50-45 ka) and MIS 5 (≈120-110 ka). The wet periods within MIS 3 and 5 coincide with major human migration events out of sub-Saharan Africa. Our results thus suggest that changes in AMOC influenced North African climate and, at times, contributed to amenable conditions in the central Sahara/Sahel, allowing humans to cross this otherwise inhospitable region.

More details from the discussion:

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American data by counties

By Razib Khan | November 29, 2009 7:55 pm

I’ve been crunching some county-by-county data at one of my other weblogs:
Where the fat folks live
Diabetes and obesity
The white vote for Obama, by county & correlates
Are over-leveraged counties seeing an increase in food stamp usage?



By Razib Khan | November 27, 2009 10:36 pm

Felines worked part-time this week due to the holiday….

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The wealth of politicians

By Razib Khan | November 26, 2009 10:09 am

Open Secrets has data on members of the House and Senate in relation to their net worth. Here are some descriptive statistics:
Democrats & Republicans:
25th percentile = $228,006
Median = $791,004
75thth percentile = $2,962,519
Mean = $6,438,210
25th percentile = $269,007
Median = $999,381
75thth percentile = $3,421,512
Mean = $6,010,456
25th percentile = $217,001
Median = $718,756
75thth percentile = $2,516,033
Mean = $6,731952
Let’s limit to those who have positive net worth (greater than zero) and less than $50,000,000. This is about two standard deviations above the median, so it removes the top ~2% who tend to skew the results.

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Marriage equality, inbreeding style

By Razib Khan | November 26, 2009 5:28 am

The New York Times has an article on cousin marriage that’s up. Here’s some important bits:

Shane Winters, 37, whom she now playfully refers to as her “cusband,” proposed to her at a surprise birthday party in front of family and friends, and the two are now trying to have a baby. They are not concerned about genetic defects, Ms. Spring-Winters said, and their fertility doctor told them he saw no problem with having children.
The couple — she is a second-grade teacher and he builds furniture — held their wedding last summer on a lake near this tiny town in central Pennsylvania. But their official marriage took place a month earlier in Maryland, at Annapolis City Hall, because marriage between first cousins is illegal in Pennsylvania — and in 24 other states, according to the National Conference of State Legislatures — under laws enacted mostly in the 19th century.

For the most part, scientists studying the phenomenon worldwide are finding evidence that the risk of birth defects and mortality is less significant than previously thought. A widely disseminated study published in The Journal of Genetic Counseling in 2002 said that the risk of serious genetic defects like spina bifida and cystic fibrosis in the children of first cousins indeed exists but that it is rather small, 1.7 to 2.8 percentage points higher than for children of unrelated parents, who face a 3 to 4 percent risk — or about the equivalent of that in children of women giving birth in their early 40s. The study also said the risk of mortality for children of first cousins was 4.4 percentage points higher.
More-recent studies suggest that the risks may be even lower. In September, Alan Bittles, a researcher at the Centre for Comparative Genomics at Murdoch University in Australia and one of the authors of the 2002 study, published a paper in Proceedings of the National Academy of Sciences that reported that the mortality rate was closer to 3.5 percentage points higher. He said he expected ongoing research to find the risk of defects to be lower than previously assumed as well.
“It’s never as simple as people make it out to be,” said Dr. Bittles, noting that very early studies did not account for factors like access to prenatal health care, and did not distinguish between couples like Ms. Spring-Winters and her husband, the first cousins in a family to marry, and those who are part of groups in which the practice is common over generations and has led to high rates of genetic disorders. “But the widely accepted scare stories — even within academia — and the belief that cousin marriage is inevitably harmful have declined in the face of some of the data we’ve been producing,” he said.

Diane B. Paul, a professor emerita of political science at the University of Massachusetts, Boston, and a research associate in zoology at Harvard, was an author of a paper published last year in the journal PLoS Biology that described the difficulty of generalizing about the potential for birth defects or increased mortality in the children of cousins. Each couple’s risk depends on the individuals’ particular genetic makeup, she said, which means “it’s very difficult to determine.” And even the small average risk of defects reported in the 2002 study, she added, represents nearly double the risk to children of unrelated parents.

As a religious Methodist, she said, she also worried that marrying her cousin would be wrong in the eyes of her church. But as it turned out, the Methodist Church has no official position on marriage between cousins, unlike the Roman Catholic Church, which requires cousins to obtain dispensation before marrying. And after talking to a relative who is a Baptist minister, Ms. Spring-Winters said, she discovered that the Bible does not say anything explicitly negative about cousin marriage, although it does list examples of sexual impurity, including relations with “close relatives,” like sisters, stepchildren, grandchildren, aunts and stepsisters; and those between mothers and sons, and fathers and daughters.
“If the Bible said no, we wouldn’t have done it,” she said.

A few salient points noted above:

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Egypt & evolution & the Muslim world

By Razib Khan | November 26, 2009 3:31 am

Last week I pointed to numbers on evolution and the Muslim world. The New York Times has an article up about the conference which inspired my investigation into that topic. The reporter focuses on the rote learning and creativity as the factors behind a lack of knowledge or understanding of evolutionary theory. Plausible, but really unlikely. East Asian nations have the same issues (which they are trying to reform), but acceptance of evolution is high there. In fact, even in non-developed nations such as the Philippines acceptance of evolution can be high. It is higher than in the United States! In Russia there is surprisingly low level of acceptance of evolution, though that might be the aftereffect of the Lysenko interlude, when conventional evolutionary biology was rejected. In other words, the reasons for skepticism of evolution are somewhat diverse, though rote learning and lack of creativity are surely neither necessary nor sufficient.
I suspect that the best analogy for what’s going on with Muslims, even elite Muslims (the samples I pointed to last week were elites), is what occurred with conservative Protestants as they faced the forces of modernism in the 20th century. Some aspects of the modern world they accepted, and others they rejected. The historical sciences, and in particular those which bear upon human nature and origins, they reject with particular vehemence. Despite the pleas of a minority, such as Francis Collins, most American Evangelicals seem to believe that rejection of evolutionary theory is necessarily entailed by their religion. Similarly, most Muslims seem to feel the same way. Even American Muslims seem to have this attitude, though not as much as American Evangelicals. While 33% of American Evangelicals accept that evolution as the best explanation for the origin of human life, 45% of Muslims do (vs. 48% of all Americans). Yet 80% of Hindu accept evolution as the best explanation for the origin of life. In any case, the citizens of Muslim nations seem to assert that religion is very important in their lives, so naturally they would be skeptical of ideas which they believe contravene the precepts of their religion.
Below the fold are results where individuals were asked how important religion was in their life from the World Values Survey 2005 by country….

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Population substructure within China

By Razib Khan | November 25, 2009 5:35 pm

The state of China has 1/5 of humanity within its borders, so it’s genetic structure is of interest. It is obviously important for medical reasons to clarify issues of population structure so that disease susceptibility among the Han is well characterized, in particular with the heightened medical needs of an aging population in the coming generation. And of course, there are the nationalistic concerns. About 20 years ago L. L. Cavalli-Sforza reported that his South Chinese samples were genetically closer to Southeast Asians than North Chinese in The History and Geography of Human Genes. This result has been somewhat muddled in the past generation with the rise of uniparental markers (NRY and mtDNA passed through the male and female lineages) along with studies which utilize hundreds of thousands of SNPs. One thing that seems to be clear is that genes vary as a function of geography in China (just as they do pretty much everywhere).
Two new articles in AJHG shed some more light on this issue, Genomic Dissection of Population Substructure of Han Chinese and Its Implication in Association Studies:

To date, most genome-wide association studies (GWAS) and studies of fine-scale population structure have been conducted primarily on Europeans. Han Chinese, the largest ethnic group in the world, composing 20% of the entire global human population, is largely underrepresented in such studies. A well-recognized challenge is the fact that population structure can cause spurious associations in GWAS. In this study, we examined population substructures in a diverse set of over 1700 Han Chinese samples collected from 26 regions across China, each genotyped at ∼160K single-nucleotide polymorphisms (SNPs). Our results showed that the Han Chinese population is intricately substructured, with the main observed clusters corresponding roughly to northern Han, central Han, and southern Han. However, simulated case-control studies showed that genetic differentiation among these clusters, although very small (FST = 0.0002 ∼0.0009), is sufficient to lead to an inflated rate of false-positive results even when the sample size is moderate. The top two SNPs with the greatest frequency differences between the northern Han and southern Han clusters (FST > 0.06) were found in the FADS2 gene, which associates with the fatty acid composition in phospholipids, and in the HLA complex P5 gene (HCP5), which associates with HIV infection, psoriasis, and psoriatic arthritis. Ingenuity Pathway Analysis (IPA) showed that most differentiated genes among clusters are involved in cardiac arteriopathy (p < 10−101). These signals indicating significant differences among Han Chinese subpopulations should be carefully explained in case they are also detected in association studies, especially when sample sources are diverse.

And, Genetic Structure of the Han Chinese Population Revealed by Genome-wide SNP Variation:

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Sex differences in ancestry in the New World

By Razib Khan | November 25, 2009 2:44 am

A new paper in PLoS ONE, Evaluation of Group Genetic Ancestry of Populations from Philadelphia and Dakar in the Context of Sex-Biased Admixture in the Americas, doesn’t add much to what we know. They looked at a several hundred individuals who are self-identified as African American and European American, as well as 49 Senegalese from Dakar. Additionally, they reanalyzed data from Latin America from whites and blacks in Brazil, as well as a group of mixed Cubans. They found what you might expect to find, African and Native ancestry shows a female bias, European ancestry shows a male bias.
But Figure 3 is nice in that it illustrates how exceptional European Americans are: they are a New World population with very little admixture, that is, a “pure race.” The data on people of white identification in most of Latin America, including in the European dominated southern cone, is that a non-trivial load of non-European genes exists in these populations (often indigenous ancestry down the maternal lineage). Similarly, African origin populations in the New World are invariably known to be admixed, more or less. Finally, even the “indigenous” generally show non-trivial European or African ancestry (this is evident in the regular notations of African or European ancestry being used to explain anomalous results).*

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CATEGORIZED UNDER: Culture, Genetics

The future of human evolution

By Razib Khan | November 24, 2009 4:50 pm

alien_face.pngSince The Origin of Species was published 150 years ago many articles on evolution are seeing the light of day today. Normally I’m all in favor of this, I ♥ evolution. But it also means that woolly thinking is put out there as conventional wisdom as journalists simply act as stenographers for any scientist who’s in their rolodex. Some of the quotes in this National Geographic article make me want to tear my hair out. Ian Tattersall, a paleoanthropologist, decides to offer up his opinions as a population geneticist:

“Everything we know about evolutionary change suggests that genetic innovations are only likely to become fixed in small, isolated populations,” he said. For example, Darwin’s famous Galápagos finches each evolved from their mainland ancestor to fit a unique habitat on the isolated islands in the Pacific.
Natural selection, as outlined in On the Origin of Species, occurs when a genetic mutation–say, resulting in a spine suited to upright walking–is passed down through generations, because it affords some benefit. Eventually the mutation becomes the norm.
But if populations aren’t isolated, crossbreeding makes it much less likely for potentially significant mutations to become established in the gene pool–and that’s exactly where we are now, Tattersall said.
“Since the advent of settled life, human populations have expanded enormously. Homo sapiens is densely packed across the Earth, and individuals are unprecedentedly mobile.
“In this situation, the fixation of any meaningful evolutionary novelties in the human population is highly improbable.” Tattersall said. “Human beings are just going to have to learn to live with themselves as they are.”

There’s a lot here.

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CATEGORIZED UNDER: Evolution, Genetics

Brown people are susceptible to diabetes

By Razib Khan | November 24, 2009 2:02 am

gandhi2.pngIn medical news which won’t be surprising to anyone, Ethnic Variation in Fat and Lean Body Mass and the Association with Insulin Resistance:

Objective: Our objective was to compare total body fat to lean mass ratio (F:LM) in Aboriginal, Chinese, European, and South Asian individuals with differences in insulin resistance.

Results: After adjustment for confounders and at a given body fat, South Asian men had less lean mass than Aboriginal [3.42 kg less; 95% confidence interval (CI) = 1.55-5.29], Chinese (3.01 kg less; 95% CI = 1.33-4.70), and European (3.57 kg less; 95% CI = 1.82-5.33) men, whereas South Asian women had less lean mass than Aboriginal (1.98 kg less; 95% CI = 0.45-3.50), Chinese (2.24 kg less; 95% CI = 0.81-3.68), and European (2.97 kg less; 95% CI = 1.67-4.27) women. In adjusted models, F:LM was higher in South Asian compared with Chinese and European men and higher in South Asian compared with Aboriginal, Chinese, and European women (P < 0.01 for all). Insulin and HOMA were greatest in South Asians after adjustment; however, these differences were no longer apparent when F:LM was considered.
Conclusions: South Asians have a phenotype of high fat mass and low lean mass, which may account for greater levels of insulin and HOMA compared with other ethnic groups.

HOMA = homeostatic model assessment, used to quantify insulin resistance and beta-cell function. The second bolded part is important, you can change your fat to lean mass ratio. Change what you eat, and exercise. I’ve seen data from England, where there are large numbers of Pakistanis and Bangladeshis, that the latter are in a higher risk category than the former when it comes to adult onset diabetes.
Update: A comment:

Minor quibble: Please be so kind as to use the term ‘type 2 diabetes’ in the future.
A large amount of type 1 diabetics get the disease in adulthood and these results have zero relevance for them or that disease.
It’s incidentally (now that we are splitting hairs…) also incorrect to use the term IDDM (insulin dependent diabetes mellitus) as a shorthand for type 1 diabetes, which is something you often see people do without thinking. A recent Danish study found that half of all type 2 diabetes patients will need insulin treatment within 6 years of diagnosis, which probably means that a majority of all insulin-dependent diabetics are type 2 patients, considering that they make out the great majority of all diabetics (in DK, 80-90% of all diabetics have type 2 diabetes).

CATEGORIZED UNDER: Anthroplogy, Health

Apocalypse 73,000 B.C.

By Razib Khan | November 24, 2009 1:07 am

FuturePundit points me to a new paper on the Toba explosion, Environmental impact of the 73 ka Toba super-eruption in South Asia:

The cooling effects of historic volcanic eruptions on world climate are well known but the impacts of even bigger prehistoric eruptions are still shrouded in mystery. The eruption of Toba volcano in northern Sumatra some 73,000 years ago was the largest explosive eruption of the past two million years, with a Volcanic Explosivity Index of magnitude 8, but its impact on climate has been controversial. In order to resolve this issue, we have analysed pollen from a marine core in the Bay of Bengal with stratified Toba ash, and the carbon isotopic composition of soil carbonates directly above and below the ash in three sites on a 400 km transect across central India. Pollen evidence shows that the eruption was followed by initial cooling and prolonged desiccation, reflected in a decline in tree cover in India and the adjacent region. Carbon isotopes show that C3 forest was replaced by wooded to open C4 grassland in central India. Our results demonstrate that the Toba eruption caused climatic cooling and prolonged deforestation in South Asia, and challenge claims of minimal impact on tropical ecosystems and human populations.

The Toba caldera is in Sumatra, but the ashfall in India was on the order of 15 centimeters to 6 feet. This might also be relevant to human evolution, The super-eruption of Toba, did it cause a human bottleneck?.
Citation Martin A.J. Williamsa, Stanley H. Ambroseb, Sander van der Kaarsc, Carsten Ruehlemannd, Umesh Chattopadhyayae, Jagannath Pale and Parth R. Chauhanf, Environmental impact of the 73 ka Toba super-eruption in South Asia, doi:10.1016/j.palaeo.2009.10.009

CATEGORIZED UNDER: Anthroplogy, Ecology, Evolution

Cannibalism & evolution

By Razib Khan | November 23, 2009 7:39 am

Cannibalism is a controversial topic. It is routine for particular societies to accuse “barbarians”, enemies, or evil mythological figures, of cannibalism. When it comes to the archaeological record some skeptics have claimed that like “sacred objects” too often human remains found in peculiar circumstances are ascribed to human sacrifice or cannibalism. In Did Adam and Eve Have Navels? Martin Gardner lays out the skeptical case for why cannibalism is rare to non-existent, and rather something which emerges from the imaginations of ethnographers and archaeologists, or is rooted in scurrilous insults hurled between ethnic groups which have antagonistic relationships. Since the arguments Gardner lays out were presented it seems that the skeptical case is looking weaker, though controversy remains in specific instances. In the domain of genetics, there is some evidence of natural selection on genetic loci which imply widespread prion diseases in the past. Diseases which are often the outcomes of cannibalism. These sorts of molecular genetic data should perhaps change our perspective as to the imaginative color which archaeologists and paleoanthropologists might add to their inferences from ancient or prehistoric human remains.
But the case of cannibalism among the Fore people of Papua New Guinea it is not speculation or a matter of historical or archaeological inference. They were engaging in the practice as late as the 1960s. So it is of interest that a new paper has come out reinforcing the finding that the kuru epidemics might have left a genetic imprint, A Novel Protective Prion Protein Variant that Colocalizes with Kuru Exposure:

Results Persons who were exposed to kuru and survived the epidemic in Papua New Guinea are predominantly heterozygotes at the known resistance factor at codon 129 of the prion protein gene (PRNP). We now report a novel PRNP variant — G127V — that was found exclusively in people who lived in the region in which kuru was prevalent and that was present in half of the otherwise susceptible women from the region of highest exposure who were homozygous for methionine at PRNP codon 129. Although this allele is common in the area with the highest incidence of kuru, it is not found in patients with kuru and in unexposed population groups worldwide. Genealogic analysis reveals a significantly lower incidence of kuru in pedigrees that harbor the protective allele than in geographically matched control families.
Conclusions The 127V polymorphism is an acquired prion disease resistance factor selected during the kuru epidemic, rather than a pathogenic mutation that could have triggered the kuru epidemic. Variants at codons 127 and 129 of PRNP demonstrate the population genetic response to an epidemic of prion disease and represent a powerful episode of recent selection in humans.

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CATEGORIZED UNDER: Anthroplogy, Genetics

Hadza heaven turning to hell

By Razib Khan | November 23, 2009 5:51 am

National Geographic has an interesting piece of ethnographic travel writing up on the Hadza of Tanzania. The Hadza are one of the few remaining hunter-gather populations in the world, and their language is an isolate which has clicks. There’s a bit too much “noble savage” archetype loaded into the piece, but this portion is of note:

The chief reason the Hadza have been able to maintain their lifestyle so long is that their homeland has never been an inviting place. The soil is briny; fresh water is scarce; the bugs can be intolerable. For tens of thousands of years, it seems, no one else wanted to live here. So the Hadza were left alone. Recently, however, escalating population pressures have brought a flood of people into Hadza lands. The fact that the Hadza are such gentle stewards of the land has, in a way, hurt them–the region has generally been viewed by outsiders as empty and unused, a place sorely in need of development. The Hadza, who by nature are not a combative people, have almost always moved away rather than fight. But now there is nowhere to retreat.

Like all extant hunter-gatherer populations* the Hadza exist precisely because their territory is unappealing or unsuitable for agriculture. It follows that the simplicity of the Hadza may be a function of the spare and marginal nature of the ecology with they depend upon for their livelihood, not the style of their livelihood. I am willing to hazard that hunter-gatherers more fertile territory would still have less inequality and social complexity than equivalent agriculturalists, but the hard-scrabble hunter-gatherers who remain surely give us an extremely distorted view of that mode of life.
* Many which anthropologists were able to study in the 20th century are no longer hunter-gatherers, so the presently extant list is shrinking fast.
H/T Michael Blowhard

CATEGORIZED UNDER: Anthroplogy, Culture

Hu Jintao vs. Barack Obama

By Razib Khan | November 23, 2009 12:36 am

I found this SNL sketch about an Obama/Jintao press conference very funny.

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CATEGORIZED UNDER: Anthroplogy, Culture

Why science fiction was better in the past

By Razib Khan | November 21, 2009 8:28 pm

Perhaps because we only remember the good stuff? Or only the good suff & famous authors get reprinted. I’m prompted to offer this hypothesis in response to Chad Orzel’s commentary that there was a lot of bad space opera even during the “Golden Age” of science fiction. I recall that Zadie Smith once noted that 99.99% (or something to that effect) of Victorian fiction is forgotten and out of print. All that remains read are the “classics,” so contemporary audiences have a biased perspective as to the median quality of Victorian-era writers. Of course the insight can be generalized to the arts overall; only the good gets reproduced or remembered.
To be fair, some science fiction authors, such as George R. R Martin (who also writes other genres obviously), have claimed that the turn away from “hard” sf rooted in physics and engineering is reflective of a cultural shift. In the 1950s the “atomic age” was viewed positively, and the possibilities seemed unbounded. Today a lot of the fiction deeply influenced by science in constructing a story may take a more ambivalent, or even pessimistic, view of how science effects human happiness (e.g., dystopian futures where nanotech gets out of control).


Chinese propensity to copy

By Razib Khan | November 21, 2009 11:54 am

No, this isn’t about intellectual property issues and piracy. Whole Genome Distribution and Ethnic Differentiation of Copy Number Variation in Caucasian and Asian Populations:

Although copy number variation (CNV) has recently received much attention as a form of structure variation within the human genome, knowledge is still inadequate on fundamental CNV characteristics such as occurrence rate, genomic distribution and ethnic differentiation. In the present study, we used the Affymetrix GeneChip® Mapping 500K Array to discover and characterize CNVs in the human genome and to study ethnic differences of CNVs between Caucasians and Asians. Three thousand and nineteen CNVs, including 2381 CNVs in autosomes and 638 CNVs in X chromosome, from 985 Caucasian and 692 Asian individuals were identified, with a mean length of 296 kb. Among these CNVs, 190 had frequencies greater than 1% in at least one ethnic group, and 109 showed significant ethnic differences in frequencies (p<0.01). After merging overlapping CNVs, 1135 copy number variation regions (CNVRs), covering approximately 439 Mb (14.3%) of the human genome, were obtained. Our findings of ethnic differentiation of CNVs, along with the newly constructed CNV genomic map, extend our knowledge on the structural variation in the human genome and may furnish a basis for understanding the genomic differentiation of complex traits across ethnic groups.

Here’s a figure which shows the distributions, CHI = Chinese and CAU = Caucasion.*
The big picture issue is CNVs may be important in gene expression, the paper cites a number that ~18% of the variance in this may be due to CNVs. An interesting recent case was CNV differences in regards to the gene which codes for amylase, with some researchers suggesting this is due to selection for the ability to digest starches for agriculturalists. In relation to the title, there might not be anything there:

A third example of ethnic variation is that the genomic coverage of CNVs in Asians is 1.6-fold higher than that in seen in Caucasians, indicating that genome variants were more common in Asians than in Caucasians. Further sensitivity analysis resulted in an only 1.2-fold elevated genomic coverage of Chinese CNVs compared to Caucasian CNVs. Considering different DNA extraction methods for Chinese and Caucasian samples, the ethnic differences seen in genomic coverage may be partially due to different binding affinities of diverse DNA extracts to the SNP chip array.

Citation: Li J, Yang T, Wang L, Yan H, Zhang Y, et al. 2009, Whole Genome Distribution and Ethnic Differentiation of Copy Number Variation in Caucasian and Asian Populations. PLoS ONE 4(11): e7958. doi:10.1371/journal.pone.0007958
* If they use “Caucasian” for European origin people, why not “Mongoloid” for Chinese?


When mammoths roamed

By Razib Khan | November 21, 2009 1:19 am

Pleistocene Megafaunal Collapse, Novel Plant Communities, and Enhanced Fire Regimes in North America:

Although the North American megafaunal extinctions and the formation of novel plant communities are well-known features of the last deglaciation, the causal relationships between these phenomena are unclear. Using the dung fungus Sporormiella and other paleoecological proxies from Appleman Lake, Indiana, and several New York sites, we established that the megafaunal decline closely preceded enhanced fire regimes and the development of plant communities that have no modern analogs. The loss of keystone megaherbivores may thus have altered ecosystem structure and function by the release of palatable hardwoods from herbivory pressure and by fuel accumulation. Megafaunal populations collapsed from 14,800 to 13,700 years ago, well before the final extinctions and during the Bølling-Allerød warm period. Human impacts remain plausible, but the decline predates Younger Dryas cooling and the extraterrestrial impact event proposed to have occurred 12,900 years ago.

Ed Yong has the bases covered:

What about humans, those pesky slayers of animals? Some scientists believed that North America’s Clovis people specialised in hunting big mammals, causing a “blitzkrieg” of spear-throwing that drove many species to extinction. But these hunters only arrive in North America between 13,300 and 12,900 years ago, around a thousand years after the population crashes had begun.
If people were responsible, they must have been pre-Clovis settlers. There’s growing evidence that such humans were around, but they weren’t common or specialised. They may have contributed to the beasts’ downfall, while Clovis hunting technology delivered a coup de grace to already faltering populati0ons.
By analysing the sediment at Appleman lake – spores, pollen, charcoal and all – Gill has replayed the history of the site, spanning the last 17,000 years. Her data rule out a few theories, but as she says, they “[do] not conclusively resolve the debate” about climate causes versus human ones. It’s possible that similar studies at different sites and other continents will help to provide more clues.

A complex story like this is perhaps more common than an event such as the extinction of the passenger pigeons. Populations of organisms often go through cycles in census size, whether due to environmental variation or coevolutionary dynamics with parasites. Consider the example of the Tasmania devil, the disease which it is susceptible to is not the doing of humans, but the introduction of dingos (probably by humans) mean that the species is restricted to Tasmania. Additionally, humans have laid claim to much of the habitat of the devil (or what was the habitat of the devil). When a virulent disease hits, the devil has a much smaller margin of error than it had before. It could be that recent megafaunal extinctions are ultimately due to humans, even if they are not always proximately due to humans.



By Razib Khan | November 20, 2009 8:55 pm

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Gene Expression

This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!

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Edifying books

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