The debate over global warming is relevant to GNXP (previous posts here and here) not so much because our readers are interested in climate science but because the dynamics of the debate — scientific “consensus” versus politically incorrect minority view — have relevance to various debates over human biodiversity. With that background, I would be curious to know what posts/arguments/sites other GNXPers find most relevant and compelling. My three favorites are:

1) Willis Eschenbach on his attempts to use the Freedom Of Information Act to access CRU data and model details.

2) Eric Raymond on details of the released code. When serious software experts like Raymond start accusing climate scientists of “blatant data-cooking,” the “consensus” started to looks much weaker.

3) Gavin Schmidt at Real Climate in defense of the scientists at CRU. Whatever the criticisms of Schmidt from folks like Steve McIntyre, you have to be impressed with his willingness to take on all comers.

In the spirit of (United States) Thanksgiving, I am thankful that the human genetics community seems to have a much broader diversity of opinion and greater committment to transparency and reproducible research than the climate science community.

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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After reading this article about the The Biggest Loser, I checked out the Wikipedia page for the show. There are international versions. Through that I found out that there is an Indian version of the show. I thought this was weird. I mean, it’s India, right? Well, around 2% of Indian women are obese (BMI 30 and above). That’s 20 million obese! In India obesity still seems to correlate with wealth and higher status. Nearly 10% of women in Delhi and Punjab are obese (vs. 0.5% in Bihar, the heart of the “Deep North”). Nearly 10% of Jains are obese. 6.5% of women who have completed secondary school are obese, vs. 1% of illiterates. 6% of people in urban areas vs. 1% in rural areas.

A few weeks ago people in the comments were nagging me a bit about some new papers on the haplogroup R1a1. This Y chromosomal lineage is found at very high frequencies from East-Central Europe into India. Initially, researchers such as Spencer Wells assumed that R1a1 signaled the arrival of Indo-Aryans to the Indian subcontinent, its frequencies decline in a northwest-to-southeast gradient, and from high to low castes. In Europe the modal frequencies are among Slavic groups, with a high representation among Germanic-speakers. The frequency of R1a1 declines sharply in Western and Southern Europe. It is very common in Central Asia as well as eastern Iran and Afghanistan. One parsimonious explanation would be that R1a1 spread with Kurgan males, along with Indo-European languages, on the order of 4-5,000 years ago.

There is a problem with this model though. One of the new papers reiterates the finding that the coalescence of the European and South Asian lineages is on the order of 10,000 years ago: Separating the post-Glacial coancestry of European and Asian Y chromosomes within haplogroup R1a (R1a1 is the dominant clade within R1a). A second paper reports the finding that R1a1 is very diverse in India, indicating deep time depth: The Indian origin of paternal haplogroup R1a1* substantiates the autochthonous origin of Brahmins and the caste system. For both R1a1 &”Ancestral North Indians” (ANI) in Reich et al.: the frequency seems intuitively way too high among tribal populations, even in South India. Remember that the low bound for ANI was ~40%. R1a1 is found at frequencies as high as 25% or so among some South Indian tribals. If this lineage arrived with the Indo-Aryans it is peculiar that it is found in such high frequencies in populations which were marginal and isolated from the dominant non-Indo-Aryan populations of South India. Back to Europe, here is a section from the abstract of the first paper:

Conversely, marker M458 has a significant frequency in Europe, exceeding 30% in its core area in Eastern Europe and comprising up to 70% of all M17 chromosomes present there. The diversity and frequency profiles of M458 suggest its origin during the early Holocene and a subsequent expansion likely related to a number of prehistoric cultural developments in the region. Its primary frequency and diversity distribution correlates well with some of the major Central and East European river basins where settled farming was established before its spread further eastward. Importantly, the virtual absence of M458 chromosomes outside Europe speaks against substantial patrilineal gene flow from East Europe to Asia, including to India, at least since the mid-Holocene.

The Holocene started 11,700 years ago. We are living in the Holocene. So the means that gene flow can’t be any later than 6,000 years ago. The paper which focuses specifically on Indian lineages reports a coalescence time on the order of 10,000 years in the past for South Asian R1a1 branches. Additionally, they confirm earlier findings that of caste ranking of R1a1 in terms of frequency, as well Brahmins having the most diversity of all groups in terms of haplotypes (ergo, the title of the paper).

Both Dienekes and Polish Genetics and Anthropology suggest that the calibration is wrong on these coalescence times. They argue that one should reduce the time to a common ancestor by a factor of 3. This would of course make a huge difference. In regards to the Reich et al. paper which argued for a plausible two-way admixture between ANI and “Ancestral South Indians” (ASI), the linkage disequilibrium has decayed too much from the time of admixture to peg a date. This was a method used to calculate the emergence of the Uyghurs as a hybrid population, on the order of 2-3 thousand years ago (admixture between two very different populations generates linkage disequilibrium which decays over time due to recombination). In terms of Fst the ANI have a value in relation to Northern Europeans which is about 3 times larger than the mean between population differences in Europe. This is somewhat greater than the pairwise values between any European populations except for the Baltic peoples (in particularly, the swath from Karelia to Lithuania) to the groups of Southern Europe. The degree of Neolithic Middle Eastern ancestry within Europe under debate, but I think one can assume that Southern Italians and Karelians are likely at opposite ends in terms of frequency of this contribution to the pre-Ice Age demographic substratum of Europe. From this I offer that it is not totally unreasonable to posit that the ANI contribution to South Asian ancestry was closer to the margins of the last Ice Age, rather than the period of the Indo-European expansion, and that its Fst values are not unreasonable in relation to modern European groups.

The main issue that is confusing is the diversity of R1a1 in South Asia. A first order model going from just this data would be that R1a1 derives from India, and spread to the Eurasian plain. But Reich et al. show data that imply little likelihood of South Asian contribution to European ancestry. The only possibility would be if ANI and ASI were totally separated when a branch of ANI left South Asia for the Eurasian plain, and which point the process of admixture between ANI and ASI began. Another possibility is that the distribution of R1a1 in Eurasia is a palimpsest. Recent work in ancient DNA is suggesting that inferring past distributions from contemporary ones may lead us astray. It could be that R1a1 was once far more diverse in Europe and Central Asia, but that subsequent demographic events eliminated most of that diversity, while such events did not occur in Europe. Y chromosomal lineages may be particularly likely to be wiped out by the expansion of new tribes as old elites are killed or marginalized. The current distribution of a particular branch of R1a1 in Europe, associated in particular with Slavs, may be an expansion of the lineage which managed to survive elimination at some point in the mid-Holocene.

Though do note I put little weight in my speculations. It seems rather confusing. But since I was asked….

Carl Zimmer reports that it might be a function of physics. Bigger whales have proportionality bigger mouths, but at some point the biological engineering runs up against constraints:

s they report today in the Proceedings of the Royal Society, Goldbogen and his colleagues found that big fin whales are not just scaled-up versions of little fin whales. Instead, as their bodies get bigger, their mouths get much bigger. Small fin whales can swallow up about 90% of their own body weight. Very big ones can gulp 160%. In other words, big fin whales need more and more energy to handle the bigger slugs of water they gulp. As their body increases in size, the energy their bodies demand rises faster than the extra energy they can get from their food.

…

If the scientists are right, they may have discovered one of the big ironies in evolution. Lunge-feeding may have allowed whales to become the biggest animals ever to roam the planet. But this was not an open-ended invitation. Once whales got large enough, lunge feeding itself became so costly it prevented them from getting any bigger. Perhaps some day another animal will evolve a new strategy that will let it get even bigger than a blue whale. But for the animal kingdom as we know it, we may be sharing the planet with the biggest species it can offer.

Given enough time and a large population one can imagine that evolution might be able to figure out a solution, or back out of the adaptive dead end.

Since 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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In 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).

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

It’s News On Academia, Not Climate:

Yup, this behavior has long been typical when academics form competing groups, whether the public hears about such groups or not. If you knew how academia worked, this news would not surprise you nor change your opinions on global warming. I’ve never done this stuff, and I’d like to think I wouldn’t, but that is cheap talk since I haven’t had the opportunity. This works as a “scandal” only because of academia’s overly idealistic public image.

It is a shame that academia works this way, and an academia where this stuff didn’t happen would probably be more accurate. But even our flawed academic consensus is usually more accurate than its contrarians, and it is hard to find reliable cheap indicators saying when contrarians are more likely to be right.

If you don’t like this state of affairs join me in trying to develop a more reliable consensus mechanism on such topics: prediction markets. It just takes time or money. Prefer instead to act shocked, just shocked, when the other side is shown to do this stuff, while reserving your side’s ability to do the same? Then I have little respect for you.

A a new paper in PLoS ONE, Genetic Variation and Recent Positive Selection in Worldwide Human Populations: Evidence from Nearly 1 Million SNPs:

Our analyses both confirm and extend previous studies; in particular, we highlight the impact of various dispersals, and the role of substructure in Africa, on human genetic diversity. We also identified several novel candidate regions for recent positive selection, and a gene ontology (GO) analysis identified several GO groups that were significantly enriched for such candidate genes, including immunity and defense related genes, sensory perception genes, membrane proteins, signal receptors, lipid binding/metabolism genes, and genes involved in the nervous system. Among the novel candidate genes identified are two genes involved in the thyroid hormone pathway that show signals of selection in African Pygmies that may be related to their short stature.

They seem to have looked at about twice as many SNPs by combining the sets of Illumina and Affymetrix chips as the norm. But they looked at only around 1/4 the number of individuals as other studies which used the HGDP panel. To a first approximation the Affy and Illumina chips are really close in the patterns of variation which they detect, but, the Illumina chip had a significantly higher heterozygosity (this is evident in some of the supplementals just by inspection).

I reformatted a figure which shows ancestral contributions to the individuals in their sample at K = 6 (6 hypothetical populations which contribute to genetic variation). In the paper they discuss the fact that the Uyghur and Hazara resemble each other, and that the Uyghur seem to have a non-trivial Central/South Asian component, and finally that the Russian and Adygei have East Asian and Central/South Asian ancestry. None of this is surprising, all this was evident in other papers which used the same sample.

First, in regards to Russians, analysis of genetic variation among East European populations sometimes show a “long tail” of variation which leads toward East Asia among Russians. That is, Russians tend to cluster with other Europeans, but a minority of individuals are deviated in the direction of East Asians, that minority shrinking in proportion to distance from Europeans. The historical reason for this presents itself plainly: a significant minority of ethnic Russians have Tatar antecedents in the recent past, and of those who do not such ancestry may be derived from Slavicized Finno-Ugric populations who may have ancient connections to the populations of Siberia. The Russian Orthodox priest who was murdered last week known for preaching to Muslims was himself an ethnic Tatar by origin.

Second, one should expect the Uyghur and Hazara to resemble each other. The Hazara likely emerged during the period of Mongol rule of Iran and Afghanistan, and are descendants in part of Mongols and Turks from greater Mongolia who settled down in Afghanistan. The Uyghurs are a Turkic-speaking people, but historically the Tarim Basin was inhabited by Europoid populations. The emergence of the Uyghur and Hazara mimic each other almost perfectly. In particular, the East Asian component of their ancestry is from the same region. The non-East Asian aspect differs a bit, but not too much when set next to the East Asian component. Interestingly, the Uyghur speak a Turkic language, while the Hazara speaking Dari, the Persian dialect. One can probably chalk that up to distance from the Turco-Mongol ur-heimat.

Third, the Central/South Asian component among the Uyghur should not be too surprising, there is significant evidence that the Tarim basin was influenced by Indo-Iranians, as well as the Tocharians. Buddhism arrived in East Asia via the Tarim Basin after all, and there have always been trade routes from the southern edge of the Tarim down into northern India. But what about the Russians and the Adygei? I think that this signal has something to do with what we’ve termed elsewhere as “Ancestral North Indians” (ANI), who were closely related to European populations, and probably emerged from somewhere in Eastern Europe to Central Asia. I’ve been told that the Fst number for ANI-Northern European populations is on the order of the distance between Baltic peoples and southern Italians. So this group may have emerged on the margins of Europe, and expanded mostly within Asia.

There’s also an interesting chart showing patterns of selection, or at least what they detected, across geographies. Even if most of the signals are false positives one may hold that the real signals within this subset will still recapitulate the geographic relationships shown to the left. The patterns of selection mirror overall phylogenetic relationships. Note the overlap patters of Central/South Asians with Europeans and East Asians, some of both, but dominated by the former.

Citation: Lopez Herraez D, Bauchet M, Tang K, Theunert C, Pugach I, et al. 2009 Genetic Variation and Recent Positive Selection in Worldwide Human Populations: Evidence from Nearly 1 Million SNPs. PLoS ONE 4(11): e7888. doi:10.1371/journal.pone.0007888