Open Thread, 2/15/2015

Origin_of_Species (1)On Twitter Ryan Baldini asked for a “top 5” list of evolutionary biologists. Even though this is a sharply delimited list, beyond the top two I think there is going to be debate. As for those, I think Charles Darwin and R. A. Fisher take those stops. Darwin for developing a theory of evolution that was more than purely descriptive in its power (pre-Darwinian theories were not powerful theoretical frameworks, even if they intuited the likelihood of various evolutionary processes). Fisher, for fusing Mendelian genetics with evolutionary biology, and also for being seminal in the creation of population genetics, which is arguably the most elementary system by which one can explore evolutionary processes. But below these top two I think one can go many disparate directions.

For example, Alfred Russell Wallace was there with Darwin as a proponent of natural selection as a mechanism for Darwinian evolution. In fact he was arguably a more staunch pan-selectionist than Darwin himself. Then you have the two other dominant figures in early population genetics, Sewall Wright and J. B. S. Haldane. The debates between Wright and Fisher were influential within evolutionary genetics for decades.

41PHSZN6AELIn the second half of the 20th century it strikes me that W. D. Hamilton and John Maynard Smith loom very large. As in the comparison between Fisher and Haldane, I think there is a difficulty in that both Hamilton and Maynard Smith were very influential and brilliant thinkers, so choosing one seems to unintentionally diminish the other. But for me W. D. Hamilton probably does rank as third on the list, behind Fisher and Darwin. And many do argue that he is their heir (in his biography Hamilton does admit his huge debt to Fisher, though later on in life he also states that he began to view Sewall Wright more favorably). Contemporary with Hamilton and Maynard Smith was George Williams, who made some important conceptual breakthroughs in the 1960s which paralleled Hamilton’s formal endeavors.

Because of the important of population genetics in modern evolutionary biology, I think I’m inclined argue that Wright and Haldane should be in the top five. That leaves only one slot, and I’d give that as I note above to Hamilton, another theorist. This is obviously a biased and subjective list. Others may differ, and I invite you to offer your own ideas.

On another note, despite my moderation policy the comments are beginning to become more frequent here. If you want a response to a comment place it on an “open thread” if it is off topic. I try and respond to queries, but I can’t keep track of it all quite a bit of the time.

East Asians are a little more ‘ooga-booga’

1-s2.0-S0002929715000142-gr3
Citation: Complex History of Admixture between Modern Humans and Neandertals

In 2010 when the Neandertal sequence paper was published the word was that all non-Africans had the same proportion of ancestry from this population, a few percent. Over the past few years researchers have looked closer, and come to the conclusion that that was wrong. In particular, East Asians seem to have ~20 percent greater Neandertal ancestry than Europeans. Why? A simple solution is that there were several admixture events with Neandertals on the way out of Africa as modern humans settled the world. But there are other options, making recourse to standard population genetic theories. So last year in The genomic landscape of Neanderthal ancestry in present-day humans proposed that the higher fraction in East Asians in Neandertals was a function of the weaker efficacy of purifying selection, which removes deleterious alleles from the genetic background, in populations which went through bottlenecks. As you may know, East Asians seem to have gone through more bottlenecks in the out of Africa migration, probably because of several choke points from west to east Eurasia.

Two new papers in The American Journal of Human Genetics seem to suggest that this explanation is unlikely. First, in Selection and Reduced Population Size Cannot Explain Higher Amounts of Neandertal Ancestry in East Asian than in European Human Populations, the authors use simulation frameworks to suggest that the extent of the bottleneck difference can not account for the difference in ancestry fractions. In other words, there isn’t that much variation in purifying selection. In the second paper the authors explicit test the ‘two pulse’ model vs. the ‘single pulse’ model. To remove the confound of selection they looked at neutral regions, and the difference persisted. Though the authors could not rule out the possibility that Europe received an influx of African-like individuals who reduced the Neandertal fraction in western Eurasian, the three ancestral populations which fused to form Europeans (i.e., hunter-gatherers, first farmers, and the steppe invaders) all had about the same Neandertal fraction. This leaves then the possibility that East Asians received a second dollop of Neandertal ancestry, ergo, the two pulse model.

A few years back Jeff Wall published a paper that showed that the Complete Genomes Gujarati samples were in between the Europeans and East Asians in Neandertal fraction. We know that the “Ancestral South Indian” (AS) fraction of Gujarati ancestry is closer to East Asians than to West Eurasian groups. To me this suggests that the second admixture may have occurred in the eastern zone of the Middle East, seem it seems basal to the eastern lineages of humans.

The topology of the human phylogenetic graph is getting somewhat more complex. But there are diminishing returns. We’re arguing over tenths of a percent now, as opposed to percents. In the near future this book will be probably be closed.

The fallibility of science

500px-Snackwells_Devils_Food_cookies
“Healthy”
I’m old enough to remember when people were advised by severe-faced nutritionists about the dangers of eggs, all the while being totally unaware of the possible downsides of gorging on high-sugar, fat-free SnackWells cookies. This was the 1980s and early 1990s, when low fat and cholesterol were all the rage. Now The Washington Post is reporting that The U.S. government is poised to withdraw longstanding warnings about cholesterol. It’s a deeply reported story, so read the whole thing. This comes in the wake of research which debunks very low sodium diets, as well Time coming out with articles such as Where Dietary-Fat Guidelines Went Wrong. There are still debates about the details, with some people moving toward a very high fat diet, somewhat as a reaction to past anti-fat excesses I believe.

41ikBliWK8L._SY344_BO1,204,203,200_A lot of this collapse of the old orthodoxy can probably be traced back to Gary Taubes, at least in the public consciousness (see his The New York Times Magazine piece from 2002). Taubes and company now put sugar into the same category that fat and cholesterol were, though for somewhat different reasons (ergo, the focus on types of calories ingested). But health is not the only concern. Hundreds of millions of people have made their food less savory over a generation because of these false recommendations.

In The Washington Post the article concludes:

“These reversals in the field do make us wonder and scratch our heads,” said David Allison, a public health professor at the University of Alabama at Birmingham. “But in science, change is normal and expected.”

When our view of the cosmos shifted from Ptolemy to Copernicus to Newton and Einstein, Allison said, “the reaction was not to say, ‘Oh my gosh, something is wrong with physics!’ We say, ‘Oh my gosh, isn’t this cool?’ ”

Allison said the problem in nutrition stems from the arrogance that sometimes accompanies dietary advice. A little humility could go a long way.

“Where nutrition has some trouble,” he said, “is all the confidence and vitriol and moralism that goes along with our recommendations.”

41WL2k2+47L._SY344_BO1,204,203,200_A lot about nutrition is tied up to morality, and our ancient psychological fixations on the “purity” of food. That’s why no matter what people say about veganism, or paleo, or high/low fat/sugar/carb, in terms of its functional health consequences, it’s really about the values that you are projecting in terms of the psychology. And that’s why we tend to get into dietary moral panics so often. Because nutrition has a lot of variables producing an output (weight or overall health) it’s difficult to assess which ones are effecting change. If gunnery specialists were using non-Newtonian physics to land hits on the enemy we’d know pretty quickly that non-Newtonian physics (or at least pre-Newtonian mechanical intuition) just didn’t work. Though heart disease rates have gone down, Americans have become more obese. The signals are mixed. Meanwhile many of us are turning our lives upside down, eliminating or adding food elements on the latest research, which is often overturned or found to be statistically not robust. No wonder many people have started to tune out any health advice from the “authorities.”

Of course there is science, and there is science. Germ theory and epidemiology in relation to viral infections and vaccinations are a robust era of science. Planetary mechanics as well. In contrast many areas of nutritional, medical, and social science remain highly uncertain and low in confidence as to the nature of the results. You wouldn’t get that from the “experts” though. Science is science when they hold forth from on high. Except it’s not.

Addendum: I forgot to mention this, but one clear issue in regards to nutrition is sensitivity to particular individuals and populations. One of the ridiculousness of modern nutrition is how lowest-common-denominator and one-size-fits-all it seems to be. Yes, I’m generalizing here, but I know people with heritable familial cholesterol who were recommended to exercise and avoid eating a wide array by nutritionists even when this condition was already known to run in the family, and, the individuals in question were relatively fit. It was obvious that lifestyle and diet were marginal variables here, but the nutritionists simply could not imagine going off script.

If you have a family history of hypertension and stroke, by all means avoid salt. But it seems that for most of the population the downside risk to flavor is small to non-existent. Apparently the same might apply to cholesterol. And sorry, I think the same also applies to sugar! There are people who are more resistant to metabolic disease. If you enjoined the whole populations to avoid food that 10-25% might gain nutritional benefit, pretty soon that means everyone will eat literally nothing, because we all have different Achilles’ heels.

The Holocene Alien Years

Fst between ancient European populations
  Ba_MN Be_LN Ben_LN Cor_LN EHG LBK_EN Mo_HG Sp_EN Sp_MN Sw_NHG Un_EBA WHG
Baalberge_MN                        
Bell_Beaker_LN 0.020                      
BenzigeroH_LN 0.021 0.004                    
CordedW_LN 0.032 0.008 0.007                  
EHG 0.082 0.041 0.038 0.034                
LBK_EN 0.009 0.021 0.025 0.035 0.084              
Motala_HG 0.083 0.057 0.053 0.060 0.048 0.093            
Spain_EN 0.021 0.028 0.035 0.044 0.092 0.015 0.099          
Spain_MN 0.014 0.022 0.026 0.035 0.077 0.016 0.081 0.009        
SwedSk_NHG 0.066 0.050 0.048 0.054 0.058 0.078 0.034 0.084 0.074      
Unetice_EBA 0.016 0.002 0.003 0.005 0.034 0.022 0.051 0.030 0.023 0.043    
WHG 0.073 0.055 0.056 0.070 0.078 0.091 0.053 0.092 0.070 0.050 0.057  
Yamnaya 0.054 0.016 0.013 0.011 0.028 0.052 0.063 0.060 0.053 0.062 0.012 0.076

It is often said that the meeting of Europeans and Amerindians in the 15th century is our best taste of what it would be like to meet aliens. The analogy is rather straightforward, as Amerindians were not part of the broad interactions between societies over the Holocene, as they had removed themselves from the scene of action ~15,000 years ago. The interaction resulted in conflict and synthesis. A new people in Latin America arose who were biologically, and to a lesser extent culturally, a compound between two very distinct antecedents. In North America the dynamic was more of replacement and marginalization, often due to organized collective action on the part of white settlers and their political systems.

41ZlHlsdYXL._SY344_BO1,204,203,200_Above I have again placed a selection of Fst statistics from the preprint Massive migration from the steppe is a source for Indo-European languages in Europe. One must be careful about not over-interpreting these statistics. But, they give a good sense of genetic divergence between two populations, on average (I have uploaded all Fst values in an Excel file). In particular above I’ve focused on the ancient populations in the data set. EN is Early Neolithic, while MN is Middle, and LN is Late. HG is Hunter-Gatherer. I’ve bolded Fst values > 0.05, because to me that’s a pretty high threshold for serious genetic divergence. The LBK brought agriculture to vast swaths of Central Europe. These were the people who encountered the hunter-gatherers who had occupied the continent since the end of the last Ice Age. The genetic distance between these two groups is incredibly high. Between the generic “Western Hunter-Gatherer” population and the LBK the Fst value is 0.091. What does that mean? The Mala are a Dalit (outside the caste system) group from Southern India. The Fst between this group and WHG is 0.11. In other words, not that much greater than between WHG and LBK. The Fst between the Mala and the LBK, two populations separated by a continent and 7,000 years is 0.077, less than between WHG and LBK. The genetic distance between the Mala and the French is 0.051. Considerably less than between the WHG and LBK. The get a sense of how small the values between modern European groups are, the genetic distance between Lithuanians and Sardinians is 0.021. The genetic distance between Belarussians and the English is 0.004, or about 4% of the distance between WHG and LBK. My claim that the contact between the first farmers and the hunter-gatherers of early Europe was one of intercontinental scale interaction is justified by the fact that the genetic distance between Han Chinese and Europeans is about ~0.10, only marginally greater than between WHG and LBK.

These sorts of genetic distances on the ancient European landscape could only be due to massive cultural revolutions which produced demographic shifts which can in no way be modeled as continuous diffusion processes. The Bantu expansion is probably a good analogy for what happened in ancient Europe, it took a little over 1,000 years to traverse the whole continent of Africa, a much larger geographic zone than Europe. But a second issue that we must also focus on are the genetic distances between European hunter-gatherers. One could chalk up 0.078 between EHG and WHG to the fact that EHG has admixture from “Ancestral North Eurasians” (ANE) at a clip of ~40 percent. But even the distance between the Motala hunter-gatherers, who are only 15% ANE, and WHG is 0.053. The uniparental markers are strongly suggestive of a relatively small group expanding to fill Europe after the last Ice Age, they are overwhelmingly haplogroup I for Y chromosomes, and haplogroup U5 for females. So what gives with the high Fst values? This is far higher than any modern intra-European distances. One hypothesis that I think might be viable is that small effective population cranked up the genetic drift in these groups, whose marriage networks were sharply delimited by cultural fractionation as well as ecological constraints which reduced population density outside of narrow specially favored areas (e.g., marine environments). One consequence of excess drift is elevated Fst values, beyond what you might think would be plausible. I’m not specialist in cultural evolution, but my intuition tells me that hunter-gatherer groups can engage in fission rather rapidly, and these divisions may have enforced greater barriers to gene flow to relatively recently diverged groups than is the norm in modern agricultural and post-agricultural societies.

Another issue that comes to mind are future analyses of ancestry tracts and linkage disequilibrium in these populations. The reason I bring this up is the fact that we need to distinguish between genetic differences due to standard workaday isolation by distance, and those produced by pulse admixture events (see Gideon Bradburd’s preprint for more elucidation of this issue). For various reasons outlined in the preprint above I’m convinced that a group like EHG, and later the hunter-gatherers of Scandinavia, did undergo admixture with a very different population during the early Holocene, after their expansion from the Ice Age refugia. But ultimately looking at patterns of this ancestry in the chromosomes as well as estimating a time since admixture would nail the coffin on this likelihood.

Finally, there’s the issue of “Nazi optics.” When word of these results started to percolate last spring a friend who is a prominent human geneticist blurted out “it sounds like the Nazis were right!” By this, he meant that this story of migrations, and demographic turnover, would be much more in place in Europe before World War 2. But there’s an immediate refutation of any attempt to Nazify these results: the Fst statistics made it clear that long term result of the clash of peoples in the early to mid Holocene has been amalgamation. The Bronze Age people of Europe, who gave rise to the historic nations, are the heirs of both the hunter-gatherers long indigenous to the continent, and disparate aliens, who arrived as strangers thousands of years ago.

The Indo-European Völkerwanderung

Fst between selected populations
Armenian Bas Cord Czech EHG Eng Fren Gre LBK Lez Lith Sard Sin WHG
Basque 0.017
Corded_Ware_LN 0.023 0.025
Czech 0.011 0.009 0.015
EHG 0.067 0.060 0.034 0.043
English 0.011 0.008 0.014 0.002 0.045
French 0.009 0.006 0.015 0.001 0.048 0.001
Greek 0.004 0.010 0.019 0.004 0.057 0.005 0.003
LBK_EN 0.023 0.024 0.035 0.024 0.084 0.024 0.020 0.016
Lezgin 0.005 0.018 0.017 0.010 0.052 0.011 0.009 0.007 0.032
Lithuanian 0.019 0.014 0.016 0.003 0.043 0.006 0.006 0.010 0.034 0.015
Sardinian 0.014 0.013 0.033 0.013 0.074 0.012 0.009 0.009 0.015 0.021 0.021
Sindhi 0.016 0.032 0.029 0.022 0.057 0.023 0.022 0.020 0.049 0.014 0.028 0.035
WHG 0.086 0.062 0.070 0.056 0.078 0.058 0.058 0.070 0.091 0.082 0.053 0.074 0.087
Yamnaya 0.030 0.034 0.011 0.020 0.028 0.021 0.022 0.026 0.052 0.019 0.022 0.044 0.028 0.076

Update: Nick Patterson writes: Much ancient DNA genotype data is “pseudo-diploid” with just one allele given for a sample at each SNP. If you want to compute F_st values for such data, the easiest way is to run smartpca (see http://genetics.med.harvard.edu/reich/Reich_Lab/Software.html) with inbreed: YES set in the parameter file.

The downside is that this option requires at least 2 samples for each population while the default option (inbreed: NO) works on a single sample.


The above table is a selection of FST values I culled from the preprint Massive migration from the steppe is a source for Indo-European languages in Europe. To get an intuition, the FST value comparing Northern Europeans and Nigerians is ~0.15 using SNP data. Before I get to the meat of the argument above, let’s take that in for a moment. You see above that the pairwise values between WHG, “Western Hunter-Gatherers,” and the LBK, the first farmer culture of Central Europe, is on the order of ~0.10. That’s about the value between Europeans and East Asians today. We also know that it is possible there was a difference in color between the hunter-gatherers and the first farmers. The meeting of farmer and hunter-gatherer in early Neolithic Europe, and down to the Bronze Age, may best be thought of as analogous to a long term racial conflict and coexistence. Rather than a gradual wave of advance I envisage that the farmers hopped from point to point along fertile stretches of maritime littoral, and pushed their way up into the heart of Europe’s ancient forests by felling the wilderness around the great rivers which issue forth from the uplands. In a world of “isolation by distance” and “clines” this sort of recourse to a term like “race” would be anachronistic, but the model of genetic disruption being reported in these results using ancient DNA strong suggests punctuated demographic transitions across a wide range of localities which would result in biologically and culturally distinct groups persisting for many generations cheek by jowl.  Over time admixture resulted in amalgamation, but it was almost certainly a millennia long process.

More specifically, the authors report unequivocally that the arrival of cultures like the Corded Ware in Northern Europe 4,500 to 5,000 years ago was accompanied by massive demographic replacement. Not only were these bands of warriors traversing the landscape, but it was a whole people on the move, men, women, and children. These were akin to the Goths fording the Danube and bursting into a new landscape of conquest. But the lands of the first farmers were not like those of Rome, heavily settled, further human cattle for the steppe agro-pastoralists to extract rents from. The preprint is not clear as to the timescale of the arrival of the eastern genetic influence across Southern Europe, but in the North the conclusion is without nuance or qualification: during the early years of the Egyptian Old Kingdom the lands of the north were being roiled by migration.

admixBut in this post I want to turn the focus away from Europe for a bit. In the text they note that “An interesting pattern occurs at K=8, with all the late LN/BA groups from central Europe and the Yamnaya having some of the “light green” component that is lacking in earlier European farmers and hunter-gatherers; this component is found at high frequencies in South Asian populations….” I’ve edited and uploaded a version of the admixture plot. One must be cautious when interpreting these plots, but with all the other information in the paper it is quite informative. As far back as Noah Rosenberg’s 2005 paper, and later on in the blogger Dienekes Pontikos’ analyses, there were suggestions of affinities between a subset of Europeans and South Asians, as well as a connection to the Caucasus. In the FST results above I note that the Sindhi population is closer to the Lezgins (Northeast Caucasians) and Yamna samples than they are to Armenians. The details are difficult to parse though. Otherwise they would have done so in this monumental paper.

I do want to add one final thing though. It’s been assumed in the past, including by me, that once farmers were established in a locale that future demographic perturbations were unlikely. By this, I mean that farmers are more useful alive to generate economic surplus for incoming elites than they are eliminated. But that is predicated on the idea of a complex specialized society where the elites view all non-elites in an almost Marxian sense of being objects of exploitation. It could very well be that this sort of cosmopolitan globalism only became common in complex societies later, and that in pre-state tribal groups even dense populations did not prevent extermination, because expropriation of vital resources necessary for survival was far more viable an option for these societies than exploitation.

There were giants in the earth in those days

horsewheellanguage
Update: The preprint is out. End update

… and also after that, when the sons of God came in unto the daughters of men, and they bare children to them, the same became mighty men which were of old, men of renown.

Genesis, 6:4

A Battle-Axe
A Battle-Axe

An emanation from the one most high…uh, I mean, David Reich, has given his talk at Oxford. Thanks to Jean Manco we have a pretty good report of what he said. The core element seems to be that a paper will soon be published using ancient DNA results to conclude that Indo-European languages came to Europe from the Yamna culture of the Pontic Steppe ~4,000 years ago. Roughly, the argument laid out by David Anthony in The Horse, the Wheel, and Language: How Bronze-Age Riders from the Eurasian Steppes Shaped the Modern World. Where Reich’s conclusions differ from those that Anthony presented in the book is that this eruption from the Eurasian heartland resulted in a genetic-demographic transformation of Europe ~4,000 years ago. Manco confirms that the genetic data from the ancient sites that Reich’s team has access too indicate that the two dominant Y chromosomal haplogroups in Europe, R1b, and R1a, arrived with the Yamna people. This is not surprising, as previous ancient DNA exhibited a surprising death of these two lineages from both hunter-gatherer and early to late Neolithic populations in Europe. And, recent whole genome sequencing of Y chromosomes indicates that both R1a and R1b lineages across Eurasia have undergone recent explosive demographic expansion on a Holocene timescale (closer to 5 than 10 thousand years). In terms of total genome ancestry it looks as if the transition to Yamna successor cultures in Central Europe (e.g., Corded Ware) was accompanied by substantial genetic turnover. In the initial Corded Ware burial grounds 60-80 percent of the ancestry seems to have derived from the Yamna. The modern Yamna-derived proportion seems to be closer to ~50 percent in a region like Germany.

The Yamna themselves are a compound population, a mix of ancient hunter-gatherer groups (analogous to the modern Karelians), and an intrusive population with Near Eastern affinities, likely from the Caucasus. I am not clear whether the Near Eastern group had  “Ancestral North Eurasian” ancestry, but the hunter-gatherers almost certainly did. The 1 to 18 percent  “Ancestral North Eurasian”  ancestry across continental Western and Central Europe today dates to the arrival of these Indo-European speakers. The very low fractions in Southern Europe, and its near absence in Sardinia, may suggest that the Indo-Europeans were demographically more significant in Northern Europe, even though they were clearly culturally effectual along the northern rim of the Mediterranean, and into Anatolia. In line with the Mal’ta results Manco relays that Reich believes that the R lineages, which are the dominant ones across Indo-European speaking populations from the North Sea down to South Asia, came into Europe via the Yamna, but ultimately derive from an “Ancestral North Eurasian” group.

220px-Yamna-en.svgThere are some phenotypic tidbits in the talk apparently. The Yamna were tall in terms of their genomic potential. Additionally, the very high frequency of lactase persistence may date to their arrival in Europe (there is some lack of clarity here). I doubt the high lactase persistence frequency and genotypes which result in greater final height are together by coincidence. Large people need a larger nutrient pipe, and adult digestion of lactose sugar would enable that.

There are two aspects which are not widely address in this talk. First, what was the exact dynamic of how the Indo-Europeans replaced the original populations? The idea of “demic diffusion” by waves of “demographic advance” promoted by Colin Renfrew seem to gradual and continuous to be responsible for this. This is basically an argument predicated on individual fitness, summed over groups. In this case I suspect that a better analogy may be the future that Genghis Khan had in mind for Northern China before his adviser Yelü Chucai dissuaded him: the North European plain was cleared out of people and turned over to pastureland. Genghis Khan and his Mongols were convinced of the value of Chinese as tax paying peasants, who could support the Mongol elite with their surplus. I suspect in a pre-state society such considerations were less relevant, as the institutional frameworks which would allow for the smooth absorption of subordinate groups were less elaborated, or even non-existent.

Hittites
Hittites

In both the Late Neolithic and after the Bronze Age the Reich group alludes to a return of the primal populations which were marginalized by the farmers, and later the Indo-European agro-pastoralists. One way to look at this is that there were larger migrations which were overlain upon the palimpsest. But, I believe one might also consider a model whereby there is ascertainment bias in the sorts of burial sites being explored and sampled, and one might be witnessing a patchy occupation of the landscape by intrusive cultures. For example, the newcomers might monopolize the rich bottom-lands for thousands of years, but huge swaths of the hinterland might be occupied by marginalized and less developed people, who over time drift into the core and become culturally absorbed. Instead of imagining the expansion of these people as purely ones of a vast uniform wave front, it might be better to conceptualize them as penetrating into virgin territory along the optimal avenues of settlement, and producing a patchy archipelago of habitation.

Second, there is the issue that though Reich and company focus on Indo-Europeans and the Yamna culture, the genetics leaves may loose threads that are difficult to tie back up. At ASHG Mait Metspalu express to me some misgivings about the term “Ancestral North Eurasian.” How do we truly know the locus and distribution of this ancestral component across Eurasia ~10,000 years ago? The Kalash of Pakistan exhibit signals of admixture with this group as high as Northern Europeans, so it is not limited to West Eurasia proper. The highest fractions today seem to be found in the North Caucasus, among many groups which are not Indo-European. If R1a was brought by Indo-Europeans to Europe, it is harder to conclude that this was the case in South Asia. Though the frequency of these lineages is higher in the Indo-Aryan North, there are relatively high fractions of R1a even among some South Indian tribal populations. R1b is found in appreciable fractions in Sardinia and among the Basques (one argument for the old idea that R1b was the legacy of European hunter-gatherers!). Obviously some of this could be due to admixture between Indo-Europeans and non-Indo-Europeans. But I think a major issue here is that Indo-European groups were a synthetic population which arose in a world where there were many synthetic populations, with ancient and recent affinities to them. I doubt the “Ancestral North Eurasian” ancestral component was limited purely to Indo-Europeans. So it seems unlikely that the R1 lineages would be purely Indo-European, even if recent expansion of some of their sub-lineages is a function of the Indo-European cultural explosion.

Of course there are only so many ancient DNA samples one can retrieve from a finite number of sites. The age of new genomic discoveries will start to close over the next few years as the paleo-demography inferred will start to exhibit some predictable solidity. That means that a deep knowledge of the archaeology, and what history there is, is essential.

Sinners in the hands of an angry mob

41Ybrs+5FTL._SY344_BO1,204,203,200_On a Bloggingheads conversation Freddie deBoer where is talking about the Jon Chait’s recent article on political correctness gone wild, he notes that points are given to those who are first to highlight the “problematic” aspect of something. Over time this leads to a constriction and strangulation of all open conversation, as the bounds of acceptability become progressively narrower. What I found fascinating is that it reminded me of something I read years ago in The Essential Talmud, where the author explains that rabbinical genius was discovered by means of further extending Jewish law into domains where it had not previously gone. The problem, which was left implicit, is that it often meant that the regulated behavior of observant Jews become more and more constricted. Much of the same applies to those who live by Islamic law, as well as Christian sects which begin to deviate into an orthopraxic direction. Once greater emphasis and reward is given to those who would make a case for the forbidding of a practice or belief, then the cultural ratchet is inevitable. And because of the dire theological consequences of transgressing what is forbidden the communal sanctions can be quite intense.

I am not particularly interested in exploring all the details of this line of thought. Rather, ruminating upon the fixation with identity and language discourse on the cultural Left, and the energy it draws, I have become convinced that the Koch brothers and their fellow travelling plutocrats have nothing to worry about. Though the Left talks a big game about economic inequality, dollars are not witches, and the rich are not numerous enough to build a witch-hunting academic career upon. This an age where Deng’s exhortation to get rich is glorious is applicable to the United States, the populist Right is inchoate and ineffectual, and the populist Left truly doesn’t exist.

Steven Pinker against those incommensurable with reason

The_Better_Angels_of_Our_NatureAt this website Steven Pinker has uploaded a PDF, Response to the Book Review Symposium: Steven Pinker, The Better Angels of Our Nature. You can find what he’s responding to in a journal with the title Sociology, which should update your probabilities if you are of a certain orientation. The response is basically “positivism porn,” so you won’t read it to be wowed by novel insights. Rather, it’s a nice “pwn” you can consume for the vicarious joy. And, on a purely sociological level it does illustrate the chasm between what passes for scholarship in some fields with the sort of endeavor that someone like Pinker is attempting.

It highlights the fact that we’re seeing an “epistemic closure” problem on some of the intellectual cultural Left. That is, if you don’t engage with a specific set of thinkers and accept particular priors, you aren’t really worth taking seriously. Of course the inverse is true for someone like me. You’re going to lose me at “critical race theory.” I just happen to think that my views match more closely the shape of reality, and it just so happens that our civilization is necessarily built upon the assumptions of a naive positivism which has great instrumental utility.

Yet I have to admit that I suspect many of our enemies in the “Post Modern” camp probably don’t deeply believe in their own presuppositions. It’s more a signalling game which yields personal gains and public acclaim. Genuine solipsism is a dead end, and subjectivism is almost always used selectively to skewer positions and views one holds in contempt, rather than eating away at one’s own dearly held beliefs. This is, by the way, in contrast to the long term arc of science, which has tended to often eviscerate the propositions which practitioners of science hold to be true and beautiful.

Eat more spice to battle weight gain?

1326-2TI really like spicy food. A lot. Though I appreciate a good habanero or ghost pepper, sometimes fresh peppers do not keep well. So I’m a bit of a connoisseur of hot sauces. Recently I ordered two bottles of Da Bomb, Ground Zero. At ~250,000 Scoville units it’s spicy enough to satisfy me, but unlike the Final Answer it doesn’t seem positively dangerous (when I put the Final Answer on a burger, I ate with gloves on). I recommend readers who trust me in this area to check this hot sauce out, it’s a really good value for the price, and though it isn’t as flavorful as milder concoctions it doesn’t taste nearly as chemical as some of the Dave’s Insanity line.

Because of the high amount of spice that I consume I’m always looking out for the scientific implications of the consumption. On the whole it seems like it’s a wash in terms of the results, so I focus on the hedonic utility. But Nautilus Magazine has a infographic up, The New Superfood? Spice. The whole idea of a “superfood” is pretty fallacious in my opinion, but it points me to the research in question, a presentation today at the Biophysical Society meeting:

Obesity contributes to diabetes, hypertension and myocardial infarction. Exercise is an effective measure to counteract obesity. Recent research demonstrates a regulatory role of transient receptor potential vanilloid 1 (TRPV1) in high fat diet (HFD)-induced obesity. Here, we evaluated the effects of exercise ± dietary capsaicin (CAP, 0.01% of total HFD), an active ingredient in natural chili peppers and a TRPV1 agonist, on HFD-fed wild type and TRPV1-/- (TRPV1 knockout) mice. We evaluated the performance of normal chow diet (NCD) or HFD (±CAP)-fed mice on computer-controlled rotarod. Trained mice were exercised for 12 min./day for five days a week. HFD+CAP-fed mice walked on the rotarod for a longer duration of the exercise regimen (630 ± 69 sec.) and showed lesser weight gain after 25 weeks of feeding (11.5 ± 2.1 g) compared to exercised HFD-fed mice (440 ± 215 sec.; 27.5 ± 2.1 g). Both sedentary and exercised HFD-fed groups exhibited similar weight gain, albeit an increase in food consumption shown by exercised HFD-fed group. Also, exercised HFD + CAP-fed mice showed an increased metabolic activity compared to exercised HFD-fed group. Further, NCD-fed WT mice walked for longer duration on the rotarod (704 ± 14 sec) and gained lesser weight at 20 weeks of feeding (4.5 ± 0.7 g) than NCD-fed TRPV1-/- mice (665 ± 50 sec.; 7.7 ± 2.1 g). CAP prevented weight gain to a similar extent in both sedentary and exercised wild type mice. Also, Dietary CAP improved the endurance of mice on rotarod and counteracted HFD-induced suppression of muscle coordination. This suggests a novel role of TRPV1 in metabolism and muscle coordination function. Collectively, our data provide evidence for the role of TRPV1 and its activation by dietary CAP and exercise to inhibit HFD-induced obesity

I’m not much into studies on mice, but those who know this area can tell me whether this is legit or not. As someone who is focused on burning the fat I’m quite happy that my consumption habits might be helping me stave off corpulence.

Open Thread, 2/8/2015

713c9hKhvqL._SL1500_So I just bought the Kindle Version of The Shape of Ancient Thought: Comparative Studies in Greek and Indian Philosophies for $3.99. At 780 pages this is a substantial work, and from what I can tell it’s an academically oriented text (not one of those Kindle “books” which are cut & paste jobs out of Wikipedia). Yet strangely the hardcover edition is much more expensive, at $39.99. That’s a huge discount. Additionally, the “digital list price” is $33.99. Is this incredible deal random? Or does Amazon know that I’m likely to buy this book at this price point? The only non-introductory population genetics text that I know of on Kindle is Matthew Hamilton’s, and it’s Kindle price is $58.99, pretty steep. I generally avoid buying books which might have figures and mathematical symbols in electronic format, because they don’t always render well on a Kindle, but if the Hamilton book was cheap enough I’d go for it (I don’t have a physical copy because I’ve got all the other major population genetics textbooks already).

Also, my friend Ryan Baldini just put up a paper on bioRxiv that some readers might find of interest, Harsh environments and “fast” human life histories: What does the theory say?. I’ll have more comment when I’ve thoroughly read the paper.