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I am travelling much of this week with the family. So expect me to be “off the grid” a bit.
But I will check this thread every day or so.
The Unz Review: An Alternative Media Selection
A Collection of Interesting, Important, and Controversial Perspectives Largely Excluded from the American Mainstream Media
The above model of the settlement of the Americas is from a new paper which utilized ancient mtDNA, Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas (open access):
The exact timing, route, and process of the initial peopling of the Americas remains uncertain despite much research. Archaeological evidence indicates the presence of humans as far as southern Chile by 14.6 thousand years ago (ka), shortly after the Pleistocene ice sheets blocking access from eastern Beringia began to retreat. Genetic estimates of the timing and route of entry have been constrained by the lack of suitable calibration points and low genetic diversity of Native Americans. We sequenced 92 whole mitochondrial genomes from pre-Columbian South American skeletons dating from 8.6 to 0.5 ka, allowing a detailed, temporally calibrated reconstruction of the peopling of the Americas in a Bayesian coalescent analysis. The data suggest that a small population entered the Americas via a coastal route around 16.0 ka, following previous isolation in eastern Beringia for ~2.4 to 9 thousand years after separation from eastern Siberian populations. Following a rapid movement throughout the Americas, limited gene flow in South America resulted in a marked phylogeographic structure of populations, which persisted through time. All of the ancient mitochondrial lineages detected in this study were absent from modern data sets, suggesting a high extinction rate. To investigate this further, we applied a novel principal components multiple logistic regression test to Bayesian serial coalescent simulations. The analysis supported a scenario in which European colonization caused a substantial loss of pre-Columbian lineages.
The key here is that looked at whole mitochondrial genomes, which gives them more information to work with. Earlier work often focused on a particular variable region of the mitochondrial genome. And, mtDNA is copious, so they got good quality data from all of their samples (really 5x is decent for population genomic work, and that was the worst). Combined with the fact that they had ancient genomes, which allow them to investigate the phylogeny in a more precise manner temporally, and have you the potential to make some really strong inferences.
Figure 3 in the paper makes everything really clear. The last common ancestors between Native American mtDNA lineages and those of Siberians is >20,000 years before the present. That is, before the Last Glacial Maximum. The next major feature you see is an explosion of lineages aroun ~15-16 thousand years ago. This is the hallmark of a rapid population expansion. But after the initial period of diversification you see the persistence of a lot of deeply divergent lineages. Additionally, further population genomic modeling indicate that there was a major extinction event ~500 years ago, no doubt due to the Columbian Exchange and the arrival of Old World populations and their diseases.
This paper is fundamentally about Native American historical genetics. It is another nail in the coffin of the “Clovis first” model of Amerindian origins. Basically, that the Clovis group of megafaunal hunters were the First Americans. No, it does seem likely now that modern humans were present in portions of the New World thousands of years before Clovis. The Monte Verde site’s occupation on the Chilean coast less than two thousand years after the opening of a coastal route from Beringia indicates that perhaps there was a strong focus on marine environments for a significant period of time. Once the New World was settled there seems to have been a lot of persistent population structure, until the arrival of Europeans, at least in comparison to what ancient DNA has told us about Europe. Additionally, the long isolation of the Beringians is also significant in my opinion.
In a world of billions of humans it may be that we lack proper intuition for how little gene flow may have occurred between populations in a sparsely populated globe. The Beringians were separated from Siberians for on the order of ~5,000 years. It only takes ~1 migrant between two populations per generation to prevent them from drifting apart in allele frequencies, so the gene flow was very low (this is mtDNA, so not strictly applicable, but the same logic holds). But it is possible that in much of northern Eurasia during the Last Glacial Maximum humans retreated to zones of survival, and vast swaths of territory became empty. This would result in islands of human habitation diverging and become very different over several thousands of years. In sharp contrast, the world over the past 4,000 years or so has been characterized by the ability of humans to travel long distances over inclement territory, and settle amongst strangers, usually through conquest. Partially this is due to the domestication of the horse, but partially it is probably due to the emergence of high density complex societies which can incubate specialist castes whose role arose initially as defense, but who often engage in offense whenever the opportunity arises.
About one week ago I wrote about bilingual education, and I admitted my mild skepticism about the research about the benefits of bilingualism. A friend emailed me and wondered why I was only “mildly skeptical.” Partly I didn’t want the comments to get sidetracked, but recently friends on Facebook have started to get exercised that Ron Unz is running for the Senate, and how bad he is for not giving the children the opportunity to be bilingual. And of course all the research that confirms how great bilingualism is referenced.
So here’s an article from last month that my friend sent me. I’ll quote the appropriate section, you’ve seen this movie before, The Bitter Fight Over the Benefits of Bilingualism: For decades, some psychologists have claimed that bilinguals have better mental control. Their work is now being called into question:
But a growing number of psychologists say that this mountain of evidence is actually a house of cards, built upon flimsy foundations. According to Kenneth Paap, a psychologist at San Francisco State University and the most prominent of the critics, bilingual advantages in executive function “either do not exist or are restricted to very specific and undetermined circumstances.”
Paap started looking into bilingualism in 2009, having spent 30 years studying the psychology of language. He began by trying to replicate some seminal experiments, including a classic 2004 paper by Bialystok involving the Simon task. In that task, volunteers press two keys in response to colored objects on a screen—for example, right key for red objects, left for green. People react faster if the position of the keys and objects match (red object on right half of the screen) than if they don’t (red object on left). But Bialystok found that twenty Tamil-English bilinguals from India were faster and more accurate at these mismatched trials than twenty English-speaking monolinguals from Canada. They were better at suppressing the location of the objects and focusing on their color—a sign of superior executive function.
“It was a really exciting finding and one that I thought would be easy to study with my students,” says Paap. “But we just couldn’t replicate any of the effects.” After years of struggling, he published his results in 2013: three studies, 280 local college students, four tests of mental control including the Simon task, and no sign of a bilingual advantage.“That broke the dam,” he says. “Others started submitting negative results and getting their articles published.”
Jon Andoni Duñabeitia, a cognitive neuroscientist at the Basque Center on Cognition, Brain, and Language, was one of them. In two large studies, involving 360 and 504 children respectively, he found no evidence that Basque kids, raised on Basque and Spanish at home and at school, had better mental control than monolingual Spanish children. “I am a multilingual researcher working in a multilingual society,” says Duñabeitia. “I’d be very happy to see an advantage for bilinguals! But science is what it is. We find no difference and we have replicated it several times, in older adults, kids, and young adults at university.”
…
For example, one group of researchers analyzed 104 abstracts on bilingualism that were presented at scientific conferences. They found that 68 percent of abstracts that found an executive-function advantage were eventually published in journals, compared to just 29 percent that found no advantage. This publication bias, a common problem in psychology and science as a whole, means that the evidence for the phenomenon seems stronger than it actually is.
But Paap doesn’t think much of the published evidence either. He found that a bilingual advantage only shows up in one in six tests of executive function, and mostly in small studies involving 30 or fewer volunteers. The largest studies, involving a hundred or more, all found negative results.
The proponents of bilingualism as a cognitive benefit have reacted angrily. Read the whole thing. But it’s probably not a real strong effect if there is any at all. Just another battle in the replication wars….
• Category: Science • Tags: Psychology
One of the major distinctions pundits made between Al Qaeda and ISIS until recently is that the latter was not as fixated on the “far enemy” (the West) as the former. That seems born out by the evidence of their behavior, focusing on conquests in the Levant and Iraq, as well as ideological arguments (e.g., What ISIS Really Wants). The New York Times now seems to be making the case that that was all wrong, How ISIS Built the Machinery of Terror Under Europe’s Gaze:
For much of 2012 and 2013, the jihadist group that eventually became the Islamic State, also known as ISIS or ISIL, was putting down roots in Syria. Even as the group began aggressively recruiting foreigners, especially Europeans, policy makers in the United States and Europe continued to see it as a lower-profile branch of Al Qaeda that was mostly interested in gaining and governing territory.
…
“All of the signals were there,” said Michael S. Smith II, a counterterrorism analyst whose firm, Kronos Advisory, began briefing the United States government in 2013 on ISIS’ aspirations to strike Europe. “For anyone paying attention, these signals became deafening by mid-2014.”
In June of 2015 The New York Times wrote about the decapitation:
… Mr. Cazeneuve emphasized that while Mr. Salhi was known to have links to Salafists, he was not believed to have links with terrorist groups.
There was no indication that Mr. Salhi was aligned with the Islamic State….
Basically the media became a telegraph service for craven politicians who didn’t want to face the crisis. I observed that The New York Times recently referred to Molenbeek as a “fifth column.” That sort of language is something that politicians and the media try to avoid, both for prudential and ideological reasons. When these “isolated” attacks occurred a few years ago the conservative press ridiculed the characterizations of the politicians and the media. It turns out that they were right, and The New York Times is admitting it. This should give us even more pause in accepting the “analysis” of the established outlets. When the evidence is confronting them this starkly they’ve had to fess up that they weren’t scratching below the surface, and perhaps even had become a cat’s-paw in the toolkit of the political class. Though I will credit The New York Times that there has been a change of direction internally when you allow Muslim communities in the West to be characterized as a possible “fifth column.” Unfortunately in Molenbeek’s case that seems operationally correct, and the evidence was too strong to obfuscate for reasons of political and ideological expedience.
• Category: Foreign Policy • Tags: ISIS
It has recently come to my attention that David Reich has two post-doctoral positions open which might interest readers of this weblog. Since I really enjoy writing about the research that his lab produces it is in my interest that he find the right people to work on the projects that he has. If you are one of those rare people in the world who has a background in history and statistical population genetics or data science this might be for you! Here are the listings, ignore the deadline date as they have been extended:
1) Post-doctoral fellow: Ancient DNA
Our ancient DNA laboratory has pioneered large-scale studies of human population history with large numbers of samples simultaneously and we are looking for a highly motivated post-doctoral researcher with appropriate experience and interests to work on analysis of these data.
The successful candidate will have previous experience in a world class ancient DNA laboratory, as well as analytical and computer skills that allow exploration of large and complex genetic data sets.
Description of additional projects in our lab, as well as papers we have recently published, is provided here.
The position will be supervised by Dr. David Reich.
Please write to reich at genetics [dot] med [dot] harvard [dot] edu by March 1, 2016 if you are interested.
2) Post-doctoral fellow: Learning about history using genetic data
We are searching for a highly motivated post-doctoral researcher to join our group.
The successful candidate will have exceedingly strong statistical / mathematical / computational skills, and an interest in history. While a background in population genetics, bioinformatics or experimental biology is advantageous, it is not necessary. Our lab has the resources to not only analyze large public data sets, but also has access to some of the world’s best new genetic data, whether generated by collaborators or in our own laboratory. Possible projects are:
• Studying human history using data from present-day populations
• Studying human history using ancient DNA
• Studying the process of speciation and the mechanisms of natural selection and mutation using genetic data
Description of projects in our lab, as well as papers we have recently published, is provided here.
The position will be jointly supervised by Drs. David Reich and Nick Patterson, and will involve work at both Harvard Medical School and the Broad Institute of Harvard and MIT.
Please write to reich at genetics [dot] med [dot] harvard [dot] edu by March 1, 2016 if you are interested.
The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans:
Some present-day humans derive up to ∼5% …of their ancestry from archaic Denisovans, an even larger proportion than the ∼2% from Neanderthals…We developed methods that can disambiguate the locations of segments of Denisovan and Neanderthal ancestry in present-day humans and applied them to 257 high-coverage genomes from 120 diverse populations, among which were 20 individual Oceanians with high Denisovan ancestry…In Oceanians, the average size of Denisovan fragments is larger than Neanderthal fragments, implying a more recent average date of Denisovan admixture in the history of these populations (p = 0.00004). We document more Denisovan ancestry in South Asia than is expected based on existing models of history, reflecting a previously undocumented mixture related to archaic humans (p = 0.0013). Denisovan ancestry, just like Neanderthal ancestry, has been deleterious on a modern human genetic background, as reflected by its depletion near genes. Finally, the reduction of both archaic ancestries is especially pronounced on chromosome X and near genes more highly expressed in testes than other tissues (p = 1.2 × 10−7 to 3.2 × 10−7 for Denisovan and 2.2 × 10−3 to 2.9 × 10−3 for Neanderthal ancestry even after controlling for differences in level of selective constraint across gene classes). This suggests that reduced male fertility may be a general feature of mixtures of human populations diverged by >500,000 years.
Take a look at the supplements for the functional stuff. I am not going to address that. Much of those results have been circulation or in other papers over the years. Rather, I want to highlight the variation in patterns of Denisovan admixture in non-Oceanian groups. Here is an important section:
Taken together, the evidence of Denisovan admixture in modern humans could in theory be explained by a single Denisovan introgression into modern humans, followed by dilution to different extents in Oceanians, South Asians, and East Asians by people with less Denisovan ancestry. If dilution does not explain these patterns, however, a minimum of three distinct Denisovan introgressions into the ancestors of modern humans must have occurred.
You see it on the figure above. The South Asian groups consistently jump well above the trend line for inferred Denisovan as a function of shared ancestry with Australians non-West Eurasian ancestry. Also, if you look at the admixture patterns for Denisovan ancestry in South Asia you see they follow the ANI-ASI cline. That is, it seems to come into the South Asian populations through the “Ancestral South Indians.” Interestingly, the Onge sample of Andaman Islanders has less Denisovan than low caste South Asian groups, reminding us that though the Onge and their kin are the closest modern populations to the ASI, they are not descended from the ASI. The highest fraction of inferred Denisovan is in the Sherpa people of Nepal.
The figure to the right is from Admixture facilitates genetic adaptations to high altitude in Tibet, and the authors find that the Sherpa are at one extreme in an ancestry cline in comparison to other East Asians. The figure is hard to make out, so I will tell you that many of the Sherpa are fixed for the red component, while other Tibetans are in positions in the middle, and most East Asians have low fractions of the red, with the Dai having none. The Gujarati sample form the HapMap have low fractions of both East Asian components. This is almost certainly an artifact of the shared ancestry of all eastern Eurasians (and perhaps Oceanians), of which the ASI were one descendant group. The proportion of Denisovan in low caste South Asians indicates that the fraction in ASI was about at the same level as the Sherpa. I suspect that ASI and the Tibetan groups got their Denisovan via different paths, but it doesn’t seem like we know yet.
Overall I do marvel at what ancient DNA can tell us. Without it we wouldn’t be talking about any of these admixture events; they’d be signals too weak to have left an obvious mark in the genome.
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Sardinian actress
Previous genetic studies have suggested a history of sub-Saharan African gene flow into some West Eurasian populations after the initial dispersal out of Africa that occurred at least 45,000 years ago. However, there has been no accurate characterization of the proportion of mixture, or of its date. We analyze genome-wide polymorphism data from about 40 West Eurasian groups to show that almost all Southern Europeans have inherited 1%–3% African ancestry with an average mixture date of around 55 generations ago, consistent with North African gene flow at the end of the Roman Empire and subsequent Arab migrations. Levantine groups harbor 4%–15% African ancestry with an average mixture date of about 32 generations ago, consistent with close political, economic, and cultural links with Egypt in the late middle ages. We also detect 3%–5% sub-Saharan African ancestry in all eight of the diverse Jewish populations that we analyzed. For the Jewish admixture, we obtain an average estimated date of about 72 generations. This may reflect descent of these groups from a common ancestral population that already had some African ancestry prior to the Jewish Diasporas.
At the time Dienekes had a pretty strong critique of the paper: the authors assumed that Northern Europeans were an unadmixed reference population, when in fact these populations may have had mixture from East Asians. He presented PCA plots which illustrated the fact that CEU (whites from Utah with British and German ancestry) sample were shifted toward Chinese in comparison to Sardinians. All these years later I think that in fact there is another explanation besides East Asian admixture to explain this: the Chinese themselves have some admixture from West Eurasians. The Sardinians are notably lacking in some admixture components common among mainland Europeans, so the West Eurasian admixture into Chinese probably is closer to mainland Europeans than it would be to Sardinians.
So what about the Sardinian admixture from Africans? The same dynamic might be at play here: old admixture from “Early European Farmers” into Africans might explain why they’re closer to Africans.
But let’s assume that the Sardinian admixture from Africans is legitimate. What does that mean for estimates of ancestral derivation from continental populations than you see in the DTC personal genomics firms that report ancestry results? It can only mean that among people of Southern European ancestry a few percent of African ancestry is being “masked” because it is part of the reference population set. This came to my mind because a half Cuban friend of mine had ~2% African ancestry. Reasonable. When I checked by running unsupervised ADMIXTURE he had ~4%. Then I noticed that the Sardinian reference set was often in the 1-2% range. One explanation for the discrepancy then would be that a few percent of African ancestry in his genome was simply swallowed up by the reference population in the supervised learning framework.
To me 1984 is really insightful not for its depiction of totalitarianism, but the way in which modern American democratic politics cynically re-imagine the past. I have always been intrigued by George H. W. Bush (and more broadly the politicians within the family) shifting from a pro-choice supporter of planned parenthood sympathetic to population control, to a conventional acolyte of New Right pro-life positions around 1980. Though some people bring this up occasionally, the reality is that there seems to be an agreement to act as if that past no longer exists (also, in the 1980s Jesse Jackson and Al Gore went from pro-life to pro-choice). Similarly, Hillary Clinton waited until 2013 to support gay marriage, after a decade opposing it. Privately I assume she supported gay marriage, but spoke against it for political expediency. When the winds had changed she shifted her public view, and now would no doubt condemn in visceral terms those who promoted a position that she herself held three years ago! A position held by most Democratic politicians in the aughts on cynical grounds of political necessity is now scourged by those same politicians as being beyond the pale.
Got Land of Two Rivers: A History of Bengal from the Mahabharata to Mujib after it was mentioned on Facebook. The more you know.
In The New York Times, Brussels Attacks Underscore Vulnerability of an Open European Society:
The cultural code of silence in the heavily immigrant district, as well as widespread distrust of already weak government authorities, has provided what amounts to a fifth column or forward base for the Islamic State.
This is in The New York Times. If Fox News said something like this the squealing about “Islamophobia” would never end. One thing that some have observed is that the terrorist networks in Belgium seem to be almost exclusively Moroccan, not Turkish. Also, there are many friends and family members involved. If you read Scott Atran’s work on terrorism these facts are not surprising. One of the most annoying things about Sam Harris’ New Atheism is that he talks as if the Koran magically transmutes normal people into ticking time bombs. The ethnographic data present a different picture, where Islamic terrorism takes root in tightly integrated social networks which exclude outsiders. As Peter Turchin says, a widening precipitation of the Islamic jihadi phenomenon was easy to predict as an outcome of the events of the past 15 years because of the historical-social premises of this civilization.
Though overall I’m not a big fan of Malcolm Gladwell, his book from 15 years ago, The Tipping Point: How Little Things Can Make a Big Difference, did describe a phenomenon which I think can shed some light on why Moroccan, but not Turkish, networks in Belgium are being sucked into the jihadi milieu. To some extent this is stochastic in terms of where the phenomenon begins, but once there is a large social network present to allow it to take off, then positive feedback loops kick in. There is a lot of talk about the causal factors for why some countries, such as Tunisia, send so many Muslims to fight for ISIS, while others, such as India, do not. There are some predictive variables here that are worth talking about, but some of it might just be random chance. But once participation in the Syria war on the side of ISIS becomes meritorious in one’s social network, then the dynamic might just feed back into itself if there are no dampening mechanisms.
Which gets to one of the major reasons that American Muslims are probably underrepresented in international jihadi activity: they lack asabiyyah due to ethnic diversity. The chart to the left actually oversimplifies. Though South Asian Muslims share a lot culturally for example, there is definitely an “inner circle” of cohesion defined by Pakistanis and Urdu speakers from India into which Bengali or South Indian Muslims, for example, are not totally integrated. Converts for obvious reasons often create their own communities of affinity unless they marry into a family, while black Americans have a separate culture altogether. The ethnic diversity combines with economic diversity to fracture Muslim-American identity in a way that makes cultural complexes like that of Molenbeek, where underclass and working class Moroccan Muslims set the tone, or Tower Hamlets, where Bangladeshi Muslims from Sylhet set the tone, very rare. Even the town of Hamtramck, Michigan, where Muslims are demographically very notable in the aggregate, exhibits a lot of ethnic diversity within the religion. The importance of ethnic homogeneity as an amplifying effect can be seen in the Buffalo Six, who grew up in a tight-knit Yemeni-American community, or the “Minnesota men” who are routinely reported to have died fighting for the Al-Qaeda affiliated Al-Shabaab in Somalia, who come out of the Somali refugee community.
To not put too fine a point on it, I think the high frequency of snitching by American Muslims is a function of the low ethnic cohesion of the religion in the United States. This is one reason why arrival of refugee communities in toto is going to be a problem in Europe. Sweden, for example, has just imported a piece of Syria, not individual Syrians. Good luck with that.
I think it’s time for Twitter to admit that it is a specialized service and focus on its core constituency.
At 10 yr anniversary, @Twitter adoption curve looks a lot different than other concurrent tech pic.twitter.com/DfldT4Uucv
— Eric Topol (@EricTopol) March 26, 2016
The Rise of Donald Trump. Important:
Many of Trump’s supporters are already convinced that mainstream America is against them. They believe, with justification, that they are mocked and ridiculed. And they are especially indignant that they are not allowed to voice their concerns about immigration, about Black Lives Matter, and about globalization and multiculturalism more broadly, without being called racists or bigots.
At minimum Trump will do better in the general elections than polls predict.
No evidence for extensive horizontal gene transfer in the genome of the tardigrade Hypsibius dujardini. “We show that the extensive horizontal transfer proposed by Boothby et al. was an artifact of a failure to eliminate contaminants from sequence data before assembly.” Oops!
Why won’t you pay to read? I’m lucky to have been paid to blog for many years (and thanks to Ron Unz in particular, obviously!). I’m also lucky that this is not, and has never been, my primary source of income. That gives me a lot of freedom to say whatever I want.
Speaking of which. “Disclosure notice,” I am joining Embark, a genomics firm which will focus on dogs for my “day job.” Also, I’m still finishing up my Ph.D., doing some consulting for Gene by Gene, and writing for publications now and then. On the last issue, please make sure to subscribe to my total feed, as I am pretty busy and might not remember to post stuff here as a link all the time. Here’s an article on what Embark aims to do: Doggie DNA startup wants to learn about human diseases from dog drool.
Vinyl record sales produce more rev ($416M) than streaming sites like YouTube, Spotify, Apple Music ($385M) https://t.co/cV9MAIyKl2 @nytimes
— Jenna Mukuno (@jmukuno) March 25, 2016
Researchers Find Fish That Walks the Way Land Vertebrates Do.
If you are interested, Support Gila monster research.
Also, I should be at the Evolution Meeting this June in Austin.
Adaptation in protein fitness landscapes is facilitated by indirect paths.
In Facebook’s Hometown, the First Responders Aren’t Local. One reason I’m leaving California is that it’s not really congenial for young families. I was talking to a friend whose family has been living in San Francisco for four generations, and we got to discussing real estate. Her family own houses because their roots are so deep in the region, and I told her it was critical to start building vertically if the area wanted newcomers to stay for the long haul. Her response was “but it would ruin the views.” My response was “views are why San Francisco is so expensive.” Basically if there was more vertical development allowed in the Bay area, as is common in an Asian city, then there’d be more housing supply. But regulatory, cultural, and contingent (i.e., stakeholders who dominate zoning boards and benefit from inflated rents and property values) make it almost impossible to change the situation in California.
It’s a great state, but if you are middle class, you had better be single, or dual-income-no-kids, or have deep roots in the state so you can inherit property your parents purchased when it was affordable to do so on less than $300,000 per year in income. Otherwise, come for your 20s if you are a professional, but move elsewhere to raise kids. Perhaps if you become wealthy you can move back to Carlsbad when you retire.
Biologists Have Learned Something Horrifying About Prairie Dogs. Vegetarians can be violent. Hitler was a vegetarian by the end of his life.
Romeo Dallaire in Rwanda. Is anyone surprised he had a soft spot for the RPF? What exactly was he supposed to do? This gives me an opportunity to promote Dancing in the Glory of Monsters: The Collapse of the Congo and the Great War of Africa. Great book that everyone should read, especially in light of what’s going on in Syria now.
It turns out there are no saints, though there are many sinners. Too often today the past and present gets reduced to Manichaean caricatures, but there’s a reason that Manichaeanism is a recurrent feature of religion, but it tends to whither over time. It doesn’t engage with reality, and appeals just to our hopes and idealism.
This is an important paper: Genetic risk for autism spectrum disorders and neuropsychiatric variation in the general population.
Minding the Beeswax. Farmers and bees have a long history together.
PCASO has already been great for collaboration/data sharing:
Got #PCA data? Be like @razibkhan, and fluidly explore it w/everyone! https://t.co/tgG1QFXQQ8 #Pcaso pic.twitter.com/7wTuBYRXbo
— Nathan Pearson (@GenomeNathan) March 22, 2016
• Category: Miscellaneous • Tags: Open Thread
Over then years ago The Genetic Legacy of the Mongols was published. This paper illustrated the surprising genetic effects that historical demographic events might have; the authors found that one particular Y chromosomal lineage was extremely common in Central Eurasia, and, that lineage exhibited an explosive growth over the past 1,000 years. Combined with the high frequency in the Khalkha Mongols in particular the natural inference made was that this lineage was reflective of the reproductive success of the group of warrior elites descended from Genghis Khan.
Some have been skeptical of this relationship. Part of this is due to ignorance or skepticism of what one can learn from genetics broadly among some scholars. In a discussion with John Horgan the cultural anthroplogist R. Brian Ferguson dismissed the possibility of something like the Genghis Khan modal haplotype. This makes sense. Here is a quote from George Orwell’s 1984:
Anything could be true. The so-called laws of Nature were nonsense. The law of gravity was nonsense. ‘If I wished,’ O’Brien had said, ‘I could float off this floor like a soap bubble.’ Winston worked it out. ‘If he thinks he floats off the floor, and if I simultaneously think I see him do it, then the thing happens.’ Suddenly, like a lump of submerged wreckage breaking the surface of water, the thought burst into his mind: ‘It doesn’t really happen. We imagine it. It is hallucination.’ He pushed the thought under instantly. The fallacy was obvious. It presupposed that somewhere or other, outside oneself, there was a ‘real’ world where ‘real’ things happened. But how could there be such a world? What knowledge have we of anything, save through our own minds? All happenings are in the mind. Whatever happens in all minds, truly happens.
Even cultural anthropologists who reject the “Post-Modern” tendencies common in the United states in this field often live at some remove from an enterprise where data dictates the set of plausible models about the world. If science fiction is a vision of the future conditioned on the priorities of the present, cultural anthropology is an ethnography of the present and history of the past conditioned on the ideological values of the present.
In 1984 the dictates of the present determine the past. One of the reasons it is useful to read Lawrence Keeley’s War Before Civilization: The Myth of the Peaceful Savage is that it serves as a record of the stated positions of many cultural anthropologists, and how they have evolved over the years in light of new evidence, without any acknowledgement that their past positions were obviously false. In a progressive conception of science error is essential for the field to slowly converge upon reality as it is over time. But one must admit that one has made errors, and is changing one’s views to match the facts. Often cultural anthropologists strike a pose that “we always knew/believed that.” Many cultural anthropologists have given upon on any pretense that learning about the world out there is possible, and at the extreme even meritorious.
The conclusions of The Genetic Legacy of the Mongols are more plausible in light of a paper which was published last year, A recent bottleneck of Y chromosome diversity coincides with a global change in culture. In the paper the authors show that a massive bottleneck and subsequent explosion of very common Y chromosomal lineages such as R1b and R1a seems to have occurred on the order of 5,000 years ago. The star-shaped phylogeny is not just the legacy of Genghis Khan.
How did this situation come to be? Read Andrew Currey’s Slaughter at the Bridge in Science. It’s riveting. Here are some interesting passages:
Before the 1990s, “for a long time we didn’t really believe in war in prehistory,” DAI’s Hansen says. The grave goods were explained as prestige objects or symbols of power rather than actual weapons. “Most people thought ancient society was peaceful, and that Bronze Age males were concerned with trading and so on,” says Helle Vandkilde, an archaeologist at Aarhus University in Denmark. “Very few talked about warfare.”
…
DNA from teeth suggests some warriors are related to modern southern Europeans and others to people living in modern-day Poland and Scandinavia
The precis: 3,200 years ago thousands of men clashed around a bridge in a narrow valley in northeast Germany near the Baltic sea. Hundreds of these men died. Their skeletons yield the facts that they were in their 20s, were often killed in the brutal manner that occurs in pitched battle, and isotope analysis suggests that most of them came from hundreds of kilometers away. Both DNA and analysis of their bones to infer their diet suggest that some were similar to modern Southern Europeans, and may have been Southern Europeans in terms of their provenance, though I do not discount that there were pockets of people who were similar to the descendants of the European European Farmers (EEF) who persisted down to that period.
What does this tell us? In The Shape of Ancient Thought, most of which was written decades ago, there are presumptions about the nature of transmission of ideas from civilized (e.g., Mesopotamian) to non-civilized (e.g., archaic Greeks and Vedic Aryans) peoples. But what these results, and books such as War Before Civilization, remind us that writing and literacy is only one of the aspects of complex human organization. Complex societies seem necessary for literacy, but literacy is not necessary for social complexity (E.g., the Inca domains). Keeley documents suggestive evidence of large-scale conflict between the first farmers to arrive in Central Europe and marine foragers along the coastal littoral thousands of years before the slaughter at the bridge. Rather than being the start of something new, I suspect what occurred at Tollense was the later stages of a tradition of preliterate conflict and competition which persisted down the period of Christianity.
A friend invited me to watch the new Batman v Superman: Dawn of Justice movie with him on a spur of the moment. I won’t say much about the film (it was OK, but way, way, too much prologue, and too little Wonder Woman). A bunch of us waited during the credits for teasers afterward. At some point an attendant came out, and told us that “this isn’t a Marvel film, there are no teasers….” I got up to leave but noticed that half the audience stayed in their seats as the attendant explained that he’d “watched the film twice already, there are no teasers. Really.” As I was exiting I looked back and it was clear that some people were stubbornly staying in their seats, and the attendant was cleaning up and mumbling there were no teasers and everyone should just go home now.
It’s going to be a long weekend for that guy.
• Category: Miscellaneous • Tags: Film
Sometimes you don’t know what is real or not real. What do people really believe? Do they really believe what they say? Even if it’s clearly ridiculous? Probably internalized 
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There's a clip of him on Howard Stern saying something like "yeah, i guess I'm pro-life, but it's not really important.." I think that's probably how he falls on a lot of issues, and I think that's what a lot of us on the pro-Trump side see - that there are so many issues on the Left/Right divid...
Might also note the role of tribal mythology. Many Amerinds like to believe that they are literally autochthonous. No Out of Africa. No migrations across the Bering Strait.Those are the White Man's myths Hence, they are not keen on scientific studies that argue otherwise.
And White scientist...
Have you seen this yet?
http://biorxiv.org/content/biorxiv/early/2016/04/06/047456.full.pdf
It claims ASI definitely came from the east.
"finally, there’s the political issue. putting women in jail is a nonstarter, so the prolife movement has avoided that at all costs. trump, being a fake prolifer, just took logic to its conclusion."
Do you believe Donald Trump is lying about being a conservative on other political issues as we...
"Now you are being either obtuse or ignorant (and certainly juvenile, e.g. “Lol”). Blacks and Hispanics account for 30% of the U.S. population, and their abortion rates are 5 times and 2 times as high as whites, respectively. Canada is 4% Black + “Latin American” in contrast. We have very...
Scottish Canadian Gavin McInnes said when he first met his Amerindian wife, he thought she was Asian.
I wonder what percentage of Amerindians look Asian to Caucasian Western eyes?
Thanks Rick. Can't believe I missed this one somehow.
This mostly applies only to "full blooded" Native Americans, but also those associated with a tribe.
Many of them believe that the purpose of these kinds of tests (not just DNA tests) is to deny them of their rightful property, history, heritage, religion, and independent political and economi...
Just search for "The ancestry and affiliations of Kennewick Man" Nature article. It is free.
What's stopping a Native American individual from taking a DNA test? Does he need permission from his tribe or the Bureau of Indian Affairs? It boggles the mind!
When most states had abandoned prohibition, alcohol consumption began to increase.
Exactly my point - it may have had a temporary effect when it was first put in force, but it's certainly not the cause of today's relatively low consumption levels, as your original statement implies.
Since we've already established that Aborigines are just as human as other Australians, that would make Amerinds a "step above" whiteys as well. In any case, definitely not fauna! ... glad we could sort that out :)
Amerinds are a step above abos, but not a big one, especially considering most of their great warriors died fighting the colonists.
Good point on Kennewick Man. Do you have a link on his affinity to South Americans? Was it to specific groups?
Even if the X2a C4c link isn't perfect, the evidence for Algonquians and other first peoples of the northern half of North America receiving input from an additional migration event...
Australia was wrong, and have corrected their mistake... you should too.
"The Algonquians are the same people identified by Reich and others as a possible second inland migration – both based on autosomal DNA, and based on rare mtDNA haplogroups like C4c and X2a."
Possibly, but probably not, related to X2a. Kennewick Man was X2a and over 8,000 years old. His genome...
The comparison with alcohol consumption today is necessary because most people are not familiar with how much alcohol was consumed at one time.
In the U.S. prohibition began at the local level in the 1830s as communities banned alcohol retail, and began statewide bans of alcohol commerce in Ma...
Actually, alcohol prohibition is making a comeback. Many Islamic states have it. Just five days ago, the Indian state of Bihar prohibited the sale AND consumption of alcoholic beverages.
They're more like fauna, Australia used to classify abos as fauna.
http://infoproc.blogspot.com/2016/04/this-is-for-pz-meyers.html#disqus_thread
Perhaps this will find the guy whose website I'm not aloud to comment at.
Steve, Thinking Changes What Is Thought About. That's why the ones who can think the hardest will end up insane less they become adepts. I hope...
Prohibition greatly reduced alcohol consumption. The average American drank about 7 gallons of alcohol per year in 1830, and today drink about 2 gallons of alcohol.
Huh? Didn't prohibition end like 80 years ago? I think widespread education and "Drink Responsibly" campaigns over the last 20 ...
Re: 1) – https://www.guttmacher.org/sites/default/files/pdfs/pubs/journals/Sedgh-Lancet-2012-01.pdfYour original claim was: "In fact, more restrictive abortion laws correlates with higher rates of abortion…" That's not what the Lancet article states. One of its interpretations is "restrictive...
Dunno. Not ice age though, the opposite. The last glacial period ended about 12 000 years ago and since then it's been warm and melty. Beringia flooded and the steppe-tundra turned into forest and crappy regular tundra.
@Robert Ford: should we turn over the land back to the buffalo that the “First People” wiped out
European settlers wiped out the buffalo. You're probably thinking of megafauna, but they weren't human either so your point still wouldn't make sense... unless you're saying we should consider ...
Prohibition greatly reduced alcohol consumption. The average American drank about 7 gallons of alcohol per year in 1830, and today drink about 2 gallons of alcohol. It greatly reduced death by cirrhosis and other alcohol-related diseases. The benefit to women who suffered abuse and poverty fro...
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