What is the impact of strict population control? Unintended consequences. Note the convergence in fertility between South Korea and the People’s Republic of China. Coercion or no, some things are inevitable.
Beating Obesity. Marc Ambinder went from 235 to 150 in a year after surgery.
For ancient hominids, thumbs up on precision grip. Many things which we perceive to be derived may be more ancestral than we’d thought.
New Genetic Framework Could Help Explain Drug Side Effects. Medicine is a crap shoot, so you want to load the die in your favor as much as you can.
Chimpanzees Prefer Fair Play To Reaping An Unjust Reward. Not too surprising, but there’s a lot of “complex behavior” whose building blocks are probably pretty ancient. The fact that humans can “socialize” with dogs and cats are somewhat suggestive to me of common mammalian cognitive furniture.
Since I’ve been talking about the possibility of admixture with “archaics” (I’m starting to think the term is a bit too H. sapiens sapiens-centric, is the Neandertal genome turning out to have more ancestral alleles?) I thought I’d point to a paper out in PLoS ONE which reiterates the basic fact that the overwhelming genetic evidence today suggests a massive demographic expansion from an African population within the last 100,000 years. Study after study has supported this contention since the mid-1980s. The question is whether this is the exclusive component of modern human genetic ancestry, which is a somewhat more extreme scenario. In any case, the paper is Formulating a Historical and Demographic Model of Recent Human Evolution Based on Resequencing Data from Noncoding Regions:
Our results support a model in which modern humans left Africa through a single major dispersal event occurring ~60,000 years ago, corresponding to a drastic reduction of ~5 times the effective population size of the ancestral African population of ~13,800 individuals. Subsequently, the ancestors of modern Europeans and East Asians diverged much later, ~22,500 years ago, from the population of ancestral migrants. This late diversification of Eurasians after the African exodus points to the occurrence of a long maturation phase in which the ancestral Eurasian population was not yet diversified.
They took 213 individuals, a little over half from diverse African groups, and the other half split evenly between Europeans and East Asians, and sequenced 20 distinct noncoding autosomal regions of the genome. ~27 kilobases per person. The noncoding part is important because they are trying to look at neutral regions of the genome, not subject to natural selection (this is obviously an approximation, as there is some evidence that even noncoding regions may have some selective value). The variation is what you’d expect, Africans more varied than non-Africans, and the two Eurasian populations are distinct from each other, but less so than either is from the Africans. Lots of statistics ensue, and an “Approximate Bayesian Computation (ABC) analysis.” I’ll cut to the chase, the highest probability model is illustrated in panel A of figure 4. Expansion out of Africa ~60,000 years ago, major bottleneck, a ~40,000 year interregnum where there was a relatively unified Eurasian population genetically, and then a separation between East and West Eurasians ~20,000 years ago.
Perhaps. Matt Stone & Trey Parker have put out a statement. I watched it online yesterday and I thought the bleeps were part of the “in joke.” I’ll spoil the episode for you by noting that it wasn’t even Muhammad in the bear a suit. Additionally I don’t get why people are that that scared, the threats were made by a group that’s very close to literally being in a basement. On the other hand, remember during the Salman Rushdie affair that translators were killed, so perhaps there’s reason that a corporation would want to stay on the safe side (one could imagine civil lawsuits if someone did get hurt against the corporation).
On final thing, the South Park episode in question depicted Moses as a dull artificial intelligence, Buddha as a cocaine junkie and Jesus as a habitual viewer of internet pornography (at least that’s Buddha’s accusation, which Jesus does not deny, rather, he minimizes its equivalence with a drug habit. I think Jesus’ logic is spot on, and am leaning toward Brit Hume’s dismissal of Buddhism on account of this interaction). There are of course Jewish,* Christian and Buddhist extremists in world. But most people judge that Jews, Christians and Buddhist are less liable to take violent action to defend the dignity of their faith than extremist Muslims. I think that’s probably a valid assessment, and I think that points to the fact that not all religions can be made equivalent in the nature and numbers of violent radicals. Why that is is a different question.
* Because Judaism is operationally coterminous with an ethnicity, at least by self-conception, I have seen some attempts to accuse those who have anti-Jewish religious views as anti-Semites. In general anti-Semites have anti-Jewish attitudes in regards to the religion, but the inverse is not always so. Some Muslims have started imitating that strategy, accusing plain anti-religious folk like Richard Dawkins of being an Islamophobe as if he is racist.
Cupp, unsupported. S. E. Cupp, sellout, or really, really, confused. That’s how you describe an atheist who accepts evolution, and, who defends the teaching of Creationism in science classes (as a conservative I’m skeptical that she’s a down-the-line majoritarian).
The Red Bias. Red as the color of success?
Of Yeast and Men. Reviews the recent attempt to finding QTLs of small effect via “Extreme QTL Mapping.” What may be doable in yeast may be harder in men.
Claim Jumper: World’s Unhealthiest Restaurant. Is it me, or do these casual dining chains which are oriented toward value always brightly lit? And their food is always super-vivid in their coloring. Contrast with higher end steak houses.
The Apple Secrecy Machine. Secrecy wouldn’t matter if the products weren’t useful.
I don’t have any deep ethical insight, but this sort of stuff is interesting because there are a lot of samples out there I assume being used from a time before consent was as formalized. Sounds like the scientists probably oversold the practical applications of their research…like they would to a grant committee. Tribe Wins Fight to Limit Research of Its DNA:
“Did you have permission,” she asked during the question period, “to use Havasupai blood for your research?”
The presentation was halted. Dr. Markow and the other members of the doctoral committee asked the student to redact that chapter from his dissertation.
But months later, tribe members learned more about the research when a university investigation discovered two dozen published articles based on the blood samples that Dr. Markow had collected. One reported a high degree of inbreeding, a measure that can correspond with a higher susceptibility to disease.
Ms. Tilousi found that offensive. “We say if you do that, a close relative of yours will die,” she said.
Another article, suggesting that the tribe’s ancestors had crossed the frozen Bering Sea to arrive in North America, flew in the face of the tribe’s traditional stories that it had originated in the canyon and was assigned to be its guardian.
Listening to the investigators, Ms. Tilousi felt a surge of anger, she recalled. But in Supai, the initial reaction was more of hurt. Though some Havasupai knew already that their ancestors most likely came from Asia, “when people tell us, ‘No, this is not where you are from,’ and your own blood says so — it is confusing to us,” Rex Tilousi said. “It hurts the elders who have been telling these stories to our grandchildren.”
I guess I have more sympathy with the idea that you might have some implied property right to how your genetic information is used than I do with being offended because your primitive beliefs might be overturned (there is no way that American Indian land claims are based on paleoanthropology in any practical terms). Creationism is primitive too, and many evangelical Christians are “offended” at the idea that they might share common descent from apes. So?
Genomics Law Report has more commentary.
There’s a lot of circumstantial evident that mtDNA haplogroup U5 was brought to Europe by the first anatomically modern populations. Though this haplogroup is extant around frequencies of ~10% in modern European populations, with the highest proportions in northern Fenno-Scandinavia and the east Baltic region, extractions of DNA from hunter-gatherer remains in northern Europe yield very high proportions of this lineage. This is not totally surprising, in the early aughts Bryan Sykes wrote a book, The Seven Daughters of Eve, and correctly pointed out that the coalescence for the U5 lineages is very deep in Europe, suggesting that it has had a lot of time to diversify. Sykes’ main thesis though was that most of the genetic heritage of Europe predates the expansion of Neolithic farmers within the last 10,000 years. The rough implication was that ~80% of the ancestry of modern Europeans could be derived from people who were resident within the modern boundaries of the continent of Europe during the last Ice Age.
Low Vitamin D Levels Associated With More Asthma Symptoms and Medication Use. Not a randomized double blind study. Rather, they look at the correlation, and they did some cell biology experiments. Looks like high levels of vitamin D enhances the action of corticosteroids.
Recreational genome sequencing for the whole family. I’m kind of irritated as the “ethical concerns” about this information. Information may not always want to be free, but this is pretty much an inevitability. Since there’s no plausible way you can cordon it off you need to educate people to use the information wisely. Unfortunately most of the populace is not too intelligent, but that just means you need to work hard in making the heuristics simple and obvious.
Genetic Basis for Health Benefits of the ‘Mediterranean Diet’. Turns out it might be a matter of gene expression.
Thinking About Tomorrow. Delaying gratification is really important, and often hard.
Why Texas is doing so much better economically than the rest of the nation. Daniel Gross focuses on the fact that Texas is globalizing and export-oriented. I note that only Utah has a lower median age. I suspect that the young work force in its peak years makes it easy for Texas to have a low public service state and focus on private sector wealth generation.
These ongoing studies are concluding that present-day genetic variation is inconsistent with a simple model where a random-mating ancestral population gives rise to today’s global population by means of a staged out-of-Africa dispersal. They next look at a model with some substantial (possibly complete) isolation between ancient human populations followed by a subsequent out-of-Africa dispersal. They show that this model fits the data significantly better.
So far, so good.
For a moment, I’m going to adopt a critical perspective. Previous results haven’t yet been able to answer an important possible question: Can they distinguish the effects of intermixture outside Africa from an ancient population structure inside Africa? Increasingly it looks like population structure inside Africa may have been very important to the evolution of Late Pleistocene Africans. How can we distinguish these kinds of structure from each other?
The short answer is that maybe we can’t, yet. Human population history was not simple. If we take a simple model and add more parameters, it will fit the data better. The question is whether there may be some even better model with the same number of parameters. Population structure within Africa, selection on some loci but not others, asymmetrical migration — all these and more might be possible.
The Out of Africa + total replacement model had a clean elegance, but it might not be viable in the near future. That being said it seems to me that the old Multiregional model implied, though proponents were often careful to reject this characterization, more regional parity than was the case. I do not expect the predominant African ancestry of modern humans to be rejected for example. There are other frameworks out there, such as Alan Templeton’s Out of Africa again and again (Richard Dawkins favors this in The Ancestor’s Tale).
Muslim Group Says It Is Warning, Not Threatening, ‘South Park’ Creators. Here’s a screen shot from the cached version of the site (it was hacked after the threat):
The website is run by a dozen crazy people. No word on crazy Buddhists objecting to the fact that Buddha was depicted as a cocaine snorting junkie in the episode. It’s a two part episode, so watch the finale tonight.
The topline is this, researchers presented the following at the recent meeting of the American Association of Physical Anthropologists:
* An analysis of 614 highly variant loci, microsatellites, in ~2,000 people from diverse populations imply some variants which seem to be derived from human lineages outside of the mainline which led to the anatomically modern humans who left Africa 50-100,000 years before the present to settle the world. I assume there were “long branches” on the phylogenies of some loci, indicating that some of the alleles were “separated” from others for long periods of time so that recombination wasn’t able to dissolve the differences between distinctive haplotypes (if we’re all descended from a small African populations which expanded demographically less than 100,000 years ago the common ancestor of the variants should have a shallow time depth).
* The data imply two admixture events, one 60,000 years ago in the eastern Mediterranean, the other 45,000 years ago in East Asia. I think of this as a floor to the number of events. The latter one seems particularly clear in Oceanic populations from the reporting.
* African populations do not have the variants for these two admixture events (there hasn’t been that much back migration to Africa aside from north of the Sahara and the Horn of Africa. I assume that’s because Africans are well adapted to their environment, and outsiders are not).
In light of the recent discovery of a Siberian hominin which lived ~30,000 years ago, and was not a H. sapiens sapiens or H. sapiens neanderthalis, as well as the confusing but intriguing Hobbits of Flores, I think we can conclude that the the evolutionary genetic past was much more complicated than we’d assumed 10 years ago. Remember three years ago when there was a spate of research on a few genes which were suggestive of introgression into the human genome from Neandertals? There are other hints here and there which pop up in the literature over the years, some in Asia. But the methods being imperfect, and interpretation being somewhat an art, a consensus of Out-of-Africa + total replacement has been assumed to be a null. So we look at isolated results with some skepticism (I think this is justified).
So is this going to be met with skepticism due to reliance on the orthodox model? This section of the article is intriguing:
There is some interest in the upcoming British election, and the renaissance of the Liberal Democrats under Nick Clegg. See this article in The New York Times about the rise of the Liberal Democrats at the expense of the two traditional parties of power, Labour and the Tories. One interesting fact from an American perspective is that Nick Clegg is an admitted atheist, though his children are being raised Roman Catholic by his wife. Of course the lack of faith of British politicians isn’t that new, two Prime Ministers were not even nominal believers, Clement Attlee was an agnostic and James Callaghan was an atheist.
This is of course in sharp contrast with the United States where all politicians operationally have to avow a religious affiliation, and the higher that a politician ascends up the ladder of achievement the more vocal and thorough the assertions of sincere faith have to become. And yet it is Britain which has an established church, where the head of state is the head of the church, and, religiously oriented schools receive public funding.
There are many models rooted in history one could propose, but the facts as they are would probably be unlikely to be inferred from prior axioms. It’s a reminder that human social affairs are the outcome of messy dynamics, and observation is often far easier than deep analysis. In 1800 one would reasonably have expected that it was in the United States where “infidel” politicians would flourish, and yet that has not been so.
Cultural innovation, Pleistocene environments and demographic change. Gene-culture coevolution gurus Peter Richerson and Robert Boyd argue that climatic fluctuations may work to the advantage of humans because of the adaptive flexibility inherent in a cultural species.
Common versus rare variants, again. Some skepticism of the new exhortation to look for rare variants of large effect instead of common variants of more modest effect. This sort of posturing by biologists strikes me as similar to what happens in social science (to a great extent all of what falls under the rubric of sociology seems to be posturing with doctorates). Does this happen in the physical sciences?
Sean Carroll Talks School Science and Time Travel. I wonder when he’s going to stop being asked about how he got together with Jennifer Ouellette. People meet up through internet. Via blogs. It happens.
Media to Tea Partiers: Can You be More Racist? Mind-reading is hard. Conservatives are racists and liberals are crypto-Leninists. Meanwhile, there’s life to be lived.
Neural Correlates of Being a Total Bad-Ass. Psychology with fMRI = telling you stuff you already know with a pretty picture to boot.
Jared Diamond famously argued in Guns, Germs and Steel that only a small set of organisms have the characteristics which make them viable domesticates. Diamond’s thesis is that the distribution of these organisms congenial to a mutualistic relationship with man shaped the arc of our species’ history and the variation in wealth that we see (though his a human-centric tale, we may enslave them, eat and use them as beasts of burden, but these are also species which have spread across the world with our expansion). This thesis has been challenged, but the bigger point of putting a focus on how humans relate to their domesticated animals, and the complex co-evolutionary path between the two, is something that we need to consider. In a plain biological and physical sense animals have utility; we eat them, and for thousands of years they were critical to our transportation networks. Some have argued that the rise of Islam, Arab monotheism, was contingent on the domestication of the camel (which opened up interior trade networks previously unaccessible). In The Horse, the Wheel, and Language: How Bronze-Age Riders from the Eurasian Steppes Shaped the Modern World the argument is made that the distribution of the Indo-European languages has to do with the facility of Central Eurasian plainsmen with their steeds. And of course there is the domestic dog, arguably the one creature which is able to read our emotions as if they were a con-specific.
I suspect that the evolution and ethology of domesticated animals will offer a window into our own evolution and ethology. Konrad Lorenz famously believed that humans were going through their own process of domestication all the while that they were selecting organisms suited to their own needs. More pliable, less intelligent, faster growing and maturing, and so forth. Know thy companions, and know thyself, so to speak.
What about an animal as intelligent as a dog, but famously tasty? (the combination of the two characters causing some ethical tension in the minds of many) I speak here of the pig. A few years ago research came out which showed that pig-culture was introduced to Europe from the Middle East. That is, Middle Eastern pigs came with Middle Eastern people in all likelihood. But modern European pigs do not derive from these lineages, rather, by comparing modern genetic variation with ancient DNA the authors showed that the Neolithic pigs had been replaced by local breeds. Just as pigs can go feral and fend for themselves rather easily, it seems that their basic morph can be derived from wild boar populations easily as well (by contrast, it will perhaps take some effort to derive a pekingese from wolf populations, offering a reason for why small dogs seem to have emerged once). A new paper explores the evolutionary history and phylogeography of the pigs of the swine-loving societies par excellence, those of East Asia. Patterns of East Asian pig domestication, migration, and turnover revealed by modern and ancient DNA:
I’ve heard some buzz about some weird new video that the Insane Clown Posse came out with, but after watching this strange parody on SNL I had to check out the original. So first the parody:
You can see the original video here. It’s actually pretty strange in and of itself. Here’s a more typical video from the group. Their stuff normally reminds me of the movie Gummo. I assume they’re mellowing since they’re pushing beyond their mid-30s and both have replicated (“Shaggy 2 Dope” up to replacement).
Note: The videos are NSFW if you have the volume on. But really, if you’re at work you should have headphones on.
Why religion can lead to racism. I think the correlations are real, but am skeptical of the causation because I think think the correlation is cultural-specific. For example, my personal experience with Muslims is that those who espouse the most “Fundamentalist” world views are the least racist. The contrast with white American Protestants probably emerges from the fact that white American Protestants and Arab Muslims have had very different recent histories (if Arab Muslims want a racial ideology, they had a good candidate in secular Baathism. Some of the same applies to Turks and Persians, who got on the 20th century racial-nationalist bandwagon, as evident in the attempt by the Shah to emphasize Iran’s Aryan antecedents, while Ataturk funded research on the racial characteristics of the Turkish people which allowed them to be a conquering race).
Air Travel Crisis Deepens as Europe Fears Wider Impact. This shows the downside of a JIT world, where we squeeze efficiencies by pushing everything to the margin and assuming stable background conditions. I worry that as the world economy becomes more interdependent, and squeezes efficiencies out through complementation via comparative advantages, there emerge problems whenever we get buffeted by a big “exogenous shock.” I think there’s some evidence that we as a species have cognitive biases toward focus on near-term conditions and discounting volatility toward the tails of the distribution. Such is nature.
S.E. Cupp On Being An Atheist & A Conservative. Some of her arguments strike me as surprisingly superficial, and I think it’s likely that she’ll convert to Roman Catholicism at some point in the next 20 years. My minimal experience with atheists who want to be religious is that they generally get their wish if they don’t die too early. Also, apparently she’s getting her masters in Religious Studies, which is a field that is often suspicious of unvarnished naturalism in the study of religion. Warning: I suspect some readers of this weblog will find her responses & viewpoints somewhat cringe-worthy. A young Heather Mac Donald she’s not, take a look at this clip, who does she remind you of? Can’t wait until she’s firmly in the Christian column.
For Goldman, a Bet’s Stakes Keep Growing. Some people are saying that investors will now be cautious of making recourse to Goldman’s services for fear that they’ll be screwed. But remember that it is assumed that many of Bernie Madoff’s investors suspected that he was front running. In other words, as long as it’s someone else being screwed they should be fine with it. The people at Goldman are the best tools you have out there, but a tool is a tool and can be used for good or ill. In any case I thought Goldman was making most of its money by trading with its own capital, leveraging the ability to get cash cheaply via the Fed window and also taking advantage of the guaranteed implicit backing of the government. I do believe that capitalism needs virtue, but I also believe that the revolution of morals has to start up top. I’m not holding my breath. Cultures go through cycles, and we’re probably due for a “correction.”
Where Paris Chefs, Not Prices, Rise. If you’re going through Paris, worth a read.
Poking around the GSS for another reason I stumbled onto something weird. Something which I’d seen hints of, or seen referred to before, but never followed up myself. It seems that support for abortion-on-demand and the death penalty peaked concurrently in the span between 1980-2000. This is evident in two GSS variables, ABANY and CAPPUN, which ask if you support a woman’s right to an abortion for any reason and the death penalty for murder. Additionally, I decided to look at attitudes toward homosexuality using HOMOSEX as a reference as a point of contrast. Unlike abortion or the death penalty attitudes toward homosexuality have been changing in the same direction for the past 30 years. Additionally, the magnitude of the change seems to be much greater than in regards to the other two controversial social issues, and especially abortion, which has exhibited notable stability.
I was particularly interested in differences by religion, so I limited the sample to whites and broke it down by Protestant, Catholic, Jew and None. To reduce sample size volatility I clustered by decade, so that “1970s” is inclusive of every year in the 1970s that the GSS asked the question for that variable.
Several months ago I put up a post which reviewed the geographical connections within the total genome content of the Cape Coloureds of South Africa. These peoples (plural because distinctive ethnic groups such as the Griqua were subsumed into this category in the 20th century) are of diverse origin, though generally their African and European ancestry has been highlighted. To the left I’ve reedited a plot which illustrates the inferred proportion of ancestry from various groups in modern Cape Coloured populations. Note that there is a substantial proportion of Asian ancestry, both South and East Asian. This makes historical sense as during the period of the founding of the Cape Colony a substantial number of Southeast and South Asian slaves were transferred from the Dutch East Indies, as well as from Madagascar, which itself has a Southeast Asian component in its population. Additionally, observe that the Bushmen & Khoikhoi element has been separated from the Bantu element. Archaeologists assume that the former are indigenous to South Africa, while the latter arrived within the last 2,000 years as the edge of the Bantu expansion which swept out of Nigeria east and south. These two populations are obviously both African, but their common ancestry is very deep. In some phylogenies Bushmen may be represented as the outgroup to all other human lineages, implying that one has to go very far back indeed for a common ancestor. In other words, the Bushmen are not the “oldest” human population, but have the oldest point of common ancestry with other human populations (e.g., the last common ancestor between a European and an East Asian may be ~30,000 years ago, but that between a Bushmen and a European may be ~80,000 years ago).
But these studies do not tell us everything about the demographic history behind the ethnogenesis of the Cape Coloureds. In this case uniparental lineages, mtDNA which traces the matriline and and nonrecombinant Y chromosomes (NRY) which trace the patriline may offer some value. Unfortunately too often because of methodological considerations we have looked at the uniparental lineages first, and then the total genome content, which I think inverts the optimal order in terms of putting genetic findings in context. A new study focuses on the Cape Coloured mtDNA and NRY lineages, with the previous findings in mind, Strong maternal Khoisan contribution to the South African coloured population: a case of gender-biased admixture:
Friday Weird Science: Smells Fishy? Check your semen. I’m not going to describe the post. You read it (though perhaps not on a full stomach).
Scientists Devise Way to Link Complex Traits With Underlying Genes. At least for some model organisms, though the authors claim at the end of their paper that they could be transfered to humans.
Mixed-Race People Perceived as ‘More Attractive,’ UK Study Finds. In general I think these sorts of studies are the inverse of the results of Charles Davenport on Jamaican mulattoes, scientists sometimes know what findings are congenial to the Zeitgeist, and will keep looking until they find them. I suspect there might be some effect here, but I doubt much in most non-inbred populations. To me the issue is diminishing returns, the same sort of problem which I think crops up in racialist arguments promoting ethnic genetic interests (that should even the balance of the scales of Political Correctness). Also, if you accept these results as rooted in heterosis you’d naturally want to compare Eurasians to European/Asian-African mixes, since the former are from much closer populations genetically than the latter, and so would exhibit proportionality more gains.
Obama, Republicans clash over financial reform. I think this is a case where David Frum’s half-a-loaf is probably wisest; the public is suspicious of Republicans when it comes to financial regulation. This isn’t an entitlement, so Republicans could probably change things in the future anyhow if they had the Presidency and majorities in Congress (though perhaps they’ll make a big stink now so that Wall Street is more positively inclined toward them in terms of political donations).
Quantum Hustles. Sometimes science blogging is not going to make intuitive sense.