linkfest – 10/19/15

First humans to leave Africa went to China, not Europe“The first humans to leave Africa decamped to far east Asia, not Europe. A trove of ancient teeth found in a cave in China adds evidence to the idea that humans reached the region thousands of years before they made it to Europe. The find suggests that modern humans reached China between 80,000 and 120,000 years ago. That challenges the widespread assumption that humans didn’t leave Africa until 60,000 years ago. It’s further evidence that Homo sapiens may have left Africa several times, says María Martinón-Torres of University College London. ‘It means we have to re-think different models of our dispersal.'” – and john hawks tweeted: “An 80kya modern human population in SE Asia w/Denisovan ancestry might help explain pattern of admixture in Philippines Mamanwa.”

Way Down South“I hear (tweets by Razib Khan, concerning Sankararaman’s talk at ASHG) that the Denisovans had substantially more genetic diversity than Neanderthals (determined mainly by the variety seen in admixed segments)….” – from greg cochran.

Lactase persistence and ancient DNA“‘…it seems plausible to me that the [European LP] allele first appeared in Central Europe, was spread around Europe by the LBK, before being introduced to the steppe later by migration from Europe.'”

Stonehenge builders had barbecue feasts at nearby party centre – and milk and cheeeeeese!

Basques are not simply a fusion of Iberian hunter-gatherers and early farmers“[T]he story told by the PCA is that Basques are the progeny of Bronze Age Iberians, who, unlike their Copper Age predecessors, experienced a pulse of steppe-related admixture from the east…. The key question now is who brought the steppe-related ancestry to Basque country. Were they Indo-Europeans or speakers of Proto-Basque?”

Sex‐specific demography and generalization of the Trivers–Willard theory – h/t owen jones! who tweeted: “Can mothers adaptively adjust offspring sex ratio? It’s complicated….”

The Great Migration and African-American genomic diversity“We find higher African ancestry in southern United States compared to the North and West. We show that relatedness patterns track north- and west-bound routes followed during the Great Migration, suggesting that admixture occurred predominantly in the South prior to the Civil War and that ancestry-biased migration is responsible for regional differences in ancestry. Rare genetic traits among African-Americans can therefore be shared over long geographic distances along the Great Migration routes, yet their distribution over short distances remains highly structured.”

Connectivity matrix predicts fluid intelligence“The enchanted loom is slowly giving up its secrets, of which it holds many. The patterns of brain activity that so many researchers have tracked with wonder are beginning to reveal a larger pattern: the possibility that each of us has a habitual pattern of brain activity which identifies us, and distinguishes us from others. So, dear reader, we are separated by the idiosyncratic rhythms of our brains, dancing to a different beat, visiting a different pattern of cortical locations, and no doubt coming to different conclusions…. The unexpected finding which I find startling is that individuals can be identified by their habitual brain patterns (not just on specific tasks) and those patterns of activity predict fluid intelligence on Raven’s Matrices at about r=0.5.” – from dr. james thompson.

Meta-analysis of associations between human brain volume and intelligence differences: How strong are they and what do they mean?“Positive associations between human intelligence and brain size have been suspected for more than 150 years…. Our results showed significant positive associations of brain volume and IQ (r = .24, R2 = .06) that generalize over age (children vs. adults), IQ domain (full-scale, performance, and verbal IQ), and sex…. We show that the strength of the positive association of brain volume and IQ has been overestimated in the literature, but remains robust even when accounting for different types of dissemination bias, although reported effects have been declining over time.”

Correlation not Causation: The Relationship between Personality Traits and Political Ideologies“Here we test the causal relationship between personality traits and political attitudes using a direction of causation structural model on a genetically informative sample. The results suggest that personality traits do not cause people to develop political attitudes; rather the correlation between the two is a function of an innate common underlying genetic factor.” – h/t robin hanson!

Generalised Anxiety Disorder – A Twin Study of Genetic Architecture, Genome-Wide Association and Differential Gene Expression“A heritability analysis of the same cohort also confirmed a significant genetic component with h2 of 0.42.” – h/t siberian fox! – and jayman tweeted: “I suspect anxiety is more common in some places than others. Perhaps due to genetic pacification.”

A Unified Crime Theory: The Evolutionary Taxonomy“Drawing on a variety of influences, we argue that many types of crime can be understood in the evolutionary context of human life history. Along these lines, we present a framework capable of explaining different patterns of criminal offending both at the individual level as well as the macro-level.” – from brian boutwell et al.

Resting heart rate and antisocial behavior: An updated systematic review and meta-analysis“Low resting heart rate was associated with higher levels of antisocial behavior…. Results were similar across behaviors, including aggression and violence.” – h/t anthony hoskin!

The association between childhood autistic traits and adolescent psychotic experiences is explained by general neuropsychiatric problems – from amir sariaslan et al. amir tweeted: “The ‘p factor’ explains assoc’s btwn childhood autistic traits and adolescent psychotic experiences.”

The Flynn Effect: IQ Testing Across Space and Time – from steve sailer.

What Extroverts and Introverts Can Learn From Snails“Genes may change a snail’s ‘personality’ and the thickness of its skin (or rather, its shell)”

Dimensional assessment of normal and abnormal personality in adults of the general population: Comparison of ‘five’ and ‘alternative five’ personality models – h/t andrew sabisky! who tweeted: “are normal and pathological personality all part of one continuum?”

So what if grammars don’t help social mobility?“On the Today programme and the New Statesman website, a statistic was quoted showing that grammar schools have a smaller percentage of pupils on free school meals than comprehensives. There are probably many reasons for this, but most likely the largest factor involved is that intelligence is hereditary and social class correlates with IQ; in other words, middle-class kids tend on average to be more intelligent than working-class ones. You could make the system fairer by replacing grammar entrance exams (for which richer parents hire tutors to help their children pass) with straight-up IQ tests, but the number of poorer children would still be disproportionately low. In fact the more social mobility we have over the generations, as everyone seems to want, the more that social class will correlate with intelligence. Richard Herrnstein pointed this out more than four decades ago. Many years earlier, Michael Young warned about this very process in The Rise of the Meritocracy. Social mobility does have its downsides; that’s because intelligence is just another privilege you inherit from mummy and daddy.” – from ed west.

The economic value of Breaking Bad: How misbehavior in school pays off for some kids“Surprisingly, we find evidence that some non-cognitive skills that manifest as childhood misbehavior in the classroom (and are predictive of lower schooling attainment) are also predictive of higher earnings later in life.”

A social science without sacred values“We argue (1) that many social scientists are paranoid egalitarian meliorists; (2) that they are therefore very sensitive to threats to a sacred egalitarian narrative; (3) that this sensitivity may be excessive (at least in the domain of science) and may cause researchers to unfairly reject research that challenges egalitarianism; (4) that this may then lead to the marginalization of individuals who forward controversial theories and/or data; and (5) that these tendencies lead to bias in the social sciences.” – from the winegard bros.

Social Status: Down the Rabbit Hole – h/t billare! who tweeted: “There are two systems of social status: Dominance & Prestige. For what selfish reasons might the latter one evolve?” – this was a really interesting read, btw.

Why Drunk Vegetarians Eat Meat – h/t jonathan haidt! who tweeted: “…esp. health vegs; moral vegs feel more disgust.”

Shame, guilt, and facial emotion processing: initial evidence for a positive relationship between guilt-proneness and facial emotion recognition ability“Guilt-prone people are highly skilled at recognising other people’s emotions.” [via] – w.e.i.r.d. study. pretty small n.

Gamblers, Scientists and the Mysterious Hot Hand“We’re all in the same boat. We evolved with this uncanny ability to find patterns. The difficulty lies in separating what really exists from what is only in our minds.” – h/t claire lehmann!

Dobzhansky and Montagu’s Debate on Race: The Aftermath

The Mutant Genes Behind the Black Death“Only a few genetic changes were enough to turn an ordinary stomach bug into the bacteria responsible for the plague.”

The End of Indian Summer“At first, human rights commissions fought discrimination only in employment and housing, and there was strong resistance to prosecution of people simply for their ideas. This situation changed from the 1970s onward. Human rights took the place in society that formerly belonged to religion, and human rights advocates acquired the immunity from criticism that formerly belonged to the clergy. Discrimination was no longer wrong in certain cases and under certain circumstances. It became evil, and people who condoned it in any form and for any reason were likewise evil.” – from peter frost.

Is Eastern Europe Any More Xenophobic Than Western Europe? – yes. but france is an exception in the west.

bonus: superforecasting conference on october 24th, if you happen to be in or near london: Superforecasting and Geopolitical Intelligence- Who can Predict the Future, and how?

bonus bonus: Did photosynthesis begin 3.2 billion years ago?“Rusty rocks from ancient ocean suggest bacteria produced oxygen far earlier than thought.”

bonus bonus bonus: The Beetle That Eavesdrops on an Ant’s Secret Language“A beetle evolves to ‘listen in’ on ants’ chemical messages to one another, changing the balance of an ecosystem.” [via]

bonus bonus bonus bonus: Ants con others into being their slaves by mimicking their scent

bonus bonus bonus bonus bonus: Sticky situation: maple syrup bandits face Quebec courts for infamous heist“Trials are under way for the 2012 attempt to steal $18m worth of Quebec’s sweetest export – a case that has succeeded in capturing Hollywood’s attention.”

bonus bonus bonus bonus bonus bonus: Pop Culture Pulsar: The Science Behind Joy Division’s Unknown Pleasures Album Cover

and the tweet of the week… (^_^)

(note: comments do not require an email. cheeeeeese!)


linkfest – 01/11/15

Genetic Variation in the Nuclear and Organellar Genomes Modulates Stochastic Variation in the Metabolome, Growth, and Defense“Systems biology is largely based on the principal that the link between genotype and phenotype is deterministic, and, if we know enough, can be predicted with high accuracy. In contrast, recent work studying transcription within single celled organisms has shown that the genotype to phenotype link is stochastic, i.e. a single genotype actually makes a range of phenotypes even in a single environment. Further, natural variation within genes can lead to each allele displaying a different phenotypic distribution. To test if multi-cellular organisms also display natural genetic variation in the stochastic link between genotype and phenotype, we measured the metabolome, growth and defense metabolism within an Arabidopsis RIL population and mapped quantitative trait loci. We show that genetic variation in the nuclear and organeller genomes influence the stochastic variation in all measured traits. Further, each trait class has distinct genetics underlying the stochastic variance, showing that there are different mechanisms controlling the stochastic genotype to phenotype link for each trait.” – h/t kevin mitchell! who tweeted: Some genomes are ‘noisier’ than others – robustness of developmental outcome is itself a genetic trait.

Evolutionary pattern in the OXT-OXTR system in primates: Coevolution and positive selection footprints“It was previously believed that placental mammals present no variability in oxytocin (OXT). The present study reports novel data on the diversity of OXT and its receptor (OXTR) in primate species, including New World monkeys. Contrary to prior expectations, we found three novel OXT forms and several OXTR nonsynonymous changes not previously described. In the Cebidae family, signals of positive selection were found for an OXT variant at position 8, which is associated with larger litter sizes. We detected positive selection for OXTR forms and report a coevolutionary process between changes in OXT and OXTR.”

Effects of the demographic transition on the genetic variances and covariances of human life history traits“The recent demographic transitions to lower mortality and fertility rates in most human societies have led to changes and even quick reversals in phenotypic selection pressures. This can only result in evolutionary change if the affected traits are heritable, but changes in environmental conditions may also lead to subsequent changes in the genetic variance and covariance (the G matrix) of traits. It currently remains unclear if there have been concomitant changes in the G matrix of life history traits following the demographic transition. Using 300 years of genealogical data from Finland, we found that four key life history traits were heritable both before and after the demographic transition. The estimated heritabilities allow a quantifiable genetic response to selection during both time periods, thus facilitating continued evolutionary change. Further, the G matrices remained largely stable but revealed a trend for an increased additive genetic variance and thus evolutionary potential of the population after the transition.” – h/t ruben c. arslan!

Mapping granny: ancestry inference for admixed individuals“In the December issue of G3: Genes|Genomes|Genetics, Yang et al. describe a method for ancestry inference of admixed individuals that uses a geographic approach to explicitly model some of the messy realities of populations. Testing the new method on data from the Population Reference Sample project, the authors were able to localize the grandparents of admixed Europeans to within around 500 kilometres of their reported ancestry, while simultaneously identifying which segments of each person’s genome were inherited from each ancestor.”

Different neurodevelopmental symptoms have a common genetic etiology“Parents of all Swedish 9- and 12-year-old twin pairs born between 1992 and 2002 were targeted for interview regarding problems typical of autism spectrum disorders, ADHD and other neurodevelopmental conditions (response rate: 80 percent). Structural equation modeling was conducted on 6,595 pairs to examine the genetic and environmental structure of 53 neurodevelopmental problems. One general genetic factor accounted for a large proportion of the phenotypic covariation among the 53 symptoms. Three specific genetic subfactors identified ‘impulsivity,’ ‘learning problems,’ and ‘tics and autism,’ respectively.” – h/t jayman! who tweeted: More evidence for the p-factor. Common genetic factor underlies many mental disorders in study of all Swedish twins.”

Measuring missing heritability: Inferring the contribution of common variants“[T]he most reasonable hypothesis concerning ‘missing heritability’ is simply that larger sample size is required to find the many remaining alleles of small effect. Fisher’s infinitesimal model will turn out to be a good first approximation for most human traits.” – from steve hsu.

Self evident but unexplored – how genetic effects vary over time – from jason collins.

Mendelian and polygenic inheritance of intelligence: A common set of causal genes? Using next-generation sequencing to examine the effects of 168 intellectual disability genes on normal-range intelligence“Despite twin and family studies having demonstrated a substantial heritability of individual differences in intelligence, no genetic variants have been robustly associated with normal-range intelligence to date. This is largely ascribed to the high polygenicity of intelligence, i.e., to its being subject to the effects of a large number of genes of individually small effect. Intellectual disability, on the other hand, frequently involves large effects of single genetic mutations, many of which have been identified…. Using an existing pool of known intellectual disability genes, we constructed a set of 168 candidate genes for normal-range intelligence, and tested their association with intelligence in 191 individuals (aged 5–18) sampled from the high and low ends of the IQ distribution. In particular, we 1) employed exon sequencing to examine the possible effects of rare genetic variants in the 168 genes, and 2) used polygenic prediction to examine the overall effect of common genetic variants in the candidate gene set in a larger sample (N = 2125, mean age 20.4, SD = 14.1). No significant association between the candidate gene set and intelligence was detected.”

IQ and Birth Order Effects: Real? No – from jayman.

Educated parents more important than rich parents“Having a mobile phone, a video recorder and a game computer are associated with lower scholastic ability, and the only substantial positive correlation is with the number of books, and of course the cause may not be the books themselves, but the intellect and character of the families who choose to buy books.” – from dr. james thompson.

The inconsistency of studies of gender differences in cognitive abilities: due to using different methods? – from emil kirkegaard.

Familial Mediterranean fever – from greg cochran.

The etiologic role of genetic and environmental factors in criminal behavior as determined from full- and half-sibling pairs: an evaluation of the validity of the twin method“Heritability estimates for CB from full- and half-siblings closely approximated those found from twins in the same population, validating the twin method.” – h/t ben southwood! who tweeted: “N=1,005,471 study of Swedish siblings and half-siblings (reared together & apart) estimates criminal behaviour is 33-56% heritable.”

Genetic polymorphisms predict national differences in life history strategy and time orientation“Polymorphisms in three genes have been linked to aspects of life-history strategy. National frequencies of these polymorphisms form a strong single genetic factor. The genetic factor is strongly associated with national differences in life-history strategy. This association remains after controlling for national socioeconomic differences.”

Genetic clue points to most vulnerable children“Some children are more sensitive to their environments, for better and for worse. Now Duke University researchers have identified a gene variant that may serve as a marker for these children….” – h/t carlos esteban!

French lesson“Modern France is founded on Western principles of equality, human betterment, and universal morality. Anyone anywhere can become French. That view, the official one, seems more and more disconnected from reality.” – from peter frost.

Is Nothing Sacred? – thosewhocansee on the charlie hebdo killings.

Twin study suggests genetic factors contribute to insomnia in children, teens

Monkeys seem to recognize their reflections“Trained macaques studied themselves in mirrors, fuelling debate over animals’ capacity for self-recognition.”

Insights into hominin phenotypic and dietary evolution from ancient DNA sequence data“Nuclear genome sequence data from Neandertals, Denisovans, and archaic anatomically modern humans can be used to complement our understanding of hominin evolutionary biology and ecology through i) direct inference of archaic hominin phenotypes, ii) indirect inference of those phenotypes by identifying the effects of previously-introgressed alleles still present among modern humans, or iii) determining the evolutionary timing of relevant hominin-specific genetic changes. Here we review and reanalyze published Neandertal and Denisovan genome sequence data to illustrate an example of the third approach.”

A New Antibiotic That Resists Resistance

There is A Scientific Reason That Cold Weather Could Cause Colds“The rhinovirus that most commonly causes colds likes chillier temperatures, where the host’s immune system doesn’t fare so well…. [W]e now know that covering your nose might actually help it stay cold-free, in more than one way.” – yes! fiiiiinally!

Remains of long-dead viruses in our genomes aid our immune response

Skip Your Annual Physical“Regardless of which screenings and tests were administered, studies of annual health exams dating from 1963 to 1999 show that the annual physicals did not reduce mortality overall or for specific causes of death from cancer or heart disease…. [S]creening healthy people who have no complaints is a pretty ineffective way to improve people’s health. If you screen thousands of people, maybe you’ll find tens whose exams suggest they might have a disease. And then upon further tests, you’ll find it is really only a few individuals who truly have something. And of those individuals, maybe one or two actually gain a health benefit from an early diagnosis. The others may have discovered a disease, but one that either would never have become clinically evident and dangerous, or one that is already too advanced to treat effectively. For instance, early detection of most thyroid cancers leads to surgery, but in many cases those cancers would not have caused serious problems, much less death. Conversely, for individuals whose annual exams lead to the diagnosis of esophageal or pancreatic cancer, the early diagnosis might extend the time they know they have cancer but is unlikely to extend their lives.” – h/t jason collins!

Variation in cancer risk among tissues can be explained by the number of stem cell divisions“Some tissue types give rise to human cancers millions of times more often than other tissue types. Although this has been recognized for more than a century, it has never been explained. Here, we show that the lifetime risk of cancers of many different types is strongly correlated (0.81) with the total number of divisions of the normal self-renewing cells maintaining that tissue’s homeostasis. These results suggest that only a third of the variation in cancer risk among tissues is attributable to environmental factors or inherited predispositions. The majority is due to ‘bad luck,’ that is, random mutations arising during DNA replication in normal, noncancerous stem cells.”

Germs May Play Key Role in Wound-Induced Skin Cancer

Race and Police Killings: Additional Thoughts – from robert verbruggen who tweeted: “Three data sets now show that racial disparities in police shootings can be explained by violent crime rates.”

In Search of an Association Between Conception Risk and Prejudice [pdf] – h/t lars penke! who tweeted: “4 large studies (1 pre-reg) by @BrianNosek et al. fail to replicate menstrual cycle effects on racial biases.”

The Strange Inevitability of Evolution“Good solutions to biology’s problems are astonishingly plentiful…. [T]wo crucial things about the RNA sequence space. First, there are many, many possible sequences that will all serve the same function. If evolution is ‘searching’ for that function by natural selection, it has an awful lot of viable solutions to choose from. Second, the space, while unthinkably vast and multi-dimensional, is navigable: You can change the genotype neutrally, without losing the all-important phenotype. So this is why the RNAs are evolvable at all: not because evolution has the time to sift through the impossibly large number of variations to find the ones that work, but because there are so many that do work, and they’re connected to one another.” – h/t billare!

Skeptic’s Guide to Debunking Claims about Telomeres in the Scientific and Pseudoscientific Literature – h/t richard harper!

Mathematicians refute oft-cited ‘diversity trumps ability’ study“‘Diverse groups of people bring to organizations more and different ways of seeing a problem and, thus, faster/better ways of solving it,’ Page told The New York Times in 2008. ‘The reason: the diverse groups got stuck less often than the smart individuals, who tended to think similarly,’ Page said. ‘What the model showed was that diverse groups of problem solvers outperformed the groups of the best individuals at solving problems.’ But Thompson’s paper in the Notices of the American Mathematical Society systematically dismantles Page’s sophistic mathematics.”

Easter Island’s Demise May Have Surprising New Explanation“The downfall of Easter Island may have had more to do with preexisting environmental conditions than degradation by humans….”

13,000 Year Old Cosmic Impact Actually Just a Stone Age House Fire

bonus: Deep bacteria may evolve even without passing genes on“Bacteria living hundreds of metres below the seafloor carry more genetic changes than their peers nearer the surface – even though the deep microbes are unlikely to reproduce and undergo natural selection in its traditional sense…. The results show – for the first time, Briggs thinks – that the bacterial genomes change with depth: the micro-organisms at 554 metres carry more mutations in genes that code for energy-related processes like cell division and biosynthesis of amino acids than are seen in their shallower counterparts…. [I]f you take evolution in its broader sense to mean genetic changes across the population, then it might be occurring even without cell division, says Briggs. That’s because in theory, bacteria in these environments grow so slowly that they may survive for hundreds of thousands of years. Individual bacteria might have begun life at the seafloor before being gradually buried, over a period of thousands of years, as more sediment accumulated at the bottom of the sea. If so, perhaps the bacteria now at 554 metres were rare cells in the initial population that have now come to dominate because the other cells, which didn’t carry their genetic mutations, have all died.”

bonus bonus: Insights into the evolution of longevity from the bowhead whale genome“The bowhead whale (Balaena mysticetus) is estimated to live over 200 years and is possibly the longest-living mammal. These animals should possess protective molecular adaptations relevant to age-related diseases, particularly cancer. Here, we report the sequencing and comparative analysis of the bowhead whale genome and two transcriptomes from different populations. Our analysis identifies genes under positive selection and bowhead-specific mutations in genes linked to cancer and aging. In addition, we identify gene gain and loss involving genes associated with DNA repair, cell-cycle regulation, cancer, and aging. Our results expand our understanding of the evolution of mammalian longevity and suggest possible players involved in adaptive genetic changes conferring cancer resistance. We also found potentially relevant changes in genes related to additional processes, including thermoregulation, sensory perception, dietary adaptations, and immune response.”

bonus bonus bonus: A Museum’s Butterfly Emerged Half Male, Half Female“The rarity is like a natural experiment that tells scientists how genes and hormones interact to produce different sexes.”

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