Archives for posts with tag: clever monkeys!

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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Questions you never thought to ask: Is inbreeding bad for democracy? – i thought to ask. so did a few other people (way before me!): steve sailer, stanley kurtz, parapundit. see also Cousin Marriage and Democracy. and, of course, see also woodley and bell. and see Question of the Day @breviosity. previously: consanguinity and democracy.

A Dose of Clannishness and What’s So Bad About Clanocracy? – @breviosity!

Where do those tensions come from?“When the Milgram experiment was done with Jordanian assistants, they were just as willing as Americans to inflict pain under orders (62.5%). But they were more willing than Americans [1.4%] to inflict pain when no orders were given, with 12.5% of them delivering shocks right up to the top end of the scale (Shanab & Yahya, 1978).” – great post from peter frost!

Modern Europe’s Genetic History Starts in Stone Age“Scientists create the first detailed genetic history of modern Europe.” – original research article. see also mtDNA haplogroup H and the origin of Europeans (Brotherton et al. 2013) from dienekes.

As women live longer and have fewer children, they are becoming taller and slimmer, study finds“‘This is a reminder that declines in mortality rates do not necessarily mean that evolution stops, but that it changes.'”

Birth Defects, FBD Marriages – from anatoly.

HBD Fundamentals – from jayman!

Why the Tropics are an evolutionary hotbed“Ant family tree shows tropical New World hosts fast speciation while also keeping older lineages alive.”

Study: People Who Believe in God Are More Responsive to Treatment of Depression“It may be that ‘the tendency to have faith in conventional social constructs’ can be generalized both to religion and the medical establishment.”

Beauty isn’t skin deep – @mangan’s.

Social psychology fraud: Just tell professors what they want to hear – from steve sailer.

Book Review: Quiet – The Power of Introverts in a World That Can’t Stop Talking (2012) by Susan Cain – from staffan. and a classic: Caring for Your Introvert. (just shush already! (~_^) )

Ethnic origins of Forbes world billionaires (2013) – @race/history/evolution notes.

Computer scientists suggest new spin on origins of evolvability“‘[E]volvable species accumulate over time even without selective pressure.'” – in their computer simulations.

Culture — Not Just a Human Thing – vervet monkeys got culture. also Parrots Barter With Nuts.

Humans Evolved Flexible, Lopsided Brains – some of us more lopsided than others. (~_^)

When Do Babies Become Conscious?“New research shows that babies display glimmers of consciousness and memory as early as 5 months old.”

Fish win fights on strength of personality“When predicting the outcome of a fight, the big guy doesn’t always win suggests new research on fish.”

Feeding our gut bacteria meat may enhance heart disease risks“Antibiotics or vegetarian diets block production of a risk-associated chemical.”

On Hold: Genes That Pause Pregnancy Discovered

Giza Secret Revealed: How 10,000 Pyramid Builders Got Fed“This meat-rich diet, along with the availability of medical care (the skeletons of some workers show healed bones), would have been an additional lure for ancient Egyptians to work on the pyramids…. ‘They probably got a much better diet than they got in their village….'”

Earliest Mayan monuments unearthed in Guatemala. see also Ancient Maya discovery sheds new light on the origins of civilization.

bonus: Levels of Commitment to the Dark Enlightenment – @habitable worlds. also What are characteristics of the Dark Enlightenment? @occam’s razor.

bonus bonus: How Cuban Villagers Learned They Descended From Sierra Leone Slaves“The amazing story of the traditional songs and dances, passed down over hundreds of years, that have tied a small Caribbean ethnic group to a remote African tribe.” – cool story!

bonus bonus bonus: Revealed: The Indian village with just 6,000 inhabitants … but more than 100 pairs of twins – another town of twins!

bonus bonus bonus bonus: Can Animals Be Mentally Ill?

bonus bonus bonus bonus bonus: not a news story, but here’s the definition of stubborn – Last Two Speakers of Dying Language Refuse to Talk to Each Other

bonus bonus bonus bonus bonus bonus: Thanks to rare alpine bacteria, researchers identify one of alcohol’s key gateways to the brain“Discovery is a step on the road to eventually developing drugs that could disrupt the interaction between alcohol and the brain.” – cool! wait. they want to disrupt the effect of alcohol on the brain?! hey!

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(sorry. the dog ate my sunday linkfest….)

And Yet Another Tale of Two Maps – from jayman.

Why are girls and boys maturing earlier? – from peter frost.

When Did Humans Come to the Americas?

Large study shows substance abuse rates higher in teenagers with ADHD“When the adolescents were an average of 15 years old, 35 percent of those with ADHD histories reported using one or more substances, as compared to only 20 percent of teens without ADHD histories.”

Tribal societies and war – from mangan.

Crime and Twins – from dienekes.

HVGIQ: Cayman Islands – from jason malloy.

Evil Genes and the Long Dark Tea Time of the Soul – @bad data, bad!

Digging Deep in the DNA“‘I think I’m one of the few people,’ she said, ‘who have taken the rectal temperature of a grizzly bear.'”

Men are from Mars Earth, women are from Venus Earth“That men and women approach their social world similarly does not imply that there are no differences in average scores between the sexes. Average differences do exist, write the authors.” – yes, average differences do exist.

Exercise linked with reduced prostate cancer risk in Caucasians but not African-Americans“Studies have also revealed that African-American men have an increased risk of developing prostate cancer and of dying from the disease compared with Caucasians.”

Gene today, gone tomorrow: Genes for autism and schizophrenia only active in developing brains“Genes linked to autism and schizophrenia are only switched on during the early stages of brain development, according to a study in mice led by researchers at the University of Oxford.” – curioser and curioser….

The Lab Accident That Led to the Discovery of Supertasters“A cloud of chemicals. One researcher detects a smell. The other does not. What happens next? Science.”

So THAT’s why women’s feet and hands are always cold! Why they are slaves to their hormones

On Genteels – @bloody shovel.

Oral Mystery: Are Agriculture and Rats Responsible for Tooth Decay?“Tooth decay is a relatively modern problem. The bacteria feasting on your teeth might have originated in the mouth of a rodent, and found their way to our teeth, thanks to agriculture.”

bonus: ‘Google for spies’ draws ire from rights groups

bonus bonus: ‘It’s a boy!’ Monkey midwife delivers baby

bonus bonus bonus: What Are Dogs Saying When They Bark? [Excerpt]“Experiments have now shown that dogs use different barks and growls to communicate different things.” – see also: Your dog really does understand you… They’re more likely to steal food if they think you can’t see, research reveals.

bonus bonus bonus bonus: Pigeons Get a New Look“Pigeons, a Darwin favorite, carry new clues to evolution.”

bonus bonus bonus bonus bonus: Do plants ‘veto’ bad genes?“Latest evidence fails to quell doubt about whether plants can access “ancestral” genes outside their parents'”

bonus bonus bonus bonus bonus bonus: Face-to-face with the earliest ancestor of all placental mammals

bonus bonus bonus bonus bonus bonus bonus: Penicillin Mold Can Reproduce Sexually, Which Could Lead to Better Antibiotics“Penicillin-producing fungus, previously thought to be asexual, has a sexual side. The finding is the latest in a kind of sexual revolution in fungal genetics.”

bonus bonus bonus bonus bonus bonus bonus bonus: Fast Food Robot Builds the Perfect Burger – won’t need mexicans for flipping burgers anymore.

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The Ignorance of Voters“Why does more education lead to less accurate beliefs? The answer returns us to the difference between rational voters (what we think we are) and rationalizing voters (what we really are). It turns out that the human mind is a marvelous information filter, adept at blocking out those facts that contradict what we’d like to believe.”

Single Out-of-Africa origin of humans: more trouble for the theory – from dienekes

Our own status affects the way our brains respond to others“People of higher subjective socioeconomic status show greater brain activity in response to other high-ranked individuals, while those with lower status have a greater response to other low-status individuals.”

Code rage: The “warrior gene” makes me mad! (Whether I have it or not) – behavioral genetics on dr. phil! whoa.

Predictors of closeness to whites among whites – from inductivist: “What predicts greater closeness to whites is: being female, being younger, having more income, being less intelligent, and more church attendance.”

Animals have personalities, too – duh.

Alcohol, Mood and Me (Not You)“Adolescents with behavioral problems drink more in general, irrespective of mood, but only adolescents without behavioral problems drink more often when feeling depressed.”

Prejudice and the president – white people are soooo waaaaaaycist

The Rewards of Doing “Something”“People don’t really care what they’re doing — just as long as they are doing something.”

Like father (country), like son – from the audacious

Monkeys, too, can recollect what they’ve seen“The researchers say that the ability of rhesus monkeys to recall what they’ve seen in the past suggests that the ability to recollect does not depend on language and may have been present in our common ancestor 30 million years ago.”

Fat, race and vitamin D – @diversity is chaos

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definitely my favorite video of the week:

bonus – a version where someone has added the appropriate music:


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