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Comparing within- and between-family polygenic score prediction | bioRxiv
https://twitter.com/StuartJRitchie/status/1116074740475736066
https://archive.is/bQnjM
See this thread for our new study on polygenic scores within fraternal twin pairs! Main point: take extra care with polygenic scores for traits like IQ & education, because they're confounded by (what seem to be) socioeconomic status effects. Not so for traits like height & BMI.
The idea is that the parenting is caused by the parental genotype, so it gets (mis)classified as a genetic effect on the children. It's really another way of looking at "genetic nurture" - see the papers from last year.
study  bio  preprint  biodet  behavioral-gen  genetics  sib-study  GWAS  class  s-factor  iq  education  attention  disease  psychiatry  embodied  health  environmental-effects  parenting  regularizer  spearhead  multi  twitter  social  commentary  backup 
10 days ago by nhaliday
Here’s How To Eliminate Negativity In 3 Minutes (or less)
It’s rough when you realize the true saboteur of your dreams is an insider. If you aren’t living up to your highest potential and achieving your goals, blame your brain’s own negativity bias…
coaching  advice  embodied 
october 2018 by lenards
An adaptability limit to climate change due to heat stress
Despite the uncertainty in future climate-change impacts, it is often assumed that humans would be able to adapt to any possible warming. Here we argue that heat stress imposes a robust upper limit to such adaptation. Peak heat stress, quantified by the wet-bulb temperature TW, is surprisingly similar across diverse climates today. TW never exceeds 31 °C. Any exceedence of 35 °C for extended periods should induce hyperthermia in humans and other mammals, as dissipation of metabolic heat becomes impossible. While this never happens now, it would begin to occur with global-mean warming of about 7 °C, calling the habitability of some regions into question. With 11–12 °C warming, such regions would spread to encompass the majority of the human population as currently distributed. Eventual warmings of 12 °C are possible from fossil fuel burning. One implication is that recent estimates of the costs of unmitigated climate change are too low unless the range of possible warming can somehow be narrowed. Heat stress also may help explain trends in the mammalian fossil record.

Trajectories of the Earth System in the Anthropocene: http://www.pnas.org/content/early/2018/07/31/1810141115
We explore the risk that self-reinforcing feedbacks could push the Earth System toward a planetary threshold that, if crossed, could prevent stabilization of the climate at intermediate temperature rises and cause continued warming on a “Hothouse Earth” pathway even as human emissions are reduced. Crossing the threshold would lead to a much higher global average temperature than any interglacial in the past 1.2 million years and to sea levels significantly higher than at any time in the Holocene. We examine the evidence that such a threshold might exist and where it might be.
study  org:nat  environment  climate-change  humanity  existence  risk  futurism  estimate  physics  thermo  prediction  temperature  nature  walls  civilization  flexibility  rigidity  embodied  multi  manifolds  plots  equilibrium  phase-transition  oscillation  comparison  complex-systems  earth 
august 2018 by nhaliday
Are visuomotor representations cognitively penetrable? Biasing action-guiding vision | SpringerLink
Are visuomotor representations cognitively penetrable? Biasing action-guiding vision
cogsci  brain  ml  vision  embodiedcogsci  embodied 
june 2018 by danbri
Moravec's paradox - Wikipedia
Moravec's paradox is the discovery by artificial intelligence and robotics researchers that, contrary to traditional assumptions, high-level reasoning requires very little computation, but low-level sensorimotor skills require enormous computational resources. The principle was articulated by Hans Moravec, Rodney Brooks, Marvin Minsky and others in the 1980s. As Moravec writes, "it is comparatively easy to make computers exhibit adult level performance on intelligence tests or playing checkers, and difficult or impossible to give them the skills of a one-year-old when it comes to perception and mobility".[1]

Similarly, Minsky emphasized that the most difficult human skills to reverse engineer are those that are unconscious. "In general, we're least aware of what our minds do best", he wrote, and added "we're more aware of simple processes that don't work well than of complex ones that work flawlessly".[2]

...

One possible explanation of the paradox, offered by Moravec, is based on evolution. All human skills are implemented biologically, using machinery designed by the process of natural selection. In the course of their evolution, natural selection has tended to preserve design improvements and optimizations. The older a skill is, the more time natural selection has had to improve the design. Abstract thought developed only very recently, and consequently, we should not expect its implementation to be particularly efficient.

As Moravec writes:

Encoded in the large, highly evolved sensory and motor portions of the human brain is a billion years of experience about the nature of the world and how to survive in it. The deliberate process we call reasoning is, I believe, the thinnest veneer of human thought, effective only because it is supported by this much older and much more powerful, though usually unconscious, sensorimotor knowledge. We are all prodigious olympians in perceptual and motor areas, so good that we make the difficult look easy. Abstract thought, though, is a new trick, perhaps less than 100 thousand years old. We have not yet mastered it. It is not all that intrinsically difficult; it just seems so when we do it.[3]

A compact way to express this argument would be:

- We should expect the difficulty of reverse-engineering any human skill to be roughly proportional to the amount of time that skill has been evolving in animals.
- The oldest human skills are largely unconscious and so appear to us to be effortless.
- Therefore, we should expect skills that appear effortless to be difficult to reverse-engineer, but skills that require effort may not necessarily be difficult to engineer at all.
concept  wiki  reference  paradox  ai  intelligence  reason  instinct  neuro  psychology  cog-psych  hardness  logic  deep-learning  time  evopsych  evolution  sapiens  the-self  EEA  embodied  embodied-cognition  abstraction  universalism-particularism  gnosis-logos  robotics 
june 2018 by nhaliday
The Religions of the Three Castes – The Neo-Ciceronian Times
The sudra caste is that which is most fitted to physical labor and bodily exercise and, as noted above, occupies the lowest position in the social hierarchy. The sudra soul is characterized by a sensual approach to life and tends to exhibit short time preferences. Thus, sudra are most often concerned with gross physical satisfaction and instant gratification. It is not surprising that it is among individuals of this caste that drug addiction, property crimes, and alcoholism are the most prevalent.

As a result, sudra religion tends to focus on feedbacks relating to the body and to the satisfaction of felt needs. It tends to be characterized the most by fleshly music, swaying, rhythmic movements, and the like. It also inclines toward specific concerns about health and physical safety, day by day provision, and so forth. Again, keep in mind that there is nothing about this that is necessarily “bad.” These are things appropriate to this caste which reflect its character and which enable it to fulfill its roles in society.

The vaisya caste is that which is most fitted to the soulish/psychical occupations which involve money and finance, technics, science, and production. The psychology of this caste involves a propensity toward materialism, empiricism, and a focus on what can be seen and felt over the intangible and faith-oriented. This caste emphasizes the pragmatic benefits provided by entrepreneurship and science, as well as exhibiting the long time preferences which enable those fields of endeavor to be successful.

The vaisya carry these concentrations over into the religious realm. Religion for the vaisya consists primarily in what can be seen and touched, whether as tangible benefits deriving from religious piety or as aids in worship itself. The intercession of gods or demigods into specific areas of life (usually pertaining to wealth or business) is considered necessary for success in those fields. Vaisya religion tends to require the reification of religious experience, rather than taking matters of religion on faith. Indeed, pure spiritualism or symbolism in religion is considered unreal, and therefore not truly efficacious.

The aristocratic caste (brahman and kshatriyan considered together) is the noble caste, and thus its tendencies are those that concern leadership and guidance, a desire to guide others in the right way. This caste tends to be focused more on eternal truths (whether specifically pertaining to religion or otherwise), and is subconsciously, and perhaps even divinely, guided toward the polar and axial tendencies which have been described by Evola in numerous places. As such, the aristocratic caste eschews materialism and the grasping for pecuniary gain and democratic political power. Instead, its focus tends to be on intangible qualities of excellence and spiritual alignment with divine and eternal realities.

Thus, aristocratic religion tends to focus more on faith and accord with spiritual realities and truths. This caste attempts to see “the reality behind the image” and is concerned with direct connection with the Divine. It will often emphasize the role of written and spoken revelation (holy books and preaching) as the means of bridging the gap between the Divine and man, ways which are used by the Divine to express His eternal laws and truths, with which man is expected to come into accord and which must be accepted through spiritual faith. The aristocratic caste, whether as priest or as king/ruler, seeks to lead and guide their people into harmony with the eternal truths espoused by religion. This caste is scrupulous to uphold the rites, while at the same time grasping and teaching the deeper spiritual realities represented by those rites.
gnon  religion  theos  gavisti  class  egalitarianism-hierarchy  military  martial  aristos  labor  things  phalanges  mystic  ascetic  empirical  new-religion  pragmatic  time-preference  embodied  realness  leadership  leviathan  sanctity-degradation  elite  social-structure  culture  society  paganism 
may 2018 by nhaliday
Who We Are | West Hunter
I’m going to review David Reich’s new book, Who We Are and How We Got Here. Extensively: in a sense I’ve already been doing this for a long time. Probably there will be a podcast. The GoFundMe link is here. You can also send money via Paypal (Use the donate button), or bitcoins to 1Jv4cu1wETM5Xs9unjKbDbCrRF2mrjWXr5. In-kind donations, such as orichalcum or mithril, are always appreciated.

This is the book about the application of ancient DNA to prehistory and history.

height difference between northern and southern europeans: https://westhunt.wordpress.com/2018/03/29/who-we-are-1/
mixing, genocide of males, etc.: https://westhunt.wordpress.com/2018/03/29/who-we-are-2-purity-of-essence/
rapid change in polygenic traits (appearance by Kevin Mitchell and funny jab at Brad Delong ("regmonkey")): https://westhunt.wordpress.com/2018/03/30/rapid-change-in-polygenic-traits/
schiz, bipolar, and IQ: https://westhunt.wordpress.com/2018/03/30/rapid-change-in-polygenic-traits/#comment-105605
Dan Graur being dumb: https://westhunt.wordpress.com/2018/04/02/the-usual-suspects/
prediction of neanderthal mixture and why: https://westhunt.wordpress.com/2018/04/03/who-we-are-3-neanderthals/
New Guineans tried to use Denisovan admixture to avoid UN sanctions (by "not being human"): https://westhunt.wordpress.com/2018/04/04/who-we-are-4-denisovans/
also some commentary on decline of Out-of-Africa, including:
"Homo Naledi, a small-brained homonin identified from recently discovered fossils in South Africa, appears to have hung around way later that you’d expect (up to 200,000 years ago, maybe later) than would be the case if modern humans had occupied that area back then. To be blunt, we would have eaten them."

Live Not By Lies: https://westhunt.wordpress.com/2018/04/08/live-not-by-lies/
Next he slams people that suspect that upcoming genetic genetic analysis will, in most cases, confirm traditional stereotypes about race – the way the world actually looks.

The people Reich dumps on are saying perfectly reasonable things. He criticizes Henry Harpending for saying that he’d never seen an African with a hobby. Of course, Henry had actually spent time in Africa, and that’s what he’d seen. The implication is that people in Malthusian farming societies – which Africa was not – were selected to want to work, even where there was no immediate necessity to do so. Thus hobbies, something like a gerbil running in an exercise wheel.

He criticized Nicholas Wade, for saying that different races have different dispositions. Wade’s book wasn’t very good, but of course personality varies by race: Darwin certainly thought so. You can see differences at birth. Cover a baby’s nose with a cloth: Chinese and Navajo babies quietly breathe through their mouth, European and African babies fuss and fight.

Then he attacks Watson, for asking when Reich was going to look at Jewish genetics – the kind that has led to greater-than-average intelligence. Watson was undoubtedly trying to get a rise out of Reich, but it’s a perfectly reasonable question. Ashkenazi Jews are smarter than the average bear and everybody knows it. Selection is the only possible explanation, and the conditions in the Middle ages – white-collar job specialization and a high degree of endogamy, were just what the doctor ordered.

Watson’s a prick, but he’s a great prick, and what he said was correct. Henry was a prince among men, and Nick Wade is a decent guy as well. Reich is totally out of line here: he’s being a dick.

Now Reich may be trying to burnish his anti-racist credentials, which surely need some renewal after having pointing out that race as colloquially used is pretty reasonable, there’s no reason pops can’t be different, people that said otherwise ( like Lewontin, Gould, Montagu, etc. ) were lying, Aryans conquered Europe and India, while we’re tied to the train tracks with scary genetic results coming straight at us. I don’t care: he’s being a weasel, slandering the dead and abusing the obnoxious old genius who laid the foundations of his field. Reich will also get old someday: perhaps he too will someday lose track of all the nonsense he’s supposed to say, or just stop caring. Maybe he already has… I’m pretty sure that Reich does not like lying – which is why he wrote this section of the book (not at all logically necessary for his exposition of the ancient DNA work) but the required complex juggling of lies and truth required to get past the demented gatekeepers of our society may not be his forte. It has been said that if it was discovered that someone in the business was secretly an android, David Reich would be the prime suspect. No Talleyrand he.

https://westhunt.wordpress.com/2018/04/12/who-we-are-6-the-americas/
The population that accounts for the vast majority of Native American ancestry, which we will call Amerinds, came into existence somewhere in northern Asia. It was formed from a mix of Ancient North Eurasians and a population related to the Han Chinese – about 40% ANE and 60% proto-Chinese. Is looks as if most of the paternal ancestry was from the ANE, while almost all of the maternal ancestry was from the proto-Han. [Aryan-Transpacific ?!?] This formation story – ANE boys, East-end girls – is similar to the formation story for the Indo-Europeans.

https://westhunt.wordpress.com/2018/04/18/who-we-are-7-africa/
In some ways, on some questions, learning more from genetics has left us less certain. At this point we really don’t know where anatomically humans originated. Greater genetic variety in sub-Saharan African has been traditionally considered a sign that AMH originated there, but it possible that we originated elsewhere, perhaps in North Africa or the Middle East, and gained extra genetic variation when we moved into sub-Saharan Africa and mixed with various archaic groups that already existed. One consideration is that finding recent archaic admixture in a population may well be a sign that modern humans didn’t arise in that region ( like language substrates) – which makes South Africa and West Africa look less likely. The long-continued existence of homo naledi in South Africa suggests that modern humans may not have been there for all that long – if we had co-existed with homo naledi, they probably wouldn’t lasted long. The oldest known skull that is (probably) AMh was recently found in Morocco, while modern humans remains, already known from about 100,000 years ago in Israel, have recently been found in northern Saudi Arabia.

While work by Nick Patterson suggests that modern humans were formed by a fusion between two long-isolated populations, a bit less than half a million years ago.

So: genomics had made recent history Africa pretty clear. Bantu agriculuralists expanded and replaced hunter-gatherers, farmers and herders from the Middle East settled North Africa, Egypt and northeaat Africa, while Nilotic herdsmen expanded south from the Sudan. There are traces of earlier patterns and peoples, but today, only traces. As for questions back further in time, such as the origins of modern humans – we thought we knew, and now we know we don’t. But that’s progress.

https://westhunt.wordpress.com/2018/04/18/reichs-journey/
David Reich’s professional path must have shaped his perspective on the social sciences. Look at the record. He starts his professional career examining the role of genetics in the elevated prostate cancer risk seen in African-American men. Various social-science fruitcakes oppose him even looking at the question of ancestry ( African vs European). But they were wrong: certain African-origin alleles explain the increased risk. Anthropologists (and human geneticists) were sure (based on nothing) that modern humans hadn’t interbred with Neanderthals – but of course that happened. Anthropologists and archaeologists knew that Gustaf Kossina couldn’t have been right when he said that widespread material culture corresponded to widespread ethnic groups, and that migration was the primary explanation for changes in the archaeological record – but he was right. They knew that the Indo-European languages just couldn’t have been imposed by fire and sword – but Reich’s work proved them wrong. Lots of people – the usual suspects plus Hindu nationalists – were sure that the AIT ( Aryan Invasion Theory) was wrong, but it looks pretty good today.

Some sociologists believed that caste in India was somehow imposed or significantly intensified by the British – but it turns out that most jatis have been almost perfectly endogamous for two thousand years or more…

It may be that Reich doesn’t take these guys too seriously anymore. Why should he?

varnas, jatis, aryan invastion theory: https://westhunt.wordpress.com/2018/04/22/who-we-are-8-india/

europe and EEF+WHG+ANE: https://westhunt.wordpress.com/2018/05/01/who-we-are-9-europe/

https://www.nationalreview.com/2018/03/book-review-david-reich-human-genes-reveal-history/
The massive mixture events that occurred in the recent past to give rise to Europeans and South Asians, to name just two groups, were likely “male mediated.” That’s another way of saying that men on the move took local women as brides or concubines. In the New World there are many examples of this, whether it be among African Americans, where most European ancestry seems to come through men, or in Latin America, where conquistadores famously took local women as paramours. Both of these examples are disquieting, and hint at the deep structural roots of patriarchal inequality and social subjugation that form the backdrop for the emergence of many modern peoples.
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march 2018 by nhaliday
Strategic height adjustment - Marginal REVOLUTION
Professor Bogin’s study, carried out in collaboration with Dr Christiane Scheffler, at the University of Potsdam, and Professor Michael Hermanussen, from the University of Kiel, also explored a second phenomenon called competitive growth — where the ruling social classes adjust their height to exceed the subordinate population.

Prof Bogin said: “This is when the mean height of colonial or military migrants, who become the socially dominant group in the conquered country, surpasses the average height of the both the conquered people and the origin population.”

In one example, the researchers found that the height of Dutch colonial masters in Indonesia in the 19th and early 20th centuries was greater than the Indonesians they ruled, and also greater than social upper classes back in the Netherlands.

“This was also the case for English colonial masters in North America,” said Prof Bogin.

“We find that it is the superior social status of the conquerors that promotes their greater height.
econotariat  marginal-rev  study  summary  links  quotes  anthropology  sociology  embodied  environmental-effects  status  conquest-empire  expansionism  history  mostly-modern  early-modern  usa  britain  europe  germanic 
march 2018 by nhaliday
The Space Trilogy - Wikipedia
Out of the Silent Planet:

Weston makes a long speech justifying his proposed invasion of Malacandra on "progressive" and evolutionary grounds, which Ransom attempts to translate into Malacandrian, thus laying bare the brutality and crudity of Weston's ambitions.

Oyarsa listens carefully to Weston's speech and acknowledges that the scientist is acting out of a sense of duty to his species, and not mere greed. This renders him more mercifully disposed towards the scientist, who accepts that he may die while giving Man the means to continue. However, on closer examination Oyarsa points out that Weston's loyalty is not to Man's mind – or he would equally value the intelligent alien minds already inhabiting Malacandra, instead of seeking to displace them in favour of humanity; nor to Man's body – since, as Weston is well aware of and at ease with, Man's physical form will alter over time, and indeed would have to in order to adapt to Weston's programme of space exploration and colonisation. It seems then that Weston is loyal only to "the seed" – Man's genome – which he seeks to propagate. When Oyarsa questions why this is an intelligible motivation for action, Weston's eloquence fails him and he can only articulate that if Oyarsa does not understand Man's basic loyalty to Man then he, Weston, cannot possibly instruct him.

...

Perelandra:

The rafts or floating islands are indeed Paradise, not only in the sense that they provide a pleasant and care-free life (until the arrival of Weston) but also in the sense that Ransom is for weeks and months naked in the presence of a beautiful naked woman without once lusting after her or being tempted to seduce her. This is because of the perfection in that world.

The plot thickens when Professor Weston arrives in a spaceship and lands in a part of the ocean quite close to the Fixed Land. He at first announces to Ransom that he is a reformed man, but appears to still be in search of power. Instead of the strictly materialist attitude he displayed when first meeting Ransom, he asserts he had become aware of the existence of spiritual beings and pledges allegiance to what he calls the "Life-Force." Ransom, however, disagrees with Weston's position that the spiritual is inherently good, and indeed Weston soon shows signs of demonic possession.

In this state, the possessed Weston finds the Queen and tries to tempt her into defying Maleldil's orders by spending a night on the Fixed Land. Ransom, perceiving this, believes that he must act as a counter-tempter. Well versed in the Bible and Christian theology, Ransom realises that if the pristine Queen, who has never heard of Evil, succumbs to the tempter's arguments, the Fall of Man will be re-enacted on Perelandra. He struggles through day after day of lengthy arguments illustrating various approaches to temptation, but the demonic Weston shows super-human brilliance in debate (though when "off-duty" he displays moronic, asinine behaviour and small-minded viciousness) and moreover appears never to need sleep.

With the demonic Weston on the verge of winning, the desperate Ransom hears in the night what he gradually realises is a Divine voice, commanding him to physically attack the Tempter. Ransom is reluctant, and debates with the divine (inner) voice for the entire duration of the night. A curious twist is introduced here; whereas the name "Ransom" is said to be derived from the title "Ranolf's Son", it can also refer to a reward given in exchange for a treasured life. Recalling this, and recalling that his God would (and has) sacrificed Himself in a similar situation, Ransom decides to confront the Tempter outright.

Ransom attacks his opponent bare-handed, using only physical force. Weston's body is unable to withstand this despite the Tempter's superior abilities of rhetoric, and so the Tempter flees. Ultimately Ransom chases him over the ocean, Weston fleeing and Ransom chasing on the backs of giant and friendly fish. During a fleeting truce, the "real" Weston appears to momentarily re-inhabit his body, and recount his experience of Hell, wherein the damned soul is not consigned to pain or fire, as supposed by popular eschatology, but is absorbed into the Devil, losing all independent existence.
fiction  scifi-fantasy  tip-of-tongue  literature  big-peeps  religion  christianity  theos  space  xenobio  analogy  myth  eden  deep-materialism  new-religion  sanctity-degradation  civil-liberty  exit-voice  speaking  truth  realness  embodied  fighting  old-anglo  group-selection  war  paying-rent  counter-revolution  morality  parable  competition  the-basilisk  gnosis-logos  individualism-collectivism  language  physics  science  evolution  conquest-empire  self-interest  hmm  intricacy  analytical-holistic  tradeoffs  paradox  heterodox  narrative  philosophy  expansionism  genetics  duty  us-them  interests  nietzschean  parallax  the-devil  the-self 
january 2018 by nhaliday
The Politics of Mate Choice
TABLE 1 Spousal Concordance on 16 Traits Pearson’s r (n)

Church attendance .714 (4950)
W-P Index (28 items) .647 (3984)
Drinking frequency .599 (4984)
Political party support .596 (4547)
Education .498 (4957)
Height .227 (4964)
pdf  study  sociology  anthropology  sex  assortative-mating  correlation  things  phalanges  planning  long-term  human-bean  religion  theos  politics  polisci  ideology  ethanol  time-use  coalitions  education  embodied  integrity  sleep  rhythm  personality  psych-architecture  stress  psychiatry  self-report  extra-introversion  discipline  self-control  patience  data  database  list  top-n  objektbuch  values  habit  time  density  twin-study  longitudinal  tradition  time-preference  life-history  selection  psychology  social-psych  flux-stasis  demographics  frequency 
december 2017 by nhaliday
Estimation of effect size distribution from genome-wide association studies and implications for future discoveries
We report a set of tools to estimate the number of susceptibility loci and the distribution of their effect sizes for a trait on the basis of discoveries from existing genome-wide association studies (GWASs). We propose statistical power calculations for future GWASs using estimated distributions of effect sizes. Using reported GWAS findings for height, Crohn’s disease and breast, prostate and colorectal (BPC) cancers, we determine that each of these traits is likely to harbor additional loci within the spectrum of low-penetrance common variants. These loci, which can be identified from sufficiently powerful GWASs, together could explain at least 15–20% of the known heritability of these traits. However, for BPC cancers, which have modest familial aggregation, our analysis suggests that risk models based on common variants alone will have modest discriminatory power (63.5% area under curve), even with new discoveries.

later paper:
Distribution of allele frequencies and effect sizes and their interrelationships for common genetic susceptibility variants: http://www.pnas.org/content/108/44/18026.full

Recent discoveries of hundreds of common susceptibility SNPs from genome-wide association studies provide a unique opportunity to examine population genetic models for complex traits. In this report, we investigate distributions of various population genetic parameters and their interrelationships using estimates of allele frequencies and effect-size parameters for about 400 susceptibility SNPs across a spectrum of qualitative and quantitative traits. We calibrate our analysis by statistical power for detection of SNPs to account for overrepresentation of variants with larger effect sizes in currently known SNPs that are expected due to statistical power for discovery. Across all qualitative disease traits, minor alleles conferred “risk” more often than “protection.” Across all traits, an inverse relationship existed between “regression effects” and allele frequencies. Both of these trends were remarkably strong for type I diabetes, a trait that is most likely to be influenced by selection, but were modest for other traits such as human height or late-onset diseases such as type II diabetes and cancers. Across all traits, the estimated effect-size distribution suggested the existence of increasingly large numbers of susceptibility SNPs with decreasingly small effects. For most traits, the set of SNPs with intermediate minor allele frequencies (5–20%) contained an unusually small number of susceptibility loci and explained a relatively small fraction of heritability compared with what would be expected from the distribution of SNPs in the general population. These trends could have several implications for future studies of common and uncommon variants.

...

Relationship Between Allele Frequency and Effect Size. We explored the relationship between allele frequency and effect size in different scales. An inverse relationship between the squared regression coefficient and f(1 − f) was observed consistently across different traits (Fig. 3). For a number of these traits, however, the strengths of these relationships become less pronounced after adjustment for ascertainment due to study power. The strength of the trend, as captured by the slope of the fitted line (Table 2), markedly varies between traits, with an almost 10-fold change between the two extremes of distinct types of traits. After adjustment, the most pronounced trend was seen for type I diabetes and Crohn’s disease among qualitative traits and LDL level among quantitative traits. In exploring the relationship between the frequency of the risk allele and the magnitude of the associated risk coefficient (Fig. S4), we observed a quadratic pattern that indicates increasing risk coefficients as the risk-allele frequency diverges away from 0.50 either toward 0 or toward 1. Thus, it appears that regression coefficients for common susceptibility SNPs increase in magnitude monotonically with decreasing minor-allele frequency, irrespective of whether the minor allele confers risk or protection. However, for some traits, such as type I diabetes, risk alleles were predominantly minor alleles, that is, they had frequencies of less than 0.50.
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november 2017 by nhaliday

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