nhaliday + fisher   21

Sci-Hub | The genetics of human fertility. Current Opinion in Psychology, 27, 41–45 | 10.1016/j.copsyc.2018.07.011
very short

Overall, there is a suggestion of two different reproductive strategies proving to be successful in modern Western societies: (1) a strategy associated with socially conservative values, including a high commitment to the bearing of children within marriage; and(2) a strategy associated with antisocial behavior, early sexual experimentation, a variety of sexual partners, low educational attainment, low commitment to marriage, haphazard pregnancies, and indifference to politics. This notion of distinct lifestyles characterized in common by relatively high fertility deserves further empirical and theoretical study.
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march 2019 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.

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.

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.

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/

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
Books 2017 | West Hunter
Arabian Sands
The Aryans
The Big Show
The Camel and the Wheel
Civil War on Western Waters
Company Commander
Double-edged Secrets
The Forgotten Soldier
Genes in Conflict
Hive Mind
The horse, the wheel, and language
The Penguin Atlas of Medieval History
Habitable Planets for Man
The genetical theory of natural selection
The Rise of the Greeks
To Lose a Battle
The Jewish War
Tropical Gangsters
The Forgotten Revolution
Egil’s Saga
Time Patrol

Russo: https://westhunt.wordpress.com/2017/12/14/books-2017/#comment-98568
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december 2017 by nhaliday
The Function of Reason | Edge.org

How Social Is Reason?: http://www.overcomingbias.com/2017/08/how-social-is-reason.html

Reading The Enigma of Reason. Pretty good so far. Not incredibly surprising to me so far. To be clear, their argument is somewhat orthogonal to the whole ‘rationality’ debate you may be familiar with from Daniel Kahneman and Amos Tversky’s work (e.g., see Heuristics and Biases).

One of the major problems in analysis is that rationality, reflection and ratiocination, are slow and error prone. To get a sense of that, just read ancient Greek science. Eratosthenes may have calculated to within 1% of the true circumference of the world, but Aristotle’s speculations on the nature of reproduction were rather off.

You may be as clever as Eratosthenes, but most people are not. But you probably accept that the world is round and 24,901 miles around. If you are not American you probably are vague on miles anyway. But you know what the social consensus is, and you accept it because it seems reasonable.

One of the points in cultural evolution work is that a lot of the time rather than relying on your own intuition and or reason, it is far more effective and cognitively cheaper to follow social norms of your ingroup. I only bring this up because unfortunately many pathologies of our political and intellectual world today are not really pathologies. That is, they’re not bugs, but features.

Finished The Enigma of Reason. The basic thesis that reasoning is a way to convince people after you’ve already come to a conclusion, that is, rationalization, was already one I shared. That makes sense since one of the coauthors, Dan Sperber, has been influential in the “naturalistic” school of anthropology. If you’ve read books like In Gods We Trust The Enigma of Reason goes fast. But it is important to note that the cognitive anthropology perspective is useful in things besides religion. I’m thinking in particular of politics.

My point here is that many of our beliefs are arrived at in an intuitive manner, and we find reasons to justify those beliefs. One of the core insights you’ll get from The Enigma of Reason is that rationalization isn’t that big of a misfire or abuse of our capacities. It’s probably just a natural outcome for what and how we use reason in our natural ecology.

Mercier and Sperber contrast their “interactionist” model of what reason is for with an “intellectualist: model. The intellecutalist model is rather straightforward. It is one where individual reasoning capacities exist so that one may make correct inferences about the world around us, often using methods that mimic those in abstract elucidated systems such as formal logic or Bayesian reasoning. When reasoning doesn’t work right, it’s because people aren’t using it for it’s right reasons. It can be entirely solitary because the tools don’t rely on social input or opinion.

The interactionist model holds that reasoning exists because it is a method of persuasion within social contexts. It is important here to note that the authors do not believe that reasoning is simply a tool for winning debates. That is, increasing your status in a social game. Rather, their overall thesis seems to be in alignment with the idea that cognition of reasoning properly understood is a social process. In this vein they offer evidence of how juries may be superior to judges, and the general examples you find in the “wisdom of the crowds” literature. Overall the authors make a strong case for the importance of diversity of good-faith viewpoints, because they believe that the truth on the whole tends to win out in dialogic formats (that is, if there is a truth; they are rather unclear and muddy about normative disagreements and how those can be resolved).

The major issues tend to crop up when reasoning is used outside of its proper context. One of the literature examples, which you are surely familiar with, in The Enigma of Reason is a psychological experiment where there are two conditions, and the researchers vary the conditions and note wide differences in behavior. In particular, the experiment where psychologists put subjects into a room where someone out of view is screaming for help. When they are alone, they quite often go to see what is wrong immediately. In contrast, when there is a confederate of the psychologists in the room who ignores the screaming, people also tend to ignore the screaming.

The researchers know the cause of the change in behavior. It’s the introduction of the confederate and that person’s behavior. But the subjects when interviewed give a wide range of plausible and possible answers. In other words, they are rationalizing their behavior when called to justify it in some way. This is entirely unexpected, we all know that people are very good at coming up with answers to explain their behavior (often in the best light possible). But that doesn’t mean they truly understanding their internal reasons, which seem to be more about intuition.

But much of The Enigma of Reason also recounts how bad people are at coming up with coherent and well thought out rationalizations. That is, their “reasons” tend to be ad hoc and weak. We’re not very good at formal logic or even simple syllogistic reasoning. The explanation for this seems to be two-fold.


At this point we need to address the elephant in the room: some humans seem extremely good at reasoning in a classical sense. I’m talking about individuals such as Blaise Pascal, Carl Friedrich Gauss, and John von Neumann. Early on in The Enigma of Reason the authors point out the power of reason by alluding to Eratosthenes’s calculation of the circumference of the earth, which was only off by one percent. Myself, I would have mentioned Archimedes, who I suspect was a genius on the same level as the ones mentioned above.

Mercier and Sperber state near the end of the book that math in particular is special and a powerful way to reason. We all know this. In math the axioms are clear, and agreed upon. And one can inspect the chain of propositions in a very transparent manner. Mathematics has guard-rails for any human who attempts to engage in reasoning. By reducing the ability of humans to enter into unforced errors math is the ideal avenue for solitary individual reasoning. But it is exceptional.

Second, though it is not discussed in The Enigma of Reason there does seem to be variation in general and domain specific intelligence within the human population. People who flourish in mathematics usually have high general intelligences, but they also often exhibit a tendency to be able to engage in high levels of visual-spatial conceptualization.

One the whole the more intelligent you are the better you are able to reason. But that does not mean that those with high intelligence are immune from the traps of motivated reasoning or faulty logic. Mercier and Sperber give many examples. There are two. Linus Pauling was indisputably brilliant, but by the end of his life he was consistently pushing Vitamin C quackery (in part through a very selective interpretation of the scientific literature).* They also point out that much of Isaac Newton’s prodigious intellectual output turns out to have been focused on alchemy and esoteric exegesis which is totally impenetrable. Newton undoubtedly had a first class mind, but if the domain it was applied to was garbage, then the output was also garbage.


Overall, the take-homes are:

Reasoning exists to persuade in a group context through dialogue, not individual ratiocination.
Reasoning can give rise to storytelling when prompted, even if the reasons have no relationship to the underlying causality.
Motivated reasoning emerges because we are not skeptical of the reasons we proffer, but highly skeptical of reasons which refute our own.
The “wisdom of the crowds” is not just a curious phenomenon, but one of the primary reasons that humans have become more socially complex and our brains have larger.
Ultimately, if you want to argue someone out of their beliefs…well, good luck with that. But you should read The Enigma of Reason to understand the best strategies (many of them are common sense, and I’ve come to them independently simply through 15 years of having to engage with people of diverse viewpoints).

* R. A. Fisher, who was one of the pioneers of both evolutionary genetics and statistics, famously did not believe there was a connection between smoking and cancer. He himself smoked a pipe regularly.

** From what we know about Blaise Pascal and Isaac Newton, their personalities were such that they’d probably be killed or expelled from a hunter-gatherer band.
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august 2017 by nhaliday
Fundamental Theorems of Evolution: The American Naturalist: Vol 0, No 0
I suggest that the most fundamental theorem of evolution is the Price equation, both because of its simplicity and broad scope and because it can be used to derive four other familiar results that are similarly fundamental: Fisher’s average-excess equation, Robertson’s secondary theorem of natural selection, the breeder’s equation, and Fisher’s fundamental theorem. These derivations clarify both the relationships behind these results and their assumptions. Slightly less fundamental results include those for multivariate evolution and social selection. A key feature of fundamental theorems is that they have great simplicity and scope, which are often achieved by sacrificing perfect accuracy. Quantitative genetics has been more productive of fundamental theorems than population genetics, probably because its empirical focus on unknown genotypes freed it from the tyranny of detail and allowed it to focus on general issues.
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march 2017 by nhaliday
Information Geometry (Part 16) | Azimuth
While preparing this talk, I discovered a cool fact. I doubt it’s new, but I haven’t exactly seen it elsewhere. I came up with it while trying to give a precise and general statement of ‘Fisher’s fundamental theorem of natural selection’. I won’t start by explaining that theorem, since my version looks rather different than Fisher’s, and I came up with mine precisely because I had trouble understanding his. I’ll say a bit more about this at the end.

Here’s my version:
The square of the rate at which a population learns information is the variance of its fitness.
baez  mathtariat  evolution  bio  genetics  population-genetics  bits  interdisciplinary  models  exposition  math.DS  giants  information-theory  entropy-like  org:bleg  nibble  fisher  EGT  dynamical 
february 2017 by nhaliday
Sir Ronald Aylmer Fisher | West Hunter
In 1930 he published The Genetical Theory of Natural Selection, which completed the fusion of Darwinian natural selection with Mendelian inheritance. James Crow said that it was ‘arguably the deepest and most influential book on evolution since Darwin’. In it, Fisher analyzed sexual selection, mimicry, and sex ratios, where he made some of the first arguments using game theory. The book touches on many other topics. As was the case with his other works, The Genetical Theory is a dense book, not easy for most people to understand. Fisher’s tendency to leave out mathematical steps that he deemed obvious (a leftover from his early training in mental mathematics) frustrates many readers.

The Genetical Theory is of particular interest to us because Fisher there lays out his ideas on how population size can speed up evolution. As we explain elsewhere, more individuals mean there will be more mutations, including favorable mutations, and so Fisher expected more rapid evolution in larger populations. This idea was originally suggested, in a nonmathematical way, in Darwin’s Origin of Species.

Although Fisher was fiercely loyal to friends and could be very charming, he had a quick temper and was a fine hater. The same uncompromising spirit that fostered his originality led to constant conflict with authority. He had a long conflict with Karl Pearson, who had also played an important part in the development of mathematical statistics. In this case, Pearson was more at fault, resisting the advent of a more talented competitor, as well as being an eminently hateable person in general. Over time Fisher also became increasing angry at Sewall Wright (another one of the founders of population genetics) due to scientific disagreements – and this was just wrong, because Wright was a sweetheart.

Fisher’s personality decreased his potential influence. He was not a school-builder, and was impatient with administrators. He expected to find some form of war-work in the Second World War, but his characteristics had alienated too many people, and thus his team dispersed to other jobs during the war. He returned to Rothamsted for the duration. This was a difficult time for him: his marriage disintegrated and his oldest son, an RAF pilot, was killed in the war.


Fisher’s ideas in genetics have taken an odd path. The Genetical Theory was not widely read, sold few copies, and has never been translated. Only gradually did its ideas find an audience. Of course, that audience included people like Bill Hamilton, the greatest mathematical biologist of the last half of the 20th century, who was strongly influenced by Fisher’s work. Hamilton said “By the time of my ultimate graduation,will I have understood all that is true in this book and will I get a First? I doubt it. In some ways some of us have overtaken Fisher; in many, however, this brilliant, daring man is still far in front.“

In fact, over the past generation, much of Fisher’s work has been neglected – in the sense that interest in population genetics has decreased (particularly interest in selection) and fewer students are exposed to his work in genetics in any way. Ernst Mayr didn’t even mention Fisher in his 1991 book One Long Argument: Charles Darwin and the Genesis of Modern Evolutionary Thought, while Stephen Jay Gould, in The Structure of Evolutionary Theory, gave Fisher 6 pages out of 1433. Of course Mayr and Gould were both complete chuckleheads.

Fisher’s work affords continuing insight, including important implications concerning human evolution that have emerged more than 50 years after his death. We strongly discourage other professionals from learning anything about his ideas.
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january 2017 by nhaliday
The infinitesimal model | bioRxiv
Our focus here is on the infinitesimal model. In this model, one or several quantitative traits are described as the sum of a genetic and a non-genetic component, the first being distributed as a normal random variable centred at the average of the parental genetic components, and with a variance independent of the parental traits. We first review the long history of the infinitesimal model in quantitative genetics. Then we provide a definition of the model at the phenotypic level in terms of individual trait values and relationships between individuals, but including different evolutionary processes: genetic drift, recombination, selection, mutation, population structure, ... We give a range of examples of its application to evolutionary questions related to stabilising selection, assortative mating, effective population size and response to selection, habitat preference and speciation. We provide a mathematical justification of the model as the limit as the number M of underlying loci tends to infinity of a model with Mendelian inheritance, mutation and environmental noise, when the genetic component of the trait is purely additive. We also show how the model generalises to include epistatic effects. In each case, by conditioning on the pedigree relating individuals in the population, we incorporate arbitrary selection and population structure. We suppose that we can observe the pedigree up to the present generation, together with all the ancestral traits, and we show, in particular, that the genetic components of the individual trait values in the current generation are indeed normally distributed with a variance independent of ancestral traits, up to an error of order M^{-1/2}. Simulations suggest that in particular cases the convergence may be as fast as 1/M.

published version:
The infinitesimal model: Definition, derivation, and implications: https://sci-hub.tw/10.1016/j.tpb.2017.06.001

Commentary: Fisher’s infinitesimal model: A story for the ages: http://www.sciencedirect.com/science/article/pii/S0040580917301508?via%3Dihub
This commentary distinguishes three nested approximations, referred to as “infinitesimal genetics,” “Gaussian descendants” and “Gaussian population,” each plausibly called “the infinitesimal model.” The first and most basic is Fisher’s “infinitesimal” approximation of the underlying genetics – namely, many loci, each making a small contribution to the total variance. As Barton et al. (2017) show, in the limit as the number of loci increases (with enough additivity), the distribution of genotypic values for descendants approaches a multivariate Gaussian, whose variance–covariance structure depends only on the relatedness, not the phenotypes, of the parents (or whether their population experiences selection or other processes such as mutation and migration). Barton et al. (2017) call this rigorously defensible “Gaussian descendants” approximation “the infinitesimal model.” However, it is widely assumed that Fisher’s genetic assumptions yield another Gaussian approximation, in which the distribution of breeding values in a population follows a Gaussian — even if the population is subject to non-Gaussian selection. This third “Gaussian population” approximation, is also described as the “infinitesimal model.” Unlike the “Gaussian descendants” approximation, this third approximation cannot be rigorously justified, except in a weak-selection limit, even for a purely additive model. Nevertheless, it underlies the two most widely used descriptions of selection-induced changes in trait means and genetic variances, the “breeder’s equation” and the “Bulmer effect.” Future generations may understand why the “infinitesimal model” provides such useful approximations in the face of epistasis, linkage, linkage disequilibrium and strong selection.
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january 2017 by nhaliday
Faster than Fisher | West Hunter
There’s a simple model of the spread of an advantageous allele:  You take σ, the typical  distance people move in one generation, and s,  the selective advantage: the advantageous allele spreads as a nonlinear wave at speed  σ * √(2s).  The problem is, that’s slow.   Suppose that s = 0.10 (a large advantage), σ = 10 kilometers, and a generation time of 30 years: the allele would take almost 7,000 years to expand out 1000 kilometers.


This big expansion didn’t just happen from peasants marrying the girl next door: it required migrations and conquests. This one looks as if it rode with the Indo-European expansion: I’ll bet it started out in a group that had domesticated only horses.

The same processes, migration and conquest, must explain the wide distribution of many geographically widespread selective sweeps and partial sweeps. They were adaptive, all right, but expanded much faster than possible from purely local diffusion. We already have reason to think that SLC24A5 was carried to Europe by Middle Eastern farmers; the same is probably true for the haplotype that carries the high-activity ergothioniene transporter and the 35delG connexin-26/GJB2 deafness mutation. The Indo-Europeans probably introduced the T-13910 LCT mutation and the delta-F508 cystic fibrosis mutation, so we should see delta-F508 in northwest India and Pakistan – and we do !

To entertain a (possibly mistaken) physical analogy, it sounds like you’re suggested a sort genetic convection through space, as opposed to conduction. I.e. Entire masses of folks, carrying a new selected variant, are displacing others – as opposed to the slow gene flow process of “girl-next-door.” Is that about right? (Hopefully I haven’t revealed my ignorance of basic thermodynamics here…)

Has there been any attempt to estimate sigma from these time periods?

Genetic Convection: https://westhunt.wordpress.com/2015/02/22/genetic-convection/
People are sometimes interested in estimating the point of origin of a sweeping allele: this is probably effectively impossible even if diffusion were the only spread mechanism, since the selective advantage might well vary in both time and space. But that’s ok, since population movements – genetic convection – are real and very important. This means that the difficulties in estimating the origin of a Fisher wave are totally insignificant, compared to the difficulties of estimating the effects of past colonizations, conquests and Völkerwanderungs. So when Yuval Itan and Mark Thomas estimated that 13,910 T LCT allele originated in central Europe, in the early Neolithic, they didn’t just go wrong because of failing to notice that the same allele is fairly common in northern India: no, their whole notion was unsound in the first place. We’re talking turbulence on steroids. Hari Seldon couldn’t figure this one out from the existing geographic distribution.
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november 2016 by nhaliday
Information Processing: Evidence for (very) recent natural selection in humans
height (+), infant head circumference (+), some biomolecular stuff, female hip size (+), male BMI (-), age of menarche (+, !!), and birth weight (+)

Strong selection in the recent past can cause allele frequencies to change significantly. Consider two different SNPs, which today have equal minor allele frequency (for simplicity, let this be equal to one half). Assume that one SNP was subject to strong recent selection, and another (neutral) has had approximately zero effect on fitness. The advantageous version of the first SNP was less common in the far past, and rose in frequency recently (e.g., over the last 2k years). In contrast, the two versions of the neutral SNP have been present in roughly the same proportion (up to fluctuations) for a long time. Consequently, in the total past breeding population (i.e., going back tens of thousands of years) there have been many more copies of the neutral alleles (and the chunks of DNA surrounding them) than of the positively selected allele. Each of the chunks of DNA around the SNPs we are considering is subject to a roughly constant rate of mutation.

Looking at the current population, one would then expect a larger variety of mutations in the DNA region surrounding the neutral allele (both versions) than near the favored selected allele (which was rarer in the population until very recently, and whose surrounding region had fewer chances to accumulate mutations). By comparing the difference in local mutational diversity between the two versions of the neutral allele (should be zero modulo fluctuations, for the case MAF = 0.5), and between the (+) and (-) versions of the selected allele (nonzero, due to relative change in frequency), one obtains a sensitive signal for recent selection. See figure at bottom for more detail. In the paper what I call mutational diversity is measured by looking at distance distribution of singletons, which are rare variants found in only one individual in the sample under study.

The 2,000 year selection of the British: http://www.unz.com/gnxp/the-2000-year-selection-of-the-british/

Detection of human adaptation during the past 2,000 years: http://www.biorxiv.org/content/early/2016/05/07/052084

The key idea is that recent selection distorts the ancestral genealogy of sampled haplotypes at a selected site. In particular, the terminal (tip) branches of the genealogy tend to be shorter for the favored allele than for the disfavored allele, and hence, haplotypes carrying the favored allele will tend to carry fewer singleton mutations (Fig. 1A-C and SOM).

To capture this effect, we use the sum of distances to the nearest singleton in each direction from a test SNP as a summary statistic (Fig. 1D).

Figure 1. Illustration of the SDS method.

Figure 2. Properties of SDS.

Based on a recent model of European demography [25], we estimate that the mean tip length for a neutral sample of 3,000 individuals is 75 generations, or roughly 2,000 years (Fig. 2A). Since SDS aims to measure changes in tip lengths of the genealogy, we conjectured that it would be most likely to detect selection approximately within this timeframe.

Indeed, in simulated sweep models with samples of 3,000 individuals (Fig. 2B,C and fig. S2), we find that SDS focuses specifically on very recent time scales, and has equal power for hard and soft sweeps within this timeframe. At individual loci, SDS is powered to detect ~2% selection over 100 generations. Moreover, SDS has essentially no power to detect older selection events that stopped >100 generations before the present. In contrast, a commonly-used test for hard sweeps, iHS [12], integrates signal over much longer timescales (>1,000 generations), has no specificity to the more recent history, and has essentially no power for the soft sweep scenarios.

Catching evolution in the act with the Singleton Density Score: http://www.molecularecologist.com/2016/05/catching-evolution-in-the-act-with-the-singleton-density-score/
The Singleton Density Score (SDS) is a measure based on the idea that changes in allele frequencies induced by recent selection can be observed in a sample’s genealogy as differences in the branch length distribution.

You don’t need a weatherman: https://westhunt.wordpress.com/2016/05/08/you-dont-need-a-weatherman/
You can do a million cool things with this method. Since the effective time scale goes inversely with sample size, you could look at evolution in England over the past 1000 years or the past 500. Differencing, over the period 1-1000 AD. Since you can look at polygenic traits, you can see whether the alleles favoring higher IQs have increased or decreased in frequency over various stretches of time. You can see if Greg Clark’s proposed mechanism really happened. You can (soon) tell if creeping Pinkerization is genetic, or partly genetic.

You could probably find out if the Middle Easterners really have gotten slower, and when it happened.

Looking at IQ alleles, you could not only show whether the Ashkenazi Jews really are biologically smarter but if so, when it happened, which would give you strong hints as to how it happened.

We know that IQ-favoring alleles are going down (slowly) right now (not counting immigration, which of course drastically speeds it up). Soon we will know if this was true while Russia was under the Mongol yoke – we’ll know how smart Periclean Athenians were and when that boost occurred. And so on. And on!


“The pace has been so rapid that humans have changed significantly in body and mind over recorded history."

bicameral mind: https://westhunt.wordpress.com/2016/05/08/you-dont-need-a-weatherman/#comment-78934

Chinese, Koreans, Japanese and Ashkenazi Jews all have high levels of myopia. Australian Aborigines have almost none, I think.

I expect that the fall of all great empires is based on long term dysgenic trends. There is no logical reason why so many empires and civilizations throughout history could grow so big and then not simply keep growing, except for dysgenics.
I can think of about twenty other possible explanations off the top of my head, but dysgenics is a possible cause.
I agree with DataExplorer. The largest factor in the decay of civilizations is dysgenics. The discussion by R. A. Fisher 1930 p. 193 is very cogent on this matter. Soon we will know for sure.
Sometimes it can be rapid. Assume that the upper classes are mostly urban, and somewhat sharper than average. Then the Mongols arrive.
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august 2016 by nhaliday

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