nhaliday + genomics   252

Manifold – man·i·fold /ˈmanəˌfōld/ many and various.
https://infoproc.blogspot.com/2019/01/a-grand-experiment.html
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What Millennials think us old folks don't understand
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Under-appreciated Genius?
Overrated Crap and Frauds?
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7 weeks ago 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
Existential Risks: Analyzing Human Extinction Scenarios
https://twitter.com/robinhanson/status/981291048965087232
https://archive.is/dUTD5
Would you endorse choosing policy to max the expected duration of civilization, at least as a good first approximation?
Can anyone suggest a different first approximation that would get more votes?

https://twitter.com/robinhanson/status/981335898502545408
https://archive.is/RpygO
How useful would it be to agree on a relatively-simple first-approximation observable-after-the-fact metric for what we want from the future universe, such as total life years experienced, or civilization duration?

We're Underestimating the Risk of Human Extinction: https://www.theatlantic.com/technology/archive/2012/03/were-underestimating-the-risk-of-human-extinction/253821/
An Oxford philosopher argues that we are not adequately accounting for technology's risks—but his solution to the problem is not for Luddites.

Anderson: You have argued that we underrate existential risks because of a particular kind of bias called observation selection effect. Can you explain a bit more about that?

Bostrom: The idea of an observation selection effect is maybe best explained by first considering the simpler concept of a selection effect. Let's say you're trying to estimate how large the largest fish in a given pond is, and you use a net to catch a hundred fish and the biggest fish you find is three inches long. You might be tempted to infer that the biggest fish in this pond is not much bigger than three inches, because you've caught a hundred of them and none of them are bigger than three inches. But if it turns out that your net could only catch fish up to a certain length, then the measuring instrument that you used would introduce a selection effect: it would only select from a subset of the domain you were trying to sample.

Now that's a kind of standard fact of statistics, and there are methods for trying to correct for it and you obviously have to take that into account when considering the fish distribution in your pond. An observation selection effect is a selection effect introduced not by limitations in our measurement instrument, but rather by the fact that all observations require the existence of an observer. This becomes important, for instance, in evolutionary biology. For instance, we know that intelligent life evolved on Earth. Naively, one might think that this piece of evidence suggests that life is likely to evolve on most Earth-like planets. But that would be to overlook an observation selection effect. For no matter how small the proportion of all Earth-like planets that evolve intelligent life, we will find ourselves on a planet that did. Our data point-that intelligent life arose on our planet-is predicted equally well by the hypothesis that intelligent life is very improbable even on Earth-like planets as by the hypothesis that intelligent life is highly probable on Earth-like planets. When it comes to human extinction and existential risk, there are certain controversial ways that observation selection effects might be relevant.
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march 2018 by nhaliday
Sacred text as cultural genome: an inheritance mechanism and method for studying cultural evolution: Religion, Brain & Behavior: Vol 7, No 3
Yasha M. Hartberg & David Sloan Wilson

Any process of evolution requires a mechanism of inheritance for the transmission of information across generations and the expression of phenotypes during each generation. Genetic inheritance mechanisms have been studied for over a century but mechanisms of inheritance for human cultural evolution are far less well understood. Sacred religious texts have the properties required for an inheritance system. They are replicated across generations with high fidelity and are transcribed into action every generation by the invocation and interpretation of selected passages. In this article we borrow concepts and methods from genetics and epigenetics to study the “expressed phenotypes” of six Christian churches that differ along a conservative–progressive axis. Their phenotypic differences, despite drawing upon the same sacred text, can be explained in part by differential expression of the sacred text. Since the invocation and interpretation of sacred texts are often well preserved, our methods allow the expressed phenotypes of religious groups to be studied at any time and place in history.
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january 2018 by nhaliday
A genetic map of the world – Gene Expression
The above map is from a new preprint on the patterns of genetic variation as a function of geography for humans, Genetic landscapes reveal how human genetic diversity aligns with geography. The authors assemble an incredibly large dataset to generate these figures. The orange zones are “troughs” of gene flow. Basically barriers to gene flow.  It is no great surprise that so many of the barriers correlate with rivers, mountains, and deserts. But the aim of this sort of work seems to be to make precise and quantitative intuitions which are normally expressed verbally.
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december 2017 by nhaliday
Use and Interpretation of LD Score Regression
LD Score regression distinguishes confounding from polygenicity in genome-wide association studies: https://sci-hub.bz/10.1038/ng.3211
- Po-Ru Loh, Nick Patterson, et al.

https://www.biorxiv.org/content/biorxiv/early/2014/02/21/002931.full.pdf

Both polygenicity (i.e. many small genetic effects) and confounding biases, such as cryptic relatedness and population stratification, can yield inflated distributions of test statistics in genome-wide association studies (GWAS). However, current methods cannot distinguish between inflation from bias and true signal from polygenicity. We have developed an approach that quantifies the contributions of each by examining the relationship between test statistics and linkage disequilibrium (LD). We term this approach LD Score regression. LD Score regression provides an upper bound on the contribution of confounding bias to the observed inflation in test statistics and can be used to estimate a more powerful correction factor than genomic control. We find strong evidence that polygenicity accounts for the majority of test statistic inflation in many GWAS of large sample size.

Supplementary Note: https://images.nature.com/original/nature-assets/ng/journal/v47/n3/extref/ng.3211-S1.pdf

An atlas of genetic correlations across human diseases
and traits: https://sci-hub.bz/10.1038/ng.3406

https://www.biorxiv.org/content/early/2015/01/27/014498.full.pdf

Supplementary Note: https://images.nature.com/original/nature-assets/ng/journal/v47/n11/extref/ng.3406-S1.pdf

https://github.com/bulik/ldsc
ldsc is a command line tool for estimating heritability and genetic correlation from GWAS summary statistics. ldsc also computes LD Scores.
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november 2017 by nhaliday
Amish Mutation Protects Against Diabetes and May Extend Life - The New York Times
What Dr. Vaughan and his colleagues discovered was striking. Amish carriers of the mutation live on average to age 85, about 10 years longer than their peers. Among the Amish who did not have the mutation, the rate of Type 2 diabetes was 7 percent. But for carriers of the mutation, the rate was zero, despite leading the same lifestyle and consuming similar diets. Tests showed that carriers of the mutation had 28 percent lower levels of insulin, a hormone whose chronic elevation can lead to Type 2 diabetes.
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november 2017 by nhaliday
Lynn Margulis | West Hunter
Margulis went on to theorize that symbiotic relationships between organisms are the dominant driving force of evolution. There certainly are important examples of this: as far as I know, every complex organism that digests cellulose manages it thru a symbiosis with various prokaryotes. Many organisms with a restricted diet have symbiotic bacteria that provide essential nutrients – aphids, for example. Tall fescue, a popular turf grass on golf courses, carries an endosymbiotic fungus. And so on, and on on.

She went on to oppose neodarwinism, particularly rejecting inter-organismal competition (and population genetics itself). From Wiki: [ She also believed that proponents of the standard theory “wallow in their zoological, capitalistic, competitive, cost-benefit interpretation of Darwin – having mistaken him… Neo-Darwinism, which insists on [the slow accrual of mutations by gene-level natural selection], is in a complete funk.”[8] ‘

...

You might think that Lynn Margulis is an example of someone that could think outside the box because she’d never even been able to find it in the first place – but that’s more true of autistic types [like Dirac or Turing], which I doubt she was in any way. I’d say that some traditional prejudices [dislike of capitalism and individual competition], combined with the sort of general looniness that leaves one open to unconventional ideas, drove her in a direction that bore fruit, more or less by coincidence. A successful creative scientist does not have to be right about everything, or indeed about much of anything: they need to contribute at least one new, true, and interesting thing.

https://westhunt.wordpress.com/2017/11/25/lynn-margulis/#comment-98174
“A successful creative scientist does not have to be right about everything, or indeed about much of anything: they need to contribute at least one new, true, and interesting thing.” Yes – it’s like old bands. As long as they have just one song in heavy rotation on the classic rock stations, they can tour endlessly – it doesn’t matter that they have only one or even no original members performing. A scientific example of this phenomena is Kary Mullins. He’ll always have PCR, even if a glowing raccoon did greet him with the words, “Good evening, Doctor.”

Nobel Savage: https://www.lrb.co.uk/v21/n13/steven-shapin/nobel-savage
Dancing Naked in the Mind Field by Kary Mullis

jet fuel can't melt steel beams: https://westhunt.wordpress.com/2017/11/25/lynn-margulis/#comment-98201
You have to understand a subject extremely well to make arguments why something couldn’t have happened. The easiest cases involve some purported explanation violating a conservation law of physics: that wasn’t the case here.

Do I think you’re a hotshot, deeply knowledgeable about structural engineering, properties of materials, using computer models, etc? A priori, pretty unlikely. What are the odds that you know as much simple mechanics as I do? a priori, still pretty unlikely. Most likely, you’re talking through your hat.

Next, the conspiracy itself is unlikely: quite a few people would be involved – unlikely that none of them would talk. It’s not that easy to find people that would go along with such a thing, believe it or not. The Communists were pretty good at conspiracy, but people defected, people talked: not just Whittaker Chambers, not just Igor Gouzenko.
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november 2017 by nhaliday
Ancient Admixture in Human History
- Patterson, Reich et al., 2012
Population mixture is an important process in biology. We present a suite of methods for learning about population mixtures, implemented in a software package called ADMIXTOOLS, that support formal tests for whether mixture occurred and make it possible to infer proportions and dates of mixture. We also describe the development of a new single nucleotide polymorphism (SNP) array consisting of 629,433 sites with clearly documented ascertainment that was specifically designed for population genetic analyses and that we genotyped in 934 individuals from 53 diverse populations. To illustrate the methods, we give a number of examples that provide new insights about the history of human admixture. The most striking finding is a clear signal of admixture into northern Europe, with one ancestral population related to present-day Basques and Sardinians and the other related to present-day populations of northeast Asia and the Americas. This likely reflects a history of admixture between Neolithic migrants and the indigenous Mesolithic population of Europe, consistent with recent analyses of ancient bones from Sweden and the sequencing of the genome of the Tyrolean “Iceman.”
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november 2017 by nhaliday
What Does a “Normal” Human Genome Look Like? | Science
So, what have our first glimpses of variation in the genomes of generally healthy people taught us? First, balancing selection, the evolutionary process that favors genetic diversification rather than the fixation of a single “best” variant, appears to play a minor role outside the immune system. Local adaptation, which accounts for variation in traits such as pigmentation, dietary specialization, and susceptibility to particular pathogens is also a second-tier player. What is on the top tier? Increasingly, the answer appears to be mutations that are “deleterious” by biochemical or standard evolutionary criteria. These mutations, as has long been appreciated, overwhelmingly make up the most abundant form of nonneutral variation in all genomes. A model for human genetic individuality is emerging in which there actually is a “wild-type” human genome—one in which most genes exist in an evolutionarily optimized form. There just are no “wild-type” humans: We each fall short of this Platonic ideal in our own distinctive ways.
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november 2017 by nhaliday
The Same Old Story | West Hunter
People often reinterpret past events, recast them in terms of some contemporary ideology. When historians talk about the Monophysites in Byzantine times, they often suggest that those struggle are a mask for a kind of proto-nationalism. Maybe they were: and maybe nobody involved was thinking anything remotely like that. The Communists tried to come up with Marxist interpretations of ancient history, which led them to spend way too much time talking about Mazdakites in Sassanian Persia and the Zealots of Thessalonika . And Spartacus: but at least Spartacus was cool.

Then there are feminist versions of history. Let us never speak of them again.

Generally, this is all crap. But we could at least hope for something new along these lines: bullshit perhaps, but at least fresh bullshit. Obviously the reality underlying both the Punic Wars and the Crusades is the ancient struggle between EEF and ANE.
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november 2017 by nhaliday
The Science of Roman History: Biology, Climate, and the Future of the Past (Hardcover and eBook) | Princeton University Press
Forthcoming April 2018

How the latest cutting-edge science offers a fuller picture of life in Rome and antiquity
This groundbreaking book provides the first comprehensive look at how the latest advances in the sciences are transforming our understanding of ancient Roman history. Walter Scheidel brings together leading historians, anthropologists, and geneticists at the cutting edge of their fields, who explore novel types of evidence that enable us to reconstruct the realities of life in the Roman world.

Contributors discuss climate change and its impact on Roman history, and then cover botanical and animal remains, which cast new light on agricultural and dietary practices. They exploit the rich record of human skeletal material--both bones and teeth—which forms a bio-archive that has preserved vital information about health, nutritional status, diet, disease, working conditions, and migration. Complementing this discussion is an in-depth analysis of trends in human body height, a marker of general well-being. This book also assesses the contribution of genetics to our understanding of the past, demonstrating how ancient DNA is used to track infectious diseases, migration, and the spread of livestock and crops, while the DNA of modern populations helps us reconstruct ancient migrations, especially colonization.

Opening a path toward a genuine biohistory of Rome and the wider ancient world, The Science of RomanHistory offers an accessible introduction to the scientific methods being used in this exciting new area of research, as well as an up-to-date survey of recent findings and a tantalizing glimpse of what the future holds.

Walter Scheidel is the Dickason Professor in the Humanities, Professor of Classics and History, and a Kennedy-Grossman Fellow in Human Biology at Stanford University. He is the author or editor of seventeen previous books, including The Great Leveler: Violence and the History of Inequality from the Stone Age to the Twenty-First Century (Princeton).
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november 2017 by nhaliday
Genetics: CHROMOSOMAL MAPS AND MAPPING FUNCTIONS
Any particular gene has a specific location (its "locus") on a particular chromosome. For any two genes (or loci) alpha and beta, we can ask "What is the recombination frequency between them?" If the genes are on different chromosomes, the answer is 50% (independent assortment). If the two genes are on the same chromosome, the recombination frequency will be somewhere in the range from 0 to 50%. The "map unit" (1 cM) is the genetic map distance that corresponds to a recombination frequency of 1%. In large chromosomes, the cumulative map distance may be much greater than 50cM, but the maximum recombination frequency is 50%. Why? In large chromosomes, there is enough length to allow for multiple cross-overs, so we have to ask what result we expect for random multiple cross-overs.

1. How is it that random multiple cross-overs give the same result as independent assortment?

Figure 5.12 shows how the various double cross-over possibilities add up, resulting in gamete genotype percentages that are indistinguisable from independent assortment (50% parental type, 50% non-parental type). This is a very important figure. It provides the explanation for why genes that are far apart on a very large chromosome sort out in crosses just as if they were on separate chromosomes.

2. Is there a way to measure how close together two crossovers can occur involving the same two chromatids? That is, how could we measure whether there is spacial "interference"?

Figure 5.13 shows how a measurement of the gamete frequencies resulting from a "three point cross" can answer this question. If we would get a "lower than expected" occurrence of recombinant genotypes aCb and AcB, it would suggest that there is some hindrance to the two cross-overs occurring this close together. Crosses of this type in Drosophila have shown that, in this organism, double cross-overs do not occur at distances of less than about 10 cM between the two cross-over sites. ( Textbook, page 196. )

3. How does all of this lead to the "mapping function", the mathematical (graphical) relation between the observed recombination frequency (percent non-parental gametes) and the cumulative genetic distance in map units?

Figure 5.14 shows the result for the two extremes of "complete interference" and "no interference". The situation for real chromosomes in real organisms is somewhere between these extremes, such as the curve labelled "interference decreasing with distance".
org:junk  org:edu  explanation  faq  nibble  genetics  genomics  bio  ground-up  magnitude  data  flux-stasis  homo-hetero  measure  orders  metric-space  limits  measurement 
october 2017 by nhaliday
Genome Editing
This collection of articles from the Nature Research journals provides an overview of current progress in developing targeted genome editing technologies. A selection of protocols for using and adapting these tools in your own lab is also included.
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october 2017 by nhaliday
Accurate Genomic Prediction Of Human Height | bioRxiv
Stephen Hsu's compressed sensing application paper

We construct genomic predictors for heritable and extremely complex human quantitative traits (height, heel bone density, and educational attainment) using modern methods in high dimensional statistics (i.e., machine learning). Replication tests show that these predictors capture, respectively, ~40, 20, and 9 percent of total variance for the three traits. For example, predicted heights correlate ~0.65 with actual height; actual heights of most individuals in validation samples are within a few cm of the prediction.

https://infoproc.blogspot.com/2017/09/accurate-genomic-prediction-of-human.html

http://infoproc.blogspot.com/2017/11/23andme.html
I'm in Mountain View to give a talk at 23andMe. Their latest funding round was $250M on a (reported) valuation of $1.5B. If I just add up the Crunchbase numbers it looks like almost half a billion invested at this point...

Slides: Genomic Prediction of Complex Traits

Here's how people + robots handle your spit sample to produce a SNP genotype:

https://drive.google.com/file/d/1e_zuIPJr1hgQupYAxkcbgEVxmrDHAYRj/view
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september 2017 by nhaliday
Second Bananas | West Hunter
Still thinking about domestication. Mostly,  the wild ancestors of domesticate animals were social: presumably, such behavioral tendencies were preadaptations that helped the domesticates come to bond with or at least tolerate people.   Social animals can have adaptive personality variation – difference behavioral strategies.  Sometimes those strategies are facultative, sometimes genetic, sometimes a mix.

I would guess that those wild individuals that account for most of the ancestry of f a domesticated species didn’t have a representative mix of personality types. Probably they were more likely to be followers rather than leaders – not the alphas of the pack, not the most aggressive stallions.  Sidekicks.  With dogs, we can probably check this hypothesis fairly easily, since wolves are still around.

https://westhunt.wordpress.com/2013/04/03/wyld-stallyns/
A few years ago, I was thinking about genetic male morphs. Turns out that you find qualitatively different forms of males in many species: Barry Sinervos’s lizards, Shuster’s isopods, Lank’s ruffs, jack salmon, etc. Logically, the Y chromosome would be the best place for a such a genetic switch, since that would avoid negative side effects in females. The problem is that the Y carries very few genes.

Alternate strategies don’t have to to be as complicated as they are in ruffs or Uta stansburiana. Different levels of aggressiveness, or different points on the cad/dad axis, would have different selective payoffs in different environments. If a new environment favored lower (or higher) aggressiveness in males , a Y-chromosome that induced lower (or higher) aggressiveness would take off. And since different Y chromosomes do indeed affect the level of aggressiveness in mice [which I just found out], possibly by affecting testosterone production – this mechanism is plausible.

This could explain a funny genetic pattern in the domestication of horses. There’s a fair amount of diversity in horse mtDNA: it looks as if many different mares were domesticated. On the other hand, it looks as if only one stallion was ever domesticated. All living stallions today are his descendants.

Stallions are pretty aggressive, and must have been hard to tame. Maybe one was genetically unusual – wimpier. Tameable.

Fortunately for all concerned, the selective value of aggressiveness, etc. has been the same for all human populations forever and ever, before and after the development of agriculture. Otherwise you might see weirdly rapid expansions of particular Y-chromosome haplogroups – common, yet only a few thousand years old.

https://westhunt.wordpress.com/2018/04/18/wyld-stallyns-part-deux/
A while ago, I wondered if modern stallions are a male morph adapted to domestication, one in which the strategy is mediated via the Y chromosome.

Looks as if I was right*. Check out “Decline of genetic diversity in ancient domestic stallions in Europe”.

Selection favored one particular kind of Y-chromosome. This had to be based on phenotype, not genealogy. Most likely it was favored under the new environment of domestication. Somehow, these stallions performed better, or were easier to get along with (my bet).

We already knew that Y-chromosomes could do things: Haplogroup I increases the risk of heart disease by about 50%, while the particular variant of Y chromosome influences aggression in mice.

Which means you have to re-examine the starburst phylogeny of R1b and R1a: it’s probably biology, rather than history, that drove those expansions. Some kind of selective advantage. Possibly one reason that those particular Y chromosomes far outraced steppe autosomal contributions. Most likely, R1a and R1b induce specific morphs – their carriers are somehow different. Maybe they’re born to be mild, or born to be princes of the universe. Maybe an R1b guy just finds it easier to cooperate with other R1b guys… Or maybe they’re resistant to typhoid.

* correct predictions mean nothing in biology. Ask any biologist.
west-hunter  scitariat  discussion  ideas  speculation  domestication  nature  egalitarianism-hierarchy  multi  genomics  recent-selection  genetics  biodet  behavioral-gen  ecology  EGT  strategy  gavisti  theory-practice  bio  paying-rent  being-right  elite  europe  antiquity  migration  conquest-empire  consilience  explanans 
september 2017 by nhaliday
tcjfs on Twitter: "Yearly legal permanent residencies 1996-2015 with a bit more disaggregated and common-sensical designations than DHS https://t.co/167ms5Xr0s"
https://archive.is/70nNG
https://twitter.com/tcjfs/status/900052649147543552
https://archive.is/5U3Mi
Asian origin according to Department of Homeland Security
not sure tbh. i was just trying to disaggregate "Asian immigration" and I was like holy shit some of these places I would never include

U.S. Lawful Permanent Residents: 2014: https://www.dhs.gov/sites/default/files/publications/Lawful_Permanent_Residents_2014.pdf
Yearbook of Immigration Statistics: https://www.dhs.gov/immigration-statistics/yearbook

https://twitter.com/tcjfs/status/933066198161469440
https://archive.is/pRTqS
Foreign born population by Chinese, Indian, Mexican birth whose residence one year ago was abroad, 2000-2013
The above chart, extended to 2000-2016, with Mexico but also all of Latin/Central/South America:
our latin american immigrants are probably getting less "huwhite"
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september 2017 by nhaliday
The Genetics of Alzheimer Disease
Twin and family studies indicate that genetic factors are estimated to play a role in at least 80% of AD cases. The inheritance of AD exhibits a dichotomous pattern. On one hand, rare mutations in APP, PSEN1, and PSEN2 virtually guarantee early-onset (<60 years) familial AD, which represents ∼5% of AD. On the other hand, common gene polymorphisms, such as the ε4 and ε2 variants of the APOE gene, can influence susceptibility for ∼50% of the common late-onset AD. These four genes account for 30%–50% of the inheritability of AD. Genome-wide association studies have recently led to the identification of 11 additional AD candidate genes.

Role of Genes and Environments for Explaining Alzheimer Disease: http://jamanetwork.com/journals/jamapsychiatry/fullarticle/209307
study  biodet  twin-study  sib-study  variance-components  candidate-gene  GWAS  medicine  neuro  neuro-nitgrit  dementia  disease  🌞  aging  multi  org:nat  genetics  genomics  immune  health 
september 2017 by nhaliday
Medicine as a pseudoscience | West Hunter
The idea that venesection was a good thing, or at least not so bad, on the grounds that one in a few hundred people have hemochromatosis (in Northern Europe) reminds me of the people who don’t wear a seatbelt, since it would keep them from being thrown out of their convertible into a waiting haystack, complete with nubile farmer’s daughter. Daughters. It could happen. But it’s not the way to bet.

Back in the good old days, Charles II, age 53, had a fit one Sunday evening, while fondling two of his mistresses.

Monday they bled him (cupping and scarifying) of eight ounces of blood. Followed by an antimony emetic, vitriol in peony water, purgative pills, and a clyster. Followed by another clyster after two hours. Then syrup of blackthorn, more antimony, and rock salt. Next, more laxatives, white hellebore root up the nostrils. Powdered cowslip flowers. More purgatives. Then Spanish Fly. They shaved his head and stuck blistering plasters all over it, plastered the soles of his feet with tar and pigeon-dung, then said good-night.

...

Friday. The king was worse. He tells them not to let poor Nelly starve. They try the Oriental Bezoar Stone, and more bleeding. Dies at noon.

Most people didn’t suffer this kind of problem with doctors, since they never saw one. Charles had six. Now Bach and Handel saw the same eye surgeon, John Taylor – who blinded both of them. Not everyone can put that on his resume!

You may wonder how medicine continued to exist, if it had a negative effect, on the whole. There’s always the placebo effect – at least there would be, if it existed. Any real placebo effect is very small: I’d guess exactly zero. But there is regression to the mean. You see the doctor when you’re feeling worse than average – and afterwards, if he doesn’t kill you outright, you’re likely to feel better. Which would have happened whether you’d seen him or not, but they didn’t often do RCTs back in the day – I think James Lind was the first (1747).

Back in the late 19th century, Christian Scientists did better than others when sick, because they didn’t believe in medicine. For reasons I think mistaken, because Mary Baker Eddy rejected the reality of the entire material world, but hey, it worked. Parenthetically, what triggered all that New Age nonsense in 19th century New England? Hash?

This did not change until fairly recently. Sometime in the early 20th medicine, clinical medicine, what doctors do, hit break-even. Now we can’t do without it. I wonder if there are, or will be, other examples of such a pile of crap turning (mostly) into a real science.

good tweet: https://twitter.com/bowmanthebard/status/897146294191390720
The brilliant GP I've had for 35+ years has retired. How can I find another one who meets my requirements?

1 is overweight
2 drinks more than officially recommended amounts
3 has an amused, tolerant atitude to human failings
4 is well aware that we're all going to die anyway, & there are better or worse ways to die
5 has a healthy skeptical attitude to mainstream medical science
6 is wholly dismissive of "a|ternative” medicine
7 believes in evolution
8 thinks most diseases get better without intervention, & knows the dangers of false positives
9 understands the base rate fallacy

EconPapers: Was Civil War Surgery Effective?: http://econpapers.repec.org/paper/htrhcecon/444.htm
contra Greg Cochran:
To shed light on the subject, I analyze a data set created by Dr. Edmund Andrews, a Civil war surgeon with the 1st Illinois Light Artillery. Dr. Andrews’s data can be rendered into an observational data set on surgical intervention and recovery, with controls for wound location and severity. The data also admits instruments for the surgical decision. My analysis suggests that Civil War surgery was effective, and increased the probability of survival of the typical wounded soldier, with average treatment effect of 0.25-0.28.

Medical Prehistory: https://westhunt.wordpress.com/2016/03/14/medical-prehistory/
What ancient medical treatments worked?

https://westhunt.wordpress.com/2016/03/14/medical-prehistory/#comment-76878
In some very, very limited conditions, bleeding?
--
Bad for you 99% of the time.

https://westhunt.wordpress.com/2016/03/14/medical-prehistory/#comment-76947
Colchicine – used to treat gout – discovered by the Ancient Greeks.

https://westhunt.wordpress.com/2016/03/14/medical-prehistory/#comment-76973
Dracunculiasis (Guinea worm)
Wrap the emerging end of the worm around a stick and slowly pull it out.
(3,500 years later, this remains the standard treatment.)
https://en.wikipedia.org/wiki/Ebers_Papyrus

https://westhunt.wordpress.com/2016/03/14/medical-prehistory/#comment-76971
Some of the progress is from formal medicine, most is from civil engineering, better nutrition ( ag science and physical chemistry), less crowded housing.

Nurses vs doctors: https://westhunt.wordpress.com/2014/10/01/nurses-vs-doctors/
Medicine, the things that doctors do, was an ineffective pseudoscience until fairly recently. Until 1800 or so, they were wrong about almost everything. Bleeding, cupping, purging, the four humors – useless. In the 1800s, some began to realize that they were wrong, and became medical nihilists that improved outcomes by doing less. Some patients themselves came to this realization, as when Civil War casualties hid from the surgeons and had better outcomes. Sometime in the early 20th century, MDs reached break-even, and became an increasingly positive influence on human health. As Lewis Thomas said, medicine is the youngest science.

Nursing, on the other hand, has always been useful. Just making sure that a patient is warm and nourished when too sick to take care of himself has helped many survive. In fact, some of the truly crushing epidemics have been greatly exacerbated when there were too few healthy people to take care of the sick.

Nursing must be old, but it can’t have existed forever. Whenever it came into existence, it must have changed the selective forces acting on the human immune system. Before nursing, being sufficiently incapacitated would have been uniformly fatal – afterwards, immune responses that involved a period of incapacitation (with eventual recovery) could have been selectively favored.

when MDs broke even: https://westhunt.wordpress.com/2014/10/01/nurses-vs-doctors/#comment-58981
I’d guess the 1930s. Lewis Thomas thought that he was living through big changes. They had a working serum therapy for lobar pneumonia ( antibody-based). They had many new vaccines ( diphtheria in 1923, whopping cough in 1926, BCG and tetanus in 1927, yellow fever in 1935, typhus in 1937.) Vitamins had been mostly worked out. Insulin was discovered in 1929. Blood transfusions. The sulfa drugs, first broad-spectrum antibiotics, showed up in 1935.

DALYs per doctor: https://westhunt.wordpress.com/2018/01/22/dalys-per-doctor/
The disability-adjusted life year (DALY) is a measure of overall disease burden – the number of years lost. I’m wondering just much harm premodern medicine did, per doctor. How many healthy years of life did a typical doctor destroy (net) in past times?

...

It looks as if the average doctor (in Western medicine) killed a bunch of people over his career ( when contrasted with doing nothing). In the Charles Manson class.

Eventually the market saw through this illusion. Only took a couple of thousand years.

https://westhunt.wordpress.com/2018/01/22/dalys-per-doctor/#comment-100741
That a very large part of healthcare spending is done for non-health reasons. He has a chapter on this in his new book, also check out his paper “Showing That You Care: The Evolution of Health Altruism” http://mason.gmu.edu/~rhanson/showcare.pdf
--
I ran into too much stupidity to finish the article. Hanson’s a loon. For example when he talks about the paradox of blacks being more sentenced on drug offenses than whites although they use drugs at similar rate. No paradox: guys go to the big house for dealing, not for using. Where does he live – Mars?

I had the same reaction when Hanson parroted some dipshit anthropologist arguing that the stupid things people do while drunk are due to social expectations, not really the alcohol.
Horseshit.

I don’t think that being totally unable to understand everybody around you necessarily leads to deep insights.

https://westhunt.wordpress.com/2018/01/22/dalys-per-doctor/#comment-100744
What I’ve wondered is if there was anything that doctors did that actually was helpful and if perhaps that little bit of success helped them fool people into thinking the rest of it helped.
--
Setting bones. extracting arrows: spoon of Diocles. Colchicine for gout. Extracting the Guinea worm. Sometimes they got away with removing the stone. There must be others.
--
Quinine is relatively recent: post-1500. Obstetrical forceps also. Caesarean deliveries were almost always fatal to the mother until fairly recently.

Opium has been around for a long while : it works.

https://westhunt.wordpress.com/2018/01/22/dalys-per-doctor/#comment-100839
If pre-modern medicine was indeed worse than useless – how do you explain no one noticing that patients who get expensive treatments are worse off than those who didn’t?
--
were worse off. People are kinda dumb – you’ve noticed?
--
My impression is that while people may be “kinda dumb”, ancient customs typically aren’t.
Even if we assume that all people who lived prior to the 19th century were too dumb to make the rational observation, wouldn’t you expect this ancient practice to be subject to selective pressure?
--
Your impression is wrong. Do you think that there some slick reason for Carthaginians incinerating their first-born?

Theodoric of York, bloodletting: https://www.youtube.com/watch?v=yvff3TViXmY

details on blood-letting and hemochromatosis: https://westhunt.wordpress.com/2018/01/22/dalys-per-doctor/#comment-100746

Starting Over: https://westhunt.wordpress.com/2018/01/23/starting-over/
Looking back on it, human health would have … [more]
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august 2017 by nhaliday
Genetic Architectures | West Hunter
Dairy cattle eventually graduate to McDonalds, so there is some interest in the genetics of beef production in dairy breeds. There is course more interest in the genetics of beef production in beef breeds of cattle.

Usually you don’t find a single allele that makes a lot of difference, but in some beef breeds, there are myostatin mutations that result in a ridiculous-looking, ‘double-muscled’ beast. Homozygosity for myostatin mutations causes difficulties in birth, so it takes really strong selection for beef production to make a myostatin null common. I don’t think you ever see this in dairy breeds.

But, as it turns out, there is a deletion that is pretty common in some dairy breeds that significantly increases milk production while killing homozygotes before birth.

Breeds under weaker selection for single traits, your typical cow of the past, probably have neither.

The point is that the genetic architecture of a quantitative trait does not have to be the same in different populations of the same species. For example, I have the impression that height is not as highly polygenic in Pygmies as it is most other human populations. There’s a particular region on chromosome 3 that seems to influence height- you don’t see such a concentration in Europeans.
west-hunter  scitariat  discussion  ideas  speculation  sapiens  pop-diff  genetics  population-genetics  QTL  homo-hetero  analogy  agriculture  nature  food  comparison  embodied  archaics  africa  genomics 
august 2017 by nhaliday
It made their brown eyes blue.. | West Hunter
Assuming population continuity, the selective advantage of the alleles they examined must have been very high. In order to see if there had been population continuity, they looked at the mtDNA frequencies of the ancient populations and compared them with mtDNA frequencies of modern populations in the same areas. Since they’re different, but not wildly different, they conclude that there has been population continuity, which was their null assumption.

That null assumption might have been reasonable, if someone had burned every history book ever written, while at the same time suppressing all the ancient DNA evidence.

Since that has not yet happened, I think their assumption is downright embarrassing. People have been moving in and out of this area for all of recorded history (as Razib Khan has also pointed out) : Cimmerians, Scythians, Goths, Khazars, Kievian Rus, the Golden Horde, eventually Russians.

There is no logical reason for geneticists to ignore information outside their field. Ignorance is no excuse. I could say the same for every other discipline. Cross the streams – it would be good.
west-hunter  scitariat  commentary  study  summary  critique  rant  sapiens  genetics  genomics  aDNA  migration  gene-flow  europe  eastern-europe  gavisti  conquest-empire  recent-selection  science  interdisciplinary  knowledge  gnxp 
august 2017 by nhaliday
Demography of the Roman Empire - Wikipedia
There are few recorded population numbers for the whole of antiquity, and those that exist are often rhetorical or symbolic. Unlike the contemporaneous Han Dynasty, no general census survives for the Roman Empire. The late period of the Roman Republic provides a small exception to this general rule: serial statistics for Roman citizen numbers, taken from census returns, survive for the early Republic through the 1st century CE.[41] Only the figures for periods after the mid-3rd century BCE are reliable, however. Fourteen figures are available for the 2nd century BCE (from 258,318 to 394,736). Only four figures are available for the 1st century BCE, and are feature a large break between 70/69 BCE (910,000) and 28 BCE (4,063,000). The interpretation of the later figures—the Augustan censuses of 28 BCE, 8 BCE, and 14 CE—is therefore controversial.[42] Alternate interpretations of the Augustan censuses (such as those of E. Lo Cascio[43]) produce divergent population histories across the whole imperial period.[44]

Roman population size: the logic of the debate: https://www.princeton.edu/~pswpc/pdfs/scheidel/070706.pdf
- Walter Scheidel (cited in book by Vaclav Smil, "Why America is Not a New Rome")

Our ignorance of ancient population numbers is one of the biggest obstacles to our understanding of Roman history. After generations of prolific scholarship, we still do not know how many people inhabited Roman Italy and the Mediterranean at any given point in time. When I say ‘we do not know’ I do not simply mean that we lack numbers that are both precise and safely known to be accurate: that would surely be an unreasonably high standard to apply to any pre-modern society. What I mean is that even the appropriate order of magnitude remains a matter of intense dispute.

Historical urban community sizes: https://en.wikipedia.org/wiki/Historical_urban_community_sizes

World population estimates: https://en.wikipedia.org/wiki/World_population_estimates
As a general rule, the confidence of estimates on historical world population decreases for the more distant past. Robust population data only exists for the last two or three centuries. Until the late 18th century, few governments had ever performed an accurate census. In many early attempts, such as in Ancient Egypt and the Persian Empire, the focus was on counting merely a subset of the population for purposes of taxation or military service.[3] Published estimates for the 1st century ("AD 1") suggest an uncertainty of the order of 50% (estimates range between 150 and 330 million). Some estimates extend their timeline into deep prehistory, to "10,000 BC", i.e. the early Holocene, when world population estimates range roughly between one and ten million (with an uncertainty of up to an order of magnitude).[4][5]

Estimates for yet deeper prehistory, into the Paleolithic, are of a different nature. At this time human populations consisted entirely of non-sedentary hunter-gatherer populations, with anatomically modern humans existing alongside archaic human varieties, some of which are still ancestral to the modern human population due to interbreeding with modern humans during the Upper Paleolithic. Estimates of the size of these populations are a topic of paleoanthropology. A late human population bottleneck is postulated by some scholars at approximately 70,000 years ago, during the Toba catastrophe, when Homo sapiens population may have dropped to as low as between 1,000 and 10,000 individuals.[6][7] For the time of speciation of Homo sapiens, some 200,000 years ago, an effective population size of the order of 10,000 to 30,000 individuals has been estimated, with an actual "census population" of early Homo sapiens of roughly 100,000 to 300,000 individuals.[8]
history  iron-age  mediterranean  the-classics  demographics  fertility  data  europe  population  measurement  volo-avolo  estimate  wiki  reference  article  conquest-empire  migration  canon  scale  archaeology  multi  broad-econ  pdf  study  survey  debate  uncertainty  walter-scheidel  vaclav-smil  urban  military  economics  labor  time-series  embodied  health  density  malthus  letters  urban-rural  database  list  antiquity  medieval  early-modern  mostly-modern  time  sequential  MENA  the-great-west-whale  china  asia  sinosphere  occident  orient  japan  britain  germanic  gallic  summary  big-picture  objektbuch  confidence  sapiens  anthropology  methodology  farmers-and-foragers  genetics  genomics  chart 
august 2017 by nhaliday
And your little dog, too! | West Hunter
It sure looks as if we’re talking near-complete replacement – which means that the historical process involved does not look much like a peaceful, diffusion-style range expansion.  Perhaps more like the Death Song of Ragnar Lodbrok, which abounds in phrases like this: “Where the swords were whining while they sundered helmets”

Interestingly, there is a very similar  pattern in canine mtDNA.  Today Europeans dogs fall into four haplotypes: A (70%), B(16%), C (6%), and D(8%).  But back in the day, it seems that the overwhelming majority of dogs (88%)  were type C,  12% were in group A, while B and D have not been detected at all.

The ancestors of today’s Europeans didn’t fool around.
west-hunter  scitariat  discussion  ideas  speculation  history  antiquity  europe  sapiens  gavisti  farmers-and-foragers  genetics  genomics  gene-flow  migration  conquest-empire  peace-violence  kumbaya-kult  nature  nihil  death  archaeology  nietzschean  traces 
august 2017 by nhaliday
The Greatest Generation | West Hunter
But  when you consider that people must have had 48 chromosomes back then, rather than the current measly 46, much is explained.

Theophilus Painter, a prominent cytologist, had investigated human chromosome number in 1923. He thought that there were 24 in sperm cells, resulting in a count of 48, which is entirely reasonable. That is definitely the case for all our closest relatives (chimpanzees, bonobos, gorillas, and orangutans).

The authorities say that that Painter made a mistake, and that humans always had 46 chromosomes. But then, for 30 years after Painter’s work, the authorities said that people had 48.  Textbooks in genetics continued to say that Man has 48 chromosomes up until the mid 1950s.  Many cytologists and geneticists studied human chromosomes during that period, but they knew that there were 48, and that’s what they saw. Now they know that there are 46, and that’s what every student sees.

Either the authorities are fallible and most people are sheep, or human chromosome number actually changed sometime after World War II.  No one could believe the first alternative: it would hurt our feelings, and therefore cannot be true.  No, we have a fascinating result: people today are fundamentally different from the Greatest Generation, biologically different: we’re two chromosomes shy of a load. .    So it’s not our fault !

http://blogs.discovermagazine.com/loom/2012/07/19/the-mystery-of-the-missing-chromosome-with-a-special-guest-appearance-from-facebook-creationists/

funny comment: https://westhunt.wordpress.com/2014/11/19/the-greatest-generation/#comment-62920
“some social environments are better than others at extracting the best from its people”

That’s very true – we certainly don’t seem to be doing a very good job of it. It’s a minor matter, but threatening brilliant engineers with death or professional ruin because of their sexist sartorial choices probably isn’t helping…

I used to do some engineering, and if someone had tried on that on me, I’ve have told him to go fuck itself. Is that a lost art?

https://www.theguardian.com/science/2014/nov/14/rosetta-comet-dr-matt-taylor-apology-sexist-shirt
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july 2017 by nhaliday
Kinship Systems, Cooperation and the Evolution of Culture
In the data, societies with loose ancestral kinship ties cooperate and trust broadly, which is apparently sustained through a belief in moralizing gods, universally applicable moral principles, feelings of guilt, and large-scale institutions. Societies with a historically tightly knit kinship structure, on the other hand, exhibit strong in-group favoritism: they cheat on and are distrusting of out-group members, but readily support in-group members in need. This cooperation scheme is enforced by moral values of in-group loyalty, conformity to tight social norms, emotions of shame, and strong local institutions.

Henrich, Joseph, The Secret of Our Success: How Culture is Driving Human Evolution,
Domesticating Our Species, and Making Us Smarter, Princeton University Press, 2015.
—, W.E.I.R.D People: How Westerners became Individualistic, Self-Obsessed, Guilt-Ridden,
Analytic, Patient, Principled and Prosperous, Princeton University Press, n.d.
—, Jean Ensminger, Richard McElreath, Abigail Barr, Clark Barrett, Alexander Bolyanatz, Juan Camilo Cardenas, Michael Gurven, Edwins Gwako, Natalie Hen- rich et al., “Markets, Religion, Community Size, and the Evolution of Fairness and Punishment,” Science, 2010, 327 (5972), 1480–1484.

...

—, —, Will M. Gervais, Aiyana K. Willard, Rita A. McNamara, Edward Slingerland, and Joseph Henrich, “The Cultural Evolution of Prosocial Religions,” Behavioral and Brain Sciences, 2016, 39, e1.

...

Purzycki, Benjamin Grant, Coren Apicella, Quentin D. Atkinson, Emma Cohen, Rita Anne McNamara, Aiyana K. Willard, Dimitris Xygalatas, Ara Norenzayan, and Joseph Henrich, “Moralistic Gods, Supernatural Punishment and the Expansion of Human Sociality,” Nature, 2016.

Table 1 summarizes
Figure 1 has map of kinship tightness
Figure 2 has cheating and in-group vs. out-group
Table 2 has regression
Figure 3 has univeralism and shame-guilt
Figure 4 has individualism-collectivism/conformity
Table 4 has radius of trust, Table 5 same for within-country variation (ethnic)
Tables 7 and 8 do universalism

Haidt moral foundations:
In line with the research hypothesis discussed in Section 3, the analysis employs two dependent variables, i.e., (i) the measure of in-group loyalty, and (ii) an index of the importance of communal values relative to the more universal (individualizing) ones. That is, the hypothesis is explicitly not about some societies being more or less moral than others, but merely about heterogeneity in the relative importance that people attach to structurally different types of values. To construct the index, I compute the first principal component of fairness / reciprocity, harm / care, in-group / loyalty, and respect /authority. The resulting score endogenously has the appealing property that – in line with the research hypothesis – it loads positively on the first two values and negatively on the latter two, with roughly equal weights, see Appendix F for details.²⁴I compute country-level scores by averaging responses by country of residence of respondents. Importantly, in Enke (2017) I document that – in a nationally representative sample of Americans – this same index of moral communalism is strongly correlated with individuals’ propensity to favor their local community over society as a whole in issues ranging from taxation and redistribution to donations and volunteering. Thus, there is evidence that the index of communal moral values captures economically meaningful behavioral heterogeneity.

The coevolution of kinship systems, cooperation, and culture: http://voxeu.org/article/kinship-cooperation-and-culture
- Benjamin Enke

pretty short

good linguistics reference cited in this paper:
On the biological and cultural evolution of shame: Using internet search tools to weight values in many cultures: https://arxiv.org/abs/1401.1100v2
Here we explore the relative importance between shame and guilt by using Google Translate [>_>...] to produce translation for the words "shame", "guilt", "pain", "embarrassment" and "fear" to the 64 languages covered. We also explore the meanings of these concepts among the Yanomami, a horticulturist hunter-gatherer tribe in the Orinoquia. Results show that societies previously described as “guilt societies” have more words for guilt than for shame, but *the large majority*, including the societies previously described as “shame societies”, *have more words for shame than for guilt*. Results are consistent with evolutionary models of shame which predict a wide scatter in the relative importance between guilt and shame, suggesting that cultural evolution of shame has continued the work of biological evolution, and that neither provides a strong adaptive advantage to either shame or guilt [? did they not just say that most languages favor shame?].

...

The roots of the word "shame" are thought to derive from an older word meaning "to cover". The emotion of shame has clear physiological consequences. Its facial and corporal expression is a human universal, as was recognized already by Darwin (5). Looking away, reddening of the face, sinking the head, obstructing direct view, hiding the face and downing the eyelids, are the unequivocal expressions signaling shame. Shame might be an emotion specific to humans, as no clear description of it is known for animals.
...
Classical Greek philosophers, such as Aristotle, explicitly mention shame as a key element in building society.

Guilt is the emotion of being responsible for the commission of an offense, however, it seems to be distinct from shame. Guilt says “what I did was not good”, whereas shame says “I am no good"(2). For Benedict (1), shame is a violation of cultural or social values, while guilt feelings arise from violations of one's internal values.

...

Unobservable emotions such as guilt may be of value to the receiver but constitutes in economy “private information”. Thus, in economic and biological terms, adaptive pressures acting upon the evolution of shame differ from those acting on that of guilt.

Shame has evolutionary advantages to both individual and society, but the lack ofshame also has evolutionary advantages as it allows cheating and thus benefiting from public goods without paying the costs of its build up.

...

Dodds (7) coined the distinction between guilt and shame cultures and postulated that in Greek cultural history, shame as a social value was displaced, at least in part, by guilt in guiding moral behavior.
...
"[...]True guilt cultures rely on an internalized conviction of sin as the enforcer of good behavior, not, as shame cultures do, on external sanctions. Guilt cultures emphasize punishment and forgiveness as ways of restoring the moral order; shame cultures stress self-denial and humility as ways of restoring the social order”.

...

For example, Wikipedia is less error prone than Encyclopedia Britannica (12, 17); and Google Translate is as accurate as more traditional methods (35).

Table 1, Figure 1

...

This regression is close to a proportional line of two words for shame for each word for guilt.

...

For example, in the case of Chinese, no overlap between the five concepts is reported using Google Translate in Figure 1. Yet, linguistic-conceptual studies of guilt and shame revealed an important overlap between several of these concepts in Chinese (29).

...

Our results using Google Translate show no overlap between Guilt and Shame in any of the languages studied.
...
[lol:] Examples of the context when they feel “kili” are: a tiger appears in the forest; you kill somebody from another community; your daughter is going to die; everybody looks at your underwear; you are caught stealing; you soil your pants while among others; a doctor gives you an injection; you hit your wife and others find out; you are unfaithful to your husband and others find out; you are going to be hit with a machete.

...

Linguistic families do not aggregate according to the relationship of the number of synonyms for shame and guilt (Figure 3).

...

The ratios are 0.89 and 2.5 respectively, meaning a historical transition from guilt-culture in Latin to shame-culture in Italian, suggesting a historical development that is inverse to that suggested byDodds for ancient to classical Greek. [I hope their Latin corpus doesn't include stuff from Catholics...]

Joe Henrich presentation: https://www.youtube.com/watch?v=f-unD4ZzWB4

relevant video:
Johnny Cash - God's Gonna Cut You Down: https://www.youtube.com/watch?v=eJlN9jdQFSc

https://en.wikipedia.org/wiki/Guilt_society
https://en.wikipedia.org/wiki/Shame_society
https://en.wikipedia.org/wiki/Guilt-Shame-Fear_spectrum_of_cultures
this says Dems more guilt-driven but Peter Frost says opposite here (and matches my perception of the contemporary breakdown both including minorities and focusing only on whites): https://pinboard.in/u:nhaliday/b:9b75881f6861
http://honorshame.com/global-map-of-culture-types/

this is an amazing paper:
The Origins of WEIRD Psychology: https://psyarxiv.com/d6qhu/
Recent research not only confirms the existence of substantial psychological variation around the globe but also highlights the peculiarity of populations that are Western, Educated, Industrialized, Rich and Democratic (WEIRD). We propose that much of this variation arose as people psychologically adapted to differing kin-based institutions—the set of social norms governing descent, marriage, residence and related domains. We further propose that part of the variation in these institutions arose historically from the Catholic Church’s marriage and family policies, which contributed to the dissolution of Europe’s traditional kin-based institutions, leading eventually to the predominance of nuclear families and impersonal institutions. By combining data on 20 psychological outcomes with historical measures of both kinship and Church exposure, we find support for these ideas in a comprehensive array of analyses across countries, among European regions and between individuals with … [more]
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june 2017 by nhaliday
10 million DTC dense marker genotypes by end of 2017? – Gene Expression
Ultimately I do wonder if I was a bit too optimistic that 50% of the US population will be sequenced at 30x by 2025. But the dynamic is quite likely to change rapidly because of a technological shift as the sector goes through a productivity uptick. We’re talking about exponential growth, which humans have weak intuition about….
https://gnxp.nofe.me/2017/06/27/genome-sequencing-for-the-people-is-near/
https://gnxp.nofe.me/2017/07/11/23andme-ancestry-only-is-49-99-for-prime-day/
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june 2017 by nhaliday
Dadly adaptations | West Hunter
If we understood how this works, we might find that individuals and populations vary in their propensity to show paternal care ( for genetic reasons). I would guess that paternal care was ancestral in modern humans, but it’s easy enough to lose something like this when selective pressures no longer favor it. Wolves have paternal care, but dogs have lost it.

This could have something to do with better health in married men. High testosterone levels aren’t cost-free.

It’s possible that various modern environmental factors interfere with the triggers for dadliness. That would hardly be surprising, since we don’t really know how they work.

All this has a number of interesting social implications. Let’s see how many of them you guys can spot.

Poles in the Tent: https://westhunt.wordpress.com/2013/07/09/poles-in-the-tent/
I’m considering a different question: what was the impact of men’s contribution on their children’s survival and fitness? That’s not quite the same as the number of calories contributed. Food is not a single undifferentiated quantity: it’s a category, including a number of different kinds that can’t be freely substituted for each other. Proteins, fats, and carbohydrates can all serve as fuel, but you need protein to build tissue. And amino acids, the building blocks of proteins, are not all fungible. Some we can’t synthesize (essential amino acids) others can only be synthesized from a limited set of precursors, etc. Edible plants often have suboptimal mixes of amino acids ( too many Qs, not enough Us) , but I’ve never heard of this being a problem with meat. Then you have to consider essential fatty acids, vitamins, and trace elements.

In principle, if high-quality protein were the long pole in the tent, male provisioning of meat, which we see in chimpanzees, might matter quite a bit more than you would think from the number of calories alone. I’m not say that is necessarily the case, but it might be, and it’s worth checking out.

Sexual selection vs job specialization: https://westhunt.wordpress.com/2017/10/02/sexual-selection-vs-job-specialization/
Pretty much every species is subject to sexual selection: heritable characteristics that lead to more mates or better mates can be favored by natural selection. Typically, sexual selection favors different strategies in males and females. Generally, males can gain fitness with increased mating opportunities, while females gain more from high-quality mates or mates that confer resources. Since the variance in reproduction is usually greater in males than females, sexual selection is usually stronger in males, although it exists and is significant in both sexes.

Usually, though, males and females of a given species have very similar ways of making a living. A male deer and a female deer both eat grass or arugula or whatever. Sexual selection may drive them to evolve in different directions, but finding something to eat mostly drives them in the same direction.

Humans are an exception. In the long past, men hunted and women gathered. The mix varied: in Arctic regions, men produce almost all the food (while women made and repaired gear, as well as raising children). In groups like the Bushmen, women produced most of the calories, but done rightly you would count more than calories: if most of the local plants had low protein or low-quality protein (wrong amino acid mix), meat from hunting could be important out of proportion to its caloric value.

This has been going for a long time, so there must have been selection for traits that aided provisioning ability in each sex. Those job-related selective pressures probably changed with time. For example, male strength may have become less valuable when the Bushmen developed poison arrows.

I was looking for an intelligent discussion of this question – but I ran into this and couldn’t force myself to read further: ” It should not simply be assumed that the exclusion of women from hunting rests upon “natural” physiological differences. ”

God give me strength.

https://westhunt.wordpress.com/2017/10/02/sexual-selection-vs-job-specialization/#comment-96323
What does Greg think about the “plows vs hoes” theory? (As seen here, although Sarah Constantin didn’t invent it.)

The claim is that some societies adopted farming (Europe, the Middle East, Asia) while some societies adopted horticulture (Oceana, sub-Saharan Africa, various primitive peoples) and that this had an affect on gender relations.

Basically: farming is backbreaking work, which favours males, giving them a lot of social capital. You end up with a patriarchal kind of society, where the men do stuff and the women are mostly valuable for raising offspring.

...

It’s kinda true, in places. There is a connection I haven’t seen explicated: the ‘hoe culture” has to have some factor keeping population density low, so that labor is scarcer than land. Tropical diseases like malaria might be part of that. Then again, crops like yams don’t store well, better to keep them in the ground until eating. That means it’s hard to tax people – easy with grain bins. No taxes -> no State – > high local violence. At times, VD may also help limit density, cf Africa’s ‘sterility belt’.

I am not a Moron: https://westhunt.wordpress.com/2017/11/03/i-am-not-a-moron/
So said Augustin Fuentes on Twitter, a few days ago. He’s the same guy that said “Genes don’t do anything by themselves; epigenetics and complex metabolic and developmental systems are at play in how bodies work. The roundworm C. elegans has about 20,000 genes while humans have about 23,000 genes, yet it is pretty obvious that humans are more than 15-percent more complex than roundworms. So while genes matter, they are only a small part of the whole evolutionary picture. Focusing just on DNA won’t get you anywhere.”

Fuentes was claiming that we don’t really know that, back in prehistory, men did most of the hunting while women gathered.

...

Someone (Will@Evolving _Moloch) criticized this as a good candidate for the most misleading paragraph ever written. The folly of youth! When you’ve been around as long as I have, sonny, you will realize how hard it is to set records for stupidity.

Fuente’s para is multidimensional crap, of course. People used to hunt animals like red deer, or bison, or eland: sometimes mammoths or rhinos. Big animals. Back in the day, our ancestors used stabbing spears, which go back at least half a million years. Stand-off weapons like atlatls, or bows, or JSOW, are relatively recent. Hunters took big risks & suffered frequent injuries. Men are almost twice as strong as women, particularly in upper-body strength, which is what matters in spear-chucking. They’re also faster, which can be very important which your ambush fails.
So men did the hunting. This isn’t complicated.

Which contemporary hunter-gather societies followed this pattern, had men do almost all of the big-game hunting? All of them.

...

Look, feminists aren’t happy with human nature, the one that actually exists and is the product of long-term evolutionary pressures. Too bad for them. When they say stuff like “It should not simply be assumed that the exclusion of women from hunting rests upon “natural” physiological differences. “, they just sound like fools.. ‘natural physiological differences” exist. They’re as obvious a punch in the kisser.

Suppose you wanted to construct a society with effective sexual equality – which is probably just a mistake, but suppose it. The most effective approach would surely entail knowing and taking into account how the world actually ticks. You’d be better off understanding that about 6,000 genes (out of 20,000) show significant expression differences between the sexes, than by pretending that we’re all the same. You would to make it so: by hook or by crook, by state force and genetic engineering.

Similarly, if you want to minimize war, pretending that people aren’t warlike is a poor start – about as sensible as fighting forest fires by pretending that trees aren’t flammable.

My advice to Augustin Fuentes, about not being a moron: show, don’t tell.

https://westhunt.wordpress.com/2017/11/03/i-am-not-a-moron/#comment-97721
Since DNA is the enduring part, the part that gets transmitted from one generation to the next, the part that contains the instructions/program that determine development and specify everything – he’s wrong. Stupid, like you. Well, to be fair, ignorant as well: there are technical aspects of genetics that Agustin Fuentes is unlikely to know anything about, things that are almost never covered in the typical education of an anthropologist. I doubt if he knows what a Fisher wave is, or anything about selfish genetic elements, or coalescent theory, or for that matter the breeder’s equation.

There are a number of complex technical subjects, things that at least some people understand: those people can do stuff that the man in the street can’t. In most cases, amateurs don’t jump in and pretend to know what’s going on. For example you don’t hear much concerning amateur opinions concerning detonation physics or group theory. But they’re happy to have opinions about natural selection, even though they know fuck-all about it.

https://twitter.com/FinchesofDarwin/status/922924692389818368
https://archive.is/AcBgh
"Significantly fewer females are present at hunts than males...females tend to appear at the hunting site once the capture has been made..."

“Women in Tech”: https://bloodyshovel.wordpress.com/2017/10/26/women-in-tech/
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june 2017 by nhaliday
Genomic analysis of family data reveals additional genetic effects on intelligence and personality | bioRxiv
methodology:
Using Extended Genealogy to Estimate Components of Heritability for 23 Quantitative and Dichotomous Traits: http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1003520
Pedigree- and SNP-Associated Genetics and Recent Environment are the Major Contributors to Anthropometric and Cardiometabolic Trait Variation: http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005804

Missing Heritability – found?: https://westhunt.wordpress.com/2017/02/09/missing-heritability-found/
There is an interesting new paper out on genetics and IQ. The claim is that they have found the missing heritability – in rare variants, generally different in each family.

Some of the variants, the ones we find with GWAS, are fairly common and fitness-neutral: the variant that slightly increases IQ confers the same fitness (or very close to the same) as the one that slightly decreases IQ – presumably because of other effects it has. If this weren’t the case, it would be impossible for both of the variants to remain common.

The rare variants that affect IQ will generally decrease IQ – and since pleiotropy is the norm, usually they’ll be deleterious in other ways as well. Genetic load.

Happy families are all alike; every unhappy family is unhappy in its own way.: https://westhunt.wordpress.com/2017/06/06/happy-families-are-all-alike-every-unhappy-family-is-unhappy-in-its-own-way/
It now looks as if the majority of the genetic variance in IQ is the product of mutational load, and the same may be true for many psychological traits. To the extent this is the case, a lot of human psychological variation must be non-adaptive. Maybe some personality variation fulfills an evolutionary function, but a lot does not. Being a dumb asshole may be a bug, rather than a feature. More generally, this kind of analysis could show us whether particular low-fitness syndromes, like autism, were ever strategies – I suspect not.

It’s bad new news for medicine and psychiatry, though. It would suggest that what we call a given type of mental illness, like schizophrenia, is really a grab-bag of many different syndromes. The ultimate causes are extremely varied: at best, there may be shared intermediate causal factors. Not good news for drug development: individualized medicine is a threat, not a promise.

see also comment at: https://pinboard.in/u:nhaliday/b:a6ab4034b0d0

https://www.reddit.com/r/slatestarcodex/comments/5sldfa/genomic_analysis_of_family_data_reveals/
So the big implication here is that it's better than I had dared hope - like Yang/Visscher/Hsu have argued, the old GCTA estimate of ~0.3 is indeed a rather loose lower bound on additive genetic variants, and the rest of the missing heritability is just the relatively uncommon additive variants (ie <1% frequency), and so, like Yang demonstrated with height, using much more comprehensive imputation of SNP scores or using whole-genomes will be able to explain almost all of the genetic contribution. In other words, with better imputation panels, we can go back and squeeze out better polygenic scores from old GWASes, new GWASes will be able to reach and break the 0.3 upper bound, and eventually we can feasibly predict 0.5-0.8. Between the expanding sample sizes from biobanks, the still-falling price of whole genomes, the gradual development of better regression methods (informative priors, biological annotation information, networks, genetic correlations), and better imputation, the future of GWAS polygenic scores is bright. Which obviously will be extremely helpful for embryo selection/genome synthesis.

The argument that this supports mutation-selection balance is weaker but plausible. I hope that it's true, because if that's why there is so much genetic variation in intelligence, then that strongly encourages genetic engineering - there is no good reason or Chesterton fence for intelligence variants being non-fixed, it's just that evolution is too slow to purge the constantly-accumulating bad variants. And we can do better.
https://rubenarslan.github.io/generation_scotland_pedigree_gcta/

The surprising implications of familial association in disease risk: https://arxiv.org/abs/1707.00014
https://spottedtoad.wordpress.com/2017/06/09/personalized-medicine-wont-work-but-race-based-medicine-probably-will/
As Greg Cochran has pointed out, this probably isn’t going to work. There are a few genes like BRCA1 (which makes you more likely to get breast and ovarian cancer) that we can detect and might affect treatment, but an awful lot of disease turns out to be just the result of random chance and deleterious mutation. This means that you can’t easily tailor disease treatment to people’s genes, because everybody is fucked up in their own special way. If Johnny is schizophrenic because of 100 random errors in the genes that code for his neurons, and Jack is schizophrenic because of 100 other random errors, there’s very little way to test a drug to work for either of them- they’re the only one in the world, most likely, with that specific pattern of errors. This is, presumably why the incidence of schizophrenia and autism rises in populations when dads get older- more random errors in sperm formation mean more random errors in the baby’s genes, and more things that go wrong down the line.

The looming crisis in human genetics: http://www.economist.com/node/14742737
Some awkward news ahead
- Geoffrey Miller

Human geneticists have reached a private crisis of conscience, and it will become public knowledge in 2010. The crisis has depressing health implications and alarming political ones. In a nutshell: the new genetics will reveal much less than hoped about how to cure disease, and much more than feared about human evolution and inequality, including genetic differences between classes, ethnicities and races.

2009!
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june 2017 by nhaliday
Genetics allows the dead to speak from the grave - The Unz Review
BOOKMARKIt is a running joke of mine on Twitter that the genetics of white people is one of those fertile areas of research that seems to never end. Is it a surprise that the ancient DNA field has first elucidated the nature of this obscure foggy continent, before rich histories of the untold billions of others? It’s funny, and yet these stories, true tales, do I think tell us a great deal about how modern human populations came to be in the last 10,000 years. The lessons of Europe can be generalized. We don’t have the rich stock of ancient DNA from China, the Middle East, or India. At least not enough to do population genomics, which requires larger sample sizes than a few. But, climate permitting, we may.

...

At about the same time the evidence for Neanderthal admixture came out, Luke Jostins posted results which showed that other human lineages were also undergoing encephalization, before their trajectory was cut short. That is, their brains were getting bigger before they went extinct. To me this suggested that the broader Homo lineage was undergoing a process of nearly inevitable change due to a series of evolutionary events very deep in our history, perhaps ancestral on the order of millions of years. Along with the evidence for admixture it made me reconsider my priors. Perhaps some Homo lineage was going to expand outward and do what we did, and perhaps it wasn’t inevitable that it was going to be us. Perhaps the Neanderthal Parallax scenario is not as fantastical as we might think?
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may 2017 by nhaliday
POPULATION STRUCTURE AND QUANTITATIVE CHARACTERS
The variance of among-group variance is substantial and does not depend on the number of loci contributing to variance in the character. It is just as large for polygenic characters as for single loci with the same additive variance. This implies that one polygenic character contains exactly as much information about population relationships as one single-locus marker.

same is true of expectation apparently (so drift has same impact on polygenic and single-locus traits)
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may 2017 by nhaliday
Edge.org: 2017 : WHAT SCIENTIFIC TERM OR CONCEPT OUGHT TO BE MORE WIDELY KNOWN?
highlights:
- the genetic book of the dead [Dawkins]
- complementarity [Frank Wilczek]
- relative information
- effective theory [Lisa Randall]
- affordances [Dennett]
- spontaneous symmetry breaking
- relatedly, equipoise [Nicholas Christakis]
- case-based reasoning
- population reasoning (eg, common law)
- criticality [Cesar Hidalgo]
- Haldan's law of the right size (!SCALE!)
- polygenic scores
- non-ergodic
- ansatz
- state [Aaronson]: http://www.scottaaronson.com/blog/?p=3075
- transfer learning
- effect size
- satisficing
- scaling
- the breeder's equation [Greg Cochran]
- impedance matching

soft:
- reciprocal altruism
- life history [Plomin]
- intellectual honesty [Sam Harris]
- coalitional instinct (interesting claim: building coalitions around "rationality" actually makes it more difficult to update on new evidence as it makes you look like a bad person, eg, the Cathedral)
basically same: https://twitter.com/ortoiseortoise/status/903682354367143936

more: https://www.edge.org/conversation/john_tooby-coalitional-instincts

interesting timing. how woke is this dude?
org:edge  2017  technology  discussion  trends  list  expert  science  top-n  frontier  multi  big-picture  links  the-world-is-just-atoms  metameta  🔬  scitariat  conceptual-vocab  coalitions  q-n-a  psychology  social-psych  anthropology  instinct  coordination  duty  power  status  info-dynamics  cultural-dynamics  being-right  realness  cooperate-defect  westminster  chart  zeitgeist  rot  roots  epistemic  rationality  meta:science  analogy  physics  electromag  geoengineering  environment  atmosphere  climate-change  waves  information-theory  bits  marginal  quantum  metabuch  homo-hetero  thinking  sapiens  genetics  genomics  evolution  bio  GT-101  low-hanging  minimum-viable  dennett  philosophy  cog-psych  neurons  symmetry  humility  life-history  social-structure  GWAS  behavioral-gen  biodet  missing-heritability  ergodic  machine-learning  generalization  west-hunter  population-genetics  methodology  blowhards  spearhead  group-level  scale  magnitude  business  scaling-tech  tech  business-models  optimization  effect-size  aaronson  state  bare-hands  problem-solving  politics 
may 2017 by nhaliday
Germline selection | West Hunter
Here’s what seems to be happening: you have cells in the testes that reproduce, producing one daughter cell like the parent and one that develops into a sperm cell. That’s the way it’s supposed to be. But carrying certain very specific mutations of FGFR2 or FGFR3 seem to cause occasional divisions that result in two daughter cells – so the pre-sperm cells that carry such mutations gradually become more and more common in the testes and produce a growing fraction of sperm with those mutations. It’s rather like cancer. You get clumps of cells producing the bad sperm.

Same things is happening with MEN2B (RET gene), which is also more common than it should be, although not as much so as achondroplasia.

Without this unusual mutational mechanism, there would be a shortage of dwarfs.
west-hunter  scitariat  discussion  ideas  trivia  biodet  genetics  genomics  disease  mutation  developmental  embodied  selfish-gene  sex  cooperate-defect  EGT  epidemiology  🌞 
may 2017 by nhaliday
The human Y chromosome: the biological role of a “functional wasteland”
“Functional wasteland,” “Nonrecombining desert,” and “Gene-poor chromosome” are only some examples of the different definitions given to the Y chromosome in the last decade. In comparison to the other chromosomes, the Y is poor in genes, being more than 50% of its sequence composed of repeated elements.
study  bio  sapiens  genetics  genomics  gender  gender-diff  survey 
may 2017 by nhaliday
Interview: Mostly Sealing Wax | West Hunter
https://soundcloud.com/user-519115521/greg-cochran-part-2
https://medium.com/@houstoneuler/annotating-part-2-of-the-greg-cochran-interview-with-james-miller-678ba33f74fc

- conformity and Google, defense and spying (China knows prob almost all our "secrets")
- in the past you could just find new things faster than people could reverse-engineer. part of the problem is that innovation is slowing down today (part of the reason for convergence by China/developing world).
- introgression from archaics of various kinds
- mutational load and IQ, wrath of khan neanderthal
- trade and antiquity (not that useful besides ideas tbh), Roman empire, disease, smallpox
- spices needed to be grown elsewhere, but besides that...
- analogy: caste system in India (why no Brahmin car repairmen?), slavery in Greco-Roman times, more water mills in medieval times (rivers better in north, but still could have done it), new elite not liking getting hands dirty, low status of engineers, rise of finance
- crookery in finance, hedge fund edge might be substantially insider trading
- long-term wisdom of moving all manufacturing to China...?
- economic myopia: British financialization before WW1 vis-a-vis Germany. North vs. South and cotton/industry, camels in Middle East vs. wagons in Europe
- Western medicine easier to convert to science than Eastern, pseudoscience and wrong theories better than bag of recipes
- Greeks definitely knew some things that were lost (eg, line in Pliny makes reference to combinatorics calculation rediscovered by German dude much later. think he's referring to Catalan numbers?), Lucio Russo book
- Indo-Europeans, Western Europe, Amerindians, India, British Isles, gender, disease, and conquest
- no farming (Dark Age), then why were people still farming on Shetland Islands north of Scotland?
- "symbolic" walls, bodies with arrows
- family stuff, children learning, talking dog, memory and aging
- Chinese/Japanese writing difficulty and children learning to read
- Hatfield-McCoy feud: the McCoy family was actually a case study in a neurological journal. they had anger management issues because of cancers of their adrenal gland (!!).

the Chinese know...: https://macropolo.org/casting-off-real-beijings-cryptic-warnings-finance-taking-economy/
Over the last couple of years, a cryptic idiom has crept into the way China’s top leaders talk about risks in the country’s financial system: tuo shi xiang xu (脱实向虚), which loosely translates as “casting off the real for the empty.” Premier Li Keqiang warned against it at his press conference at the end of the 2016 National People’s Congress (NPC). At this year’s NPC, Li inserted this very expression into his annual work report. And in April, while on an inspection tour of Guangxi, President Xi Jinping used the term, saying that China must “unceasingly promote industrial modernization, raise the level of manufacturing, and not allow the real to be cast off for the empty.”

Such an odd turn of phrase is easy to overlook, but it belies concerns about a significant shift in the way that China’s economy works. What Xi and Li were warning against is typically called financialization in developed economies. It’s when “real” companies—industrial firms, manufacturers, utility companies, property developers, and anyone else that produces a tangible product or service—take their money and, rather than put it back into their businesses, invest it in “empty”, or speculative, assets. It occurs when the returns on financial investments outstrip those in the real economy, leading to a disproportionate amount of money being routed into the financial system.
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may 2017 by nhaliday
Genetically engineered humans will arrive sooner than you think. And we're not ready. - Vox
lol "epigenetics" makes an appearance ofc

https://www.theatlantic.com/science/archive/2017/06/the-moral-question-that-stanfords-bioengineering-students-get/531876/

For now, that’s prohibitively expensive, but it won’t always be that way. In 2003, it cost 4 dollars to press one of the keys on Endy’s hypothetical synthesizer. This month, it costs just two cents—a 200-fold decrease in price in just 14 years. In the same time frame, the cost of tuition at Stanford has doubled, and is now around $50,000. Given all of that, the first question that Stanford’s budding bioengineers get is this:

At what point will the cost of printing DNA to create a human equal the cost of teaching a student in Stanford?
And the answer is: 19 years from today.

But the follow-up question is a little more complicated:

If you and your future partner are planning to have kids, would you start saving money for college tuition, or for printing the genome of your offspring?
The question tends to split students down the line, says Endy. About 60 percent say that printing a genome is wrong, and flies against what it means to be a parent. They prize the special nature of education and would opt to save for the tuition. But around 40 percent of the class will say that the value of education may change in the future, and if genetic technology becomes mature, and allows them to secure advantages for them and their lineage, they might as well do that.

https://www.nytimes.com/2016/05/14/science/synthetic-human-genome.html
http://www.nature.com/news/plan-to-synthesize-human-genome-triggers-mixed-response-1.20028

https://ipscell.com/2017/06/crispr-human-genetic-modification-a-needed-course-correction/
news  org:data  org:lite  enhancement  biotech  longevity  genetics  CRISPR  epigenetics  westminster  morality  ethics  inequality  futurism  patho-altruism  speedometer  multi  org:mag  stanford  higher-ed  values  poll  elite  org:nat  org:sci  frontier  genomics  🌞  🔬  current-events  org:rec  science  events  announcement  scitariat 
may 2017 by nhaliday
Estimating the number of unseen variants in the human genome
To find all common variants (frequency at least 1%) the number of individuals that need to be sequenced is small (∼350) and does not differ much among the different populations; our data show that, subject to sequence accuracy, the 1000 Genomes Project is likely to find most of these common variants and a high proportion of the rarer ones (frequency between 0.1 and 1%). The data reveal a rule of diminishing returns: a small number of individuals (∼150) is sufficient to identify 80% of variants with a frequency of at least 0.1%, while a much larger number (> 3,000 individuals) is necessary to find all of those variants.

A map of human genome variation from population-scale sequencing: http://www.internationalgenome.org/sites/1000genomes.org/files/docs/nature09534.pdf

Scientists using data from the 1000 Genomes Project, which sequenced one thousand individuals from 26 human populations, found that "a typical [individual] genome differs from the reference human genome at 4.1 million to 5.0 million sites … affecting 20 million bases of sequence."[11] Nearly all (>99.9%) of these sites are small differences, either single nucleotide polymorphisms or brief insertion-deletions in the genetic sequence, but structural variations account for a greater number of base-pairs than the SNPs and indels.[11]

Human genetic variation: https://en.wikipedia.org/wiki/Human_genetic_variation

Singleton Variants Dominate the Genetic Architecture of Human Gene Expression: https://www.biorxiv.org/content/early/2017/12/15/219238
study  sapiens  genetics  genomics  population-genetics  bioinformatics  data  prediction  cost-benefit  scale  scaling-up  org:nat  QTL  methodology  multi  pdf  curvature  convexity-curvature  nonlinearity  measurement  magnitude  🌞  distribution  missing-heritability  pop-structure  genetic-load  mutation  wiki  reference  article  structure  bio  preprint  biodet  variance-components  nibble  chart 
may 2017 by nhaliday
Human genome - Wikipedia
There are an estimated 19,000-20,000 human protein-coding genes.[4] The estimate of the number of human genes has been repeatedly revised down from initial predictions of 100,000 or more as genome sequence quality and gene finding methods have improved, and could continue to drop further.[5][6] Protein-coding sequences account for only a very small fraction of the genome (approximately 1.5%), and the rest is associated with non-coding RNA molecules, regulatory DNA sequences, LINEs, SINEs, introns, and sequences for which as yet no function has been determined.[7]
bio  sapiens  genetics  genomics  bioinformatics  scaling-up  data  scale  wiki  reference  QTL  methodology 
may 2017 by nhaliday
Missing heritability problem - Wikipedia
The "missing heritability" problem[1][2][3][4][5][6] can be defined as the fact that single genetic variations cannot account for much of the heritability of diseases, behaviors, and other phenotypes. This is a problem that has significant implications for medicine, since a person's susceptibility to disease may depend more on "the combined effect of all the genes in the background than on the disease genes in the foreground", or the role of genes may have been severely overestimated.

The 'missing heritability' problem was named as such in 2008. The Human Genome Project led to optimistic forecasts that the large genetic contributions to many traits and diseases (which were identified by quantitative genetics and behavioral genetics in particular) would soon be mapped and pinned down to specific genes and their genetic variants by methods such as candidate-gene studies which used small samples with limited genetic sequencing to focus on specific genes believed to be involved, examining the SNP kinds of variants. While many hits were found, they often failed to replicate in other studies.

The exponential fall in genome sequencing costs led to the use of GWAS studies which could simultaneously examine all candidate-genes in larger samples than the original finding, where the candidate-gene hits were found to almost always be false positives and only 2-6% replicate;[7][8][9][10][11][12] in the specific case of intelligence candidate-gene hits, only 1 candidate-gene hit replicated,[13] and of 15 neuroimaging hits, none did.[14] The editorial board of Behavior Genetics noted, in setting more stringent requirements for candidate-gene publications, that "the literature on candidate gene associations is full of reports that have not stood up to rigorous replication...it now seems likely that many of the published findings of the last decade are wrong or misleading and have not contributed to real advances in knowledge".[15] Other researchers have characterized the literature as having "yielded an infinitude of publications with very few consistent replications" and called for a phase out of candidate-gene studies in favor of polygenic scores.[16]

This led to a dilemma. Standard genetics methods have long estimated large heritabilities such as 80% for traits such as height or intelligence, yet none of the genes had been found despite sample sizes that, while small, should have been able to detect variants of reasonable effect size such as 1 inch or 5 IQ points. If genes have such strong cumulative effects - where were they? Several resolutions have been proposed, that the missing heritability is some combination of:

...

7. Genetic effects are indeed through common SNPs acting additively, but are highly polygenic: dispersed over hundreds or thousands of variants each of small effect like a fraction of an inch or a fifth of an IQ point and with low prior probability: unexpected enough that a candidate-gene study is unlikely to select the right SNP out of hundreds of thousands of known SNPs, and GWASes up to 2010, with n<20000, would be unable to find hits which reach genome-wide statistical-significance thresholds. Much larger GWAS sample sizes, often n>100k, would be required to find any hits at all, and would steadily increase after that.
This resolution to the missing heritability problem was supported by the introduction of Genome-wide complex trait analysis (GCTA) in 2010, which demonstrated that trait similarity could be predicted by the genetic similarity of unrelated strangers on common SNPs treated additively, and for many traits the SNP heritability was indeed a substantial fraction of the overall heritability. The GCTA results were further buttressed by findings that a small percent of trait variance could be predicted in GWASes without any genome-wide statistically-significant hits by a linear model including all SNPs regardless of p-value; if there were no SNP contribution, this would be unlikely, but it would be what one expected from SNPs whose effects were very imprecisely estimated by a too-small sample. Combined with the upper bound on maximum effect sizes set by the GWASes up to then, this strongly implied that the highly polygenic theory was correct. Examples of complex traits where increasingly large-scale GWASes have yielded the initial hits and then increasing numbers of hits as sample sizes increased from n<20k to n>100k or n>300k include height,[23] intelligence,[24] and schizophrenia.
article  bio  biodet  behavioral-gen  genetics  genomics  GWAS  candidate-gene  methodology  QTL  missing-heritability  twin-study  measurement  epigenetics  nonlinearity  error  history  mostly-modern  reflection  wiki  reference  science  bounded-cognition  replication  being-right  info-dynamics  🌞  linearity  ideas  GCTA  spearhead 
may 2017 by nhaliday
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