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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
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.
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september 2017 by nhaliday
Why was the Catholic Church so opposed to heliocentrism (for example, in the Renaissance)? Why did they not simply claim that God lived in the Sun, so we go around Him? - Quora
The main reason the Catholic Church opposed the teaching of heliocentrism as a fact was that it was contrary to the science of the time.

Amongst the modern myths about early science is the persistent idea that the opposition to heliocentrism was one of "science" versus "religion". According to this story, early modern astronomers like Copernicus and Galileo "proved" the earth went around the sun and the other scientists of the time agreed. But the Catholic Church clung to a literal interpretation of the Bible and rejected this idea purely out of a fanatical faith, insisting that the earth had to be the centre of the cosmos because man was the pinnacle of all creation. Pretty much everything in this popular story is wrong.
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september 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
Jan Gotlib Bloch - Wikipedia
Bloch became intrigued by the devastating victory of Prussia/Germany over France in 1870-1871, which suggested to him that the solution of diplomatic problems by warfare had become obsolete in Europe. He published his six-volume master work, Budushchaya voina i yeyo ekonomicheskie posledstviya (Russian: Будущая война и её экономические последствия - Future war and its economic consequences), popularized in English translation as Is War Now Impossible?, in Paris in 1898.

His detailed analysis of modern warfare, its tactical, strategic and political implications, was widely read in Europe. Bloch argued that:

-New arms technology (e.g. smokeless gunpowder, improved rifle design, Maxims) had rendered maneuvers over open ground, such as bayonet and cavalry charges, obsolete. Bloch concluded that a war between the great powers would be a war of entrenchment and that rapid attacks and decisive victories were likewise a thing of the past. He calculated that entrenched men would enjoy a fourfold advantage over infantry advancing across open ground.
- Industrial societies would have to settle the resultant stalemate by committing armies numbering in the millions, as opposed to the tens of thousands of preceding wars. An enormous battlefront would develop. A war of this type could not be resolved quickly.
- Such a war would become a duel of industrial might, a matter of total economic attrition. Severe economic and social dislocations would result in the imminent risk of famine, disease, the "break-up of the whole social organization" and revolutions from below.

http://journals.sagepub.com.sci-hub.cc/doi/abs/10.1177/096834450000700302
http://www.historytoday.com/paul-reynolds/man-who-predicted-great-war
https://archive.org/details/futurewar00unkngoog
https://archive.org/details/iswarnowimpossib00bloc
https://westhunt.wordpress.com/2016/12/30/the-secret-histories/#comment-86474
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june 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?
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may 2017 by nhaliday
Germ theory of disease - Wikipedia
The germ theory was proposed by Girolamo Fracastoro in 1546, and expanded upon by Marcus von Plenciz in 1762. Such views were held in disdain, however, and Galen's miasma theory remained dominant among scientists and doctors. The nature of this doctrine prevented them from understanding how diseases actually progressed, with predictable consequences. By the early nineteenth century, smallpox vaccination was commonplace in Europe, though doctors were unaware of how it worked or how to extend the principle to other diseases. Similar treatments had been prevalent in India from just before 1000 A.D.[2] [N 1] A transitional period began in the late 1850s as the work of Louis Pasteur and Robert Koch provided convincing evidence; by 1880, miasma theory was struggling to compete with the germ theory of disease. Eventually, a "golden era" of bacteriology ensued, in which the theory quickly led to the identification of the actual organisms that cause many diseases.[3][4] Viruses were discovered in the 1890s.
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may 2017 by nhaliday
The Advent of Cholera | West Hunter
Two main factors interfered with an effective policy response to cholera (not counting ever-present human stupidity and obstinacy): bad science and 19th century liberalism.

Scientists at the time had convinced themselves that the germ theory of disease was just wrong. Yellow fever’s decimation of the French force in Haiti made it important, and when yellow fever hit Barcelona in 1822, French scientists were all over it. They concluded that there was no possibility of contact between yellow fever victims in Barcelona, and ruled out contagion. Mosquito transmission didn’t occur to them.

Worse yet, they generalized their error: they concluded that contagion was never the answer, and accepted miasmas as the cause, a theory which is too stupid to be interesting. Sheesh, they taught the kids in medical school that measles wasn’t catching – while ordinary people knew perfectly well that it was. You know, esoteric, non-intuitive truths have a certain appeal – once initiated, you’re no longer one of the rubes. Of course, the simplest and most common way of producing an esoteric truth is to just make it up.

On the other hand, 19th century liberals (somewhat like modern libertarians, but way less crazy) knew that trade and individual freedom were always good things, by definition, so they also opposed quarantines – worse than wrong, old-fashioned ! And more common in southern, Catholic, Europe: enough said! So, between wrong science and classical liberalism, medical reformers spent many years trying to eliminate the reactionary quarantine rules that still existed in Mediterranean ports.

some history: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3559034/
In some countries, the suspension of personal liberty provided the opportunity—using special laws—to stop political opposition. However, the cultural and social context differed from that in previous centuries. For example, the increasing use of quarantine and isolation conflicted with the affirmation of citizens’ rights and growing sentiments of personal freedom fostered by the French Revolution of 1789. In England, liberal reformers contested both quarantine and compulsory vaccination against smallpox. Social and political tensions created an explosive mixture, culminating in popular rebellions and uprisings, a phenomenon that affected numerous European countries (29). In the Italian states, in which revolutionary groups had taken the cause of unification and republicanism (27), cholera epidemics provided a justification (i.e., the enforcement of sanitary measures) for increasing police power.

...

Anticontagionists, who disbelieved the communicability of cholera, contested quarantine and alleged that the practice was a relic of the past, useless, and damaging to commerce. They complained that the free movement of travelers was hindered by sanitary cordons and by controls at border crossings, which included fumigation and disinfection of clothes (Figures 1,​,22,​,3).3). In addition, quarantine inspired a false sense of security, which was dangerous to public health because it diverted persons from taking the correct precautions. International cooperation and coordination was stymied by the lack of agreement regarding the use of quarantine. The discussion among scientists, health administrators, diplomatic bureaucracies, and governments dragged on for decades, as demonstrated in the debates in the International Sanitary Conferences (31), particularly after the opening, in 1869, of the Suez Canal, which was perceived as a gate for the diseases of the Orient (32). Despite pervasive doubts regarding the effectiveness of quarantine, local authorities were reluctant to abandon the protection of the traditional strategies that provided an antidote to population panic, which, during a serious epidemic, could produce chaos and disrupt public order (33).
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may 2017 by nhaliday
How Samuel Huntington Predicted Our Political Moment - The American Interest
The views of the general public on issues of national identity differ significantly from those of many elites. The public, overall, is concerned with physical security but also with societal security, which involves the sustainability–within acceptable conditions for evolution–of existing patterns of language, culture, association, religion and national identity. For many elites, these concerns are secondary to participating in the global economy, supporting international trade and migration, strengthening international institutions, promoting American values abroad, and encouraging minority identities and cultures at home. The central distinction between the public and elites is not isolationism versus internationalism, but nationalism versus cosmopolitanism.

https://www.washingtonpost.com/news/book-party/wp/2017/07/18/samuel-huntington-a-prophet-for-the-trump-era/
The book looks back to the Revolutionary War, the Jacksonian age, the Progressive era and the 1960s as moments of high creedal passions, and Huntington’s descriptions capture America today. In such moments, he writes, discontent is widespread, and authority and expertise are questioned; traditional values of liberty, individualism, equality and popular control of government dominate public debates; politics is characterized by high polarization and constant protest; hostility toward power, wealth and inequality grows intense; social movements focused on causes such as women’s rights and criminal justice flourish; and new forms of media emerge devoted to advocacy and adversarial journalism.

Huntington even predicts the timing of America’s next fight: “If the periodicity of the past prevails,” he writes, “a major sustained creedal passion period will occur in the second and third decades of the twenty-first century.”

We’re right on schedule.

...

Over the subsequent two decades, Huntington lost hope. In his final book, “Who Are We?,” which he emphasizes reflect his views not just as a scholar but also as a patriot, Huntington revises his definitions of America and Americans. Whereas once the creed was paramount, here it is merely a byproduct of the Anglo-Protestant culture — with its English language, Christian faith, work ethic and values of individualism and dissent — that he now says forms the true core of American identity.

...

The Huntington of 1981, apparently, was just wrong. When listing academics who had — inaccurately, he now insists — defined Americans by their political beliefs, Huntington quotes an unnamed scholar who once eloquently described Americans as inseparable from the self-evident truths of the Declaration. Unless you recognize the passage from “American Politics” or bother to check the endnotes, you have no idea he is quoting himself. It’s as close to a wink as you’ll find in Huntington’s angriest book.

...

Little wonder that, long before Trump cultivated the alt-right and Hillary Clinton denounced the “deplorables” in our midst, Huntington foresaw a backlash against multiculturalism from white Americans. “One very plausible reaction would be the emergence of exclusivist sociopolitical movements,” he writes, “composed largely but not only of white males, primarily working-class and middle-class, protesting and attempting to stop or reverse these changes and what they believe, accurately or not, to be the diminution of their social and economic status, their loss of jobs to immigrants and foreign countries, the perversion of their culture, the displacement of their language, and the erosion or even evaporation of the historical identity of their country. Such movements would be both racially and culturally inspired and could be anti-Hispanic, anti-black, and anti-immigration.” The more extreme elements in such movements, Huntington notes, fear “the replacement of the white culture that made America great by black or brown cultures that are . . . in their view, intellectually and morally inferior.”

...

This is a conflict he had long anticipated. In his 1996 book proclaiming a clash of civilizations, he writes that the West will continue its slow decline relative Asia and the Islamic world. While economic dynamism drives Asia’s rise, population growth in Muslim nations “provides recruits for fundamentalism, terrorism, insurgency, and migration.” Much as Trump mocks politicians who refuse to decry “radical Islamic terrorism,” Huntington criticizes American leaders such as Bill Clinton who argued that the West had no quarrel with Islam, only with violent extremists. “Fourteen hundred years of history demonstrate otherwise,” he remarks.

Huntington’s clash has been caricatured as a single-minded call to arms against Muslims, and certainly the argument is neither so narrow nor so simple. He is probably more concerned with China and fears a “major war” if Washington challenges Beijing’s rise as Asia’s hegemon. Yet the threat Huntington sees from the Muslim world goes far beyond terrorism or religious extremism. He worries of a broader Islamic resurgence, with political Islam as only one part of “the much more extensive revival of Islamic ideas, practices, and rhetoric and the rededication to Islam by Muslim populations.” Huntington cites scholars warning of the spread of Islamic legal concepts in the West, decries the “inhospitable nature of Islamic culture” for democracy and suggests that Islam will prevail in the numbers game against Christianity. In the long run, “Mohammed wins out,” he states. “Christianity spreads primarily by conversion, Islam by conversion and reproduction.”

https://twitter.com/tcjfs/status/918662411669917697
https://archive.is/Z2FlF
I am rereading Huntington. The only options he foresees are:
* cultural decay
* political breakup
* white re-assertion
* Christian revival
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may 2017 by nhaliday
None So Blind | West Hunter
There have been several articles in the literature claiming that the gene frequency of the 35delG allele of connexin-26, the most common allele causing deafness in Europeans, has doubled in the past 200 years, as a result of relaxed selection and assortative mating over that period.

That’s fucking ridiculous. I see people referencing this in journal articles and books. It’s mentioned in OMIM. But it’s pure nonsense.

https://westhunt.wordpress.com/2013/03/05/none-so-blind/#comment-10483
The only way you’re going to see such a high frequency of an effectively lethal recessive in a continental population is if it conferred a reproductive advantage in heterozygotes. The required advantage must have been as large as its gene frequency, something around 1-2%.

So it’s like sickle-cell.

Now, if you decreased the bad reproductive consequences of deafness, what would you expect to happen? Gradual increase, at around 1 or 2% a generation, if the carrier advantage held – but it probably didn’t. It was probably a defense against some infectious disease, and those have become much less important. If there was no longer any carrier advantage, the frequency wouldn’t change at all.

In order to double in 200 years, you would need a carrier advantage > 9%.

Assortative mating,deaf people marrying other deaf people, would not make much difference. Even if deaf people substantially out-reproduced normals, which they don’t, only ~1-2% of the copies of 35delG reside in deaf people.
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may 2017 by nhaliday
A sense of where you are | West Hunter
Nobody at the Times noticed it at first. I don’t know that they ever did notice it by themselves- likely some reader brought it to their attention. But this happens all the time, because very few people have a picture of the world in their head that includes any numbers. Mostly they don’t even have a rough idea of relative size.

In much the same way, back in the 1980s,lots of writers were talking about 90,000 women a year dying of anorexia nervosa, another impossible number. Then there was the great scare about 1,000,000 kids being kidnapped in the US each year – also impossible and wrong. Practically all the talking classes bought into it.

You might think that the people at the top are different – but with a few exceptions, they’re just as clueless.
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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
Low-Hanging Poop | West Hunter
Obviously, sheer disgust made it hard for doctors to embrace this treatment.  There’s a lesson here: in the search for low-hanging fruit,  reconsider approaches that are embarrassing, or offensive, or downright disgusting.
west-hunter  scitariat  stories  discussion  medicine  meta:medicine  being-right  info-dynamics  epistemic  emotion  sanctity-degradation  education  low-hanging  error  bounded-cognition  embodied  policy  ideas  the-trenches  alt-inst  innovation  discovery 
may 2017 by nhaliday
Call Him George | West Hunter
I hear that Rasmus Nielsen (speaking at SMBE 2014) has evidence that Tibetans picked up some of their altitude adaptation (EPAS1) from Denisovans.

Who could have imagined that?

https://westhunt.wordpress.com/2012/02/17/islands-in-the-sky/
There are three major high-altitude regions inhabited by humans: highland Ethiopia, Tibet, and the Andean altiplano. In each of these three cases, the locals have adapted in various ways to high altitude – physiological adaptations, as well as cultural. To make it even clearer, those physiological changes are, to a large extent, a consequence of natural selection, rather than individual acclimatization.

https://westhunt.wordpress.com/2013/05/16/tibet/
The Tibetans deal with high altitude much more effectively than the Amerindians of the Altiplano. You have to think that they’ve lived there longer, been exposed to those selective pressures longer – and that’s quite feasible. Anatomically modern humans have been in Asia much longer than in the Americas, and it’s even possible that they picked up some adaptive altitude-adaptation genes from archaic humans that had been there for hundreds of thousands of years.

There’s another interesting point: the hunter-gatherers of Tibet appear to account for a lot of Tibetan ancestry, probably most of it, rather than than being almost entirely replaced by a wave of neolithic agriculturalists, which is the more common pattern. They had a trump card – altitude adaptation. A story like that which has left Bolivia mostly Amerindian.

Modern Eugenics: https://westhunt.wordpress.com/2013/11/13/modern-eugenics/
Recent work in genetics has made it clear that Tibetans, Andean Indians, and Ethiopians adapted independently to high-altitude living. It’s also clear that the Tibetan adaptations are more effective those in Andean Indians. Infant survival is better in Tibet, where babies average about half a pound heavier, and the suite of Tibetan adaptations doesn’t seem to fail with increasing age, while a significant fraction of Andean Indians develop chronic mountain sickness in later life. The Andean pattern look something like an exaggerated acclimatization response, while the Tibetan pattern is more like that seen in mammalian species have lived at high altitude for a long time.

...

The obvious solution to these apparently permanent problems in Bolivia and Peru is a dose of Tibetan genes. Since Tibetan alleles are more effective, they must confer higher fitness, and so their frequencies should gradually increase with time. This doesn’t mean that Bolivians would turn Tibetan overall – the change would only happen in those genes for which the Tibetan version was more efficient. It wouldn’t take all that high a dose: in fact, if you’re not in a hurry, just a few tens of Tibetans could transmit enough copies of the key alleles to do the job, although admittedly you’d have to wait a few thousand years to complete the process.

Logically, the easiest way to do this would be to encourage some young Tibetan men to immigrate to the Andes. Clearly, men can be more effective at this than women. We could pay them to donate to the local sperm banks. We could subsidize the process, _giving cash rewards to the mothers of part-Tibetan kids, a la the Howard Foundation_ [lmao]. We could give our heros Corvettes. Considering the general level of discontent in Tibet, it might not be too hard to recruit young men for this kind of work.

The project would take longer than the usual NIH time horizon, so probably the best approach is to find some wealthy sponsor. You could get a sure-fire version of this program going, one big enough to make ultimate success a racing certainty, for under a million bucks. The backer would never see the end result, but so what? When we build, let us think that we build forever.

https://westhunt.wordpress.com/2014/08/07/powerful-stuff/
I was thinking again about that Denisovan allele of EPAS1 that plays a big role in Tibetan altitude adaptation. Considering modern humans, it has only been found in Tibetans (high frequency) and in the Chinese (couple of percent). The preferred model in the paper is that it entered the common ancestors of Tibetans and Han, rising to high frequency among the Tibetans because of its advantage. I doubt this: the authors are clinging to a claim of a recent split in a previous publication of theirs – but the idea that the modern Tibetans are a fusion of a Han-like population with a long-established group of Tibetan hunter-gatherers seems more likely to me. So the few copies of the high-altitude EPAS1 allele among the Chinese are probably a result of recent gene flow, possibly from the Tibetan empire (618-841) that controlled parts of China, or from ethnic Tibetans identifying as Chinese.

This allele has some pretty powerful effects on the hypoxia response, which is there for a reason. The usual evolutionary rule is that change is bad: even though the Denisovan allele confers a big advantage at high altitude, the odds are that it is disadvantageous at low altitude. This would explain why it is rare in China and apparently unknown in Japan. This would also explain why it never made it to the Andes – even though there might have been a copy or two in the long-ago East Asian ancestors of the Amerindians, who have a bit of Denisovan admixture admixture (at least, I think they do – interesting if that isn’t the case) , it would most likely have been lost in Beringia. Along the same lines, altitude adaptations probably never managed to travel from Ethiopia to Tibet, which is why they have different approaches to altitude adaptation today.

It is therefore no surprise that this EPAS1 allele does not exist in Melanesians, even though they have 25 times as much Denisovan ancestry as mainland East Asians.

https://westhunt.wordpress.com/2016/12/11/tibetan-mastiff/
The Tibetan Mastiff can take high altitude better than generic dogs, or so breedists would like you to think. Some of the genetics changes are similar to those seen in human Tibetans – regulatory changes in EPAS1, for example. Domesticated dogs haven’t lived in Tibet all that long – but wolves have. The Tibetan Mastiff picked up some of those useful variants from local wolves, even though the amount of admixture wasn’t large. Adaptive introgression, just as Tibetans seem to have acquired their high-altitude version of EPAS1 from Denisovans.

Andean Indians didn’t have any archaic humans around to steal adaptations from. They have had to develop their own altitude adaptations (in a relatively short time), and they aren’t as effective as the Tibetan adaptations.

Naturally you are now worrying about sad Inca puppies – did they suffer from hypoxia? There are canids in South America, like the maned wolf and the bush dog, but they are probably too divergent to be able to hybridize with dogs. The chromosomes are different, so pre-Columbian dogs probably couldn’t acquire their alleles. Moreover, the dogs of the Amerindians seem to have done poorly in competition with Eurasian dogs: I know of only a few breeds [the Carolina Dog, for example] that are known to have significant pre-Columbian ancestry. Perhaps Amerindian dogs were also scythed down by Eurasian diseases.
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may 2017 by nhaliday
Faces in the Clouds | West Hunter
This was a typical Iraq story: somehow, we had developed an approach to intelligence that reliably produced fantastically wrong answers, at vast expense. What so special about Iraq? Nothing, probably – except that we acquired ground truth.

https://westhunt.wordpress.com/2013/06/19/faces-in-the-clouds/#comment-15397
Those weren’t leads, any more than there are really faces in the clouds. They were excuses to sell articles, raise money, and finally one extra argument in favor of a pointless war. Without a hard fact or two, it’s all vapor, useless.

Our tactical intelligence was fine in the Gulf War, but that doesn’t mean that the military, or worse yet the people who make and influence decisions had any sense, then or now.

For example, I have long had an amateur interest in these things, and I got the impression, in the summer of 1990, that Saddam Hussein was about to invade Kuwait. I was telling everyone at work that Saddam was about to invade, till they got bored with it. This was about two weeks before it actually happened. I remember thinking about making a few investments based on that possible event, but never got around to, partly because I was really sleepy, since we had a month-old baby girl at home.

As I recall, the “threat officer” at the CIA warned about this, but since the higher-ups ignored him, his being correct embarrassed them, so he was demoted.

The tactical situation was as favorable as it ever gets, and most of it was known. We had near-perfect intelligence:: satellite recon, JSTARS, etc Complete air domination, everything from Warthogs to F-15s. . Months to get ready. A huge qualitative weapons superiority. For example, our tanks outranged theirs by about a factor of two, had computer-controlled aiming, better armor, infrared sights, etc etc etc etc. I counted something like 13 separate war-winning advantages at the time, and that count was obviously incomplete.. And one more: Arabs make terrible soldiers, generally, and Iraqis were among the worst.

But I think that most of the decisionmakers didn’t realize how easy it would be – at all – and I’ve never seen any sign that Colin Powell did either. He’s a “C” student type – not smart. Schwartzkopf may have understood what was going on: for all I know he was another Manstein, but you can’t show how good you are when you beat a patzer.

https://westhunt.wordpress.com/2013/06/19/faces-in-the-clouds/#comment-15420
For me it was a hobby – I was doing adaptive optics at the time in Colorado Springs. All I knew about particular military moves was from the newspapers, but my reasoning went like this:

A. Kuwait had a lot of oil. Worth stealing, if you could get away with it.

B. Kuwait was militarily impotent and had no defense treaty with anyone. Most people found Kuwaitis annoying.

C. Iraq owed Kuwait something like 30 billion dollars, and was generally deep in debt due to the long conflict with Iran

D. I figured that there was a fair chance that the Iraqi accusations of Kuwaiti slant drilling were true

E. There were widely reported Iraqi troop movements towards Kuwait

F. Most important was my evaluation of Saddam, from watching the long war with Iran. I thought that Saddam was a particular combination of cocky and stupid, the sort of guy to do something like this. At the time I did not know about April Glaspie’s, shall we say, poorly chosen comments.
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april 2017 by nhaliday

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