Open Thread, 7/31/2016

They say to write about what you know. One thing I know are peppers, and hot sauce. So in addition to my writings on genetics, history, and assorted odds & ends, probably more pepper writing than before.

Class is important, but it doesn’t seem to be a good organizing principle around which an organic social movement can develop, like race or religion. The Soviet Union and Peoples’ Republic of China have both evolved into nationalistic states because the ideology of Communism never erased, and in fact only complemented, the nationalist ethos which served as the true substrate of the modern polities.

The is an important book because it gives an impression of the possibilities of much of the human future. These poor white people can be described in unvarnished terms because they’re white, and white people can be described somewhat objectively. Their world is in crisis, as the world economy leaves them behind. The golden age of well-paid unskilled and semi-skilled work is gone. The future is uncertain, and without dignity.

This is the lot of the bottom 90 percent of all races. But because class can’t motivate human emotions in the same way as race and religion, we might see a return to more nationalist organizing principles in the near future because the elites really don’t have anything to give in terms of dignity and economic hope to the masses. Yes, they’ll live at a marginal consumer level, but they won’t obtain honor and self-worth through work, because they will have been rendered redundant by productivity gains and globalization.

I had a discussion about gentrification at a start-up event recently. As a gentrifier and small-l libertarian I don’t have a problem as such with gentrification. My interlocutor had local roots, and talked about the dislocation imposed upon his maternal Mexican American side. I was sympathetic, but, I suggested that America is a global nation, and a diverse one. He made the case for non-economic social capital, and cultural cohesion, and I suggested that sounds a lot like the sort of thing working class whites might also offer up for why mass immigration is a problem (he was taken aback by the analogy).

Ultimately the public discussion tends to avoid the hard questions. And that’s why we’re where we are.

A tutorial on how (not) to over-interpret STRUCTURE/ADMIXTURE bar plots. Unless you’ve produced a lot (a lot) of these plots, please read this. Whether you read my blog, or plan to do admixture analysis in the future.

The Strange Rites of the Ancient Olympics.

The domesticated brain: genetics of brain mass and brain structure in an avian species.

The lack of progress in science: sex differences

The above visualization is from a Reddit thread, Almost all men are stronger than almost all women. It’s based on grip strength, and basically reiterates my post from last year, Men Are Stronger Than Women (On Average). The same metric, grip strength, is highlighted. The plot above shows that the “great divergence” occurs on the cusp of puberty, exactly when secondary sexual characteristic of males and females become much more pronounced. In my post I pointed out that the Olympic caliber female German fencers were on the lower end of the male distribution.

This came to my mind when reading this nice piece in The New York Times Magazine, The Phenom: The most dominant swimmer in the pool this summer is 19-year-old Katie Ledecky. The question isn’t whether she’ll win, but by how much:

It’s not unusual for men and women swimmers to train together, but being in the pool with Ledecky is something that many men can’t handle. In April, Conor Dwyer, a 6-foot-5, 27-year-old American swimmer who won a gold medal in the 4-by-200 freestyle relay in London, gave a revealing interview posted online by USA Swimming. In it, he talked about male swimmers being “broken” by Ledecky when they practiced together at the Olympic Training Center in Colorado Springs.

Ledecky’s ability to crush men in practice does not necessarily mean she would defeat them in competition. There’s a difference between imposing her will, and perhaps superior conditioning, over the course of a two-hour practice and doing it in a shorter race in which men’s generally greater strength provides an advantage. Her best chance would probably be in the 1,500 freestyle, which women race at the FINA World Championships but not at the Olympics. (The men don’t swim the 800 in the Olympics, so there are the same number of events for male and female swimmers.) Ledecky’s best time in the event would put her among the dozen or so top American men and is 25 seconds faster than their qualifying time at the United States Olympic trials — but it is much too slow to earn a medal at the Games. On the other hand, because no other woman offers a real challenge to her, she is never pushed in that event. I asked Andrew Gemmell, who specializes in the 1,500 free, a hypothetical question: What if, in some dystopian swim universe, Ledecky was told that there would be no women’s events and that she would have to try to make the American team by competing with the men in the 1,500?

His father, who trains her, had told me that he did not think she could qualify, a feat that under current rules would require her to finish first or second at the trials. Andrew, who trains side by side with her, had a different answer. “It would be really difficult, but I would never bet against her,” he said. “I don’t think anybody knows yet what she’s capable of.”

I’m a little surprised honestly that the term “dystopian” got in there, because there are now people with academic appointments arguing for the ending of sex segregation in sports. Often they are sociologists, who believe all things are socially constructed, and take some element of non-binary aspect to gender to meaning that the distribution of possibilities are entirely flat and arbitrary.

Katie Ledecky has preternatural gifts, as well as opportunities afforded to her by her class status. The whole piece highlights Ledecky’s exceptional physical abilities and mental attributes. But even it acknowledges she would likely not beat the top men in her events.

One of the authors of the above book, , Adrienne Milner, was interviewed last year on NPR about the thesis. The interviewer was polite, but a little incredulous. When he brought up biological differences, her response was illuminating, after a fashion.

First, she argued that sex segregation in sport denoted women’s inferiority, and that was a problem. The fact is that when it comes to strength, especially upper body strength, all the data do suggest that women, on average, are markedly inferior to men. This is a fact. This fact causes problems. But the fact that this fact causes problems does not entail that we literally deny the fact. At least that’s my opinion.

Second, she analogizes sex and gender as social constructs to race as a social construct. I knew she was going to go there, because this is a rhetorical nuclear option which is going to quickly defenestrate interlocutors. She observes that:

“We look at race as a social construction. It is not genetic, it is not biological, and we believe the same is [true] for sex … The male-female dichotomy doesn’t cover everyone, right? We have trans people, intersex people.”

As I said above, the reporter was incredulous, but he had a hard time responding after Dr. Milner explicitly connected race and sex, because it is the mainstream position now that race is a social construct and lacks any biological basis. The facts may not be on Milner’s side, but she has the theory and the “moral arc of history” backing her. It would take great courage to still dig in and defend reality as it is, as opposed to her preferences.

The reality is that race and sex/gender are social constructs. The atom is a social construct. Matter and energy are social constructs. Cities are social constructs. Everything is a social construct, as we look through the glass darkly. But social constructs operate on various levels of clarity and distinctiveness and exhibit different levels of pliability and utility. Dalton’s atomic model is profoundly wrong. It has long been superseded by quantum physical models, which have the utility of making correct predictions, whatever their correspondence to reality on a metaphysical level might be. But the Daltonian model is still often implicitly the one introduced to children to allow them to gain some intuition as to the nature of how matter is constituted. In contrast, the metaphysical ideas of the ancients as to the material nature of the universe are both wrong, and, lacking in utility.

All models are wrong, but there are still superior and inferior models. Their measure is in how they correspond to, and predict, reality. Not how they correspond to our ethical judgements of how the universe should be.

Many sociologists dissent from this position. They’ve marched into the academy and taken it over. Because of their ideology that all things are social, they believe they can reshape the fabric of the universe through their own normative preferences. To me this is a problem. I struggle against it. Our deep human intuitions often reject, and recoil, against fragments of reality. But to successfully grapple with reality we need to attempt to understand reality on its own terms, not our own.

I may struggle in vain. Could it be the liberal Whiggish scientific moment in history is over? History is written by the winners, but perhaps in the future science will also be written by the winners. I’m not sure that the truth will win out. Perhaps the glass will become darker, rather than clearer. There are genuine difficult empirical questions about the nature of human variation and our dispositions, and how it relates to the values that we hold to be true. The fact that we’re still discussing sex segregation in sports and how it is unjust illustrates how far we’ve come in the solipsistic and socially constructionist direction.

Imagine that in the end of days all the mandarins will be sociologists, who come not to bring illumination of the truth, but to determine the nature of the truth for us to agree upon. Perhaps this is the true end of history, as humanity returns to an equilibrium where the bracing aspects of reality are shielded from the masses, which lay indolent in their delusions, while the technocrats and artificial intelligences confront the outside.

Yellowbird hot sauce should engage in some truth in advertising

is a pretty good hot sauce. As you can see it gives you quantity, and the quality is decent. But there’s a major problem with the serrano and habanero brands.

According to the scoville scale the habanero is about 10 times spicier than the serrano. That sounds about right to me. So if you buy a habanero sauce, it should be around 10 times spicier, right? Well, not exactly since a sauce has other ingredients. But, it should be considerably spicier, at least.

That’s not what I perceive in the brand. The serrano sauce is nearly as spicy as the habanero line. What’s going on? If you look at the ingredients serrano is listed first for its sauce, but habanero is not first. Carrot is first. A lot of hot sauces use carrot puree in their sauces, but I find that a lot of “habanero” sauces overwhelm you with carrot flavor so that you can say you bought a habanero sauce, without tasting much habanero.

I suspect that that adds a lot more serrano to that lien than they add habanero to that sauce. So the label is officially accurate, but when you buy the two sauces they are not that different in spice levels, because the concentration of capsaicin is actually pretty close.

Overall I would say that the isn’t worth it. The though is a good sauce. Because there’s a lot of pepper there is a fresh green flavor to it, and it’s not so sweet as some hot sauces. Like most good hot sauces there’s an astringency, but it doesn’t overpower.

The gods curse the sin of incest!

440px-Heraclius_tremissis_681357The Emperor Heraclius is a great man. It’s a shame most people don’t know more about him. His campaigns against the Persians in the early 7th century were truly audacious. But, he also lived long enough to witness the loss of Syria and Egypt. If you haven’t, I would highly recommend .

In any case, I was double-checking the marriage to his niece Martina because of some comments below, and came upon this interesting passage on Wikipedia:

Martina and Heraclius had at least 10 children, though the names and order of these children are questions for debate…

Of these at least two were handicapped, which was seen as punishment for the illegality of the marriage.

The coefficient of relatedness between uncles and nieces is 1/4. Twice as close as cousins, and the same as that between half-siblings. It isn’t entirely surprising that debilities would show up at this genetic distance, though two out of ten at that extreme might be a bit high.

Middle Eastern populations have higher recessive disease load

A new paper in Nature Genetics, Characterization of Greater Middle Eastern genetic variation for enhanced disease gene discovery, is both interesting and important. But, as with the paper on the Andaman Islander genomes it starts out with a naive and misleading utilization of model -based clustering to frame the later results. Here’s a major offending section:

The least admixed samples were found in the NWA, AP, and PP subregions, suggesting that populations in these regions are derived from founder populations, but there was evidence of inter-regional variation in GME-specific components, suggesting the occurrence of local admixture (Fig. 1b) and potentially supporting historical events. The NWA component was found in regions from west to east across North Africa, likely representing the Berber genetic background…The AP component likely represents ancestral Arab populations and was observed in nearly all regions, possibly as a result of the Arab conquests of the seventh century coincident with the expansion of the Arabic language now spoken over much of the GME. Similarly, the Persian expansion into the TP and SD regions and parts of NEA in the fifth century was the most likely contributor of the PP signal.

Patterns of human migration and drift were recapitulated using TreeMix for GME subregions, on the basis of 1000 Genomes Project control populations…The inferred tree with no migration showed tight clusters for European and Asian populations but much greater apparent divergence among subjects from GME regions. The ordering of the GME subregional populations from the root corroborated much of the ‘out-of-Africa’ ordering of subsequent founder populations…For GME populations, distance from the root emulated the west-to-east organization of GME samples, with the PP population showing the largest inferred drift parameter, supporting a west-to-east trajectory of human migrations.

You can’t assume that a population which is near fixed for a cluster, K, is actually not admixed. If you don’t have enough variation within your data set then the ‘least admixed’ populations will come out as similar to the reference, even though they themselves are admixed.

Second, I am quite open to the idea that the Arab conquests of the 7th century were demographically significant, but these results don’t show that. The Tuscan population is not 25% Arab, due to the Arab conquests. Additionally, Arabs did not permanently alter the interior of Anatolia. Their raids went rather rather far to the west, such as the one of Amorium, but the high water mark of Arab rule in relation to the Byzantines, arguably in the decades around ~800 A.D., simply resulted in a “no man’s land” along the borders (though some Semitic peoples, some of them Arabic speaking, of Christian background did migrate into Byzantium).  Similarly, the Persian-Pakistani modal cluster has nothing to do really with the Persian Empire.

This is not a big deal, but, these passages are just silly. They’re wrong on the face of it. But the “peer reviewers” that Nature Genetics assigned to this paper were probably not well versed in human historical phylogenomics. Probably they saw that the methods were sound in the broadest sense (e.g., Admixture, Treemix, PCA, etc., are all fine methods), and were unaware that the inferences made were totally wrong. Anyone who had read Lazaridis’ et al.’s The genetic structure of the world’s first farmers would see how these passages needed to be revised and changed. The clusters in admixture above are to a great extent artifacts (useful ones for GWAS, but still artifacts). The historical inferences made have little basis in reality.

Second, the genetic pattern of variation above has nothing to do with the “out-of-Africa” migration. Rather, it has to do with the fact that there is cryptic Sub-Saharan African admixture even in the “pure” samples from some regions, because Sub-Saharan admixture is rather well mixed in some groups (e.g., in Northwest Africa). The cline is less about “out-of-Africa,” and more about a cline of African ancestry. These patterns of variation have literally nothing to say about the “out-of-Africa” migration. The whole passage should have been excised.

ng.3592-F3It’s a shame that there’s all this wrong stuff in the paper. I’m a big fan of Jean-Laurent Casanova because his medical genetics is going to make a difference in lives, and, his hairdo is awesome. Andy Clark is on the paper, he’s my St. Jerome for having co-authored . I feel a little ridiculous making these criticisms, but I think I’m right, and it’s a shame that the authors didn’t have anyone who knew enough human population genomics to fix this portion of the paper, and it’s a shame that Nature Genetics couldn’t find peer reviewers to steer them the right direction.

Aside from the the random wrong historical inference stuff, the paper is kind of a big deal (I think Nature Genetics worthy, but I don’t know anything about this stuff in regards to publications). It confirms in the broadest outlines a lot of what we knew. The further you go from Africa the less genetically diverse populations get when it comes to looking at polymorphism diversity. Native Americans have fewer segregating polymorphisms than Eurasian populations, for example. One way to model this is as serial bottlenecks out of Africa. I think that’s too simple of a picture, as there has been a lot of gene flow and admixture over the last 10,000 years, but on the coarsest of all scales it’s not totally misleading.

But a peculiar aspect of these dynamics is that when you look at runs of homozygosity in the genome, which usually measure more recent inbreeding, the Middle East and South Asia tends to have higher lower genetic diversity. To get a sense of South Asian populations, you can read The promise of disease gene discovery in South Asia. Because of caste/jati endogamy a lot of the South Asian groups have less genetic diversity than you might expect. This has disease implications.

Middle Eastern, North African, and Pakistani populations are even more extreme. You can see it in the figure above. Across short runs of homozogosity the results converge onto what you’d expect, roughly. But Middle Eastern populations are a huge anomaly at long runs. That’s because of this:

From 20–50% of all marriages in the GME are consanguineous (as compared with <0.2% in the Americas and Western Europe)1, 2, 3, with the majority between first cousins. This roughly 100-fold higher rate of consanguinity has correlated with roughly a doubling of the rate of recessive Mendelian disease19, 20. European, African, and East Asian 1000 Genomes Project populations all had medians for the estimated inbreeding coefficient (F) of ~0.005, whereas GME F values ranged from 0.059 to 0.098, with high variance within each population (Fig. 2c). Thus, measured F values were approximately 10- to 20-fold higher in GME populations, reflecting the shared genomic blocks common to all human populations. F values were dominated by structure from the immediate family rather than historical or population-wide data trends (Supplementary Fig. 8). Examination of the larger set of 1,794 exomes that included many parent–child trios also showed an overwhelming influence of structure from the immediate family, with offspring from first-cousin marriages displaying higher F values than those from non-consanguineous marriages (Fig. 2d).

Screenshot 2016-07-28 20.09.42The authors masked alleles which were part of the reason that individuals were included in the data set in the first place (to prevent ascertainment bias). Rather, they were focused on genome-wide patterns of loss of function and derived alleles. Because they were looking at many low frequency variants naturally they found a lot of new variation, totally unobserved in European dominated genetic data sets. This is why bringing genomics to the world is kind of a big deal.

For me this was the most interesting, and sad, result:

Despite millennia of elevated rates of consanguinity in the GME, we detected no evidence for purging of recessive alleles. Instead, we detected large, rare homozygous blocks, distinct from the small homozygous blocks found in other populations, supporting the occurrence of recent consanguineous matings and allowing the identification of genes harboring putatively high-impact homozygous variants in healthy humans from this population. Applying the GME Variome to future sequencing projects for subjects originating from the GME could aid in the identification of causative genes with recessive variants across all classes of disease. The GME Variome is a publicly accessible resource that will facilitate a broad range of genomic studies in the GME and globally.

The theory is simple. If you have inbreeding, you bring together deleterious recessive alleles, and so they get exposed to selection. In this way you can purge the segregating genetic load. It works with plants. But humans, and complex animals in general, are not plants. More precisely the authors “compared the distributions of derived allele frequencies (DAFs) in GME and 1000 Genomes Project populations.” If the load was being purged the frequency of deleterious alleles should be lower in the inbreeding populations. It wasn’t.

Middle Easterners should stop marrying cousins to reduce the disease load. But that’s just a recommendation. Some of these nations, like Qatar, have a lot of money to throw at Mendelian diseases. Perhaps they’ll use preimplantation genetic diagnosis? I don’t know.

Frieda’s ghost peppers are great

ghostRecently I was at the supermarket, getting some shrimp at the fish counter. The clerk noticed I had some habanero peppers, and he asked if I’d checked out the ghost peppers. My interest was piqued, but I had no idea what he was talking about. He told me to look at again.

They were Frieda’s ghost pepper chilis. My first question: are these really ghost peppers? Comparing to the standard orange habaneros you’d get at the supermarket I’d stay these peppers were about three times as spicy. So probably real ghost peppers then. But here’s the great thing: there was a tangy astringency which made them much less bland that mass produced orange habaneros. The pepper was legitimately delicious.

The main caution I’d give is that what goes in easily may not come out with grace and comfort.

Ancient archaic admixture into the Andamanese

Screenshot 2016-07-25 21.52.42
Update: If Pontus Skoglund fails to replicate your results it is not an optimal outcome….

end update
A new paper on on archaic admixture in Andaman Islanders has come out. It’s in Nature Genetics, Genomic analysis of Andamanese provides insights into ancient human migration into Asia and adaptation. If you don’t have access, just read the supplements, they have the good stuff as usual.

The results here range from intriguing to clarifying. But I want to engage in a little post-publication criticism: I think the fact that the authors highlighted model-based admixture results is a disservice to the rest of their results. will be out with a paper on best practices (or not) in relation to the utilization of model-based admixture soon enough, but the plot that is part of figure 1 is really in my opinion misleading in the broader context of their results. The JAR and ONG are Andamanese samples, while ILA and BIR are isolated tribal group in south to central India. These four groups are not very numerous, and, they are characterized by very small effective populations. In other words, the model-based admixture framework immediately infers these to be extremely close to idealized reference populations because they are so drifted. One can call this the “Kalash effect”, as the original STRUCTURE based analyses of the middle 2000s would routinely yield a “Kalash cluster.”

One consequence of the mix of populations that they have in this reference panel is some of the results are difficult to interpret. The Andamanese and Irula (a South Indian tribe) become nearly fixed for a major cluster respectively, and in the text the authors are interested enough to observe that these Andaman samples don’t show admixture because of this result. This is not necessarily true though. If these are the ‘purest’ of the samples that remain, then they will serve as the ‘pure’ reference. That doesn’t mean there hasn’t been recent gene flow into them. The same with the Irula. Because these two are highly drifted populations they are quite often going to arrive at these very high fractions in some particular K cluster.

Because of the large sample these rather obscure tribal groups, you have the result that Rajputs seem to share more ancestry with Chinese than the Bengalis (RAJ and BEN). This is in contradiction to everything we know. In reality, the Rajput samples have very little recent East Asian admixture, while the Bengalis are about ~10% East Asian on the time scale of the past one to two thousand years. I can offer a hypothesis for why the clustering algorithm converged on this result, but I’ll just suggest you read Lucy van Dorp’s Evidence for a Common Origin of Blacksmiths and Cultivators in the Ethiopian Ari within the Last 4500 Years: Lessons for Clustering-Based Inference.

But what of the results overall? The intriguing aspect is the evidence that there is archaic admixture into the Andamanese, Australian indigenous peoples, and to some extent Indians (via their “Ancestral South Indian”) form a mystery hominin. The time scale they infer is on the order of divergence at least several hundred thousand year ago in the past. Presumably these results became clear because they had good high quality whole genome sequences (~10x and more coverage) with millions of SNPs to work with (and well ascertained), as opposed to the few hundred thousand in earlier work.

One of the models the authors were testing is the idea that there were two waves out of Africa, with South Asian and Oceanian peoples in particular exhibiting hallmarks of admixture from an earlier migration. There are smattering of population genomics papers which support this proposition, but I will tell you most researchers who work with these data are skeptical. There were some methodological issues with some earlier findings, and limitations on the sample sizes and quality (whole genome sequence), or marker set (the SNP studies).

By and large these results support the idea of one migration. If one assumes Africans are one branch of the modern human race, all non-Africans are approximately equally related to Africans, because there is one major bifurcation between Africans and non-Africans. In contrast, the two migration thesis often posits that there was an earlier migration, that was later overwhelmed by a later migration. In that case, you might have scenarios where the second population shared more genetic drift with modern Africans because of a later separation. Or, there could be a scenario where the South Eurasian substrate shared more drift with Africans, shifting the affinities of the Andaman Islanders in that direction.

In any case, they did not see evidence of any of this. Rather, Andamanese share no more ancestry with Africans than you’d expect of generic non-Africans…sort of. As it turns out when using an outgroup with only ancestral allelic states as inferred from using the chimpanzee reference Andamanese actually have fewer African alleles that Europeans and East Asians. The same is true of indigenous Australians, though the authors did not tackle this issue in detail. Of course this could be Neanderthal and Denisovan ancestry. But it isn’t. We have the ancient genomes of these populations, and the Andamanese seem typical for a East Eurasian population.

They make the inference of a few percent admixture from a population which diverged from modern humans on the order of ~300,000 years ago through a lot of testing of explicit models. Again, read the supplements. Unfortunately they don’t have the genome of the mysterious ghost population, so they can’t make definitive conclusions.

The fact that East Asians and Europeans both lack this ancestral element is peculiar, because all the evidence puts the Andamanese on the same branch as the East Asians. So you can have models whereby a composite East Asian/European population engages in back migration to Africa. Or, perhaps Ancient North Eurasians, who contributed to both Europeans and East Asians? In any case, of the models they tested it does seem that archaic admixture from a ghost population is the most likely, but that does not mean that that is the correct answer. Obviously they did not exhaust the possibilities of models and scenarios. For several years now people have been seeing strange things in the data from Australasian and isolated Southeast Eurasian groups. There’s a story here, we just don’t know much of the outlines, we’re just grasping. Both Mait Metspalu and Luca Pagani have papers in the works….

What about the clarifying? It strikes me that they used some stringent selection tests (e.g., focusing on hard sweeps?), and still hit pay-dirt on positive results for the Andamanese. Both selection tests, and polygenic scores, suggest there’s a bias toward being small in these two groups. I’m curious if the Sentinelese would be the same. The thesis here is that islands result in dwarfism. But I wonder if the selection here is very recent indeed. The authors note that some of the sweeps are not complete. In the last few hundred years there has been a massive demographic collapse of the Andaman Islanders, and only the Sentinelese preserve their lifestyle in a pristine fashion.

This relates to the question in regards to phylogenetics. The authors indicate the the phenotype of these Austro-Melanesian populations is not necessarily due to shared descent from Africans, but adaptation to local circumstances. I don’t think they’ve proven it as such, but they’ve definitely shown that there’s a lot of selection occur in their new habitats. Curiously they don’t detect that there’s been adaptive introgression from the archaic, but I’m not sure if they have the power to detect that sort of thing anyhow. But, it might indicate that the admixture occurred further north?

Finally, I should mention that the Andamanese genomes are now online.

Class status matters more for success than performance

Though Nassim Taleb is more well known for , I actually liked his earlier book , better. It seemed aimed toward more general issues than .

One of Taleb’s hobby-horses in is that the book was based on faulty inferences, and misleading many people. This was back in the heady days before the property bust, so many middle class individuals were investing in the “can’t miss” and eternally appreciating real estate bubble. In any case, had a simple strategy: observe the characteristics of millionaires, and so gain insight into what might make you a millionaire. The problem pointed out by Taleb is that the sample set is highly biased; you see all the millionaires with the characteristics of interest, but not the more numerous non-millionaires. One of the major variables, perhaps the major variable, in becoming a millionaire is what we’d all luck. There may be many necessary conditions, but luck is one we can’t cultivate. One might increase the chance that one is a millionaire…but misled many people into thinking that just by doing what millionaires had done any person could become on themselves.

So consider this from The Wall Street Journal, Best-Paid CEOs Run Some of Worst-Performing Companies:

The analysis, from corporate-governance research firm MSCI, examined the pay of some 800 CEOs at 429 large and midsize U.S. companies during the decade ending in 2014, and also looked at the total shareholder return of the companies during the same period.

MSCI found that $100 invested in the 20% of companies with the highest-paid CEOs would have grown to $265 over 10 years. The same amount invested in the companies with the lowest-paid CEOs would have grown to $367. The report is expected to be released as early as Monday.

The original report is also online. There are other studies which support this conclusion. The correlation between CEO pay and firm performance is relatively weak to non-existent.

Does this mean CEOs are worthless? Not necessarily. There’s some range constriction going on. The average person on the street wouldn’t have the minimum necessary skills and aptitudes to be a CEO of a large firm. But the variation among CEOs in pay might be due to a whole different set of skills than the characteristics which constrain the set of individuals who might become CEOs. For example, the average CEO might be far more conscientious and intelligent than the average person. But, it may be that the less conscientious CEOs actually get paid more. And then of course there is luck in falling into a good board situation, which anchors you to a particular set point in terms of future salary expectations. And the outcome of a firm may have only the most marginal relationship to the CEO performance (consider how we attribute macroeconomic performance to American presidents, when they probably have only marginal influence on the business cycle).

And once you make it into a particular class, social connections can help prevent you from sliding back down. To a great extent the same of Yahoo to Verizon is a failure for Marissa Mayer. But she’ll be fine, and obtain another CEO position if she so chooses. If she had turned around Yahoo, always a long shot, she would have been dubbed a genius. As it is, she’ll get a golden parachute and look to future opportunities.

What’s the take-home less? Social mobility is a thing in the United States. But the reality is that what you really need to do is somehow make it into a particular segment of the class structure. Once you are there, the reality is that your own competence probably matters less than chance and necessity. Even if you don’t become a superstar, the nature of the American class structure will probably make it so you’ll be shielded from the bracing consequences of creative destruction.

Open Thread, 7/24/2016

When people ask me what they should read to understand genetics, I don’t really know what to say. But is what I reviewed for my genetics qualifying exam. If you want to understand what PCA is, the Wikipedia page should suffice, especially if you have taken linear algebra. Perhaps ironically for someone interested in evolution and genetics I’ve read only a few textbooks devoted to these topics. Rather, I try and read papers. And with the preprint revolution there’s really far less of an excuse to not engage with the literature in such a direct fashion if you are interested.

re: question about inferring admixture from allele, as opposed to genotype data. One could convert to diploid genotype. Or, one could use a PCA based admixture method which takes allele data as inputs.

. In China.

finished with a bang. I’d recommend it, though it is a difficult and frustrating read. Even being conditioned by the previous books that the protagonist is pretty creepy, it went even further in . But R Scott Bakker shines where you’d expect, in world-building and haunting evocations and expositions of what had heretofore been beyond the horizon. In particular the sections in Ishterebinth illustrate Bakker’s ability to take a tired trope, elves (he calls them nonmen), and transform it into something novel and multi-textured. Interestingly, as I was reading these sections I began to think that the nonmen looked just like the engineers in the world of the Alien films, and someone also added that observation to their entry in the wiki.

is kind of like reading . It’s hurtling toward tragedy. For the section on the “Great War in Africa” I’d just recommend . One might ask, why read books like this? Because to confront reality is hard, but to understand the world one must expose oneself to horrible truths.

One of the aspects of American culture that I have long disliked is the inability to acknowledge that democratic polities will naturally lead to an element of populism, and the people are often illiberal. The Founders were aware of the pitfalls of democratic populism, but the skepticism of the 18th century gave way to the embrace of democracy in the Age of Jackson. I’ve long been skeptical of this, but it’s interesting to watch people attempt to deny legitimacy to popular will where in other cases that is all that matters.

Joshua Schraiber is looking to get some post-docs.

In other news, why do people with Ph.D.s aim to get post-docs so that they can get a job in the private sector? Shouldn’t the 5+ years in a Ph.D. program in the biological sciences train you for jobs outside of academia? If not, then we’re doing it wrong.

I don’t talk about contemporary politics much. That’s because I don’t have much to say. On some topics, such as international affairs, not to be immodest, I’m actually more well informed on history and ethnographic detail than many people who write columns. But because I know a fair amount I’m also conscious of how little we can say concretely. Stuff happens. Big coarse heuristics are probably for the best, because this isn’t like sending a probe to Jupiter. We just don’t have a good grasp of mechanics. As for domestic politics, my current attitude is to ask my friends every now and then what’s happening. My time is better spent on intellectual interests, working, and spending time with my family.

So are there neighborhoods where kids hang around on the block? A suburban cul-de-sac? That’s the childhood I want for my kids, but the streets seem to be empty of children. Are they playing video games?

Uncle Sam Wants You — Or at Least Your Genetic and Lifestyle Information.

Someone asked me about a few weeks back. Everything seems to moving in directions you’d predict. I suspect that much of the narrative in the book is not going to be so pat. The show-runners for the HBO series seem to want to squeeze an incredible amount into the last two seasons, while Martin has at least two books to go, and probably three (his books are barely physically feasible, there are so many pages).

One thing watching the television show has impressed upon me: the average IQ of people watching television is much lower than those who read books. The “theories” promoted by those who primarily watch the television show are often far stupider than anything I remember from the message boards of the late 1990s and early 2000s, when those who read the books came up with plausible models such as R+L=J.

Unlike most of my friends I don’t have a problem with gentrification. If a city is expensive, then only people who can afford there should be able to live there. That might impact the cost or availability of services provided by low wage earners, but that’s just how life goes. But being a gentrifier myself it’s interesting to see neighborhoods in transition. The demographic switch can happen very rapidly (e.g., if I see young white women on a block I assume it’s safe). But there is the phenomenon of established businesses often being geared toward the lower-income population that was previously dominant. Eateries and churches might still be frequented by old-timers, who hang around in some way almost as ghosts, strangers in the neighborhoods that grew around them.

The Kindle version of was free yesterday, so I bought it. There are some awesome things going on in space right now, and it’s fascinating to look back to a time when this was the science which captured the public imagination. It strikes me we are in the golden age of planetary probes, so who is the Richard Dawkins of this field?

The whole DNC email leak and Debbie Wasserman-Schultz resignation strikes me as strange. Obviously I don’t follow politics, because everyone knew they were engaging in these shenanigans. Is it different because we know for a fact?

Detecting Heterogeneity in Population Structure Across the Genome in Admixed Populations. I think the method is a bit under-powered…but I think that’s because local ancestry deconvolution hasn’t progressed that far in the past 3-4 years. I hear things will change soon. Also, high-quality whole genome sequences will change things.

Evolution Is Happening Faster Than We Thought.

I’ve started a Blue Apron subscription. Pretty impressed so far in that it has “nudged” me to start cooking.