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510bcY7t15L I spruced up my personal website recently. It was getting sort of cluttered. Also, the new theme should look better on mobile.

Not sure how long Twitter will be around, but as long as it’s around, make sure to follow me.

Screenshot 2016-11-27 00.59.01 Got my copy of The Atheist Muslim: A Journey from Religion to Reason. I’m personally opposed to a term like “atheist Muslim,” because a Muslim by definition to me is not atheist. But the author, Ali Rizvi, is an interesting fellow.

Going to try and get to Land of Promise: An Economic History of the United States before Christmas. Don’t know if I’ll get to it, but it’s been on my “to-read” list for a while.

Has anyone ever thought that the novel Musashi was somewhat reminiscent of Cúchulainn? No idea why I think this, but it’s always been on my mind…

I think someone keeps asking about South Asian genetic signatures in Southeast Asia, and I keep forgetting to respond to them. I think there was old (say Iron Age) gene flow from South Asia to various parts of Southeast Asia (basically the cores of Hindu-Buddhist archaic semi-historical polities such as Angkor era Cambodia), and, also more recent gene flow due to colonialism era migration mediated by Europeans. Also, I suspect there was more gene flow from early Holocene Southeast Asia into South Asia than we currently comprehend.

2978777 Ten years after first reading it I appreciate Adam K Webb’s Beyond the Global Culture War more. Why? Probably because universal liberal democracy seems less assured as the final stationary state of society in all places now than it did then. It’s an interesting book in part because it attacks the global cultural element with which it is probably easiest to identify me with.

 
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ls Went to Z & Y in San Francisco recently. Second time. Still have to give Mala in Houston better marks. A friend who has been to both agrees.

Been busy working recently. But obviously a lot is going on in science and non-science….

 
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51jUZQV3r1L._SX329_BO1,204,203,200_ (1) Now reading Hume: An Intellectual Biography. David Hume was a man of moderation in his private life. Something to consider.

I was in New York City yesterday. I got a cab from the Upper East Side to Columbus Circle. The cabby did not anticipate the anti-Trump protest. When I said it was the anti-Trump protest probably, he turned around and said “Trump?” I said, “Donald Trump. You know.” He shrugged. By his accent I assume he was an African immigrant. I wonder if his English just wasn’t very good, as I have a hard time how you could be a cab driver in New York City and be surprised at who Donald J Trump was.

Met some friends. Some of them are in the ‘conservative establishment’, at least the more intellectual parts. They are cautiously hopeful. Or hoping for the best.

If you are a Trump supporter, perhaps this is a time to consider that tribal exultation will eventually fade and real life will again intrude. If you are a ‘conservative’, and not married, and without children, and above 30, perhaps you should consider what you need to do to get to a point where you can embody the values you purportedly support. If you are not a Trump supporter, and if you do have a family, perhaps you should reflect that at the end of the day the ultimate thing of substance is your relationship to them, and taking care of them. You have to get up every morning and work to support them, love them, and let them flourish. Politics is just a means toward the end of this sort of flourishing. But just one means.

510bcY7t15L I pre-ordered a copy of The Atheist Muslim: A Journey from Religion to Reason. Skeptical that one can be an “Atheist Muslim,” but the author is someone who I respect from Twitter, and it is important to read differing views. I myself am careful to state that I am not a “cultural Muslim” for two reasons. First, I am not part of the “Muslim community” in any way in my day to day life. I do not attend Muslim celebrations with my family in a nominal fashion. My children will have no affiliation to Islam except their surname indicating some connection to a South Asian Muslim. Second, unlike some people I do not have fond memories of a past life as a believer. I never really believed. My family as isolated enough that I was never part of the Muslim community anywhere that I lived. And my distaste for religion generally increased in a monotonic fashion as I grew into adulthood.

But other people have different experiences. So I’m curious.

Finally, I know people on all sides are binging on analysis of the election results. I understand. I get it. I just wish people would be more enthusiastic about immersing themselves in the life of the mind. People always ask me how I make time to be able to read. Some of the answer is prosaic. I stopped playing video games when I was sixteen. This is not without cost in hedonic utility and the ability to bond with people of my similar social profile. But it freed up a lot of time (similarly, I do not own a television, and have not for over ten years, so I don’t get caught up in passive viewing). Though I work a lot and have a family, various reasons allow for some level of flexibility in time allocation. And, unfortunately, I often do not sleep as much as I should.

But another reason I take time to read is that it is who I am, and who I have always been. I don’t read books and try to learn things to impress people or seem smart. I don’t really care that much about that stuff compared to actually knowing stuff. If that’s not important as an end in and of itself, and it isn’t for most people from what I can grasp (in contrast to winning arguments), that’s fine. But, I think a lot of people aspire to read more, and know more, because its important to them. If so, a little Buddhist or Stoic equanimity again the currents of the world really does help.

 
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Screenshot 2016-11-06 09.57.53

51deNffGPJL._SX327_BO1,204,203,200_ (1) My prediction above. Based on a few minutes scanning online. Also, I suspect that Trump supported is being overestimated. Low confidence that I’m adding value with my opinion.

After finishing Unfinished Empire: The Global Expansion of Britain I’m struck by the fact that the author had to make some criticisms of Edward Said’s Orientalism, because Orientalism is so weak on both details and overall theoretical framework. That’s why I dismissed it fifteen years ago when I read it, but today I have to say that Orientalism is the model of scholarly sophistication compared to what prevails today in postcolonial theory.

 
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51deNffGPJL._SX327_BO1,204,203,200_ I’m reading Unfinished Empire: The Global Expansion of Britain. Not as well paced as his previous After Tamerlane: The Rise and Fall of Global Empires, 1400-2000, but pretty good nonetheless.

Politics exhausts me. This is an exhausting time for me mentally as I’m overwhelmed by the din of political chatter and fixation. I’m very excited for November 8th to come and go.

There’s lots of stuff in science I want to write about, but the combination of lack of time, and politics saturation all over the place, has been demotivating me. So as the month proceeds I’ll probably get my energy back.

 
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2016-10-23 08.40.37 Bought Marie Sharpe’s green habanero sauce at Granville Market. The spice level is nothing to sneeze at, and it’s got a nice flavor. But the salt is out of control.

danbo There is a lot of good Asian food in Vancouver. A pretty good meal at the downtown Kirin, but I want to highlight Ramen Danbo. The servers were all young women from Japan, so the ambience and food exhibited an authenticity that’s not typical.

Annexation_Bill_of_1866_mapAfter four days in Canada I really don’t see why at minimum we don’t have a customs union and open borders so we can dispense with these sorts of friction to travel. Canadians are easier to understand in terms of their English for most people who speak General American than some of our fellow citizens. Vancouver in particular reminds me a lot of Seattle, a city I know decently well since I’m from the Pacific Northwest originally and still go back to visit family.

Pandora was blocked in Canada for some reason. And I had to call to make special provisions to maintain data on my phone. Really is there a reason for this?

I am struck by the colonialism described by Colin Woodard in American Nations when it comes to Reconstruction. In his telling Yankees swarmed to the South believing that they could recreate New England in the post-war societies. Eerily familiar in light of what happened after the Iraq War.

51y9UBanyFL._SX386_BO1,204,203,200_ Someone in a comment below asked what population genetics they should read. Start with Principles of Population Genetics. It’s the gold standard. Some people would suggest starting with Population Genetics: A Concise Guide, but I didn’t start with that and I’m fine.

Joe Felsenstein and Graham Coop have some good notes online.

Spent some time with “reiver” online. He seemed curious as to my ability to read a lot and read fast. There’s nothing very impressive or amazing about it actually. I’ve been reading a lot in several areas since I was an early elementary school student, and so I can read and process new information fast because I already have a lot of preexistent structure.

416NQwBS-+L._SY344_BO1,204,203,200_ But you can lose things. For example I read books on cognitive neuroscience more slowly than I used to because I stopped reading in this topic when I went to grad school. I’m a big fan of Stanislas Dehaene’s work, but I get less out of it than I used to. That’s unfortunate.

Overall I do worry that I’ve focused too narrowly in my interests as my brain has aged and I’ve matured. My knowledge of specific areas is deeper, but I am not as broad in my curiosity as I used to be.

ASHG was good. I’ll say more later, but the popgen was a little thinner than in previous years.

It was interesting that many seemed to know about the company I work for. The fact is that our canine genomic test is the most comprehensive and robust out there. That’s not marketing fluff, and geneticists can discern bullshit from reality pretty easily. So the discussions were more brass-tacks about the value customers. I had a pretty good case for why a purchase is justified or feasible, so easy discussions.

417otmYuMcL._SX303_BO1,204,203,200_ Reading about Poststructuralism, and having a hard time understanding how people take this stuff seriously. That’s a problem, because people do. Perhaps a validation of its weirdly grand take on the power of language to shape the structure of reality.

It will be nice to read about something different. In particular, functional programming. Need to get my NumPy skills up, as I spend so much time struggling with data-types.

 
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51I3Hux0TsL._SY344_BO1,204,203,200_ I reread Colin Woodward’s American Nations: A History of the Eleven Rival Regional Cultures of North America on the plane recently. It’s a less scholarly work than Albion’s Seed or The Cousins’ Wars: Religion, Politics, Civil Warfare, And The Triumph Of Anglo-America, but arguably more straightforwardly relevant to modern conditions and events. I’m rather sure that Woodward would be interested in a further edition which updated with the goings on of the 2016 election campaign, if he’s not working on it already (an important complement, Replenishing the Earth: The Settler Revolution and the Rise of the Angloworld, 1783-1939, which takes a broader Anglospheric view).

The important point here is that initially developed cultural folkways can be persistent and reinforcing. The author observes that Nordic immigrants seem to have almost invariably chosen the region of the American frontier dominated by a Yankee ethos, the Upper Midwest. Though they overwhelmed this region demographically, rather than changing the culture, they simply accentuated its longstanding features, which were established by Yankees (e.g., social progressivism and communitarianism).

What else is going on? Going to be at ASHG a lot this week.

 
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8412068Episode 728: The Wells Fargo Hustle. Elizabeth Warren is right, there won’t be any accountability at the top. Hope I’m wrong.

Started reading A New History of Western Philosophy last summer, but got bogged down in the medieval section. I started reading it last week and it’s going much faster now that I’m in the “modern” section.

Sensitivity of quantitative traits to mutational effects and number of loci.

Reference-based phasing using the Haplotype Reference Consortium panel.

The genetic history of Cochin Jews from India.

How the compact disc lost its shine.

Actually, Facebook’s New Craigslist Competitor Should Be a Little Debauched. How is it that CraigsList is still around?

Piece of carved wood suggests Persian taught maths in Japan 1,000 years ago.

Ages of Discord: My Third Independently Published Book (Peter Turchin’s).

A Review of Cognitive Abilities in Dogs, 1911 Through 2016: More Individual Differences, Please!.

 
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9780192805577Online Life Is Real Life, Aleph-Nought in a Series:

I thought of this while I was reading John Scalzi’s epic post about self-presentation, prompted by someone who complained that he behaved differently in person than that person had expected from Scalzi’s online persona. (Personally, having met John in person several times, I don’t see it, but whatever…) Scalzi rightly notes that there’s nothing at all wrong with this, and that much of the difference is (probably) just basic courtesy and politeness.

It’s a major pet peeve of mine that people deduce from what they see on this blog and Twitter to generate a full picture of whom I am. If the data you saw were representative, then that might be one thing, but they really aren’t. Rather, they’re strongly biased.

A long time reader (as in, back to the ScienceBlogs days) is someone who I now socialize with semi-frequently. One observation he makes is that I tend to engage in more unguarded bloviating in real life. That sounds about right. In real life everything I say is not recorded for posterity.

The basic insight thought is that there is much you don’t see when you consider just what you see.

When people engage in others, they use theories to fill in the background of their interlocutors. It’s pretty impossible not to do so. On the other hand, theories are always imperfect, and you shouldn’t get surprised when those who you theorize about are angry when your theories miss the mark.

One way that my “non-internet” and internet personas do align well is that I’m rather aggressive. If think you’ve mischaracterized me, I won’t be happy in person, or online.

I read Foucault: A Very Short Introduction on a plane last week. I have the “very short introductions” series a great deal (have also read Hegel). It strikes me they’re good to orient and refresh you before a deeper dive.

A commenter below dismissed the importance of the genealogy of intellectuals and their movements in comparison to mass culture. But reading Foucault: A Very Short Introduction you see clearly the lexical armamentarium on display decades before it would percolate to Facebook threads and MSNBC.

51k6n6ma-NL._SY344_BO1,204,203,200_ Reading about Postcolonialism, I’m really struck by the possibility its intellectual apogee was already attained by Edward Said in Orientalism. I read Said about 15 years ago, but dismissed the work. My objection? It was simply wrong on many facts. In hindsight, it strikes me that I was naive in regards to what people admired about Said’s work, and its significance. That is, it’s importance was not as a narrative about the historical past, but possibilities for narrative frameworks relevant for organizing the political present.

Campus debate on Black Lives Matter called racist, shut down by protesters (VIDEO). If state campuses are to be thought of as arms of the Left-progressive movement in America, I can’t see any reason for states where the majority of the population is not Left-progressive to continue funding them.

My friend David Bachinsky has a GoFundMe to help fight his brain cancer.

Next Big Tech Corridor? Between Seattle and Vancouver, Planners Hope. Next year in Jerusalem. There is only one. There shall be only one.

Pre-Industrial Societies Reward High Status Men With More Children.

ASHG in Vancouver in two weeks….

 
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4197TkGD1DL._SY344_BO1,204,203,200_ At a readers’ suggestion I got Explaining Postmodernism: Skepticism and Socialism from Rousseau to Foucault. Unlike The Dialectical Imagination this is not necessarily a detached academic book. Rather, the author has a definite perspective. About 20 years ago I read George H. Smith’s Atheism: The Case Against God, and there are a lot of similarities between the two books. From that I suspected before doing some research that the author had some influence from Objectivism, and that seems correct. I don’t care too much, and I probably broadly share the authors’ libertarian/classical liberal politics, but the middle sections of the Explaining Postmodernism got a little preachy for my taste.

Nevertheless the first half especially is excellent, and it outlines a genealogy of the Postmodern movement very concisely and in an illuminating manner. There are some details where one might quibble (e.g., the relationship of Immanuel Kant to religion is much more in dispute than presented in Explaining Postmodernism, though that’s a minor objection). But the progression of Transcendental Realism down to the morass we see around us today is a familiar story told more crisply here then elsewhere.

The author does outline a sociological origin for Postmodernism which is very intriguing, as it explains why it is an overwhelmingly far Left movement, despite the implications toward extreme relativism and subjectivism one might infer from the worldview. But there is something that is omitted here, perhaps because the author was not aware of this fact: there is a relationship of Postmodernism to elite intellectual religious revival in the past few decades.

418lqzfRjwL._SY344_BO1,204,203,200_ Alister McGrath is a proponent of this school, and outlines his thesis in The Twilight of Atheism: The Rise and Fall of Disbelief in the Modern World. To condense McGrath’s argument, if everything is a superstition, then people will fall back on the tried and true superstitions. McGrath asserts the collapse of the authority of rationality and philosophical realism signal the end of the Enlightenment project, and undermines the secular world. As an empirical matter there is a lot one can quibble with here; in particular, though Postmodernism may be vigorous in the academy, science and technology are concrete witness to power of naive realism and rationalist presuppositions. But McGrath’s position is philosophically cogent. And, it is not well known, but the doyen of modern Intelligent Design, Phillip E. Johnson, has admitted that the he was strongly shaped by Critical Theory:

I used to refer jokingly to myself as the entire right wing of the Critical Legal Studies movement, which in their view was a contradiction in terms. Their critique was purely the instrument of a left-wing political program, which was chosen arbitrarily and presumed to be good. It was a faith commitment.

So I’m reading a lot of things on Postmodernism. I’m going back to Hegel. On the one hand this is a major opportunity cost. There’s a lot of science and programming stuff I want to read that I don’t have time to read. On other hand, much that I was suspecting becomes very clear. Ultimately I’m respecting Postmodernism more insofar as it is a reasonable tool from what I can see in destroying certainty and realism for those who are innumerate. If you have any understanding of statistics you’re pretty insulated from Postmodernism. But very few people think statistically. I also now believe it is ultimately far more dangerous than before, because it is a serious intellectual tool that can deconstruct much that is precious and rare in the world. In particular, the Enlightenment project, which in many ways goes against the world historical grain, or at least the grain of human intuitions and preferences. Postmodernism as an intellectual exercise is easy to dismiss. But as a tool of political battle it has to be taken seriously.

A Single Migration From Africa Populated the World, Studies Find. I will blog these papers. It’s a question of time. Please don’t pester me on non-open threads about this stuff.

Widespread allelic heterogeneity in complex traits.

14390818_10153997292567984_5603508903928344619_nGunman kills Jordanian Christian writer charged over anti-Islam cartoon. The title is misleading, as the cartoon was making fun of jihadists, not Islam. He posted the cartoon on Facebook.

Chinese Jews of Ancient Lineage Huddle Under Pressure. Most of the Kaifeng Jewish community was absorbed into the Han, though some became Muslim.

Academic Research in the 21st Century: Maintaining Scientific Integrity in a Climate of Perverse Incentives and Hypercompetition.

Please use the “open thread” for random stuff. The OT comments early in threads are pretty annoying.

Also, if you follow me on Twitter if you tweet at me a lot, and I don’t respond, but you keep tweeting at me demanding a response, I’m probably going to block you. Also, I get annoyed at readers and Twitter followers who presume they know my state of mind or aspects of my life from what they see on the interwebs. If you do that and tweet at me, I’m going to block you, just as if you do that in the comments here your chances of me publishing future comments goes way lower. If you have read me for a while you should be aware that I have a really long memory and recall commenters who have crossed me in some way for years, so even if I let you comment again please don’t think I’ve forgotten. The major problem is commenters who presume over-familiarity with me. Probably a function of the low social intelligence of many of my readers.

Finally, Sean don’t post anything on sexual selection on this thread. I won’t post the comments.

 
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What’s going on?

51I89uOM0AL._SX331_BO1,204,203,200_ Very busy, so haven’t gotten much further in The Dialectical Imagination, but I do have to say that the distinction between “positive freedom” and “negative freedom” is a useful one to highlight at this point. The comments below make me unsure about the influence of the Frankfurt School on modern socio-political movements, but the ideal of a utopian end state for society which enshrine a vision of the good definitely seems to be one of the things that moderns have lost. Rather, a lot of identity politics talk seems to be about positional games and status competition. The perpetual revolution.

At the suggestion of a reader I purchased Explaining Postmodernism. The Kindle version is $4.99.

There was an ancient DNA convention in England. It turns out that the original Polynesians may not have had much Melanesian ancestry, implying multiple migrations into Far Oceania.

The impact of recent population history on the deleterious mutation load in humans and close evolutionary relatives.

 
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51I89uOM0AL._SX331_BO1,204,203,200_ Reading The Dialectical Imagination: A History of the Frankfurt School and the Institute of Social Research, 1923-1950.

A good book. Dense. But it is clear (the author so admits) that it’s only a superficial exploration of the ideas of the Frankfurt School.

That being said, a lot of the abstruse and in my opinion wrong-headed tendencies of Critical Theory types does seem to get back to the roots. In relation to impenetrability, the influence of Heidegger on Marcuse makes a lot of sense.

 
• Category: Ideology • Tags: Open Thread 

Parents Didn’t Just Dislike Super Nintendo 25 Years Ago—They Thought It Was a Scam. Fun fact: I stopped playing video games when I was 16. Mostly because it was taking up too much of my time. This means that I’m excluded from a lot of conversation and pop culture. So be it.

Excited to be going to ASHG 2016. Is Vancouver really part of Canada? Isn’t it like Seattle with a queen? In any case, the abstracts aren’t online yet. They should drop this week….

1584203._UY200_ The Ezra Klein podcast has a recurring question: name three books. Taking about five seconds, mine are the following: The Fall of Rome: And the End of Civilization, Principles of Population Genetics, and In Gods We Trust: The Evolutionary Landscape of Religion. The next three? Albion’s Seed: Four British Folkways in America, The Genetical Theory Of Natural Selection, and From Dawn to Decadence, 1500 to the Present: 500 Years of Western Cultural Life.

ngs48_0187 As a change of pace I’ll be checking out Christie Wilcox’s new book, Venomous: How Earth’s Deadliest Creatures Mastered Biochemistry. It’s often joked that geneticists don’t know real biology, and despite an undergrad background in biochemistry that’s probably somewhat true for me.

Got a copy of The Dialectical Imagination: A History of the Frankfurt School and the Institute of Social Research, 1923-1950. If history is written by the winners, I figured I should get to know the winners a little better!

I was doing most of my Python object-oriented, but everyone kept telling me that I should go functional (online and offline). As I don’t have too much time, I got Treading on Python Series: Intermediate Python Programming: Learn Decorators, Generators, Functional Programming and More.

People have been talking about this for a while. Gwern did some real analysis, Embryo selection for intelligence.

How does India’s caste system work in the 21st century? Quora user hits the bull’s eye.

Using Genetic Distance to Infer the Accuracy of Genomic Prediction.

Tabs Or Spaces – One Billion Files Later An Answer. Sorry Richard, it’s all spaces all the way….

5 racist stereotypes that historically were the opposite of what they are today. Vox is doing well because they’re very cautious about challenging the preconceptions of their readers. Often they reinforce them. Too easy to deconstruct, but please note that stereotypes which might be held about Asians may not be common for certain types of Asians. This sort of banal observation is difficult to make when you are experiencing an orgasm because of the smug-saturation.

Walmart automation will eliminate 7,000 jobs.

Dissecting the genetics of complex traits using summary association statistics.

More Ancient Jomon DNA.

Steak That Sizzles on the Stovetop.

I had forgotten this was once #1 in the early 90s:

 
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21_SM_indian_ocean_2979858e About 2/3 of the way through The Ocean of Churn: How the Indian Ocean Shaped Human History by Sanjeev Sanyal. It’s a wide-ranging book which synthesizes diverse disciplinary threads. The big over-arching thesis seems to be that movement of peoples and ideas was far less unidirectional than we often tend to think and are told. Probably one of the major examples of this which I think has been somewhat misleading to many people has been the idea that migration out of Africa can be purely defined unidirectional migration in a series of stepwise events.

Human_migration_out_of_AfricaThat being said, there are the usual problems that occur when you synthesize diverse disciplines. Since I know a fair amount about the intersection of genetics and history I can say with great confidence that some of the genetics in the book is now outdated. The reason is that it relies on work that was published ~5 years ago. Also, there is the unfortunate reality that sometimes high-impact journals publish works that are almost certainly wrong. For example, Sanyal cites Genome-wide data substantiate Holocene gene flow from India to Australia. This paper is interesting, but it was clear to many that it was probably wrong almost immediately upon publication.

Longer review when I have time.

I need to read the paper closely. But the demographic-historical implications of this are pretty straightforward. (it’s open access)

G.E., the 124-Year-Old Software Start-Up. The story is interesting to me mostly because it illustrates how contingent how modern civilization is. There are so many people doing so many specialized things that we take for granted.

518EQMWHB0LForget “Earth-Like”—We’ll First Find Aliens on Eyeball Planets. M. J. Engh’s Wheel of Winds was set on one of these planets.

Ohana:

Ohana is a suite of software for analyzing population structure and admixture history using unsupervised learning methods. We construct statistical models to infer individual clustering from which we identify outliers for selection analyses.

It may be better than ADMIXTURE, but we’re reaching a point where “good-enough” tools are achieving “lock-in.”

Empirical assessment of published effect sizes and power in the recent cognitive neuroscience and psychology literature. No surprise.

Down in the valley, up on the ridge. On Melungeons.

Leon Hadar is now a contributor to Secular Right, Will Trump Usher the GOP’s Secular Age?

The crescent and the globe. I wrote this.

 
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61lWPI+qpGL._SY344_BO1,204,203,200_ Guy Gavriel Kay’s Children of Earth and Sky is set in the same world as the Sarantine Mosaic duology, and the Lions of Al-Rassan, The Last Light of the Sun, and A Song for Arbonne. I’ve enjoyed Kay’s work for more than half my life at this point, so no surprise that I enjoy Children of Earth and Sky. As I’ve noted before, Kay is arguably the world’s greatest historical fantasist, and for someone like me it’s always pleasurable to make connections between our own real history, and his secondary creation. This sort of fantasy is more magical, than characterized by magic.

I know I have readers in India because of IP addresses. Keep an eye out for my byline in India Today, where I’ll make some contributions now and then. The first should drop this Friday in print and online, a short review of Shadi Hamid’s Islamic Exceptionalism. An Indian friend told me that India is one nation where the sales of print are actually increasing, so I’m curious how this will go.

On Twitter most of my blocks come because I’m being tweeted at directly by someone. If I don’t follow you on Twitter in most cases I don’t want to be bothered. The main reason I block isn’t because I’m a coward or I feel unsafe. It’s because the person is probably stupid, and starting to annoy me. Sometimes, it’s because they want me to make a point that they want to make. Needless to say, I don’t take kindly to that. Between all my various adult responsibilities that I have now at this age, I don’t really feel guilty at all muting stupid people (who invariably think they’re genius, because you know, they’re stupid).

So you’ve convinced me that functional programming is the way to go.
Screenshot 2016-08-21 02.02.00 Since my genotype is public somehow it got used in an rnsnps tutorial. Pretty funny.

Also, Running Structure-like Population Genetic Analyses with R. Looks like there are some interesting visualizations of admixture components which are feasible with the new program.

People keep emailing me about the HGDP plink data set. I think I removed where it initially was, and it’s linked to my old Admixture tutorials. Well, download this zip, and look at the .fam file. It has clear population labels, so you should be able to do what you want in Plink.

Should We Be Having Kids In The Age Of Climate Change? The arguments really go all the way back to the ZPG movement. Actually, they’ve popped up in philosophical movements from the beginning of time. The world is a “vale of tears”, etc. Myself, I have no guilt about having children. My children are attractive, and seem rather intelligent so far. Would that more children like mine exist in the world!

Stop Tweeting Your #Firstsevenjobs: It’s just a way to disguise your privilege. FUCK YOU. The author of the piece has a degree in French language and literature from Columbia university according to her Linkedin. She gets to write for a living for Slate about food, and was editorial assistant for Mark Bittman. What. The. Fuck. She gets paid to write about food! She was Mark Bittman’s assistant. I guess it takes one to know one. Not that the author tries to mask her privilege: “But this list doesn’t tell you that I went to an Ivy League school and graduated without debt, since my parents were able and willing to pay for my tuition.”

I hate it when people say that gender is a continuum, because that tacitly brings to mind a uniform distribution. It’s not. It’s highly bimodal.

Lou Pearlman is dead. The weirdest thing about his career is that several stories have implied he became a boy-band impresario because he was a closeted gay man, and that was a way for him to have access to young vulnerable teenagers. The fact that he became very prominent in the late 1990s boy-band boom was almost a coincidence.

Sarah Haider has been accused of being a white supremacist.

Let Caster Run! We Should Celebrate Semenya’s Extraordinary Talent. As they would say, “I don’t even.”

The company I work for has a 20% discount on kits right now. So if you want your dog to get genotyped on 200,000 markers, and get ancestry and health, it’s a good time as any.

What are you reading?

The Amazing Atheist youtube channel has some pretty funny videos. E.g.,

 
• Category: Miscellaneous • Tags: Open Thread 

The-Ocean-of-Churn I just bought my friend Sanjeev Sanyal’s book, The Ocean of Churn: How the Indian Ocean Shaped Human History. Sanjeev is a polymath with varied interests, some of which intersect with my own. A few years back I had the pleasure of having dinner with him and Reihan Salam, and the server kept unapologetically offering drinks one of us had ordered to the wrong person. I don’t think we look that much alike!

The top start-up mecca in America is far from Silicon Valley. It’s cheap to live here, and fun for young brogrammers. Also, not too long a flight from elsewhere. As Mark Krikorian observed on Twitter being a blue bubble in a red state means that Austin can take advantage of low-cost and low-tax public policies, while maintaining a culturally liberal social aesthetic.

Bought Python Essential Reference.

Hubby and Lewontin on Protein Variation in Natural Populations: When Molecular Genetics Came to the Rescue of Population Genetics.

Sausage Party is a surprising mix of high and lowbrow.

Update: If I don’t post your initial comment, posting five additional times won’t result in your comment being posted.

 
• Category: Miscellaneous • Tags: Open Thread 

pydata_cover (1) Sorry about the light posting. I’ll get back into gear in a few days. Very busy professionally and personally the past week or so.

I’ve been getting into writing Python code, as opposed to reading it. It’s a different beast altogether, obviously. I’m a lot slower than I would be in Perl, but I’m getting stuff done, so that’s something. I would highly recommend Python for Data Analysis: Data Wrangling with Pandas, NumPy, and IPython, if you have a background in R and another scripting language.

I went to my high school reunion. It was fun and interesting. Apparently people change in a few decades…

 
• Category: Miscellaneous • Tags: Open Thread 

pepper
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.

51G93vyEl5L 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 Hillbilly Elegy: A Memoir of a Family and Culture in Crisis 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.

 
• Category: Miscellaneous • Tags: Open Thread 

51Qh5-h64SL._SX384_BO1,204,203,200_ When people ask me what they should read to understand genetics, I don’t really know what to say. But An Introduction to Genetic Analysis 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.

First CRISPR trial in humans is reported to start next month. In China.

The Great Ordeal 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 The Great Ordeal. 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.

Congo: The Epic History of a People is kind of like reading Oedipus Rex. It’s hurtling toward tragedy. For the section on the “Great War in Africa” I’d just recommend Dancing in the Glory of Monsters. 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 Game of Thrones 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.

51ucb328bdL The Kindle version of The High Frontier: Human Colonies In Space 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.

 
• Category: Miscellaneous • Tags: Open Thread 

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Been busy with work. Lots of data coming in. Will be good to turn around some science.

But I’m eating OK. Location matters….

Here’s a FB post from a researcher on Eran Elhaik’s weird results which regularly make press. I’ve started ignoring Elhaik’s stuff because it’s also so crazy.

I’ll try to monitor the open thread better this week and respond to questions.

 
• Category: Miscellaneous • Tags: Open Thread 
Razib Khan
About Razib Khan

"I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. If you want to know more, see the links at http://www.razib.com"


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