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Open Thread, 7/12/2015

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9780199589883 To give my brain a break after reading Reading in the Brain I am reading A New History of Western Philosophy. I know I should tackle The Shape of Ancient Thought: Comparative Studies in Greek and Indian Philosophies or Warriors of the Cloisters: The Central Asian Origins of Science in the Medieval World, but I feel that that would have taken more mental energy. Histories of Western philosophy are easier hauls since I already know the roadmap and have a conceptual armamentarium. Though if you want to read a history of Western philosophy, I recommend The Truth About Everything: An Irreverent History of Philosophy. It’s written with more humor than most of the books on this topic! The style obviously differs from that in more academic works, but the general structure of The Truth About Everything is pretty much always recapitulated. A yellow-brick road instead of an asphalt one perhaps.

51lW5fpojzL._SY344_BO1,204,203,200_ Reflecting on Western philosophy and its beginnings you always need to go back to Aristotle and Plato. The order in which I listed these two individuals despite their chronology should tell you about my bias. In a A New History of Western Philosophy the author recounts an assertion by Gilbert Ryle, people could be divided into two categories on the basis of four dichotomies: green versus blue, sweet versus savoury, cats versus dogs, Plato versus Aristotle. I suppose three out of four isn’t bad! Like Armand Leroi (see The Lagoon: How Aristotle Invented Science) I have strong sympathies with Aristotle probably because I am a natural scientist, and in particular, a biologist. It is in the domain of biology that Aristotle was mostly wrong, as opposed to not-even-wrong, as in physics. And often he wasn’t even wrong, not too shabby for a man who lived ~2,500 years ago was literally inventing whole fields on the fly. Aristotle’s lack of recourse to mathematical formalism rendered his physics laughable, but his observational acumen lent itself to biology, and his inferences were often quite perspicacious.

But the history of philosophy makes me wonder at contingency and necessity. It strikes me that it is important to observe that Aristotle was a family man. He had a wife and children. Though if you dig into his presonal life it seems to have been conventionally complicated. Plato, in contrast was a lifelong bachelor. Whether he was a homosexual in a physical sense, as a wealthy aristocrat who never married he was somewhat detached from the normal course of affairs in a way the more bourgeois Aristotle never was. Did their life choices affect their philosophy? Or were their philosophies and life choices outcomes of a common cause and personality difference? As the years progress I am less and less convinced by the importance of contingency, in particular reading the ideas of Chinese and Indian thinkers, which in many ways have analogs to the Greeks (even if the emphases might differ). Complex civilization has a Plato-shaped hole, and it has an Aristotle-shaped hole.

This piece in the new TNR, It’s Not Easy Being a Guy in a Country Song, Either, is actually not too bad, as it avoids too much sneering at the subjects. But when implicitly bemoaning the lack of voices in “bro country” which are not white straight, male and culturally* Southern, as well as the topicality of blonde babes, dirt roads, and beer, I’m a little confused as to how the author expects the genre to diversify. If, for example, urban underclass black males were represented in the genre, the topicality would shift. But pretty soon I think it would be hard to differentiate it from hip-hop, because the topics reflect a historical experience. It seems entirely reasonable that the mores and lifestyle of working class Southern white men would be somewhat distasteful to cosmopolitans with a Ph.D.. But if a genre termed “bro country” ever appealed to a feminist whose profession is to be a cultural critic, they’re doing it wrong. If you took Luke Bryan, and just changed his sexual orientation, I doubt that there would be a big audience for songs about his life growing up as a closeted gay man on the dirt roads of Georgia, kicking back with a beer and meeting other guys in the back of his big rig. The cultural landscape is not flat, and some experiences will be more commonly reflected in the arts because they are…more common.

I guess diversity is great, unless it operates outside your narrow ideological purview.

I’ve been busy for the past week. So I’ll answer some of last week’s “open thread” questions here.

First, I’ve been looking for something about ancient+early medieval Arab history. Any suggestions? Here are three: Great Arab Conquests, When Baghdad Ruled the Muslim World, and A History of the Arab Peoples.

9780307819383 Everyone is talking about and asking me about The New York Times piece, The Mixed-Up Brothers of Bogata. Two pairs of identical twins were “switched” at birth in a fashion so that two families raised what they thought were fraternal twins. If the piece fascinated you, you really should read Born that Way. Also, there’s a confusing section in the piece: “On average, the researchers found, any particular trait or disease in an individual is about 50 percent influenced by environment and 50 percent influenced by genes. ” I suspect most readers will take this to mean that the trait in the individual is 50 percent genetic and 50 percent environmental. That is wrong. Rather, 50 percent of the variation in the population is due to variation in genes. There is an obviously implication for individuals, but there is a lot of variation, and for most traits it doesn’t make sense to say that in an individual it is any percent genetic or environmental.

There’s a large section on epigenetics in the article, but they never report results. I assume there’s a publication down the line, and we’ll hear about it. Could epigenetics explain some of the environmental component of variation? Perhaps. But behavior genetics already suggests that non-shared environment is quite large in its effect.

Finally, my wife recommends you watch the documentary (42 minutes) if you have any fluency in Spanish. The article elided a lot of the inter-individual differences which are visible in their manner, speech, and overall physiognomy.

In response to a question about aDNA in China and its utility. The key is sample size. If you are working with Y or mtDNA there is a lot more noise and randomness than intuition would suggest, due to their small effective population sizes.

* Some major figures in the genre, such as Dierks Bentley, were not raised in the South but have assimilated to Southern culture.

 
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  1. Finally gonna give Steven Soderbergh’s 5 hour film “Che” a try. Pray tell, what is the official Razib Khan (TM) opinion on Che Guevara? Hero, tyrant or something in between?

    • Replies: @Razib Khan
    @Robert Ford

    not important.

  2. I again recommend “The Spirit of Medieval Philosophy” by Etienne Gilson to Mr. Khan.

  3. https://www.youtube.com/watch?feature=youtu.be&v=b86dzTFJbkc

    This is a great speech by Jonathan Haidt in which he not only describes his theory about liberals and conservatives in moral terms, but also how the liberal domination of science (and the subsequent conservative distrust of it) are quite new. I was shocked to learn this phenomenon seems to date only to the 1990’s. The science part of the discussion starts at 48 minutes into the video.

    I was particularly pleased to see him single out the denial of IQ, heritability, and sex differences as problems among liberal social scientists.

  4. Hi Razib,

    Are there any books you would recommend for someone who wants to understand the Stone Age and the different cultures that existed during it (for example, the Aurignacian culture)?

    Thanks,

    Beowulf

    • Replies: @Razib Khan
    @Beowulf

    picked it up ad hoc. i'd be curious too.

    Replies: @Beowulf

  5. @Robert Ford
    Finally gonna give Steven Soderbergh's 5 hour film "Che" a try. Pray tell, what is the official Razib Khan (TM) opinion on Che Guevara? Hero, tyrant or something in between?

    Replies: @Razib Khan

    not important.

  6. @Beowulf
    Hi Razib,

    Are there any books you would recommend for someone who wants to understand the Stone Age and the different cultures that existed during it (for example, the Aurignacian culture)?

    Thanks,

    Beowulf

    Replies: @Razib Khan

    picked it up ad hoc. i’d be curious too.

    • Replies: @Beowulf
    @Razib Khan

    Thanks for the reply.

    By the way, how close is each human being to another genetically? Because I keep hearing people say that all human beings are 99.7% or 99.9% identical which makes no sense to me considering that Melanesians are about 5% Denisovan for example, not to mention the fact of neanderthal admixture in non-africans vs africans.

    -Beowulf

    Replies: @Razib Khan

  7. Razib – have you seen this: Sequencing an Ashkenazi reference panel supports population-targeted personal genomics and illuminates Jewish and European origins?

    “Reconstruction of recent AJ history from such segments confirms a recent bottleneck of merely ≈350 individuals.”

    “We used the lengths of shared segments (Fig. 3c) to infer the parameters of a recent AJ bottleneck (effective size 250–420; 25–32 generations ago) followed by rapid exponential expansion (rate per generation 16–53%; Fig. 4, bottom)”

    • Replies: @Anonymous
    @Anthony

    Thanks for linking to this paper. The calculated bottleneck is smaller and more recent than I would have thought.

    I'm always intrigued by Principal Component maps such as the one in that paper's Supplementary Information, but I think I tend to read more into them than I should. It would have been interesting to see non-Jewish Italians, Greeks, Turks on that plot as well.

    , @Razib Khan
    @Anthony

    saw it. good paper. not much to say. i think jews are best modeled as sw euro + iron age middle eastern (like assyrians).

  8. @Razib Khan
    @Beowulf

    picked it up ad hoc. i'd be curious too.

    Replies: @Beowulf

    Thanks for the reply.

    By the way, how close is each human being to another genetically? Because I keep hearing people say that all human beings are 99.7% or 99.9% identical which makes no sense to me considering that Melanesians are about 5% Denisovan for example, not to mention the fact of neanderthal admixture in non-africans vs africans.

    -Beowulf

    • Replies: @Razib Khan
    @Beowulf

    it's confusing. but you need to distinguish identity-by-state and identity-by-descent (IBS vs IBD). markers which are IBS are not always IBD, but markers which are IBD are pretty much always IBS (i guess if u have a mutation that's not so, but this is a tiny % of cases). the 99.9% is measuring IBS. that's how you get the "we are 98% like chimps." since you're 99.5% like a denisovan, the 5% ancestry (IBD) from that doesn't change the 99.9% identity much. make sense?

    Replies: @Beowulf

  9. @Beowulf
    @Razib Khan

    Thanks for the reply.

    By the way, how close is each human being to another genetically? Because I keep hearing people say that all human beings are 99.7% or 99.9% identical which makes no sense to me considering that Melanesians are about 5% Denisovan for example, not to mention the fact of neanderthal admixture in non-africans vs africans.

    -Beowulf

    Replies: @Razib Khan

    it’s confusing. but you need to distinguish identity-by-state and identity-by-descent (IBS vs IBD). markers which are IBS are not always IBD, but markers which are IBD are pretty much always IBS (i guess if u have a mutation that’s not so, but this is a tiny % of cases). the 99.9% is measuring IBS. that’s how you get the “we are 98% like chimps.” since you’re 99.5% like a denisovan, the 5% ancestry (IBD) from that doesn’t change the 99.9% identity much. make sense?

    • Replies: @Beowulf
    @Razib Khan

    My understanding of IBS is that it means you share an identical marker with someone at a certain location in your genome, but that this marker did not come from a shared ancestor.

    And my understanding of your comment is that even though humans are 99.5 % identical with Denisovans this is mainly because of IBS, and 5% of the markers that are ibd are shared between Denisovans and Melanesians. Is this a correct summary?

    That being said, you say "markers which are IBD are pretty much always IBS". I don't understand this part because I thought that by definition IBS Segments cannot be IBD in the strictest sense. Or are you just saying that IBS segments can masquerade as IBD?

    Alternatively, I may just not understand IBS vs IBD fully.

    Thanks for your time,
    -Beowulf

    Replies: @Razib Khan

  10. Of course, bro-country IS mostly hip-hop. Guns, alcohol, babes, and male bragging.

  11. Anonymous • Disclaimer says:
    @Anthony
    Razib - have you seen this: Sequencing an Ashkenazi reference panel supports population-targeted personal genomics and illuminates Jewish and European origins?

    "Reconstruction of recent AJ history from such segments confirms a recent bottleneck of merely ≈350 individuals."

    "We used the lengths of shared segments (Fig. 3c) to infer the parameters of a recent AJ bottleneck (effective size 250–420; 25–32 generations ago) followed by rapid exponential expansion (rate per generation 16–53%; Fig. 4, bottom)"
     

    Replies: @Anonymous, @Razib Khan

    Thanks for linking to this paper. The calculated bottleneck is smaller and more recent than I would have thought.

    I’m always intrigued by Principal Component maps such as the one in that paper’s Supplementary Information, but I think I tend to read more into them than I should. It would have been interesting to see non-Jewish Italians, Greeks, Turks on that plot as well.

  12. @Anthony
    Razib - have you seen this: Sequencing an Ashkenazi reference panel supports population-targeted personal genomics and illuminates Jewish and European origins?

    "Reconstruction of recent AJ history from such segments confirms a recent bottleneck of merely ≈350 individuals."

    "We used the lengths of shared segments (Fig. 3c) to infer the parameters of a recent AJ bottleneck (effective size 250–420; 25–32 generations ago) followed by rapid exponential expansion (rate per generation 16–53%; Fig. 4, bottom)"
     

    Replies: @Anonymous, @Razib Khan

    saw it. good paper. not much to say. i think jews are best modeled as sw euro + iron age middle eastern (like assyrians).

  13. @Razib Khan
    @Beowulf

    it's confusing. but you need to distinguish identity-by-state and identity-by-descent (IBS vs IBD). markers which are IBS are not always IBD, but markers which are IBD are pretty much always IBS (i guess if u have a mutation that's not so, but this is a tiny % of cases). the 99.9% is measuring IBS. that's how you get the "we are 98% like chimps." since you're 99.5% like a denisovan, the 5% ancestry (IBD) from that doesn't change the 99.9% identity much. make sense?

    Replies: @Beowulf

    My understanding of IBS is that it means you share an identical marker with someone at a certain location in your genome, but that this marker did not come from a shared ancestor.

    And my understanding of your comment is that even though humans are 99.5 % identical with Denisovans this is mainly because of IBS, and 5% of the markers that are ibd are shared between Denisovans and Melanesians. Is this a correct summary?

    That being said, you say “markers which are IBD are pretty much always IBS”. I don’t understand this part because I thought that by definition IBS Segments cannot be IBD in the strictest sense. Or are you just saying that IBS segments can masquerade as IBD?

    Alternatively, I may just not understand IBS vs IBD fully.

    Thanks for your time,
    -Beowulf

    • Replies: @Razib Khan
    @Beowulf

    IBS ultimately is IBD if you go back far enough ;-) IBD usually refers to more recent ancestry.

    let's make it concrete. if you just count markers and see if they are identical or not >99% are identical between any two people. IBS. pretty much same for sib vs sib and sib vs non-sib. but the IBD is totally different. 0 vs 0.50.

    Replies: @Beowulf

  14. @Beowulf
    @Razib Khan

    My understanding of IBS is that it means you share an identical marker with someone at a certain location in your genome, but that this marker did not come from a shared ancestor.

    And my understanding of your comment is that even though humans are 99.5 % identical with Denisovans this is mainly because of IBS, and 5% of the markers that are ibd are shared between Denisovans and Melanesians. Is this a correct summary?

    That being said, you say "markers which are IBD are pretty much always IBS". I don't understand this part because I thought that by definition IBS Segments cannot be IBD in the strictest sense. Or are you just saying that IBS segments can masquerade as IBD?

    Alternatively, I may just not understand IBS vs IBD fully.

    Thanks for your time,
    -Beowulf

    Replies: @Razib Khan

    IBS ultimately is IBD if you go back far enough 😉 IBD usually refers to more recent ancestry.

    let’s make it concrete. if you just count markers and see if they are identical or not >99% are identical between any two people. IBS. pretty much same for sib vs sib and sib vs non-sib. but the IBD is totally different. 0 vs 0.50.

    • Replies: @Beowulf
    @Razib Khan

    Ok that makes sense.

    Thanks

  15. @Razib Khan
    @Beowulf

    IBS ultimately is IBD if you go back far enough ;-) IBD usually refers to more recent ancestry.

    let's make it concrete. if you just count markers and see if they are identical or not >99% are identical between any two people. IBS. pretty much same for sib vs sib and sib vs non-sib. but the IBD is totally different. 0 vs 0.50.

    Replies: @Beowulf

    Ok that makes sense.

    Thanks

  16. That “Girl In a Country Song” video is kind of funny; I like it. Of course it works in part because the two girls who do it are good enough looking to be girls in country songs. Plus the female equivalent of the fat guy washing the truck in revealing attire would never be a “girl in a country song.” For it to be a good analogy, the guys should all have been studmuffins.

    The article also fails to mention a former country singer by the name of Taylor Swift. Sure, she’s moved over to pop now — she is too big for country — but she began her career well within the country genre, with songs about Tim McGraw and pickup trucks and slammin’ screen doors . . . .

    Sort of undermines her thesis.

    • Replies: @Razib Khan
    @Zippy

    re: maddie & tae. that's always bothered me. both are pretty attractive and got there partly through their wholesome looks.

  17. @Zippy
    That "Girl In a Country Song" video is kind of funny; I like it. Of course it works in part because the two girls who do it are good enough looking to be girls in country songs. Plus the female equivalent of the fat guy washing the truck in revealing attire would never be a "girl in a country song." For it to be a good analogy, the guys should all have been studmuffins.

    The article also fails to mention a former country singer by the name of Taylor Swift. Sure, she's moved over to pop now -- she is too big for country -- but she began her career well within the country genre, with songs about Tim McGraw and pickup trucks and slammin' screen doors . . . .

    Sort of undermines her thesis.

    Replies: @Razib Khan

    re: maddie & tae. that’s always bothered me. both are pretty attractive and got there partly through their wholesome looks.

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