Open Thread, 4/24/2018

Finished She Has Her Mother’s Laugh: The Powers, Perversions, and Potential of Heredity. To be honest I was pleasantly surprised that the narrative wasn’t overly fixated on the ‘perversions.’ Sometimes it’s hard to move past that.

I think different people will benefit from reading the book differently. If you are a layperson a serial reading from front to back is optimal. She Has Her Mother’s Laugh is a long book, so this will take a while. But you need to do this to get situated. If you are a geneticist, you may benefit from jumping around chapters, and sampling what people in other fields are doing. Additionally, some geneticists would actually benefit from reading the historical chapters.

Started reading The Fate of Rome: Climate, Disease, and the End of an Empire. Yes, it’s very good. Will see if it’s better than The Fall of Rome: And the End of Civilization after I’ve finished.

Thanks for whoever reviewed the podcast I cohost on iTunes and Sticher. If you haven’t done so, please do so!

Appreciate the feedback so far.

Found out today that India Today posted my review of Who We Are a few weeks ago! Pretty funny I didn’t see it.

Meanwhile, The Genetic History of Indians: Are We What We Think We Are? It looks like Indian scientists are bending before reality: ““How do I say it? See, I am a nationalist,” Rai says over the phone. “People will be upset. But that’s how it is. All the studies are showing that people came here from elsewhere.”

A friend asked again “how do I learn population genetics?” My opinion has not changed in the 15 years I’ve become interested in the field, read Principles of Population Genetics. If you need a gentle introduction, Population Genetics: A Concise Guide is probably that. But I read Principles of Population Genetics in 2004 without any formal training in the field. It’s not that difficult if you put time into it.

Supervised machine learning reveals introgressed loci in the genomes of Drosophila simulans and D. sechellia. Gotta do it on flies first!

California, Coffee and Cancer: One of These Doesn’t Belong. The cancer warnings in California are treated as a joke by the population. Unfortunately, there are real carcinogens out there.

Genomic SEM Provides Insights into the Multivariate Genetic Architecture of Complex Traits.

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16 thoughts on “Open Thread, 4/24/2018

  1. Razib,

    Do you know anybody who plans to write a “Who We Are…” book that takes into account Prof. Reich’s population genomic insights, but incorporates them into a larger historical/archaeological perspective? Prof. Reich’s work was good but I had to continually double check references just to learn more interesting details about the various prehistoric civilizations such as Indus Valley, Corded Ware, etc.

    -Riordan

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  2. Reich notes that Europe and India seem to exhibit a parallelism. Both Eurasian peninsulas’ genetic character emerges from the collisions between herders from the Eurasian steppe, farmers from West Asia, and indigenous hunter-gatherers.

    From your India Today piece. I wonder if thinking of it that way will make it easier for Indian nationalists to accept.

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  3. Razib: I follow your super feed and read your postings here and on Brown Pundits. The subject of the ancestry of South Asians comes up frequently. It seems to have a political valence that I, as an outsider, do not understand.

    Can you explain it? or point us to an explanation?

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  4. A friend of mine has a congenital condition in which two particular adult teeth never came in (I believe it is the upper canines). He had the corresponding baby teeth, but the adult teeth simply weren’t there (x-rays revealed they weren’t “hiding”, either).

    His father has the same issue. One of his sons does as well.

    All of his other teeth are normal and developed normally.

    There has to be a very specific and rare genetic origin for this — is it “known”?

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  5. Fate of Rome‘s sections on Bubonic Plague and the climate are so good. The line he had about Earth being a “heaving platform” sticks with me as well. We tend to read stability into the past that often wasn’t there.

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  6. Since you say there’s not much about the “perversions” of heredity in Carl Zimmer’s book, I am now willing to buy it. I wasn’t going to read the book if it contained a lot of fearmongering about genes.

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  7. There has to be a very specific and rare genetic origin for this — is it “known”?

    don’t know this one, but dental mutations are common. it’s probably in the literature.

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  8. I had to continually double check references just to learn more interesting details about the various prehistoric civilizations such as Indus Valley, Corded Ware, etc.

    nope. and i do the same.

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  9. “british colonialism and culture wars in modern day india.”

    Those are things, but they do not explain who is upset, and why they process this genomic information as being inimical to them. Who are these people? What political postion have they taken that would be undermined by genomics?

    I am genuinely puzzled.

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  10. “nope. and i do the same.”

    I think there is a real market for “all in one” books on this topic. A logical way to do it is to focus on one region per book, eg- one book on GB, one on Ireland etc.
    (I have heard it said that the structure of these particular regions is fairly completely understood…)

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  11. @Roger Sweeny, as I understand it, in a way the parallelism kind of both is and isn’t there. The “is” is just what’s quoted and as simple as that. But the “isn’t” is that European hunter gatherers shared quite a bit of drift with both the Anatolian farmers who entered Europe (who can model to a first approximation as WHG+Basal Eurasian) and the Yamnaya, in a way that is less the case comparing at least HG in South Asia and the other waves.

    To take an imaginary (and probably unlikely) example, if we find in a few years that Koreans for instance had a population history with layers of a mix of East Eurasian “Altaic” speaking herders, East Eurasian North Chinese farmers and local East Eurasian hunter gatherers. In a way that would be like what happened in Europe / South Asia, but the actual degree and timescale to which the groups involved were evolving separately could be quite different.

    All that said, thinking in terms of parallelism might be useful from certain perspectives.

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  12. Let me ask here about a comment you made yesterday at Brown Pundits:
    as for the constructs, people like zack ajmal and i have assumed that they’re not real singular pops as early as 2010. we’ve been saying there must have been a different west asian migration event (we were right). ANI + ASI are easy abstractions…but obv they weren’t real peoples. just statistical averages.

    Glad to hear these are just statistical averages, since my brain exploded seeing Narasimhan etc. talking of them as actual people (may be there were being loose with their language in the interest of efficiency).

    Can you confirm if my following understanding of the above is basically correct: you represent the genetic data of a large number of south Asians as points in some n-dimensional space, and it so turns out that the points mostly lie in a two dimensional subspace. This is why people came up with the idea of ANI or ASI in the first place.

    ANI and ASI are then nothing but two reasonable vectors that span this subspace (reasonable meaning a property like: all the points should lie in the “first quadrant” in the sense that the component with respect to a source population cannot be negative). This doesn’t determine ANI or ASI uniquely since the same space can have different pairs of vectors spanning it (and satisfying additional constraints of reasonability).

    So, speculation for Reich’s figures: first, you basically have a three dimensional, not n-dimensional, subspace to look at – with a natural coordinate system given by Steppe, Near Eastern farmer and AASI. Reich simply assumed that ANI cannot have AASI, and that ASI cannot have Steppe. **These two constraints determine the spanning vectors for the two dimensional subspace uniquely**, so you come up with what the composition of ANI and ASI must have been. And this was upset by Narasimhan et al, when it was found that a reasonable ANI must have had a little bit of AASI. Was this likely the basis of Reich’s deduction? Thanks again.

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  13. Walter, Razib:

    Here’s a recent blog post/article by one of the proponents of OIT (he even wrote a book on it and has always claimed that he has refuted the AIT): http://talageri.blogspot.sg/2018/04/what-is-value-of-new-genomic-evidence.html. He’s often approvingly cited by Koenraad Elst, another OIT proponent, too.

    It may provide some of the context you seek.

    The key point to note is that the OIT proposition draws heavily on the Vedic textual form and content of the Vedic scriptures. So some of the emotion involved in this debate may simply by of the “their theory refutes the texts dear to us” form.

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  14. Razib, do you believe that India will be able to overcome issues regarding caste, or will it simply be part of Indian culture and inequality forever? Are you optimistic or pessimistic in regards to the future of South Asia economically? Are the HBDers right, and Indians (particularly low-caste Indians) are simply fated to be nothing more than another population of “dumb brown people?”

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