Open Thread, 04/28/2019

Reading The Race for Paradise: An Islamic History of the Crusades. A bit too many names and battles (narrative), rather than social and economic dynamics. But it’s a good inversion of the traditional narrative, and illustrates just how chaotic and fractions the Islamic world in the last decades of the 11th-century was. Western European society was coming back to Roman levels of density and complexity after 1000 A.D., and for various reasons, the last half of the 11th-century was a period of disunity in the lands of Islam, so the Crusades were timed very fortuitous for the Franks.

Speaking of the Crusades, Christopher Tyreman’s God’s War: A New History of the Crusades is one of my favorite books (I remember staying up to 3 AM on worknights reading this book). But for some reason, it has much worse Amazon reviews than Thomas Ashbridge’s The Crusades: The Authoritative History of the War for the Holy Land. Does anyone know why?

Interesting historical fantasy I stumbled across, The City of Brass. The author is a white ethnic woman from New Jersey who converted to Islam as a teen, and now has a last name which is associated with Bengali Brahmins (she also pronounces very peculiarly). The reviews are good, but I’m not a fan of historical fantasy. Mixing the real and fantastic doesn’t appeal to me.

Dante is still selling 30x WGS for $229 as of this writing. No, I have no idea how Dante works in regards to this price point. But apparently, it’s not a fraud.

Speaking of personal genomics, this week on The Insight I’ll be talking to Rodrigo Martinez, an officer at Veritas. Follow the link above to see the different ways you can subscribe.

Endgame is worth watching.

Speaking of podcasts and the like, I’m told that three people on a single Extremely Offline podcast that will go live next month will all have been podcasts on the Browncast. Can you guess who? It shouldn’t be too hard.

Evolutionary dynamics of culturally transmitted, fertility-reducing traits.

A genetic hazard score to personalize prostate cancer screening, applied to population data.

This thread is worth reading:

Gencove announces Phase I SBIR grant to validate polygenic risk score estimation from low-pass sequencing.

Angiosperm speciation speeds up near the poles. “Overall, our results show that speciation rates follow an opposite pattern to global variation in species richness.”

The continuing impact of an ancient polyploidy on the genomes of teleosts. “…lend support to recent suggestions that the TGD was the source of a morphological innovation in the structure of the teleost retina.”

Darwin Devolves: The New Science About DNA That Challenges Evolution. Michael Behe has a new book out. Richard Lenksi has responded in detail on his weblog.

I read Darwin’s Black Box and Michael Denton’s Evolution: A Theory in Crisis 20 year ago. Not convinced. That being said, people without a scientific background can be impressed easily. I still remember the stupid reader who incredibly blown-away by the pig-headed sophistry in David Stove’s Darwinian Fairytales: Selfish Genes, Errors of Heredity and Other Fables of Evolution. I read the book because the reader was impressed, and the reader was someone who I didn’t have a strong opinion about. I came away concluding that the reader must be kind of a moron since the book itself was just plain ignorant in the literal sense.

I’m still trying to place a piece in The Federalist on evolution. They gave me a few suggestions. Friends who have read my draft were already impressed, so I’m 90% sure I can get this placed in the conservative media. I actually interviewed the author of this piece, Why One-Third Of Biologists Now Question Darwinism, for the Browncast. The podcast will go live tomorrow.

Genome-wide sexually antagonistic variants reveal long-standing constraints on sexual dimorphism in fruit flies. This is a really interesting paper. The citations are interesting too.

Efficient use of genomic information for sustainable genetic improvement in small cattle populations.

Direct-to-Consumer Genetic Testing and Potential Loopholes in Protecting Consumer Privacy and Nondiscrimination.

16 thoughts on “Open Thread, 04/28/2019

  1. Dante: It is really 30X. Mine took about 5 months to arrive, but if there are any hiccups with mailing labels etc. then it could take a lot longer because their customer service is nearly non-existent. Unpaired reads. Point mutations, indels, and CNVs called in separate VCF files, and occasionally phased (if they are very adjacent). BAM files are $59 extra.

    I wanted to phase it more reliably using SNP array data and local ancestry painting, to separate grandparents’ DNA contributions, but haven’t done it yet. Also hoped to use divergent rare variation to improve TMRCA estimates for the shared array-data segments, but my co-participants couldn’t ever get her DNA processed because of the shipments snafus, so it got nowhere as well.

    A really good Y-chromosome SNP map caught my attention, but there is no way to upload it to the database of the only commercial lab matching Y’s, and there is nobody in my clade on the open site YFull. Hmmm, what else to do with the genome sequence?

  2. I’m not Australian, but aren’t R J Stove (“Unsleeping Eye”) and David Stove (“Darwinian Fairytales”) two different people?

  3. Apologize in advance if this is a dumb question, I am a non-STEM layman:

    I was reading something about Elizabeth Warren’s native american ancestry, where you mentioned that due to recombination it is possible that it could have been 0% on her Ancestry.com DNA test even if she had a native american ancestors. Found that to be quite counter-intuitive.

    Go me thinking about Neanderthal and Denisovans admixture in humans.

    What are some possible scenarios in someone could have 2% Neanderthal DNA (in terms of different discrete combinations of Sapien vs Neanderthal great, great…. grandparents) ? Is this even possible to estimate at all ?

    I think would be a good way for a layman like me to intuitively understand what these findings actually mean. Thanks.

  4. So I’m curious Razib – since I know you’re an ASOIAF fan, and watched the last episode of Game of Thrones – what your thoughts are?

    I’m seeing a lot of butthurt people online. They seem to be under the impression that The Night King arc was the core of the story – that it was really attempting to show the futility of all of the little squabbles for the throne when there was this giant existential threat to all of mankind bubbling away in the background. Thus, by resolving the arc with three episodes left to go – without Jon being “the hero” as well – that the showrunners somehow destroyed their own show, and spending the last thee episodes focusing on (presumably) Cersei is a let down. They also seem sure this is all the idea of “D&D,” and GRRM would write the story they prefer.

    This all seems very strange to me. First, it misses that GRRM is a big Tolkien fan, and in both The Hobbit and Lord of The Rings what seems like the big conflict (Smaug and Sauron) are both resolved with five chapters left to go, leaving a whole secondary conflict which needs to be resolved. A denouement certainly seems like a good idea with a cast as big as Game of Thrones, given we just have so many personal arcs to resolve.

    Secondly, even though most of these people claim to have read the books, they seem to have completely missed the point of the stories. If it was really all about defeating the White Walkers, why wouldn’t it all just be told from the perspective of Jon? Obviously the book TL is still way behind, so we don’t know how GRRM intends to develop it, but if anything I get the idea that TV played up the existential stakes in a way Martin never planned to do. You don’t write thousands of pages dedicated to a complicated story about intrigue over a throne without that being the main point of your friggin story.

  5. “Fossil Points to a Vanished Human Species in Himalayas: Fossil jaw discovered in highlands of Tibet shows the Denisovans lived at an altitude that would leave many people today starved for oxygen”
    https://www.wsj.com/articles/ancient-humans-dwelled-at-great-heights-scientists-find-11556730001

    Robert Lee Hotz
    May 1, 2019 1:00 p.m. ET

    A fossil jaw found in the Himalayan highlands of Tibet belongs to a vanished human species called Denisovans, deepening the mystery of human evolution in Asia, scientists said Wednesday in a new study probing the roots of humankind.

    Discovered by a local Buddhist monk, the fossil shows these archaic human relatives lived on the roof of the world in the rarefied air at almost 11,000 feet—an altitude that would leave many people today starved for oxygen. They settled at these frigid heights at least 160,000 years ago, more than 120,000 years before modern humankind arrived, said the scientists, who published their work on the fossil in the journal Nature.

  6. KZ, good points. i liked the episode, though i thought the night-king angle got resolved too quickly for my taste. also, in the books, there is no night-king. i didn’t mind that the girl got to do the deed, i thought that was a nice twist.

    we know the ending is going to be bittersweet. jon has risen from the dead. i think he’s on borrowed time. when his task is done, he will go….

  7. What are some possible scenarios in someone could have 2% Neanderthal DNA (in terms of different discrete combinations of Sapien vs Neanderthal great, great…. grandparents) ? Is this even possible to estimate at all ?

    your neanderthal variation is chopped up into lots and lots and lots of little segments. that means you are unlikely to have zero unless SS african and unlikely to have much more than 2%. the variance is low cuz it’s widely distributed across 1/3 of the human genome.

    recent ancestry is choppier and distributed in blocks.

  8. I remember years ago reading William McGowan’s Only Man is Vile: The Tragedy of Sri Lanka (1992). Everyone in Sri Lanka, he said, felt they were an oppressed minority. Tamil Hindus were a minority on the island, but combined with their mainland brethren, they outnumbered the Sinhalese Buddhists. As I recall, the book was a plea for a “liberal” society that was not race/ethnic conscious, either in an old style right wing way or a modern left wing way.

  9. “I was reading something about Elizabeth Warren’s native american ancestry, where you mentioned that due to recombination it is possible that it could have been 0% on her Ancestry.com DNA test even if she had a native american ancestors. Found that to be quite counter-intuitive.”

    Both American Americans and European American populations have a lot of Ancient Northern Eurasian ancestry – a huge percentage in the case of American Americans, varying percentages in the case of northern and western European populations. In other words there’s enough shared genetic material that you could be missing some of the non-shared American American genetic material and still have a good chunk of the shared material and the test could identify that as European when really it’s just ANE.

    And that is one of the biggest weakness of Ancestry.com and it’s geographical model of reporting your ancestry. Populations =/= territories.

  10. In other words there’s enough shared genetic material that you could be missing some of the non-shared American American genetic material and still have a good chunk of the shared material and the test could identify that as European when really it’s just ANE.

    jim is wrong. the comment is bullshit (sorry). the method used wouldn’t pick up ANE as a false positive. it’s looking for long chunks of recent ancestry, not old recombined stuff that might show up as a false signal in genotype-based method’s.

  11. Razib, in the wake of the recent Syrian Christian blog post you did, you might find this interesting.

    “King Alfred and India: an Anglo-Saxon embassy to southern India in the ninth century AD”

    https://www.caitlingreen.org/2019/04/king-alfred-and-india.html

    It’s possible that King Alfred may have sent emissaries all the way to Kerala/South India to give alms to the supposed resting place of St. Thomas and St. Bartholomew as well as possibly trade with existing Christians there.

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