Razib Khan One-stop-shopping for all of my content

July 16, 2018

Open Thread, 07/17/2018

Filed under: Open Thread — Razib Khan @ 11:57 pm

History of Japan: Revised Edition. As I said, a pretty good and short history. Recommended.

CRISPR/Cas9 gene editing scissors are less accurate than we thought, but there are fixes. I know the focus is on human genetics. And rightly so. But this isn’t going to be as much of an issue in animal and plant breeding.

Patterns of speciation and parallel genetic evolution under adaptation from standing variation.

Genome-wide analysis in UK Biobank identifies over 100 QTLs associated with muscle mass variability in middle age individuals.

Amazon told me R for Everyone: Advanced Analytics and Graphics was on sale. Great. But I already own it. That being said, I can tell you it’s a pretty good book.

Genome doubling shapes the evolution and prognosis of advanced cancers.

Against Moral Equivalence. “The talking heads trafficking in examples of U.S. interference neglect to mention that the goal of American policy has always been to prop up anti-totalitarian, pro-market leaders.” I dislike the tendency of American conservatism to conflate anti-authoritarian and pro-market. The two are distinct (I’m pro-market for what it’s worth, but capitalism is amoral, even though it leads to greater human well-being).

Large randomized controlled trial finds state pre-k program has adverse effects on academic achievement.

Archaeobotanical evidence reveals the origins of bread 14,400 years ago in northeastern Jordan.

Confronting Implicit Bias in the New York Police Department. Implicit bias stuff is sketchy science. But people want solutions for social problems.

How Social Science Might Be Misunderstanding Conservatives. I got introduced to the “authoritarian personality” in college. I didn’t think much about it, but over the years it seemed pretty clearly a bit rigged. But whatever. Then I read The Dialectical Imagination: A History of the Frankfurt School and the Institute of Social Research, 1923-1950. That’s where it comes from. Enough said, right?

Tides of History is a great podcast. Now Patrick Wyman is talking about the “Hundred Years War.”

Should I post “open threads” anymore? It seems that the number of comments keeps dropping. Really “everything” is moving to Twitter nowadays though Twitter is a wasteland.

Open Thread

Filed under: Open Thread — Razib Khan @ 9:11 pm

Please keep the other posts on topic. Use this for talking about whatever you want to talk about.

July 10, 2018

Open Thread

Filed under: Open Thread — Razib Khan @ 11:58 am

Please keep the other posts on topic. Use this for talking about whatever you want to talk about.

July 9, 2018

Open Thread, 07/09/2018

Filed under: Open Thread — Razib Khan @ 6:31 pm

My review of The University We Need: Reforming American Higher Education is up at National Review Online (it’s already posted to my total content feed). The book’s publication date is tomorrow.

A  review can only pack in so many things. So if there is something missing that seems obvious, it’s probably something that I cut in the interests of space (e.g., the author is not a fan of the emphasis on football and such at many universities, but I didn’t touch on that in the review). The University We Need is a short book, but it’s very dense in ideas and suggestions. Unfortunately, comments on NRO and Twitter indicate many people haven’t really read the review, so they won’t read the book.

Surely one reason I enjoyed the book is that the author is someone who I’m coincidently on the same wavelength. I first encountered his work nearly twenty years ago, when I read A History of the Byzantine State and Society, a ~1,000 survey of the topic. In many ways a scholarly “core dump”, it has served me in good stead all these years. But at the time I was totally unaware that the author, Warren Treadgold, and I shared broadly similar politics in the grand scheme of things. That is, we were intellectually oriented people who were also not on the Left.

I don’t consider myself a conservative intellectual. I’m just an intellectual happens to be conservative because the Left terrifies me (I have real personal reasons!). Treadgold’s work similarly is not informed by him being a conservative intellectual. Rather, he’s a scholar whose views default to the Right as opposed to the center or Left because of where the dominant tendency in academia today is.

I’m currently reading A History of Japan. I think I’m getting stale and predictable. I read John Keay’s Midnight’s Descendants: A History of South Asia since Partition really quickly a few weeks ago. Need to move out beyond my tendency of reading long histories and lots of genetics papers.

I have a stack of books on cognitive psychology and cultural evolution I need to get through, though I think papers are probably more useful in the latter area, since I’ve read a fair number of books already on this topic (e.g., Cultural Evolution: How Darwinian Theory Can Explain Human Culture and Synthesize the Social Sciences).

Speaking of psychology, there are some really good podcasts in that field out. Part of it is there is so much to talk about with the replication crisis. I really enjoyed Two Psychologists Four Beers, for example. Though not surprisingly they sort of still mischaracterize the views and issues of conservatives or non-liberals in academia…there are so few who are “out” and vocal with their politically normal colleagues that people just don’t know what’s going on in their heads and it’s easy to mischaracterize.

This is the week when you follow the #SMBE2018 hashtag on Twitter. I assume a lot of papers are going to come out in the next few weeks after people present at SMBE.

Estimating recent migration and population size surfaces. This seems important. Definitely going to read.

How eliminating the ‘kill box’ turned Mosul into a meat-grinder.

Genetic analysis of social-class mobility in five longitudinal studies.

Male homosexuality and maternal immune responsivity to the Y-linked protein NLGN4Y.

Hung out with Stuart Ritchie this week. Still recommend his book, Intelligence: All That Matters.

There was some discussion on ancient DNA and archaeology on Twitter. Has ancient DNA changed everything? Or not?

First, I think it’s important to acknowledge that many of the models which have emerged out of ancient DNA are resurrections of older anthropological, archaeological, and historical frameworks, which emphasize migration. But these were long dismissed within many of these fields. Like David Reich in Who We Are and How We Got Here I believe that there was a political rationale for this. As someone who has read deeply in paleoanthropology and history for twenty years, I reject the idea that ancient DNA is actually not that revolutionary because I remember what passed as conventional wisdom 10-20 years ago.

July 3, 2018

Open Thread

Filed under: Open Thread — Razib Khan @ 11:57 am

Please keep the other posts on topic. Use this for talking about whatever you want to talk about.

July 1, 2018

Open Thread, 07/01/2018

Filed under: Open Thread — Razib Khan @ 4:49 pm

Thanks to everyone for getting us above 100+ reviews. Would be nice to have more than 10 reviews on Stitcher.

War! What Is It Good For? is a good book. Though it’s really more about social complexity than inter-group conflict. In this way, there are obvious resemblances to Ultrasociety. If you really want to read about war, War in Human Civilization is the way to go.

The decline in South Asian poverty.

The World Bank. Lots of interesting research on that website.

Happy birthday America!

June 27, 2018

Open Thread

Filed under: Open Thread — Razib Khan @ 10:14 am

Please keep the other posts on topic. Use this for talking about whatever you want to talk about.

June 24, 2018

Open Thread, 6/24/2018

Filed under: Open Thread — Razib Khan @ 7:58 pm

I recently read John Keay’s Midnight’s Descendants: A History of South Asia since Partition. No particular reason. But I’ve read earlier books on the history of India and China and I sort of wanted to fill a hole in my knowledge. I would recommend if you don’t know much about this period and place. It’s probably somewhat important in the future.

Thanks to all the readers of this weblog who have given iTunes ratings to my podcast. We’re almost to 100 ratings, so you won’t be hearing me go on and on about it.

Though speaking of the podcast, we’re going to talk to Ian Morris, author of War! What Is It Good For?: Conflict and the Progress of Civilization from Primates to Robots, soon. So subscribe now.

Erdogan’s Election Win Gives Him Vastly Expanded Powers in Turkey.

The Trailer for The Man Who Unlocked the Universe Is a Gorgeous Mixture of Science and Action. This looks like a good complement to Lost Enlightenment: Central Asia’s Golden Age from the Arab Conquest to Tamerlane.

It’s curious how many Central Asian warlords were patrons of culture. Mahmud of Ghazni, for example, supported Ferdowsi.

Just found out that Reihan has a new book out this fall, Melting Pot or Civil War?: A Son of Immigrants Makes the Case Against Open Borders.

Demographic inference in a spatially-explicit ecological model from genomic data: a proof of concept for the Mojave Desert Tortoise.

Bangladesh’s Secular Bloggers: Risking Their Lives for Freedom. A lot of atheist podcasts aren’t really “edgy” anymore. The Secular Jihadists is an exception.

Evolution of correlated complexity in the radically different courtship signals of birds-of-paradise.

The citizen scientist who finds killers from her couch.

Human demographic history has amplified the effects of background selection across the genome.

June 20, 2018

Open Thread, 6/20/2018

Filed under: Open Thread — Razib Khan @ 8:19 pm

I try to limit the shilling, but since readers of this weblog know what this means: Helix has a sale on kits until the end of the month. The three Insitome products can be purchased for app-only cost ($29.99) as an entrance into the ecosystem. In other words, for $29.99 you can get millions of markers in your exome sequenced, as well as some positions in the rest of your genome. Helix keeps the data, but there will be no kit cost if you see a future app that you want to purchase.

* Regional Ancestry
* Metabolism
* Neanderthal

If you are not subscribed to my total feed, you might not know that my review of She Has Her Mother’s Laugh went up at National Review Online. One thing that I’ve reiterated: it’s a very big book. A single review can’t really cover many aspects of what Carl touches on, and unfortunately even during the podcast I didn’t get to chimeras.

We’re almost at 100 reviews on iTunes on 10 on Sticher. I’ll stop bugging when we reach those milestones.

It’s been obvious to me that more and more people are protecting their Twitter accounts. Instead of a conversation the platform is about snooping on blow-ups and controversies.

In rapidly adapting asexuals, the orientation of G can reflect selection rather than functional constraints. Evolutionary, population, and quantitative genetics have been long-term interests of mine, so I love stuff like this. Adding a little genomics would be even better.

The most important study of the Mediterranean diet has been retracted and The collapse of a $40 million nutrition science crusade. Basically, it seems you should just eat what you want. Probably avoid processed food and trans-fats.

Diverse haplotypes span human centromeres and include archaic lineages within and out of Africa. Centromeres are crazy.

Harvard Office of Institutional Research on Discrimination Against Asian-American Applicants. I will blog about this at some point…and I’ve been making semi-serious/jokey tweets. But people are probably not clear on my “position.” My main irritation about Harvard is the extent of the doublethink that they get away with. Drew Gilpin Faust’s pablum about inclusion and diversity being central values at Harvard is a classic “Shaggy defense”. Faust helms a finishing school for the overclass, and as such accepts the necessity of discrimination when it comes to anointing future overlords. Some hypocrisy is necessary for the ruling caste, but the juxtaposition between “neoliberal” reality of what Harvard is, and the “progressive” rhetoric of it presents to the gullible and ignorant public, is starting to become indecent.

Speaking of overclass, Tim Draper is a third generation member of the capital class, and still defends Elizabeth Holmes.

With tantalizing early results, Sarepta’s gene therapy for Duchenne raises hopes for ‘real change’.

Close inbreeding and low genetic diversity in Inner Asian human populations despite geographical exogamy.

Genetic ancestry and population differences in levels of inflammatory cytokines in women: Role for evolutionary selection and environmental factors.

Population Genomics blog. The author is Chad Rohlfsen.

Re-identification of genomic data using long range familial searches.

Inference of species histories in the presence of gene flow.

How Much Does Education Improve Intelligence? A Meta-Analysis. It’s probably time to start reviewing stuff on psychometrics. The Ian Deary book is pretty good.

Open Thread

Filed under: Open Thread — Razib Khan @ 10:12 am

Please keep the other posts on topic. Use this for talking about whatever you want to talk about.

June 13, 2018

Open Thread

Filed under: Open Thread — Razib Khan @ 10:12 am

Please keep the other posts on topic. Use this for talking about whatever you want to talk about.

June 11, 2018

Open Thread, 06/11/2018

Filed under: Open Thread — Razib Khan @ 1:14 am

A few years ago a reader sent me a copy of Edward Feser’s Five Proofs of the Existence of God. Though I haven’t read that book, I did read a substantial proportion of Feser’s Aquinas: A Beginner’s Guide on a plane trip recently. I’m not a big believer in whole-hog Thomism, but I’ve read some Aquinas before and always admired his incredible intellect. Feser’s treatment seems to be a good introduction to that.

So a friend emailed me and wondered why I’m so hard on R.A. Fisher. To be honest the number one reason is that his own daughter seems to have written a rather unflattering biography when it comes to his personal temperament. That being said, let me pass on E. B. Ford’s R. A. Fisher: An Appreciation.

When it comes to any individual it’s easy to be at some remove from a situation and pass on lies because you don’t know any better. It has certainly happened to me.

Which brings me to what’s happened to someone named Wajahat Ali. He’s a Muslim American (Pakistani) public intellectual who has gotten in trouble with some Muslims because he violated some of the norms of BDS (though he never joined on with BDS as such, it’s become normative in many Muslim circles). To me, there are two curious aspects.

First, the general one that in some cultural milieus lies are very powerful, and became truth. If some people generate enough smoke, other people will assume there’s fire. It’s pretty obvious that the people accusing Ali of being an Islamophobe and Zionist-stooge are either liars or enthusiastic witch-burners. But there’s no huge penalty for making this stuff up, so only “upside” for the accusers.

It is also interesting that Ali contends that some people are finally standing up and admitting they know him, and all the accusations are lies, and they can’t listen to the lies any longer. The implication though is that these people were silent for a long while because they were afraid to stand by him when he was maligned unjustly.

A pretty honest commentary about our society today.

Second, Ali exposes the tacit racial hierarchy which is taken for granted in the Muslim American community. A few months ago a friend of mine who is a liberal (white) academic was saying some negative things about Hindu nationalism in relation to Islamophobia and wondered what Muslim students on campus would think about the tolerance that Hindu nationalist speakers are shown in the United States. My first thought: the only Muslims who care about Hindu nationalists are South Asians. Arabs probably don’t even know anything about Hindu nationalists.

The reality is there is one overwhelming concern of Muslim Americans, and that’s Palestine. To be entirely frank many Arab Muslims don’t give a shit what happens to South Asian Muslims. They’re not as callous to proactively not care. It’s just that it never really comes onto their radar. What matters to them is what is happening in the Middle East.

The converse is not true. South Asian Muslims care a great deal about Palestine. As they should: Arabs and Middle Eastern people, in general, are the center of Islam’s mental hierarchy. Not explicitly so. But implicitly, obviously. In general, Arabs will not listen to South or Southeast Asians, or black Africans tell them anything about Islam. In contrast, non-Arabs will listen to Arabs about Islam (Turks and Persians are a special case, and may not defer as much to Arabs).

Ali’s transgressions led to pretty straightforward observations he was being an uppity Pakistani who should leave Israel-Palestine to Arabs. He doesn’t seem to have been traumatized by this, but that’s because I assume he expected that that would happen. South Asians who don’t defer on these sorts of religious issues will be put back in their place. The mosque in New York I went to as a small child had an ethnic division of labor. The South Asians, mostly Pakistani and Indian doctors, provided funds when needed, and the Arabs ran the mosque and took on adult and childhood religious education.

What Really Happens in China’s ‘Re-education’ Camps. You probably know about the ethnic and religious targeting of Uighurs, and the fact that hundreds of thousands have been placed in re-education camps.

Back in the day, I used to read Tariq Ramadan’s books to get a sense of what intellectual Muslims think from a moderately conservative viewpoint. Today he stands accused of multiple rapes and admits that he had many affairs. The thing for me to reflect on is that I have no doubt that Ramadan believes in an all-powerful God. And yet he knowingly commits what he believes to be sin (extra-marital sex). And he may have raped women.

High-resolution comparative analysis of great ape genomes.

In to Asia. Lots of human evolution and paleoanthropology happened in Asia.

The Lifespan of a Lie: The most famous psychology study of all time was a sham. Why can’t we escape the Stanford Prison Experiment?

The expected time to cross extended fitness plateaus.

Remember to listen to this week’s podcast:

June 5, 2018

Open Thread, 06/05/2018

Filed under: Open Thread — Razib Khan @ 1:12 am

The Cultural Brain Hypothesis: How culture drives brain expansion, underlies sociality, and alters life history. I keep suggesting to everyone that they need to read more cultural evolution! But to be honest it’s hard for me to keep up. So much earlier reading evolutionary genomics, since I know the literature and the models far better.

Book recommendations, The Secret of Our Success: How Culture Is Driving Human Evolution, Domesticating Our Species, and Making Us Smarter. Yeah, it’s good. But for the more technically inclined, Mathematical Models of Social Evolution: A Guide for the Perplexed.

Two issues of guilt: I haven’t been keeping up with the comments, and also the South Asian Genotype Project. I’ll try to do better on that in the near future. Though a major cost there is I will then post less.

Probably keep an eye out for more stuff from me in NRO and India Today in the near future. Though if you follow my total content feed the NRO stuff already gets pushed into that automatically.

She Has Her Mother’s Laugh was reviewed in The New York Times. I plan on trying to get a review into NRO. Here is an important point: it’s a pretty diverse and long book, so any review is going to run with only a small sliver of the narrative. Honestly the stuff about marine cancer and chimerism is probably the most novel material, but that’s probably not going to take center stage in most reviews because it would take a lot of explanation.

In contrast, people “get” race, eugenics and epigenetics (or so they think).

I found the second half of The Rise and Fall of American Growth: The U.S. Standard of Living since the Civil War more of a slog than the first half. Why? I think it’s because I didn’t viscerally understand as well the difference between 1870 and 1940. In contrast, I get what’s changed between 1940 and 2010 (I think?).

I still think it’s worth a read. Lots of facts and footnotes.

So many in my “stack” before I could ever get to The Rise and Fall of the Dinosaurs: A New History of a Lost World. But this looks like a really good book.

Lots of debate on the Twitter on whether the Enlightenment “invented” racism. The problem that I see is that this is correct if you define racism in a very specific way. To be frank, an entirely Eurocentric way.

In God’s War: A New History of the Crusades, there is a section which covers tensions in the Egyptian court during the period of the Crusader kingdom. Basically, black slaves who traditionally guarded the harem had take a more prominent leadership role. The Circassian military slaves found this offensive on grounds of race and caste. The cultural context was clearly not anything that a 17th century Englishmen would recognize, but it’s pretty clear that the tensions at court organized themselves around race. You might say it wasn’t racism because there wasn’t an explicit Linnean taxonomy. But the implication is clear that the Circassians were not going to tolerate domination by black slaves who were customarily, if not by statute, subordinate. Kind of sounds racist.

Though I’ve read books like The History of White People, in general I find them too Eurocentric, with a particular focus on Anglo-America. Not that that matters as such, it’s just not to my taste to understand the general human condition.

But when we get into arguments about racism being invented in a clear and distinct fashion during the Enlightenment, it helps to have read books like God’s War, and have really good recall. Or a bit of Ibn Khaldun and his rather crass ethnography. Or you might read a history of Ming dynasty China, and recall that sometimes Portuguese sailors who were washed ashore were executed by officials, because they had blonde hair and blue eyes sometimes, and so were assumed to be Dutch (who were a priori pirates). The Ming were not racist as such, but they generalized racially in a manner which was unfortunate for fair Portuguese (and probably for dark Dutch, those these instances are not recorded, for obvious reasons).

Of course we know most people don’t know any of this, or Aristotle’s taxonomies, or the literature on folk biology.

Additionally, one thing I’ve noticed over the years is that in public debates historians often lie. They don’t lie in a bald-faced manner, they lie like Protagoras might lie. They play fast and loose with terminologies and shade the conclusions in a way that benefits their chosen tribe. Unlike physics history is really hard, and requires a lot of honesty. Unlike physics, historians seem to lack that quite often.

I know enough to be able to see them in action, because I know enough to know when they’re engaging in misdirection.

Speaking of history, John Julius Norwich has died. His Byzantium books are decent. Though you should always graduate to Warren Treadgold’s A History of Byzantine State and Society.

Uncertainty about social interactions leads to the evolution of social heuristics.

The genetic basis of mutation rate variation in yeast.

Andy Ngo Patreon. Honestly, I agree with him too much to read him a lot!

Outstanding questions in the study of archaic hominin admixture. Follow the citations.

The Discourse of Race in Modern China. I read this book 13 years ago. It was written 25 years ago. Seems like it is more relevant today than it was then.

Mystery ghost ape species found hidden in bonobo’s genome. Sometimes I wonder if the term “specie” and “population” are just getting totally overwhelmed with the complexity of the models that genomics is now throwing at us.

I don’t think genomics has transformed evolutionary biology in the broad sketches. But, it’s really specified a lot of details, and filled in gaps, and terms which had previous been pretty clear and distinct are getting really muddled.

Don’t usually say it straight out, but I might not be posting as frequently for a while. Need to catch up on family, keep up on work, etc. I feel like I’ll probably crank it up again when the next batch of ancient DNA papers come out.

Also, Patrick Wyman is on this week’s episode of The Insight. We take ancient DNA and Late Antiquity. I think you’ll like it.

May 28, 2018

Open Thread, 05/28/2018

Filed under: Open Thread — Razib Khan @ 11:45 pm

She Has Her Mother’s Laugh is now available. The interview with Carl Zimmer will be live on The Insight Wednesday night (EDT).

If you haven’t, please consider leaving a 5-star review on iTunes or Stitcher.

I’ve told that you can already read The University We Need on Google Books. I can’t vouch for this, but on Amazon the publication date is July 10th.

I suspect the field of cultural evolution is going to become big in the next ten years, breaking out its relatively rarified ghetto. If you haven’t, I’d recommend The Secret of Our Success by Joe Henrich.

The older, more technical books, are Cultural Transmission and Evolution, Culture and the Evolutionary Process.

I noticed the other day that the spam filter was a little overactive recently. Just in case you notice comments not going through….

May 20, 2018

Open Thread, 5/20/2018

Filed under: Open Thread — Razib Khan @ 3:40 pm

Warren Treadgold’s The University We Need: Reforming American Higher Education is going to come out in early July, but I’ve written my review. Don’t know when NRO will post it. In general, I’m positive. Though Treadgold has some ideological issues with Leftism in the academy, much of the book is apolitical and shines the light structural problems with contemporary academia.

It’s not a secret that I’m a fan of the author’s earlier work, A History of the Byzantine State and Society. So I checked some of the footnotes in The University We Need, and it turns out he’s a skeptic about the accolades given to Chris Wickham’s Framing the Early Middle Ages. Myself, I think both of these huge books are worth reading.

Bernard Lewis has died. He gets a lot of bad press from people like Edward Said of Orientalism fame, and over the last 20 years has become inextricably connected to neoconservatives who cheered on our nation’s foreign adventures. But a lot of his work is pretty interesting, especially the earlier stuff. I like The Middle East: A Brief History of the Last 2,000 Years.

On The Number Of Siblings And p-th Cousins In A Large Population Sample. I can’t say I follow all the mathematical details but jump to equation 7. But this preprint heavily informs Edge & Coop’s How lucky was the genetic investigation in the Golden State Killer case?

The Coming Wave of Murders Solved by Genealogy. The horse has left the barn and the great rush is on. Ultimatley this all going to be a normal part of forensic work soon enough.

I’m not sure that there’s a single fact yet in The Rise and Fall of American Growth: The U.S. Standard of Living since the Civil War that’s surprised me. Is this because so much of this stuff has now percolated across our culture (e.g., the increased demand for horses in the late 19th century due to complementarity with railroads).

That being said there is a lot of specific detail that’s of interest. For example, the proportion of households with telephones during the Great Depression dropped, but those with radios kept increasing as a fraction of the American populace. The reason is that telephones were rented and required recurrent payments, which many families could no longer afford, while radios were purchased once, after which usage was free.

I don’t know much about Jordan Peterson. Curiously the people who talk to me about him the most are moderate liberals who are annoyed about the demonization of him by the further Left. I don’t have much to say, except it’s shocking how many patrons he has, and, the Left-media attacks on him probably are making him more popular.

Men are far more dangerous than women:

Problematic anti-Semitism bill passes in South Carolina:

The Act, which if not challenged in court and struck down as unconstitutional, will require South Carolina’s public institutions of higher education to “take into consideration the [State Department’s] definition of anti-Semitism for purposes of determining whether the alleged practice was motivated by anti-Semitic intent” when “investigating, or deciding whether there has been a violation of a college or university policy prohibiting discriminatory practices on the basis of religion.”

Heavy-handed suppression of anti-Semitism on campus is going to lead to more, not less, anti-Semitism. You know why.

Genetic analysis of Sephardic ancestry in the Iberian Peninsula.

Hybridization and postzygotic isolation promote reinforcement of male mating preferences in a diverse group of fishes with traditional sex roles.

A New Way for DTC? Nathan Pearson, Root Deep Insight.

Was Kevin Cooper
Framed for Murder?

Farmers, tourists, and cattle threaten to wipe out some of the world’s last hunter-gatherers.

May 13, 2018

Open Thread, 05/13/2018

Filed under: Open Thread — Razib Khan @ 9:23 pm

The University We Need: Reforming American Higher Education is a funny book. The author, Warren Treadgold, is someone I know from his magisterial A History of the Byzantine State and Society. One of the complaints about A History of the Byzantine State and Society is that it’s too dry and academic. The University We Need is not dry at all, unless you are referring to the mordant wit on display.

Since I’ll be reviewing The University We Need for NRO I won’t say much more than that, except that Treadgold is most definitely in a “gives no fucks” mood. Yes, he attacks administrators as you’d expect, but he also slams Hillsdale, the professoriate, and students. He also has opinions about cafeteria food!

Italy’s 5 Star, League Reach Deal to Govern Nation. This sort of Left-Right hybrid to me illustrates that we’re in a “crisis of capitalism,” or more precisely a crisis of Western civilization. Italian total fertility rate is ~1.40. The rest is commentary.

Localizing and classifying adaptive targets with trend filtered regression. In Who We Are David Reich talks about his ambition to create a sort of encyclopedia of human genomic history. But once that history is established, we’ll need to move on to understanding selection. This preprint looks like it will be important.

23andMe Hits Ancestry.com With Patent Suit Over DNA Kit. One thing they are doing is suing over notifying about identity-by-descent. The “non-obvious” reason for awarding the patent is apparently the notification.

Intellectual property is a joke. But it’s also big business.

This week on the podcast we talked about the grandmother hypothesis with Kristen Hawkes. I should have been more aggressive in jumping in to get her to clarify what “life history theory” was. Live and learn.

We are now at 20 podcasts. If you can, please subscribe with iTunes or Stitcher. Also rate us highly and leave positive views if you can!

Carl Zimmer’s podcast has been recorded already, but won’t be dropped until close to when She Has Her Mother’s Laugh is published. We’re also recording a podcast with Patrick Wyman of Tides of History. This should be “evergreen”, at least on the scale of a year, so expect that in June or later.

The next few weeks we’re going to go it alone with just Spencer and myself, talking about a few topics we’re both interested in. It’s a good change of pace. We’ve got some ideas for what we’re going to talk about in June. I think it is most definitely important to follow-up on the Indo-Aryan podcast, which we actually recorded in July of 2017, though we didn’t drop it until 2018.

There was an interesting fiasco on Twitter recently where some semi-prominent people asserted that Andrew Sullivan was against gay marriage. This is really bizarre because Sullivan was a major proponent of the idea before it was ever mainstream, and for a period also got resistance from the more radical anti-bourgeois faction of the gay rights movement.

Anyway, the mistaken tweets occurred because Sullivan is transforming into a hate-figure on the Far Left, and a lot of people are Twitter are stupid and ignorant, so they just inferred facts from their theory that Sullivan is right-wing. Some of these people retracted the falsehood grudgingly but as usual you can see that retweets and likes are/were more evident on the original tweet.

The point is repeating all this is this is how “knowledge” is created now. If you have a prominent Twitter account it’s trivial to inject falsehoods into the debate. I’ve seen people doing this pretty consciously several time (this is really common in anonymous/pseudo accounts).

At the Brown Pundits weblog, I put up a post on this strange Slate piece on how the 1990s TV show Friends is contributing to sexism and homophobia in India. Though ostensibly about India, and narrated by an immigrant from India, the piece is about preoccupation within American culture in 2018.

A publication like Slate is going to get a lot of clicks if they post something about misogyny and homophobia in Friends, but how to make it novel? Pretend it’s actually about India! To me, this is to journalism to science fantasy is to science fiction.

Societies and cultures in relative decline and undergoing stagnation tend to undergo a period of involution. Narcissism writ-large.

I also wrote a post on Brown Pundits on why India did not become mostly Muslim. Need to think a lot more on this. Not all the comments were dumb.

Reading the coalescent chapter in Molecular Population Genetics, and it’s amusing to note that the coalscent’s big advantage over forward-simulations in terms of computational horsepower needed isn’t really that big of a deal today. Even a few years back this was a huge issue. This is like in phylogenetics where everyone runs Bayesian stuff, where 15 years ago people were having a hard time imaging max-likelihood!

While reading Molecular Population Genetics I keep hearing the author’s voice in my head. I think this has to do with the fact that I know the author before I read his books. This didn’t happen when I read She Has Her Mother’s Laugh because I had read Carl Zimmer before I got to know Carl in person. At least that’s my theory (The 10,000 Year Explosion was all in Greg Cochran’s voice).

Reading too much about Rome. So Carthage Must Be Destroyed is in the stack.

A systematic assessment of ‘Axial Age’ proposals using global comparative historical evidence. The argument here is that the “Axial Age” wasn’t a singular time period, but a continous event that spanned thousands of years. I think this is probably right, though “ages” are conceptually useful mental bookkeeping. This is similar to the idea that age cohorts are a real thing, but generations are not.

The Infectious Enthusiasm of Breaking the Bee.

Detection of shared balancing selection in the absence of trans-species polymorphism.

Self domestication and the evolution of language.

I need to set aside a day to catch up on the South Asian Genotype Project (SAGP). Also, figure out which plugin is causing the 500 errors.

May 7, 2018

Open Thread, 5/07/2018

Filed under: Open Thread — Razib Khan @ 11:29 pm

Longtime readers are well aware that A History of the Byzantine State and Society is one of my favorite books. To understand the Middle East right before the arrival of the Mongols and the emergence of the Crusader states, one has to understand the expansion of Byzantium in the early 11th century, and it’s subsequent regression in the late 11th and 12th centuries. In 2005 I actually did a 10 questions with the author, Warren Treadgold.

So I’m very excited to be reviewing his new book, The University We Need: Reforming American Higher Education, for NRO.

Had a chance to read Matt Hahn’s Molecular Population Genetics. The con is that it’s an $80 book that’s 350 pages. This is not a replacement for Principles of Population Genetics or Introduction to Quantitative Genetics. Rather, as alluded to by the title there’s a lot of focus on molecular evolutionary and population genetics. Imagine a population genetics book written with an assumption that you know what a SNP-chip is and have access to genome-wide sequence data. In some ways, it’s similar to Rasmus Nielsen’s (and Slatkin) An Introduction to Population Genetics. But these books reflect the authors.

For example, if you look up “site frequency spectrum” in An Introduction to Population Genetics there are seven pages. In Molecular Population Genetics there is one page on this topic. Anyone familiar with the work of these researchers would totally expect this. If you are a pop-gen nerd, there’s really no debate. You need to get Molecular Population Genetics or steal it from a friend. But a bigger question is why I recommend seemingly esoteric books to my readers. I say seemingly because understanding the population genetics in the generality makes a lot of the detailed more specifically interesting stuff much more comprehensible.

The readership of this weblog is small but self-selected. If you consider yourself an intellectual person and have some disposable income and leisure you should be developing yourself in various ways outside of the professional sense.  If you are reading this weblog you are likely to be the type of person who wants to understand things not just because one gets paid to understand things, but because understanding things is an end unto itself.

I am privileged to be paid to explore various topics related to certain intellectual interests (human population genomics), but I believe that something would be seriously wrong with me if I limited my inquiries to this narrow topic. Therefore I read a fair amount of history, and take an interest in topics like cognitive science and Biblical scholarship. Part of my attempt on this weblog to is to add population genetics to the list of interests of people who are professionally not engaged with the topic, whether they be in closely related fields (e.g., a theoretical ecologist) or in a totally different line of work (union organizer).

The Neutral Theory in Light of Natural Selection. This review is free. One of the great things about this is that it kind of revived a corner of science Twitter which had started to go into senescence (Patrick Phillips has been at the center of several of these discussions).

Related to our podcast topic from this week, Doc Edge and Graham Coop have read the definitive formal take, How lucky was the genetic investigation in the Golden State Killer case? The TL;DR version is not that lucky. They show formally that with a database of ~1 million individuals with SNP-data it’s likely that you’ll get relative matches that might be useful. More precisely, a database of ~1 million means that there is a ~90% chance of at least one 3rd cousin match. There’s even a 25% chance of a 2nd cousin match! A database of ~5 million gives a 75% chance of a 2nd cousin match, and ~10 million gives a 90% chance of a 2nd cousin match. These are around the range of the databases of 23andMe and Ancestry right now.

As the authors say: “it’s a question of deciding the circumstances under which we as a society want these familial searches to be used.”

Tales of Human Migration, Admixture, and Selection in Africa.

The evolutionary history of human populations in Europe. Preprint by Iosif Lazaridis.

There is a certain number of traditional liberals with a libertarian bent who I’ve always admired. Nadine Strossen is one of those (Wendy Kaminer is another). Strossen is out with a new book, HATE: Why We Should Resist It with Free Speech, Not Censorship (Inalienable Rights). It strikes me this is conservative in the literal sense in that she is attempting to defend a late 20th-century liberalism which is now on the wane.

The Liberal Media Can Have Ideological Diversity Without Conservatives. Two sections jump out at me. First, “the social conservative’s view on fetal personhood is unfalsifiable — and does boast a significant constituency — but it doesn’t generally lend itself to novel or engaging debates.” The issue with abortion is not about debating, as much as it is important to not always put forward writers who implicitly assume that the pro-choice position is the only view that one might entertain. I’m skeptical of some of the leaps that pro-life writers make based on their political position…but then, I’m not pro-life. It’s important to at least know the views of other people.

Second, the author suggests that Left-wing socialists who believe that the people should control the means of production (as opposed to simply redistributive socialism as is the case in Scandinavia) should be given a fair hearing, though they observe “concentrating financial power in the state apparatus has often been an invitation to tyranny.” Yeah. That.

Pretty straightforward establishment liberals, such as Matt Yglesias, are starting to assert that publications like The Atlantic and The New York Times are equivalent to National Review, in their ideological valence (the argument being that they shouldn’t have to hire conservatives since they’re liberal publications). Conservative critics have long asserted this, but now liberals are agreeing.

Conservatives have lost the universities and the press. Both these institutions don’t even make a pretense at evenhandedness at this point. The broadly liberal center is eroding. I suspect that people like Nadine Strossen will be viewed in the future like Cato the Younger.

Stuff You Missed in History Class podcast, Mohenjo Daro. People don’t really know much.

Interviewing Carl Zimmer for the podcast this week. Taking suggestions for questions to ask him (we have a finite time so might not get it in….)

 

April 29, 2018

Open Thread, 04/29/2018

Filed under: Open Thread — Razib Khan @ 10:05 pm

One of the strange things about getting old is that your friends start to become kind of a big deal. Matthew Hahn has a new book out, Molecular Population Genetics. If there is one single reason I keep blogging, it’s to get awareness of the field of population genetics to spread beyond the small circle who are “in the know.” I joked on Twitter that buying this textbook is like spending money to talk to Matt about pop-gen, and that’s surely worth it.

Another one for the stack!

Speaking of worth it, Kyle Harper’s The Fate of Rome: Climate, Disease, and the End of an Empire is definitely worth a read. Not done, and I’m not sure it’s better than The Fall of Rome: And the End of Civilization. Perhaps my issue is that exogenous shocks are to be expected in my view of the world. Though the details in The Fate of Rome are novel, the general thesis and framework were what I’d assumed were taken for granted.

What Happens When Geneticists Talk Sloppily About Race. I don’t think that David Reich was sloppy…though the op-ed was edited in a way that was confusing. That being said I’ve heard through the grapevine that some prominent human population geneticists may write a response to David’s op-ed, which is something I want to see. Part of me still thinks that these vigorous public discussions are important (another part of me just thinks that when Sulla or Marius take over all this old-fashioned fixation on truth will be irrelevant).

One thing stated in the piece above is that regular people have a Platonic model of race. This is true. But it is also a fact that geneticists have not done a good job of explaining to the educated public what population structure is, and why it’s not trivial or arbitrary. I know this from personal experience over 15 years interacting with people about genetics online (some of the funniest interactions are on Facebook where a person of professional class background/status “genetics-splains” me about how I don’t understand the extent [lack] of human genetic variation and how arbitrary population cluster identity is).

With The Genomic Formation of South and Central Asia I obviously think we have the broad outlines of the peopling of South Asia in hand. There will be lots of detailed elaborations of how/what happened, but I think the big picture is nailed down.

That being said some of the objections remind me a lot of Creationist tendencies. Creationists often focus on weak points and hammer in on them over and over.

One of the weird things about Indian genetics is that a lot of people think new research will overturn Hindu nationalism. But I know several Hindu nationalists, and privately they tell me that most Hindu nationalists don’t care about these abstruse issues, and many of the more intellectual ones don’t have a major problem with the science.

GEDmatch, Ysearch and the Golden State Killer.

Anthropogenic habitat alteration leads to rapid loss of adaptive variation and restoration potential in wild salmon populations.

Bracketing phenotypic limits of mammalian hybridization.

A few people have asked about the podcast. We skipped a week, but we’ll be back. Taking some feedback in relation to various aspects of the show. A common issue seems to be that my voice is too quiet though Spencer’s is “just right.”

Again, if you use Stitcher or iTunes please remember to give us positive reviews and 5-stars!

If you have ideas for shows, we’re game.

April 24, 2018

Open Thread, 4/24/2018

Filed under: Open Thread — Razib Khan @ 12:23 am

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.

April 17, 2018

Open Thread, 4/17/2018

Filed under: Open Thread — Razib Khan @ 3:01 am

Almost done with She Has Her Mother’s Laugh: The Powers, Perversions, and Potential of Heredity. To be honest I’m a little relieved that there wasn’t that much focus on the “perversions” of heredity. Lots of interesting stuff. This is definitely a book that scientists and lay people could benefit from.

Carl is a great writer so he makes rather abstruse concepts clear and engaging to nonspecialists. As for those of us who have our noses close to the ground, we sometimes lose the bigger perspective. There is a lot of interesting research that he surfaces in She Has Her Mother’s Laugh that I wasn’t very familiar with, though I had probably read about it or seen it in one of his columns (or Ed Yong’s).

Met a lot of cool people, and touched base with others who I knew ahead of time, at the AAPA 2018. Compared to ASHG or even SMBE the conference was very white. I guess that’s why there were all the diversity sessions?

Lee & I

I had a lot of discussions with Lee Berger about science on a broad philosophical level. Unfortunately, specialization is such that it can be hard to communicate across disciplines such as human genomics and paleoanthropology. But as Lee brings enough samples into the open to do some real statistics I think that will change how constrained to the elect paleoanthropological knowledge is.

Braai

Lee’s son introduced me to the concept of South African barbecue. I haven’t had any yet, but I’m curious about it.

Lee will be on this week’s episode of The Insight. Again, please subscribe on iTunes, Stitcher, Google Play. The last episode with Stuart Ritchie was our most successful yet in terms of traffic. We’re suspecting that Lee’s episode will do quite well as well. People keep finding the podcast by chance. We really need reviews to get featured by iTunes!

Spencer and I will probably shift back to a two-person conversation next week. We should probably do an AMA again soon.

Was There a Civilization On Earth Before Humans? Very interesting piece, especially for those of us who have read science fiction. But my issue is straightforward: humans have scrambled biogeography so much in such a short amount of time. I think any other industrial species would have done the same. Even after they went extinct, the phylogeographic chaos they wrought would remain.

It seems very likely that all Australian marsupials descend from one South American ancestor species. The explosive emergence of very different placentals all across Australia simultaneously in the fossil record would be quite suspicious (or red deer descendants in New Zealand).

I spent some time with the people who were associated in some way with the Reich lab a fair amount during the AAPA meeting. I also talked to a few friends about what they thought about David’s op-ed and book. It’s no surprise that there are legitimate human population geneticists considering writing a response of some sort. It’s also no surprise that even critics of David within the population genetics community think that the Buzzfeed op-ed was so bad that it makes it harder for them say something, as the water has been nuddied.

In some ways the reaction has made one of David’s major points: population geneticists need to offer their unvarnished opinions, rather than cosigning people in other fields who mangle their findings.

Some people feel that David “threw me under the buss” in his now infamous chapter. I don’t see it that way.

As many of you know (if you subscribe to my total content feed you know) I have a few other blogs, one of them Brown Pundits. It actually receives substantial traffic from India now. It will be “interesting” to say the least.

A population genetic interpretation of GWAS findings for human quantitative traits. Stuck in the weeds of ancient DNA these past few years I haven’t been paying attention to the storm of GWAS and PRS approaching.

Signatures of negative selection in the genetic architecture of human complex traits.

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