Open Thread, 12/11/2017

Thinking back to The Turks in World History the author points out that even the most explicit Islamic of the late Turkic empires, that of the Ottomans, persisted with a customary law similar and cognate to the Mongol yasa. Perhaps then the folkway of the nomadic Turk was sublimated and integrated into the Islamic superstructure of the Ottoman ruling ideology?

I went to a work-related Christmas party thrown by my company’s law firm. There were a lot of VC guys there. Two of them confused me for a blockchain entrepreneur (one of them was asking about a conflict with the CFO). I think I better get into blockchain….

So the website Everyday Feminism has an article, 10 Things Every Intersectional Feminist Should Ask On a First Date. I only know about this website because of conservative Twitter. It could be that 90% or more of the hits on this website are through viral “hate-clicks”.

Second, I feel the image that goes along with the article is problematic as fuck. The woman pictured seems to be geared toward appealing to cishet male norms of “attractiveness.” On the other hand, if intersectional feminists typically look something like Josie Maran…well, I won’t go there.

I will observe also that I find out about a lot of far-right movements and individuals through Left and Centrist Twitter (the two groups are interested for different reasons).

As noted in the comments, The Irish DNA Atlas: Revealing Fine-Scale Population Structure and History within Ireland. At this point, I think I can say this: unless it’s ancient DNA I’m done with the historical genetics of the British Isles. We know enough. Period.

Why the #MeToo Movement Should Be Ready for a Backlash. I don’t care too much about Al Franken, but digging a little deeper I think there might be some dirty tricks going on there…. I was rather dim on the prospects for Republicans in 2018, but at this rate, the Dems might “struggle-session” their way into defeat.

India Warily Eyes AI: Technology outsourcing has been India’s only reliable job creator in the past 30 years. Now artificial intelligence threatens to wipe out those gains. When I believed in the End of History and the Last Man this would matter to me. Now it’s all a big shrug.

The ancestral animal genetic toolkit revealed by diverse choanoflagellate transcriptomes.

Another reason that helper-AIs can’t come to medicine soon enough:

Chronicler of Islamic State ‘killing machine’ goes public.

As home DNA tests become more common, people must grapple with surprises about their parents:

Until recently, Andrea Ramirez, 43, thought she was part Mexican.

But the results from an at-home genetic test from 23andMe revealed that she is a mix of Northern European, North African and a little Native American.

And not at all hispanic.

There can be no genetic test for being Hispanic because that is a socio-cultural identity. There are Korean, Arab, and Nordic Hispanics. Even the most common genetic profile varies, from mostly European Argentines to mostly indigenous Bolivians to Afro-Cubans and Afro-Colombians.

When I read stuff like this I really wonder what they teach journalists (the Census explicitly declaims the the idea that Hispanic is a racial category).

I spent a fair amount of time this weekend cleaning up scripts that can batch process 23andMe, Ancestry and FamilyTree DNA input files and push them down the pipeline toward generating admixture percentages. I have posted the most current results from the South Asian Genotype Project have been posted.

Two things

1) I’m not happy with the clusters that I used. I may change them (in which case I’ll rerun everything).
2) Once I’ve done that I’ll probably send some of my scripts to Zack Ajmal and he can run all the Harappa individuals with this new cluster.

Finally, people from the “Cow Belt” don’t get genotyped. No submissions from UP or Bihar so far. Very frustrating.

The word problematic is problematic in my opinion. I really want to punch people when they use that word. But I’ve lost that battle.

My friend Chad Niederhuth is starting his plant genomics lab at Michigan State. He’s looking for graduate students and postdocs.

My friend Nathan Pearson’s HLA genomics start-up, Root is out of stealth mode.

Looking at my Kindle stack wondering about which of these five books to tackle next:

Open Thread, 11/4/2017

A disproportionate number of submissions to the South Asian Genotype Project have been Bangladeshi. That surprised me. Though I’ve gotten a few obscure submissions, so all for the good. I’ll update submitters by email in the next day or two and probably note something on next week’s open thread.

If my original post wasn’t clear: I really hope to get more samples from the “cow belt.”

One thing I should be explicit about: my reading of history leads me to believe that social and cultural revolutions can happen really fast because of nonlinear dynamics. This is why ‘predicting’ history is such a mug’s game. The way it seems to work is that everything is fine, then next thing you know you’re face is smashed against a windshield with no warning. To give a concrete example, in 1785 it would have been hard to imagine the religious dimension in the War in the Vendée less than 10 years later. Similarly, Germany in the 1920s was one of the most socially liberal societies on the planet. And, in the Europe-wide context for several decades German Jews were among the most assimilated and tolerated populations on the continent.

Been busy with work and stuff leading up to Holidays. What’s going on?

Open Thread, 11/26/2017

A few days ago there was a Twitter thing about top five books that have influenced you. It’s hard for me to name five, but I put three books down for three different reasons:

  • Principles of Population Genetics, because it gives you a model for how to analyze and understand evolutionary processes. There are other books out there besides Principles of Population Genetics. But if you buy this book you don’t need to buy another (at SMBE this year I confused Andy Clark with Mike Lynch for a second when introducing myself. #awkward)
  • The Fall of Rome. A lot of historical writing can be tendentious. I’ve also noticed an unfortunate tendency of historians dropping into contemporary arguments and pretty much lying through omission or elision to support their political side (it usually goes “actually, I’m a specialist in this topic and my side is 100% correct because of obscure-stuff where I’m shading the facts”). The Fall of Rome illustrates the solidity that an archaeological and materialist take can give the field. This sort of materialism isn’t the final word, but it needs to be the start of the conversation.
  • From Dawn to Decadence: 1500 to the Present: 500 Years of Western Cultural Life. To know things is important in and of itself. My own personal experience is that the returns to knowing things in a particular domain or area do not exhibit a linear return. Rather, it exhibits a logistic curve. Initially, it’s hard to make sense of anything from the facts, but at some point comprehension and insight increase rapidly, until you reach the plateau of diminishing marginal returns.

If you haven’t, I recommend you subscribe to Patrick Wyman’s Tides of History podcast. I pretty much wait now for every new episode.

The big Washington food fight. GMO labeling is coming.

In Our Time has two very good episodes recently I recommend on the Picts and Thebes.

The Unexamined Brutality of the Male Libido. When I read the title I assumed that the piece was somehow informed by evolutionary psychology. No. It’s larded with Freudianism.

Evolutionary psychology has taken its hits over the last 15 years, and rightly so when it’s basically re-warmed social psychology, but the stuff informed by primatology is 21st century science (you can agree to disagree, but there’s something to grab onto there). Freudianism sometimes gets a bad rap even though its origins were not nearly as woolly as we might think, but cutting-edge early 20th century psychology is really beyond its sell-by date today.

This is the stuff that makes me pessimistic that the “replication crisis” is going to have any impact on the media or the public. For example, At Yale, we conducted an experiment to turn conservatives into liberals. The results say a lot about our political divisions in The Washington Post. The author of the op-ed is a major person in the center of the controversy around replication. In particular, “ego depletion.” This op-ed is based on studies with p-values of 0.034 and such.

That being said, Radiolab has an episode on Stereotype Threat which acknowledges worries about its replication. Really all that matters to me is the funnel plot.

Detecting past and ongoing natural selection among ethnically Tibetan women at high altitude in Nepal. It’s polygenic and we don’t understand the architecture of the trait that well it seems. Basically, early selection sweep analysis detected some major loci, but it’s not the whole story. Reminds me of pigmentation.

An endogenous retroviral envelope syncytin and its cognate receptor identified in the viviparous placental Mabuya lizard. This is pretty cool, the same process seems to be occurring over and over.

Rethinking phylogenetic comparative methods. I think this is will be an impactful paper once it gets published.

Meanwhile, this looks interesting: The role of chromosomal inversions in speciation.

I posted some Taylor Swift memes to Twitter as a joke. They seem quite popular, especially the ones related to string theory and evolution, though the one related to Arminian and orthodox Calvinist soteriology took off in a different sector of Twitter.

The funny thing is several people were angry because they thought I was putting down Taylor Swift. I was just making fun of the media fixation on famous people and their stupid thoughts.

My friend D. Allan Drummond has gone “full artiste.” He’s now selling some of his incredible biologically-themed 3-D printing. You can read about his work in this profile at Nerdist (by day he’s a biochemist who used to be an evolutionary geneticist who used to be an engineer).

Open Thread, 11/19/2017

So we put up a 3rd reviewer mug. Kind of an “inside joke”, but we liked it. One thing we have noticed: people really like the DNA helix logo. They click it. They buy it. More visual, less wordy.

One thing that’s funny, when it paternal haplogroups I1 clicks a lot, but they never buy (in contrast to R1b).

Thousands of horsemen may have swept into Bronze Age Europe, transforming the local population. The piece is pretty expansive, though something of a mess. But it’s a mess because there are still unresolved issues.

There’s a Digital Media Crash. But No One Will Say It. Privately my friends in the media tell me exactly this. It’s going to get worse before it gets better. There are many reasons, but it’s happening.

The Evolutionary Genomic Dynamics of Peruvians Before, During, and After the Inca Empire. Similar thing in Mexico: old population structure is still there!

Singleton Variants Dominate the Genetic Architecture of Human Gene Expression. Genomics is a little overhyped, at least in evolution, but it can really do incredible things nailing down the specific details of what’s going on.

The nature of nurture: effects of parental genotypes and Estimating heritability without environmental bias.

Don’t throw out the sympatric species with the crater lake water: fine-scale investigation of introgression provides weak support for functional role of secondary gene flow in one of the clearest examples of sympatric speciation.

I’ve spent a little time reading Oathbringer this week, mostly before I go to sleep. It’s a little hard to keep track of everything because it’s been seven years since the first book and over three since the last one. Since Brandon Sanderson projects ten books in the series I doubt I will finish this out. At the current rate of production I will be thinking about retirement when the Stormlight Archive is near completion!

But reading Oathbringer it did come to my mind that Sanderson has done a really good job in building a world which is fundamentally not just a European Middle Ages retread, as is the norm in much of fantasy. There are so many new words and characters to keep track of I think I didn’t internalize this in the earlier books. So I did a little Googling and found that Sanderson was trying to do the same thing that Frank Herbert did in Dune, by creating a whole new and novel ecology.

Secondly, he has mentioned that most of his characters are not white and that he has struggled to make sure that they are not depicted in stereotypical European fashion in cover art. The primary protagonists are in fact a people who he imagines to be a hybrid between East Asians and Middle Easterners (his time in Korea as a Mormon missionary inflected his world-building), though that is simply the closest analog. He specifically states that the one human race without epicanthic folds, and look the most European in feature and complexion, are often assumed to be East Asian in by readers because of their exoticism and name (Shin).

Charles Manson has died. I haven’t read it, but have heard good things about Jeff Guin’s Manson: The Life and Times of Charles Manson (it seems like it’s a cultural history).

Precise dating of the Middle-to-Upper Paleolithic transition in Murcia (Spain) supports late Neandertal persistence in Iberia. What we’re learning is that our patchy understanding of the human past also understates how patchy and uneven many dynamics were.

The day the Pintupi Nine entered the modern world. The story of nine people who were totally isolated from the modern world until 1984. They were scared when they met relatives who had lived in a town. To convince them to stay the relatives had them taste sugar.

Open Thread, 11/12/2017

One of the major insights of contemporary cognitive psychology is that a lot of human mental processes emerge from the intersection of lower level intuitions/models/instincts. The key is to remember that a lot of mental operations occur implicitly and rapidly, and we often construct ad hoc rationalizations after the fact (see The Enigma of Reason).

Because rationality is such a good talker many of us have deluded ourselves into thinking that instead of being a mouthpiece and a lawyer that gets us out of sticky situations, it’s actually calling the shots. No.

Anyone interested in these topics should check out Paul Bloom’s Descartes’ Baby: How the Science of Child Development Explains What Makes Us Human (or his other books).

This comes to mind when thinking about issues that have been bubbling up in our society. A friend on Facebook who is an evolutionary anthropologist wondered about the context of Harvey Weinstein’s serial rapes. I think A Natural History of Rape: Biological Bases of Sexual Coercion get’s a bad rap because of the incendiary topic, but in this case, I think cognitive psychology yields a quicker and clearer answer. Weinstein is a very wealthy man, so if it was sex with nubile women he could have paid for high-priced escorts (and it seems he did on occasion). But cognitive psychology suggests that people crave “authenticity.” Weinstein’s targeting and abuse of women he knew professionally and personally clearly provided for him an addictive frisson that paying for sex wouldn’t have given him.

Today people are passing around this “shock poll,” Poll: 37 percent of Alabama evangelicals more likely to vote for Moore after allegations. Probably most of these people think this is a politically motivated hit. That being said, it brought to mind a passage from In Gods We Trust where respondents asserted that disconfirming evidence in regards to their beliefs actually made them stronger in their beliefs.

In other words, when it comes to deeply held beliefs people aren’t going to react in a straightforward manner to reason and logic. Don’t be surprised if they behave irrationally. If the irrationality is consistent across individuals there’s probably some deeper psychology you aren’t accounting for.

The problem of doctors’ salaries. The AMA licensing cartel is keeping the supply of medical services constrained. Yes, we need more doctors. But we need more non-doctors to be able to do things that only doctors can do right now.

On the other hand, medical doctors have on average $200,000 of educational debt when they graduate. The high debt load is probably in part because there is the assumption that they will be making between $200,000 and $400,000 per year (though with income tax rates, as well as malpractice insurance, remember their net take home is considerably less).

These sorts of structural features are why we can’t have nice things. I suspect most people agree that the American tax code should be reformed…but peoples’ choices have been made with deductions in mind!

We’re rolling out more shirts for DNAGeeks. Eight people have bough GNXP t-shirts. Would be curious to post a picture of someone wearing one of those. A little surprised, but the Evo-Devo t-shirts are selling well. Anyone have any ideas for something more pop-gen related?

I love maps [THE MAP IS FAKE!] which have more granularity than country vs. country comparisons. I really hate when people compare the USA to European countries. California alone is nearly as populous as Spain, which isn’t even a small European country.

The map to the left shows the areas of high GDP in South Asia, though resizing region by the size of the population would help give a better sense. The distinction between urban and rural is very stark in Bangladesh.

I predict Twitter will be clearly in a death spiral in a year. The proportion of highly polarized political chatter on my timeline keeps increasing, even though I’m not following anyone different. The vibrant years of “genomics twitter” seem to be a thing of the past.

The above tweet has gone somewhat viral. What did I mean above? The sort of thing in The End of History and the Last Man, that the terminal stable state of humanity would be post-materialist secular individualist liberalism. Though secularism seems to remain ascendant in the West, for now, the post-materialist individualism liberal project seems to be fraying. Instead of Western culture being a stand-in for global culture, it may be in the near future it will again be just another culture among cultures.

Open Thread, 10/29/2017

Read some of The Red Flag: A History of Communism. In the interests of being candid, I do have to say that many intellectuals today who are skeptical of Communism might be much more open to the ideology in the early 20th century. Marxism literaly hadn’t been tried.

The key issue is that it has been tried.

Kids very excited about Halloween.

The CRISPR stuff is exciting.

Open Thread, 10/22/2017

Reading The Turks in World History and confused how any state whose elite were non-nomads held out before the gunpowder revolution. Also, the persistent defection of Chinese generals and soldiers to the side of the barbarians is interesting light of other conversations we’ve had.

Are there any (post-)Roman examples of this? I know that an early Dark Age a major Slavic warlord was actually a Frankish merchant (Samo). But did whole units “go native”? Seems likely in Francia and Britain.

ASHG in Orlando is over. Much more excited by ASHG in San Diego next year, because it’s in San Diego. That being said the conference seems to be moving into a strong clinical genomic direction.

Lots of stuff going on. Still recuperating. My company released a Metabolism app.

A paper from a few years ago argues that we could sequence the whole world by 2025 (capacity).

This paper argues 60 million will be sequenced in healthcare context by 2025. Seems conservative.

Went to a Broad Institute presentation where they said they had 300,000 exomes and 85,000 whole genomes sequenced.

Now that researchers are converging in the likelihood that  modern humans spend the vast majority of their time in Africa, it looks like evolutionary population genomics in the next 10 years will really focus on that continent.

 

Open Thread, 10/15/2017

E. O. Wilson has a new book out, The Origins of Creativity. Did you know about it? Honestly totally surprised. Wilson’s been retired for a while now, so his profile isn’t as high as it was. He’s 88, so you got to give it to him that he can keep cranking this stuff out.

The New Yorker introduced me to Against the Grain: A Deep History of the Earliest States. This is a topic that I’m interested in, but I’m not sure I disagree with the author at all, so I doubt I’d get much out of it for the time invested.

Basically, I agree with the proposition that for the average human being quality of life was probably somewhat better before agriculture, until the past few hundred years when innovation increased productivity and the demographic transition kicked in.

Will be at ASHG meeting Tuesday night until Saturday morning. Going to be at the Helix session on Wednesday and probably man their booth for an hour.

This year seems a little light on evolutionary genomics. Perhaps the methods posters will be good though.

Wolf Puppies Are Adorable. Then Comes the Call of the Wild. Basically, it looks like there are some genetically based behavioral differences which makes dogs amenable to being pets and wolves not so much.

Na-Dene populations descend from the Paleo-Eskimo migration into America. Not entirely surprised, but kind of nails it down for good. One thing to remember is that New World and Old World were not totally isolated before the arrival of the Norse and later Iberians. For example, the Asian War Complex shows up in northwest North America 1,300 years ago.

The Decline of the Midwest’s Public Universities Threatens to Wreck Its Most Vibrant Economies. I think it is important to remember that economics is a means, not an ends. There is plenty of evidence that conservatives in the USA see academia as hostile to them and inimical to its values. On a thread where Alice Dreger asserted the importance of truth as the ultimate goal of an academic, one scientist unironically wondered how they could make their research further social justice goals.

So yes, many people who are going to try and defund academia understand that might not be optimal for economic growth. But if they believe that they’re funding their own cultural and political elimination, they don’t care.

An Alternate Universe of Shopping, in Ohio. Another story about the transformation of retail. One thing that is curious and strange to me is the evolution of the idea and perception of the mall over the past 25 years. Back in the 1980s malls were modernist shrines to the apogee of American capitalism. Today they seem mass-market and declasse. Part of it is that you don’t want to be a member of a club that everyone can join.

California Fires Leave Many Homeless Where Housing Was Already Scarce. This is horrible on so many levels.

An Unexpectedly Complex Architecture for Skin Pigmentation in Africans.

Over at Brown Pundits I wrote Race is not just skin color. I didn’t post it here because frankly it just seemed a silly thing to even have to explain.

Variation and functional impact of Neanderthal ancestry in Western Asia .

A few weeks ago over at Secular Right I wrote Why Trump could murder someone and people would still support him.

1977–2017: A Retrospective. Peter Turchin reminds us that for Russians the 1990s were horrible.

This graph from Planet Money blew up for me a bit on sci-twitter. The thing is that it’s easy to talk about racial and sexual diversity (or lack thereof) because it’s visible. On the other hand, people from less affluent backgrounds may not want to advertise that, so many are unaware of the implicit class assumptions that many people make:

Open Thread, 10/01/2017

Thinking about Big Gods: How Religion Transformed Cooperation and Conflict. It’s a good book. I’d recommend it. But a lot of the research highlighted pre-dates the era of the “reproducibility crisis.” That is, some of the positive results just didn’t end up being replicated after this book was written (more ethical behavior if you show people false eyes is mentioned, as are priming studies).

I think this is a general issue for anything written before 2015 that deals with psychology (unless it’s a book that to some extent tries to refute the ubiquity of overly sexy ideas, like The Invisible Gorilla).

Patrick Wyman has a podcast, The Fall of Rome Podcast. He comments on this weblog now and then. Recommended.

Over at Anatoly Karlin’s some confusion because his comments, from a Russian IP, were labeled “spam.” He thought I had banned him. Unfortunately, I don’t understand the logic of some comments labeled as spam, and I have to retrieve them many weeks later, as I check the spam folder only once a week or so. The ones with lots of links make sense, but sometimes there must be some semantic similarity with comment spam (and a lot of the spambots for a while had .ru addresses, so that explains why they don’t like Russian IP addresses).

Also, since for a while they thought I banned him some of his commenters who I had probably legitimately banned at some point decided to rant about how I don’t know anything about genetics or history and I’m a poo-poo head. There are lots of things you could criticize me for…but not knowing genetics or history are weird ones to fix upon. But hey, perhaps I’m the stupid one here with the blog that they were reading, while they, the anonymous commenters, are really so genius I can’t even Grokk their incandescent brilliance (there is a strange similarity in criticisms from both frog-Nazis and SJWs directed toward me as to my ignorance of all the facts they know).

Emails Show How An Ivy League Prof Tried To Do Damage Control For His Bogus Food Science. And Why We Find And Expose Bad Science. The researcher at the center of this scientific scandal actually seems like a decent human being from what I can tell. Unfortunately, he also seems to have likely been committing very basic statistical errors in his research and enabled a culture of sloppiness. The problem with not coming down with a hammer on a prominent professor at Cornell is that leniency will give the green light to more researchers that sloppiness and statistical shoddiness will “pay.”

If you don’t follow my RSS you might know, but I’m posting more at Brown Pundits and Secular Right.

I do have one opinion on Catalonia: seems like the government in Madrid took a low flame and sprayed gasoline all over it.

People regularly confuse that Africa has the most genetic diversity with the idea that African populations have the most genetic diversity among them in terms of ‘genetic distance.’ I realized an easy way to explain why this does not follow: Bantu populations diverged over the past 3,000 years, Eurasians over the past 40,000 years. The Eurasians went through a massive bottleneck, and so are less genetically diverse than all Sub-Saharan Africans. But the genetic distance between two Eurasian populations can be greater than between two Bantu populations because there is ten times as much time to accumulate between-group differences in the case of Eurasians than Bantus (in contrast, the high between-group difference among San Bushmen indicates really deep divergences).