Open Thread, 2/11/2018


The podcast that Spencer Wells and I are doing, The Insight, now has got eight episodes up. It’s nice that people are stumbling upon it now. Additionally, we’re pretty satisfied with the uptake. So far. To break out of our “core” audience we need more people to know about us.

First, please subscribe via iTunes, Stitcher or Google Play. Second, mention the podcast on social media. Tell your friends. Third, we have the next two or three podcasts planned, we’re still taking suggestions for ideas and possible guests (so far we’ve had John Hawks and Joe Pickrell on).

I now have Amazon Associates for Canada and the UK. The links to US Amazon items I post on this page should now change depending on your IP.

Cheddar Man changes the way we think about our ancestors. This is a pretty good article. But a few points. First, anyone who followed the literature would have predicted that Cheddar Man would contribute ~10% of the genomes to modern Britons and that he would lack alleles for light skin, but have them for blue eyes. I can’t believe any of the researchers were shocked in light of the La Brana etc. results. Second, we’re not extremely confident that he had very dark skin after the past few years when it’s clear pigmentation genetics involves more than just a few major loci. Seeing as how selection methods have detected lots of sweeps for skin lightening alleles over the last 5,000 years in Northern Europe, it seems implausible that they were as light as modern Northern Europeans, but not necessarily dark.

Spencer and I will probably an episode of The Insight on Cheddar Man after the documentary is out on the 18th (and the paper, probably in Nature).

I’ve blogged on female circumcision/FGM before. There are variations of opinion within Islam on this practice. It is mandatory, meritorious, or there is no comment. Muslims from areas where this is not practiced, such as South Asia or the Maghreb, naturally assume that this is a “cultural practice” that has nothing to do with Islam.

This is simply false. The Shafi school of Sunni Islamic jurisprudence considers female circumcision obligatory, for example. The complicated issue is that a) not all women subject to female circumcision/FGM are Muslim, for instance, in Africa, including Egyptian Copts b) not all Muslims are subject to the practice, obviously. These facts allow all sorts of confusions and obfuscations to emerge.

But the bigger issue is that if you are not Muslim it is not really coherent to say that something is a “cultural” practice as opposed to a “religious” one. Religion is part of the culture, and to a great extent on the reflective conscious scale the defining element of culture. Muslims disagree as to the religious acceptability of many practices. Those disagreements are cultural because Islam is cultural.

Land of Promise is a book I’ve mentioned many times. It’s one whose premises rub me the wrong way: the vigorous mixing of state fiat with the market. I’m not a fan of “industrial policy.” And yet I read the book because Michael Lind, the author, knows his history, and he’s honest about it.

I do think on some level I’m rethinking my commitment to the free market as opposed to institutions, and the short-term benefits of market efficiency set against the long-term advantages of social stability. That’s probably part of a general trend toward conservatism away from libertarianism.

Let’s Ban Porn. Don’t laugh. It took some boldness for The New York Times to publish something as laugh-out-loud implausible. But in the end, I think porn is the symptom. Really we as a culture don’t agree on what sex is supposed to be about. Without that agreement, porn is a sideshow.

Also, the proliferation of porn in the last 20 years hasn’t led to the explosion of sex crimes that critics on the Left and Right would have predicted.

Some of you may wonder about DNA Geeks. What’s the deal? Well, I can tell you that we are building a nice brand, and periodically there are traffic spikes. And the microscope is killing it.

The main sadness for me is that the ratio of R1b to R1a t-shirts sold is like 20:1. But I guess it’s quality over quantity?

While I was taking a Twitter break I got a few DMs about the latest controversy about hours worked by academics:

The stupidest thing on science twitter is how crazy and nasty people get over the idea that you have to work hard in science to succeed. Everybody knows you have to work hard and long to succeed, and yet everyone is willing to outright lie about the truth, lest you be publicly destroyed.

It’s pretty clear some people work fewer hours than other people and do fine. It’s also clear that other people have higher sweet spots in terms of return-on-time-worked. The problem is when people presume there’s a one-size-fits-all formula. I think it would be best if people reacted with a little more charity to those who extrapolate from what’s worked for them.

Open Thread, 2/4/2018

One of the things that reading Land of Promise has prompted in me is the need to read Matt Stoller’s book, when it comes out. Land of Liberty in many ways was a historical foil of Stoller’s article, How Democrats Killed Their Populist Soul.

And yet both exhibit an intellectual honesty which I generally find lacking in the modern pundit class, agree or disagree.

Steven Pinker’s new book, Enlightenment Now: The Case for Reason, Science, Humanism, and Progress, is now being published a few weeks earlier. Apparently this now one of Bill Gates’ favorite books.

I’m a big fan of Steven Pinker. But I’ve become much more pessimistic than him over the past few years. Here’s hoping that Enlightenment Now turns that around.

DNA Geeks has a total site redesign! Check it out.

I haven’t been saying this on the podcast yet, but you should be subscribing to it on iTunes, Stitcher, and Google Play, and review and rate it. Spencer and I have a certain audience already, and we’d like to expand it.

This has probably always been so, but I’m really getting tired by the emergence of different verbal ticks in various socio-political subcultures. For example, when liberals say “my dude” -“bros”, it’s dismissal-by-identity. Both NRx, and what is now called the Altright, also have their own subculture languages, which makes understanding what they’re trying to say hard for outsiders. A feature or a bug?

Taking a Twitter break for a week.

Open Thread, 01/28/2108

For various reasons we focus Classical Greece and Rome, but neglect the Hellenistic period, with the exception of the biography of Alexander. If you want to read something besides Alexander to Actium, check Dividing the Spoils.

A heads up, this week on The Insight we’ll be talking to Joe Pickrell of Gencove. The main topic will be DNA and ancestry.

Is the United States the new Saudi Arabia? This stuff is crazy if you read books about “Peak Oil” in the 2000s. Also, I really don’t ever want to hear about this stuff from random guys who read these books and thought they had all the answers ever again.

DNA Geeks is now gearing toward more general STEM and items for children. The 100x LED Microscope for Mobile Devices has been quite popular, and shipping is right now free. Also, we have European vendors for our t-shirts, so shipping is cheaper and faster.

Following many liberals on Twitter has confirmed my right-wing identity, though modified by policy beliefs. In particular, far Left people, such as Matt Stoller, seem to make coherent criticisms of capitalism and what it has wrought. Criticisms which I don’t always have a good answer for.

In contrast, moderate liberals, with their mild platitudes and thin policies are not persuasive, but their adherence to sex/race identity politics and smearing of all those to the Right of them as white supremacists means that it’s pretty obvious all of those who are “Other” need to band together as one when the time comes. We hang together, or we’ll go to the re-education camps separately.

The Follower Factory. This makes sense.

Why Ursula Le Guin Matters.

Nicholas Christakis is being treated pretty unfairly. I don’t expect that he’ll get satisfaction. This isn’t the age for honorable men.

Big Data Comes to Dieting.

The new gnomAD is pretty dope.

Dissecting historical changes of selective pressures in the evolution of human pigmentation. Not sure of the demographic model.

Sarah Haider on Secular Jihadists.

Open Thread, 01/21/2018

Don’t know when I’ll get to Kyle Harper’s book, The Fate of Rome: Climate, Disease, and the End of an Empire, but it looks very interesting (Patrick Wyman interviewed him for his podcast).

One thing though: climate always changes. It’s how organisms react to that change and why that is perhaps more informative. The way the Roman political order reacted the way it did to the exogenous environmental shocks had more to do with the nature of the Roman political order than the sui generis character of the shocks (they were going to happen….).

If you haven’t subscribed to my podcast with Spencer Wells, The Insight, you should (so far it’s on iTunes, Google Play and Stitcher). We’re coming out with episodes every week now. The next one will include Spencer’s recollections of the Paleolithic period of personal genomics, before 2005. We’re also recording a podcast with Gencove’s Joe Pickrell on ancestry testing this week.

DNA Geeks has more Gene Expression themed gear now, including a redesigned “Are you genotyped” shirt.

A new blog, mtDNAwiki.

An Ethnolinguistic and Genetic Perspective on the Origins of the Dravidian-Speaking Brahui in Pakistan. Have not read. Though I anticipated the conclusion over 5 years ago.

I contribute regularly to the Insitome Blog. So, No genetic test will tell you if you are Hispanic or Latino, was written after watching days of DNA-test reveals on YouTube. There’s a lot of education that needs to be done! As the Regional Ancestry product rolls out results expect many more blog posts (and probably explainers in podcast/video format at some point).

The convergences between the racialist Right and the identity politics Left have always been sad. But now that both are the waxing it’s quite sinister. For example, both would agree that science is Eurocentric in some deep way. And, both pay close attention to marriages which are racially mixed to draw broader lessons.

How genetics is unlocking the secrets of ancient human migration. On the Scandinavian hunter-gatherers.

Open Thread, 1/14/2018

Steven Pinker is one of my favorite public intellectuals. The Language Instinct is probably my favorite book from Pinker.

Last week I started seeing scientists who I respect(ed) starting to tweet that Steven Pinker, a moderately liberal academic of Jewish background, is a fan of Neo-Nazis. This stuff started to litter my timeline since I follow many scientists on Twitter. To find all the links and commentary, start with Jerry Coyne, who is a friend of Steve’s. All I have to say is that a substantial portion of the science Twittersphere is OK with bracketing Steven Pinker with Neo-Nazis. True fact.

I read Consciousness and the Brain: Deciphering How the Brain Codes Our Thoughts two years ago. I don’t remember much about that book though.

CBC under fire for documentary that says first humans to colonize New World sailed from Europe. There is less evidence for the Solutrean Hypothesis now than there was 20 years ago (in a relative sense). We also now know from ancient DNA that almost no Solutrean ancestry is present in modern Europeans.

If you don’t believe me, read this paper, The genetic history of Ice Age Europe.

At least most of my Twitter followers don’t seem to be anti-Pinker.

Having a hard time saying anything about Anhui of note. Perhaps that says something?

Genomweb story that mentions both my day-job and side-hustle.

Predictions for 2018

I don’t normally do year-end stuff. But I figured, why not? After all, I put up a post at my work blog about the major things that happened in historical human pop gen this year.

Indian population genomics will move forward notably. The ancient DNA work really feels like vaporware sometimes. Some of the researchers involved reach out to journalists (people of my acquaintance) and leave tantalizing clues, but they disappear off the face of the earth. I assume that some sort of Indo-Aryan intrusion from Central Asia will seem clear from the data and results, though the Indian media and intellectual class will claim the opposite. In this way they are just like the American media and intellectual class; if the evidence does not fit just say that the evidence says the opposite of what it does. People will believe because they want to believe.

The current protests in Iran won’t go anywhere. Someone with guns needs to be on the side of the protestors. That’s it. Also, if a group with guns ends up favoring them, the West will find that anti-clerical Iranians are quite nationalistic and not necessarily liberal democrats.

The Democrats will win the House of Representatives. I think there’s about a 50/50 chance that they’ll get the Senate.

The United States will be in a recession by the last quarter of 2018. We’re overdue. All OECD countries are growing, to the point where Brent crude prices are going up. This isn’t sustainable, especially since many developed nations have been kicking the bucket down the line.

Personal genomics is going to be more of a presence as the year progresses. I was surprised by all the attacks from the tech-press on direct to consumer genomics over the past few months. That indicates to me that the industry is getting big enough to be a click-bait target.

George R. R. Martin will publish Winds of Winter.

More ancient DNA from the New World. This has been in the works for a while. I’m really skeptical that they won’t be able to push it out in 2018.

Twitter will continue to not be able to find its way. Basically, it can’t win, and won’t win.

More work in complex trait genetics published. This is has been long in the works, so this I know for a fact. Whatever the results, don’t worry, it will confirm all your priors no matter what those priors are.

Open Thread, 12/24/2017


Well, Merry Christmas Eve!

I’ve been rereading Zero to One: Notes on Startups, or How to Build the Future. Recommended. A little different now that I’ve been involved in start-ups.

I would say that a lot of it is a pretty straightforward application of stuff you’ll encounter in economics and economic history to Silicon Valley (e.g., economic growth through technology vs. Smithian growth through globalization).

Haven’t had time to work on the South Asian Genotype Project much since I’ve burned a lot of hours on the margin moving websites. I’ll get back to it in the next few days.

Just a reminder, two days now to get $80 off Helix products (say early hours of December 26th), including Neanderthal, Metabolism and Regional Ancestry.

A friend asked about which podcasts I listen to. Here are the ones I listen to habitually:

In Our Time. I’ve been listening to this podcast for 10 years now. The Glenn Show on bloggingheads.tv. Probably listen to 75% of these discussions. Planet Money and Tides of History.

Secular Jihadists. One of the cohosts pointed out on the last episode that Stalin and Mao killed more people than Hitler. Oh, and that white people are the “least racist.” We live in a predictable world, and this podcast always surprises me with the originality of the hosts (though I demur from their New Atheism).

Chap Trap House. I don’t really get it, but the bro-banter is pretty amusing to me.

Stuff You Missed In History Class.

Politics Podcast from FiveThirtyEight.

Also, my podcast with Spencer Wells is going well (if downloads are any measure). We have some stuff coming up on Neanderthals (two episodes), as well as the Aryan invasion of India. You can find it on iTunes, Stitcher, and Google Play too (Spotify hasn’t gotten back to me).

I’ll be taking some time off from this weblog and my day job spending some time with my kids the week after Christmas. I’ll probably post stuff if I really have to, but otherwise might be a little quieter….

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).