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).

Open Thread, 09/24/2017

Reading Harold Marcus’ A History of Ethiopia. So far a little too heavy on diplomatic as opposed to social history. My curiosity was piqued when reading The Fortunes of Africa when the author observed that the geopolitical extend of the modern Ethiopian state was partially a function of a relatively late state expansion in the 19t and 20th centuries from the Abyssinian highlands.

It’s one of those facts which allow other facts to snap into place. I’ve always been curious about the huge number of Muslims and Somalis in modern Ethiopia. Well, it turns out to be a function of the fact that the borders were drawn at a particular moment and time.

Neolithization of North Africa involved the migration of people from both the Levant and Europe.

A stray thought I had. For years people have been wary about Richard Dawkins’ conflation of atheism with science, and evolution more particularly. I am starting to wonder if the more self-conscious political activism of scientists, almost uniformly on the Left, will start to have an impact.

The problem is that at for now scientists depend on the public for their funding by and large (there are exceptions obviously). A polarized public which does not esteem science and has a faction which sees it as hostile may be less interested in cutting checks for “blue sky” projects (i.e., NIH will be fine, but the NSF….). Since academics are overwhelming of one political orientation I suspect they have a poor intuition of how quickly such a change could come about (there is more real diversity there than is vocalized, but many people I know personally have no inclination for public denunciations due to any heterodoxy, so they keep their mouths shut).

Going to the ASHG meeting in one month. I doubt I will venture out into Orlando. I have been to a conference in that city before, but never left the convention center attached to the airport! Am I missing something?

In general, I avoid national politics. But the whole controversy around football is curious because I’m skeptical that the sport will be around in a generation.

One thing that I have been thinking recently is dropping my Twitter follow back down to 300 or so. I still use Twitter obviously…but it’s getting too dumb. And lots of interesting and smart voices are going passively into lurk mode because it’s exhausting having to deal with dumb people.

Open Thread, 9/17/2017

Reading Vietnam: A New History. The author has an apologia/explanation for why he is focusing not just on European colonialism, but the history of what became Vietnam back to the first contacts with Han China (with some perfunctory archaeological passages). This is great in theory, but from what I have read so far we’re going to have a tryst with the French sooner than later. So I don’t think he really delivered here (though perhaps “normal” people want to read about evil European colonialism immediately?).

By coincidence, there is a Ken Burns documentary on the Vietnam War now. One of my friends from when I was a kid had (has) a dad who was a Vietnam vet. He’d have night terrors. Only now do I realize how recently in the past it was for him back in the 1980s.

I did enjoy The Best and the Brightest.

Sent out my second newsletter. Here’s a stat that I divulged: more than 50% of traffic to this site is directly due to Google+Twitter+Facebook. In 2011 it was 35%. Much of the difference is due to the decline in RSS feeds, and the rise of mobile.

Why is Twitter not what it was in the early 2010s? I think part of it is that there are too many people on Twitter, and the average user is less intelligent overall. Unlike Facebook on Twitter the “genius” is anyone can talk to you. This is a problem.

The grandmaster of Mormon dweeb fantasy (I say this affectionately) Brandon Sanderson is coming out with the third book in his projected ten book Stormlight Archive series.

I’m at peace with the likelihood that I won’t finish this series. Sanderson is a great world-builder, so I’m looking at these books more as fictional ethnographies. Just along for a short ride.

Finally in the homestretch of A New History of Western Philosophy. After the classical period I haven’t really enjoyed this book, it was a slog. I began to read it at the same time as I read Consciousness and the Brain, which I finished in a week. Two years on I’m finally finishing the other book I started then.

Finally, again I highly recommend The Fortunes of Africa. Great read. I do have to say that it was hard not to be particularly appalled by Arab slave traders. It’s not like the European trade isn’t appalling, but that’s widely known. In contrast the driving of black Africans across the Sahara is less in the Western consciousness.