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

October 29, 2017

Open Thread, 10/29/2017

Filed under: Open Thread — Razib Khan @ 9:33 pm

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.

October 28, 2017

Video is for consumption and text is for production

Filed under: Uncategorized — Razib Khan @ 9:22 am

The Information has a piece up, The Case Against Video. The Information charges a decent amount for its services which are in text form, so of course there is some bias here insofar as this belief was probably preexistent.

But I happen to agree. It strikes me that video is relatively low density, and it often takes reading to be able to combine facts/concepts together to form something new. It can be done via video, but it ends up taking more time.

For most people video will be sufficient, just as for most people television news is sufficient. But real depth will require reading.

The summer of ’99

Filed under: Culture — Razib Khan @ 12:27 am

Every generation has its nostalgia. Some of them have their year. For the boomers it’s the summer of ’67. For Bryan Adams it was the summer of ’69. For people born between 1965 and 1980, I will bet the summer of 1999 is that special summer. It was near the end of the long boom of the 1990s, and the United States of America was the hyperpower. We hadn’t gotten mired in wars, and terrorism seemed like a nuisance.

Apes just being apes

Filed under: Genomics — Razib Khan @ 12:10 am

A while back I made from of bonobos and chimpanzees for being kind of losers for looking across at each other on either side of the Congo river for ~1.5 million years the time elapsed since their diversion. I finally ended up reading the paper from last year, Chimpanzee genomic diversity reveals ancient admixture with bonobos, which reported complex population history between these two species. In other words, “they got it on”.

The key was a reasonable sample size of N=40 and high coverage genomes (>20x), to give them the amount of information necessary to have the power to detect admixture. If you aren’t human and have a reasonable size genome, and all mammals do, get to the back of the line. But the Pan‘s turn finally arrived.

The paper primary result is that over past few hundred thousand years there have been reciprocal gene flow events of small, but detectable, magnitude between chimpanzees and bonobos. Naturally, there was some geographic specificity here, in that chimpanzees from far West Africa lack much evidence of this while those from Central Africa have a great deal. The admixture is directly proportional to proximity to b0nobo range.

To obtain the result their initial focus on high-frequency bonobo derived alleles that were at low to moderate frequencies in chimpanzees. There was a notable excess for this class among Central African chimpanzees. And, these alleles seem to have introgressed recently.

I suppose the major takeway is that hominids do it like they do it on the Discovery Channel.

October 27, 2017

Without a sense of what is right everything is wrong

Filed under: Culture,Halloween — Razib Khan @ 10:50 pm

When I was a kid Halloween was my favorite holiday. First, candy! Second, costumes! Third, you could be a little naughty!

Finally, my parents were not the most inquisitive people and didn’t realize the pagan and Christian influences on the holiday. They liked it because unlike Christmas, at least to their perceptions, it didn’t have a religious connotation which conflicted with Islam. They allowed me to participate with any guilt.

I try not to live through my kids, so holidays for me are not about recreating my own childhood. It’s for allowing them to have fun. Holidays are a big deal for kids.

With Halloween coming up we’ve been giving thought to our kid’s costumes. My daughter and elder son have some opinions. There was some mention that perhaps my daughter could be Tiana from The Princess and the Frog. My daughter is not really too into princesses. I’ve heard her spend more time talking about dwarf planets than princesses (especially her favorite, Haumea). But she likes Tiana, and we’ve watched the movie together.

Ultimately we went with something animal related (in keeping with some previous years when she was a lion and a duck).

Nevertheless, this email I received from her elementary school today is deeply annoying to me:

It’s Halloween, but we can’t scare the kids too much? (fake blood does seem like it would be a huge mess so I can understand that) No masks, of course, nixes many costumes, but I guess I can go along with that for security reasons?

But the part about “No costumes representing an ethnicity, race, religion or culture, other than your own” kind of rubbed me the wrong way. My wife was livid. Our children are mixed race, so what does that mean for them? In fact, half of my daughter’s elementary school class is mixed race. Also, my daughter already knows she is an atheist. Does that mean she couldn’t dress up as a nun like Mother Theresa if she admired her? The whole email seemed to presuppose that the world consists of discrete and separable races and cultures. You simply identify with one, and that delimits your possibilities.

My daughter attends an Asian language immersion school where one of the teachers is a recent immigrant who clearly does not understand American culture very well. She wouldn’t have even known to write about much of this. This mandate was clearly written by an administrator. The aim of the whole email was to head off any complaints from parents. But it’s written in such a heavy-handed and general manner that it’s bound to cause widespread irritation.

We’re a diverse country with many ethno-racial, religious, and ideological groups. There are no common standards at this point on what is and isn’t offensive. Perhaps some Christian parents would be offended if a little kid showed up at a school-sponsored Halloween party as the devil? I strongly suspect that the race and religion bans above really target mostly white kids who dress up as racial minorities…but it’s written in a general way so as not to offend those parents too (but in the process irritates others).

Whatever we’re doing, it’s not making many people happy, though it is insulating administrators from making personal judgments. My daughter is a smart kid (she has shocked even me in her ability to infer general principles from specific cases), and my wife and I have already had conversations about how to insulate her or make her aware of the low level of intellect which now dominates our public ideologies. My wife has studied the Chinese language and the history of the Cultural Revolution, and though obviously there is a difference of degree she regularly contends that there are analogies between what is now happening in the United States and what happened in China in the 1960s. I do unfortunately believe that my daughter will grow into maturity into a country which is in many ways second-rate and mediocre in the things which our family values. We are thinking hard about how to prepare her for a different future than the ones we expected when we were children in the 1980s.

In 2546 Richard Dawkins will be remembered for “memes”

Filed under: Cultural Evolution,Memetics — Razib Khan @ 5:15 pm

In 2006 South Park premiered Go God Go. The episode synthesized Buck Rogers in the 25th century, the Wii craze of the middle 2000s, and Richard Dawkins’ God Delusion engendered fame. In some ways, this was a sad reflection on Dawkins’ reputation, because before he got full-bore into atheist activism he was a great science popularizer, most famously for The Selfish Gene. Many would contend that George C. Williams’ Adaptation and Natural Selection outlined The Selfish Gene‘s ideas better and earlier, while Dawkins himself is most proud of The Extended Phenotype. But warranted or not The Selfish Gene stands head and shoulders above his other work in terms of recognition, in large part due to the sexy title (which Dawkins has expressed some ambivalence about due to its misinterpretation).

When God God Go premiered it was plausible, as the episode suggested, that ~500 years into the future Dawkins would be remembered as the prophet of irreligion. But times change. I now believe that Richard Dawkins’ reputation will in the future hinge on the word and concept of the meme. That is because Dawkins introduced the idea in The Selfish Gene in 1976. Despite Susan Blackmore’s attempt to revive interest in the specific idea in The Meme Machine I think it is fair to say that “memetics” as an analog to “genetics” was moribund. This is not to say that cultural evolution as a field did not exist, but that field is distinct from memetics and emerged around the same time as Dawkins’ suggestion of memetics.

Today we are in a very different position than 2006. The word “meme” has entered the lexicon. As the Google Trends chart above shows the increase began in the late 2000s, but it is has been rather precipitous of the last decade. Among the younger set, the word meme is not exotic. It’s just another word. In fact I mentioned offhand to a co-worker that Richard Dawkins invented the neologism and he was incredulous. He simply couldn’t believe it. And that to me illustrates how ubiquitous it’s gotten in a bizarre way.

Of course, memetics and memes as Dawkins originally envisaged them never developed in the way he’d have imagined. But culture has a knack for evolving in directions we wouldn’t expect….

October 25, 2017

New Atheism is dead, long live New Atheism

Filed under: atheism,Religion — Razib Khan @ 11:50 pm

Scott Alexander asks How Did New Atheism Fail So Badly? It’s in response to an obnoxiously fact-free Baffler rant. I think what Scott is alluding to here is the lack of fashionability of “New Atheism.”

But in the American context, I do think that New Atheism arose is a particular time and context, George W. Bush’s America, and has declined in salience in another one, where standard-bearer of the Republican party is a cultural Christian at best. The previous President, Barack Obama, was a liberal Christian who admitted that he believed in evolution more than angels.

Today a larger fraction of Millennials are irreligious than they are Evangelical Protestants. The proportion of Americans who said they had “No religion” in 2000 was 8%. Today it is 18%.

Addendum: I think some of Scott’s commenters are correct that the rise to prominence of Islam as something that good liberals need to defend in public, no matter their private contempt for the religion (which they share with me candidly of course), also makes New Atheism kind of less attractive.

Recollections of Mel Green

Filed under: Genetics — Razib Khan @ 5:50 pm

Mel Green co-taught a “history of genetics” course that I took as a first-year grad student at UC Davis. It was fitting because Mel Green was a living embodiment of the history of genetics. Mine was one of the last years that Mel co-taught that class, so I feel quite privileged.

Unlike some of my friends who have gone through Davis I only had a few conversations with Mel. But he gave us the wisdom of a life of learning and seeing genetics evolve as a discipline over the 20th century. It isn’t often that you talk to someone who could dismiss Charles Davenport because he had talked to the man and judged that he had a poor grasp of Mendelian theory!

Most everyone has a “Mel Green story.” So let me recount mine. Though it doesn’t have to do me with as such. Mel lived 101 years, and was active in science by the 1940s. In our history of genetics course we had to give a presentation on a particular topic (mine was on polytene chromosomes). The student who was giving the presentation on Drosophila research was not a genetics student. I had assumed she would be a bit nervous because Mel was a renowned Drosophilist, and he was sitting right there listening to everything.

At some point they began to refer to a researcher, “M Green.” They went on about “M Green” and his work for about five minutes, at one point pausing to note that “M Green” even worked at Davis! At this point the co-instructor had to stop her and tell her that “M Green” was sitting in the room, right next to her. Because the research was published in the 1940s the student had assumed that this was from someone who could never have been alive in the present. But there it was, Mel Green was still there, a witness to all that history and come and gone.

October 23, 2017

The presumption of parental choice in genetics

Filed under: Genetic Engineering,In Virto — Razib Khan @ 6:35 pm

In various forms, I’ve been talking about genetic modification and testing of children for years. As most of you know my older son was whole-genome sequenced before he was born. This was in large part scientific activism. I wanted to show people it could be done, and it’s not scary. Genes are not destiny, they’re information.

In the current year of 2017 we’ve gotten much further than when I first began talking about this sort of stuff. The Washington Post and Stat have two articles on the topic that are relevant, Discounts, guarantees and the search for ‘good’ genes: The booming fertility business and A baby with a disease gene or no baby at all: Genetic testing of embryos creates an ethical morass.

I’m prompted to comment on them for two reasons. A simple one is that Michael Brendan Doughtery wondered if the recourse to “super-male” sperm donors would lead to inadvertent consanguineous marriage. I doubt the math works out there. There are tens of millions of children. Even with 1,000 sperm donors genetic diversity would mostly be retained, and you can find plenty of partners. And of course in the near future with ubiquitous genetic testing, most individuals will immediately detect consanguinuity. This is not a problem practically.

A second, broader issue, is in regards to genetic testing and sperm donation I do not believe we should treat parents who make recourse to these technologies any differently from parents (like myself) who can have children without assistance. Most humans make choices on characteristics of their spouses, and those choices aggregate into assortative mating. To me, this is a difference of degree, not kind, from selecting sperm donors. It simply seems creepy because of the technological aspect. The impulses are the exact same.

I do understand that some people have religious, ethical, and normative objections to these new technologies. Personally, I disagree with this viewpoint, but I think it is healthy for us to have the debate openly and candidly.

For example, a few years ago Radiolab had an episode where a gay Israeli couple went looking for egg donors. More specifically they wanted eggs from someone who was white. Obviously, I don’t prioritize my children looking like me that much even though they are biologically mine, so I have a hard time relating to fixating on this issue (my wife and I discussed this topic and I didn’t care too much whether the kids looked like dad, though other people on playgrounds seem to care way too much for my taste). But at the end of the day, it is a choice. And, it is the same choice that the vast majority of humans make by marrying and having children with people of the same race. In multiracial societies like the United States of America, this choice is explicit and implicit in terms of revealed preferences. People want kids to be the same race as themselves. They want to see themselves physically. The Radiolab episode simply exposed what generally occurs on the down-low.

Perhaps we are uncomfortable with the expense and artifice of assisted reproduction. Perhaps it violates our values. This is reasonable. These are issues and debates we need to hash out. But ultimately many of the same issues apply to assisted reproduction and genetic selection as do with “natural” or unassisted parenthood. I think it is important not to put parents who need assistance to a higher standard than those who don’t.

Addendum: I think the argument is ultimately somewhat low stakes because parents who really want a specific child and don’t want to adopt will spend as much as needed to get what they want. And if these technologies were banned in the United States people would just go abroad for the duration of the pregnancy.

Political polarization in the Twitter-sphere and how it will end

Filed under: Politics — Razib Khan @ 5:34 pm

A few weeks ago a very Left-wing (I believe Marxist?) reciprocal follow on Twitter quoted Sebastian Gorka. I couldn’t see what was being said, so I assumed Gorka had blocked him. I clicked the link only to find that I was blocked by Gorka!

This really confused me because to my knowledge I have never spoken about Gorka. My working assumption is that I was on a “block-list” that Gorka had subscribed to. But what sort of block-list was I on? Honestly, the most likely conclusion is that I probably follow or am followed by someone blacklisted by Gorka’s block-list. The strangest thing is that some people who are literal Communists (with substantial followings) were not blocked by Gorka!

The criteria I use to follow people is probably pretty strange. If they follow me and work in a scientific field close to my own professional interests I will usually follow them back (e.g., I pretty much follow back every evolutionary and population genomicist and geneticist, but not every genomicist or geneticist). Since the vast majority of this group are vocally liberal, or keep their politics to themselves (there is a non-trivial minority of libertarian-leaning scientists who are closeted), I see a lot of tweets I disagree with.

After that, I will follow people I interact with a lot or post interesting stuff outside-of-my-field. For example, I often, but not always, follow back economic historians. Then there are science journalists who focus on biology with some following and who I interact with or know personally. I don’t like following people who have no information on their profile.

Finally, there are libertarian and conservative pundits. They often follow me, and I follow back since I respect that they actually bother to follow someone who often tweets about abstruse and technical topics. After the recent hit piece that was written about me in a well respected science journalism publication* (which has really updated my priors what I think about journalism and how much, or honestly little, I respect the profession) there is really no point in engaging with any prominent liberal that is outside of science because their minds are made up. I am honestly OK with that since I’m not liberal, and I still retain influence and following on the Right, where people are more open-minded about the world in my opinion (basically I think anyone who has sympathies that they have the courage to make vocal with classical liberalism will end up on the Right eventually; I’m looking at you, Bret Weinstein).

And yet because most of the people I follow are science-related I’m exposed to different opinions all the time…and that probably explains how I got on Gorka’s block-list. So I was really curious when I saw Kai Ryssdal, the NPR journalist, tell people to follow “5 people you disagree with.” To me that was a really bizarre statement. I assume I follow about 500 to 600 people I disagree with. This is pretty much in evidence when people re-tweet stuff about how all conservatives are Nazi’s approvingly (even though they follow me perhaps they don’t notice I am a conservative!). I guess I’ve gotten really good at ignoring smugness and screaming that is at total polar opposite of mine politically (though I agree with the Left on many positions, so it’s not always in disagreement).

Out of curiosity, I decided to put up a poll to survey what my follower’s politics were. Since there were only four options allowed, I allowed for liberal, moderate, conservative, and libertarian. Though I wasn’t surprised by the political diversity, I was surprised by the balance. In a classical “world’s smallest political quiz” my followers are almost equally split across the four quadrants!

As for how this polarization will end, I think it will end with the cessation of politics and the assertion of an old-fashioned authoritarianism. It will be Sulla. Or Caesar. Or Shihuangdi. Liberalism in the classical sense of the Right and Left dies in meekness, and most people are quite meek. Many liberals privately admit to me that they’re terrified of a Spanish Civil War type denouement to our culture wars, while many non-liberals are resigned (the people on the extremes, who are very vocal, of course, are thrilled and anticipatory). Social change is nonlinear, and it would not surprise me if in the coming generation the polarization and dehumanization come to a head and it ends badly for one side. Ultimately people will have to pick a side or be persecuted by both groups (also, an international exit plan is probably necessary for many people who have expressed opinions in public). The only way to win and be safe is to have a tribe.

But until then life goes and we try to make the best of it. Knowledge and learning existed before liberal democracy, and it will persist after it. As someone who follows a lot of liberals honestly I’m just more and more convinced that there will never be healing because there is so little lack of charity, grace, or humility when it comes to political differences. I really relate to Maajid Nawaz talking to Islamists in unguarded moments in prison realizing how they would give no quarter the opposition if they came to power. My twitter feed pretty much makes more, not less, Right-leaning. It’s the same on the conservative side, though since I don’t follow too many conservatives I wouldn’t know** Perhaps amusingly most of the crazy conservative stuff I see is hate-RTed by liberals. I guess it would be different if I picked “Salon conservative” type of liberals, but in science, you don’t really have a choice when you are in such a small minority.

Addendum: When people find out I’m conservative or identify me as such the liberals are often confused and want clarification. First, political quizzes often show me to be a moderately conservative libertarian (if that makes sense). But even if I was a Left-liberal if you are vocal about things which are considered third-rails on the Left it doesn’t matter what the preponderance of views turns out to be. A few deadly sins count more than one thousand mitzvahs. At the end of the day, a pragmatist picks the side which won’t persecute him. I am no longer surprised when a publically very orthodox liberal scientist confides me in thoughts that would get them scourged. It’s basically my tribe, right or wrong, for most people. But the disjunction between private and public views really just reinforces that there’s not really as much to preserve as we think, and we’re already extremely far down the path to cultural cognition overwhelming individual reason.

* Several journalists privately DMed to say they thought it was unfair, but of course they can’t break ranks with their peers and say that in public (with very rare exceptions). It’s a guild, and you don’t cross powerful people in the guild who want to shape reality as they see it. I really respect Foucault a lot more than I used to after seeing how journalism works.

** Just because someone is an intolerant screamer on politics doesn’t mean they don’t have a lot of interesting things to say, so I keep following usually. Until the last day of this republic, we’ll have plenty to exchange of value.

October 22, 2017

ScienceBlogs is shutting down at the end of the month

Filed under: Blogs — Razib Khan @ 7:12 pm

The people, whoever they are, at ScienceBlogs have announced that they’ll be shutting down at the end of the month. I actually should have all my archives, so there’s no worry on that end for me.

The first few years for Seed were pretty flush for a small operation. There were a couple of blogger meet-ups in New York City (and a fair number of ad hoc meet-ups in the San Francisco Bay area, as several of us lived there and many people traveled there). But the Great Recession hit media hard, and that included Seed. Some attrition of bloggers started to occur in 2008 and 2010, and then presumably in an attempt to get more revenue they started a Pepsi sponsored blog, and that caused a further set of defections.

But there are some great blogs still there. Respectful Insolence and Uncertain Principles I’ve followed on and off since the beginning. The latter blog has had some continuity as a science blog since the spring of 2003, so along with Gene Expression it’s been around for 15 years or so.

Here is an article in The New York Times from January 20th of 2006, Science Blogs as a Vehicle for Upscale Ads. I remember where I was then, chilling out in Prospect Heights at my friend’s apartment in New York City. Honestly, a nearly 12-year run is not that bad. Some great journalists started at or grew their careers at ScienceBlogs.

ScienceBlogs’ wiping away of the whole site illustrates the major problem with relying on someone else’s platform to gain scale and synergy. It might be a short-term strategy. Unfortunately, I think the areas of science twitter I’m familiar with are already in steep decline from the vibrant and spirited by collegial conversations dominant between 2010-2015. It’s not quite as far gone as ScienceBlogs’ neglect.

Open Thread, 10/22/2017

Filed under: Open Thread — Razib Khan @ 2:04 pm

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.


Selection swimming against the genomic tide

Filed under: Africa Genetics,Africa Genomics,Genetics,Genomics — Razib Khan @ 1:32 pm

One of the major issues that confuses people is that the distribution of a trait or gene is often only weakly correlated with overall phylogeny and the rest of the genome.

To give a strange but classic example, the MHC loci are subject to strong balancing selection. This means that novel alleles do not substitute and replace ancestral alleles. Substitution of this sort results in “lineage sorting,” so that when you look at chimpanzees and humans you can see many polymorphic loci where all humans carry one variant and all chimpanzees the other. In contrast at the MHC loci there is frequency-dependent selection for rare variants, so the normal cycling process does not occur. Humans and chimpanzees overlap quite a bit on MHC, and any given human may have a more similar profile to a given chimpanzee than another human.

There are 19,000 human genes. At 3 billion base pairs only about ~100 million are polymorphic on a worldwide scale (using some liberal definitions). There are lots of unique stories to tell here.

A new preprint, Inferring adaptive gene-flow in recent African history, illustrates how certain genes with functional significance may differ from genome-wide background. The authors find that among the Fula (Fulani) people of West Africa there has been introgression from a Eurasian mutation that confers lactase persistence. The area of the genome around this gene is much more Eurasian than the rest of the genome. In contrast, the area around the Duffy allele is much less Eurasian. The variation in this locus is related to malaria resistance. Finally, in other African populations, they found gene flow of MHC variants.

None of this is entirely surprising, though the authors apply novel haplotype-based methods which should have wider utility.

Machine learning swallowing population genetics = understanding patterns in population genomics

Filed under: Machine Learning,Population genetics — Razib Khan @ 1:09 pm

Dan Schriber and Andy Kern have a new review preprint out, Machine Learning for Population Genetics: A New Paradigm. On Twitter there has already been a little snark to the effect of “oh, you mean regression?” That’s fair enough, and the preprint would probably benefit from a lower key title, though that’s really the sort of titles journals seem to love.

I would recommend this preprint to two large groups of my readers. There are those with strong computational skills who are curious about biology. It makes it clear why population genomics benefits from machine learning methods. Second, those who are interested or trained in genetics with less of a computational and pop gen background.

Yes, all models are wrong. But some give insight, and some are just not salvageable. In population genomics some of the model-building is obviously starting to yield really fragile results.

The backlash against social psychology was pent up demand

Filed under: Psychology,Social Psychology — Razib Khan @ 12:02 pm

Both Slate and When the Revolution Came for Amy Cuddy, have pieces deconstructing the fall from grace of an idea like “power posing.”

This is all obviously wrapped up in the “replication crisis”, which is impacting most sciences which use some statistics and are generally characterized by modest and complex causal effects (social and biological sciences in particular then).

Obviously, I am no social psychologist, but can I just say that everyone knew there was a problem in the field. By everyone, I mean psychologists. I had friends who worked in related fields who told me as early as 2006 not to trust anything coming out of social psychology. Others described how p-hacking and “unconscious” data manipulation was relatively common in psychological experimentation, and the personal stands they had to take.

When everyone knows that something is wrong, but no one says anything, you have a coordination problem. But once the snowball starts rolling down the hill…everyone decides to speak their mind.

Finally, there’s the demand-side problem: ideas like power posing, implicit bias, and stereotype threat, offer neat, clean, and powerful explanations and oftentimes solutions for social problems. Wonkish Left-liberal publications and pundits in particular literally mine the literature to “show what the science says” (don’t worry, it overwhelmingly confirms prior beliefs).

As a testament to power of the likely wrong (not robust) viewpoints, consider that John Bargh has a book out, Before You Know It: The Unconscious Reasons We Do What We Do. Bargh’s work was one of the first research programs to be critiqued in the early 2010s. Of course he doesn’t agree with the critics, but it does strike me that the field as a whole (e.g., people like Daniel Kahneman) believe that these subliminal effects are much weaker than originally claimed, at best. Nevertheless Bargh is going to sell his books, and people in coffee shops and airports all over the country are going to eat it up.

October 16, 2017

The rise of the word “weaponized”

Filed under: Linguistics,Weaponized — Razib Khan @ 8:41 pm

The gratuitous use of the word “weaponized” really annoys me.

October 15, 2017

Why farming was inevitable and miserable

Filed under: Agriculture,Culture — Razib Khan @ 10:48 pm

There are many theories for the origin of farming. A classic explanation is that farming was simply a reaction to Malthusian pressures. Another, implied in Big Gods: How Religion Transformed Cooperation and Conflict, is that ideological factors may also have played a role in the emergence of sedentary lifestyles and so eventually farming.

I don’t have a strong opinion about the trigger for farming. What we know is that forms of farming seem to have emerged in very disparate locales after the last Ice Age. This is a curious contrast with the Eemian Interglacial 130 to 115 thousand years ago when to our knowledge farming did not emerge. Why didn’t farming become a common lifestyle then? One explanation is that behavioral modernity wasn’t a feature of our species, though at this point I think there’s a circularity in this to explain farming. It seems plausible that biological and cultural factors over time made humans much more adaptable,

Why didn’t farming become a common lifestyle then? One explanation is that behavioral modernity wasn’t a feature of our species, though at this point I think there’s a circularity in this to explain farming. It seems plausible that biological and cultural factors over time made humans much more adaptable, protean, and innovative. We can leave it at that, and assume that the time was ripe by the Holocene.

Also, we need to be careful about assuming that modern hunter-gatherers, who occupy marginal lands, are representative of ancient hunter-gatherers. Ancient hunter-gatherers occupied the best and worst territory in terms of productivity. If territory is extremely rich in resources, such as the salmon fisheries of the Pacific Northwest, then a hunting and gathering lifestyle can coexist with dense sedentary lifestyles. But the fact is that in most cases hunting and gathering can support fewer humans per unit of land than agriculture.

The future belongs to the fecund, and if farming could support larger families, then the future would belong to farmers. Though I don’t think it was just a matter of fertility; I suspect farmer’s brought their numbers to bear when it comes to conflicts with hunter-gatherers.

Of course, farming is rather miserable. Why would anyone submit to this? One issue that I suspect needs to be considered is that when farming is initially applied to virgin land returns on labor are enormous. The early United States is a case of an agricultural society where yeoman farmers, what elsewhere would be called peasants, were large and robust. They gave rise to huge families, and never experienced famine. By the time the frontier closed in the late 19th century the American economy was already transitioning to industry, and the Malthusian trap was being avoided through gains in productivity and declining birthrates.

The very first generations of farmers would have experienced land surplus and been able to make recourse to extensive as opposed to intensive techniques. Their descendants would have to experience the immiseration on the Malthusian margin and recall the Golden Age of plenty in the past.

And obviously once a society transitioned to farming, there was no going back to a lower productivity lifestyle. Not only would starvation ensue, as there wouldn’t be sufficient game or wild grain to support the population, but farmers likely had lost many of the skills to harvest from the wild.

Finally, there is the question of whether farming or hunting and gathering is preferable in a pre-modern world. I believe it is definitely the latter. The ethnography and history that I have seen suggest that hunters and gatherers are coerced into settling down as farmers. It is never their ideal preference. This is a contrast with pastoralism, which hunting and gathering populations do shift to without coercion. The American frontier had many records of settlers “going native.” Hunting was the traditional pastime of European elites. Not the farming which supported their lavish lifestyles.

Many of the institutional features of “traditional” civilized life, from the tight control of kinship groups of domineering male figures, to the transformation of religion into a tool for mass mobilization, emerged I believe as cultural adaptations and instruments to deal with the stress of constraining individuals to the farming lifestyle. Now that we’re not all peasants we’re seeing the dimishment of the power of these ancient institutions.

Open Thread, 10/15/2017

Filed under: Open Thread — Razib Khan @ 6:09 pm

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:

Another great-great-great…great-uncle in Asia

Filed under: Ancient DNA,Human Genetics,Tianyuan — Razib Khan @ 4:48 pm

The paper which surveys the relationship of the 40,000 year old Tianyuan sample is finally out in Current Biology, 40,000-Year-Old Individual from Asia Provides Insight into Early Population Structure in Eurasia. There isn’t anything too surprising here. Here is the part of the abstract that presents new finding:

…we generated genome-wide data from a 40,000-year-old individual from Tianyuan Cave, China…We find that he is more related to present-day and ancient Asians than he is to Europeans, but he shares more alleles with a 35,000-year-old European individual than he shares with other ancient Europeans, indicating that the separation between early Europeans and early Asians was not a single population split. We also find that the Tianyuan individual shares more alleles with some Native American groups in South America than with Native Americans elsewhere, providing further support for population substructure in Asia [8] and suggesting that this persisted from 40,000 years ago until the colonization of the Americas. Our study of the Tianyuan individual highlights the complex migration and subdivision of early human populations in Eurasia.

The Tianyuan sample lived about ~40,000 years ago in China, and it does not seem to have been the direct ancestor of modern East Eurasians. It also seems to have had some relationship to the Australo-Melanesian affiliated population which contributed ancestry to the indigenous peoples of South America. Additionally, it also shares ancestry above what you’d expect with a 35,000 year old Paleolithic European, the GoyetQ116-1 sample, which is found in an Aurignacian context.

There are some direct conclusions that one can infer from this paper. First, as known beforehand the divergence between East Eurasians and West Eurasians has to predate 40,000 years before the present since this sample already shares drift with East Eurasians far more than West Eurasians. In the paper, the authors give an interval of 40,000 to 80,000 years before the present, which seems advised. Remember that “Basal Eurasians” separated before the divergence of East and West Eurasians.

Second, “ghost” populations were common. There are at minimum two ancient Eurasian populations, represented by the Oase1 sample in Romania from 40,000 years ago, and the 45,000 year old Ust’-Ishim from Siberia, who were not closely related to any populations which left descendants today.

Third, the human “family tree” looks more like a human “family bramble.” One of the interesting points in this paper is that Tianyuan shares drift with Goyet, but does not share drift with El-Miron, which seems to be descended in large from a population like Goyet. The key here is to note that Goyet is the closest proxy to some of the ancestors of El-Miron, but it may not be the ancestor at all. So if Goyet-like populations were heterogeneous in relation to East Eurasian, then El-Miron may descend from a group which never mixed with East Eurasians.

This is clear when you read many of these ancient DNA papers closely. The Mal’ta boy was representative of a population which contributed to both Northern Europeans (via Eastern Hunter-Gatherers) and Amerindians, but the deeper results also indicated that the common contributor to these populations was not the Mal’ta population, but related to them. That is, there is no expectation that the sparse sampling of ancient DNA in many regions and epochs will find the ancestral populations, as opposed to groups related to the ancestral populations.

This is a looking-through-the-glass-darkly situation. The true pattern of population relationships of the past needed to be inferred from a finite set of individuals randomly drawn from those populations. If most of those populations left no descendants due to common and repeated local extinction events, then it may be that most of the time we’re going to have to triangulate to the “true” ancestral groups, who left descendants simply due to luck.

Finally, this should really put the nail in the coffin of the idea that we can think of ancient populations are algebraic recombinations of modern populations. Modern groups almost certainly sample only a small part of the distribution of ancient populations.

October 12, 2017

Race is not just skin color

Filed under: Genetics,race — Razib Khan @ 8:56 pm

“The southern Indians resemble the Ethiopians a good deal, and, are black of countenance, and their hair black also, only they are not as snub-nosed or so woolly-haired as the Ethiopians; but the northern Indians are most like the Egyptians in appearance.”

– Arrian

I might almost say that the same animals are to be found in India as in Aethiopia and Egypt, and that the Indian rivers have all the other river animals except the hippopotamus, although Onesicritus says that the hippopotamus is also to be found in India. As for the people of India, those in the south are like the Aethiopians in colour, although they are like the rest in respect to countenance and hair (for on account of the humidity of the air their hair does not curl), whereas those in the north are like the Egyptians.


The plot above is from Genetic Evidence for the Convergent Evolution of Light Skin in Europeans and East Asians. It’s a 2007 paper. For those of you not versed in genetics, 10 years is like the difference between the First Age and Third Age on Middle Earth. For those of you not versed in Tolkien, 10 years is like the difference between Gupta India and Maratha India? I think?

Basically, the authors looked around the regions of the genome of loci known to be implicated in pigmentation variation in 2007, which mostly started from differences between Europeans and Africans. In the plot above you see pairwise genetic distances visualized in a neighbor-joining tree. The populations are:

SA = Asians, IM = Island Melanesians, WA = West Africans, EU = Europeans, EA = East Asians, and NA = Native Americans

What you see is that pigmentation loci are not phylogenetically very informative. Because of ascertainment bias in discovery Europeans are an out-group on many of the genes. But overall you see that the trees generated by a relationship on pigmentation genes do not conform to what we’d expect, where Africans are an outgroup to non-Africans. This is not surprising, as any given locus is not too phylogenetically informative. Additionally, pigmentation is a trait where selection has likely changed allele frequencies a lot, so it’s not a very good trait to look at to determine evolutionary relationships.

A white actress?

I bring this up because The New York Times and other publications are reporting on a new paper in Science, Loci associated with skin pigmentation identified in African populations, with headlines like Genes for Skin Color Rebut Dated Notions of Race, Researchers Say.

The Science paper is very interesting because it helps to make up for the long-term ascertainment bias in the literature, whereby European differences from other groups helped to discover pigmentation loci of interest. The big topline result is that there’s a lot of extant variation within Africans, and much of it is very old, pre-dating modern humans by hundreds of thousands of years, implying long-term balancing selection to maintain polymorphism.

Here’s a quote from The New York Times piece:

For centuries, skin color has held powerful social meaning — a defining characteristic of race, and a starting point for racism.

“If you ask somebody on the street, ‘What are the main differences between races?,’ they’re going to say skin color,” said Sarah A. Tishkoff, a geneticist at the University of Pennsylvania.

The widespread distribution of these genes and their persistence over millenniums show that the old color lines are essentially meaningless, the scientists said. The research “dispels a biological concept of race,” Dr. Tishkoff said.

I can go along with all the sentences more or less except the last. Skin is the largest organ we have, and it’s pretty salient. West Asian Muslims regularly referred to Indians as “black” (early Islamic Arabs referred to the people of Sindh as “black crows”). They defined themselves as white (though contrasted their own olive complexion with ruddy Europeans). The Chinese referred to themselves as white, and Southeast Asians, such as the inhabitants of the ancient Cambodian kingdom of Funan, as black. Among South Asians, skin color is also very salient. During the period when Pakistan included a western and eastern half the West Pakistanis were known to refer to the Bengalis as blacks, while East Pakistanis who went to study in the West, like my father, were surprised that not all Pakistanis were white like Ayub Khan.

Sharon Muthu, Indian American actress

But racial perception and categorization are not identical with skin color. The ancients knew this intuitively, as the quotes from Arrian and Strabo above suggest. They were aware that South Asians were dark-skinned, but those in the north were lighter than those in the south, and that those in the south resembled Africans in the range of their complexion. But, they also knew that it was not difficult to distinguish a South Asian from an African in most cases, because South Asians have different hair forms and to some extent facial features, from Africans.

I know this myself personally. Living in almost white areas of the United States for most of my childhood I encountered some racism. My skin tone is within the range of African Americans. But when it came to racial slurs I was usually called “sand nigger”, or more sometimes “camel jockey.” Please note that the modifier sand. Even racists understood to distinguish people of similar hues who were clearly physically distinctive.

Conversely, African Americans did not usually recognize me as African American. Living in the Pacific Northwest there aren’t many non-whites. It’s also very rainy. Sometimes when I was wearing my Columbia jacket with hood black men walking from the other direction on the sidewalk would start to nod at me, assuming I was black. But mid-way through the nod as they approached me they recognized that despite my brown color I was not African American and would stop the motion and switch to a manner of distanced politeness as opposed to informal warmth.*

Finally, I also had East Asian friends who were very light-skinned. As light-skinned as any white person of Southern European heritage. That did not prevent racists from calling them “chinks” or (more rarely) “gooks.” These racists were seeing beyond the skin color.

If ancient authors from 2,000 years ago understood that race is more than skin color, and if genuine bigots understand race is more than skin color, I fail to understand why so often the public discourse in the United States acts as if race is just skin color. We know it’s not so.

The reason I’m posting this on Brown Pundits is that the focus on skin color made sense to me growing up in the United States, but as someone of South Asian ancestry I also knew it was not sufficient as a classifier. I knew when I was probably around five. Many South Asians see a huge range in skin color within their immediate families. That is, empirically the fact that there were large effect QTLs segregating within South Asians is obvious to any South Asian who grew up around South Asians.**

My mother is of light brown complexion. My father is of dark brown complexion. My mother’s complexion is fair enough that she is usually assumed to be Latina if she doesn’t speak (her accent is clearly South Asian), and in cases has been misjudged to be Southern European. My father, like his mother, is in contrast on the darker side. Their Bengali friends would joke that they were an interracial relationship.

My father’s father was very light skinned, and his mother was very dark skinned. Some of his siblings were dark, some of them were light, and some of them were between. One of my father’s brothers is basically a doppelganger of my father, except he is lighter skinned.

And yet there was never a question that both my parents were ethnically Bengali. They were both people with deep roots in Comilla in eastern Bengal. Now that I have their genotypes I can tell you that my parents are genetically clearly from the same region of Bengal; they cluster together even compared to other Bangladeshis. In fact, my father is more Indo-Aryan (every so slightly) shifted than my mother. I suspect it is through his mother, whose father was born into a family of recently converted Brahmins. It is clear that skin color is not predicting phylogeny in this case, and I am sure many South Asians intuitively grasp this because of the variation in complexion they see across their families, who are usually from the same sub-ethnic group in any case.***

A multiracial United States is going to be more complex world than the situation before 1965, when America’s racial consciousness was partitioned between black and white (notwithstanding Native Americans, Hispanos and other Latinos in the Southwest, and a residual of Asian Americans). But sometimes I feel the intellectual and cultural elite of this nation is stuck in the paradigm of 1964.

* I have a friend from Kerala in South India who has talked about being mistaken for being Ethiopian.

** I am the only South Asian my daughter has grown up around, and her complexion is far closer to her mother’s than my own. She did have a difficult time distinguishing me from black males in her early years because to her my dark-skin is very salient. When her mother asked her to give reasons why African American males might look different from her father, she immediately clued in on the hair and facial features.

*** Black Americans and Middle Easterners, and a whole host of other groups where pigmentation loci segregation in appreciable frequencies, can all see that differences in skin color do not necessarily denote differences in race, since there is so much intra-familial variation.

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