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

November 6, 2017

Our time in the sun

Filed under: Evolutionary Biology — Razib Khan @ 9:14 pm

The New York Times has a story up, After the Dinosaurs’ Demise, Many Mammals Seized the Day. It’s a write-up of a new paper that is open access, Temporal niche expansion in mammals from a nocturnal ancestor after dinosaur extinction.

This research illustrates how computational power has changed evolutionary biology. There has long been an intuitive verbal model that mammals were ancestrally night-adapted creatures based on aspects of their biology, as well as the evolutionary reality that for most of the lineages’ existence they were overshadowed by dinosaurs (remember, more than half of our evolutionary history predates the Cenozoic).

But today we do more than posit models which match and predict the fossil (or genetic) data. Computationally intensive phylogenetic frameworks are tested using extant lineages to generate probabilities of given scenarios generating the data we see given particular models. Something like the Reversible-jump Markov chain Monte Carlo (which is used in this paper) could actually be done manually…if a phylogeneticist had thousands of slaves to do all the computations. Obviously, the emergence of powerful computers accessible to all really changed the game in terms of analytic power.

And yet I wonder about the sense of precision that people gain from these methods. Verbal models are necessarily vague. When you give a probability of a given hypothesis being 0.71, that gives understanding a solidity. But is it warranted? Though researchers understand all the individual moving parts of the phylogenetic framework, only a computer can really bring it all together.

It’s something to consider. This is to a great extent the future of evolutionary biology. Positing models, and put it into a calculating machine like Leibniz dreamed of.

Citation: Temporal Niche Expansion In Mammals From A Nocturnal Ancestor After Dinosaur Extinction
Roi Maor, Tamar Dayan, Henry Ferguson-Gow, Kate Jones

Addendum: This is stupid of me, but only after reading the above paper did I reflect that most amniotes are diurnal and that mammals are the exception. Think about it, birds. And reptiles are probably more sluggish at night.

The end of the Kingdom of Saudi Arabia

Filed under: International Affairs,Saudi Arabia — Razib Khan @ 6:49 pm

The most important thing happening in the world that is different this week from last week from what I can tell is that the the Kingdom of Saudi Arabia is going “full Ishmael” on us. By this I mean the reference in the Hebrew Bible to Abraham’s firstborn son, Ishmael, and the legendary ancestor of the Arabs: “And he will be a wild man; his hand will be against every man, and every man’s hand against him….”

What’s going on now? As you know there seems to be an internal purge going on, and a centralization of power around the Crown Prince. This, after the rollback of the power of the religious establishment.

Externally the quagmire in Yemen continues, and the Saudi state is now becoming more belligerent toward both Iran and Lebanon.

Most of you probably know the general issues about why the Saudi state is attempting to change and reform. Though petroleum will remain important for plastics and jet fuel, it is quite possible that the proportion used for gasoline will decline with the rise of electric cars. Additionally, there seem more supply-side possibilities with fracking technologies.

But perhaps the biggest factors are demographic. Over ten years ago Peter Turchin wrote a paper, Scientific Prediction in Historical Sociology: Ibn Khaldun meets Al Saud. It’s pretty useful in understanding what’s going on right now. The big issue which Turchin talks about more generally and is relevant to Saudi Arabia is elite overproduction. The Royal House is highly fecund. And all the scions demand unsustainable leisured lives….

November 5, 2017

Open Thread, 09/05/2017

Filed under: Open Thread — Razib Khan @ 7:07 am

Over the weekend DNAGeeks put up some Gene Expression t-shirts. Check it out!

Saudi Crown Prince’s Mass Purge Upends a Longstanding System. This is a big deal with major ramifications.

Genomic Signatures of Sexual Conflict.

Finished Red Flag: A History of Commumism. Recommedned.

November 2, 2017

China’s wealthiest come from only a few regions

Filed under: China — Razib Khan @ 10:53 pm

In Kenneth Pomeranz’s The Great Divergence: China, Europe, and the Making of the Modern World Economy he argues that the difference in per capita economic wealth between Europe and China is a relatively recent phenomenon. One of the major arguments he makes is that one has to make an apples-to-apples comparison. Comparing Northwest Europe to China is not apples-to-apples, but comparing Northwest Europe to the lower Yangzi Delta region of Central China is apples-to-apples. Using this measure Europe and China are roughly comparable.

At least that’s the argument. Others argue for much deeper and older roots for the differences between Western Europe and the rest of the world, most articulately in Gregory Clark’s A Farewell to Alms.

I don’t have a dog in this fight and am not decides, though I follow the field closely. Rather, I’ve always been curious about differences between Chinese regions, and how they never undermine national unity. I recall reading years ago in The Age of Confucian Rule that imperial examinations to determine candidates for the bureaucracy had quotas on candidates from the southeastern province of Fujian. They were simply filling up too many slots, at the expense of northern Chinese candidates.

The tension between social and economic orientations of different regions of China cropped up periodically. Basically, the Overseas Chinese community is derived from southern regions such as Guangdong and Fujian, the central government over the centuries attempted to stamp out these regions’ propensity toward international commerce. A figure like Howqua is typical, though he certainly would not be met with approval by stern Neo-Confucians such as Zhu Xi (also a southern Chinese born and bred).

With all this in mind, I was curious about the origins of the 20 wealthiest Chinese as of 2017. Below you see the results:

Name Net worth (USD) Sources of wealth Province Certainty
Wang Wenyin 14 billion mining, copper products Anhui  
Liu Yongxing 6.6 billion agribusiness Fujian  
Ma Huateng 24.9 billion internet media Guangdong  
He Xiangjian 12.3 billion home appliances Guangdong  
Yang Huiyan 9 billion real estate Guangdong  
Yao Zhenhua 8.4 billion conglomerate Guangdong ?
Zhang Zhidong 8.4 billion internet media Guangdong ?
Hui Ka Yan (Xu Jiayin) 10.2 billion real estate Henan  
Lei Jun 6.8 billion smartphones Hubei  
Liu Qiangdong 7.7 billion e-commerce Jiangsu  
Zhang Shiping 6.7 billion aluminum products Shandong  
Wang Wei 15.9 billion package delivery Shanghai  
Robin Li 13.3 billion internet search Shanxi  
Wang Jianlin 31.3 billion real estate, Sichuan  
Xu Shihui 21.1 billion solar power equipment Sichuan  
Jack Ma 28.3 billion e-commerce Zhejiang  
William Ding 17.3 billion online games Zhejiang  
Zong Qinghou 7.2 billion beverages Zhejiang  
Li Shufu 21.1 billion automobiles Zhejiang  
Guo Guangchang 6.3 billion diversified Zhejiang

A few of the individuals I’m not totally sure about in terms of where they were born, but I think I guessed correctly. Comparing representation on the list to national population by province, and you get:

Province Pop % On list
Guangdong 8% 25%
Zheijiang 4% 25%
Sichuan 8% 10%
Fujian 3% 5%
Anhui 5% 5%
Henan 7% 5%
Hubei 4% 5%
Jiangsu 6% 5%
Shanghai 2% 5%
Shanxi 3% 5%
Shandong 7% 5%

Zheijang-Jiangsu-Shangai is the core economic region highlighted by Pomeranz. About 12% of China’s population resides in these jurisdictions, but 35%, 7 out of 20, of its 20 wealthiest individuals were born here. Guangdong, as ground zero of the new economic revolution has clearly benefited.

Introducing DNAGeeks.com

Filed under: DTC personal genomics,Personal genomics — Razib Khan @ 8:27 am

Four years ago my friend David Mittleman and I wrote Rumors of the death of consumer genomics are greatly exaggerated. The context was the FDA crackdown on 23andMe. Was the industry moribund before it began? The title gives away our opinion. We were personally invested. David and I were both working for Family Tree DNA, which is part of the broader industry. But we were sincere too.

Both of us have moved on to other things. But we still stand by our original vision. And to a great extent, we think we had it right. The consumer genomics segment in DTC is now nearing 10 million individuals genotyped (Ancestry itself seems to have gone north of 5 million alone).

One of the things that we observed in the Genome Biology piece is that personal genomics was still looking for a “killer app”, like the iPhone. Since then the Helix startup has been attempting to create an ecosystem for genomics with a variety of apps. Though ancestry has driven nearly ten million sales, there still isn’t something as ubiquitous as the iPhone. We’re still searching, but I think we’ll get there. Data in search of utility….

David and I are still evangelizing in this space, and together with another friend we came up with an idea: DNAGreeks. We’re starting with t-shirts because it’s something everyone understands, but also can relay our (and your) passion about genomics. We started with “Haplotees.” Basically the most common Y and mtDNA lineages. This might seem silly to some, but it’s something a lot of people have an interest in, and it’s also a way to get ‘regular people’ interested in genetics. Genealogy isn’t scary, and it’s accessible.

We are also field-testing other ideas. If there is a demand we might roll out a GNXP t-shirt (logo only?). The website is obscure enough that it won’t make sense to a lot of people, but perhaps it will make sense to the people who you want it to make sense too!

Anyway, as they say, “keep watching this space!” We don’t know where DNAGeeks is going, but we’re aiming to have fun with genomics and make a little money too.

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.

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