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

March 29, 2017

10 Things About Roman History You Should Know

Filed under: Culture,History,rome — Razib Khan @ 9:42 pm

Since Since the earlier “10 Things” was quite popular, I thought I’d try my hand at another one on a topic I know rather well. This involves Roman history. Unfortunately, history is a less clear and distinct topic than evolutionary biology, so there may be some disagreement with the assertions below.

But here we go….

1) Constantine did not make Christianity the official religion of the Roman Empire. The Roman Empire did not have an established religion, at that point, in any way we could understand today. Rather, there were customary subsidies given to traditional cults, and favor shown to particular religions by particular emperors. The subsidies from the state coffers to pagan cults were cut off more than two generations after Constantine.

2) By the late Republic most of the “noble” families of Roman society were originally plebeian, rather than patrician, in origin. They were defined by their wealth, power, and achievements, as opposed to their blood. There were still powerful patrician lineages, such as the Julii and Claudii, by they no longer held a monopoly on the public square (Julius Caesar may have been from an old patrician line, but his mother was a Cotta, who were plebeians).

3) Most of the emperors who were “not Roman,” were thoroughly Roman. Septimius Severus, the “African emperor,” born in Libya, did come from a paternal lineage of Punic (so Phoenician) origin. But his mother descended from Italian colonists in North Africa. He was culturally a man of the Latin West.

4) At the elite level Roman culture was to some extent dual-culture, with many Latin elites cultivating aspects of Greek culture and learning. But Western (Latin) and Eastern (which usually been Greek or Hellenized non-Greek) societies remained sharply differentiated in many ways. The first emperor who may have spoken Greek as his first language, Anastasius, reigned at the end of the 5th century. Greeks dominated philosophy, while Latins dominated rhetoric.

5) Though Latin political control collapsed in Italy in 476, the cultural and economic destruction of the Italian peninsula occurred during the East Roman reconquista of the 6th century.

6) The forms of Republican Rome persisted for centuries during the imperial period. The transformation of Roman Emperors into purely naked autocrats did not occur until after the chaos of the middle 3rd century.

7) Speaking of which, the Roman system almost collapsed during the “Crisis of the Third Century”.

8) The early “bad emperors,” such as Nero or Caligula, often caused problems for the Roman elites. But the overall institutional system persisted and was minimally impacted. In contrast, Julius Caesar would almost certainly be judged to have committed genocide in Gaul were he judged by modern standards.

9) Most of the expenditure of the Roman state went to the military.

10) Romans arguably invented Western bureaucracy. Though the Roman state in was incredibly understaffed by modern standards, one consequence of the Western Empire’s fall was the collapse of tax collection in specie as opposed to kind or service.

When the gods come crashing down

Filed under: Culture,Evolution,History — Razib Khan @ 9:03 pm

Sometimes the old gods slowly fade into oblivion. Contrary to popular perception this seems likely the case for ancient paganism. The conversion of Constantine to the Christian religion began the process of a hand-off and the commanding heights of classical culture that took over a century to complete. There were punctuating moments, such as the apostasy of Justinian in the 360s, or the mostly symbolic ban on public paganism by Theodosius in the 390s (the Serapeum was destroyed by a vigilante mob). But pagans in the form of the Neoplatonic school persisted into the 6th century, while elite pagans such as Marcellinus maintained power and influence deep into the second half of the 5th century.

Call this “normal” cultural evolution. Antiquity evolved from being predominantly pagan to predominantly Christian (though a small cultured pagan minority persisted even until the Islamic conquest in the Near East, such as the Sabians of Haran).

The Reformation period was different. In a single generation one thousand years of a coherent and unified Western Christian ideology collapsed, and was replaced by something very different.

Note here that I said Western Christian ideology. The reality is that Western Christianity was never as unified or coherent as Western Christians themselves envisaged themselves to be (or aspired to be). There were episodes of hostility between particular kingdoms and the Roman papacy. Heresies such as that of the Cathars, and popular revolts with a religious tinge such as that of the Hussites. And finally, there were periods of multiple popes, which undermined the credibility of the institution of the Church in the medieval period.

But all this pales next to the magnitude and scope of the revolt against the establishment of the Western Christian church that occurred in the 1520s. Martin Luther went from being a Christian cleric within the established Church to declaring the pope the anti-Christian! Previously devout peasants in Switzerland turned on the relics and churches which they had only recently venerated, and engaged in mob iconoclasm. Whereas monarchs, such as Henry IV, ultimately compromised with the clerical estate (or, submitted), Henry VIII of England managed to destroy or subordinate the institutions of the church to his own will and pleasure.

There are many theories for why the Reformation occurred when it did. Some of them are rooted in technology, in particular the printing press. Others point to the development of proto-national identities, such as the rise of German nationalism and its leveraging by Luther against his “Roman” persecutors.

These specific issues are not interesting to me. Rather, what they point out to us that there can be cultural revolutions that occur very rapidly. One can point to the pacific post-World War II Japanese, and contrast them with the militaristic Japanese of the first half of the 20th century. Or the shift of Russia from being a conservative autocracy in the 1910s to a revolutionary society in the 1920s. But these are modern events, and moderns are liable to suggest that our own epoch is sui generis in these sorts of turnovers of values. But the Reformation shows that revolutionary changes in whole societies can occur rather rapidly even in a pre-modern context.

In other words, cultural revolution is not a derived characteristic of our species, but perhaps a very old one. The rapid expansion of the Austronesians. Or the radiation of non-African humanity. These come out of a vacuum, a cultural-demographic analog to the inflationary universe. But given enough time perhaps our species is simply subject to these sorts of explosions of creative change and innovation.

List of top 10 evolutionary biologists in history

Filed under: Evolution,Evolutionary Biologists,Genetics — Razib Khan @ 4:00 am

What is your list of the top 10 evolutionary biologists in history? I’m asking because this came up in a discussion with a friend. Obviously the composition of the list will have to do with disciplinary bias and geography and history (there are Russian population geneticists from the 20th century who should be more famous who aren’t).

Here are my top 10 (with two minutes thought given):

1. Charles Darwin
2. R. A. Fisher
3. Sewall Wright
4. J. B. S. Haldane
5. W. D. Hamilton
6. G. G. Simpson
7. John Maynard Smith
8. August Weismann
9. Motoo Kimura
10. Theodosius Dobzhansky

What’s your list? (in the comments)

March 28, 2017

How Indians are a lot like Latin Americans

Filed under: Anthroplogy,Genetics,India — Razib Khan @ 5:45 am


Pretty much any person of Indian subcontinental origin in the United States of a certain who isn’t very dark skinned has probably had the experience of being spoken to in Spanish at some point. When I was younger growing up in Oregon I had the experience multiple times of Spanish speakers, probably Mexican, pleading with me to interpret for them because there was no one else who seemed likely. It isn’t a genius insight to conclude I was most likely South Asian…but it wasn’t out of the question I was Mexican. This applies even more to lighter skinned South Asians. In the Central Valley of California, where there are many Sikhs from Punjabi and Mexicans, this confusion occurred a lot for some Indian kids.

Of course biogeographically there isn’t that much connection between South Asia and the New World. But it isn’t crazy that Christopher Columbus labelled the peoples of the New World “Indian.” After all, they were a brown-skinned people whose features were not African, East Asian, or West Eurasian. And, it turns out genetically there is a coincidence that connects the New World and South Asia: the mixed peoples of Latin America with Amerindian and European ancestry recapitulate an admixture which resembles what occurred in South Asia thousands of years ago. It looks as if about half the ancestry of South Asians is West Eurasian and half something more like eastern Eurasians.

On principles component analysis that means that South Asian and Mexican and Peruvian samples often overlap. This is somewhat curious because the non-West Eurasian ancestors of South Asians and Amerindians diverged in ancestry on the order of 25 to 45 thousand years before the present. And the Iberian ancestry of the mixed people of the New World is almost as far from the character of South Asian West Eurasian ancestry as you can get (in the parlance of this blog, lots of EEF, less CHG, not too much ANE).

A new paper, A genetic chronology for the Indian Subcontinent points to heavily sex-biased dispersals, highlights another similarity: massive bias in biogeographic ancestry by sex. More precisely, the rank order of West Eurasian ancestry in South Asia is skewed like so: Y chromosome > whole-genome > mtDNA (as is evident in the above figure).

I actually began writing about this in the late 2000s, when the fact that South Asian mtDNA was very different from West Eurasian mtDNA, and South Asian Y chromosome was mostly West Eurasian, was obvious. Then work using genome-wide data sets began to point to massive intra-Eurasian admixture between very diverged lineages. The paper is not revolutionary, but worth reading for its thoroughness and how it brings together all the lines of evidence.

Finally, no ancient DNA. That’s probably for the future, but I don’t expect any surprises.

Citation: A genetic chronology for the Indian Subcontinent points to heavily sex-biased dispersals.

March 27, 2017

It doesn’t get better, blogging vs. YouTube and Twitter

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

Many of you know I use Twitter. It’s replaced a lot of the “link posts” I might have done in the early 2000s or so. Some have argued that Twitter cannibalized a lot of blogging, and that seems true. And that hasn’t always been for the good…there are some arguments and discussions which don’t work well on Twitter. There have been many Twitter misunderstandings which simply wouldn’t have happened in the blogging format, because of the artificiality of Twitter strips context.

Until recently I didn’t much pay attention to YouTube except for movie trailers and Games of Thrones stuff. Oh, and How it Should Have Ended. Any other YouTube I probably just found via a share on Facebook and Twitter.

But of late I have been watching some YouTube channels. I was prompted partly by the fact that after the hit piece came out on me about my incredible influence on the alt-right someone emailed me to explain that in fact the most influential people on the alt-right were on YouTube, where they spread interpretations of genetics congenial to their racialist worldview. Honestly I didn’t watch these channels for very long because:

Fathering the next generation of white non-whites

1) I don’t need genetics lectures.

2) I don’t need primers on Western history.

3) I am not concerned about white genocide, I am white genocide.

Rather, I found a channel called The Rubin Report, which had come recommended to me by my friend Sarah Haider. I agreed with the host, Dave Rubin, on most issues, and often disagreed with his guests. It made for reasonably compelling listening (I rarely watch really, but treat this stuff like a podcast). He also introduced me to a lot of different vloggers. Among the people he interviewed was someone called Roaming Millennial, an early 20s Eurasian Canadian woman with broadly center-right/classical liberal views.

I don’t mean to spotlight her, but her channel illustrates three facts:

1) Relatively short, pithy, commentaries.

2) A huge number of views.

3) Many of these vloggers are “TV-friendly” in their appearance.

Comparing traffic can be hard across years and platforms, so I’ll focus on the first and last issue. When it comes to the early generation of bloggers there are plenty who became famous on pithy quick links. But there were also long-form essayists and commenters. To give one example, Cosma Shalizi’s posts on IQ were extensively linked for many years because of their thoroughness and depth (obviously few people read everything or understood much, but the posts were there, and many at least skimmed a fair amount).

These sorts of discursive commentaries are not really possible on YouTube. From what I can tell when vloggers allow themselves to go more than 20 minutes on a single topic they start to ramble, repeat themselves, and get boring. You can’t engage in extemporaneous speaking for too long and sound like you have your shit together. The data density of blogging is potentially much higher than vlogging.

The third issue…. Many bloggers had a face for radio, and a voice for silent film. The extremely popular liberal blogger Steve Gilliard was morbidly obese, and died of illnesses related to his weight issues. But his appearance was not a big deal when he began blogging. Many of the early bloggers concealed many details of their private life, let alone their image. Similarly, a lion of the warblogging cohort, Steve Den Beste, looked to be out of central casting for “middle aged software/anime nerd.” But Den Beste became hugely influential before his retirement from blogging, which was partly triggered by health issues.

Obviously things aren’t that different. There was television in the 2000s. And many webforums existed which had a Twitter-like feel. But they are different nevertheless. Someone like Roaming Millennial could have made it on TV, but there are only so many spots for non-blondes at Fox, and in any case she speaks at a higher level of analysis than what you see in talking heads. There are many more of these vloggers than there would ever have been slots on television. This is a whole new information universe, and it’s different.

A the end of the day it makes me appreciate text, and blogging. There are newer technologies, but they aren’t better.

Adaptation is ancient: the story of Duffy

Filed under: Duffy allele,Duffy antigen,Genomics,History,Malaria — Razib Khan @ 10:06 pm

Anyone with a passing familiar with human population genetics will know of the Duffy system, and the fact that there is a huge difference between Sub-Saharan Africans and other populations on this locus. Specifically, the classical Duffy allele exhibits a nearly disjoint distribution from Africa to non-Africa. It was naturally one of the illustrations in The Genetics of Human Populations, a classic textbook from the 1960s.

Today we know a lot more about human variation. On most alleles we don’t see such sharp distinctions. Almost certainly the detection of these very differentiated alleles early on in human genetics was partly a function of selection bias. The methods, techniques, and samples, were underpowered and limited, so only the largest differences would be visible. Today we often use single base pair variations, single nucleotide polymorphisms, and the frequency differences are much more modest on average. Ergo, the reality that only a minority of genetic variation is partitioned across geographic races.

Why is Duffy different? Obviously it could be random. Assuming you have a polymorphism, you’ll get a range of frequencies across populations, and in some cases those frequencies which map onto different geographic zones just by chance. Imagine constant mutation, and high structured bottlenecks. You could get a sequence of derived mutations fixing in populations one after the other, just by chance.

This is probably not the case with Duffy. I’ll quote from Wikipedia:

The Duffy antigen is located on the surface of red blood cells, and is named after the patient in which it was discovered. The protein encoded by this gene is a glycosylated membrane protein and a non-specific receptor for several chemokines. The protein is also the receptor for the human malarial parasites Plasmodium vivax and Plasmodium knowlesi. Polymorphisms in this gene are the basis of the Duffy blood group system.

Malaria is one of the strongest selection pressures known to humanity. The balancing selection which results in sickle-cell disease is well known even among the general public. But the likely selection pressures due to the vivax variety are well commonly talked about, partly because they don’t as a side-effect induce a serious disease. Duffy may be canonical if you are a human population geneticist, but it is of less interest more generally.

But a recent paper in PLOS GENETICS shows just how dynamic the evolutionary genetic past of our species was, through the lens of the Duffy system, Population genetic analysis of the DARC locus (Duffy) reveals adaptation from standing variation associated with malaria resistance in humans. Here’s the author summary:

Infectious diseases have undoubtedly played an important role in ancient and modern human history. Yet, there are relatively few regions of the genome involved in resistance to pathogens that show a strong selection signal in current genome-wide searches for this kind of signal. We revisit the evolutionary history of a gene associated with resistance to the most common malaria-causing parasite, Plasmodium vivax, and show that it is one of regions of the human genome that has been under strongest selective pressure in our evolutionary history (selection coefficient: 4.3%). Our results are consistent with a complex evolutionary history of the locus involving selection on a mutation that was at a very low frequency in the ancestral African population (standing variation) and subsequent differentiation between European, Asian and African populations.

Why is it that regions of the genome subject to selection due to co-evolution with pathogens are hard to detect in relation to selection? My response would be that it’s because selection and adaptation are always happening in these regions, constantly erasing its footprints in these regions of the genome.

You may be familiar with the fact that the major histocompatibility complex (MHC) are some of the most diverse regions of the genome. That’s because negative frequency dependent selection makes it so that rare variants never go extinct, as the rarer they get the more favored they are.

Many classical and modern techniques of selection require less protean dynamics when it comes to the model which they attempt to detect. Basically, many of the standard selection detection methods are looking for a simple perturbation in the pattern of variation that’s expected. A strong powerful recent sweep on a single mutation is like the spherical cow of evolutionary genetics. It happens. And it’s easy to model and detect. But it may not be nearly as important as our ability to detect these “hard sweeps” may suggest to us.

In contrast, if selection targets a larger number of independent mutations, then you get a “soft sweep,” which is harder to detect, because it is no singular event. Complexity is the enemy of detection. As a thought experiment, if you selected for height within a population you may catch some large effect alleles that would leave strong signals, but most of the dynamic would leave a polygenic footprint, distributed across innumerable genes.

The Duffy locus is somewhat in the middle. The authors distinguish between selection on standing variation (the allele frequency is higher than a single new mutation within the population) and a soft sweep, where multiple variants against different haplotypes are subject to selection. Their models and results strongly support selection on standing variation for the FY*O variant, and perhaps selection for the FY*A variant.

These selection events were very old, and very strong. Selection coefficients on the order of 4% are hard to believe in a natural environment. Curiously the coalescence times for the haplotypes some of these alleles indicate that selection was contemporaneous with the emergence of modern humans out of Africa, about ~50,000 years ago. From their sequence data analysis the different alleles have been segregating for a long time in the collective human population, and powerful sweeps fixed FY*O in both the ancestors of the Bantu and Pygmies before they diverged from each other. In contrast the Khoisan samples suggest that FY*O introgressed into their population from newcomers, while variants of FY*A are ancestral.

The big picture here is that selection is ancient, that it is powerful, and it was a dynamic even before our species diversified into various lineages.

If you read the paper, and you should, it’s pretty clear that a lot of the adaptive story was suspected. It’s just with modern genomics and fancy ABC methods you can put point estimates and intervals on these hunches. But another issue, as they note in the piece, is that we have a better grasp of African population structure today than in the past, and this allows for better framing.

But it is here I have some caution to throw. At one point citing a 2012 paper the authors suggest “The KhoeSan peoples are a highly diverse set of southern African populations that diverged from all other populations approximately 100 kya.” I can tell you that some credible researchers who have access to whole genome sequences and have been looking at this question peg the divergence date closer to 200,000 years. Some of the issue here is that you need to decompose later gene flow, which will reduce the distance between populations. Easier said than done.

The genetic prehistory of the African continent is almost certainly much more complex than what is presented in the paper, largely due to lack of ancient DNA within Africa. Northern Eurasia turned out to be far more complex than had earlier been guessed…and it is likely that Northern Eurasia has had a simpler history because of its much shorter time of habitation.

If I had to guess I suspect that the ancestors of the Khoisan as we understand them were a separate and distinct group who diverged between ~100,000 and ~200,000 years ago from other extant African populations. But I suspect our clarity is very low in relation the sort of structure which eventually resulted in the shake-out of only a few large groups of Sub-Saharan Africans aside from the Khoisan.

Citation: Population genetic analysis of the DARC locus (Duffy) reveals adaptation from standing variation associated with malaria resistance in humans.

March 26, 2017

1967 imagines the home and life of 1999

Filed under: Future — Razib Khan @ 2:32 pm

We’re almost two years past 1999, but some of the things imagined in this conception of the future in the 1960s for the turn of the century are only now just coming true (e.g., electronic medical records, home health monitoring). I was surprised how well they anticipated a lot of the function of information technology, though of course as it was the 1960s there are a lot of turning of knobs.

Second, they didn’t anticipate how traditional humans can be about certain things. It turns out that instant meals have always remained a niche, rather than taking over the whole sector. Additionally, just because people could engage in ‘e-learning’ by the mid-1990s with the internet, didn’t mean that schools and their social aspect didn’t remain important. And we’ve been able to do video-conferencing for a while, but most of us prefer to take calls in the old-fashioned way, when we take calls at all (with email and various messaging services cannibalizing a lot of the function of the telephone).

Finally, they were totally unrealistic about the nature of transportation for middle class families. Yes, people travel, depending on your socioeconomic status. But an impulsive jaunt to Mexico City to go play golf just doesn’t happen.

Open Thread, 03/26/2017

Filed under: Open Thread — Razib Khan @ 2:08 pm


Lots of tweaks and changes on regards to the blog platform recently. As they say in the start-up world we’re “iterating.” The content/substance is going to remain pretty much the same, but over time I’ll be trying to figure out different ways to deliver.

This might cause some minor issues in terms of continuity (I do have the full archives from Unz and earlier, so I’ll load them up once I’m confident we aren’t going to change platforms for a while). I did some fiddling with the permlink URLs, so if you shared anything on Facebook, I’d appreciate if you reshared again.

No matter the details, the old Gene Expression website will point to where you need to go, gnxp.com, but you can also keep track of me through razib.com as well. Also, Twitter and my permanent feed (this feed always hooks into wherever my blog is, so it’s the one you want).

Finally, I also have set up a newsletter with MailChimp. The primary reason is really that I’m worried that some day Twitter will disappear and I figured it is important to have another way to contact people who follow me. I have only sent out one notification, and the next one will probably be when I’m more settled in terms of platform tweaks.

Mostly done with Reformations: The Early Modern World, 1450-1650. I’m a big fan of Diarmaid MacCulloch’s The Reformation, and this is a somewhat different book. Reformations focuses more on intellectual history and theological details, while MacCulloch’s magisterial survey hits political, social, cultural, and theological angles in equal measures. If I had to pick the order in which to read it would definitely be The Reformation first, but Reformations is a good compliment.

It’s annoying to me that journalists are pretty ignorant. I understand that that’s the deal when you are a generalist and get assigned to a diverse array of topics. But the public takes journalists seriously, so the fact that so many are so bad at what they do is frustrating. At this point I assume I’m being misled in a lot of areas where I don’t have domain knowledge.

I have a little knowledge about what happened in East Pakistan in the period of the late 1960s and early 1970s. The writer above probably doesn’t have domain knowledge. So they fit the Pakistan military’s killings in the framework of intra-Muslim conflict. Obviously there is something to this. But it is critical, in my opinion, to note that the ruling elites of West Pakistan viewed East Pakistanis as racially and culturally inferior, and that the large population of Hindus who remained in East Pakistan after partition bore a disproportionate brunt of the genocide. Foregrounding attacks on Muslims by this journalist arguably “erases” and misleads many of the readers of this piece, though I assume this is inadvertent.

On many topics my knowledge comes through “book-learning.” The conflict around 1970, and the cultural context beforehand, I know through oral history. For example, older Muslim Bengalis, such as my maternal grandfather, remained pro-Pakistan, in large part because their formative years were during the British Raj, and they retained strong memories of their religious marginalization during the time when the Hindu upper classes dominated Bengal. He was born in 1896, and recalled being the only Bengali Muslim doctor in many areas.

My parents, growing up after partition, had different memories. From what they have told me if you were a Muslim Bengali it certainly wasn’t similar to the experience of blacks in the American South, but there were events that occurred which made it clear who was on top. In Bangladesh after partition there was a community of people who migrated from India termed “Biharis” (many, but not all, were from Bihar province to the west of Bengal). As Urdu-speakers they identified more strongly with West Pakistan, and perceived themselves to be superior to the native population.

After independence they have been the subject of persecution in Bangladesh. Obviously this is bad, and my family does not have any animus toward Biharis. Many of them have assimilated and become Bengali. As most are Sunni Muslims and don’t look that different from the range of physical types among Bengalis it is not that difficult. Some of my cousins for example have a Bihari grandmother, a fact I only became aware of because despite having perfect Bengali there are some words she uses which point to an Urdu-speaking background.

But, my mother does admit during the 1960s she was witness to incidents where Biharis in Bengal behaved as if they were better and had more rights. One case which will have resonance with American readers: a Bihari man got on a bus and began shouting in Urdu for someone to get off because there were no seats left on the bus. Since the bus driver did not know Urdu someone had to be found to interpret for him, at which point a poor soul at the front of the bus was ejected and room was made for the Bihari man.

The killings of hundreds of thousands to millions of Bengalis was a bad thing. But the root causes and historical context shouldn’t be misrepresented.

RNA viruses drove adaptive introgressions between Neanderthals and modern humans. Here’s the important sentence: ” Our results imply that many introgressions between Neanderthals and modern humans were adaptive.”

I got a review copy of The Neuroscience of Intelligence. We’ll see when I get to it.

So some people are still asking me about the hit piece. I think I can tell you it was mostly written before the guy ever talked to me. Second, I’m to understand the editor of Undark is a serious person by journalist friends, but there is one link in there where the implication made does not follow at all from the content at the link (I rather argue the opposite of what was implied from the title).

I’m pretty sure that the journalist and the editor assumed most people would not read it (I can check the Google Analytics, very few people clicked through). If that isn’t true, they’re incompetent. Basically, it’s been a little sad because I am now concluding that the media is fine with just lying about people by implication without even the barest pretense. Meanwhile, someone like Michael Oman-Reagan is more mainstream in science than I am.

Honestly I’ve given up on the future of classical liberalism in the West. Most people are cowards and liars when push comes to shove. I don’t want to speak of this at length, as it’s a bit like a God-is-dead moment for me, but I thought I’d come clean and be frank. The Critical Theorists are right, power trumps truth. I’m not sure they’ll enjoy what’s to come in the future when objectivity is dethroned, but I think I will probably laugh as the liars scramble to lie different lies, because that is almost certain to happen.

So I have another son. He’s healthy. That’s all you can ask for. I still think now and then about the cat who died in January though.

Open Thread, 03/26/2017

Filed under: Open Thread — Razib Khan @ 2:08 pm


Lots of tweaks and changes on regards to the blog platform recently. As they say in the start-up world we’re “iterating.” The content/substance is going to remain pretty much the same, but over time I’ll be trying to figure out different ways to deliver.

This might cause some minor issues in terms of continuity (I do have the full archives from Unz and earlier, so I’ll load them up once I’m confident we aren’t going to change platforms for a while). I did some fiddling with the permlink URLs, so if you shared anything on Facebook, I’d appreciate if you reshared again.

No matter the details, the old Gene Expression website will point to where you need to go, gnxp.com, but you can also keep track of me through razib.com as well. Also, Twitter and my permanent feed (this feed always hooks into wherever my blog is, so it’s the one you want).

Finally, I also have set up a newsletter with MailChimp. The primary reason is really that I’m worried that some day Twitter will disappear and I figured it is important to have another way to contact people who follow me. I have only sent out one notification, and the next one will probably be when I’m more settled in terms of platform tweaks.

Mostly done with Reformations: The Early Modern World, 1450-1650. I’m a big fan of Diarmaid MacCulloch’s The Reformation, and this is a somewhat different book. Reformations focuses more on intellectual history and theological details, while MacCulloch’s magisterial survey hits political, social, cultural, and theological angles in equal measures. If I had to pick the order in which to read it would definitely be The Reformation first, but Reformations is a good compliment.

It’s annoying to me that journalists are pretty ignorant. I understand that that’s the deal when you are a generalist and get assigned to a diverse array of topics. But the public takes journalists seriously, so the fact that so many are so bad at what they do is frustrating. At this point I assume I’m being misled in a lot of areas where I don’t have domain knowledge.

I have a little knowledge about what happened in East Pakistan in the period of the late 1960s and early 1970s. The writer above probably doesn’t have domain knowledge. So they fit the Pakistan military’s killings in the framework of intra-Muslim conflict. Obviously there is something to this. But it is critical, in my opinion, to note that the ruling elites of West Pakistan viewed East Pakistanis as racially and culturally inferior, and that the large population of Hindus who remained in East Pakistan after partition bore a disproportionate brunt of the genocide. Foregrounding attacks on Muslims by this journalist arguably “erases” and misleads many of the readers of this piece, though I assume this is inadvertent.

On many topics my knowledge comes through “book-learning.” The conflict around 1970, and the cultural context beforehand, I know through oral history. For example, older Muslim Bengalis, such as my maternal grandfather, remained pro-Pakistan, in large part because their formative years were during the British Raj, and they retained strong memories of their religious marginalization during the time when the Hindu upper classes dominated Bengal. He was born in 1896, and recalled being the only Bengali Muslim doctor in many areas.

My parents, growing up after partition, had different memories. From what they have told me if you were a Muslim Bengali it certainly wasn’t similar to the experience of blacks in the American South, but there were events that occurred which made it clear who was on top. In Bangladesh after partition there was a community of people who migrated from India termed “Biharis” (many, but not all, were from Bihar province to the west of Bengal). As Urdu-speakers they identified more strongly with West Pakistan, and perceived themselves to be superior to the native population.

After independence they have been the subject of persecution in Bangladesh. Obviously this is bad, and my family does not have any animus toward Biharis. Many of them have assimilated and become Bengali. As most are Sunni Muslims and don’t look that different from the range of physical types among Bengalis it is not that difficult. Some of my cousins for example have a Bihari grandmother, a fact I only became aware of because despite having perfect Bengali there are some words she uses which point to an Urdu-speaking background.

But, my mother does admit during the 1960s she was witness to incidents where Biharis in Bengal behaved as if they were better and had more rights. One case which will have resonance with American readers: a Bihari man got on a bus and began shouting in Urdu for someone to get off because there were no seats left on the bus. Since the bus driver did not know Urdu someone had to be found to interpret for him, at which point a poor soul at the front of the bus was ejected and room was made for the Bihari man.

The killings of hundreds of thousands to millions of Bengalis was a bad thing. But the root causes and historical context shouldn’t be misrepresented.

RNA viruses drove adaptive introgressions between Neanderthals and modern humans. Here’s the important sentence: ” Our results imply that many introgressions between Neanderthals and modern humans were adaptive.”

I got a review copy of The Neuroscience of Intelligence. We’ll see when I get to it.

So some people are still asking me about the hit piece. I think I can tell you it was mostly written before the guy ever talked to me. Second, I’m to understand the editor of Undark is a serious person by journalist friends, but there is one link in there where the implication made does not follow at all from the content at the link (I rather argue the opposite of what was implied from the title).

I’m pretty sure that the journalist and the editor assumed most people would not read it (I can check the Google Analytics, very few people clicked through). If that isn’t true, they’re incompetent. Basically, it’s been a little sad because I am now concluding that the media is fine with just lying about people by implication without even the barest pretense. Meanwhile, someone like Michael Oman-Reagan is more mainstream in science than I am.

Honestly I’ve given up on the future of classical liberalism in the West. Most people are cowards and liars when push comes to shove. I don’t want to speak of this at length, as it’s a bit like a God-is-dead moment for me, but I thought I’d come clean and be frank. The Critical Theorists are right, power trumps truth. I’m not sure they’ll enjoy what’s to come in the future when objectivity is dethroned, but I think I will probably laugh as the liars scramble to lie different lies, because that is almost certain to happen.

So I have another son. He’s healthy. That’s all you can ask for. I still think now and then about the cat who died in January though.

March 23, 2017

Ancestry inference won’t tell you things you don’t care about (but could)

Filed under: Anthroplogy,Genetics,Genomics,Personal genomics — Razib Khan @ 5:59 pm

The figure above is from Noah Rosenberg’s relatively famous paper, Clines, Clusters, and the Effect of Study Design on the Inference of Human Population Structure. The context of the publication is that it was one of the first prominent attempts to use genome-wide data on a various of human populations (specifically, from the HGDP data set) and attempt model-based clustering. There are many details of the model, but the one that will jump out at you here is that the parameter defines the number of putative ancestral populations you are hypothesizing. Individuals then shake out as proportions of each element, K. Remember, this is a model in a computer, and you select the parameters and the data. The output is not “wrong,” it’s just the output based how you set up the program and the data you input yourself.

These sorts of computational frameworks are innocent, and may give strange results if you want to engage in mischief. For example, let’s say that you put in 200 individuals, of whom 95 are Chinese, 95 are Swedish, and 10 are Nigerian. From a variety of disciplines we know to a good approximation that non-Africans form a monophyletic clade in relation to Africans (to a first approximation). In plain English, all non-Africans descend from a group of people who diverged from Africans more than 50,000 years ago. That means if you imagine two populations, the first division should be between Africans and non-Africans, to reflect this historical demography. But if you skew the sample size, as the program looks for the maximal amount of variation in the data set it may decide that dividing between Chinese and Swedes as the two ancestral populations is the most likely model given the data.

This is not wrong as such. As the number of Africans in the data converges on zero, obviously the dividing line is between Swedes and Chinese. If you overload particular populations within the data, you may marginalize the variation you’re trying to explore, and the history you’re trying to uncover.

I’ve written all of this before. But I’m writing this in context of the earlier post, Ancestry Inference Is Precise And Accurate(Ish). In that post I showed that consumers drive genomics firms to provide results where the grain of resolution and inference varies a lot as a function of space. That is, there is a demand that Northern Europe be divided very finely, while vast swaths of non-European continents are combined into one broad cluster.

Less than 5% Ancient North Eurasian

Another aspect though is time. These model-based admixture frameworks can implicitly traverse time as one ascends up and down the number of K‘s. It is always important to explain to people that the number of K‘s may not correspond to real populations which all existed at the same time. Rather, they’re just explanatory instruments which illustrate phylogenetic distance between individuals. In a well-balanced data set for humans K = 2 usually separates Africans from non-Africans, and K = 3 then separates West Eurasians from other populations. Going across K‘s it is easy to imagine that is traversing successive bifurcations.

A racially mixed man, 15% ANE, 30% CHG, 30% WHG, 30% EEF

But today we know that’s more complicated than that. Three years ago Pickrell et al. published Toward a new history and geography of human genes informed by ancient DNA, where they report the result that more powerful methods and data imply most human populations are relatively recent admixtures between extremely diverged lineages. What this means is that the origin of groups like Europeans and South Asians is very much like the origin of the mixed populations of the New World. Since then this insight has become only more powerful, as ancient DNA has shed light as massive population turnovers over the last 5,000 to 10,000 years.

These are to some extent revolutionary ideas, not well known even among the science press (which is too busy doing real journalism, i.e. the art of insinuation rather than illumination). As I indicated earlier direct-to-consumer genomics use national identities in their cluster labels because these are comprehensible to people. Similarly, they can’t very well tell Northern Europeans that they are an outcome of a successive series of admixtures between diverged lineages from the late Pleistocene down to the Bronze Age. Though Northern Europeans, like South Asians, Middle Easterners, Amerindians, and likely Sub-Saharan Africans and East Asians, are complex mixes between disparate branches of humanity, today we view them as indivisible units of understanding, to make sense of the patters we see around us.

Personal genomics firms therefore give results which allow for historically comprehensible results. As a trivial example, the genomic data makes it rather clear that Ashkenazi Jews emerged in the last few thousand years via a process of admixture between antique Near Eastern Jews, and the peoples of Western Europe. After the initial admixture this group became an endogamous population, so that most Ashkenazi Jews share many common ancestors in the recent past with other Ashkenazi Jews. This is ideal for the clustering programs above, as Ashkenazi Jews almost always fit onto a particular K with ease. Assuming there are enough Ashkenazi Jews in your data set you will always be able to find the “Jewish cluster” as you increase the value.

But the selection of a K which satisfies this comprehensibility criterion is a matter of convenience, not necessity. Most people are vaguely aware that Jews emerged as a people at a particular point in history. In the case of Ashkenazi Jews they emerged rather late in history. At certain K‘s Ashkenazi Jews exhibit mixed ancestral profiles, placing them between Europeans and Middle Eastern peoples. What this reflects is the earlier history of the ancestors of Ashkenazi Jews. But for most personal genomics companies this earlier history is not something that they want to address, because it doesn’t fit into the narrative that their particular consumers want to hear. People want to know if they are part-Jewish, not that they are part antique Middle Eastern and Southwest European.

Perplexment of course is not just for non-scientists. When Joe Pickrell’s TreeMix paper came out five years ago there was a strange signal of gene flow between Northern Europeans and Native Americans. There was no obvious explanation at the time…but now we know what was going on.

It turns out that Northern Europeans and Native Americans share common ancestry from Pleistocene Siberians. The relationship between Europeans and Native Americans has long been hinted at in results from other methods, but it took ancient DNA for us to conceptualize a model which would explain the patterns we were seeing.

An American with recent Amerindian (and probably African) ancestry

But in the context of the United States shared ancestry between Europeans and Native Americans is not particularly illuminating. Rather, what people want to know is if they exhibit signs of recent gene flow between these groups, in particular, many white Americans are curious if they have Native American heritage. They do not want to hear an explanation which involves the fusion of an East Asian population with Siberians that occurred 15,000 to 20,000 years ago, and then the emergence of Northern Europeans thorough successive amalgamations between Pleistocene, Neolithic, and Bronze Age, Eurasians.

In some of the inference methods Northern Europeans, often those with Finnic ancestry or relationship to Finnic groups, may exhibit signs of ancestry from the “Native American” cluster. But this is almost always a function of circumpolar gene flow, as well as the aforementioned Pleistocene admixtures. One way to avoid this would be to simply not report proportions which are below 0.5%. That way, people with higher “Native American” fractions would receive the results, and the proportions would be high enough that it was almost certainly indicative of recent admixture, which is what people care about.

Why am I telling you this? Because many journalists who report on direct-to-consumer genomics don’t understand the science well enough to grasp what’s being sold to the consumer (frankly, most biologists don’t know this field well either, even if they might use a barplot here and there).

And, the reality is that consumers have very specific parameters of what they want in terms of geographic and temporal information. They don’t want to be told true but trivial facts (e.g., they are Northern European). But neither they do want to know things which are so novel and at far remove from their interpretative frameworks that they simply can’t digest them (e.g., that Northern Europeans are a recent population construction which threads together very distinct strands with divergent deep time histories). In the parlance of cognitive anthropology consumers want their infotainment the way they want their religion, minimally counterintuitive. Consume some surprise. But not too much.

Your ancestry inference is precise and accurate(ish)

Filed under: 23andMe,Ancestry,Culture,Family Tree DNA,Genetics,Genomics — Razib Khan @ 6:29 am

For about three years I consulted for Family Tree DNA. It was a great experience, and I met a lot of cool people through that connection. But perhaps the most interesting aspect was the fact that I can understand the various pressures that direct-to-consumer genomics firms face from the demand side. The science is one thing, but when you are working on a consumer facing product, other variables come into play which are you not cognizant of when you are thinking of it from a point of pure analysis. I’m pretty sure that my insights working with Family Tree DNA can generalize to the other firms as well (23andMe, Ancestry, and Genographic*).

The science behind the ancestry inference elements of the product on offer is not particularly controversial or complex, but the customer aspect of how these results are received can become an intractable nightmare. The basic theory was outlined in the year 2000 in Pritchard et al.’s Inference of Population Structure Using Multilocus Genotype Data. You have lots of data thanks to better genomic technology (e.g., 300,000 SNPs). You have computers to analyze that data. And, you have scientific models of population history and dynamics which you can test that data against. The shape of the data will determine the parameters of the model, and it this those parameters that yield “your ancestry.”

In broad sketches the results make sense for most people. It’s in the finer details that the confusions emerge. To the left you see my son’s 23andMe ancestry deconvolution. The color coding is such you can tell that his maternal and paternal chromosomes have very different ancestry profiles (mostly Northern European and South Asian, respectively).

But his “Northern European” chromosomes also are more richly colored, with alternative segments denoting ancestry from different parts of Northern Europe. So in terms of proportions I am told my son is about 15 percent French and German, and 10 percent Scandinavian and 10 percent British and Irish. This is reasonable. On the other side he’s nearly 50 percent “broadly South Asian.” The balance is accounted for by my East Asian ancestry, which is correct, as my South Asian ethnicity is from Bengal, where there is a fair amount of East Asian ancestry (my family’s origin is on the eastern edge of Bengal itself).

And it is here that the non-scientific concerns of consumer genomics comes into focus. The genetic differences and distance between various South Asian groups are far higher than those between various Northern European groups. Depending on the statistic measure you use intra-South Asian variation is about one order of magnitude greater than intra-Northern European differences. This is due to geographic partitioning, the caste system, and differential admixture in South Asians between extreme diverged ancestral elements (about half of South Asian ancestry is very similar to Europeans and Middle Easterners, and half of it is extremely different, so how far you are from the 50 percent mark determines a lot).

Broadly South Asian

In Northern Europe there is very little genetic variation from the British Isles all the way the Baltic. The reason for this is historical: massive population turnover in the region 4,500 years ago means that much of the genetic divergence between the groups dates to the Bronze Age. It is this the genetic divergence, the variation, that is the raw material for the inferences and proportions you see in ancestry calculators. There’s just not that much raw material for Northern Europeans.

Broadly South Asian

Remember, the methods require lots of variation in the data as a raw input. You’re making the inference machine work real hard to produce a reasonable robust result if you don’t have that much variation. In contrast to the situation with Northern Europeans, with South Asians the companies are leaving raw material on the table, and just combining diverse groups together.

What’s going on here? As you might have guessed this is an economically motivated decision. Most South Asians know their general heritage due to caste and regional origins (though many Bengalis exhibit some lacunae about their East Asian ancestry). In contrast, many Americans of Northern European ancestry with an interest in genealogy are extremely curious about explicit proportional breakdowns between Northern European nationalities. The direct-to-consumer genomic firms attempt to cater to this demand as best as they can.

As I have stated many times, racial background is to various extents both biological and social. When it comes to the difference between Lithuanians and Nigerians the biological differences due to evolutionary history are straightforward, and clear and distinct. You can generate a phylogenetic history and perform a functional analysis of the differences. Additionally, you also have to note that the social differences exist, but are not straightforward. Like Lithuanians Nigerians of Igbo background are generally Roman Catholic, while most other Nigerians are not. The linguistic differences between Nigerian languages are great enough that it is defensible to suggest that Hausa speakers of Afro-Asiatic dialects are closer to Lithuanians in their phylogenetic history than to the dialects of the Yoruba.

A Lithuanian American

Contrast this to the situation where you differentiate Lithuanians from French. To any European the differences here are incredibly huge. The history of France, what was Roman Gaul, goes back 2,000 years. After the collapse of the West Roman Empire by any measure the people who became French were at the center of European history. In contrast, Lithuanians were a marginal tribe, who did not enter Christian civilization until the late 14th century. In social-cultural terms, due to history, the differences between French and Lithuanians are extremely salient to people of French and Lithuanian ancestry. But genetically the differences are modest at best.

If a direct-to-consumer genetic testing company tells you that you are 90 percent Northern European and 10 percent West African, that is a robust result that has a clear historical genetic interpretation. The two element’s of one’s ancestry have been relatively distinct for on the order of 100,000 years, with the Northern European element really just a proxy for non-Africans (though it is easy to drill-down within Eurasia). In contrast, notice how 23andMe, with some of the best scientists in the business, tells people they are “French-German,” and not French or German. What the hell is a “French-German”? Someone from Alsace-Lorraine? A German descendent of Huguenots? Obviously not.

“French-German” is a cluster almost certainly because there are no clear and distinct genetic differences between French and Germans. Yes, there is a continuum of allele frequencies between these two groups, but having looked at a fair number of people of French and German background in Family Tree DNA’s database I can tell you that France and Germany have a lot of local structure even among people of indigenous ancestry. Germans from the Rhineland are quite often genetically closer to French from Normandy than they are to Germans from eastern Saxony. Some of this is due to gene flow between neighboring regions, but some of this is due to cultural fluidity as to who exactly is German. It is clear that some Germans from the eastern regions are Germanized Slavs. Some Germans from the north exhibit strong affinities to Scandinavians, while Germans from Bavaria and Austria are classically Central European (whatever that means). The average German is distinct from the average French person, but the genetic clustering of the two groups is not clear and distinct.

Remember earlier I explained that the science is predicated on aligning data and models. The cultural model of Northern Europeans is conditioned on diversity and difference which has been very salient for the past few thousand years since the rise and fall of Rome. But the evolutionary genetic history is one where there are far fewer differences. The data do not fit a model that makes much sense to the average consumer (e.g., “you descend from a mix of Bronze Age migrants from the west-central steppe of Eurasia and Mesolithic indigenous hunter-gatherers and Neolithic farmers”). What makes sense to the average American consumer are histories of nationalities, so direct-to-consumer genetic companies try to satisfy this need. Because the needs of the consumer and their cultural expectations are poorly served by the data (genetic variation) and models of population history, you have a lot of awkward kludges and strange results.

Imagine, for example, you want to estimate how “German” someone is.  What do you use for your reference population of Germans?  Looking at the data there are clearly three major clusters within Germany when you weight the numbers appropriate, with affinities to the northern French, Slavs, and Scandinavians, and various proportions in between. Your selection of your sample is going to mean that some Germans are going to be more Germans than other Germans. If you select an eastern German sample then western Germans whose ancestors have been speaking a Germanic language far longer than eastern Germans are going to come out as less German. Or, you could just pick all of these disparate groups…in which case, lots of Northern Europeans become “German.”

Consumers want genetic tests to reflect strong cultural memories which were forged in the fires of rapidly protean and distinction-making process of cultural evolution. But biological and cultural evolution exhibit different modes (the latter generates huge between group differences) and tempos (those differences emerge fast). The ancestry results many people get are the outcomes of compromises to thread the needle and square the circle.

All the above is half the story. Next I’ll explain why “deep history” has to be massaged to make recent history informative and comprehensible….

* Also, I have a little historical perspective because of my friendship with the person who arguably created this sector, Spencer Wells.

March 21, 2017

The Return

Filed under: Culture,Video — Razib Khan @ 9:45 pm

Plato, St. Ambrose, Marcuse: heralds for our age

Filed under: Culture,philosophy,Tolerance — Razib Khan @ 9:23 pm

It galls me to agree with the proposition that Western philosophy consists of footnotes to Plato, but it is at least fair to admit that Western intellectual thought exists in dialogue with him and his thinking. But the spare and arrogant idealism which Plato and his followers promoted is not entirely alien to the landscape of human cognition. It is not purely invention, but has a basis in intuition. A tendency to abstract, and confuse the abstract with reality, seems hard-wired into our mental architecture. As Paul Bloom would say, we are natural born essentialists (and dualists).

One implication of Platonic idealism seems to be that striving for the perfect form of truth bleeds over into a conceited belief that one’s understanding of the truth is Truth itself. I do not believe that Christianity is necessarily understood only in the light of the mental universe which Plato and his detractors created, but it is hard to deny the Platonic tincture of much of early Christian thought as it diffused throughout the ancient world and began to make converts among the elites. Christian thinking may hinge upon divine revelation, but its theistic illuminations gained rigor and steel via philosophical certitudes.

St. Ambrose was a man of such steel. A scion of the West Roman elite he matured in an era when the heights of society were still religiously pluralistic, with the most eminent and ancient families and men of renown, such as Quintus Aurelius Symmachus, exhibiting clear pagan sympathies. Or perhaps they might characterize it as a fondness for the customary gods of Rome.

In 382 there was a dispute in Rome over the removal of the Altar of Victory from the Roman Senate. Symmachus entered into the record an apologia for the restoration of the statue. He makes a plea:

We ask, then, for peace for the gods of our fathers and of our country. It is just that all worship should be considered as one. We look on the same stars, the sky is common, the same world surrounds us. What difference does it make by what pains each seeks the truth? We cannot attain to so great a secret by one road; but this discussion is rather for persons at ease, we offer now prayers, not conflict.

St. Ambrose, whose faith was on the march, and the future, did not mince words:

But if you deny Christ to be God, because you believe not that He died (for you are ignorant that death was of the body not of the Godhead, which has brought it to pass that now no one of those who believe dies), what is more thoughtless than you who honour with insult, and disparage with honour, for you consider a piece of wood to be your god. O worship full of insult! You believe not that Christ could die, O perversity founded on respect!

Symmachus asked for tolerance, because that was all his kind could ask for. St. Ambrose and the other militants saw no gain to such tolerance, because they had truth before them, and denying the truth was an insult to all. Tolerance of idolatry and superstition was no tolerance.

In 1965 Herbert Marcuse wrote Repressive Tolerance. He begins:

THIS essay examines the idea of tolerance in our advanced industrial society. The conclusion reached is that the realization of the objective of tolerance would call for intolerance toward prevailing policies, attitudes, opinions, and the extension of tolerance to policies, attitudes, and opinions which are outlawed or suppressed. In other words, today tolerance appears again as what it was in its origins, at the beginning of the modern period–a partisan goal, a subversive liberating notion and practice. Conversely, what is proclaimed and practiced as tolerance today, is in many of its most effective manifestations serving the cause of oppression.

These ideas find relevance today, where one descendent of Critical Theory has transformed dissent and offense into violence, and so justifies suppression of disagreeable thought. St. Ambrose would have used different logic because of a differing metaphysical basis, but I believe the psychological impulses are not so different. Tolerance of error is problematic when that error leads to injustice, impiety, and diminishes the “good society,” however it is imagined.

There are those who believe that they know the Truth. Plato and his acolytes had their conceit as philosopher kings. St. Ambrose and his fellow believers had divine revelation, and were seeking to bring all those in the darkness who disagreed with their views to the light. Following St. Augustine the pre-modern Catholic Church asserted that “error has no rights”.

The latest flare up of this sentiment among particular cultural elites, sometimes termed the “regressive Left” (somewhat of a contradiction clearly), is but latest incarnation of this viewpoint. They believe that the time for tolerance is over, as tolerance gives sanction and space to error and impiety (these are called “oppression” now). The liberal “end of history” seems to be evading us, the old battles reoccur with a regularity that hints at an eternal recurrence.  Every few generations the battle with Tiamat must be joined, as monsters issue from the darkness of our cultural Id.

As a descriptive matter it strikes me that some have now denied that words as a tool of discussion, dialogue, and dispute, have utility to discover truth. Those who object with words are engaged in a likely futile exercise, just as pleas for the tolerance of the old religion were futile. A new world was upon them, they simply lacked our hindsight to see the dawning of the age of the One True God. Perhaps in a different universe history took a different course. In those universes I doubt the old gods survived through persuading the believers of the new Lord with words.

The age of words is over. If words become violence, then violence becomes the tool of ultimate persuasion, compulsion. If truth is all about power, then power is all there is. In a Whiggish telling we as a species came out of the blood and darkness, the struggle for power and zero-sum contests for collective domination. But perhaps we are destined to become what we were, creatures forged in blood and power, unable to resist the temptations of coercion and compulsion.

March 20, 2017

10 Questions for Sarah Haider

Filed under: 10 questions,Sarah Haider — razibk @ 5:22 pm

Sarah Haider is co-founder of ex-Muslims of North America. She is prominent in social media as an activist, after bursting onto the scene by giving a speech at The American Humanist Association conference in 2015. More recently I would highly recommend watching her defend the novel idea that there shouldn’t be safe spaces on a panel discussion. Sarah has also been profiled recently in Quillette, On Betrayal by the Left – Talking with Ex-Muslim Sarah Haider

1. I know that you were a sincere believer in religion at some point. Did this affect you in your day to day life in any discernible manner?

When I was religious, I practiced what I believed. Even today, I have difficulty understanding the perspective of believers who choose aspects of the faith to practice or ignore. If you have an ethical code you believe to be true and you *don’t* follow it, you are admitting yourself to be an immoral person. Having said that, my parents were liberal Muslims (liberal being a strictly relative term), and I was educated with a more humanist version of the faith than commonly practiced.

I left the religion at about 15, the age when it no longer seemed sufficient to parrot the beliefs of my parents. I had begun to look deeper into the faith, questioning aspects that seemed nonsensical or immoral in an attempt to better understand (and therefore align closer to the revealed truth). I dressed modestly to deflect attention from my body, and to the bemusement of my parents, I chose to don the hijab for a short period. I stayed away from drugs or sexual encounters of any kind, complied with dietary restrictions, and prayed as regularly as I could. My practice decreased as my doubts grew – and by the end of high school, I no longer felt tied to any observance. Given the years of shame over my body, however, I continued to have hang-ups about sex and sexuality for some time. I remember (at 18 years of age) putting on thigh-length shorts in public for the first time – I had never felt more naked.

2. Do you believe that Islam is in some way sui generis when compared to other world religions in how capable of embracing modernity?

It is hard to dispute the idea that Islam has remained resilient in the face of modernity. Vast majorities of Muslims and Eastern Islamic scholars believe literalism alone can bring us closer to the commandments of god – while biblical literalists are truly a fringe phenomenon. Meanwhile, the unchanging “perfection” of the text is a central claim of the faith – it is what gives the Quran supremacy over the Bible, why Muhammad is the “Seal of the Prophets”. There isn’t a long history of revisionism either, but there have been many efforts to revert religious practice to the time of Muhammad.

Despite all of that, I am hesitant to make broad claims of the “capability” of the religion to embrace modernity, although I will say I expect the faith is as likely to break as it is to bend. Comparisons to the slow modernization of Christianity fall flat in the face of the very different world we live in today. Islam’s backwardness and limited ability to flex may be its undoing – I’ve noticed an increase of atheists and agnostics as literature/media critical of Islam becomes more widely accessible. Christianity never had to face such a rapid onslaught of challenges.

3. Is there any particular philosopher who most exemplifies your own thought?

I’ll admit I can’t think of one in particular – but I’ve been influenced by John Stuart Mill, Bertrand Russell and Peter Singer.  Lately I’ve been exploring Hannah Ardent’s work more closely, particularly her essays on civil disobedience and violence in politics.

4.  Do you read any languages besides English? If yes, does this impact how you view the world (e.g., being able to access a wider array of news sources)?

Sad to say, not particularly.

5. People of a materialist and irreligious orientation seem to align in the United States, and more broadly internationally, on the political Left. Do you think this is contingent, or a necessary outcome of the psychology of the irreligious?

It appears to be a bit of both.

Most versions of conservatism understand religion to be a worthwhile institution in society, and so long as that stands it is safe to assume atheist sympathies will continue to lie (on the whole) with the Left.

GOP leaders often use an appeal to religious authority in order to justify policies and regularly bend over backwards to court the most religious Americans – terribly repellant to many atheists. The American political right appears to be subservient to dictates of Christianity rather than secular morality or reason.

I don’t think that other conservative or right-wing values are inherently unappealing to nonbelievers, however. I’ve also noticed some recent trends which may affect political allegiance.

I’ve felt an increasing hostility to some fields of science coming from the political Left, particularly a denial of biological influence in human behavior and outcomes. As this tendency becomes better known, so may some scientific-minded atheists distance themselves from the politics that fuel it. Islam may be the biggest game changer of all – the Left’s refusal to acknowledge the problems within the religion have left some atheists (myself included) feeling betrayed and abandoned.

6. Do you think it is possible in the future, barring trans/posthumanism, that human beings could ever become a mostly nonreligious species?

If by religion, you mean simply “a belief in the supernatural”, then yes, given a greater understanding of the natural world it is possible humans become a mostly nonreligious species. However, irrational “faith” is not exclusive to religions and I am not too sure that we can overcome dogmatic tendencies and instill skeptical thinking within the majority.

I think a greater danger than religion in and of itself is the propensity to reject the existence of an objective reality and disavowal of our own rationality as a means of understanding the world.

I can sometimes find quite a bit of irrational behavior among secular individuals, and I find their inability to see the similarities between religious and nonreligious dogma to be distressing. Is this tendency something deeply and irremovable human?

7. You’re a Texan. I’m curious whether that’s influenced your outlook on life in any way.

While in Texas, I was staunchly progressive but ever since I left the state, I find myself moving gradually to the political center. This may mean that a contrarian spirit rather than a true ideological alignment motivated my leftist tendencies – but I believe that isn’t entirely the case. I had a very negative view of conservatism and libertarianism while surrounded by their excesses, and since I’ve left that particular bubble (and walked into another) my feelings have tempered.

8. You go home to Texas and visit your family, but do you ever go to Pakistan? If not, do you plan to?

I do not regularly visit Pakistan, and since I’ve become more public with my activism I believe it would be unwise to do so in the future. I find it curious (but unsurprising) that in discussions of the supposed unbearable hostility experienced by Muslims in the West, the plight of non-Muslims/apostates in Muslim countries is never really brought up. Safe to say that a Muslim is far safer in any Western country than a public apostate like me is in any Muslim one. In fact, I can go further than that. Safe to say that a Muslim is far safer in any Western country than someone like me is *in that very same* Western country.

9. What’s your most unpopular obscure opinion that those who follow your work might be surprised by?

Generally speaking, individual rights and freedoms are central to my understanding of a healthy, functioning society. I also lean progressive, so I hold many leftist ideas about what constitutes a family. Having said that, I’m not “on board” with the idea shared by some progressives that a society that moves beyond the two-parent family is desirable. I am alarmed by the rise of single parenthood, and I believe that, on the whole, children raised by single parents are at a severe disadvantage compared to dual-parent households, no matter how loving and dedicated the single parent. While shaming such parents is despicable, women should be discouraged from having children without a committed, long-term partner. In fact, I think an ideal atmosphere for child rearing is closer to the joint-family common in South Asia. It may not be the most desirable or “liberating” environment for some individuals (certainly wouldn’t be for me), but parents have a duty to consider their children’s needs.  Conservatives reading this might think that was a spectacularly benign thing to say – but it really is controversial in some circles I frequent.

10. In no particular order, could you list five books that have influenced you? Don’t spend more than a minute or so, not an issue if you’d give a somewhat different list if asked again tomorrow! (here’s mine: Principles of Population Genetics, The Fall of Rome and the End of Civilization, From Dawn to Decadence, In Gods We Trust, and The Blank Slate).

1.       Kindly Inquisitors – Jonathon Rauch

2.       Thinking Fast and Slow – Daniel Kahneman

3.       On Writing Well – William Zinsser

4.       The Red Queen – Matt Ridley

5.       Why I am not a Christian – Bertrand Russell.

10 Questions for Sarah Haider

Filed under: 10 questions,Sarah Haider — razibk @ 5:22 pm

Sarah Haider is co-founder of ex-Muslims of North America. She is prominent in social media as an activist, after bursting onto the scene by giving a speech at The American Humanist Association conference in 2015. More recently I would highly recommend watching her defend the novel idea that there shouldn’t be safe spaces on a panel discussion. Sarah has also been profiled recently in Quillette, On Betrayal by the Left – Talking with Ex-Muslim Sarah Haider

1. I know that you were a sincere believer in religion at some point. Did this affect you in your day to day life in any discernible manner?

When I was religious, I practiced what I believed. Even today, I have difficulty understanding the perspective of believers who choose aspects of the faith to practice or ignore. If you have an ethical code you believe to be true and you *don’t* follow it, you are admitting yourself to be an immoral person. Having said that, my parents were liberal Muslims (liberal being a strictly relative term), and I was educated with a more humanist version of the faith than commonly practiced.

I left the religion at about 15, the age when it no longer seemed sufficient to parrot the beliefs of my parents. I had begun to look deeper into the faith, questioning aspects that seemed nonsensical or immoral in an attempt to better understand (and therefore align closer to the revealed truth). I dressed modestly to deflect attention from my body, and to the bemusement of my parents, I chose to don the hijab for a short period. I stayed away from drugs or sexual encounters of any kind, complied with dietary restrictions, and prayed as regularly as I could. My practice decreased as my doubts grew – and by the end of high school, I no longer felt tied to any observance. Given the years of shame over my body, however, I continued to have hang-ups about sex and sexuality for some time. I remember (at 18 years of age) putting on thigh-length shorts in public for the first time – I had never felt more naked.

2. Do you believe that Islam is in some way sui generis when compared to other world religions in how capable of embracing modernity?

It is hard to dispute the idea that Islam has remained resilient in the face of modernity. Vast majorities of Muslims and Eastern Islamic scholars believe literalism alone can bring us closer to the commandments of god – while biblical literalists are truly a fringe phenomenon. Meanwhile, the unchanging “perfection” of the text is a central claim of the faith – it is what gives the Quran supremacy over the Bible, why Muhammad is the “Seal of the Prophets”. There isn’t a long history of revisionism either, but there have been many efforts to revert religious practice to the time of Muhammad.

Despite all of that, I am hesitant to make broad claims of the “capability” of the religion to embrace modernity, although I will say I expect the faith is as likely to break as it is to bend. Comparisons to the slow modernization of Christianity fall flat in the face of the very different world we live in today. Islam’s backwardness and limited ability to flex may be its undoing – I’ve noticed an increase of atheists and agnostics as literature/media critical of Islam becomes more widely accessible. Christianity never had to face such a rapid onslaught of challenges.

3. Is there any particular philosopher who most exemplifies your own thought?

I’ll admit I can’t think of one in particular – but I’ve been influenced by John Stuart Mill, Bertrand Russell and Peter Singer.  Lately I’ve been exploring Hannah Ardent’s work more closely, particularly her essays on civil disobedience and violence in politics.

4.  Do you read any languages besides English? If yes, does this impact how you view the world (e.g., being able to access a wider array of news sources)?

Sad to say, not particularly.

5. People of a materialist and irreligious orientation seem to align in the United States, and more broadly internationally, on the political Left. Do you think this is contingent, or a necessary outcome of the psychology of the irreligious?

It appears to be a bit of both.

Most versions of conservatism understand religion to be a worthwhile institution in society, and so long as that stands it is safe to assume atheist sympathies will continue to lie (on the whole) with the Left.

GOP leaders often use an appeal to religious authority in order to justify policies and regularly bend over backwards to court the most religious Americans – terribly repellant to many atheists. The American political right appears to be subservient to dictates of Christianity rather than secular morality or reason.

I don’t think that other conservative or right-wing values are inherently unappealing to nonbelievers, however. I’ve also noticed some recent trends which may affect political allegiance.

I’ve felt an increasing hostility to some fields of science coming from the political Left, particularly a denial of biological influence in human behavior and outcomes. As this tendency becomes better known, so may some scientific-minded atheists distance themselves from the politics that fuel it. Islam may be the biggest game changer of all – the Left’s refusal to acknowledge the problems within the religion have left some atheists (myself included) feeling betrayed and abandoned.

6. Do you think it is possible in the future, barring trans/posthumanism, that human beings could ever become a mostly nonreligious species?

If by religion, you mean simply “a belief in the supernatural”, then yes, given a greater understanding of the natural world it is possible humans become a mostly nonreligious species. However, irrational “faith” is not exclusive to religions and I am not too sure that we can overcome dogmatic tendencies and instill skeptical thinking within the majority.

I think a greater danger than religion in and of itself is the propensity to reject the existence of an objective reality and disavowal of our own rationality as a means of understanding the world.

I can sometimes find quite a bit of irrational behavior among secular individuals, and I find their inability to see the similarities between religious and nonreligious dogma to be distressing. Is this tendency something deeply and irremovable human?

7. You’re a Texan. I’m curious whether that’s influenced your outlook on life in any way.

While in Texas, I was staunchly progressive but ever since I left the state, I find myself moving gradually to the political center. This may mean that a contrarian spirit rather than a true ideological alignment motivated my leftist tendencies – but I believe that isn’t entirely the case. I had a very negative view of conservatism and libertarianism while surrounded by their excesses, and since I’ve left that particular bubble (and walked into another) my feelings have tempered.

8. You go home to Texas and visit your family, but do you ever go to Pakistan? If not, do you plan to?

I do not regularly visit Pakistan, and since I’ve become more public with my activism I believe it would be unwise to do so in the future. I find it curious (but unsurprising) that in discussions of the supposed unbearable hostility experienced by Muslims in the West, the plight of non-Muslims/apostates in Muslim countries is never really brought up. Safe to say that a Muslim is far safer in any Western country than a public apostate like me is in any Muslim one. In fact, I can go further than that. Safe to say that a Muslim is far safer in any Western country than someone like me is *in that very same* Western country.

9. What’s your most unpopular obscure opinion that those who follow your work might be surprised by?

Generally speaking, individual rights and freedoms are central to my understanding of a healthy, functioning society. I also lean progressive, so I hold many leftist ideas about what constitutes a family. Having said that, I’m not “on board” with the idea shared by some progressives that a society that moves beyond the two-parent family is desirable. I am alarmed by the rise of single parenthood, and I believe that, on the whole, children raised by single parents are at a severe disadvantage compared to dual-parent households, no matter how loving and dedicated the single parent. While shaming such parents is despicable, women should be discouraged from having children without a committed, long-term partner. In fact, I think an ideal atmosphere for child rearing is closer to the joint-family common in South Asia. It may not be the most desirable or “liberating” environment for some individuals (certainly wouldn’t be for me), but parents have a duty to consider their children’s needs.  Conservatives reading this might think that was a spectacularly benign thing to say – but it really is controversial in some circles I frequent.

10. In no particular order, could you list five books that have influenced you? Don’t spend more than a minute or so, not an issue if you’d give a somewhat different list if asked again tomorrow! (here’s mine: Principles of Population Genetics, The Fall of Rome and the End of Civilization, From Dawn to Decadence, In Gods We Trust, and The Blank Slate).

1.       Kindly Inquisitors – Jonathon Rauch

2.       Thinking Fast and Slow – Daniel Kahneman

3.       On Writing Well – William Zinsser

4.       The Red Queen – Matt Ridley

5.       Why I am not a Christian – Bertrand Russell.

March 19, 2017

10 things about human evolution (genetics) you should know (simpler)

Filed under: Evolution — razibk @ 3:25 am

In response to my earlier post some people suggested that the language was impenetrable. Nathan Taylor​ offered to make it more plain spoken, so here is this go at it. I think it’s pretty good.

(text below is from Nathan)  

1) Modern humans stayed in Africa for tens of thousands years of before expanding beyond it. Most of the ancestors of non-African humanity seem to have started expanding rapidly from a small founder group of less than 1,000 people, starting around 50-75 thousand years years ago. African humanity has a more complex pattern. Some groups diverged as early as 200,000 years ago, then mixed back together.


2) Don’t think of humanity as a branching tree. Rather think of humanity as groups of streams. Some streams end, many fold back on one another, and some suddenly have massive expansions. Surprisingly, all major human population groups we know today seem to be the product of relatively recent fusions. Even Africa, the source of modern humanity, has seen streams flow back from Eurasia.


3) Many of the characteristics people focus on today are of recent origin. At least as measured in thousands or tens of thousands of years. 8,000 years ago parts of Europe were populated by brown skinned hunter gatherers with blue eyes. Whiter skin is a (relatively) recent development. And the thick straight hair now common among East Asians is recent as well.

4) The genetic variant which helps Tibetans tolerate very high altitudes comes from a human lineage as divergent from modern humans as Neanderthals are. The Denisovans. This illustrates a general trend: we have adaptations from other very diverged human lineages in our genes today. Even if the genetic percentage is small.


5) The transition to agriculture and complex civilization seems correlated with the explosive growth of a few select male Y chromosomes. Think Genghis Khan.


6) It seems unlikely there is one genetic change which made humans humans. This is less certain than 1-5, but I’m pretty sure it’s true. Researchers have been looking for this for years and haven’t turned up anything definitive. I think the reason is simple enough: many genetic changes came together to make us distinctive.


7) A lot of variation between human groups is not due to novel genes. Rather it comes from increasing the popularity of pre-existing genetic variants. For example, the lightening of skin across parts of Eurasia is due to an increase of genetic variants which are common to many human populations. Height is another example.


8) Cultural flexibility does not means humans are not evolving. On the contrary, strong shifts in cultural norms seem to drive human evolution. Lactase persistence (the ability to drink milk as an adult) is a clear case. But even genetic tolerance to malaria was ultimately driven by human created environmental changes.


9) There are no “most ancient” human group. By definition, we are all equally separated in time from our common ancestors.


10) There are hints of possible new discoveries coming from ancient human DNA.  For example there is evidence of humans leaving Africa ~100,000 years ago into Eurasia in both genetic and fossil data. These earlier humans may have been overrun by a later group. But this is hard to determine with the current data. The DNA of current and ancient humans still has many stories to tell.

10 Questions for Henry Louis Gates Jr.

Filed under: 10 questions,Henry Louis Gates Jr. — razibk @ 2:34 am

Henry Louis Gates Jr. is the Director of the Hutchins Center for African & African American Research. He is also the host of Finding Your Roots, and Africa’s Great Civilizations (among many other documentaries).

Below are 10 questions.

  1. If you were eighteen and had to choose a different profession from the one you have now, what would that be? (a professor in a sufficiently different scholarly discipline would count.)

 

Hollywood Film Producer or Psychiatrist/Novelist.

 

  1. About ten years ago you began bringing genealogical research to the public. Personal histories, if you will. Obviously you’ve continued down this path and expanded your purview in terms of topic, as well as the methods you use. The ‘use case’ for why genetics and genomics matter for personal health straightforward. But for genealogy, one’s ancestry, it is often more vague, and perceived to be a matter of entertainment. And yet I know many people for whom it is an emotionally rewarding endeavor. Why do you think this is so?

 

When I conceived of the series that has become Finding Your Roots, my goal was to use the new science of ancestry-tracing through mt- and y-DNA to enable African Americans to learn more about their distant ancestry in Africa.  I had no idea how the science worked, but I had been tested by Dr. Rick Kittles and given a startling result, a result, as it turned out, that turned out to be much more complicated than it initially appeared.  (But that is another story.). I approached my friend, Quincy Jones, and asked him if he would be in the series, should we raise the funding.  He readily agreed.  Quincy himself was fascinated with genealogy, as it turned out; he had scored the music for “Roots,” and had introduced me to Alex Haley, the king of black genealogy.  When I pitched the story to potential corporate sponsors, I sold the idea around the recovery of lost African ethnic ancestry.  “How would you like your corporation’s brand associated with the world learning the ‘tribe’ from which Oprah Winfrey descended?”  That was the pitch.  And that was it!  So we launched “African American Lives,” and it was a hit.  We followed it, at PBS’s urging, with “African American Lives II,” another hit.  When I received a letter from a woman of Russian Jewish descent, asking if I was a racist because we only tested black people in the series, we “expanded the brand,” as they say, and decided to trace everybody’s roots.  I shall forever be grateful to that person for making that bold suggestion to me.  It had never occurred to me before that I could test white people, and that they might find the process as riveting as black people did.

 

Here’s the surprise:  initially, I thought the climax of the reveal would be the discovery of an African American’s African ethnic ancestry, on their mother’s mother’s line, or their father’s father’s line.  But to my surprise, this is not the part of the process that moved my guests the most.  What moved them was learning the names of their recent ancestors on their family trees, their great-grandparents and great-great grandparents, etc., the names of the people who had survived slavery and then the Jim Crow era.  I almost fell off my chair when the first person we interviewed began to cry, just seeing the name of an enslaved ancestor on a musky old document.  It was a revelation to me!  Distant ancestry–always, by definition, anonymous– is intellectually fascinating; recent ancestry–learning the names of the people on your own family tree going back a few hundred years–can be powerfully gripping emotionally.  And that has turned out to be true for all of the guests in all of our genealogy series.

 

Why?  Because genetic genealogy is, in the end, ultimately about yourself.  It is a way of learning more about the human being you have become.  You literally inherit DNA from all of the ancestors on your family tree going back 5 or 6 generations; but you also, it seems some-times, inherit preferences, habits, choices, inclinations, from recent ancestors, ancestors whom you have never met and will never meet.  It’s uncanny.  But it is true.  Habits are passed down, invisibly, generation to generation, just as surely as DNA is.  My work has been blessed with wonderfully generous mentors in the field of genetics, who have shared developments in this fascinating field as they have unfolded.  So each year, our DNA reveals have become more and more sophisticated.  I’m thinking of people such as George Church, Eric Lander, Mark Daly, David Altshuler, Steve Hyman, Joanna Mountain, Kasia Bryc, Razib Khan, CeCe Moore and most recently David Reich.

 

  1. No matter how intimate you are with someone it is not possible to understand an individual in every single detail of their thought process and viewpoints. But oftentimes it is useful to collect some informative data so as to make one’s own inferences. Here is an example. I’m going to name two philosophers who shape my thinking and align with my own viewpoints who both lived before 0 A.D., one Western and one non-Western. That would be Aristotle and Xunzi. I’d be curious as to your picks.

 

Kant and Hegel fascinate me, in part because of what they wrote about race.  What they wrote was not, shall we say, very flattering to people of African descent.  But my all time favorite philosopher is Plato.  I am also partial to the great Greek tragedians as well, Aeschylus, Sophocles and Euripides.  But that’s my day job, teaching literature!

 

  1. Genetics and history are progressing rather fast. Because of the cost and lack of information a lot of the work on ancient DNA has involved prehistory. But soon that will change. I know that some African Americans hold Egypt to be a ‘black’ civilization. When ancient DNA begins to come back my prediction is that ancient Egyptians will be shown to be a predominant mixture of Levantine farmers, Natufians, with a minority component of Sub-Saharan ancestry with strong affinities to the populations which in-habit the current Sudan. This mixture is probably old, and may date to the ‘Green Saha-ra’ period, so well-mixed throughout the population. For those of Afrocentrist perspective would this be sufficient? Would it be controversial? To be frank, I know that in many circles population genetics is ignored when it is inconvenient to the narrative, so perhaps it would only be of scholarly interest?

 

Though we’ve inherited many representations of Egyptians created by themselves, we don’t yet know what the Egyptians actually looked like, because their mode of portraiture was not realism.  However, if you consult “The Image of the Black in Western Art,” volume one (edited by David Bindman and myself), you will see that we know what colors they used to represent themselves, and the skin tones they used to represent Nubians, who lived south of the 3rd cataract.   And from what I can tell, they were the color of North Africans today, not white, not black, but somehow in-between.  The Nubians–Egypt’s sometime trading-partner, sometime friend, sometime enemy, sometime conquered sometimes conqueror–however, are always represented as darker and with what anthropologists used to call “Negroid” features.  Just look at the statues recently recovered by the great anthropologist, Charles Bonnet, of the Black Pharaohs of the Nile[5]​, the Nubians who conquered Egypt and established The 25th Dynasty.  Let’s just say that had they shown up in Mississippi in the 50’s, they’d be sitting in the back of the bus.  The Egyptians and the Kushites or the Nubians exchanged many things, including, without a doubt, genetic material.  But on the whole, I believe that DNA will reveal exactly what you predict, and will show that the Nubians, by contrast, have a much larger component of sub-Saharan autosomal DNA, just like their descendants do today in the country of Sudan.  I’ll take Nubia any day!  It was an extraordinary civilization, it lasted through three iterations from 3000 BC to about 400 AD (as Kerma, Napata, and Meroe), it had a written language (Meroitic), and it was undeniably and indisputably “black.”

  1. As a scholar there is always a tension between production of knowledge geared toward colleagues, and that geared toward the broader public. The tension is not something that many in the public are aware of, but within the scholarly world there is a spectrum of acceptability, with some academics asserting that anything geared toward the broader public is a ‘waste’ of time. Those who hold this view in public are the minority, but my experience has been that this position is held privately to a much greater degree. Most people would say you are a ‘public intellectual,’ so you clearly have opted for engagement. Have there been ramifications or consequences in the world of scholarship? And why do you choose to engage the public? Is it because you think it is important for the public? Because it is important for you to share what you know? Both?

 

I have had a long, fruitful and blessed career.  At its beginning, understandably, I wrote scholarly pieces in the jargon of critical theory which only a few people could read–only people within the guild, as it were; the initiated.  I enjoyed–and enjoy–that kind of writing.  One of the happiest days of my professional life was the day I received an acceptance letter about my first essay on “The Signifying Monkey”  from Professor W.J.T. Mitchell, the Editor of “Critical Inquiry,” still the finest journal in the field of critical theory.  I became the first African American to publish an essay on critical theory in that august journal, and that was hugely gratifying for me.  But I also want to be able to share my views of the world, how I see things, with people fluent in languages other than that of critical theory.  So I like to thing that I’m multi-lingual.  And I love good storytelling, like my father used to do.

 

  1. The ‘futurist’ Ray Kurzweil talks about exponential change and the Singularity. Setting aside your specific opinions on the Singularity, what is the greatest technological change you hope to see by 2030? (I’ll give my answer to give you a flavor of what I’m looking for: gene editing technologies becoming advanced enough to cure adults with Mendelian diseases)

 

I want to know what color Homo sapiens were 50,000 years ago, and what the Egyptians looked like.

 

  1. I was a bookish child, and I’m a bookish adult. But I know others who had a life changing moment when they realized that they wanted to explore the world of ideas. When did you realize that your aim in life was to become a professional scholar?

When I went to the University of Cambridge and met Professor Wole Soyinka and my fellow student, Kwame Anthony Appiah.  They brought me to the party.  Until that time, I thought I’d become a medical doctor.  They told me, in their own different ways, that I had been called to be a scholar.  The call is irresistible.

 

  1. We live in a world of paradoxes. On the one hand economic development in China has resulted in a massive gain in human well being. On the other hand inequality in developed societies, and the possibility of a ‘post-work’ world looms for many lower on the skill hierarchy. I’m pessimistic about any real solution to this problem in the medium term. It doesn’t strike me that the political Left or Right have any ideas beyond rhetoric and appeals to 20th-century social-political tools in response to 20th century conditions. What is your stance on this? Are you optimistic? Pessimistic?

 

We just aired “Black America Since MLK:  And Still I Rise[6]​” on PBS in November.  It’s about the class divide within the black community.  It’s a wake up call.  While the black middle class has doubled since Dr. King died and the black upper middle class has quadrupled over the same period, the percentage of black children living at or beneath the poverty line has dropped from about 42% to about 38%.  In other words, there is a huge class gap within the black community and those of us most privileged, those of us who have benefited from affirmative action, need to insist that the government and private industry undertake the wide variety of programs necessary to restart class mobility in this country.

 

  1. I know that you’ve dug really deep into human prehistory of late, with a focus on human evolution. If the public take away one thing, what would that be?

 

We are all Africans.  And mutations matter.

 

  1. In no particular order, could you list five books that have influenced you? Don’t spend more than a minute or so, no worries if you’d give a somewhat different list if asked again tomorrow! (Here’s mine: Principles of Population Genetics[7]​, The Fall of Rome and the End of Civilization[8]​, From Dawn to Decadence[9]​, In Gods We Trust[10]​, and The Blank Slate[11]​).

A Tale of Two Cities[12]​, Les Miserables[13]​, Death and the King’s Horseman[14]​, Macbeth[15]​, Cosmopolitanism[16]​ (by Kwame Anthony Appiah), Notes of a Native Son[17]​, Cane[18]​, Invisible Man[19]​, Frederick Douglass 1845 Narrative of the Life[20]​, Their Eyes Were Watching God[21]​.

 

10 things about human evolution (genetics) you should know

Filed under: Evolution — razibk @ 1:53 am

In 2011 I had dinner with a friend of mine from college. He’s a smart guy. Ph.D. in chemistry form M.I.T and all that. I mentioned offhand how it was rather proven to good degree of certainty there was Neanderthal gene flow into modern humans (our lineage)[1]​. He was somewhat surprised by this information, and I was aghast that he didn’t know. 1It was one of the biggest science stories of the year. Right?

What that brought home to me is that something that seems revolutionary near to your heart or field of occupational interest may not be so visible to those who are not similarly situated. My friend is a well educated person with a science Ph.D., but it was just not on his radar. Similarly, I had very smart friends in college who were evangelical Christians who were surprised by the high degree of identity between the chimpanzee and human in regards to our DNA sequence (they were Creationists, and skeptical of any close kinship).

Here’s a final example that might interest readers. I had a long conversation with a relatively prominent journalist a month or so ago. Someone who writes in biology, and in particular genetics (who is not Carl Zimmer). I mentioned offhand to them that the work of various labs utilizing ancient DNA is showing rather conclusively that the vast majority of human populations are relatively recent admixtures between highly diverged lineages. To put it in plainer language: we are all mestizos! This journalist was totally surprised by this fact.

This indicates to me again that facts which are “known” in the “in-group” may be surprising to those who are not as hooked in. It isn’t a matter of being educated, smart, or interested. It’s a matter of narrowly constrained social channels.

Here are 10 facts that we’ve recently discovered about human evolution, with a focus on genetics since that’s what I know best, which you should probably know. Or might find interesting.

1) The expansion/development of modern humans occurred within Africa for tens of thousands of before their expansion “Out of Africa.” Most of the ancestors of non-African humanity seem to have started expanding rapidly from a small founder group of 100-1,000 50-75 thousand years years ago. African humanity has a different and more complex historical pattern, with lineages which began diverging as early as 200,000 years before the present, and then mixing back with each other.

2) Related to #1, we’re one species, so rather than an expanding “tree” from common ancestors, it’s better to think of a mesh which keeps coming back together, as some branches are pruned, and the whole pulses out periodically. All major human populations seem to be the product of relatively recent fusions between diverged branches. Africa was the source of modern humanity, but clearly there has been “back migration” from Eurasia.

3) Many of the phenotypes we define as characteristic of various human populations are relatively recent. E.g., the depigmented look of Northern Europeans, or the thick straight hair of East Asians.

4) The Denisovan version of EPAS1 which is found in Tibetans illustrates a general trend: we have adaptations from other very diverged human lineages through low levels of gene flow[2]​.

5) The transition to agriculture and complex “civilization” seems correlated to pulses of highly fecund male paternal lineages. Many of the common Y chromosomes today exhibit a pattern of diversification indicative of explosive population growth.

6) It seems unlike there is one singular genetic change which makes us sui generis or distinctive in relation to our hominin cousins. This is less certain than 1-5, but I’m pretty sure that this is so. Researchers have been looking for years, and not finding anything definitive, and I think there’s a reason. There isn’t anything definitive. Many genetic changes come together to make our lineage distinctive.

7) A lot of adaptation occurs through reemergence of old variation which is floating around in the human population. For example, the lightening of skin across parts of Eurasia co-opt common mammalian pigmentation pathways.

8) Cultural flexibility does not negate biological evolution. On the contrary, strong shifts in cultural norms seem to drive biology. Lactase persistence is a clear case, but even something like malaria adaptation is ultimately due to anthropogenic environmental changes.

9) We are all equally descended from common ancestors. There are no “most ancient” human lineages. We’re all equally recent by definition.

10) There are evolutionary genetic events in our history which are hinted at in the most recent data, so there are major lacunae in our knowledge. The picture is well formed, but not complete. E.g., there is evidence of pulses out of Africa ~100,000 years ago into Eurasia in both genetic and fossil data. These lineages may have gone extinct, or, their contribution may be difficult to detect with current data sets. But there is clearly more to be told in this story.

On the passing of Mike B. McKeown Razib Khan

Filed under: Friends,Mike B. McKeown — razibk @ 12:56 am

In the years that I’ve had this blog I’ve had many correspondents and communications with people who I’ve come to consider friends. Some of these correspondences go back over 10 years now. Some of them are people you would know. But many are not known to you insofar as they do not leave comments in this space, nor do they interact with me on Twitter, etc.

One of these individuals is Mike McKeown. When he began emailing me in the middle 2000s Mike was a tenured professor of biology at Brown[1]​. I was a dilettante blogger and web developer. I’m not sure he “mentored” me as such, but he gave me a lot of encouragement and feedback on my various projects over the years. It was through Mike that I was introduced to Ken Miller[2]​, the biologist who has written against Creationism over the years, as well as religion and science[3]​.

Here’s the last email I received from Mike, on February 13th of 2012:

Congratulations on your lovely daughter.

You probably intellectually understand that you have already done all you can to mold her personality. I had the luck to have this pounded into me when our DZ (XX & XY) twins were showing completely different personalities from the very start. For me it was liberating because ‘IT IS NOT MY FAULT.”

One other thing, reading to her even now will get you and her into the feel of it. Of course you can find kid books you like, especially when she gets a bit bigger you get into various classics. I amused myself by trying to give each character a personality-linked voice, now all three kids can tell just a little bit from a line and they understand the whole context.

Best to all,

Mike

I had never ended up meeting Mike in person, though we wondered if we’d ever overlap at a conference when I began grad school. Today I realized that I hadn’t received an email from Mike in years. Five years in fact now that I checked!

There’s a reason. A little Googling immediately yielded the fact that Mike died from Alzheimer’s this last December[4]​. I’m sad that I didn’t know what he was going through, because I did consider him a friend, but such are the wages of a purely cyber-friendship. Presumably over the years emailing became more difficult for Mike.

I put this post up partly to acknowledge all the people I’ve met via email over the years, including those who I’ve never met in person. These relationships matter. I know they matter because I am feeling rather sad right now after finding out about Mike.

Anyway, I’m privileged to have known Mike. When I have time I’ll probably be rereading my emails with him, since I have all of them still.

Addendum: I still haven’t processed Henry Harpending’s passing[5]​. I’ll write about that some day perhaps when I can say something worth sayin

March 12, 2017

Open Thread, 3/12/2017

Filed under: Uncategorized — Razib Khan @ 2:44 pm
Updates on the changing situation...
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