Basically, a thread to unlurk if you want.
Journey of Man, Spencer Wells’ book and documentary, came out 15 years ago. To a great extent the impact of TV is such that one can argue it introduced genetic anthropology to a whole generation.
A lot has happened since then. On this week’s The Insight we review what’s happened since then, and how Spencer, who started out a conventional academic scientist, became a documentarian.
If you subscribe on iTunes, Sticher or Google Play, make sure to post a review.
One of the main reasons I listen to the Secular Jihadists podcast is that there’s an earnest honesty from the hosts which is fading from our society in public discourse. Though I’m not a “New Atheist” personally (just an atheist), I don’t mind, and even appreciate, people who can discuss the reality that according to the Sunnah, Muhammad, PBUH, was a child rapist and sex slaver by the norms of the current year.
As I am not Muslim and I don’t wish to emulate Muhammad I don’t have to reconcile traditional Islam’s understanding of him with modern norms (not that Muhammad is special, Moses was a child slaughterer). But I am also not sure that airing the reality of Muhammad’s life is productive, or forwards any broader conversation. But the fact of the traditions of his life is true. If facts are never aired, then facts fade from comprehension, and people may confuse polite ommissions with reality.
Because attitudes toward Islam have been ideologized honesty about the religion in public is dangerous, as the truth is a weapon in partisan games. For example, a few months ago I noticed Jerry Coyne had linked to an old post of mine on why being Muslim is not a racial thing on Twitter. Curiously, Twitter flagged the post as sensitive.
So what did I say? You can see….
Obviously, I didn’t say anything too crazy. Rather, the text flagger probably saw “race” and “Islam” and wondered if I this was frog-nazi talk. But more generally there has been heightened sensitivity around Islam and Muslims over the past 17 years, and frank discussion of the religion is now difficult. I recall watching the PBS’ To the Contrary in the 1990s and at one point there was a discussion about Muslim women and their plight. The most stridently Left on the regular panel, Julianne Malveaux, stated plainly that there was perhaps something about Islam which was constitutively anti-woman.
I happen to disagree with the idea that there is anything constitutively anti-woman about Islam, but that’s because I take a very dim view of religious essentialism. But it’s not an unreasonable assertion given the huge body of shariah where women are given inferior status in relation to men. Malveaux wasn’t crazy. And none of her fellow panelists said much in relation to her observation about the essential anti-feminism of Islam. It was the 1990s and anti-religious outbursts by a very Left-wing person wasn’t surprising. Islam was a religion, ergo….
Today the situation is different. I doubt Malveaux would say something similar in public. And I assume that her panelists, especially the conventional liberals, would come to the defense of Islam if she did. This despite the fact that privately many liberals will admit that Islam and women’s rights do not exactly correlate too well. I have a friend who chides Islamophobes on Facebook who will state it is a “fucked up religion” in personal conversation (and to be entirely frank, this is really common from non-Muslim South Asians in the West, who tend to come from Islamo-skeptic backgrounds and yet cultivate strong SJW public personas).
What I’m alluding to here is the ubiquity of preference falsification. The term was popularized in Timur Kuran’s Private Truths, Public Lies: The Social Consequences of Preference Falsification. Chinese “Communism” today is arguably just one huge game of preference falsification. Late stage Soviet Communism was also preference falsification writ large.
The Secular Jihadists don’t engage in preference falsification, and I find that refreshing because it’s so rare. I don’t agree with their New Atheist beliefs on a lot of the details, nor do I share their liberal politics, but I know where I agree and disagree. There’s no reading between the lines. They say what they mean and mean what they say.
While listening to podcasts and viewing YouTubes one thing I’ve come to realize is that Far Left and Far Right views are more interesting because the two groups are so marginal they don’t have an incentive to preference falsify. I disagree with both perspectives, but it’s honest disagreement. When I listen to mainstream Center Left and Center Right folks it’s generally much more boring. They are keen on telling truths that won’t rock the boat and will make the fewest waves. They will lie, omit, and manipulate, to also minimize rocking the boat.
Back in the 2000s Andrew Sullivan came up with the “Yglesias Award”, named after Matt Yglesias, now of Vox. From the page about the award: “This award…is for writers, politicians, columnists or pundits who actually criticize their own side, make enemies among political allies, and generally risk something for the sake of saying what they believe.” Can anyone imagine him criticizing his own side today? Vox and its coterie of writers have become well-off on cozying up to establishment power. They are now the system. Or at least one of the two primary systems (the Right and Left).
There is an equivalent on the Right. Back in the 2000s The Weekly Standard wrote some positive pieces on Intelligent Design. This was strange because The Weekly Standard was a flagship journal of neoconservatism, and so decidedly secular and urban, with a large contingent of Jewish writers and editors. In contrast, Intelligent Design was being pushed forward by evangelical Protestants, and to a lesser extent a small number of conservative Catholics. At the time most people understood that The Weekly Standard was engaged in coalition building. Privately no one there probably found Intelligent Design creditable, but they were part of a coalition of people who took these ideas seriously and sincerely. Though on some level everyone understood what The Weekly Standard was doing, the important thing was that it did what it did in public, and expended some of its capital among secular intellectuals to support religious conservatives as a costly signal to its commitment to the Right.
One reason that Heather Mac Donald began to speak out about atheism and the Right in the 2000s is that she’s a sincere person and was aggravated by the juxtaposition in public respect for religion that conservative intellectuals were prone toward, despite many of them privately having little use for faith.
There’s another dynamic where preference falsification and revealed preferences are connected. I recently observed that Joe Kennedy III seems to be evidence of the royal family of the Democratic party getting whiter while the party gets browner. Joseph P. Kennedy and Rose Kennedy now have many great-grandchildren, such as Joe Kennedy III. Most are no doubt liberal Democrats who think diversity is great and good. But take a look at who these Kennedys are marrying. Since they’re a prominent family, their weddings are noted in the public record. Though the Kennedy’s of the current generation say the correct thing for liberals about racial diversity in public, their private choices are more in alignment with being in sympathy with a white ethnostate.
Why does any of this matter? As I said above, if the public lying is ubiquitous enough, people begin to confuse polite ommissions or accepted public distortions with reality. Eventually the public and private come into alignment. An analogy to religion is appropriate. All of the living descendants of Moses Mendelssohn descend from Christian branches of his lineage. The conversion in the early 19th century of prominent German Jews to Christianity was often a conscious act of assimilation, or a means toward professional advancement. There is evidence that some of these individuals were never sincere Christians in a deep theological sense, and many people understood this. But over time the preference falsification in these families faded, and they became sincere Christians in public and private.
Now consider the case of sex differences. One of the reasons I post on sex differences on strength is to remind people who de facto preference falsify about the truth, and expose newbies to the truth who might otherwise confuse falsification-by-omission with the truth. By this, I mean that over the past generation sex differences are not an issue that many among the cultural elite (on the Left) want to talk about in depth. Most people know that there are differences in strength, though they may be fuzzy on the details. But some younger people actually confuse the lack of attention to sex differences with the fact of no sex differences, and take maximal gender social constructionism at face value!
Because the truth is not fashionable preference falsification will become more and more common. Demands for politeness by omission will become more strident and all-encompassing. Old-fashioned positivists and empiricists who naively make testable truth claims will still exist, but their prestige will be low. Instead of truth being telos, an ends, it will become purely techne, a means or artifice.
Truth, positivism, scientism. All these are the affectations of a small cult. Over time this cult needs to recede out of public view because they are inconvenient to power. The flourishing of truth in the dark and hidden corners of the world must occur through the cult’s service of power. The destruction of falsehood must occur not through argumentation, which falsehood will always win, but through fiat. Falsehood always bends more quickly to fiat.
Going back to where this post started, “ex-Muslims” are a particular affront to the modern order of things. Their existence is an offense, and uncomfortable to most Muslims. Their witness as to Islam’s illiberality is highly inconvenient for the modern Western Left, which maintains a public alliance with Islam. And yet most of these individuals are committed to Left social progress in all areas outside of Islam.
My prediction is that Left critics of ex-Muslims will become more and more vociferous. Not because they believe in their case. Rather, they know that marginalizing this one group despite the injustice of that course of action is an excellent “hard-to-fake” signal of their sincerity and commitment to their Muslim allies. They will destroy this small group not because it is right, but specifically because it is wrong. Innocence is not a defense.
I’m proposing on an upcoming episode of The Insight that we should talk about natural selection in the context of humans. The reason is that there seems to be a lot of it. It may even be ubiquitous. But, in most cases which aren’t trivial, we have no good idea what’s going on.
By not being trivial, I mean when there is selection on loci implicated in immunological variation in response, it’s pretty clear what’s going on. Infection by pathogens is arguably the reason that humans have sex, where some sort of frequency-dependent selection is obvious.
When it comes to something like lactose tolerance (lactase persistence), the genomic evidence seems indisputable that there was natural selection (a very long haplotype in Eurasia sweeping up in frequency recently). And there’s a reasonably plausible story. The adoption of agro-pastoralism by disparate populations across the world has produced similar adaptions, albeit via different genetic pathways. But, it isn’t as if we have experimental or ecological evidence as to the differential fitness of humans “in the wild” on this trait. Does milk sugar really make that huge of an impact? (disease kills, its selective power is clear)
Then, you have cases like pigmentation where there are numerous explanations which part of the story, but not most of it. And finally, you have situations like the EDAR variant among East Asians and Amerindians where selection seems likely, but there is zero plausible explanation of what the target of selection is.
If you are American you have probably heard about “Cheddar Man” in Bryan Sykes’ Seven Daughters of Eve. If you don’t know, Cheddar Man is a Mesolithic individual from prehistoric Britain, dating to 9,150 years before the present. Sykes’ DNA analysis concluded that he was mtDNA haplogroup U5, which is found in ~10% of modern Europeans, and which ancient DNA has found to be overwhelmingly dominant among European hunter-gatherers. But for years there has been controversy as to whether this result was contamination (after all, if it’s found in ~10% of modern Europeans it wouldn’t be surprising if the DNA was contaminated).
Today that is a moot point. On February 18th Channel 4 in the UK will premier a documentary that seems to indicate genomic analysis of Cheddar Man’s remains have been performed, and he turns out to be exactly what we would have expected. That is, he’s a “Western Hunter-Gatherer” (WHG) with affinities to the remains from Belgium, Spain, and Central Europe. These WHG populations were themselves relatively recent arrivals in Pleistocene Europe, with connections to some populations in the Near East, and with unexplored minor genetic admixture from an East Asian population. Their total contribution to the ancestry of modern Europeans varies, with lower fractions in the south of the continent, and the highest in the northeast.
Overall, the consensus seems to be that in Western Europe the genuine descent from indigenous hunter-gatherers passed down through admixture with Neolithic farmers, and then the Corded Ware and Bell Beaker groups, is around ~10%. This is the number that shows up in the press write-ups. But, there are some researchers who contend it is far less than 10%, and that that fraction is misattribution due to early admixture with relatives of these hunter-gatherers as steppe and farmer peoples were expanding.
Phylogenetics aside, one of the major headline aspects of the Cheddar Man is that reconstructions are now of a very dark-skinned and blue-eyed individual. Some of the more sensationalist press is declaring that the “first Britons were black!” As far as the depiction goes, this is literally true. The reconstruction is of a black-skinned individual in the sense we’d describe black-skinned.
But on one level it is entirely expected that this is what Cheddar Man would look like. The hunter-gatherers of Mesolithic Western Europe were genetically homogenous. They seem to derive from a small founder population. And, on the pigmentation loci which make modern Europeans very distinctive vis-a-vis other populations, SLC24A5, SLC45A2 and HERC2-OCA2, they were quite different from anything we’ve encountered before. First, these peoples seem to have had a frequency for the genetic variants strongly implicated in blue eyes in modern Europeans close to what you find in the Baltic region. The overwhelming majority carried the derived variant, perhaps even in regions such as Spain, which today are mostly brown-eyed because of the frequency of the ancestral variant. Second, these European hunter-gatherers tended to lack the genetic variants at SLC24A5 and SLC45A2 correlated with lighter skin, which today in European is found at frequencies of ~100% and 95% to 80% respectively.
The reason that one of the scientists being interviewed stated that there was a “76 percent probability that Cheddar Man had blue eyes” is that they used something like IrisPlex. They put in the genetic variants and popped out a probability. The problem is that the training set here is modern groups, which may have a very different genetic architecture than ancient populations. Recent work on Africans and East Asians indicate that the focus on European populations when it comes to pigmentation genetics has left huge lacunae in our understanding of common variants which affect variation in outcome.
East Asians, for example, lack both the derived variants of SLC24A5 and SLC45A2 common in Europeans but are often quite light-skinned. A deeper analysis of the pigmentation architecture of WHG might lead us to conclude that they were an olive or light brown-skinned people. This is my suspicion because modern Arctic peoples are neither pale white nor dark brown, but of various shades of olive.
As far as blue eyes go, it is reasonable that these individuals had that eye color because that trait seems somewhat less polygenic than skin color. There are darker complected people with light eyes, from the famous “Afghan girl” to the first black American Miss America, Vanessa Williams. The homozygote of the derived HERC-OCA2 variant seems relatively penetrant. From what I recall the literature indicates many people with blue eyes are not homozygotes on this locus for the derived haplotypes, but those who are homozygotes for the derived haplotypes invariably have blue eyes.
Addendum: It isn’t clear in the press pieces, but it looks like they got a high coverage genome sequence out of Cheddar Man. They refer to sequencing, and, they seem to have hit all the major pigmentation loci. This indicates reasonable coverage of the genome.
Unless you were sleeping under a rock today you saw what SpaceX did. I don’t really follow Musk closely. My friends in Silicon Valley speak highly of him. He shares an interest in some of the same topics I do (he’s a fan of Nick Bostrom’s Superintelligence). But in general on an analytical level I think he’s a long-term thinker who may seem crazy, but actually is simply less pedestrian in his focus than the typical billionaire.
T. Boone Pickens has given hundreds of millions of dollars to Oklahoma State University…with the majority going to its athletic programs. And yet to my knowledge, Pickens’ philanthropy has attracted less opprobrium than Musk’s focus on quixotic topics such as hostile strong AI. Musk is weird. Pickens just furthers the cause of traumatic head injury so that his fellow Okhlahomans can cheer on Saturday.
Today at work one of my coworkers hooked up the conference screen to the coverage of the SpaceX launch and landing. I had one eye on the screen…when I saw the descent of the two boosters which landed successfully. I literally jumped out of my chair and ran over to watch them land. It was like seeing a CGI “artist’s conception” of the future of space travel come to life!
As many of you know I am not a fan of Joseph P Kennedy II. When I was a child in the 1980s he gave a speech on the floor of the House of Representatives where he argued against funding for space exploration because of the opportunity cost in relation to social spending. His delivery was quite appallingly poetic from what I recall, something like “why must we take food from the poor so that spaceships can sail high above us?”
Because I was a science nerd with a child’s lack of understanding of the “real world,” where some people were poor and destitute, my reflex was very negative. I still remember Kennedy’s pained expression and can feel my rictus of rage. It’s a flashbulb memory for me. I probably didn’t appreciate the substance of Kennedy’s argument, but the spirit of it was clear.
Some might argue that we don’t need to make a choice. But what if we did? What if space didn’t return much on our investment?
These are fundamentally ancient arguments. In China, during Warring States periods there was a stylized debate between the partisans of Mozi, who we can characterize as a utilitarian, and the followers of Confucius, as to the value of frivolities such as music. Those who aligned with Mozi were fixated on human well-being on the most general and universal scale possible. Music and other cultural productions were pure aesthetic consumption which took away from labor which might otherwise have gone into alleviating human suffering. In the end, history weighed in on the side of the Confucians…with the exception of Communist revisionists in the 20th century.
Musk, and Jeff Bezos, envisage us as an inter-planetary (and perhaps extra-planetary) species. This is laudable so as to avoid the risk of mass extinction on a single “lifeboat Earth.” But perhaps humans becoming inter-planetary is like art? Perhaps it is part of our telos?
These are ideas explored in science fiction. In Against the Fall of Night Arthur C. Clarke writes about a human race which is immortal and geriatric, inward-looking and lacking the spirit of curiosity that defines us, except for a young boy named Alvin. Francis Fukuyama’s End of History and the Last Man prophesies a pedestrian future untouched by the chiliastic passions we see today in Islamic fundamentalism or the dragons of pre-liberal nationalism awakening from their slumber. Space offers a way out of these two visions of conflict and ennui. The eternal frontier.
There is also a deeper evolutionary historical framework for understanding why we are fascinated by the possibilities of space, crazy as they are. Our own modern human lineage was the first to cross over from Sundaland to Sahul. No matter whether you accept a new date of 65,000 years BP, or the more traditional date of 45,000 years, modern humans show up in Australia very early after their exit en masse from Africa.
These humans crossed 90 kilometers of open sea. In Guns, Germs, and Steel Jared Diamond proposed that Australia may have been settled by a pregnant woman who clung to a floating tree branch. Genetics tells us this is false. Oceanian peoples went through a bottleneck, but not such an extreme one.
The implication is that the proto-Oceanian people who left Sundaland for Sahul did so as a unit, impelled by some cultural human prerogative. We may think that going to Mars is crazy, but we know Mars exists. What would have driven these proto-Oceanian peoples eastward into the great blue ocean? And how did they go east during the Pleistocene, before seafaring traditions?
The lesson from prehistory is that modern humans are a crazy species. We journey across the deep blue sea into the unknown. To a great extent, this is irrational for the groups and individuals who engage in this activity. The vast majority of voyagers probably expired. And yet something within us kept pushing some of us until we made it.
In a different lingo, one might say that staying home, focusing on safety and comfort, is a local maximum. International space agencies and private firms such as Lockheed Martin were chasing the local maxima. That was safe and defensible. Only someone as crazy as Elon Musk would push SpaceX into an endeavor which was insane and likely to fail. And yet sometimes humans don’t fail, and crazy is actually saner than we could ever imagine.
Over the past ten years or so the idea of “adaptive introgression” in the human context has gone from seeming ludicrous to banal. When I first began entertaining this idea in 2006 some commenters literally heckled me, because the idea of admixture with Neanderthals seemed so ludicrous. Then, in 2010 the maturation of the field of ancient human DNA confirmed that it was likely non-Africans had Neanderthal admixture. Over the next few years, specific instances of introgression were discovered (e.g., EPAS1 from a Denisova-relative).
Today the whole landscape of adaptive introgression from other lineages is now being mapped. An open access paper in Molecular Biology and Evolution, Disentangling Immediate Adaptive Introgression from Selection on Standing Introgressed Variation in Humans, examines the distinction between the immediate sweep of an introgressed allele after admixture, and later selection on alleles which are segregating neutrally within the absorbing population.
The authors developed a statistic which detected “immediate adaptive introgression (iAI).” Instances where alleles increased in frequency immediately after the admixture in the modern human background from Neanderthals (or possibly other archaics?).
One interesting gene was LYPD6B. This seems to have been subject to selection immediately, and it’s widely distributed in modern non-Africans. This locus controls “cholinergic signaling in the brain” and the authors suggest that the “results suggest that selection on this introgressed haplotype may have been due to beneficial behavioral and/or physiological traits.” The other possible cases of iAI seem mostly involved immune response, not entirely surprising.
But perhaps the bigger issue is that there may be a lot of selection on segregating variants that came in from Neanderthals. That is, introgression may be more important for selection on standing variation. This is is probably the dominant mode of adaptation in humans in any case. Think of it is portfolio diversification.
Speaking of variation, there’s a paper in the works which suggests that admixture with Neanderthals replenished some of the genetic diversity that the Out-of-Africa modern lineage lost:
“They left many beneficial variants behind in Africa,” says evolutionary genomicist Tony Capra of Vanderbilt University in Nashville, who reported the results. “Interbreeding with Neandertals provided an opportunity to get back some of those variants, albeit with many potentially weakly deleterious Neandertal alleles as well.”
Carl Zimmer has an incredible piece up, This Mutant Crayfish Clones Itself, and It’s Taking Over Europe:
All the marbled crayfish Dr. Lyko’s team studied were almost genetically identical to one another. Yet that single genome has allowed the clones to thrive in all manner of habitats — from abandoned coal fields in Germany to rice paddies in Madagascar.
In their new study, published in the journal Nature Ecology and Evolution, the researchers show that the marbled crayfish has spread across Madagascar at an astonishing pace, across an area the size of Indiana in about a decade.
Basically, it looks like a crayfish mutated and now is able to reproduce clonally. That is, it’s asexual. Also, because of its chromosomal structure, it’s no longer inter-fertile with the species from which it emerged.
As it happens there are a fair number of lineages which have sexual and asexual species. Asexual species seem to be much younger. The implication then is that they’re going extinct and emerging over and over again.
One of the things that reading Land of Promise has prompted in me is the need to read Matt Stoller’s book, when it comes out. Land of Liberty in many ways was a historical foil of Stoller’s article, How Democrats Killed Their Populist Soul.
And yet both exhibit an intellectual honesty which I generally find lacking in the modern pundit class, agree or disagree.
Steven Pinker’s new book, Enlightenment Now: The Case for Reason, Science, Humanism, and Progress, is now being published a few weeks earlier. Apparently this now one of Bill Gates’ favorite books.
I’m a big fan of Steven Pinker. But I’ve become much more pessimistic than him over the past few years. Here’s hoping that Enlightenment Now turns that around.
DNA Geeks has a total site redesign! Check it out.
I haven’t been saying this on the podcast yet, but you should be subscribing to it on iTunes, Stitcher, and Google Play, and review and rate it. Spencer and I have a certain audience already, and we’d like to expand it.
This has probably always been so, but I’m really getting tired by the emergence of different verbal ticks in various socio-political subcultures. For example, when liberals say “my dude” -“bros”, it’s dismissal-by-identity. Both NRx, and what is now called the Altright, also have their own subculture languages, which makes understanding what they’re trying to say hard for outsiders. A feature or a bug?
Taking a Twitter break for a week.
In human populations a SNP in ABCC11 is correlated with two salient traits: 1) wet or dry earwax 2) body odor. When I had my first son sequenced before his birth the main variant of phenotypic consequence that I noticed (aside from him being a heterozygote on KITLG), was that he carried a derived mutation on this position. Meaning that he was going to have dry earwax and fewer issues with body odor.
My wife and I are both heterozygotes. This is not too surprising. The derived variant is actually greater than 50% in Bengalis in the 1000 Genomes (in South India the derived variant is also around ~50%), while about ~25% of Northern Europeans are heterozygotes.
This genetic story came to my mind again because of this article in The New York Times, Aiming at China’s Armpits: When Foreign Brands Misfire:
There’s another reason few Chinese consumers buy deodorant: basic biology.
Scientists in recent years have shown that many East Asians, a group that includes China’s ethnic Han majority, have a gene that lowers the likelihood of a strong “human axillary odor” — scientist-speak for body stink.
That lowers the likelihood that they will use deodorant to begin with, according to a 2013 study by researchers at the University of Bristol and Brunel University in Britain, after a survey of nearly 6,500 women of various backgrounds.
“It is likely that deodorant usage is not widely adopted because there is, for much of the East Asia population, no need for it,” it said. (For those curious about such matters, that same genetic difference also leads to drier earwax.)
A friend of mine in undergrad of East Asian background told me once that she had never worn deodorant. So this shouldn’t be very surprising.
Today I found a paper, A missense variant of the ABCC11 gene is associated with Axillary Osmidrosis susceptibility and clinical phenotypes in the Chinese Han Population, which explicitly probes the correlation between body odor (“Axillary Osmidrosis”) and the SNP in question in the Han Chinese population.
The chart below makes the association obvious:
The correlation between carrying the G, ancestral, allele, and body odor is very strong. Though it is imperfect. Going through this literature human smells are clearly a polygenic trait (see The effect of ethnicity on human axillary odorant production). That being said, this case-control study in a Han population shows ABCC11‘s importance in at least East Asian populations (earlier work in Japan showed that those with body odor tended to have wet earwax and carry the G allele as well).
In regards to the genotype proportions the authors observe:
The excessive heterozygosity observed in AO individuals is probably due to the effect of selection, particularly nonrandom mating against AO phenotype.
This doesn’t make sense to me. Wouldn’t people who have body odor tend to pair up in a society where they are a minority? The authors note that the excess of heterozygotes was observed in earlier studies too.
If you dig into the frequencies it seems that the derived mutation is absent among populations in Africa without recent Eurasian back-migration. I looked it up, and it’s segregating in ancient Eurasian samples, with Ust Ishim being a heterozygote. It is curious that in no population has the derived frequency swept to fixation, nor has the ancestral variant fixed in other groups (such as in Europe).
I strongly doubt that there is any selection on this locus due to earwax or body odor. It is a pleiotropic locus, there are other effects from the mutation. One of those other effects is probably the target of any selection. And in regards to selection, it seems likely that that would be a balancing sort since neither the ancestral nor the derived variant are fixed in most populations.