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

November 30, 2017

The great rollback

Filed under: Culture — Razib Khan @ 11:33 pm

Derek Thompson in The Atlantic has a piece up, How to Survive the Media Apocalypse, which gets at something I’ve come to believe:

Advertising has been critical to the affordable distribution of news for a century and a half in the U.S. Today’s media companies don’t have to reach all the way back to the early 1800s for a business plan, to when newspapers were an elite product, selling at the prohibitive price of six pennies per bundle. But they are going back in time, in a way, and excavating a dusty business model that relies more on readers, and less on advertisers, than the typical online publisher….

There are two groups of people who as readers truly value the truth in anything but the workaday (e.g., weather, traffic reports, etc.): nerds and those with money on the line.

The idea that news is about giving people the Truth is a conceit that was never attainable, but the American media had aspirations. Really most people want to be entertained, amused and vindicated. Conservatives complaining about the perceived Leftward drift of The New York Times who cancel their subscriptions are accelerating an inevitable process (as the readership gets more and more liberal). The fat profits generated by both advertising, in particular classifieds, and subscriptions, allowed the 20th-century media to not be beholden to one master. This is a new world, though a generation that grew up in the old world has not internalized the now.

Outfits which are geared toward the wealthy or business, such as Bloomberg, will retain a more straightforward positivist orientation. Facts will basically be a luxury consumption good, as well an input necessary for greater productivity on the margins for efficient allocation of capital. Those journals with mass audiences will fragment and develop sharper viewpoints and pay less attention to facts if they impede sensationalism and audience preferences. Basically, we’re going to become Britain!

Thompson’s reference back to the early 1800s made me think of Carl Friedrich Gauss. Like Gottfried Wilhelm Leibniz Gauss did not have absolute leisure to pursue intellectual activities. At some point, he was employed as a surveyor in Hanover. To the modern mind, this was a terrible waste of incredible talent. It is for this sort of reason that institutions of higher education with some independence arose to give scholars leisure and freedom to pursue their interests.

But will it always be so? The science fiction genre of steampunk obtains its novelty from injecting advanced technology into a Victorian world on its own terms. Perhaps in a few decades, many of our social and cultural arrangements will seem very quaint and antiquated to those of us who came into maturity in the fin de siècle of the 20th century, with all culture was mass culture.

Crescent over the North Sea

Filed under: Europe,Islam — Razib Khan @ 12:03 am

Pew has a nice new report up, Europe’s Growing Muslim Population. Though it is important to read the whole thing, including the methods.

I laugh when people take projections of the year 2100 seriously. That’s because we don’t have a good sense of what might occur over 70+ years (read social and demographic projections from the 1940s and you’ll understand what I mean). Thirty years though is different. In the year 2050 children born today, such as my youngest son, will be entering the peak of their powers.

First, one has to note that these statistics include a lot of people who are what some would term “Muslimish”. That is, they are not religious believers, but have some identification with Muslim culture. That’s explicitly noted in the methods.

The problem with this is that there is a wide range of religious commitment and identification across Europe’s Muslim communities. On the whole, they are more religiously observant than non-Muslims in their nations of residence,  but, for example, British Muslims are consistently more religious than French Muslims on surveys (or express views constant with greater religious conservatism).

Here are the results of a 2006 survey:

  France Britain Germany
Yes, Westerners are respectful of women 77 49 73
Yes, there is a conflict between being devout Muslim and living in modern society 28 47 36
Yes, sometimes violence against civilian targets in order to defend Islam can be justified 16 15 7
Did Arabs carry out 9/11? (yes) 48 17 35
People in Western countries are selfish (yes) 51 67 57
People in Western countries are arrogant (yes) 45 64 48
People in Western countries are violent (yes) 29 52 34
Do you consider yourself Muslim first? (yes) 46 81 66
In my country Muslims are perceived to adopt customs of nation 78 41 30

Numbers such as those above indicate even if France and the United Kingdom both have Muslim minorities on the order of 17% of the population, the nature of those populations differs to such an extent that that similarity in value may mislead.

In God’s Continent Philip Jenkins observes that public statistics of Christians often work to exclude cultural Christians, but those of Muslims include cultural Muslims. What many estimates of “Muslims” in the European context do is give a sense of the proportion of the population which is of Muslim background. This is especially true in a nation like France where religious survey data is not collected by government agencies.

Overall I think this data is important to consider, but there’s nothing really new in a qualitative sense. And, it is important to keep in mind the details. It is highly probable that the idea of a European superstate will have faltered by 2050, and each nation will its own Muslim minority, and engage with them differently depending on local values and context. Though Muslims, broadly construed, will form about the same proportion of the French and British general population, I suspect that in Britain the distinction between Muslim and non-Muslim will be much more obvious and strict than in France.

November 28, 2017

The Elephant, dragon and eagle

Filed under: Asia,China,Economics,India — Razib Khan @ 12:24 am

The relationship between China and India is clearly one-sided: India is obsessed with a China which is approaching lift-off toward becoming on the verge of a developed nation within a generation (certain urban areas are already basically developed, albeit not particularly wealthy in comparison to Hong Kong or Singapore).

Often when I see interviews with regular Chinese about their opinions of the other country the fixation is upon the manifest Third World nature of India, which seems to be changing much more slowly than their own nation. For me GDP is less important that vital statistics like child mortality or life expectancy. And it is in these sorts of statistics where you see the gap opening up between the two nations. India is developing…. but China is leading, and converging faster with developed nations.

It is in this context that this piece in The New York Times jumped out at me, Amazon, in Hunt for Lower Prices, Recruits Indian Merchants:

While Amazon.com has sellers hailing from many countries, Mr. Cheris said that India and China are the two most important places for Amazon to recruit new merchants since both nations are sources of cheap manufactured goods.

Unlike China, where local companies dominate e-commerce, India is also a huge domestic market for Amazon. Although most of India’s commerce is conducted offline, Indians are coming onto the internet at a rapid clip through their smartphones. Amazon’s chief executive, Jeff Bezos, views India and its 1.3 billion residents as vital to his company’s future, and he has vowed to spend at least $5 billion building up his India operations.

a, I was aware that Amazon really hadn’t gotten any traction in the Chinese market. I did not know that Amazon was so competitive in India, though Flipkart is still dominant there.

The story outlined seems to be part of a bigger trend whereby India is on a very different path from China in its relationship to the rest of the world. China’s economy is big enough and insular enough that it sees the world as either an export market or a source of commodities. It is quickly taking back its place of old as a lumbering hegemon. India, in contrast, seems to be developing a more integrative relationship with large economies such as the United States, despite its command and regulatory economy legacy.

Of course, the India-USA relationship is nothing like “Chimerica” in terms of magnitude, but the Sino-American relationship strikes me as very transactional. Despite the recent tendency of Indian society to espouse a stronger Hindu nationalist line, which is at odds with the West, it seems that there is more cultural exchange between elite Indians and Western societies in the deep sense of values, than has occurred with the Chinese and the West. And, yoga and aspects of spirituality notwithstanding, most of the cultural exchange seems to be toward cosmopolitan elites Indians assimilating to global values which draw from the mode of the West.

Ultimately all of this seems to have geopolitical implications. I’m assuming smarter people than me are keeping track of these trends….

November 27, 2017

Razib Khan’s raw genotype data on 23andMe, Family Tree DNA, Geno 2.0 and Ancestry

It has been a while since I posted an update on my genotype. Since then I’ve been tested on most of the major platforms. I don’t see any harm in releasing this to the public or researchers who want to look at it (though I don’t know why anyone would).

You can download all the files here.

Having my genotypes public is pretty useful for me. If I inquire about someone’s genetics oftentimes people get weirdly defense and ask “what about you?” I Just invite them to look at my raw data and analyze it for themselves! I’m not a hypocrite about this.

Over the years I’ve had researchers inquire about my ethnicity when they stumble upon my genotype on platforms such as openSNP. So in full disclosure, most of my ancestry is pretty standard eastern Bengali. I’m more East Asian shifted than most Bangladeshi samples in the 1000 Genomes project, but then my family is from Comilla, in the far east of eastern Bengal (anyone who cares, my Y is of course R1a1a-Z93 and my mtDNA U2b).

As before I’ll put the genotype under a Creative Commons license:Creative Commons License

Understanding prehistory through genetic inference and ancient DNA

Filed under: Ancient DNA,Population genomics — Razib Khan @ 8:23 pm

Before David Reich’s book, Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past, I highly recommend a new preprint from Pontus Skoglund and Iain Mathieson*, Ancient genomics: a new view into human prehistory and evolution.

It’s basically at the sweet spot for a lot of readers: doesn’t overemphasize methods or archaeological minutiae that’s hard to follow. That being said I do think you would benefit if you read two things which would complement in those directions, First Farmers: The Origins of Agricultural Societies, and Ancient Admixture in Human History.

* I have to say, I consider Iain a friend, but am I the only one a bit perplexed by how a British person can have such a difficult to spell version of his name? I always have to look it up!

Most popular GNXP post of all time?

Filed under: GNXP,Most popular post on GNXP — Razib Khan @ 3:30 pm

Was talking to a friend and mentioned offhand that the most popular GNXP post of all time was written in 2010 very casually and because of a question on Twitter posed by Jason Goldman. At 700,000 Google Analytics sessions it periodically still gets bumped up by places like Reddit.

The book to the right is a pretty big clue. Can you guess the post? I’m posting the link in the comments below….

November 26, 2017

Neanderthal vs us: for wont of a SNP?

Filed under: Human Evolution,Human Evolutionary Genomics — Razib Khan @ 6:49 pm

Recently at a human evolution conference in England Svante Paabo (or someone in his group) was alluding to discovering how modern humans and Neanderthals differed by looking at the ~30,000 genetic positions (bases) where modern humans and Neanderthals exhibit fixed differences. That is, Neanderthals and modern humans exhibit totally disjoint frequencies.

I’ve been saying this for years, but I’ll say it again: this is probably a fool’s errand. I do think there are major differences at loci which we know about, such as at FOXP2. But, it isn’t clear that even at FOX2 Neanderthals and modern humans exhibited complete lineage sorting. That is, there’s evidence that the Altai Neanderthal had introgression from modern (or modern-related) human populations, and that those variants were sweeping. And there is still variation in modern human populations at FOXP2.

All Homo exhibit encephalization

It looks like Soft Sweeps Are the Dominant Mode of Adaptation in the Human Genome (also see Detecting polygenic adaptation in admixture graphs). But it may be that soft selections and recurring gene flow are common features of the broader Homo lineage for several million years.

In other words, looking for silver bullet variants which can explain why we are so special may always fail, because there are no silver bullets (for several years at ASHG I note that there were presentations which attempted to determine the locus of humanity by looking at the loci of functional interest where Neanderthals and modern humans differed). Rather, human exceptionalism is no exceptionalism, and human populations explore a wide space of phenotypes defined by a huge range of allelic variance which spans many of our extant lineages.

Open Thread, 11/26/2017

Filed under: Open Thread — Razib Khan @ 5:59 pm

A few days ago there was a Twitter thing about top five books that have influenced you. It’s hard for me to name five, but I put three books down for three different reasons:

  • Principles of Population Genetics, because it gives you a model for how to analyze and understand evolutionary processes. There are other books out there besides Principles of Population Genetics. But if you buy this book you don’t need to buy another (at SMBE this year I confused Andy Clark with Mike Lynch for a second when introducing myself. #awkward)
  • The Fall of Rome. A lot of historical writing can be tendentious. I’ve also noticed an unfortunate tendency of historians dropping into contemporary arguments and pretty much lying through omission or elision to support their political side (it usually goes “actually, I’m a specialist in this topic and my side is 100% correct because of obscure-stuff where I’m shading the facts”). The Fall of Rome illustrates the solidity that an archaeological and materialist take can give the field. This sort of materialism isn’t the final word, but it needs to be the start of the conversation.
  • From Dawn to Decadence: 1500 to the Present: 500 Years of Western Cultural Life. To know things is important in and of itself. My own personal experience is that the returns to knowing things in a particular domain or area do not exhibit a linear return. Rather, it exhibits a logistic curve. Initially, it’s hard to make sense of anything from the facts, but at some point comprehension and insight increase rapidly, until you reach the plateau of diminishing marginal returns.

If you haven’t, I recommend you subscribe to Patrick Wyman’s Tides of History podcast. I pretty much wait now for every new episode.

The big Washington food fight. GMO labeling is coming.

In Our Time has two very good episodes recently I recommend on the Picts and Thebes.

The Unexamined Brutality of the Male Libido. When I read the title I assumed that the piece was somehow informed by evolutionary psychology. No. It’s larded with Freudianism.

Evolutionary psychology has taken its hits over the last 15 years, and rightly so when it’s basically re-warmed social psychology, but the stuff informed by primatology is 21st century science (you can agree to disagree, but there’s something to grab onto there). Freudianism sometimes gets a bad rap even though its origins were not nearly as woolly as we might think, but cutting-edge early 20th century psychology is really beyond its sell-by date today.

This is the stuff that makes me pessimistic that the “replication crisis” is going to have any impact on the media or the public. For example, At Yale, we conducted an experiment to turn conservatives into liberals. The results say a lot about our political divisions. The author of the op-ed is a major person in the center of the controversy around replication. In particular, “ego depletion.” This op-ed is based on studies with p-values of 0.034 and such.

Detecting past and ongoing natural selection among ethnically Tibetan women at high altitude in Nepal. It’s polygenic and we don’t understand the architecture of the trait that well it seems. Basically, early selection sweeps detected some major loci, but it’s not the whole story. Reminds me of pigmentation.

An endogenous retroviral envelope syncytin and its cognate receptor identified in the viviparous placental Mabuya lizard. This is pretty cool, the same process seems to be occurring over and over.

Rethinking phylogenetic comparative methods. I think this is will be an impactful paper once it gets published.

Meanwhile, this looks interesting: The role of chromosomal inversions in speciation.

I posted some Taylor Swift memes to Twitter as a joke. They seem quote popular, especially the ones related to string theory and evolution, though the one related to Arminian and orthodox Calvinist soteriology took off in a different sector of Twitter.

The funny thing is several people were angry because they thought I was putting down Taylor Swift.

One month of DNAGeeks & Cyber Monday sale

Filed under: DNAGeeks — Razib Khan @ 5:02 pm

For a while, one of the weird things about DNAGeeks sales in quantities has been that people who look at haplogroup I1‘s page have not been buying the shirts. This is in contrast to haplogroup R1b. The geographically the two groups overlap a fair amount. It’s not totally implausible to guess that 75% of the humans who have stepped foot on the moon have been paternal haplogroup’s R1b and I1. And the two have had about the same number of page-views.

I began to make gross generalizations about the type of man who carries I1. Well, the joke’s on us: turns out that the previous font made it look like “I1” was lowercase L, as in “l1.” Well we’ve fixed that problem, so let’s see how that works out!

When my friends and I started DNAGeeks over a weekend we didn’t have a precise idea where it was going to go and what was going to be popular. People keep asking “so what it’s about about?” Well DNA obviously, but the journey is just starting.

We knew genetics and genomics and have a wide diversity of other skills (I can write, others handle the code and business sides), but “DNA-themed products” was not something which I saw a lot of market testing on. So as they say in the start-up world we’re trying to iterate and figure out what works and doesn’t. The goal is make more people passionate about genetics, and also target people who are already passionate about genetics.

One thing we have learned is that the DNA helix symbol is very popular (thanks Joel!). We’re putting it on shirts, mugs, and now cellphone cases (iPhone only, since only iPhone owners spend money). Also, I’m happy to report a fair number of Gene Expression t-shirts have sold.

Until tomorrow if you used DNAEXPLAINED17 as a coupon code on checkout you get 15% off. Viva la consumerism!

November 25, 2017

What does Ajit Pai’s race have anything to do with net neutrality?

Filed under: Ajit Pai,race — Razib Khan @ 3:33 pm

Not surprise that Hari Kondabolu goes there. The problem with making everything about racial dynamics is that more white people in the United States might take a page from that. I don’t wish to encourage that.

Also, believe it or not racializing a topic that the majority probably agrees with on might make it less popular. But if you now talk to people who just agree with you all the time on these things you might not remember that.

November 24, 2017

The question should be “Who Are Salafi Muslims and Why Are Many So Extreme?”

Filed under: Islam,Islamic State,Salafism — Razib Khan @ 7:45 pm

Because of the horrible massacre at a mosque with Sufi tendencies in Egypt, there are a lot of “explainers” out there about sectarian divisions in Islam. The one in The New York Times, Who Are Sufi Muslims and Why Do Some Extremists Hate Them? could be worse. This portion especially gets at the major issue:

For a time, beginning in the 12th century, Sufism was a mainstay of the social order for Islamic civilization, and since that time it has spread throughout the Muslim world, and to China, West Africa and the United States. As Sufism spread, it adapted elements of local culture and belief, making it a popular practice.

Alexander D. Knysh, a professor of Islamic studies at the University of Michigan and expert in modern Sufism, describes it as a “very wide, amorphous movement” practiced within both the Sunni and Shiite traditions.

Specific claims about Sufism beyond the most general fail because vast swaths of Islamic history and Muslim peoples and practice are Sufi. In the modern western media, there is an unfortunate tendency to dichotomize Islam into a harsh and fundamentalist form and a moderate and mystical Sufi variety. Though a small minority of Sufis have drifted toward very heterodox beliefs, the vast majority are orthodox Muslims who also adhere to a school of Islamic law.

And Sufis are not all pacific saints. In the 19th century Libya the Sensussi Sufi movement was critical in the continuation of the trans-Saharan slave trade, and later served as a major focal point for violent resistance against the Italian colonial project. The great anti-philosopher of the medieval period, Al-Ghazali, who is generally agreed to have ushered in the decline of philosophical thinking within orthodox Sunni Islam, was a Sufi.

The question should not be about Sufis. Sufis are not moderate or mystical Muslims, they are simply Muslims. That is, they’re the mainstream. Rather, the crux of the issue is that violent radicals have emerged from the soil of Salafism. Not all Salafis are violent. But violent Salafis are the ones who regularly target other Muslims and their holiest of sites.

Salafism is a modern movement of the past few centuries. Like Protestant Fundamentalism, it is a product of the engagement of traditional religion with the modern world. Self-consciously Salafist Muslims have never known a world where the West was not dominant. Therefore it is no surprise that they look to the accrued tradition of Islamic civilization and see in it failure and decay.

Like some Radical Protestants, the Salafists imagine that they are creating a community of Muslims who are true to the path of the religion in its earliest years before it became tainted with monarchy. Basically, Salafists wish to transform Islam from a religion of history to one of pure axiomatic abstractions.

Why do Salafi radicals attack Sufis? Their tendency to engage in takfir against other Muslims goes back to the proto-Salafi Wahhabists. And Sufi Islam, with a venerable history going back more than 1,000 years, is naturally going to be the target of Salafi rage because it was the Islam that failed to stem the tide of Western ascendancy, the Islam that witnessed the slow and gradual decline from the greatness of the 8th and 9th centuries. The children shall eat their own parents.

Cultural and religious relics as clues to cultural process

Filed under: Paganism,Religion — Razib Khan @ 5:27 pm

Much of the public is given the impression that Christianity became the official religion of the Roman Empire under the reign of Constantine. Though it is hard to deny that it was the favored religion, especially by the end of his rule, modern ideas of the “official” religion of a given state are somewhat anachronistic for this period and place. In The Last Pagans of Rome Alan Cameron argues that the true death-blow to non-Christian religions in the Roman Empire occurred during the reign of Gratian, 50 years after Constantine, with the cessation of subsidies to the traditional religion (a contrasting view is that elite paganism was vital as a public force up until Theodosius the Great’s conquest of the Western Empire).

In The Final Pagan Generation the author reviews the almost imperceptible change that occurred in the lives of the Roman elite, who looked back to a continuous cultural lineage that drew from the late republic. These elite men and women exhibited passivity and complacency, as the norms which had come before would presumably obtain until the end of time. What they did not understand is that there are periods when societies go through rapid changes, so that a rupture occurs between the past and the future in the span of a lifetime.

Whether you think elite public paganism lost its vitality in the last decades of the 4th century or sometime in the 5th, the reality is that it was a spent force by the time Justinian began his the marginalization of the last of the Neoplatonic philosophers around 500.

Of course, this does not mean that sub-pagan practices did not persist among the European peasantry for centuries. But the reality is that they were at least nominally Christian, and a coherent sense of traditional religious identity apart from that outward affiliation did not exist (at least after Christianization).

Which brings me to the people of the Mani peninsula, in the southern Peloponnese. This isolated region was reputed to retain the practices of Greek paganism as late as the year 1000 A.D. Let me quote Constantine VII, Byzantine emperor from 913 to 959:

Be it known that the inhabitants of Castle Maina are not from the race of aforesaid Slavs (Melingoi and Ezeritai dwelling on the Taygetus) but from the older Romaioi, who up to the present time are termed Hellenes by the local inhabitants on account of their being in olden times idolaters and worshippers of idols like the ancient Greeks, and who were baptized and became Christians in the reign of the glorious Basil. The place in which they live is waterless and inaccessible but has olives from which they gain some consolation.

The Basil in question reigned from 867 to 886.

Of course, we don’t know if Constantine and his contemporaries were correct in all the details of the people of Mani. It seems unlikely that he would have misidentified them as Greek as opposed to Slavs (whose paganism was more recent), but perhaps they practiced a debased form of folk Christianity mixed with old superstitions? But, if they did continue to practice the religion of ancient Greece it illustrates how persistent traditional beliefs than be in a world where the state and cultural elites have more limited purview than one might have thought. It seems unlikely that the people of Mani would have been unfamiliar with Christianity (there are ruins of churches going back to the 4th century in the area), but they may have been socially isolated enough that the incentives to convert to the new religion did not exist.

The Tengerrese people of East Java, who remain Hindu, maybe a modern analogy. The worshippers of the gods of the old Norse were by chance the Sami, who did not become fully Christian until after the Reformation. And up until the Islamic period, the city of Harran remained predominantly pagan (the Persians were close enough that the East Roman authorities respected the religious liberties of these people lest they defect).

Soft selection for gentleness in Puerto Rican African Honeybees

Filed under: Population genetics,Population genomics,Soft Selection,Soft Sweep — Razib Khan @ 3:07 pm

When I was a kid “killer bees” were a major pop culture thing. There were movies about the bees, and we would get updates about their march northward in the news. They were a cautionary tale of our species’ hubris.

Today we have a little bit more perspective. These bees were actually just African honeybees, the ancestral population to European honeybees, which were introduced to the New World with Europeans centuries earlier than the African honeybees. African honeybees were not that different from European honeybees, but they were more aggressive and tended to outcompete European honeybee colonies. They are a major problem for the beekeeping industry, but not a major threat to human life.

Today the African and European populations in the United States seem to have stabilized in their ranges, with a hybrid zone between them. African bee’s migratory behavior makes them less competitive with European bees in colder climates.

A friend of mine once mentioned to me that if he had to do it all over again he would do research on the evolutionary genomics of Hymenoptera, and in particular bees. People care about bees. So it ‘s no surprise that I noticed this paper out in Nature Communications, A soft selective sweep during rapid evolution of gentle behavior in an Africanized honeybee:

Highly aggressive Africanized honeybees (AHB) invaded Puerto Rico (PR) in 1994, displacing gentle European honeybees (EHB) in many locations. Gentle AHB (gAHB), unknown anywhere else in the world, subsequently evolved on the island within a few generations. Here we sequence whole genomes from gAHB and EHB populations, as well as a North American AHB population, a likely source of the founder AHB on PR. We show that gAHB retains high levels of genetic diversity after evolution of gentle behaviour, despite selection on standing variation. We observe multiple genomic loci with significant signatures of selection. Rapid evolution during colonization of novel habitats can generate major changes to characteristics such as morphological or colouration traits, usually controlled by one or more major genetic loci. Here we describe a soft selective sweep, acting at multiple loci across the genome, that occurred during, and may have mediated, the rapid evolution of a behavioural trait.

Come for the bees, but stay for the soft selection! If you talk to anyone in evolutionary and population genomics you know that the future is in understanding patterns of soft selection and polygenic selection from standing variation. Though these are related phenomena which are associated with each other, all are all distinct.

Standing variation just refers to the diversity which is segregating in the population at any given time. At any given moment many loci exhibit polymorphism. This polymorphism can be a target of natural selection if it is correlated with heritable variation and differentials in fitness. Though soft selection can be quite wooly it’s inverse, hard selection, is clear: in genetic terms hard selection can be seen in allele frequency changes at a single variant in a locus, going from the point where it is a novel mutation to nearly fixed in the population. In Haldane’s original conception hard selection involved excess deaths, and imposed a limit on the rate of evolution as well as the amount variation you could expect within a given population. This model was convenient in the pre-genomic and early genomic era because empirical selection tests had to focus on large allele frequency changes around singular loci. Researchers didn’t have large numbers of whole-genome samples available (nor the computational ability to analyze them).

Today this is not a limitation. In the analysis above the authors had 30 individuals of the 3 populations sequenced at high quality (20x). They ended up with millions of genetic variants they could analyze.

The plot to the left shows that “gentle African honeybees” (gAHB) tend to be closer to the African honeybee populations (AHB) overall (though with some hybridization with European honeybees, EHB). This is not surprising.

But the key observation was that over 12 generations the African honeybees of Puerto Rico became progressively less aggressive, despite maintaining overall morphological similarities to the mainland Mexican African bees from which they likely derive. Though buried in the discussion, there is a rationale for why this morphological change may have occurred: the Puerto Rican bees are subject to a lot of negative selection against aggression because of the density of the island, as well as the reality that aside from humans there aren’t other many species where their aggressive tendencies are beneficial. Basically, if you are an aggressive colony, it’s harder to make a go in densely settled areas (the implication here then is that there are probably “gentle” African honeybee populations across Latin America, they just are never disaggregated from the broader meta-population).

Credit: Phillip Messer and Nandita Garud

It’s the genomics where the real evolutionary insight comes in: they found that there were multiple soft sweep events around genetic regions implicated in behavior. In their overall genome the gAHB of Puerto Rico resembled mainland AHB, but in this subset of genetic loci they resembled EHB. Many of these loci had also been known to be targets of selection when the original European bee population diverged from the ancestral African population. Basically this is a genomic illustration of convergent evolution.

Regular readers of this blog will recognize the ways they detected selection. They used a modified form of EHH, which is reasonable since the selection event was recent enough to have been associated with distinct haplotype blocks. Also, standard Fst analysis showed that these were outliers in relation to the broader genetic pattern of relatedness (these loci were more like EHB than AHB, while most loci were more like AHB than EHB).

So this a form of polygenic selection. Remember, natural selection only knows genes through the phenotype (with intra-genomic selection being an exception). A behavior like aggression is probably subject to the fourth law of behavior genetics. That is, variation won’t be defined around a single genetic locus. Rather, variation across the genome will be correlated with variation in the phenotype. As selection favors a particular value of the phenotype across the distribution the allele frequencies across many genetic loci will shift, but they will not necessarily fix. Polygenic selection operates on the dispersed standing genetic variation which explains much of the variation of the phenotype in question. Instead of total sweeps to fixation due to large fitness differences between a given allele and its alternative form, the selection impact is distributed and diffused across the genome.

Though most of the genetic variants seem to recapitulate the evolution of the less aggressive phenotype that occurred with the original migration north of African honeybees, some of the selection signatures were novel. This points to the reality that when you have soft selection on standing variation you may have similar phenotypes which evolve via different means. Additionally, the authors noted that these results were in contrast to controlled breeding experiments in mammals where selection for gentility (“domestication”) often targeted a few loci and exhibited strong pleiotropic effects (due to the genetic correlation). These results point to the limitations of inferences made from human-directed selection.

Soft selection is probably ubiquitous. Consider the evolution of skin color in humans. There are lots of variants and lots of variation, and most of the variation seems to be ancestral. Only at the locus SLC24A5 do you have a perfect illustration of a hard selective sweep, probably from a de novo mutation that emerged around the Last Glacial Maximum.

From a geneticists’ perspective evolution is basically conceived of as changes in allele frequencies over time. Much of this is due to natural selection. Now that the world of soft selection is opening up, I suspect that we’ll understand a lot more of what we see around us, at least in the generality.

Citation: A soft selective sweep during rapid evolution of gentle behaviour in an Africanized honeybee.

Dodging the Apple Premium (still)

Filed under: Technology — Razib Khan @ 11:53 am

Because of what I have been provided by my employers over the last few years I’ve been working on a Macbook Pro. These are fine machines, but they have not converted me to being a convert to all things Apple. I have two machines with Ubuntu at home that I have no problem with using (one of them has a dual-boot where I have a copy of Windows which I use every six months or so to make sure that security updates are installed).

In any case, my current phone has been acting erratically over the past few weeks. Up until now I had been resisting getting a new phone because it wasn’t as if I really needed one…but when there is a jeopardy that your phone will decide to not boot up, one has to act.

So I was agonizing over the Samsung 8 or iPhone 8. I’ve had multiple Samsung’s before. And the Samsung 8 seemed fine. The flip side is that everyone in my office uses an iPhone 8, and I get crap for staying with Android. This is not a major issue…but I can’t lie, I’m curious about the iPhone.

In the end, I probably stayed with Android for one primary reason: people in the Apple ecosystem seem totally hostage to Apple. Upgrades are a total pain, and there are minor things I need to get fixed in regards to my Macbook Pro‘s OS which is going to require a “Genius.” The whole situation strikes me as farcical and not futuristic. I’d rather tinker with my Ubuntu distribution than wait in line at a crowded Mac store.

So pass for now….

Regional Ancestry by Insitome

Filed under: Ancestry,ancestry inference,Helix,Regional Ancestry — Razib Khan @ 11:27 am

Shill alert!

When readers and friends found out I was going to work with Spencer Wells, many asked about ancestry analysis. By and large I said “wait.”

Wait no longer. This is now a 3 day pre-sale promotion for our Regional Ancestry product. Basically, you can get it for $19.99. I wrote a blog post on the product, Ancestry as a window onto your past.

The customers who have already purchased Neanderthal and Metabolism will probably get their results first, because remember that Helix apps reuse the original data sequenced and typed. Those who have already gotten previous results on any Helix app will be able to get results almost immediately when the app is live (the constraint here is compute time).

Currently, we are projecting the appl to be live starting January 8th, 2018 (being conservative).

Also, at $19.99 this is a great way to get into the Helix ecosystem.

(note the current ancestry product is autosomal analysis. no Y and mtDNA)

November 21, 2017

The Neanderthal-modern human handover

Filed under: Neanderthal,Neanderthal admixture — Razib Khan @ 3:11 am

We live in a time of transitions when it comes to Neanderthals. Since the 2010 discovery of strong genomic evidence for Neanderthal ancestry in most humans they’ve been…humanized. This was pretty much inevitable, but, I also think it was right. Neanderthals were a big-brained human species which dominated much of Eurasia for hundreds of thousands of years. Their culture did exhibit a certain stasis, but then so did that of our modern African ancestors ~200,000 years ago.

There has been a recent debate about how far back the divergence between Neanderthals and modern humans goes back. My own views is that it’s probably further back than 500,000 years, perhaps closer to 750,000 years, but that there may have been ancient gene flow between lineages as well.

A new paper is now out which suggests that Neanderthals persisted in southern Spain for 3,000 years after they disappeared elsewhere, Precise dating of the Middle-to-Upper Paleolithic transition in Murcia (Spain) supports late Neandertal persistence in Iberia. Obviously, I can’t evaluate the taphonomy and all that. There have long been debates by paleoanthropologists about this region and its Neanderthal habitation (some earlier dates suggested Neanderthals persisted down to 29,000 years ago in southern Spain, but those seem to be rejected). What I can say is that it is entirely expected that the Neanderthal range as it contracted would exhibit an s-shaped trajectory, with a tail where they persisted as relic populations in areas which they were particularly well adapted to.

As paleoanthropology and genetics progress I’m rather sure that we’ll drill-down on very detailed dynamics of interaction, and local succession and replacement. Though humans leave cultural artifacts behind, as a rule the first and last fossils in paleontology usually underestimate the time span that a species flourished. I wouldn’t be surprised if the same applied to Neanderthals, and some day someone with a suspiciously high Neanderthal ancestral fraction was sequenced or genotyped who lived just before the Last Glacial Maximum.

Also, I should mention for those of you looking for a pre-Christmas gift, my company’s Neanderthal product (which does a functional analysis of a set of characteristics where modern humans segregate ancestral and derived variants from the two lineages) can be had for $29.99, as Helix is discounting the $80.00 kit cost (the same applies to the $39.99 Metabolism product, though if you bought Neanderthal earlier then Metabolism is always$39.99 since Helix has banked your data).

People keep asking us the details of the Helix-Insitome relationship and how it works. So we decided to write a blog post addressing that (it’s very short), How does Helix work?.

P.S. we’re probably the only start-up in the world where regular office conversation occurs about Neanderthals.

Against the rectification of names of the enemy

Filed under: Culture,Culture Wars,Semiotics — Razib Khan @ 2:32 am

Since the beginning of this weblog, a particular tick that is common to humans emerges over and over. A tick that is seductive, inevitable, and which I periodically react negatively to (and surely do engage in). That tick is the one where peculiar or exotic terms, or common terms in specific senses, are deployed to demarcate ingroup vs. outgroup.

This is clearly illustrated by example. Libertarians will often call non-libertarians statists. In some ways, this is a defensible term descriptively. But statists never call themselves statists, and often are confused what that even means. Really the term “statist” is just a way you can tell other libertarians that this person is not of the tribe. It’s not about communicating with the statist in question. It’s about labeling them…a witch!

Another example is ally. This is a banal and general word, but on the cultural Left it’s become transformed into a very specific thing. If you are a white male, you are by constitution an oppressor with privilege, so you must by necessity aim toward being an ally. Ally here means those with privilege joining the struggle against oppression and the liberation of marginalized people.

Almost all of the above terms are pretty standard English words, but bundled together into that paragraph you know the perspective and Weltanschauung it’s expressing.

In the United States those who oppose the right to an abortion because they think the fetus is a person define themselves as pro-life.  Those who support the right to an abortion define themselves as pro-choice. Pro-choice people sometimes call pro-life people anti-choice, while pro-life people call pro-choice people pro-abortion. The terms themselves are not important as descriptions. Rather, they’re about tribal mobilization.

On occasion, I’ve seen the term TERF, for trans-exclusionary feminist. The people who are called TERFs never call themselves TERFs. Often people who are denounced as TERFs don’t see to be TERFs at all.

When someone brings up the term “civic nationalism,” I’m usually pretty sure that that person is probably a white nationalist, because that’s a term that they seem to use a lot (to describe non-racial nationalists). People who are civic nationalists don’t describe themselves as such in normal conversations.

Because my views are generally more conservative than liberal people on the Right often believe that I am aware of all the tribal divisions and lexical nuances deployed by conservatives today. Or, more honestly people who spend a lot of time reading and discussing politics online with the tribe. I have finite time, I don’t really really track of all the new fashionable terms. Political philosophy and history interest me, but the contemporary ephemera, not so much. One of the most irritating aspects of “Neoreaction” was that they had all those terms which made no sense to outsiders without a glossary.

This sort of behavior makes sense ingroup. But when you start spouting off in public forums with new-fangled vocabulary accessible to the initiates you exclude them. Which is fine, but you also make it clear you just want to hear yourself talk.

Though sometimes scientists are guilty of this sort thing, by and large the utilization of words in a peculiar context has a precise meaning which is clear and distinct. For example, the term heritable. Transformed into heritability, it is the proportion of variance in the phenotype explained by variance in the genotype. Now could say “the proportion of variance in the phenotype explained by variance in the genotype” every time, but it’s usually easier just to say “heritability.”

I’ve made it pretty clear I take a dim view of the prospects for this liberal democracy of ours over the next generation or so. A day shall come when you stand with the Frost Giants or you stand with the Aesir. There’s really no avoiding a choice. I would recommend on that day pick you pick the strongest side, not who you think is the right side. Power is truth, truth is not power.

But this day is not that day. Until then there is still time to listen and cultivate one’s mind. Let’s dispense with bleeding private language into public. It’s just unseemly.

Cystic fibrosis as the sickle-cell anemia of the north

Filed under: cystic fibrosis,Medical Genetics — Razib Khan @ 1:40 am

Cystic fibrosis is one of those ‘classical’ recessive diseases you learn about in medical genetics. It’s frequent enough that doctors will always be interested in it, and its inheritance pattern is relatively simple, following a rough Mendelian pattern of recessive expression. The reality is a little more complicated than that though, as there are different mutations in the CFTR gene, and some variants can complement so that two carriers don’t necessarily have a risk of producing a child which expresses the disease.

But CF is also interesting from an evolutionary perspective. Why is such a lethal disease present at such high frequencies in Northern Europeans? On the order of 1 out of 25 Northern Europeans carry a mutant allele on CFTR. Apparently, 1 in 19 Irish carries a mutation for CF, while Finland it’s prevalent at a frequency of around 1 in 90, which is actually in the range of non-European populations.

Though it is well known that inbred populations can manifest high frequencies of deleterious alleles, as a whole Northern Europe is not an inbred population. So what’s going on? One hypothesis is that heterozygotes for CF (carriers) have a higher fitness than wild-type individuals, so the low but persistent frequency of CF expressing individuals is an outcome of this overdominant effect. The analogy then presents to sickle-cell anemia.  Heterozygotes are more resistant to malaria, an endemic and pervasive disease in much of the tropics and subtropics.

So what might be causing the high frequency of mutant CF alleles in Northern Europe? One candidate has been tuberculosis, a very common disease in the recent past in Europe. A new paper out of Brazil supports this contention with epidemiological methods, Cystic fibrosis carriership and tuberculosis: hints toward an evolutionary selective advantage based on data from the Brazilian territory:

Applying spatial epidemiology, we studied the link between CF carriership rate and tuberculosis (TB) incidence in Brazil. We corrected for 5 potential environmental and 2 immunological confounders in this relation: monthly income, sanitary provisions, literacy rates, racial composition and population density along with AIDS incidence rates and diabetes mellitus type 2. Smoking data were incomplete and not available for analysis.

A significant, negative correlation between CF carriership rate and TB incidence, independent of any of the seven confounders was found.

The immediate objection is that one may not have controlled for all the confounds. Though do note there are molecular biological rationales for why CFTR heterozygotes may be more fit when infected with tuberculosis.

All that being said Brazil is a diverse place, and it is hard to imagine there might not be a confound out there geographically. Fortunately, we won’t be doing a randomized controlled field trial by infecting individuals with tuberculosis, so we’re just going to have to keep looking at these correlational studies.

Something has to be driving selection for this nasty disease as part of the genetic correlation.

November 19, 2017

Open Thread, 11/19/2017

Filed under: Open Thread — Razib Khan @ 10:33 pm

So we put up a 3rd reviewer mug. Kind of an “inside joke”, but we liked it. One thing we have noticed: people really like the DNA helix logo. They click it. They buy it. More visual, less wordy.

One thing that’s funny, when it paternal haplogroups I1 clicks a lot, but they never buy (in contrast to R1b).

Thousands of horsemen may have swept into Bronze Age Europe, transforming the local population. The piece is pretty expansive, though something of a mess. But it’s a mess because there are still unresolved issues.

There’s a Digital Media Crash. But No One Will Say It. Privately my friends in the media tell me exactly this. It’s going to get worse before it gets better. There are many reasons, but it’s happening.

The Evolutionary Genomic Dynamics of Peruvians Before, During, and After the Inca Empire. Similar thing in Mexico: old population structure is still there!

Singleton Variants Dominate the Genetic Architecture of Human Gene Expression. Genomics is a little overhyped, at least in evolution, but it can really do incredible things nailing down the specific details of what’s going on.

The nature of nurture: effects of parental genotypes and Estimating heritability without environmental bias.

Don’t throw out the sympatric species with the crater lake water: fine-scale investigation of introgression provides weak support for functional role of secondary gene flow in one of the clearest examples of sympatric speciation.

I’ve spent a little time reading Oathbringer this week, mostly before I go to sleep. It’s a little hard to keep track of everything because it’s been seven years since the first book and over three since the last one. Since Brandon Sanderson projects ten books in the series I doubt I will finish this out. At the current rate of production I will be thinking about retirement when the Stormlight Archive is near completion!

But reading Oathbringer it did come to my mind that Sanderson has done a really good job in building a world which is fundamentally not just a European Middle Ages retread, as is the norm in much of fantasy. There are so many new words and characters to keep track of I think I didn’t internalize this in the earlier books. So I did a little Googling and found that Sanderson was trying to do the same thing that Frank Herbert did in Dune, by creating a whole new and novel ecology.

Secondly, he has mentioned that most of his characters are not white and that he has struggled to make sure that they are not depicted in stereotypical European fashion in cover art. The primary protagonists are in fact a people who he imagines to be a hybrid between East Asians and Middle Easterners (his time in Korea as a Mormon missionary inflected his world-building), though that is simply the closest analog. He specifically states that the one human race without epicanthic folds, and look the most European in feature and complexion, are often assumed to be East Asian in by readers because of their exoticism and name (Shin).

Charles Manson has died. I haven’t read it, but have heard good things about Jeff Guin’s Manson: The Life and Times of Charles Manson (it seems like it’s a cultural history).

Precise dating of the Middle-to-Upper Paleolithic transition in Murcia (Spain) supports late Neandertal persistence in Iberia. What we’re learning is that our patchy understanding of the human past also understates how patchy and uneven many dynamics were.

The day the Pintupi Nine entered the modern world. The story of nine people who were totally isolated from the modern world until 1984. They were scared when they met relatives who had lived in a town. To convince them to stay the relatives had them taste sugar.

November 16, 2017

PCA remains the swiss-army-knife to explore population structure

Filed under: PCA,Population Structure,Population Substructure — Razib Khan @ 5:14 pm

I put up a poll without context yesterday to gauge people about what methods they preferred when it came to population genetic structure.* PCA came out on top by a plural majority. More explicitly model-based methods, such as Structure/Admixture, come in right behind them. Curiously, the oldest method, pairwise Fst comparisons (greater Fst means more variance partitioned between the groups), and Treemix, the newest method, have lower proportions of adherence.

Why is PCA so popular? Unlike Treemix or pairwise Fst you don’t have to label populations ahead of time. You just put the variation in there, and the individuals shake out by themselves. Pairwise Fst and Treemix both require you to stipulate which population individuals belong to a priori. This means you often end up using PCA or some other method to do a pre-analysis stage. Structure/Admixture model-based methods make you select the number of distinct populations you want to explore, and often assume an underlying model of pulse admixture between populations (Treemix does this too when you have an admixture edge).

PCA is also better at smoking out structure than Structure/Admixture for the same number of markers, and, it’s pretty fast as well. This is why the first thing I do when I get population genetic data where I want to explore structure is do a PCA and look for clusters and outliers. After this pre-analysis stage, I can move onto other methods.

Further reading:

* I stipulated “genotyped-based” methods to set aside some of the new-fangled techniques, which often assume phasing and analysis of haplotypes, such as Chromopainter or explicit local ancestry deconvolution (some local ancestry deconvolution does not require phased haplotypes, but the most popular do).

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