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 Gene Expression Blog

Screenshot 2016-11-27 20.15.36 It’s been exactly three years since I moved on from Discover. Change is timeless. So I thought it would be a good time to announce the move to another project today.

Until further notice this is my last post as a blogger at Unz Review. Just as when I left Discover, this shouldn’t impact regular readers very much in terms of substance and content. As always you can follow me through my RSS feed, http://feeds.feedburner.com/RazibKhansTotalFeed, Twitter, http://twitter.com/razibkhan, and of course, my website, http://www.razib.com (I’m surprised how many people bookmark that website, as I got some emails when I changed the formatting).

Screenshot 2016-11-29 15.20.38 The new site where I will host my content is not up yet, but it should be live within less than two weeks as engineers and designers work to get the final pieces in place (~2 weeks is within 95% confidence interval of the expected value, obviously hope it will be closer to now than not). If you want to be notified by email when the site goes live, subscribe to my newsletter. I probably won’t send out an email more than once a month, but I realize that not everyone uses RSS or Twitter, so it is probably best to start collecting a list of addresses for those who follow my work and would prefer to be contacted that way. If you are old school and just want to bookmark and check the site to see when it goes live, this will work:

http://gnxp.nofe.me

If you have a blog, please update your link to: http://gnxp.nofe.me. It will help me with getting some PageRank (I’m also going to point the front page of http://gnxp.com to the new site).

There will be some changes and flux. I’m starting “my own thing” over at N of Everyone, where I’m working with some friends to develop a new way of disseminating science to the masses. That is, I’m not just going to be a blogger, but am taking an active role in running the shop. A few of the big ideas motivating this move can be found in the piece I coauthored with David Mittleman from a few years back, Dragging scientific publishing into the 21st century. So expect the newest iteration of Gene Expression to be somewhat more experimental in terms of playing around with feature set and evolving more over time.

Also, honestly I’m not sure that Twitter will be around in its current form in another five years, so the Gene Expression at N of Everyone is going to be my attempt to create an independent platform so that I can communicate to who I want to communicate without relying on intermediaries…indefinitely (as long as I’m interesting in doing this, my professional path is definitely going to remain in science so I can express my opinions honestly without having to toe party lines).

Addendum: I’ll be moderating comments here for a bit as long as stray threads continue as long as Ron lets me continue with my permissions, but eventually I’ll stop checking.

 
• Category: Miscellaneous • Tags: Last Post 

Razib_Khan
The Eurogenes blog is running a fundraiser. I chipped in mostly to support his continued blogging. I don’t agree with everything he posts, but the site is a good and valuable resource. “Genome blogging” hasn’t gotten as far as I’d have thought it would have in 2010, mostly because the initial burst of enthusiasm wasn’t followed up by a consistent producer community (in addition to the commentariat). But Eurogenes soldiers on….

0780e5c94be98d65256f715b26529e90 In any case, as part of the donation I got an analysis of my genotype. I wasn’t super interested in this because I know a fair amount about my genotype, and the analysis isn’t too informative for someone like me who is >10% East Eurasian. But I thought I would post the PCA because it’s interesting. It’s hard to see in the image above (click it for a larger version), but you notice that I am almost equally positioned between the antipodes of Eurasia (Western Europeans vs. East Asians). Most South Asians occupy a position in between, but definitely skewed toward West Eurasians (the green). But you notice I’m nearly the most “eastern” of the main cluster of South Asians. Depending on how you calculate it I’m between 10% and 20% East Eurasian. This “pulls” me in that direction more than almost all other South Asians. Like a colossus I look east, and I look west, and stand athwart Eurasia bridging the gap.

In any case, if you have $12 to spare, think about donating to Eurogenes. Logistics are at the link.

 
• Category: Science • Tags: Genomics 

heart_of_what_was_lost_tad_williams Tad Williams has a new book set in Osten Ard, The Heart of What Was Lost. At only 224 pages it seems more like a novella compared to what he produced for his original series. The last of that of that trilogy, Memory, Sorrow, and Thorn, To Green Angel Tower, weighed in at more than 1,000 pages in the original print hardcover edition (of course it was split in two for paper back).

People are talking about how Memory, Sorrow, and Thorn Book was an inspiration for series such as A Song of Ice and Fire. First, Williams finished the series in three books. So that’s a huge difference. Memory, Sorrow, and Thorn Book produced large narratives on a per publication basis, but the story was relatively spare compared to what people are attempting now (Brandon Sanderson’s The Stormlight Archive is already coming out with 1,000 pages books in a projected ten book series). Additionally, William’s world-building was relatively thin and superficial, while the ultimate resolution of the plot threads of Memory, Sorrow, and Thorn Book struck me as a bit cliche and pat.

This is not to denigrate what Tad Williams achieved with Memory, Sorrow, and Thorn Book. But to be honest I think the past generation has seen huge changes in epic fantasy. Whether for the worse or better, that is up to you….

 
• Category: Miscellaneous • Tags: Fantasy 

Screenshot 2016-11-28 02.43.45
MIT Technology Review has an article up, Do Your Family Members Have a Right to Your Genetic Code?, which is now part of the genomics-human-interest-piece genre you see regularly. Here you have the exemplar of this sort of narrative: what do you do when one twin gets a test and the other does not, and they disagree on how much they want to know? (obviously the twin being tested is a “I-want-to-know”) In this case though there is a twist: both of them are scientifically highly trained. And, it turns out that the twin who was worried/nervous about genetic results turned out to have ‘actionable’ results from the other twins’ decision.

There’s a major problem I have with this genre: genomics is not magic, genetics predates genomics by 100 years, and genetics predates DNA based molecular biology by 50 years. That means the basics of this dilemma have been present for over a century. Here are the conditions:

1) You have a condition
2) That condition is heritable
3) You have family members with varying degrees of relatedness to you

If it’s a highly penetrant variant, by which I mean that a very high proportion of individuals with the mutant allele will develop the condition, then the very fact of any individual being diagnosed has implications across the whole pedigree. Do you then keep it a family secret? Do you speak of it to friends? Do you avoid support groups based on the disease for reasons of genetic privacy?

Obviously sequencing an identical twin is a reductio ad absurdum. There’s very little uncertainty for highly penetrant alleles in this case. You know what the allele simply by inspecting the genome, even before diagnosis of any disease or condition (it may be a late in life disease). And, identical twins are almost perfect concordant in their genome. But qualitatively the same concerns have been present in some form for over a century.

Every disease you manifest and every trait you show on your face is a reflection on the genetics of your extended pedigree. Any information you divulge as a matter of course or happenstance then becomes a “bioethical dilemma.” The choices you make will smoke out values. For example, I weight the interests and privacy of the nuclear family far more than even the nearest circle of relations. I would without much thought sacrifice the diluted expectation of privacy (diluted because of diminished relatedness) for my extended kin (siblings, parents, cousins) if I needed information to help my children. In contrast, if I lived in a Hindu joint family my calculus might be different.

 
• Category: Science • Tags: Genetics 

Screenshot 2016-11-27 23.50.40
Screenshot 2016-11-27 23.53.36 I began playing video games as a child after the crash of 1983. At the time I wasn’t aware of the tumult in the culture and the technology scene that that had caused. Video games were just fun, not the it thing I suppose. Perhaps as an analogy it would be like getting online in the early 2000s, after the dot-com crash of 2000. The internet by then was a normal part of everyday life, but the excitement and cultural omnipresence abated.

In that context the original NES took center stage rather slowly and organically in the mid-1980s, eventually triggering the competition between Sega, TurboGrafx, Nintendo, and later Sony. I got off that particular train when I was about seventeen, seeing the amount of time that the hobby swallowed. But I couldn’t help but be amused by this article in The New York Times, Nintendo’s New Console May Feed Your Nostalgia, if You Can Get One:

When she heard that Nintendo was planning to reproduce its iconic Nintendo Entertainment System video game console for the holiday season, Emily Bradbury put a note on her calendar and set an alarm on her phone.

She was not interested in buying it for her children. She wanted it for her husband.

“He’s 40 years old and grew up with a Nintendo,” Ms. Bradbury said. “It’s a nostalgia thing.”

 
• Category: Miscellaneous • Tags: Video Games 

51OftfuYlSL._SX316_BO1,204,203,200_ So I have an Amazon referrer account. I’ve had one since 2003. Pretty much I use it to get money when people buy books (or other items) through links here. It’s a non-trivial, though not princely, sum of money. Especially since it’s passive. These are books I’ve read and want to talk about anyhow (usually around Christmas someone follows a book link, and ends up purchasing a computer or two, which is a way of “supporting my work” that I can get behind).

But one of the more interesting side effects is that I can see what my readers are buying (or if they are). For example, it heartens me when I see someone purchase Principles of Population Genetics. That means “I’m making a difference,” as I doubt that these are advanced undergraduates or graduate students. An interesting aspect is that I can see what interests people in terms of “clickbait”, before clickbait was a thing. Bobbi S. Low’s Why Sex Matters routinely gets a lot of clicks because of the title, despite the fact that I don’t flog it. In contrast, In Gods We Trust gets a lot of clicks because I tell people to read it to understand my thinking on religious phenomena.

51gYdVvOoQL._SX379_BO1,204,203,200_ As the year ends I like to tally books people have ordered. It turns out that the most purchased book through this website for the year leading into December is The Monkey’s Voyage: How Improbable Journeys Shaped the History of Life. For Kindle, it’s Congo: The Epic History of a People.

Another category is conversion rate. In relation to number of clicks what proportion purchase. Tops for the books in that category is Bioinformatics Data Skills: Reproducible and Robust Research with Open Source Tools. My personal experience is that for technical books many people still prefer print for physicality and rendering of figures and graphs. For Kindle the highest conversion was Intelligence: All That Matters and Longitude: The True Story of a Lone Genius Who Solved the Greatest Scientific Problem of His Time. I think there was a “daily deal” or something at one point, and that prompted many purchases of the latter.

1846077 Finally, there are books I see which I didn’t recommend, and didn’t know about. An intriguing one off this list is Barry Cunliffe’s By Steppe, Desert, and Ocean: The Birth of Eurasia. The main issue I’ve had with Cunliffe’s work of late is that he doesn’t seem to be reading enough of the Reich/Willerslev duopoly’s papers. Not that everyone has time to engage in such primary literature diving, but at this point you’re remiss if you write about archaeology and don’t include genetics. Unfortunately a search inside doesn’t indicate that By Steppe, Desert, and Ocean is DNA-heavy, but sometimes you take history and archaeology on its own terms and integrate them into your overall model of the world, rather than having someone else do that for you….

 
• Category: Miscellaneous • Tags: Books 

510bcY7t15L I spruced up my personal website recently. It was getting sort of cluttered. Also, the new theme should look better on mobile.

Not sure how long Twitter will be around, but as long as it’s around, make sure to follow me.

Screenshot 2016-11-27 00.59.01 Got my copy of The Atheist Muslim: A Journey from Religion to Reason. I’m personally opposed to a term like “atheist Muslim,” because a Muslim by definition to me is not atheist. But the author, Ali Rizvi, is an interesting fellow.

Going to try and get to Land of Promise: An Economic History of the United States before Christmas. Don’t know if I’ll get to it, but it’s been on my “to-read” list for a while.

Has anyone ever thought that the novel Musashi was somewhat reminiscent of Cúchulainn? No idea why I think this, but it’s always been on my mind…

I think someone keeps asking about South Asian genetic signatures in Southeast Asia, and I keep forgetting to respond to them. I think there was old (say Iron Age) gene flow from South Asia to various parts of Southeast Asia (basically the cores of Hindu-Buddhist archaic semi-historical polities such as Angkor era Cambodia), and, also more recent gene flow due to colonialism era migration mediated by Europeans. Also, I suspect there was more gene flow from early Holocene Southeast Asia into South Asia than we currently comprehend.

2978777 Ten years after first reading it I appreciate Adam K Webb’s Beyond the Global Culture War more. Why? Probably because universal liberal democracy seems less assured as the final stationary state of society in all places now than it did then. It’s an interesting book in part because it attacks the global cultural element with which it is probably easiest to identify me with.

 
• Category: Miscellaneous • Tags: Open Thread 

Haplogroup_R1b_World
300px-Hamito-Semitic_languagesIf you follow Y genealogy you know that the distribution of R1ba2 exhibits a peculiar pattern. R1b is the most common haplgroup in Western Eurasia, and shares a deep common ancestry with R1a. It seems to have risen to high frequencies in Europe only during the Bronze Age, though has been found in earlier periods. But within Africa R1b is found in very high concentrations around Lake Chad. This particular R1b lineage seems to have diverged from other Eurasian branches in the latter portion of the Pleistocene, so one possible consideration is that this was an instance of Eurasian backflow during the Ice Age.

One reason I have been somewhat skeptical of this model is that the Sahara desert was much more extensive and arid during much of the Pleistocene than today. And during this period humans had less cultural technology to endure the rigors of the deep desert. Or, if they did, their population densities were likely much lower, which probably served as an impediment to gene flow.

A new paper in The American Journal of Human Genetics sheds light on what might have been going on here. Chad Genetic Diversity Reveals an African History Marked by Multiple Holocene Eurasian Migrations. The major findings are straightforward. First, much greater sampling of populations, and a better depth/density of marker coverage, allowed the researchers to detect low levels, on the order of ~1%, Eurasian admixture in some Central African groups. This admixture seems to date to the Holocene, ~5,000 to ~7,000 years before the present (they used LD based methods on the autosome). Interestingly, the R1b lineage common in Central Africa also seems to coalesce during this time. Finally, the admixture seems to be closest to Sardinians among extant populations.

The Sardinian affinity of much of African Eurasian admixture may seem peculiar, but it makes more sense when one considers that Sardianians are probably the best modern proxies for the earliest Neolithic farmers from the Eastern Mediterranean. Modern Middle Eastern populations are very different from those which flourished in the prehistory between the rise of agriculture and complex civilizations because of admixture within Middle Eastern groups. The initial push into Africa by the agriculturalists dates to a period before we have a good understanding of the ethnographic balance.

Very high frequencies of R1b in modern Central Africa groups may indicate drift. But another possibility is that the migration was male-mediated. This seems to have been the case in much of Eurasia, so it would not be surprising in this context. The status of these males was such that despite their diminishing genetic impact on overall ancestry, their Y chromosomes, and possibly their language, with varied forms of Afro-Asiatic, persisting down to the present.

Finally, here’s the last paragraph of the discussion:

Our study has shown that human genetic diversity in Africa is still incompletely understood and that ancient admixture adds to its complexity. This work highlights the importance of exploring underrepresented populations, such as those from Chad, in genetic studies to improve our understanding of the demographic processes that shaped genetic variation in Africa and globally.

 
• Category: Science • Tags: Africa, Genetics 

gr2 A new paper in The American Journal of Humans Genetics, The Divergence of Neandertal and Modern Human Y Chromosomes, reports on possible reasons why we don’t see Y chromosomes in modern humans from this archaic lineage, despite exhibiting detectable levels of autosomal admixture. As you might recall the clear lack of deep branching Y and mtDNA lineages was long one of the major genetic rationales for why gene flow between Neanderthals and modern humans was presumably not very significant. This, despite suggestive evidence from morphological analysis as well as inferences from autosomal data. The problem is that it is harder to do the sort of clean phylogenetic reconstruction via a coalescent model utilizing autosomal data (which recombines, as opposed to the Y and mtDNA, which do not for the regions of interest), so ancient genome sequences were really what was needed to convince most people with these sorts of markers.

This makes us ask: why are Neanderthal Y and mtDNA lineages not found in modern humans which exhibit indications of gene flow from other hominin lineages? After all, the lack of these really led many people off on the wrong track for years. I recall in 2008 going to a talk by Svante Paabo who reported that the Neanderthal mtDNA he had sequenced was definitely very different from anything in the current databases for our species, which confirmed his assumption that there was no admixture into modern populations (Paabo changed his tune very soon after due to the whole genome sequencing obviously). One simple explanation is that because effective population sizes of Y and mtDNA are smaller than autosomal regions of the genome they’ll be more strongly subject to drift, and exhibit higher extinction rates. In other words, it wouldn’t be that surprising of all Neanderthal Y and mtDNA went extinct after admixture because they were a small minority, and most lineages went extinct in any case. Researchers who work in non-human phylogeography who relied on mtDNA in particular can tell of many stories of being led astray by looking at one informative locus.

But chance may not be what is at work here. Buried in the discussion of the paper:

…polypeptides from several Y-chromosome genes act as male-specific minor histocompatibility (H-Y) antigens that can elicit a maternal immune response during gestation. Such effects could be important drivers of secondary recurrent miscarriages30 and might play a role in the fraternal birth order effect of male sexual orientation.31 Interestingly, all three genes with potentially functional missense differences between the Neandertal and modern humans sequences are H-Y genes, including KDM5D, the first H-Y gene characterized…It is tempting to speculate that some of these mutations might have led to genetic incompatibilities between modern humans and Neandertals and to the consequent loss of Neandertal Y chromosomes in modern human populations. Indeed, reduced fertility or viability of hybrid offspring with Neandertal Y chromosomes is fully consistent with Haldane’s rule, which states that “when in the [first generation] offspring of two different animal races one sex is absent, rare, or sterile, that sex is the [heterogametic] sex.”

The origin of species is obviously one of the founding questions which arose with the emergence of evolutionary biology. Haldane’s rule dates to the 1920s. In mammals the heterogametic sex are males, so these the hybrids which will be selected against (or, they may be sterile). There’s been a lot of research of late on why Neanderthals went extinct, and whether there were speciation barriers in keeping with the biological species concept between our two lineages. This result suggests that there is going to be interesting stuffed coming out of the population genomics of ancient hominins in the near future….

 
• Category: Science • Tags: Genetics, Neanderthals 

ls Went to Z & Y in San Francisco recently. Second time. Still have to give Mala in Houston better marks. A friend who has been to both agrees.

Been busy working recently. But obviously a lot is going on in science and non-science….

 
• Category: Miscellaneous • Tags: Open Thread 

 
• Category: Miscellaneous • Tags: WestWorld 

pid_23819 Listened to an interesting interview this morning with the author of a new book, The Latinos of Asia: How Filipino Americans Break the Rules of Race. There was a lot to agree with and disagree with, but it rang true in many ways for me because I have had a fair number of students with roots in the Philippines. An early portion of the interview illustrates an important dynamic. The author himself has parents from the Philippines and when his university was running a study on alcohol consumption and those of “Asian” ancestry. When he approached to be a participant though the researchers said that what they were looking for were people of Japanese, Korean and Chinese ancestry, because they had the right “population structure.”

Screenshot 2016-11-15 09.39.56 Naturally this was somewhat offensive. The author pointed that as a sociologist he believes race is a “social construct.” It is also the case that people from the Philippines occupy a someone liminal position of both “Asian” and “Latino” identities. As a South Asian I can relate, as I am “Asian”, but not “typically” Asian.

From what I can gather the research group was rather artless in the way they communicated their necessary conditions for their project, but the researchers probably were correct in excluding the author. Alcohol flush reaction segregates in only a finite set of East Asians. With limited resources it is rational for them to exclude individuals from populations where the variants of interest are not present, or at very low frequencies.

The problem is that the author confuses the terminology, “Asian”, with reality. A common tendency in the “post-modern” style of thought is putting primacy in the power of language to shape our perception of reality. The fact is that people from the Philippines have very distinct genetic structure in relation to Northeast Asians. Whether they are categorized as Asian or Latino does not truly impact that fact, unless one is of Chinese background and from the Philippines. To me it is ironic that so many scholars place into language so much power when language is only an imperfect mapping onto reality.

 
• Category: Science • Tags: Genomics, Science 

51r8Ph-vcaL Back in the 2000s I used to write a lot about “adaptive introgression.” This was partly due to conversations with, and influence from, people like John Hawks and Greg Cochran. The theoretical framework can be found in papers such as A genetic legacy from archaic Homo. And planet geneticists, such as Loren Rieseberg, have been studying gene flow between structured populations for decades.

That was why I was a bit surprised when the authors of A Draft Sequence of the Neandertal Genome kept emphasizing there was no selection detected in their work. This is true in the strict sense, but it seems reasonable that the expectation was that this will change.

Nearly ten years after John Hawks et al. began talking about introgression and adaptation in humans, their views are now commonplace, and perhaps even orthodox. A case in point, Archaic Hominin Admixture Facilitated Adaptation to Out-of-Africa Environments:

Here, we describe a comprehensive set of analyses that identified 126 high-frequency archaic haplotypes as putative targets of adaptive introgression in geographically diverse populations. These loci are enriched for immune-related genes (such as OAS1/2/3, TLR1/6/10, and TNFAIP3) and also encompass genes (including OCA2 and BNC2) that influence skin pigmentation phenotypes. Furthermore, we leveraged existing and novel large-scale gene expression datasets to show many positively selected archaic haplotypes act as expression quantitative trait loci (eQTLs), suggesting that modulation of transcript abundance was a common mechanism facilitating adaptive introgression. Our results demonstrate that hybridization between modern and archaic hominins provided an important reservoir of advantageous alleles that enabled adaptation to out-of-Africa environments.

The more we learn, the more we comprehend that the patterns of selection and phylogenetic relationships in hominins was quite complex.

 
• Category: Science 

51jUZQV3r1L._SX329_BO1,204,203,200_ (1) Now reading Hume: An Intellectual Biography. David Hume was a man of moderation in his private life. Something to consider.

I was in New York City yesterday. I got a cab from the Upper East Side to Columbus Circle. The cabby did not anticipate the anti-Trump protest. When I said it was the anti-Trump protest probably, he turned around and said “Trump?” I said, “Donald Trump. You know.” He shrugged. By his accent I assume he was an African immigrant. I wonder if his English just wasn’t very good, as I have a hard time how you could be a cab driver in New York City and be surprised at who Donald J Trump was.

Met some friends. Some of them are in the ‘conservative establishment’, at least the more intellectual parts. They are cautiously hopeful. Or hoping for the best.

If you are a Trump supporter, perhaps this is a time to consider that tribal exultation will eventually fade and real life will again intrude. If you are a ‘conservative’, and not married, and without children, and above 30, perhaps you should consider what you need to do to get to a point where you can embody the values you purportedly support. If you are not a Trump supporter, and if you do have a family, perhaps you should reflect that at the end of the day the ultimate thing of substance is your relationship to them, and taking care of them. You have to get up every morning and work to support them, love them, and let them flourish. Politics is just a means toward the end of this sort of flourishing. But just one means.

510bcY7t15L I pre-ordered a copy of The Atheist Muslim: A Journey from Religion to Reason. Skeptical that one can be an “Atheist Muslim,” but the author is someone who I respect from Twitter, and it is important to read differing views. I myself am careful to state that I am not a “cultural Muslim” for two reasons. First, I am not part of the “Muslim community” in any way in my day to day life. I do not attend Muslim celebrations with my family in a nominal fashion. My children will have no affiliation to Islam except their surname indicating some connection to a South Asian Muslim. Second, unlike some people I do not have fond memories of a past life as a believer. I never really believed. My family as isolated enough that I was never part of the Muslim community anywhere that I lived. And my distaste for religion generally increased in a monotonic fashion as I grew into adulthood.

But other people have different experiences. So I’m curious.

Finally, I know people on all sides are binging on analysis of the election results. I understand. I get it. I just wish people would be more enthusiastic about immersing themselves in the life of the mind. People always ask me how I make time to be able to read. Some of the answer is prosaic. I stopped playing video games when I was sixteen. This is not without cost in hedonic utility and the ability to bond with people of my similar social profile. But it freed up a lot of time (similarly, I do not own a television, and have not for over ten years, so I don’t get caught up in passive viewing). Though I work a lot and have a family, various reasons allow for some level of flexibility in time allocation. And, unfortunately, I often do not sleep as much as I should.

But another reason I take time to read is that it is who I am, and who I have always been. I don’t read books and try to learn things to impress people or seem smart. I don’t really care that much about that stuff compared to actually knowing stuff. If that’s not important as an end in and of itself, and it isn’t for most people from what I can grasp (in contrast to winning arguments), that’s fine. But, I think a lot of people aspire to read more, and know more, because its important to them. If so, a little Buddhist or Stoic equanimity again the currents of the world really does help.

 
• Category: Miscellaneous • Tags: Open Thread 

Screenshot 2016-11-09 21.41.13

51PboR9SpFL._SY344_BO1,204,203,200_ I do not spend much time thinking about politics at this point in my life. Therefore I have little to say that is very important or interesting, though I take a passing casual interest. The map above is very curious. Donald Trump did not simply ride on a wave of expected gains. He changed the map. Yes, he was solid in core Republican regions (except Mormon America), but he really gained in more “purple” areas of the Midwest and Middle Atlantic. Trump crushed it in West Virginia and lost Virginia. That would be very peculiar in the 1990s. More relevantly, the Driftless went for Trump, despite being the most prominent area of rural white America outside New England to support Obama in 2008 and 2012 (the area also favored Democrats in 2000 and 2004). In the near future, when I have more time, I will be looking at the county-level data.

Second, the exit polls are interesting. One has to be careful here with these sorts of results, but it does not look as if Trump lost with minorities and gained with whites nearly as much as the press would have you believe. Granted, disaggregation is important here. Trump lost among wealthier and more educated whites, but made up for it with the downscale. Anyone trying to sell a simple story is probably taking you for a ride.

There are many stories here. Though you can probably go elsewhere for most of them. I plan on focusing on science and history, which I find more fascinating than politics.

 
• Category: History • Tags: Politics, Trump 

7531-1477645031Eurogenes points me to this interesting conference with a book of abstracts, Human Dispersals in the Late Pleistocene – Interdisciplinary Approaches Towards Understanding the Worldwide Expansion of Homo sapiens. Below are those of interest to me….

Philipp Gunz

Max Planck Institute for Evolutionary Anthropology
Leipzig, Germany

Evolution and development of the modern human
face and brain

A number of fossils from North, South, and East Africa document the early stages of our species, and fossils from the Levant document the presumed first wave of migration out of Africa. The exact place and time of our species’ emergence remain obscure as large gaps in the fossil record and the chronological age of many key specimens make it difficult interpreting the evolutionary processes and population dynamics shaping the cranial diversity of modern humans. Here we use 3D geometric morphometrics based on landmarks and semilandmarks to compare facial and endocranial shape in a worldwide sample of recent and fossil humans from Africa, Europe, and Asia.

Our data support a complex evolutionary history of our species involving the whole African continent. Regarding facial shape, we find that even the early H. sapiens specimens fall within the shape variation of recent modern humans. Endocranial shape, however, changes considerably within the Homo sapiens lineage.

51t3ZeiK+vL._SY344_BO1,204,203,200_ I think I understand archaic introgression better now. Humans really care about faces. Brains? Not as much. If our species developed its normal range of species-typical faces rather early on than we’d recognize each other as conspecifics, despite widespread phenotypic differences (including likely cognitive and behavioral) and genetic divergence. Basically, it’s just like the Trojan War; a face can launch ships, and mediate gene flow.

John Hawks

University of Wisconsin-Madison, USA

African population diversity and its relevance for human dispersals

As modern humans dispersed throughout the world, they encountered and mixed with populations with much greater genetic distinctiveness than any living humans today. This process is now relatively well documented by ancient DNA in Eurasia and Australasia due to the ancient DNA records of Neanderthal and Denisovan samples. Within Africa this process of contact and mixture between genetically differentiated populations also took place, evidenced by the evidence of population mixture from genomes of some African populations today. The process began earlier, well before 100,000 years ago, and may have extended over a longer period of time. The evidence suggests that modern humans originated and began their dispersals within an African continental context equally or more genetically structured than Eurasia. However the fossil record of this population is very sparse, and it is not evident how archaeological distributions may relate to biological populations. Here I discuss the implications of this population structure for human dispersal and adaptability. T he modern human phenotype originated as one well adapted for dispersal within a long-existing network of successful populations of potential competitors.

Basically it strikes me that John is developing and extending the neo-multiregionalist framework that he was operating within in the early 2000s. Also, African substructure is a thing. A major thing.

Finally, but not least:

Stephan Schiffels

Max Planck Institute for the Science of

Human History, Jena, Germany

Analysing Australian genomes to learn about early modern human dispersal out of Africa

When and how modern humans left the African continent is still a debated question. Recently, three projects have analysed new genetic data from modern populations in Papua New Guinea and Australia, which has provided new insights on this topic. I will present analyses from one of these publications (Malaspinas et al. 2016), and compare results with findings from the two other projects (Mallick et al. 2016, Pagani et al. 2016). Here, we used MSMC2, a novel computational framework to analyse the distribution of times to the most recent common ancestor along multiple sequences. We find that all non-African populations that we analysed, including Australians, experienced a very similar population bottleneck in the past, consistent with only one out-of-Africa migration for all extant non-African populations. At the same time, we find evidence that some African populations are more distantly related to Australians than to Eurasian populations, and we show that this result is robust to haplotype phasing errors and archaic introgression. We interpret our result as evidence for gene flow between some Africans and Eurasians after the initial split, which is also consistent with results from other population genetic methods. Our analysis suggests that in order to understand human dispersal out of Africa, we need to better understand ancient population substructure within Africa, which is an important direction for future research.

Again, ancient African substructure. No coincidence. Talk to the cutting edge people in the field, and this is the fabric of reality that the knife’s edge is going to slice in the near future. Second, I do believe it is likely that there was non-trivial gene flow between Sub-Saharan Africa and Western Eurasia over the past 50,000 years. Some of this is masked perhaps by low levels, but, just as likely in mind, ancient African structure which has been erased due to population turnover.

 
• Category: Science • Tags: Genetics, Human Evolution 

relig One of the first things I wrote on the internet related to Indonesian Islam, and what we could expect in the future. This was before Gene Expression, and I don’t have archives of that blog. There are many issues where my views have changed over the past fifteen years, but that is a piece of writing whose contents I think hold up rather well, if I recall it correctly! (when I go back and reread things I wrote 15 years ago I often wince at my naivete)

Yesterday I noticed that The Wall Street Journal had a piece up, Hard-Liners’ Show of Force Poses Thorny Challenge for Indonesia’s President, and an accompanying sidebar: Examples of Indonesia’s Turn to Conservative Islam. The details are not super important. Basically, the Christian and ethnic Chinese governor of Jakarta has gotten himself into some blasphemy trouble. Some of this critics are probably sincere, while some of his critics are probably being opportunistic. The political elite of the country must make a pretense toward neutrality, and genuflect toward religious sensibilities, since Indonesia is famously a 90% Muslim nation. Most people on some level know it’s bullshit, but at minimum you have to go through the motions. Religion aside this is a great chance to make sure that an assertive ethnic Chinese and Christian politician doesn’t get too uppity.

More interesting than what is happening is why this is occurring now. Not only is “Indonesia” famously the world’s most populous Muslim “nation,” it is also “tolerant” and “syncretic”, though recently “conservative” religious movements have become prominent, changing the nature of “Indonesian” Islam. Normally the usage of quotation marks in this manner is asinine, but I was conscious in what I was trying to “problematize.”

Indonesia is not truly a nation. Or at most it is a nation like India, a nation which encompasses a civilization with several related nationalities. Second, the tolerance of illiterate peasant cultivators for religious heterodoxy is different from the tolerance which 51T9NDF7GPL emerged (for example) in England on matters of religious belief and practice in the 18th century. And the syncretism of Indonesians is not like the syncretism you see in the development of the Sikh religion, which is a genuinely novel positive religious vision from a Dharmic base engaging questions and presuppositions derived from Islam. And Indonesian Islam which is called conservative is not conservative if conservatism harks to the customary, traditional, and organically evolved religious folkways of the populace. Rather, the “hard-line” Islam comes up from the aspirant middle classes and is connected with a broader movement of world-wide Islamic reformism and revivalism across the Ummah, and is consciously marginalizing the traditional Islamic religious establishment of rural regions.

What I’m getting at here is a general phenomenon, not limited to Islam. Eric Kaufmann alludes to it in Shall the Religious Inherit the Earth. Dianne Purkiss in The English Civil War points to it too. What is that phenomenon? The terminal state of postmaterialist modernity is not attained in a linear and unidirectional fashion. In fact, it may not be a terminal and stationary state at all!

When engaging many progressive friends and acquaintances who have little interest in international relations it is often asserted that material deprivation is the root of Islamic terrorism and Islamism writ large. This is demonstrably false empirically. Marc Sageman in Understanding Terror Networks did an extensive ethnography of the Salafist terror international of the 2000s, and there was an extreme overrepresentation of the highly educated, affluent, and technical professionals. Scott Atran has also done ethnographic research, and converged on the same result: it is not economic deprivation that fuels these violent explosions, because the participants and principles are not economically deprived.

51r6r4q8HiL._SY344_BO1,204,203,200_ Even a superficial analysis of Islamist movements, the necessary parent movement for violent terrorism, show that they are often driven by the middle class and prosperous, just as most radical movements are. This reminds me of a particular religious movement: Reform Protestantism. In the Anglo-American case this is most starkly illustrated by the Puritans, who were attempting to complete the Reformation within the English Church (purging all “Popish” rituals and institutions, as well as removing theological diversity, such as Arminianism). The Puritans were often from the industrious and prosperous classes of London and eastern England. The New England colonies were arguably the world’s first universal literacy societies.

I have stated before that whenever I read about the Reformation and English Civil War I undergo some cognitive dissonance. My consciousness as an American was formed in a region of upstate New York which was heavily Dutch, but later became demographically dominated by the great migration out of New England. Either way, a particular Anglo-Protestant, even Puritan, vision of history was what was taught to me. And yet the Protestants in the Reformation were often the heralds of intolerance, violence, and iconoclasm. Just as they were the heralds of toleration and liberality (in addition to the Netherlands, see Reform Transylvania and to some extent Poland). Protestantism unleashed many different tendencies sublimated within the Western Christian Church up until the 16th century (the exceptions of the Hussites and John Wycliff aside). And some of those forces and tendencies were not ones which postmaterialist liberals in the broad sense would have much sympathy with. It gave rise to both the pluralism of the Pennsylvania project and the tolerance of Rhode Island, as well as the demands toward public conformity and private uniformity which were the Puritan Congregationalist colonies.

In Red State, Blue State, Rich State, Poor State Andrew Gelman points out that ideological polarization is maximized at the upper income brackets. Values are to some extent luxuries, consumption goods for those beyond the subsistence level. What Kaufmann analyzes this on a sociocultural level, Gelman does so on an individual scale. And it explains why so little international Islamic terrorism comes out of the poorest Muslim countries in relation to their populations. The battle between the Taliban and the government in Afghanistan is between an Islamist movement and elements which are more diverse, but ultimately it recapitulates divides between country and city, and Pashtun and non-Pashtun, which give it local valence. The international aspect of Islamic terror is Afghanistan, or Yemen, or Somalia, comes from forces and threads which are international. Osama bin Laden was of Yemeni ancestry, but raised wealthy in Saudi Arabia. The influence of Al Qaeda and the Islamic State in poor Muslim countries has clear connections with migration from wealthier nations and Diasporas. Poverty may be fertile ground, but it is almost never the seed.

Going back to Indonesia, let’s bring together these strands and try and understand what’s going on. First, Indonesia is a collection of various nationalities with long histories of contact but distinction. The tolerant folk Islam that is often assumed to be the sine qua non of Indonesian Islam is really the culture of central and Borobudur_Templeeastern Java, that of the Javanese. At 40% of the Indonesian population the Javanese loom large, but they are not the totality of Indonesian culture and society. The people of Aceh came under Islamic influence centuries before Java, and they have traditionally had closer connection to the Middle East, and practice a more Middle East normative form of Islam. Second, many of the outlying islands have Muslim populations without the civilizational overhang of pre-Islamic greatness which characterizes Java. To this day a small minority of Javanese remain Hindus, while conversion to Hinduism from nominal Islam is not unheard of. This history though is truly the history of Java, and to a lesser extent the region around the Malacca strait. Hindu-Buddhist civilization’s impact on most of the Indonesian archipelago was much more diffuse and marginal (Sanksrit loan words as far as the Philippines and Madagascar are signs of this civilization’s contact with groups outside of Java and Sumatra). Outside of the areas of most intense Hindu-Buddhist domination history begins with Islam and the Dutch. They do not have much of a Hindu-Buddhist identity to synthesize with Islam in the first place.

Additionally, identity is not much of an issue in a village folk context. This is why syncretistic and tolerant Islam is common in many parts of the world characterized by subsistence farming. Individual lives are delimited by the custom and tradition of the village, which self-regulates. Rather than looking toward textual scripture, or religious professionals, long established folkways guide lives in a seamless fashion. Though these people may be tolerant when it comes to poorly understood or practiced religious orthodoxy and orthopraxy, they are also often very superstitious, and liable to murder the local “witch.” There are more tolerances than those of religious orthodoxy alone!

The major “problem” though occurs when you urbanize peasants. In an urban context village spirits are irrelevant, and the folk cultural currency which smoothes relationships no longer apply. If you are very wealthy this may not be relevant, as social networks of the elite have long had purchase in urban centers, and old connections can be leveraged at the commanding heights of industry and government. For the lower classes within slums the day to day may be a matter of survival and subsistence. A new identity is secondary to making to the next day. Where the need for identity likely comes to the fore is in the urban middle class. These the classes not connected to the levers of power in the social heights, but still have resources and leisure to ponder their place in the world, and how their nation should be ordered. In a village context these may have been prosperous farmers and gentry, already more closely connected to religious professionals than the more marginal peasant. Translated to the urban milieu their rural accumulated social capital accounts for little, with the inchoate Javanese mysticism and syncretism dissipating in the new environment for which it was never adapted in the first place.

This is where reformist and international Islam comes into play. This is a religion that is portable, and culturally neutral (ostensibly). Different local sub-elites transplanted into an urban milieu can meet and communicate with the lexicon of a religion which was defined from its beginning by urbanity. Not only does Islam allow for connections between people between different regions, but it also integrates oneself into an international network, previously only accessible to those with financial resources to travel extensively. Common belief in a transnational religion allows for immediate rapport with those from other nations, without the need for prior extensive personal interactions. Subscription to various forms of Islam allow for immediate inclusion into an international brotherhood.

The United States is perhaps the best example of what mobility and lack of solidity do to religious institutions. American religion is exceedingly confessional and decentralized. The Roman Catholic Churches attempt to create a corporate pillar on the model of the European society in the 19th century failed. Rather, operationally American Catholicism has become confessional at the level of the believers, if not the exterior institutions. Similarly, American Judaism took a very different trajectory from that of European Judaism. While European Reform Judaism was marginalized between the two poles of Orthodoxy and secularism, in the United States Reform Judaism was arguably the dominant form of Judaism for most of the nation’s history.

American religions are characterized by a wide range of levels of tension with the surrounding society, and are generally confessional, rather than communities of birth (though Judaism is arguably a hybrid, as Reform Judaism has again embraced the ethnic dimension of the religion). Some groups, which are often termed “conservative”, are at high tension with society. The reality is that they are not necessarily conservative, as much as they exhibit strong ingroup dynamics, and marginalize outgroups, and are marginalized by outgroups. Consider Mormonism, a religion which is conservative in its mores, but whose theology is highly exotic, and arguably radical. The key toward understanding Mormonism is its high internal cohesion. But this results in a side effect of tension with the surrounding society.

41cpg1ESArL._SY344_BO1,204,203,200_ Indonesia is a nation of 250 million. The rise of “conservative” Islam is natural. As Indonesia urbanizes, its folk Islamic subculture s are dissolving. They evolved organically over thousands of years, and they are adapted to local conditions, utilizing local lexicon. Their strength was their deep local roots. They are not transplantable. It is natural that many urban dwellers would find that a culturally stripped down form of Islam based on textual sources, though extending from them, would be amenable to their needs. This form of Islam allows for strong ingroup ties that are not contingent on local histories or ethnic identities. But, it also throws up walls toward those who it considers outsiders and competitors. That is, non-Muslims. Other Indonesian urbanites are not becoming “conservative” Muslims. Rather, they are probably subscribing to what one might term “liberal international,” the transnational globalist class which is united by their affluence and postmaterialism, and a form of individualism well characterized by Jonathan Haidt.

Indonesian Muslims are arguably more “liberal” and more “conservative.” But this increased variation and solidity of large bloc social units is salient in a form which is more threatening. To readers of The Wall Street journal the transnational Muslims identifying with the Islamic Reformist international bloc are threatening, and a danger, due to their hostility toward outgroups. In contrast, the liberal globalists take a more relaxed attitude toward group identity, though they too have their own redlines and normative preferences.

The details may be local, but the dynamics are global.

 
• Category: Foreign Policy, History • Tags: Indonesia, Religion 

Screenshot 2016-11-06 09.57.53

51deNffGPJL._SX327_BO1,204,203,200_ (1) My prediction above. Based on a few minutes scanning online. Also, I suspect that Trump supported is being overestimated. Low confidence that I’m adding value with my opinion.

After finishing Unfinished Empire: The Global Expansion of Britain I’m struck by the fact that the author had to make some criticisms of Edward Said’s Orientalism, because Orientalism is so weak on both details and overall theoretical framework. That’s why I dismissed it fifteen years ago when I read it, but today I have to say that Orientalism is the model of scholarly sophistication compared to what prevails today in postcolonial theory.

 
• Category: Miscellaneous • Tags: Open Thread 

40_weeks_pregnantWould You Want To Know The Secrets Hidden In Your Baby’s Genes? Turns out most people don’t. The article profiles the BabySeq Project, and the offer of whole exome sequencing (exomes are the parts of the genome which code for proteins).

In some ways, the results were discouraging:

One thing Green hadn’t anticipated is how hard it has been to convince new parents to do this screening in the first place. Early research showed the majority of parents were interested in the medical information. But 94 percent of parents Green and his team are approaching are saying no.

So that leaves 6 percent. That’s not a trivial number. There are about 4 million babies born per year, so that would be 240,000 newborns with their exome sequenced. And part of the balking is just fear. People will get over this. Technologies like this have an S-shaped adoption curve. It starts out low at first, and then expands to most of the population. Some portion will always opt-out, and that’s their right.

Probably the bigger issue is that people need to not overreact. A lot of loss-of-function mutations turn out to be innocuous in many people.

 
• Category: Science • Tags: Genomics 

CLIMAP

51ABT97467L._SX325_BO1,204,203,200_ Three major events have shaped the distribution and abundance of modern humans across planet earth over the past 50,000 years. First, the “Out of Africa” event. Second, the Last Glacial Maximum ~20,000 years ago. And third, the changes wrought by the Holocene, foremost amongst them agriculture, but also including other developments, such as the utilization of the horse to increase human mobility.

There are two major phylogenetic and population genetic consequences of these dynamics. First, human phylogeny is highly reticulated. That is, it can be better thought of as a graph rather than a branching tree over the past ~50,000 years, due to repeated pulses of massive gene flow between tips of the diversifying human lineages. Second, abiotic and biotic selection pressures in the context of population turnover mean that adaptation has been a continuous process. Additionally, the complex feedback loops engendered by cultural evolution mean that biological evolution through adaptation is driven by endogenous forces, emerging from changes within human societies, rather than simply external exogenous shocks.

Two new papers on Australian archaeology and genetics illustrate this. First, today, Cultural innovation and megafauna interaction in the early settlement of arid Australia:

Elucidating the material culture of early people in arid Australia and the nature of their environmental interactions is essential for understanding the adaptability of populations and the potential causes of megafaunal extinctions 50–40 thousand years ago (ka). Humans colonized the continent by 50 ka1, 2, but an apparent lack of cultural innovations compared to people in Europe and Africa3, 4 has been deemed a barrier to early settlement in the extensive arid zone2, 3. Here we present evidence from Warratyi rock shelter in the southern interior that shows that humans occupied arid Australia by around 49 ka, 10 thousand years (kyr) earlier than previously reported2. The site preserves the only reliably dated, stratified evidence of extinct Australian megafauna5, 6, including the giant marsupial Diprotodon optatum, alongside artefacts more than 46 kyr old. We also report on the earliest-known use of ochre in Australia and Southeast Asia (at or before 49–46 ka), gypsum pigment (40–33 ka), bone tools (40–38 ka), hafted tools (38–35 ka), and backed artefacts (30–24 ka), each up to 10 kyr older than any other known occurrence7, 8. Thus, our evidence shows that people not only settled in the arid interior within a few millennia of entering the continent9, but also developed key technologies much earlier than previously recorded for Australia and Southeast Asia8.

The paper is archaeology, with a lot of stuff on dating and stratigraphy, which I can’t add much to. But, it confirms hints that modern humans really spread rapidly once they had a chance. It does seem that the pulse of migration out of the fringe of Africa that resulted in all non-Africans (or most of their ancestry) moved very rapidly across the world once it got a head of steam going. The genetic and archaeological evidence seems to indicate that movement did not predate 50,000 years B.P. by that much (this doesn’t mean there weren’t earlier waves which were absorbed or died off from the same region of a similar ancestral population).

Then, from a few months ago, A genomic history of Aboriginal Australia:

The population history of Aboriginal Australians remains largely uncharacterized. Here we generate high-coverage genomes for 83 Aboriginal Australians (speakers of Pama–Nyungan languages) and 25 Papuans from the New Guinea Highlands. We find that Papuan and Aboriginal Australian ancestors diversified 25–40 thousand years ago (kya), suggesting pre-Holocene population structure in the ancient continent of Sahul (Australia, New Guinea and Tasmania). However, all of the studied Aboriginal Australians descend from a single founding population that differentiated ~10–32 kya. We infer a population expansion in northeast Australia during the Holocene epoch (past 10,000 years) associated with limited gene flow from this region to the rest of Australia, consistent with the spread of the Pama–Nyungan languages. We estimate that Aboriginal Australians and Papuans diverged from Eurasians 51–72 kya, following a single out-of-Africa dispersal, and subsequently admixed with archaic populations. Finally, we report evidence of selection in Aboriginal Australians potentially associated with living in the desert.

There are a few things going on in this paper. First, they had a lot of whole genomes, rather than just SNP data. They used this whole genome data to get a really good sense that once you correct for excess Denisovan ancestry the “two-wave” model out of Africa is just not that well supported in comparison to a single expansion.

Second, because the Australians and Papuans were isolated from other populations for most of history, it turns out you can see evidence of gene flow between Sub-Saharan Africans and Eurasians, in particular West Eurasians, after the divergence of the non-African groups. This is not entirely surprising. And, that gene flow is found in the Dinka and Yoruba samples, but not the San. Again, not surprising. Note, more recent Holocene gene flow form Eurasians into Sub-Saharan populations is clear in Nilotic populations, such as the Masai. This is something different. Perhaps it is older gene flow back into Africa, or, perhaps it is evidence of substantial African gene flow into Eurasia, possibly during the Pleistocene.

Map_of_Sunda_and_Sahul But big inferences were about the timing and divergence of Australian and Papuan groups. As noted in the paper Australia was not separate from New Guinea for much of the Pleistocene. They were one continent, Sahul. But the divergence between modern Australians and Papuans seems to predate the rising of the sea levels by tens of thousands of years. Part of this is probably some level of ecological isolation, as the highlands of New Guinea would always have been very distinct from the much drier Australian landmass. But I suspect that part of is that there was a lot of ancient structure in Sahul. The existence of two major lineages is probably simply a function of the fact that meta-population dynamics in humans are subject to a lot of local extinction events, and most of the deeply diverged lineages are gone.

Modern Australians seem to date from a common population which may have arisen around the Last Glacial Maximum. This comports with the model above. Basically, a lot of the other groups in the broader family of Australian populations probably went extinct for various reasons. This means ancient DNA from Australia which is substantially old enough will be from highly diverged lineages with no modern descendants. Think of the ancient samples from Siberia and Romania which seem to have had minimal impact on the modern Eurasian populations.

 
• Category: Science • Tags: Australians 
Razib Khan
About Razib Khan

"I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. If you want to know more, see the links at http://www.razib.com"