Open Thread, 10/31/2016

51deNffGPJL._SX327_BO1,204,203,200_I’m reading Unfinished Empire: The Global Expansion of Britain. Not as well paced as his previous After Tamerlane: The Rise and Fall of Global Empires, 1400-2000, but pretty good nonetheless.

Politics exhausts me. This is an exhausting time for me mentally as I’m overwhelmed by the din of political chatter and fixation. I’m very excited for November 8th to come and go.

There’s lots of stuff in science I want to write about, but the combination of lack of time, and politics saturation all over the place, has been demotivating me. So as the month proceeds I’ll probably get my energy back.

No one knows about the third human admixture into Melanesians

Vanuatu_blondeThere are several reports in the media about a third hominin group besides Denisovans and Neanderthals, and how they contributed to Melanesians. Science News has a sober summary of it all.

Several people have asked me on email and Twitter about this, and I told them to ignore it. The reason I say this is that I was in the room when the presentation was given, and it was clear people were having a hard time following what was going on. Afterward several pretty intelligent statistical human geneticists expressed great confusion.

A few things to take away. First, it was a presentation at a conference. One can’t expect very novel findings to be understood easily in a 15-30 minute talk. Wait for the preprint at least. Second, this was a presentation at a conference. A lot of presentations don’t pan out. If it’s a really surprising theoretical or interpretative finding, as opposed to sequencing a new species (an empirical result), generally I don’t pay close attention. A lot of time the reason that no one else has stumbled onto the surprising results is that they are wrong, or trivial upon further inspection.

Finally, there are complexities of human history we don’t have a good grasp on. There may indeed be other hominins which contributed to the human gene pool to the point of detectable admixture. I think it is likely. But it is a different thing to have specified all the details.

Basically, I wish the press would set a higher bar for presenting on new results from conferences. It’s not even that it’s not been peer reviewed. Often the results are provisional, and they don’t end up turning into the paper that’s promised.

The Egyptians live

61kCcH+1C9L._SY344_BO1,204,203,200_For various sociocultural reasons ancient Egyptians are a big deal. The pyramids of Giza are about as distant from the time of Augustus as Classical Rome is from us. When the pyramids were rising the world was mostly prehistory. Africa was dominated by hunter-gatherers, as was much of Southeast Asia. The genetic cluster which we recognize as Northern Europeans was only coming into focus, while South Asians as we understand them today may not totally have been a coherent group.

It was a very different time. Down to the present day one population can plausibly claim a connection to ancient Egypt, and that population are the Copts. Though now extinct, their language was a direct descendant of ancient Egyptian, which was not a Semitic tongue. As Christians in a nation which as been Muslim for over 1,000 years, with the period after 1000 A.D. likely majority Muslim, they likely have experienced less genetic perturbation than other groups in the area.

The paper The genetics of East African populations: a Nilo-Saharan component in the African genetic landscape has some Coptic, and other, samples. There are 175,000 markers on this chip. Merged with the HGDP populations you get about 30,000.

sudanThe PCA shows that Copts are mostly West Eurasian in ancestry. But they seem shifted to Northeast African Sub-Saharan groups The Mozabite Berbers are shifted toward West Africans, but their West Eurasian ancestry looks to be more like that of the Copts than West Asians. Though not shifted toward West Asians, the Copts do seem to have affinities with various Sudanese groups.
Screenshot 2016-10-28 00.34.13This TreeMix graph was run on 30,000 markers, with the Sudan skewed sample and some HGDP populations. Not surprisingly, there are gene flow arrows from the Copts to the others. In particular, the two Nubian groups, who have long been resident right to the south of Egypt. But, there is also gene flow from a position between the Copts and Sub-Saharan Africans. Finally, observe that Northeast African Bantus, who have some Nilotic admixture from the Bantu, receive gene flow from a more “European” like population, while the Copts receive gene flow from near the Sardinians. All this points to a complex population history.

It seems likely that the Eurasian backmigration into Sub-Saharan African over the Holocene involved several distinct events. Some of them probably date to the period of the Pleistocene.

Why 23andMe is no longer leading on personal genomics

23andme_logoI really admire what 23andMe has done. To a great extent they are the “Uber” of DTC personal genomics. FamilyTree DNA really pioneered the sector in the early 2000s, while The Genographic Project scaled things up massively in the middle 2000s. But in the late 2000s 23andMe brought Silicon Valley “disruption” to the game, pushing into disease and traits in a way that both the two earlier efforts consciously avoided. We know how that ended.

But it wasn’t all in vain. 23andMe is today a healthy company, and its shoot-first-ask-questions later actions in the first half of the teens really brought personal genomics into peoples’ lives.

So what’s going with stories like this, 23andMe Has Abandoned The Genetic Testing Tech Its Competition Is Banking On:

For years, genetic-testing startup 23andMe was working to develop a cutting-edge technology that could dramatically expand what its customers might learn about their DNA. While the company’s core product, a $199 “spit kit,” can tell you about your health and ancestry based on small bits of your genetic code, tests based on the new technology — called next-generation sequencing — could provide much more comprehensive information, including your potential risks for many diseases.

But 23andMe has given up on the technology for now, BuzzFeed News has learned.

I think one way to understand what’s going on is that though the firm’s consumer face is still as a DTC personal genomics outfit, it is really banking on becoming a genetically savvy pharmaceutical corporation. Genomics is the future, but pharm is the present.

51cz5E2hKTL._SX378_BO1,204,203,200_23andMe probably has ~1.5 million genotypes now. They’ll confirm more than 1 million. If they had more than 2 million I assume they would tell us they did. What are they doing with those genotypes? It was always understood by most that 23andMe was increasing its database to the point where they could generate associations that academics could not because of lack of statistical power. The problem now, with more than 1 million genotypes, is that they need phenotypes.

It is much more valuable for 23andMe to get rich data on one customer, than it is to gain one hundred more random genotypes. That’s probably why they’re not sweating that the $199 price point discourages people, especially when those people are getting less than they did in the past. That’s also why they are pulling out of the game in next generation sequencing. Sequencing is basically a commodity business now, and just not as good a return on investment as gearing toward the pharmaceutical market. Sequencing deeply has some benefits, but there is no way 23andMe would be able to subsidize the $1,000 cost of a good 30x genome to get enough of a sample size to return the investment.

None of this is a big secret. A friend of mine was talking about this in the broadest sketches at the 23andMe party at ASHG.

Moving along the Roman Peace

Rami_Malek_in_Hollywood,_CaliforniaA friend of mine introduced me to Mr. Robot a month ago. The show was difficult for me to follow, and I don’t watch much TV in the first place (“watching TV” is like making a “mix tape”; there’s not television involved anymore). But, the star, Rami Malek, had an intriguing look.

It was only later that I realized why: his face resembled the Fayum portraits. These miniatures represented people in Roman Egypt from all walks of life. They are one of the best set of representations we have of normal individuals, albeit, prosperous enough to commission these works.

Malek is from a Coptic family, so presumably genetically representative of people in Roman Egypt during that time. It stands to reason that he’d look quite like many of these ancient Romans.

italianAnyway, I happen to have some data laying around put it through PCA, Treemix and ADMIXTURE. If you click the plot to the left PC 1 shows a cline from Sardinians to Lithuanians. PC 2 is from (modern) Egyptians to Basques. The Egyptians are clearly being shifted by their Sub-Saharan African admixture, which in other analyses usually comes in at between 10% to 25% depending on the individual. The Assyrian Christian samples, and Cypriots, are much closer to the other populations on PC 2 (several of the Lebanese). Then the Sicilians, Tuscans, Bergamo Northern Italians, and Spanish (before the Basque).

Sometimes Treemix is more informative. Below is a pretty representative graph with 5 migration edges (I set Egyptians to be the root):

Screenshot 2016-10-24 22.39.38

And here’s K = 4.


These sorts of plots are a Rorschach test. But, I’m pretty sure ancient DNA will confirm that migration around the Mediterranean during the Classical Era was non-trivial, but, the minor component in the ancestry of most modern populations.

Game of Thrones spoiling A Song of Ice and Fire

51OMI4Jez3L._SX260_I finally “broke” last year, and began watching Game of Thrones, the HBO show. As a longtime reader of the series I had held out hope that The Winds of Winter would come out early enough not to be spoiled by the series, but it was not to be. In fact, it is probably likely that that book will come out after next season.

Say whatever you will about the “fork” between the television series and the books, Benioff and Weiss have made it clear that they know the conclusion, and that they’ll tie the threads back together broadly in line with the books. That means unless Martin engages in a major course correction, we’ll know conclusion of the series years before last book.

I began to watch the show because it was pretty much impossible to avoid spoilers on Twitter as they began to push the story forward rapidly. What’s the point in waiting another ten years? But that also means that I now have access to other material which can spoil the show: below the fold is footage of the actors in what is clearly a very important scene. The scene brings together two characters who are so important that I have a hard time believing that this is a major difference between the book and the television show. It is entirely likely that this scene occurs in the book in some form. It isn’t an entirely unlikely occurrence, but, it still brings into realization what was only a probability.

If you want to be spoiled, click below the fold. Even if you don’t want to be spoiled, it will happen. If you haven’t read the book and are waiting on George R. R. Martin to finish, probably a good time to read all the books that are out and hope Winds comes out shortly.
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Open Thread, 10/23/2016

2016-10-23 08.40.37Bought Marie Sharpe’s green habanero sauce at Granville Market. The spice level is nothing to sneeze at, and it’s got a nice flavor. But the salt is out of control.

danboThere is a lot of good Asian food in Vancouver. A pretty good meal at the downtown Kirin, but I want to highlight Ramen Danbo. The servers were all young women from Japan, so the ambience and food exhibited an authenticity that’s not typical.

Annexation_Bill_of_1866_mapAfter four days in Canada I really don’t see why at minimum we don’t have a customs union and open borders so we can dispense with these sorts of friction to travel. Canadians are easier to understand in terms of their English for most people who speak General American than some of our fellow citizens. Vancouver in particular reminds me a lot of Seattle, a city I know decently well since I’m from the Pacific Northwest originally and still go back to visit family.

Pandora was blocked in Canada for some reason. And I had to call to make special provisions to maintain data on my phone. Really is there a reason for this?

I am struck by the colonialism described by Colin Woodard in American Nations when it comes to Reconstruction. In his telling Yankees swarmed to the South believing that they could recreate New England in the post-war societies. Eerily familiar in light of what happened after the Iraq War.

51y9UBanyFL._SX386_BO1,204,203,200_Someone in a comment below asked what population genetics they should read. Start with Principles of Population Genetics. It’s the gold standard. Some people would suggest starting with Population Genetics: A Concise Guide, but I didn’t start with that and I’m fine.

Joe Felsenstein and Graham Coop have some good notes online.

Spent some time with “reiver” online. He seemed curious as to my ability to read a lot and read fast. There’s nothing very impressive or amazing about it actually. I’ve been reading a lot in several areas since I was an early elementary school student, and so I can read and process new information fast because I already have a lot of preexistent structure.

416NQwBS-+L._SY344_BO1,204,203,200_But you can lose things. For example I read books on cognitive neuroscience more slowly than I used to because I stopped reading in this topic when I went to grad school. I’m a big fan of Stanislas Dehaene’s work, but I get less out of it than I used to. That’s unfortunate.

Overall I do worry that I’ve focused too narrowly in my interests as my brain has aged and I’ve matured. My knowledge of specific areas is deeper, but I am not as broad in my curiosity as I used to be.

ASHG was good. I’ll say more later, but the popgen was a little thinner than in previous years.

It was interesting that many seemed to know about the company I work for. The fact is that our canine genomic test is the most comprehensive and robust out there. That’s not marketing fluff, and geneticists can discern bullshit from reality pretty easily. So the discussions were more brass-tacks about the value customers. I had a pretty good case for why a purchase is justified or feasible, so easy discussions.

417otmYuMcL._SX303_BO1,204,203,200_Reading about Poststructuralism, and having a hard time understanding how people take this stuff seriously. That’s a problem, because people do. Perhaps a validation of its weirdly grand take on the power of language to shape the structure of reality.

It will be nice to read about something different. In particular, functional programming. Need to get my NumPy skills up, as I spend so much time struggling with data-types.

On the Reformation

MacCulloch_Reformation_smSince we’re on the topic of religion, I thought I would make a book recommendation. If there is one book I would read on the Reformation if there was one book, it is Diarmaid MacCulloch’s The Reformation. I read this magisterial work in 2004 over a week and it has stuck with me in a way no other work on this topic before or since, has (similarly, if you are going to read one book on Byzantine history, it would be A History of the Byzantine State and Society).

MacCulloch’s history of Christianity was relatively disappointing (thin gruel, stretching out a deep topic too far in a survey). But I see he’s come out with a new book on an old topic, All Things Made New: The Reformation and Its Legacy. I just got a copy and it seems interesting. More thematic than narrative in comparison to the earlier survey.

Justified by more than logos alone

41I42XDmNfL._SX335_BO1,204,203,200_There are some topics which I have some interest in, such as prehistory illuminated by genetics, in which there is constant change and new discoveries every few months. If a new paper doesn’t drop in a six month interval, I think something is wrong.

There are other topics where I don’t perceive much change, and have stopped paying much attention. Psychometrics for example is one area where I basically just stopped paying much attention after reading The g factor. I understand that it’s a live field, but at this point to me the details are academic, as the broad sketch seems well established (this will change in some ways over the next decade due to genomics, but since I think genomics will confirm what we already know it won’t be very revelatory for me).

The scientific study of religion is another topic where I once had a lot of interest, but where I concluded that the basic insights have stabilized. Since I stopped reading much in this area I stopped writing much about it too. To get a sense of where I’m coming from, Scott Atran’s In Gods We Trust: The Evolutionary Landscape of Religion is probably the best place to start. It’s about 15 years old, but I don’t see that much has changed since then in the basics of the field.

9780195178036And what are those basics? At its fundamental basics religious impulses must be understood as an outcome of our cognitive mental intuitions. All religion operates on top of this basic kernel of our mental OS. Religion may have functional utility as a social system of control, or channeling collective energies, as argued by David Sloan Wilson in Darwin’s Cathedral. Or, one might be able to fruitfully model “religious marketplaces” as argued in Marketplace of the Gods. But these are all basically simply applications installed into on top of the operating system.

Why does this matter? For me this is a personal issue, because I’m one of those people who has never really had a strong religious impulse. Since I didn’t have a religious impulse, my model of religion was as that of an outsider, which led to some confusions. For example, there was a point perhaps around the age of 18 where I thought perhaps if someone just read a book like Atheism: A Philosophical Justification they’d be convinced. Just as if I’d been a Roman Catholic I would have thought a reading of Summa Theologica would have convinced. This was all wrongheaded.

Very few are Roman Catholic because they have read Aquinas’ Five Ways. Rather, they are Roman Catholic, in order of necessity, because God aligns with their deep intuitions, basic cognitive needs in terms of cosmological coherency, and because the church serves as an avenue for socialization and repetitive ritual which binds individuals to the greater whole. People do not believe in Catholicism as often as they are born Catholics, and the Catholic religion is rather well fitted to a range of predispositions to the typical human.

One thing that the typical human does not have is intensive need for rationalization of our daily life, and the totality of their beliefs. There are a non-trivial subset of Catholics who have heard of the Five Ways, or might be conversant in the Ontological Argument. But this is a very small minority of Catholics, and for even these this philosophical element is a sidelight to most of their spiritual practice and orientation.

The reason I am posting this is in response to something Rod Dreher wrote, Mystery Of The Ages:

Here’s something I have never figured out. In theory, Catholics ought to be a lot more theologically conservative on such matters. They have a clear teaching proclaimed by a clear church authority, with a deep Biblical theology behind it. And yet, on the whole, it doesn’t seem to matter to lay Catholics. Evangelicals, on the other hand, have the Bible, but no binding interpretive authority to keep them from diverging. Yet, on these issues, they are more morally conservative than Catholics — even by Catholic standards.

Why is this? I’m asking in a serious way. Any of you have a theory? I’m not going to publish gratuitous Catholic bashing or Evangelical bashing in the comments.

The best book to fully address this paradox would be D. Jason Slone’s Theological Incorrectness: Why Religious People Believe What They Shouldn’t. But that’s the generality. If you want specifics, see Jay P. Dolan’s In Search of an American Catholicism: A History of Religion and Culture in Tension. Though American Catholics retain identity and affiliation with the Roman Catholic Church, it has operationally become Protestantized when it comes to how people view their relationship to the religion (in a similar way, American Reform Jews also transformed their religion to conform with American confessional Protestantism).

There are a subset of believers who are not well captured by the generalizations in books such as Slone’s, or in ethnographic descriptions which trace the assimilation of Catholicism into the American scene. They are usually highly intellectual and analytical in their orientation. Often, they seem to be converts. Rod Dreher was a convert to Catholicism from Methodism, before he became Orthodox. Leah Libresco and Eve Tushnet also seem to fall into this category. Highly intellectual. And, converts to Catholicism.

Because they are analytical and articulate, these sorts of religious people are highly prominent on the public stage, and, they also write the histories that come down to us through the centuries. These are also the type of people who are overrepresented in the clerical apparatus of any organized religion. This is a problem, because their prominence can obscure the reality that they are not as influential as you might think. As a metaphor, imagine mountainous islands scattering amidst a featureless ocean. The islands are salient. But it is the vast ocean which will ultimately be determinative. Similarly, the vast number of believers who move along a nexus of inscrutable social forces, and driven by powerful universal psychologies, may be hidden from our view.

51jUZQV3r1L._SX329_BO1,204,203,200_And yet even for the “analytics” reason does not dictate. Both Dreher and Tushnet have made references to mystical and emotional occurrences and impulses which are beyond my ken. I have no need, no wish, no impulse, and no intuition as to what they are talking about in that dimension (Libresco seems a somewhat different case, but I haven’t read much of what she’s written; I suspect I’ve been in the same room with her since she worked for an organization which I have many personal connections with, but I’m not sure).

It isn’t a surprise that I think Hume was onto something when he asserted that “reason is a slave to the passions.” In many instances I suspect theological analysis is simply the analytic engine being applied to a domain whose ultimate rationale is driven by a passion.

Addendum: Leah Libresco seems to have been associated with the broad umbrella group of Bay Area rationalists. I’ve been associated in some fashion with these people as friends and acquaintances for nearly 10 years. I will admit that I’ve generally found the conceit of rationality as an ends, as opposed to a means, somewhat off-putting. Ultimately I’m more of a skeptic than a rationalist I suppose at the root.

Open Thread, 10/17/2016

51I3Hux0TsL._SY344_BO1,204,203,200_I reread Colin Woodward’s American Nations: A History of the Eleven Rival Regional Cultures of North America on the plane recently. It’s a less scholarly work than Albion’s Seed or The Cousins’ Wars: Religion, Politics, Civil Warfare, And The Triumph Of Anglo-America, but arguably more straightforwardly relevant to modern conditions and events. I’m rather sure that Woodward would be interested in a further edition which updated with the goings on of the 2016 election campaign, if he’s not working on it already (an important complement, Replenishing the Earth: The Settler Revolution and the Rise of the Angloworld, 1783-1939, which takes a broader Anglospheric view).

The important point here is that initially developed cultural folkways can be persistent and reinforcing. The author observes that Nordic immigrants seem to have almost invariably chosen the region of the American frontier dominated by a Yankee ethos, the Upper Midwest. Though they overwhelmed this region demographically, rather than changing the culture, they simply accentuated its longstanding features, which were established by Yankees (e.g., social progressivism and communitarianism).

What else is going on? Going to be at ASHG a lot this week.