The media needs clicks and people are rather myopic. This explains patently false pieces such as this in Buzzfeed, This Is How We Radicalized The World. It is a rather unorganized list of facts, but they are assembled in a way to convince and persuade the reading audience that modern information technology has facilitated the rise of political radicalism, as if it is something new and notable. So wrong it hurts.
Anyone who knows history will realize this is patently false. Anyone who is aware of the Taiping Rebellion, the October Revolution, or the unrest of 1848. Of course, that “anyone” is a small set of individuals because most people don’t know history. Their minds are devoid of most facts not having to do with the Khardashians. And journalists are not much better. Many of them are in the game of creating stories rather than interpreting the world. If public relations operatives are well paid propagandists on a short leash, many journalists are poorly paid propagandists compensated with the freedom to be fabulists.
A piece like the above could convince, but only with a scatterplot. Social science can convince whether history says otherwise, because it is systematic and clear. But most people are not fluent and competent enough to do such data analysis, so they create a conclusion that is congenial to their audience, and marshal evidence in a biased manner (wittingly or unwittingly) to support their conclusion.
To get a sense of what we’re seeing today in the world, we need to go back centuries.
In the early 16th century, the unity of Western Christianity shattered. The standard story you see in the movies is that a German Augustinian monk named Martin Luther led a rebellion against the Roman Church, what became the Roman Catholic Church after it was clear that the Protestants were going to go their own way.
Sex in humans may not be binary, but it’s surely bimodal. Jerry Coyne is a well known evolutionary biologist who is also a vocal atheist. He’s now emeritus from the University of Chicago, and so I feel he’s kind of “out of step” with the culture. For example, within this post, which I generally agree with, he uses the term “transsexual” when most academics would use “transgender” to mean what he means. A lot of biologists don’t comment on this issue for two reasons. First, it’s politically fraught and you can’t really win. Second, the terms, norms, and frameworks are changing fast and constantly, so that people don’t even know what they’re addressing.
Speaking of fraught, the first robust SNP hits for male nonheterosexual behavior were reported at ASHG. The preprint should be out in less than four months. Antonio Regalado has already reported on it, Genes linked to being gay may help straight people get more sex. We plan to interview one of the authors on our podcast.
Recently talked to some people from Andy Kern’s lab about implications of Wright-Fisher vs. non-Wright-Fisher models in terms of spatial heterogeneity. It really makes me excited for the “forward simulation revolution.” Talking to people in evolutionary genomics that isn’t focused on getting NIH grants for human research, and it is clear why Matt Hahn has stated that there’s already enough data produced for many years to come.
A Tentative OUT OF INDIA Model To Explain The Origin & Spread Of INDO-EUROPEAN LANGUAGES. I’m skeptical of the conclusion, but this post has a lot of interesting information. Additionally, I think that AASI ancestry is going to be found in the Indus Valley between 3000 and 2000 BC…but I’m not totally sure. Johanna Nichols’ work is recommended though.
Recently I’ve been thinking about China and Saudi Arabia. Recently we’re looking skeptically at our elite’s ties with Saudi Arabia. But what about China? Many researchers and businesspeople “have” to work with China, and unlike Saudi Arabia, it seems implausible that we can “avoid” interactions. But there are plenty of human rights issues with the Chinese state. The only conclusion I draw is that people need to be careful about getting on their high horses. Researchers who criticize working with the Saudis or in Israel should also consider them working with Chinese colleagues who are under the purview of a problematic state…but that penalize their Chinese colleagues, and would be harder and harder to maintain over the years.
The Blanning Frederick the Great book really is good. Though some of you might want to speed through the details of campaigns (and some of you may not).
Income inequality and intergenerational mobility—the degree to which (dis)advantage is passed on from parents to children—are among the defining political challenges of our time. While some scholars claim that more unequal countries exhibit a stronger persistence of income across generations, others argue that mobility rates are unaffected by social equality and are equally low in most societies. We compare economic opportunity across U.S. areas populated by different European ancestral groups, and find a substantial variation that mirrors current differences across descendants’ countries of origin: mobility is highest in areas dominated by descendants to Scandinavian immigrants, lower in places where the Italian, French, or Germans settled, and lower still in areas with British ancestral origins. A similar pattern is observed for income equality, which gives rise to a gradient closely resembling the “Great Gatsby Curve” across European countries. We provide suggestive evidence that these differences arise mainly at the community level and that similar mobility patterns apply to the black minority population, so they are not simply a function of ancestral groups themselves being more or less mobile. A more plausible explanation is that cultural differences among immigrant groups gave rise to local economic and social institutions that are more or less conducive to mobility. Our findings suggest that present cross-country differences in inequality and intergenerational mobility are real and may have deeper historical origins than has hitherto been recognized.
Looking at county-level ethnicity data from the 1980 census as well as the income tax data that Raj Chetty uses, the authors found some interesting patterns in the “synthetic countries” within the USA:
The overall thesis that the culture immigrants brings persists for generations seems plausible. In Not By Genes Alone Robert Boyd and Peter Richerson report data from Illinois where farmers of German-American background behave very differently from their neighbors of Anglo-American background when given the same conditions. Anglo-Americans behaved much more like homo economicus . They sold their farms when the market price was right. In contrast, the German-Americans would attempt to keep the farms within the family even through periods when it was not economically rational.
My point is that there are non-economic aspects of culture that may not be picked up by these analyses which have economic consequences.
The second issue is that not all Americans of “British” origin are the same culturally. Long-time readers know where I’m going with this. The argument in Albion’s Seed: Four British Folkways in America is that English American New England Yankees are culturally very distinct from British Americans from the South, whose origins often range from southwest England to the borders with Scotland, as well as Ulster-Scots who arrived in the middle of the 18th century.
If you look at at the map within the preprint you see that Utah has a high fraction of British Americans, but its socio-demographic profile is more like the Upper Midwest, dominated by Scandinavians and Germans. The British Americans of Utah, of course, descend to a great extent from New England Yankees, as well as various Northern European immigrant groups converted to Mormonism by 19th-century missions. Though similarly socially and politically conservative, Utah Mormons are culturally very different from white Southerners. One way to describe it is that Utah Mormons have a lot of social cohesion and an orientation toward communalism. This is in line with their Yankee origins. Yankee migrants to the West organized their towns very differently from those from the South (to be frank, Southerners didn’t much organize their towns at all in comparison to Yankee rationalism and collectivism).
A reader pointed out a very interesting passage in Richard Dawkins’ The Greatest Show on Earth: The Evidence for Evolution on the future possibilities of genome sequencing. Since the book was published in the middle of 2009, it is quite possible the passage was written in 2008, or even earlier.
Unfortunately for Dawkins’ prognostication track-record, but fortunately for science, he was writing at the worst time to make a prediction:
…the doubling time [data produced for a given fixed input] is a bit more than two years, where the Moore’s Law doubling time is a bit less than two years. DNA technology is intensely dependent on computers, so it’s a good guess that Hodgkin’s Law is at least partly dependent on Moore’s Law. The arrows on the right indicate the genome sizes of various creatures. If you follow the arrow towards the left until it hits the sloping line of Hodgkin’s Law, you can read off an estimate of when it will be possible to sequence a gnome the same size as the creature concerned for only £1,000 (of today’s money). For the genome the size of yeast’s, we need to wait only till about 2020. For a new mammal genome…the estimated date is just this side of 2040
The cost for a sequence here is somewhat fuzzy. The first assembly of a genome sequence of an organism is much more difficult than subsequent alignments of later organisms (though more in computation than in the sequencing). But, the upshot is that Dawkins was writing when “Hodgkin’s Law” was collapsing. From 2008 to 2011 Moore’s Law was destroyed by the sequencing revolution pushed forward by Illumina.
Though you can get a $1,000 consumer human sequence today, the reality is that this is for 30× coverage. For lower coverage, which means you aren’t as sure of the validity of any given variant, the price drops rapidly. And for the type of evolutionary questions Dawkins is interested in, the coverage needed is far lower than 30× (you probably want to get a larger number of samples than a single high-quality sample).
After reading the supplements to the new Siberian paper I have a few general thoughts that I want to layout.
First, the clines vs. clusters considerations seem to be one we need to revisit. Like the expansion of Native American peoples ~15,000 years ago, it seems that the “Out of Africa” migration pulse happened so quickly that a lot of different groups emerged at the same time. In the new paper the earliest proto-“Ancient North Eurasians” can be modeled as most similar to the West Eurasian branch of humanity (sans Basal Eurasian), but with some minor component affinity to East Eurasians. It could be that this is a function of admixture between the distinct lineages. Or, it could be that there was a fair amount of substructure within the post-Basal Eurasian “Out of Africa” meta-population.
The problem with the idea of lots of structure within this population that I see is that it might depend on the plausible effective population sizes. I’d need to know more ethnography than I do, but it seems not impossible for ~10,000 humans to be highly structured in Paleolithic social contexts, even if they were close geographically. But, this would entail a great deal of xenophobia and likely inter-group conflict.
Second, I am convinced that there were earlier “Out of Africa” migrations. Many of them. As John Hawks pointed out at ASHG the Neanderthals and Denisovans seem to be descended from a migration of African hominins that dates to somewhere after 1 million years ago. This means they replaced hominins that were present in Eurasia for ~1 million years already. Geneticists and paleontologists have both also discovered suggestive clues to likely “proto-modern” human populations that were present and admixing before the rapid expansion of Eurasians and Australasians ~40-50,000 years ago. With more ancient DNA and subtle analysis, I think we’ll find that modern human absorbed some layers between that of Denisovans and Neanderthals and the most recent expansion.
Finally, I think multi-regionalism within Africa is between plausible and likely, and that major back-to-Africa migrations that modify/challenge “Out of Africa” are possible. We are learning a lot. But that means simple elegant models are falling by the wayside.
…Here, we report 34 ancient genome sequences, including two from fragmented milk teeth found at the ~31.6 thousand-year-old (kya) Yana RHS site, the earliest and northernmost Pleistocene human remains found. These genomes reveal complex patterns of past population admixture and replacement events throughout northeastern Siberia, with evidence for at least three large-scale human migrations into the region. The first inhabitants, a previously unknown population of “Ancient North Siberians” (ANS), represented by Yana RHS, diverged ~38 kya from Western Eurasians, soon after the latter split from East Asians. Between 20 and 11 kya, the ANS population was largely replaced by peoples with ancestry from East Asia, giving rise to ancestral Native Americans and “Ancient Paleosiberians” (AP), represented by a 9.8 kya skeleton from Kolyma River. AP are closely related to the Siberian ancestors of Native Americans, and ancestral to contemporary communities such as Koryaks and Itelmen. Paleoclimatic modelling shows evidence for a refuge during the last glacial maximum (LGM) in southeastern Beringia, suggesting Beringia as a possible location for the admixture forming both ancestral Native Americans and AP. Between 11 and 4 kya, AP were in turn largely replaced by another group of peoples with ancestry from East Asia, the “Neosiberians” from which many contemporary Siberians derive. We detect additional gene flow events in both directions across the Bering Strait during this time, influencing the genetic composition of Inuit, as well as Na Dene-speaking Northern Native Americans, whose Siberian-related ancestry components is closely related to AP. Our analyses reveal that the population history of northeastern Siberia was highly dynamic, starting in the Late Pleistocene and continuing well into the Late Holocene. The pattern observed in northeastern Siberia, with earlier, once widespread populations being replaced by distinct peoples, seems to have taken place across northern Eurasia, as far west as Scandinavia.
The preprint is very interesting and thorough, and the supplements are well over 100 pages. I read the genetics and linguistics portions. They make for some deep reading, and I really regret making fun of Iosif Lazaridis’ fondness for acronyms now.
I will make some cursory and general observations. First, the authors got really high coverage (so high quality) genomes from the Yana RS site. Notice that they’re doing more data-intense analytic methods. Second, they did not find any population with the affinities to Australo-Melanesian that several research groups have found among some Amazonians. Likely they are hiding somewhere…but the ancient DNA sampling is getting pretty good. We’re missing something. Third, I am not sure what to think about the very rapid bifurcation of lineages we’re seeing around ~40,000 years ago.
The ANS population, ancestral by and large to ANE, seems to be about ~75% West Eurasian (without much Basal Eurasian) and ~25% East Eurasian. Or at least that’s one model. Did they then absorb other peoples? Or, was there an ancient population structure in the primal ur-human horde pushing out of the Near East? That is, are the “West Eurasians” and “East Eurasians” simply the descendants of original human tribes venturing out of Africa ~50,000 years ago? Also, rather than discrete West Eurasian and East Eurasian components, perhaps there was a genetic cline where the proto-ANS occupied a position closer to the former, as opposed to some later pulse admixture?
Without more ancient DNA we probably won’t be able to resolve the various alternative models.
You may have noticed I haven’t been posting much. Busy with other things, like ASHG, work, family, etc. I don’t normally post “won’t be posting often” notices, as no one really cares much about blogs…but when I go into lower production mode people sometimes worry. No reason to worry.
There was talk about ASHG about the Amy Harmon article, Why White Supremacists Are Chugging Milk (and Why Geneticists Are Alarmed). It seems most of the geneticists I know personally were contacted by Harmon at some point over the last two years. A lot of work went into this. Many of our quotes were obviously not used. That’s called journalism.
There was a period when many frog-Nazis were on Twitter brandishing a particular STRUCTURE bar plot (since frog-Nazism has been severely purged by Twitter I see this far less often). I understand that many journalists and people of the “chattering-thinking” classes are strongly influenced by what they see on Twitter in terms of their perception of what’s going on in the world.
Additionally, to be honest for many white people racism is somewhat an abstraction. They need to make recourse to instrumental variables. The SNL election night sketch which shows white liberals talking about how it’s never been so bad, and black comedians nodding along, illustrates a real trend, and that is that many white liberals feel like there has been a massive upsurge of racism over the past few years.* But as a nonwhite person who has lived in this country since the early 1980s, it is clear that America is far less racist than it was back then, and our society has been defined by a gradual decrease in racial prejudice. White support for laws banning interracial marriage went from about 25% in the 1980s to 10% in 2002, when the question stopped being asked because it was such a marginal viewpoint.
A story about the social and political of implications evolutionary population genetics is a reasonable one. And, it might make a somewhat interesting academic paper as well. But the prominence of this piece to me cuts to a deep disagreement about the nature of racial conflict and difference within human societies. Immanuel Kant’s abstract and intellectual reflections on race may be alarmingly white supremacist to many moderns, but the profitable character of exploitation of sugar and the utility of slavery in the West Indies, and the rise of the West in a much more robust manner as signified by the McCartney Mission in the 1790s, was far more important in shaping the emergence of a very vigorous white supremacist ideology in the late 19th century which culminated in Madison Grant and Lothrop Stoddard.
I enjoy discourses on the intersection of race and genetics as much as the next person. I write them myself. But the most concrete thing I can do for the “racial question” is what I’m doing already: participating in the amalgamation of very distinct pedigrees and producing Americans related to a much larger fraction of the world’s population. White Americans who believe in the cause of racial social justice and anti-racism can do something very easily if they so choose: select a non-white partner and produce mixed children. If you are already partnered up, encourage your children to do so. This will make a bigger difference than retweeting how great diversity is, while not living it in your own life. For white progressives, do understand that your nonwhite allies notice the overwhelming pallor of the types of people who become and remain your intimates. You spend an afternoon on a racially diverse panel. Why not spend life in a racially diverse manner? Because I am a political outsider to these issues nonwhites probably feel more comfortable telling me how they perceive you don’t have much skin in the game. An ounce of action is worth a pound of talk (also, you can proactively give money to nonwhite people from your own disposable income).
The above is not a troll at all. I’m not the sort of person who thinks that the type of person another human being becomes friends with, or partners with, is my business. Do as you wish. But if you accept the premises of most forms of anti-racist talk, then Norman Podhoretz’s 1963 essay which enjoins action still applies.
This Elizabeth Warren fact-check by the Daily Caller Foundation’s Emily Larsen is pretty good. Having to listen to political pundits talk about ancestry testing all week has been painful. More need for education….
ASHG photo that I find most amusing.
As most of you probably know, the human genome still has gaps. I felt this year more people talked about those gaps, and how to fill them in. Also, lots of African genetics (this was by plan).
May write some more tutorials soon. Depends on the time.
The Slow Burn podcast ended with talking about Juanita Broderick. The Broderick allegations really have shot into prominence over the last few years. But if the Republicans knew about them in detail, that does make their determination to impeach Bill Clinton far more comprehensible.
I don’t have much to say about the Khashoggi thing you haven’t heard elsewhere.
A new analysis of CEU mutation rates is there is an age effect, most mutations are paternal, and, there might be variation in increases in mutations with older individuals by family.
* Most of my white friends tend to point to particular media anecdotes. As a nonwhite person I have not perceived any difference, and I travel in various parts of the country. Your experience may vary.
There were five parts of Warren’s DNA that signaled she had a Native American ancestor, according to the report. The largest piece of Native American DNA was found on her 10th chromosome, according to the report. Each human has 23 pairs of chromosomes.
“It really stood out,” said Bustamante in an interview. “We found five segments, and that long segment was pretty significant. It tells us about one ancestor, and we can’t rule out more ancestors.”
He added: “We are confident it is not an error.”
The proportion of ancestry is not large. But it is clearly there. They compared to the Utah white and British European 1000 Genomes populations, which is a good standard for Old Stock Anglo-Americans. She’s clearly an outlier, with about an order of magnitude more “Native American” ancestry. So it’s unlikely to be some artifact.
There is some talk in the article about lack of reference populations. But remember, the key is to identify Native American ancestry, so all of this should coalesce back 10-15,000 years ago. Compared to the divergence from Northern Europeans, this is going to jump out against the genetic background.
So does Elizabeth Warren have Native American ancestry? 99% sure that that is a yes. Is she going to run? Well, I wouldn’t say 99%, but that seems likely too….
(I doubt she’ll do it, but it would be neat if she released her raw results)
Update II: Some quick responses to comments. I’m going to address the genetic aspects. I’ll leave the cultural and political angles to others.
The analyst, who I know personally as well as by reputation, did exactly what I’d have expected he do with this data. So nothing atypical in terms of method/analytic pipeline. You can download and use the tools yourself!
The number of markers used in the analysis, 660,000, is a good number. Sufficient most definitely for the local ancestry analysis done here (and probably on some level necessary to gain a high level of confidence).
Some people wonder about the sample size of the reference population. Is the number sufficient? Yes, for the purposes of this analysis. For the scope of the questions asked. You aren’t looking for recent relatives, you are looking for a good representation of the genealogical networks from a given geography/ethnicity. The Utah whites are an industry standard sample set that is well known. The British data set in the 1000 Genomes is also pretty well known. Both seem representative of people of Northwest European heritage, a set of populations which are genetically very similar to each other.
People are asking about the robustness of this result. One thing you have to remember when comparing reference sets against an individual is that the genetic distance of the reference sets is important. Applying local ancestry to an individual of Dutch ancestry with training sets of Germans and English heritage is going to produce results, but the training sets themselves are going to overlap in some ways. Now, if you take someone with Dutch ancestry and do local ancestry for English vs. Javanese ancestry, then you’re going to get really clear results in comparison.
Some serious individuals are questioning the representativeness of the European panel and the Native American panel. As well as the lack of Siberian groups, who are closely related. But we know that Warren’s family background is such that a shift toward a Northeast Asian group is likely to be Native American. Not Chukchi. Further analysis could confirm, but the most likely hypothesis is that this is a woman of Northwest European ancestry with some Native American ancestry. Other models could fit these results. But those are not likely models in the first place (also, the PCA on Native American groups makes it likely that she is not Siberian, and she is not shifted to the northern groups).
A huge issue is that people are worried about the representativeness of the Native American groups. First, if you are looking for someone with indigenous North American ancestry, Mexican groups are sufficient. If anything this will reduce your power to detect, not produce false positives. Second, look at the plot, Warren’s haplotype is positioned between Canadian and Mexican natives:
People are interpreting this local ancestry method, which assigns segments of the genome to particular populations with a probability, to the point estimates provided in most consumer genomics results. From what I can see, they assigned 0.4% of Warren’s genome as Native American. But 8% was not assigned. This is almost certainly mostly European, but some of it may be Native as well. Basically, the method here was less about assigning a specific proportion, and more about testing whether it was likely she had detectable indigenous American ancestry (she did), and, the range of periods in which that ancestry could have admixed into the Northern European genetic background. This is not comparable to the estimates you are getting from personal genomics tests.
One way you can try to assess whether these are artifactual is to compare an individual to populations of known ancestry and see the distribution of empirical results. Warren’s results are very atypical in comparison to Northern European reference sets. If this is a “false positive” due to the training sets, then you would expect the same type of problem to crop up when test out sample individuals.
Some are asking whether Warren is just a typical white American. You would need to do apples-to-apples comparisons. But my intuition is that she’s not. Most Old Stock white Americans probably have a genealogical relationship to Native Americans, but they may not have any segments of DNA because it is too far back. Warren is part of the minority of white Americans who have detectable Native American ancestry.
Basically, I think it is very likely that Warren has Native American ancestry. Follow-up analysis would probably just increase our confidence.
I pinned the above chart to my Twitter profile because I’m “trying to make it happen.” It was David Mittelman’s idea, and the data was courtesy of ISOGG, but putting it together as a graph has really brought home to people how the consumer genomic landscape has changed over the last half a decade.
The plot to the right, which shows a smoothed chart of the total number of kits over time, is also important.
I recorded a podcast for the Urbane Cowboys last week. It should go up today, so watch for it. I talked about a variety of topics, so I don’t know how it will drop in regards to editing.
Was talking to a friend about the importance of emotion in reasoning, or at least how emotion allows us to reason better. He asked about books, and Descartes’ Error came to mind. But I’ve read about critiques of its interpretation of the history of science and philosophy, though I think the big picture conclusion is probably still valid.
Will be at ASHG this week. Mostly I’m going to learn more about African genomics. Not as much on pop-gen as in previous years. If I approach your poster, don’t worry that I’m going to tweet or write about. Just be cool.
I’m listening to John Keegan’s A History of Warfare on Audible. To be honest I think I’m much better at reading than listening. This shouldn’t be surprising. In courses, I generally prefer to learn from the textbook as opposed to listening to lectures. And I have a lot of experience reading over my lifetime. Less so listening.
Xunzi: The Complete Text has been a difficult read for me. I’ve gone back and reread passages several times. It is definitely on the discursive side. That being said, I have come to a strange observation: Xunzi’s view of religion is similar to Ludwig Wittgenstein’s. Here from the Stanford Encylopedia of Religion:
He opposed interpretations of religion that emphasize doctrine or philosophical arguments intended to prove God’s existence, but was greatly drawn to religious rituals and symbols, and considered becoming a priest. He likened the ritual of religion to a great gesture, as when one kisses a photograph. This is not based on the false belief that the person in the photograph will feel the kiss or return it, nor is it based on any other belief. Neither is the kiss just a substitute for a particular phrase, like “I love you.” Like the kiss, religious activity does express an attitude, but it is not just the expression of an attitude in the sense that several other forms of expression might do just as well….
This seems similar to Xunzi’s belief that religious rituals were an important part of life, even if supernatural beings did not exist. Though Wittgenstein seems to have had some sort of fundamental mystical religious beliefs, whereas Xunzi was more of a naturalist.