A Song of Ice & Fire: the maesters lie!

Below in my post on there were two comments which I think are important to keep in mind. First, George R. R. Martin has admitted that accounts of distant lands and ancient times may not be precisely accurate in a modern sense, but rather hew to the sort of scholarship one might have found in the High Medieval period which his world is generally an analog with. Second, one commenter points out that the long lineages asserted in Martin’s books make no sense in light of high rates of elite conflict and attested extinctions and near extinctions. The problem is the same one you see in uniparental DNA lineages (mtDNA and Y) and surnames which come down through one sex. In Augustan Rome the elite families were going extinct, to the consternation of the princeps. But it was basic math. If family lines are perpetuated through males, and a certain proportion of families in each generation do not produce males who live to adulthood to perpetuate the line, then there is going to be a slow extinction of the old lineages. As a stylized example, if a given nuclear family has a 95% chance of having an adult son each generation, a quite high rate, within 15 generations more than half of these lineages would still be extinct. That’s 375 years. The idea that the Starks would be able to maintain the paternal lineage for thousands of years, let alone keep their status as the apex lineage, is simply unbelievable.

Because I’m interested in biology I naturally fixated on the genetic aspects of Martin’s secondary-world which raised my ire, but really they’re minor issues in the grand scheme.* Rather, it’s the broad geographic and historical sweep which leave me skeptical of the world-building. George R. R. Martin’s complex and multi-textured narrative in a world which is recognizably High Medieval, but not exceedingly isomorphic with our own, has reshaped fantasy over the past generation, engendering many imitators. Martin’s protagonists are human in a fully developed fashion which makes them more believable to readers who aren’t 12 year old males, or late/post-Victorian dons. Aragorn would never have had a bastard. The true blood of Númenor was not capable of such things by the nature of his being. By introducing a dark and realistic pre-modern sensibility akin to Bernard Cornwell’s Martin’s work has won praise for its verisimilitude. A world not just of imagination, but perhaps could just be.

And yet when you take a step back much does not make sense. The First Men arrived ~10,000 years ago. But they all spoke the same language even ~2,000 years ago, when the Andals arrived. Two thousand years after the Andal arrival different peoples on the continent sized Westeros speak with different accents. The dates given for the arrival of the First Men in particular can be thought of as legendary, but they are recorded as being a Bronze Age people. Therefore their arrival must have been long ago. The Andals have a more well attested history, because they are the dominant people of Westeros. The level of cultural diversification simply does not comport with what we know about evolutionary rates of change of societies on the scale of thousands of years. Very little happens on Westeros in comparison to our own world, where the rate of change has been much faster since the emergence of agriculture.

Second, institutions such as the Night’s Watch are totally implausible. Societies which are of High Medieval nature are unlikely to be able to plan for disasters on the order of thousands of years. Nor are the men of the Night’s Watch likely to maintain neutrality as to goings on south of the Wall for so many generations. Humans exhibit group conformity and cohesion around ideals, but these decay over time, and a time of selfishness always breaks free to tear down institutions before they are built back anew. What Martin has constructed in his secondary-world is a landscape which is not nearly as subject to episodic regressions and cycles of cultural efflorescence as our own, despite its peculiar climatic regime which would militate in favor of such a pattern. It is a world of radical cultural stasis and torpidity. In ways they do not resemble modern humans at all, but other groups of hominins.

OK, to take a step back, I’ve really lost it, haven’t I? The reality is no secondary-world replicates the complexity and nuance of the real world in terms of the religions, languages, and peoples, which we see around us. None of them are able to have as much historical background as the real world. In fact if someone attempted to do this they’d not be able to write novels! Secondary-worlds by their nature have to be stripped down. The same problem crops up in far future science fiction. If it is too exotic and changed it is simply not able to be turned into a narrative which we as modern humans could relate to. Authors like George R. R. Martin have to strike a balance between plausible social texture, exoticism which doesn’t leave us incredulous, and simplification which does not render the canvas blank. It’s a tough balancing act. They make different choices, and I respect Martin’s.

* If the Targaryen ability to master the dragons is genetic, then they should have followed the Walder Frey strategy and bred themselves an army.

Math kills the analogies, a good thing

A few weeks ago an interesting article was published in PLOS Biology, Not Just a Theory—The Utility of Mathematical Models in Evolutionary Biology. Importantly the authors emphasize the importance of ‘proof-of-concept’ mathematical models, which lay out verbal logic in a way that might expose contradictions. The emptiness of many verbal models was well illustrated to me in Jerry Coyne and H. Allen Orr’s survey of “models” in . There wasn’t even an internal check on the speculative frenzy. Mathematical models are also analogy killers, which is usually a good thing because people often end up obfuscating rather than illuminating when they have to make recourse to these verbal structures. Since I promoted a few weeks ago, I thought I’d also higlight Sarah Otto and Troy Day’s . It really covers all the bases, though it might be heavy-going for some.

Speaking of math and biology, Lior Pachter has a non-jeremiad post up, The two cultures of mathematics and biology, which is worth reading in full. It’s a fact that many biologists are the sort of scientists who have the attitude toward math which takes the form, “yes, some equations for statistical testing, just not too much.” But things are a changing. I’ve never talked to a biologist who has complained that they had to take too much math, rather, it’s always the other way around. With the explosion in genomics some level of mathematical fluency now extends beyond population biological fields within ecology and genetics. As an example, a friend who was trained as a biochemist told me that he had to take a course on graph theory as a postdoc to keep up with the demands of his research. But one portion of Lior’s post caught my attention:

Biologists have their papers cited by thousands, and their results have a real impact on society; in many cases diseases are cured as a result of basic research. Mathematicians are lucky if 10 other individuals on the planet have any idea what they are writing about.

But these aren’t comparable! Just because a paper is cited thousands of times doesn’t mean that those citing understand the paper. Case in point, W. D. Hamilton’s papers are often cited, but not understood to any formal depth. With the mathematicization of population genomics and phyologenomics I’ve seen the problems of specialization and incomprehensibility which are common in math and theoretical physics creeping into biology. A few years ago I mentioned offhand to an acquaintance how difficult some of the mathematical and statistical logic in his papers were. He named a half a dozen young researchers who he was confident could vet said papers. When I brought this conversation up with one of those very researchers he admitted to me that some of the work he was asked to “peer review” was so opaque even to his mathematically trained mind that he was at a loss. Obviously I have no solution, but the event horizon of the small puddles of research communities barely able to communicate in the vast sea of scholarship is now upon us in some areas of biology. Our own Tower of Babel is at hand.

Genome sequencing of newborns

This is coming, Genome Sequencing in Babies to Begin as Part of Study, with high risk cases first:

Stephen F. Kingsmore, director of the Center for Pediatric Genomic Medicine at Children’s Mercy and a leader of the study, says he expects any expanded program of newborn genome sequencing to be applied to some of the approximately 14% of the four million babies born in the U.S. each year who are admitted to neonatal intensive care units. Genome sequencing can be helpful when babies don’t exhibit typical symptoms of known diseases or have rare or unknown genetic conditions, he says.

There is “strong logic and good evidence that in acutely ill babies this makes sense. It is not clear at all it makes sense in a healthy baby,” Dr. Kingsmore says.

Right now I agree that the benefits for sequencing high risk newborns seems much more obvious than for healthy infants. But it’s just a matter of time that longitudinal studies will want to include healthy infants, who after all have varying degrees of later-in-life risks with heritable components. Speaking of which:

But Nicholas Catella, an engineer from Jamaica Plain, Mass., says he wouldn’t be interested in newborn screening unless his child’s health was at acute risk. Mr. Catella, who has two children, ages 3 years and 16 months, says sequencing might reveal information about health risks like Alzheimer’s disease, which occurs later in life and for which effective interventions aren’t yet available. In the case of his healthy children, “I would need a good reason to want that information,” he says.

This is a common objection. But the issue really isn’t new, it began when people developed tests for Huntington’s disease. What’s the benefit in knowing your child is highly likely to develop a fatal disease by the time they’re 50 for which there is no viable cure for? It’s a matter of choice, but it strikes me that knowing your risk of dying at a particular time would change your life calculations a great deal. Many people live full lives by the time they’re 50.

Why genomic transparency matters

Gina Kolata has a new piece in The New York Times, In a New Approach to Fighting Disease, Helpful Genetic Mutations Are Sought. The gist is pretty straightforward: some people seem to have compensatory mutations which can mask the effects of well known deleterious variations. So, the man who is the focus of the article has a variant well known to result in early onset Alzheimer’s disease. In fact, this has been the case in his extended pedigree. But he does not exhibit any symptoms into his 60s. But this part caught my attention:

Now, a year later, “we are in this interesting place between excited and frustrated,” Dr. Friend says. They analyzed data from over 500,000 people and found 20 who seem to be protected from a fatal disease. But because of privacy issues there were no names attached to the data.

Four of the subjects are in China. Dr. Schadt and Dr. Friend are trying to find a way to contact them, but “it is very difficult,” Dr. Schadt said.

Dr. Friend and Dr. Schadt are now looking at other databases that might make it easier to contact subjects, but also decided they need to try different approaches. One will be to simply ask healthy people to let them sequence their DNA, putting out the word that they are looking for volunteers, perhaps hundreds of thousands of them. People who agreed would be contacted only if they appeared to be protected from a fatal disease.

I suspect the main long term benefits of sequencing is going to be when the scale really ramps up, and we start to soak up all the rare variants. Kind of like the strategy of Long Term Capital Management hoovering up pennies. OK, perhaps I shouldn’t have used that analogy, but I think that’s really where the future in actionable genomic medicine is going to be. And that brings up the issue of genetic privacy and comfort in the broader public with this sort of data sharing. So yes, I still think that the “Rumors of the death of consumer genomics are greatly exaggerated”. This baby hasn’t been born yet. We’re not talking a 9 month gestation, more like 9 years.

The World of Ice & Fire isn’t the Silmarillion

For Christmas I gifted myself a physical copy of . I actually went down to the local bookstore, but balked when I noted that Amazon charges while they were offering $50 retail. I don’t go for cheap in every case, but that was a ridiculous difference. After reading the reviews and browsing a bit at the bookstore (yes, I’m a bad person!) I wasn’t too surprised with what I received (no, I was not getting the ebook version because the illustrations matter for this, and ebook renderings are often suboptimal). It’s not , because George R. R. Martin is just not the “world creator” that J. R. R. Tolkien was. I think it’s fair to say that Martin’s world has been created as a vessel for the stories, while Tolkien’s narrative served to flesh out his world. As someone on an Amazon review stated much of what you find in will be online soon enough, so why purchase the book? Mostly because though many of us are fans of Martin’s series we’re no longer obsessively reading over websites like Westeros. We’re OK with getting the authorized gist.

And that’s what this book is. The subhead is mildly misleading, because most of the text is predictable if you read between the lines of the book, and fill in missing pieces of the histories alluded to in passing. Also, some of it strikes me as a bit hasty. In online interviews Martin seems to basically admit that he had to create some elements of the background on demand, because he actually didn’t have anything in mind. This reminds of Tolkien complaining that he received letters from bontanists demanding a more thorough treatment of the biogeography of the plants of Middle Earth.

My main gripe is that I could have done without the section on the Targaryen kings. Perhaps this is setting the scene for prequals to the current series, but that seems getting ahead of yourself if I may say so. Also, the Targaryen practice of brother-sister royal marriage is probably not as genetically sustainable as it seems to be in the family tree depicted at the end of the book (no, I haven’t calculated the inbreeding coefficient). I say this after reading , where it seems rather obvious that some royal lines simply expired due to inbreeding.

Finally, I was rather surprised that it seems that the Martin’s world is inhabited by three species of humans. The inhabitants of the southern continent, originally labelled Sothoryos, seem to be analogous to a robust Australopithecus. The people of Ib seem to be Neandertal analogs. Both of these populations are explicitly stated to not be inter-fertile with other human populations due to post-zygotic barriers. I have to wonder if this was just created on the stop to add exotic color to the book, since it seems pretty outlandish.

Note: I have not watched the HBO show. Nor do I plan to in the near future.

Open Thread, 12/28/2014

is a great book. A bit theory poor, but data rich. Much more readable than . I don’t recommend it enough, and I should reread it someday (though it’s got a big queue ahead of it). Also, Kevin Phillips’ is excellent. I avoided it for a long while because Phillips had a history as a political operative, so I thought it would be superficial. I was very wrong.

In the post below on Planet Fitness my wife thought that I was going to mention that I’ve gotten a bit obnoxious and insufferable about working out. About 6 months ago I decided to make a life change, and now I lift and run 5 miles 2 out of 3 days. It’s gotten extreme enough that before travel I check to see if the hotel has weights, or if there’s a good gym nearby (here in Palm Springs, where I’ll be when this post goes up, that isn’t hard). My goal is lose some fat and gain some muscles. The latter is pretty much one, I’m just working on definition now. As for the fat, I still have some work to do around my stomach though it’s getting much better (I don’t really have appreciable fat elsewhere, such as moobs).

I’m curious what readers who have a fitness regime do. For example, what do you think about protein shakes? I did creatine for a bit, but I don’t want to get totally jacked so I stopped. Running before or after lifting? I seem to feel much better running after I lift. What works for you in terms of diet?

Merry Christmas!

Merry Christmas! No one in my family is Christian (inclusive of first degree in-laws) so there’s no explicit religious content in the celebration of the holiday, but it’s still a big deal. I think that a mid-winter holiday is a pretty straightforward aspect of “evoked culture” in the temperate climes. That is, it was bound to arise, and it is no surprise that modern Christmas was unable to slough off the many strands of European pagan custom and belief which threaded these mid-winter festivals together.

I’m going to queue the open thread for Sunday now as I’ll be sporadic checking in on this website for a bit.

A greener future is a high-tech future

700px-BIG_LEAF_MAPLES_HOHIn an article titled Restored Forests Breathe Life Into Efforts Against Climate Change, there’s an interesting portion which talks about how farming techniques relate to reforestation:

Around the world, trees are often cut down to make room for farming, and so the single biggest threat to forests remains the need to feed growing populations, particularly an expanding global middle class with the means to eat better. Saving forests, if it can be done, will require producing food much more intensively, on less land.

Life is about trade-offs, even if you don’t want to admit it. Organic farming uses more land to produce the same amount of food. Basically, it’s a luxury good if you can afford it (and highly profitable for agribusiness!). The poorest farmers in the world are organic producers because they have to. There are many downsides with industrial agriculture, but one of its upsides is that it produces the maximum amount of calories using the minimum amount of land. New England reforested in part because much of the farmland was abandoned due to low productivity (and the availability of much better land in the Old Northwest territories amenable to farms which could take advantage of economies of scale). One major tool of modern farming, genetically modified organisms (GMO), has been resisted and stymied for several decades by public suspicion and adherence to the precautionary principle (e.g., many types of plants which could be easily GMOed are not even in the United States). Most of the time environmentalists are quite skeptical of GMO because of the precautionary principle, but the fact is that “natural” local organic farming can have a much larger carbon footprint than something artificial. To some extent all of human life is touched by artificiality today.

27-shanghai-artist-impressionAnother developing trend which opens up the potential for rewilding spaces now given to human habitation, would be a transition toward greater density and urbanization. As someone who grew up in the Pacific Northwest it is striking that here you have a land of contrasts, as small rural towns dependent on logging decline, and the greater Portland and Seattle metropolitan areas have ballooned. Urban dwellers venture to the outdoors quite often, but they do not live in the wild. A shift toward density and vertical habitation would likely result in greater economic efficiency and reduced carbon footprints.

The irony is that the lowest impact future in relation to the environment may be the most ‘high tech.’ A world of mechanized farms growing bioengineered crops, meat cultures grown in vast industrial vats, and the predominant form of habitation being within organically developing arcologies which replace the megacities of today is positively out of science fiction. But, it would also be a much greener world than the ‘natural’ alternatives. With the exception of a scenario that includes mass die off of most of the human race.

American racial boundaries are quite distinct (for now)

Rashida Jones

Geneticists are people of their time. I’m rather sure that if Charles Davenport had written a book with the title today it would end with a far different moral, because the dominant Zeitgeist in regards to racial admixture in the United States is far different nearly 100 years on. In my post below where I review interesting aspects of the new study from researchers in David Reich’s lab and 23andMe, The Genetic Ancestry of African Americans, Latinos, and European Americans across the United States, I didn’t cover the variation in admixture in black and white Americans too much in detail. Partly that’s because this study only improved the bigger picture on the margins, and with finer geographic grain (though these were interesting obviously). We knew that the vast majority of white Americans who are not Hispanic do not have detectable non-European ancestry. It has also long been reported and verified that a substantial minority of the total ancestry of black Americans is of European origin, with a small Native American fraction as well. Additionally, this non-African ancestry in black Americans varies by geography as well as individual to individual a great deal.

euroSo I have to take issue when The New York Times posts articles with headlines such as White? Black? A Murky Distinction Grows Still Murkier. What genetics is showing is that in fact white Americans are shockingly European to an incredibly high degree for a population with roots on this continent for 400 years. If we removed all the history that we take for granted we’d be amazed that the indigenous peoples had so little demographic impact, and, that the larger numbers of people of partial African ancestry did not move into the general “white” population. This is in fact the case across much of Latin America, where many self-identified whites, blanco, have African and indigenous ancestry. But we do know the reasons for why North America was unique, a combination of a smaller indigenous population which underwent a mass die off, and folk migrations on a huge scale previously unimaginable in human history. Whole villages in Poland and Norway, not just working age males, decamped for the New World. The original Anglo settler stock on the North American seaboard underwent a period of incredible demography expansion driven by high birthrates, in particular in New England, which in the 17th century had some of the highest total fertility rates recorded in human history.

The peculiar nature of white Americans is evident in the figure to the left. You see that black Americans span the gamut from being mostly African to mostly European (I believe that individuals who are 100% European but state they are black are probably due to error in self-identification on the survey). Though it isn’t quite clear on these sorts of plots (yes, I know why there’s moderate opacity), the black American distribution of African/European ancestry is not symmetrical, but is skewed, so that a small minority of black Americans are more than 50% European in ancestry, while the majority are less than 25% European. With the Latino populations you see admixture with both Africans and Native Americans. Though typical Mexican people are presumed to be mixed between European and Native, most Mexicans seem to have low, but detectable, levels of African ancestry. This is almost certainly due to the attested slave population across the Spanish colonies. And, this is contrast to the situation in the United States, where even “Old Stock” Anglo-Americans whose ancestors have been coexistent with people of African origin for at least 250 years by and large.

My own hunch is that the contrast between Anglo-America and Latin America when it comes to admixture has a lot to do with the fact that a far larger proportion of the European settlers were female. This allowed for a total replication of European populations, norms, and mores, rather than enforcing a sort of synthesis, as was necessary in Latin America. In the Spanish colonies European males were initially very polygynous, establishing liaisons with many women, both indigenous and black. A modest stream of men from Europe could quickly “whiten” what had initially been a mixed first generation, resulting in a elite creole caste which was predominantly European, but whose Europeanization had been male mediated atop a foundational base which featured non-European women. This can explain with the mtDNA lineages are so much more indigenous than total genome content might lead one to suspect. In Latin America individuals with obvious non-European ancestry, such as Vincente Guerrero, could rise to positions of prominence, and forward the project of a European-dominated society. In contrast someone with mixed blood in the United States would have been socially marginalized, and had minimal prospects outside of a few exceptional cases (e.g., among the mixed race Creoles of Louisiana).

Of course even with balanced sex ratios relations across racial lines occurred. This brings us to the next step of a peculiarity in the ideology of white American racial supremacy: hypodescent. This is the rule by which mixed offspring inherit the racial identity and social status of the parent whose is of the inferior race. In the United States this operationally meant that children born to slave mothers of free white fathers were considered black, and condemned to slavery (this is in contrast to the official rule in Islam, where children of the master who were recognized were free). In some ways this practice seems similar to lack of rights which non-legitimate offspring experience in many societies. But in the American context it was highly racialized. The norm of hypodescent also resulted in scientific theories which buttressed it, such as Madison Grant’s contention that mixing between superior and inferior races always resulted in a population which resembled the inferior race (the law of “reversion toward the lower type”). Charles Davenport even went so far as to argue that admixture produced offspring inferior to both parental types, a form of hybrid breakdown.

It is entirely reasonable to argue that racial categories in the United States are blurred if one holds to a Platonic and essentialist view which resembles that which underpinned white racial supremacy and the law of hypdoescent. But as it is these views have no necessary scientific basis, and a percent or two of African ancestry in someone who is ~98 percent of European ancestry does not make them non-white in any rational sense. The 12 year old paper, Categorization of humans in biomedical research: genes, race and disease, has aged well in my opinion. A conclusion that 10 percent of whites in South Carolina are actually black because they have detectable African ancestry strikes me as crazy. But then, hypodescent also strikes me as somewhat crazy, though the rationale which drove it is also eminently understandable (i.e., the exclusion of illegitimate children and maintenance of a racial order). I hold that the racial lines are “blurred” only if you hold to the criteria which arose in the 17th and 18th centuries in the culture of the American South.

There is one aspect of paper and The New York Times article which I think is worth commenting on:

Most Americans with less than 28 percent African-American ancestry say they are white, the researchers found. Above that threshold, people tended to describe themselves as African-American.

Katarzyna Bryc, a 23andMe researcher and co-author of the new study, didn’t want to speculate about why people’s sense of ethnic identity pivots at that point.

I will speculate. The 28 percent proportion is about where African ancestry becomes salient, or not. In a de facto sense today the law of hypodescent applies only those who have visible African ancestry. In the United States these individuals are classified as black, no matter the preponderance of their lineage. A good example here is Rashida Jones, the daughter of Quincy Jones and Peggy Lipton. Quincy Jones has had some genetic analysis done, and he is about 2/3 African and 1/3 European. The expected value then for Rashida Jones is that she is 1/3 African in ancestry, though that may vary up or down a bit (her mother is an Ashkenazi Jew). Rashida Jones regularly plays white characters in film and television, and she does so because African features are not very evident in her. In contrast, her sister Kidada is just a bit more African in her features, and profiles of them growing up have indicated that while Rashida identified with her Jewish side (and still does), Kidada felt more black. In contrast, people who are 1/4th Asian, such as Keanu Reeves, are not subject to hypodescent in the United States, because Asian features are not as salient to white and black Americans, and white supremacy in the American South was generally aimed at blacks (my friend David Boxenhorn, who is Ashkenazi Jewish, finds it amusing that both my children have lighter eyes than any of his children).

Geetali Norah Jones Shankar
Geetali Norah Jones Shankar

But, with the rise in intermarriage and a clearly mixed-race Latino population the lines between the races will become blurred genetically more and more. A substantial number of American children today are multiracial, and that fraction looks to increase. If 23andMe did a survey of American genetics 25 years from now I’d be much more amenable to the interpretation that the media is putting on this survey. In one generation the world of the Baby Boomers, American, black and white, will be gone. With all that being said, I think it is highly likely that many people with known non-white ancestry (e.g., 1/4th Japanese, as a blonde haired and blue eyed friend of mine is) are going to identify as white. That means that to be “white” in the United States will be much more in keeping with the norm in Latin America, where a generally European appearance and preponderant ancestry are sufficient. And, it also means that race and racism will continue to be features of American life, just as they are in Latin America. Just differently.

Related: Steve says many of the same things.

Men have been more pro-choice over the past 30 years

abany2One of the weird things that annoys me about American politics is the idea that support for abortion rights is particular in some way to women. This is very common on the Left side of the political spectrum, but strangely for the self-described “reality based community” it has basically no correspondence with reality at the first pass.* All you need to do is look at the General Social Survey, which as a variable “ABANY” which asks respondents if it should be legal for a woman to have an abortion for any reason. The question has been asked every few years since 1977. I limited the data to whites only, and what you can see above is that year to year there is actually a correlation between men and women when it came to a “Yes” response. I was actually surprised by that. The jumps are not total noise, but reflect changes in the Zeitgeist (the rule of thumb is that the populace becomes more pro-choice during Republican presidencies and more pro-life during Democratic ones).

The second plot illustrates that for most of the years since 1977 men have supported abortion on demand at a higher clip than women. It doesn’t prove anything, except that reality is a little more “problematic” than some people who regularly call in to NPR might think (that’s what triggered this post).

* If you look close, there is evidence that a smaller well educated segment of liberal women are particularly intense about abortion rights.