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 Gene Expression Blog

Michelangelo-David_JB01About a year and a half ago I decided to get serious about my health. The primary reason had to do with the fact that I have children, and I wanted to reduce my risk of mortality as well as morbidity (yes, I have life insurance). A more specific reason to me is that for years my blood sugar has been on the high end of normal. Not pre-diabetic, but too close for my comfort. This is not abnormal for South Asians. And, my father developed type 2 diabetes around my current age (some context, he’s 4 inches shorter than me, and was a bit heavier and much paunchier than I’ve ever been). Within a combination of lifting and running, and mild changes to how I eat (more “Paleo”, though I’m not strict about it), I’ve gone from 155-160 lbs to 145-150 lbs (I’m 5’8). My body fat has gone from ~20% to ~15% from April 2014, to right now.

But I still have a distance to go. I want to push my body fat percentage closer to ~10%. Part of it is health, but at this point much of it is aesthetic. A friend of mine finds this all quizzical, since I haven’t been single in more than 10 years. But then again, he’s single, so what does he know about motivations? The reality is that everyone is not beautiful, and that almost everyone can get more beautiful. And that’s a good thing, and not just because it’s a social construct. Eating junk food and being lazy feels good too. But it doesn’t make you feel good about yourself.

The low hanging fruit is gone. At this point I’m running about 3.5 to 4.0 miles 4-5 days a week, and hitting the weights a similar number of days. Though I think I’m making slow but steady progress, I’m worried that I’m trying to do too much. E.g., am I running so much that I’m losing muscle mass? (I’m starting to suspect this) Do I need to eat more? Do I suffer from low T? There are lots of questions I have.

Of course you can go to bodybuilding.com and “get all the answers.” But you then know how that goes. Next there are informative websites like Skinny-Fat Transformation. What’s one to believe? I believe in personal experimentation, so I think I can get there by iterating. But it’s a tough haul, and I’d like to cut a few corners. (though one thing that’s consensus is that pull-ups are good)

So I’m putting this post up mostly to get reader feedback. My ultimate goal is to get down to the body fat percentage above, and gain definition. I’m not aiming for a lot of bulk. I’m only 5’8, and I don’t want to turn into what I like to term the “brick-guys” (the guys build like bricks). What’s worked for you? What’s not? People of South Asian ancestry especially would be useful.

Note:
I have a very young looking face and my skin hasn’t aged much at all, so one issue that I suspect I have is a lot of subcutaneous fat. My suspicion is that this means that it’s not for me not to look smooth and fatty.

 
• Category: Science • Tags: Fitness

51D2RoDDkXL._SX329_BO1,204,203,200_ A friend sent me a link to this long piece in The New Republic, What’s a species anyways?. Its subtitle is “The search for the red wolf’s origins have led scientists a new theory about how evolution actually works.” This is wrong. In fact, the article itself admits that there’s nothing revolutionary here. You just need to get to the second half of the piece, where the truth, as opposed to sensationalism, steps front and center. Many types of biologists have different ideas about what a species is. Often they are divided by disciplinary focus; phylogeneticists have different priorities than evolutionary geneticists. My friend John Wilkins wrote a book on the issue, top to bottom, Species: A History of the Idea. John’s a philosopher of science, so he has a precise take. Working biologists are often not so clear, and that’s sort of the point. In Speciation, a book co-written by two evolutionary geneticists (that you should read!), the authors are frank that their idea about what a species is is purely instrumental. That is, what are their end goals, and what does the species concept get us? The biological species concept, which for many is the species concept, is optimal for mammals. But less relevant to most of the tree of life, and even within mammals it’s not absolute, but just a rule-of-thumb.

519gldjJoAL._SY344_BO1,204,203,200_Bob Wayne is almost certainly right that the red wolf is a stabilized hybrid to a first approximation. He has the best genomes in the business of canids that I know of, and his 48,000 study was broadly persuasive in any case. The major issue isn’t scientific, it’s political. The federal government needs a clear and distinct set of criteria for the Endangered Species Act, but species are not really a clear and distinct concept.

Ultimately the question has to be what’s the point? That’s really how biologists figure out what species concept to use. To put my cards on the table it strikes me that a more honest and useful end goal is to focus on an ecological species concept. That way government bureaucrats wouldn’t be reduced to arguments about “genetic purity.” And I say this as a geneticist!

 
• Category: Science • Tags: Genomics, Red Wolf

ejhg2015233f1

Claudia_Cardinale_1963 The question of Italy population genetic structure comes up rather often for various reasons. I haven’t visited this topic in much detail since reading Consanguinity, Inbreeding, and Genetic Drift in Italy, a very old book using classical genetic techniques. L. L. Cavalli-Sforza did not find much structure in Italy at the time, but it turns out that there wasn’t enough power in the methods. I have some access to Italian data sets and I can tell you that there is a lot of variation. Sicilians in particular are mixed in ways unique outside of the Iberian peninsula A few years ago using the PopRes data set Peter Ralph and Graham Coop found in The Geography of Recent Genetic Ancestry across Europe some interesting facts about Italy:

In addition to the very few genetic common ancestors that Italians share both with each other and with other Europeans, we have seen significant modern substructure within Italy (i.e., Figure 2) that predates most of this common ancestry, and estimate that most of the common ancestry shared between Italy and other populations is older than about 2,300 years (Figure S16). Also recall that most populations show no substructure with regards to the number of blocks shared with Italians, implying that the common ancestors other populations share with Italy predate divisions within these other populations. This suggests significant old substructure and large population sizes within Italy, strong enough that different groups within Italy share as little recent common ancestry as other distinct, modern-day countries, substructure that was not homogenized during the migration period. These patterns could also reflect in part geographic isolation within Italy as well as a long history of settlement of Italy from diverse sources.

There were limitations in terms of how much geographic specificity the PopRes data set provided them, so there was only so much you could say. One hypothesis could be that unlike much of Europe deep local structure within the Italian peninsula predating the Roman Empire persists to this day. The Latinization of Italy then during the late Republican and early Imperial period could be thought of primarily as a matter of cultural diffusion and elite emulation. This stands to reason in part because much of the Italian peninsula was inhabited by peoples who were already speaking languages very close to Latin. But, another possibility is that this deep structure exists became of more recent migrations. For example, the existence of Magna Graecia in southern Italy and Sicily was due to the migration of males from Greece in the centuries before the rise of Rome. The genetic distance of this population would be inflated due to this gene flow, and if Italian demographic history is such that gene flow across regions is low, then it would persist.

italyBut things have changed since 2013. We know a fair amount more about European genetic history, thanks to ancient DNA. Just read Ancient human genomes suggest three ancestral populations to get a flavor. In short, it turns out that most European populations can be modeled as a three-way admixture, between one group with ancient Middle Eastern affinities, but different from modern Middle Easterners. Modern Sardinians are very close to this group. A second group are the indigenous European hunter-gatherers, who presumably expanded after the retreat of the tundra and had deeper roots in the continent, possibly at least back to the Gravettian period. Finally, a third group is a compound with a different Middle Eastern group, the European hunter-gatherer ancestry, and an ancient North Eurasian population more distant to other West Eurasians.

ejhg2015233x3 Most readers of this weblog are familiar with this song and dance. Now I want to submit new results from a paper in EJHG, The Italian genome reflects the history of Europe and the Mediterranean basin. A minor nit: I would assume that the Italian genome reflects the history of Europe and the Mediterranean basin! It would be really surprising if the Italian genome reflects the history of East Asia and the South China Sea!

What immediately jumped out for me about the results form this paper is that it seems clear that all non-Sardinian populations exhibit equal distance to Sardinians. That is, there is no “Sardinian-cline” in these data. Perhaps there are populations on the mainland that do exhibit a Sardinian-cline, but they haven’t been sampled in this study. What does this mean? The circumstantial evidence is strong that there was an intrusive population across Europe which arrived from the steppes spread across Northern Europe about ~4,500 years ago. The linguistic evidence tends to bind the Celtic and Italic branches of the Indo-European language family, so it seems the case that there was likely an intrusive population from Northern Europe that arrived sometime between 500 BC, when the Italian populations start to edge into history, and 2500 BC, when the Indo-Europeans swept Northern Europe. These people would presumably have amalgamated with the original Sardinian-like group. The best work suggests that though Sardinians have the most of this ancestry, it is still predominant in Southern Europe overall. It is curious then that the Sardinian fraction is so low, and, that it is relatively even. In fact, it is lowest in the southernmost Italian groups, and highest in Lombdary! Part of this is probably because Sardinian is not the same as Sardinian-like farmer. But I still would have expected some cline (I presume the Sardinians shifted toward the mainland are due to migration from the mainland). On the other hand, there is a large north-south gradient that you can see on the admixture plot .

ejhg2015233x5 The plot to the left is too small to make out well, but as people allude to Italian population structure in a world-wide context, this PCA does just that. The bright green are the Southern Italians, the bright light blue the Central Italians, and the red the Northern Italians. You see that the Southern Italians are shifted toward the Middle Eastern groups, while the Northern Italians are closer to groups like the Spanish and French. To the top right are Northern European groups, in purple, and the bottom right are Mozabites, with Turks in dark green in the middle, shifted toward Italians. Sardinians occupy the far left. As you can see, contrary to a commenter earlier this week, Italians of all stripes are not that distinct from other Europeans.

But, Southern Italians, and from what I have seen in private data Sicilians in particular, are distinct because of a possible admixture signal with exotic groups you don’t normally see in Europeans. If you look in the supplements the possibility becomes clearer. There is a lot of evidence that this admixture is North African. You see this in the ADMIXTURE plots in the supplements, as well as the IBD sharing patterns. The South Italian groups are enriched with the Mozabites and Moroccans, not groups from the eastern Mediterranean. The likely period when this admixture occurred is when Sicily was an Arab emirate, from 830 to 1070. More or less Sicily was then part of the greater Maghreb. Calabria also had a Muslim presence, though more tenuous.

Finally, the authors used LD patterns and reference populations to attempt to estimate admixture times:

We found evidence of the presence of a mix of Central-Northern European and Middle Eastern-North African ancestries in the Italian individuals (Supplementary Table S5). The estimated times of admixture ranged between ~2050 and 1300 years ago (y.a.), with an average of about 1650 y.a. – assuming 29 years per generation– for Northern Italians, and between ~3000 and 1450 y.a. (~2100 y.a. on average) for Central Italians. Finally, for the Southern Italian individuals, admixture between European and Northern African-Middle Eastern ancestry was estimated to have occurred about 1000 y.a. (see Supplementary Table S5 and Supplementary Results for a complete report of significant results).

The admixture in Southern Italy is estimated to have occurred ~1000 years ago. That’s pretty much what you’d expect. These methods tend to pick up the last signal of admixture, so there may have been ones earlier (e.g., Magna Graecia?). That might explain the relatively low fraction of “Sardinian” ancestry, as this area of Italy has had significant gene flow from outside Italy over the past 2,500 years, whether it be Greeks, people from other parts of the Mediterranean, and last Maghrebis.

The difference between Northern and Central Italians is intriguing. The reference populations are not optimal, and the dates have a wide interval. We actually know what was happening 2,100 years ago in Central Italy, and there was no admixture between Middle Eastern and Northern European groups. The Roman world empire was still in a nascent state. The Northern Italian admixture date might align with a German migration into Italy, or perhaps the Gauls in the centuries earlier. I really don’t know. I am of the inclination to suggest that the Central Italian signal might be somehow low balling the Indo-European admixture.

The authors say that their data will be released. But I looked up the accession number, and it’s not up there yet.

 
• Category: Science • Tags: Genomics, Italy

71+K3llKhVL The banana is in the news again. You won’t be surprised about the topic if you read Dan Koeppel’s Banana: The Fate of the Fruit That Changed the World. As you may already know, the banana that we eat today was resistant the Panama disease which took out Gros Michel variety, which was the dominant one before 1960. I’m mildly hopefully that breeders will figure something out, technology is changing fast now. But, one interesting thing I learned is that artificial banana flavor, which most people are not impressed by, actually might resemble the Gros Michel pretty well. It’s just that two generations have come to think of the waxy and more astringent Cavendish as banana qua banana.

Saudi Arabia is a problem. They’re going to execute a Sri Lankan maid for adultery by stoning. The nation seems to have played in a role in radicalizin Tashfeen Malik. The vast majority of the 9/11 hijackers were Saudi. But here’s the question: what do we do with our ally? Invade and replace the monarchy with a democracy? Here’s a sad prediction: the outcome will be worse than what we’ve got now!

After 60 Years, B-52s Still Dominate U.S. Fleet. The article claims that some of them are going to be used until 2040! Attempts to replace them have failed. Why? Perhaps the B-52 is just a optimal design for the sort of missions it undertakes.

VW Destroys Myth of Efficient Germans.

Can Everyone Tell I’m Skinny-Fat?

In Utah Feud Over ‘Dirty’ Sodas, Flavored Darts Are Fired.

 
• Category: Miscellaneous • Tags: Open Thread

UltrasSoc_cover_epub Over the past few years one of the major finds of ancient DNA is that human genetic patterns as a function of time often exhibit discontinuity. In plain language, the people who live in a given location are often unlikely to have descendants at that location 10,000 years down the line. This has resulted in an update to long held null and consensus models of of modern human dispersal across the world. To sum it up, that family of models tended to be predicated on a sequence of unidirectional migrations out of Africa in a step-wise fashion. This resulted in the stylized fact that genetic diversity decreased as a function of distance, with groups like Native Americans and Oceanians the most “steps” from Africans. Though all non-African populations are separated by the same number of generations from Africans, one result that would be implied and was seen in the data is that genetic distance from Africans of these populations was often higher than Eurasians, likely a function of their elevated drift (more drift means more divergence from ancestral shared allele frequencies). Once these regions were settled at a given time in the past genetic diversity so partitioned would slowly equilibrate through gene flow between adjacent demes.

F1.large (1) Though this model captures some element of the truth, the reality of sharp local discontinuities in a given region is strongly indicative of the fact that there was no stable state achieved once the initial founders arrived. Geographical reality seems to dictate the sort of pattern of settlement outlined by the model of serial bottleneck Out-of-Africa model, but it seems likely that future population arrivals could be drawn from both closer to, and further out, from Africa. Second, it turns that most of the world’s populations are the product of relatively recent admixtures between very different ancestral lineages. Instead of overlaying a phylogenetic tree over a spatial landscape, one has to conceive of it as a reticulate network. This revised model is outlined in Joe Pickrell and David Reich’s Towards a new history and geography of human genes informed by ancient DNA. In place of diffusion and continuous genetic exchange between adjacent demes, the empirical data seems to point to a non-trivial proportion of “pulse admixtures.” That is, people who were very genetically different arrived, and mixed in with the local population, in a very short period. Sort of what happened in the New World with the arrival of Europeans.

But that’s all talk. A new paper in Molecular Biology & Evolution formally models these processes, Long distance dispersal shaped patterns of human genetic diversity in Eurasia (open access):

…However, it is likely that the Last Glacial Maximum (LGM) affected the demography and the range of many species, including our own. Moreover, long-distance dispersal (LDD) may have been an important component of human migrations, allowing fast colonization of new territories and preserving high levels of genetic diversity. Here, we use a high-quality microsatellite dataset genotyped in 22 populations to estimate the posterior probabilities of several scenarios for the settlement of the Old World by modern humans. We considered models ranging from a simple spatial expansion to others including LDD and a LGM-induced range contraction, as well as Neolithic demographic expansions. We find that scenarios with LDD are much better supported by data than models without LDD. Nevertheless, we show evidence that LDD events to empty habitats were strongly prevented during the settlement of Eurasia. This unexpected absence of LDD ahead of the colonization wave front could have been caused by an Allee effect, either due to intrinsic causes such as an inbreeding depression built during the expansion, or to extrinsic causes such as direct competition with archaic humans. Overall, our results suggest only a relatively limited effect of the LGM-contraction on current patterns of human diversity. This is in clear contrast with the major role of LDD migrations, which have potentially contributed to the intermingled genetic structure of Eurasian populations.

One of the things the authors found is that low population pairwise genetic distances across a wide range of human populations in Eurasia is probably due to LDD events homogenizing the landscape. Continuous gene flow between demes after the initial settlement Out-of-Africa would not have resulted in these patterns. Second, it seems reading the paper that the weak effect of the LGM population reductions on genetic diversity are partly a function of this mixing across long distances. Finally, it is notable in within Eurasia at least (they suggest that the Americans and Oceania may not fit this pattern) a sort of diffusion/wave of advance model does hold for the initial arrival of modern humans in Eurasia. They posit that this might be because archaic populations prevented long distance movements, or, that population fitness became too low when the bands were too small, the reference to the allee effect. Additionally, they also note that the evidence in Europe suggests both replacement with minimal admixture, and then later admixture with the local substrate.

But the details are less important than the big picture. The authors note that there are aspects of the data (dozens of microsatellites) that leave something to be desired, but this is a first pass. At the top of this post you see Peter Turchin’s Ultrasociety. Though the authors don’t get into much specificity in the discussion, I think the solution to what’s going on, and how LDD seems prevalent when you have a populated landscape, is that cultural complexity resulted in sharply increased returns to the victors in inter-group competition. Though some of the dynamics date back to the Pleistocene, the re-patterning of the world with “LDD”, what I call “leapfrogging”, is probably most salient for Eurasia during the Holocene. And, as the story about the Yakutian horses implies, this is also relevant to many domestic lineages.

 
• Category: Science • Tags: Demography, Genetics, History

Лошади_темная_3_малень_wiki

Screenshot - 12042015 - 05:32:56 PM How fast can evolution occur? More precisely, how fast can adaptation occur? The rough answer is pretty fast. For humans that’s clear when you read a book like 10,000 year explosion, or see the results from ancient DNA in papers, that selection (~1% coefficient) on variation can drive allele frequency changes rapidly (~0% to ~100%).

A new paper in PNAS on Yakutian horses is interesting because it highlights the power of selection and how quickly it can change populations when there’s enough genetic variation for adaptation to proceed. These horses are a stocky and hairy breed optimized for life in extreme cold, as Yakutia is in the heart of Siberia, as everyone who has played Risk knows. As a Palearctic species (with origins in North America!) horses have been present in this region since the last last Ice Age. So one model is that the Yakutian horses are a long present population adopted by the Yakut Turkic people, who arrived form the Altai in the last ~1,000 years. The alternative model is that they’re descended from populations brought by the Yakuts, and have undergone recent adaptation. Finally, there is a synthetic model which allows for admixture between the local and intrusive groups, so that adaptation can occur through introgression of alleles from the former to the latter.

To answer these questions they took a genomes from the extant population, as well as ancient or historical genomes. The TreeMix plot makes it pretty clear that the Yakutian horses are intrusive, and do not descend from the ancient populations, represented by Batagai. CGG101397 is from the 19th century, and you can see that is placed near modern individuals from the region, as you’d expect if they arrived with the Yakuts. Interesting, the Batagai individual is even further out that the Mongolian wild horse, which itself is rather diverged from the domestic population, which is not derived from it. They tested for non-trivial admixture between the Batagai lineage and the modern Yakutian horses, and did not find any evidence. This tilts the playing field toward the idea that Yakutian adapatations occurred from their own variation. Mind you, I don’t think they’ve totally eliminated the population of introgression with their sample sizes, as you can have alleles move between populations even if there is almost not detectable admixture.

61DFNJkqyGL._SY344_BO1,204,203,200_ But there are other elements which suggest that ancient variation wasn’t used. They note that selected variants seem to often be cis-regulatory elements, and not nonsynonymous ones. The former alter gene expression, while the latter presumably impact the function of the proteins, as they’re ultimately transcribed and translated from genes. There is a long argument in the geneticists community around this topic, and Sean B. Carroll’s book from the 2000s, Endless Forms Most Beautiful makes the case for cis-regulatory elements. Here’s a paper from Hopi Hoekstra and Jerry Coyne taking the other side. The authors argue that because the population didn’t have enough standing genetic variation there was a focus on these noncoding elements, which can alter regulation in a quantitative fashion.

The list of genes are what you’d expect when it comes to climate adaptation in this region. What is interesting, and noted in the abstract, is that mammoth and human also seem to have used the same mechanisms and pathways. What this implies is that there are certain genetic constraints, or at least low hanging adaptive fruit, at the level of the mammalian taxonomic rank. I’d go further judging by what we know of pigmentation. Basically, genetic variation is not endlessly pliable and infinite. The wheel is always reinvented, but from the same parts that have long been handy.

 
• Category: Science • Tags: Genomics

41dbipeX+pL._SX319_BO1,204,203,200_ I was talking to a friend recently about life and its aims and meaning. Offhand I mentioned I was reading Meditations, by Marcus Aurelius, arguably the most powerful man in the world when he was composing it. There is debate about whether he wrote Meditations for public consumption, but that is somewhat irrelevant to why we moderns read it.

I could attempt to derive the fundamental theorem of calculus and reconstruct vast swathes of modern mathematics from first principles. But I don’t. Part of it is that I don’t have the skill or time. But another aspect is that I can stand on the shoulders of those who have come before, and lean upon the hard work that has come before. And so with natural science, which has a institutional backdrop I can’t recapitulate. There’s no point in reinventing the wheel.

There are those, like Steven Pinker, who suggest that the nature of modern philosophy is that it has been relegated to answering questions which seem well night insoluble. And I am in broad sympathy with this perspective. But the reason I look to the ancients is that often I find their musings more human and real than those of the philosophers of today, who in the analytic tradition put passion in thrall to reason, and on the Continent place a premium on stylistic verve at the cost of coherency. I don’t think that Marcus Aurelius, or Seneca or Christ for that matter, had any specific deep insight into the general human condition. But they probably addressed most of the same questions that the average person today has. There may be benefit then in seeing what their answers to the deep questions were, because presumably the generations that have intervened have selected at least some for memetic clarity, if it not depth.

 
• Category: Miscellaneous • Tags: Philosophy

Screenshot - 12032015 - 01:57:15 AM

The guy who runs the Pop vs. Soda page has really improved it. You can look at county level metrics just by hovering over the county. You can see counts, to get a good sense of the confidence in the representation of the underlying demographics. One thing that must be amended is that it’s not just soda vs. pop, there’s also coke in the South.

Screenshot - 12032015 - 01:54:14 AM

It is now very clear from these maps that there is an extremely sharp cline between the Middle Atlantic/New England region and the Great Lakes/Midwest on this dialect difference. I grew up in a soda region of upstate, though in the upper Hudson valley (95% soda), closer to New England than Syracuse. But in west-central New York you have counties right next to each other which are 60% vs. 15% pop, with reasonable sample sizes. Pennsylvania is similar. Clearfield county is 83% pop. Centre county just to the east is 19% pop (I know Centre county has Penn State, but the other counties around it are mostly soda as well).

In some places state lines matter a lot. Look at Oregon vs. California. The two “soda counties” in Oregon are more tied to the far north of California than the Willamette valley (the state of Jefferson). The Wisconsin-Illinois state line is a huge barrier as you approach Lake Michigan. But in other areas borders don’t matter so much. South Florida is part of soda territory, but that makes sense with its cultural history (lots of Jews with family roots in the Northeast). And there’s the huge zone that radiates out of St. Louis.

Screenshot - 12032015 - 02:11:39 AM

But in some ways the distribution of coke is the most interesting. First, state lines matter a lot in some areas. In the west there is a sharp drop off as one moves into Oklahoma, but an even sharper one into Kansas. Basically it’s the old Confederacy states, as Missouri has very little coke. As you move east it becomes more complicated. Northern Florida is part of the south, but you see in parts of Indiana that coke is a very common term for soft drinks. Why? It’s the “butternut” folk; descendants of Southerners who had settled large swaths of the Old Northwest. They retain connections and affinities with the South to this day.

Finally, on the Atlantic coast, you see the impact I suspect of border position and Northeastern migration into Virginia and North Carolina. The far west of North Carolina is like eastern Tennessee. West Virgina has an Appalachian extension in eastern Kentucky. State borders are less important in the east, just as is in the case further north. Cultural patterns that emerged organically when states were rather inchoate exist today in these regions, while newer states to the west were defined partly by their borders in terms of their cultural background (e.g., Kansas as a free state would be less appealing to Southern settlers culturally than if it was a slave state).

Those will more local knowledge can probably say more.

 
• Category: Miscellaneous • Tags: Geography

I recently watched the above video of a Demi Lovato song. I like Michelle Rodriguez’s stomach as much as the next guy (OK, perhaps more), but one thing that struck me in particular is that throughout the whole narrative arc Lovato, a 5’3 tall female, beats the crap out of many much larger men. Obviously this is a stylized fantasy, and the trope of “butt-kicking babes” is pretty well established in our culture now that we can slot it into the appropriate schema (Lara Croft?). But, recently I’ve been made aware of the magnitude of the strength differences between men and women, so these sorts of scenes are even more fantastical than were before. It’s almost as strange to me as an episode of Sailor Moon. It starts to violate the need for a “minimally counter-intuitive” scenario which is the criterion for a good realistic fantasy (yeah, that’s an oxymoron!).

sexdiff The table to the left is from Costs and benefits of fat-free muscle mass in men: relationship to mating success, dietary requirements, and native immunity. I’m not too interested in the evolutionary psychological details at the heart of the paper. Rather, let’s focus on some statistics which are given. The key is to focus on the d column, this is the effect size, which indicates the differences between the means of the two distributions in standard deviation units. The mean ages of the two distributions were the same, 33. So d is naturally 0 for this measure. For height men are 1.75 standard deviations taller, on average, than women. This seems about right. You can see in body fat percentage that women have higher values than men. The d here is negative. It gets interesting once you get to muscles. These are measuring volumes. When it comes to arm muscles the average male has 2.5 standard deviation units more than the average female! I was also surprised by the thigh muscle, as arm musculature differences have always been more salient. Finally, there’s the fat free mass.

Some have pointed out to me before that the standard sexual dimorphism calculation in relation to humans may not be informative in the way we might think. There’s about a 10% size differences between men and women. But as you see in the “fat free mass” row the size difference is much more extreme if you account for the higher body fat of women. This is relevant because fat does not make you strong, it just adds more weight and volume. In terms of upper body muscle mass there’s less than a 10% overlap between the two distributions. The vast majority of men have more muscle mass than all women. 99.9% of females have less upper body muscle mass than the average male. The 61% greater average muscle mass in male upper bodies translates into 90% greater average strength (the respective values for the lower body are 50% and 61%). The authors of the paper note that “The sex difference in upper-body muscle mass in humans is similar in magnitude to the sex difference in lean body mass in gorillas, the most sexually dimorphic primate.” Obviously humans don’t engage in obligate harem building, and males are not totally devoted to agonistic behavior as their raison d’etre. So one should be cautious about extending the analogy too far. But this result will likely surprise many. It surprised me.

k10359 I spent a lot of time fixating on numbers above because I don’t beat women. More pointedly, I’ve never hit a woman. That’s not because of the way I was raised by my parents. Though they don’t countenance beating women, they came as adults to this country from Bangladesh, so their attitudes toward violence are more “liberal” in a literal sense than the average America. The culture in which I grew up though affected me more in regards to proper behavior in this dimension (the United States, and more particularly, middle class mores). I have a cousin who was beaten up by her husband several times (for the record, they both grew up in Bangladesh into their adulthood). She’s about 4’10 and he’s 5’8. Though I abhorred this behavior I didn’t have any concrete understanding of what this might have meant. I’ve gotten into fights, but only with guys, and they weren’t ever that much smaller than me. Now I understand better why a 5’8 man should never get violent with a 4’10 woman. The discrepancy is far greater than height would suggest, because the woman has less muscle mass per pound. I have some intuition about this because my wife is about my height and of athletic disposition for a woman, and when she tried to throw down my sorry out of shape ass it was pretty easy for me to prevent her. How is it possible that despite us being the same height, and her being in shape and me not being in shape*, I could still best her? Because I still had more upper body muscle mass due to being a male.

Now, mind you, there are a small minority of women who are stronger than a small minority of men. The statistics above make it clear. But it is very unlikely that in a pairwise interaction the very strongest females will randomly face the very weakest males. In terms of relationships, where domestic violence occurs, it is very unlikely for reasons of assortative mating that the very strongest females will be paired up with the very weakest of males. On the contrary.

There are two reasons I’m posting this. First, I’m assuming most of my male readers have never beaten a woman, so they too lack good intuition about what they might be capable of if they did do such a thing. There isn’t the sort of thing you really want first-person experience of, so scientific research which can gain you some sense of the shape of reality is useful. Second, the general skepticism and rejectionism of biological differences in behavior between the sexes which is now common on the cultural Left can start to bleed into other domains in the most surreal ways. I’ve had friends with science backgrounds who balk somewhat when I attempt to start any discussion about sex differences with the contention that there is a difference in upper body strength. They don’t necessarily even want to concede this without dispute. In these earlier conversations I didn’t know of any research on the magnitude of the difference, it just seemed “common sense.” But perhaps the positive diminution of domestic violence in some sectors of American society has had the side effect that people forget how strong the magnitude of difference in strength is?

Related: Men Are Stronger Than Women (On Average). In which I report that the average German man has a grip strength more powerful than the majority of the woman’s Olympic level fencing team.

* This was in the past, now that I lift my upper body muscle mass has increased considerably.

 
• Category: Science • Tags: Sex Differences

41TiKtcNqlL._SX322_BO1,204,203,200_ Over at Heterodox Academy there’s a post, Heterodox Academy’s Guide to the Most (and Least) Politically Diverse Colleges, First Edition, geared toward those looking for “unsafe spaces.” This isn’t on the list, but there’s another option: just be around me! Recently a friend found out I was a conservative, and he expressed total wonderment at the exotic specimen sitting before him, as he admitted he had never had a conservative friend (he, a Harvard graduate). I don’t mean to be what I am, but as an conservative brown person I diversify my white liberal milieu by dint of living and breathing in their presence!

One thing that I wondered in relation to that post: why not just read books which don’t align with your opinions? I know this is an exotic thought for many, but it does wonders for perspective, and it’s far cheaper than going to a university. One strategy is to read old books. It is highly likely that you will not align in totality with Aristotle on issues such as slavery, for example. If that is too heavy going, then perhaps the Epic of Gilgamesh or the The Iliad. To lighten the mood even more, The Golden Ass.

51oviG6d1aL._SX341_BO1,204,203,200_ But the ancients are no more. Perhaps we want some more contemporary thinkers who are still alive, or represent more living traditions, oppositional to our own viewpoints? Years ago I read Tariq Ramadan’s Western Muslims and the Future of Islam. Unlike Reza Aslan Ramadan has scholarly heft, and is religiously orthodox in the eyes of the majority of the world’s Muslims (I enjoyed No God but God despite its occasional sloppiness, but Aslan is really not an alien perspective, he’s a person rather like me who happens to be broadly religious in some vague manner and so more sympathetic to Islam than I). It shows when someone like me, an atheist, an irtidad, attempts to read his verbal circumlocutions around concepts such as tawhid. Ramadan’s thought is extremely alien to me. It reminds me somewhat of attempting to read passages of Heidegger in translation. Such an exercise is useful, at least in understanding the incoherency of the believers.

Another book which has stuck with me is Michael Parenti’s Blackshirts and Reds: Rational Fascism and the Overthrow of Communism. I read it a long time ago, but I recall it is the sort of book that Southern romantics wrote about the lost cause, except in this case the lost cause was actually international Communism and Marxist-Leninism. Though Parenti doesn’t defend Stalin in the totality, he actually does defend him in some specifics! Obviously I’m not a Communist, and never have been. Though I did have a good friend in college who was a self-described Communist and Fidel groupie, she was a sociology major so I didn’t give it much thought. Here though is a man who lives in our time, an ex-friend of Bernie Sanders, defending the lost cause of Communism and bemoaning the fall of the Soviet Union as a grand experiment that was no more.

41KQE93RKGL._SX338_BO1,204,203,200_ Next let’s move to Creationist books I’ve read which have challenged my views. Though I find both Parenti and Ramadan’s views abhorrent and objectionable, I give the nod to them as scholars. But Darwin’s Black Box was a dumb book by a smart man (that is, Behe is a competent biochemist, but as an evolutionary biologist he’s a professional imbecile). Darwin on Trial I recall being slick and sophisticated, but it was just what a lawyer would write. It did not challenge me, it disgusted me, as it was sophistry. In contrast, Larry Witham’s By Design: Science and the Search for God is a sympathetic portrait of some researchers associated with the Intelligent Design movement, more or less. Like Islam, Creationism and Neo-Creationism (Intelligent Design), are stupid and false ideas. Creationism has the demerit of being promoted for most of its history by evangelical Protestants, so it has never developed intellectual richness which would impress outsiders (unlike Islam, which has a 1,500 year history). But, some of the people promoting Intelligent Design are quite clever, and their motives are illuminating.

A_Theory_of_Justice_(original_edition) John Rawls’ A Theory of Justice is not bed-time reading, but it is important to understanding modern political philosophy (Robert Nozick’s Anarchy, State, and Utopia was a response). Philosophy doesn’t have a direct impact on modern society, but it does shape the frameworks of intellectuals, who eventually become political actors and influences. E.g., Matt Yglesias, a philosophy grad from Harvard, is pretty obviously influenced by Rawls, though this was more evident when he was an undergraduate. Rawls’ hyper-logical system building isn’t something that I’m too congenial with at this point in my life (rationalist models of society made more sense when I was a virgin). I am a conservative, I obviously disagree in a lot of details with Rawls. But the tendencies which he evinces are common among intellectual liberals, libertarians, and even free market zealots in the conservative camp.

51oBb9Js1ZL._SY344_BO1,204,203,200_ We live in a Whiggish age, so John Horgan’s The End of Science is an audacious book. I’m a scientist who loves science, so obviously I’m not convinced, to say the least. But Horgan gives it a good college shot, and sometimes the effort can result in illumination. Scientists are filled with hubris. A “cure for cancer” has been around the corner for decades, and robotics is going to go mainstream any day now. Some caution is warranted.

51hcmhp1YsL._SX343_BO1,204,203,200_ When I first read Garrett Hardin’s The Ostrich Factor: Our Population Myopia I was actually rather concerned with overpopulation. Today, for various reasons, I am not nearly as alarmed. But Hardin’s work is essential toward understanding how many people, especially biologists, think about these issues. Carrying capacity and the logistic curve of growth and saturation with “checks” are concepts drilled into the heads of most biologists, especially those with an ecological focus. Hardin, with his “tragedy of the commons”, was exceptional at being able to communicate this internal logic in a way that the public could understand. As such, his work channels many of the concerns in the environmental movement, in particular those which are more Deep Ecology tinged.

debt Randall Robinson wrote The Debt: What America Owes to Blacks during a period of time when there was a fair amount of talk about reparations for slavery. Though I agree most that American blacks have suffered injustice, and to some extent continue to do so, I do not hold to Left liberal positions on racial relations or the means of reconciliation. At the time I read The Debt I was a rather strident libertarian, so I was skeptical of Robinson’s case, and remained so after having finished it. Though some sections, as when he depicts Cuba as a racial paradise for blacks, were totally implausible, Robinson did not toss off a wild eyed screed. Impractical and unlikely as reparations were, The Debt was a serious effort offered in good faith.

7186SZ78EWL._SX310_BO1,204,203,200_ It seems this list is heavily skewed toward politics. But that’s one area where I have strong affirmative and negative positions, and am less open because these are grounded in a priori norms. It is strange to think of having a “diversity of views” on physics, for example. In the mid-1990s I read a fair amount of feminist material. Most of it did not stay with me. For example, I think I read Mary Daly’s The Church and the Second Sex, but I have no recollection what it was about in the specifics. In contrast Andrea Dworkin’s Woman Hating haunts me (in contrast, Mary Wollstonecraft’s A Vindication of the Rights of Woman inspires me as to the possibilities of my daughter’s life). Woman Hating is an unhinged radical feminist take on sexual relations. Even many feminists have accused her work to be a distorted reflection of the misogyny under which she suffered. Dworkin’s views are not representative of mainstream feminism, but they definitely reflect the fringe rather well, if in an unpleasant tone. The ubiquitous idea of “violence” through speech rather than deed took root early in this group of thinkers.

That is all for now. Readers can chime in with books which were influential for them, despite disagreeing with their viewpoints or perspective.

 
• Category: Ideology, Miscellaneous • Tags: Diversity

Screenshot - 12012015 - 10:22:42 PM

The above is from an article in Nature, A test that fails. Two stories first. One of my good friends who went to grad school at MIT got a good ribbing from his roommates because he was the only one who didn’t get a perfect score on the math portion of the GRE. Luckily for him, he was a chemist, so they let him into the program. It is a truth universally acknowledged among the quantitatively ept that the quantitative GRE is just way too easy, and is compressed at the top scale and does not allow for differentiation of the good from the great. That is, there are a wide range of competencies which are bracketed among those who score a “perfect” 800 on the quantitative GRE. And there are many people in fields like physics who score 800; the average score on quantitative reasoning for those who intend to study physics in graduate school (not those who get accepted!) is in the 740s. Second, a friend of mine was complaining about the lack of underrepresented minorities in the biological sciences at my graduate school. To her surprise and irritation I just pointed out that all the underrepresented minorities within the range of GRE scores that our program takes would be going to Stanford or Berkeley. There weren’t enough of them that we’d be competitive. Data like the above is just not well known.

Another point is that the article above is very anti-GRE. They claim that the GRE score is not very predictive of ultimate outcome. One of my professors pointed to a study at University of California San Francisco (UCSF) where they tracked future successes (e.g., tenured position in academia x years out), and correlated them with GPA and GRE. Neither were very strong predictors. Rather, their Ph.D. research productivity was highly predictive. This isn’t that surprising, because GPA and GRE are just proxies to get at whether one can be a productive researcher, and being productive in graduate school is probably the best guide as to whether you’ll be productive later. But, one thing I want to point out is that UCSF is a very selective school. The range of GRE scores in particular is likely to be narrow, because they’re going to simply not even look at applicants with low scores. Whenever people point out that MCAT or GRE is poorly correlated with professional outcomes, remember that you’ve already compressed the distribution toward the higher end. If schools allowed a much wider range of applicants in, then these aptitude tests would be much more predictive.

Screenshot - 12012015 - 11:12:23 PM In fact, the reality is that there is variation in outcomes according to general intelligence among graduate students. As I stated above, the maximum score of the GRE, especially the quantitative reasoning section, is too low to get at that. But Camilla Benbow’s group has been tracking mathematically precocious children for decades. As the data to the left shows, the smartest-of-the-smart are more likely to become scientists, and much more likely to attain tenure. The cut-off was scoring in the top 1% of their age group on the mathematical SAT test, a 390 score. You can see how much better those very rare students who score 700 or more at age 13 are doing later in life.

Finally, obviously these tests are very robust and predictive, but they’re population statistics. There are people who do not do well on the GRE who do well in academia, and vice versa. But, the reality is that these tests are not useless, and just how “not useless” they are will become more obvious if no one made recourse to them.

Addendum: My physicist friends always enjoy a chuckle whenever I honestly state that physicists are smarter than biologists, as I am a biologist. There are rare cases, such as Ed Witten, of people entering physics from other fields, but in general it’s the physicists who are the imperialists. And that’s because they’re smart, able to decompose general problems rapidly and decisively. In contrast, biologists are somewhat narrow in their focus, and plodding in their reasoning. These are generalizations, but I think they’re roughly correct (I had a friend at a prominent non-profit who was irritated with how difficult it was to find Ph.D. biologists who were flexible thinkers in interviews). And standardized tests bear out my generalization (though honestly, it is a pleasure talking to physicists and mathematicians about out of topic fields compared to biologists partly because they’re so mentally acute; you don’t need GRE stats to get this).

But, another implication of this logic is that some minority groups are also not too bright. If you don’t think these tests are accurately reflecting real intellectual skills that groups have though you don’t have to go there. And my experience is that this is a common belief, including among physicists. But then I suppose they shouldn’t get so full of themselves about their GRE scores in relation to biologists?

 
• Category: Science • Tags: Academia, GRE, Psychometrics

2015-11-29 10.54.09 Over Thanksgiving I tried Marie Sharp’s Habanero Pepper Sauce. It is apparently from Belize. Highly recommended. It’s a genuine habanero sauce, in that it actually is spicy. The additives don’t overwhelm the habanero flavor and impact. I would say it is very mildly on the sweet rather than vinegar side, but the other flavors don’t interfere with the impact, nor are they dissonant.

51zlgfgrs2L._UY250_ So apparently I forgot that Marcus Aurelius was like Adolf Hitler. More precisely, I read Frank McLynn’s biographies of Genghis Khan and Marcus Aurelius in sequence, and while the exterminationist practices of the Mongols were well covered, I had forgotten that the great philosopher emperor had wanted to blot the Iazyges Sarmatians from the earth during his Danube campaigns. The reason was that unlike the German agro-pastoralists whose mode of life was such that they could have been transferred to the empire and become taxpayers, the Iazgyes were nomadic pastoralists who were likely to be a perpetual thorn in the side of the Roman state who were also not ideal settlers within it. This brings me to a curious historical analogy: that between the Kangxi Emperor and Marcus Aurelius. The two have both been termed philosopher emperors, who wrote down their reflections for posterity. Marcus Aurelius famously in his Meditations, while you can find that of the Kangxi Emperor in Jonathan Spence’s Emperor of China: Self-Portrait of K’ang-Hsi.

And like Marcus Aurelius the Kangxi Emperor also endeavored upon a “final solution” for an ethno-political problem: the destruction of the Dzungar polity which he began, and his successors completed, entailed genocide on a large scale through famine and displacement. More Holodomor than Holocaust. The ethnic character of the northern half of modern day Xinjiang, what was Dzungaria, has been radically reshaped over the past 250 years due to the efforts of the Kangxi Emperor and his heirs (what was once a Oirat Mongol domain passed over to Kazakhs and Uygurs).

UltrasSoc_cover_epub As promised, Ultrasociety: How 10,000 Years of War Made Humans the Greatest Cooperators on Earth, is now available in trade paperback. I’ve started to read it. One thing that I like about Peter’s work is that he’s relatively economical in regards to prose, and like a scientist he balances powerful analytic frameworks which allow for general inferences ,with rich empirical description of specifics. You should probably read his 2013 PNAS paper before you read this book.

ISIS’ Grip on Libyan City Gives It a Fallback Option. Look at the map. The Islamic state has hegemony over a huge swath of the coast between Tripoli and Benghazi. We, the West, and France and the United States in particular, created this situation. This was a war of choice. Liberals who abhorred the Iraq intervention somehow thought that the Libyan one was warranted. The Gaddafi regime was not a good thing. He was a mercurial dictator who sponsored terror against the West and was a source of trouble for his neighbors in the Middle East and Africa. But, he was aging, and beginning to slide into his “bunga bunga” years. Libyans are arguably worse off now than they were before the intervention. The rest of the world most definitely is.

The Heart Disease Conundrum. Here’s the important part:

However, Framingham risk models do not tell the whole story for nonwhite ethnic groups. In 1959, the first study was published showing the increased risk of premature heart disease in Indian immigrant males, who had four times the rate compared with the men in Framingham, despite having lower rates of hypertension, smoking and high cholesterol, and more often following a vegetarian diet.

What is it about South Asian genetics or environments that lead to so much heart disease? We need a Framingham-type study to answer this question.

The problems exhibit themselves among well off South Asians in the West. And, frankly, well off South Asians in South Asia. All four of my grandparents died of issues relating to their cardiac health or the circulatory system (e.g., heart disease, hypertension leading to stroke, etc.). Mind you, they died in their mid-70s, early 80s, and at 100, so one needs to keep in mind that at those ages something was going to happen. Luckily cancer doesn’t seem to run in my family. I’ve got a large pedigree at least to check for these things.

I’ve been running and lifting to various degrees over the past year and a half, going from 155-160 lbs (at 5’8) to 145-150 lbs. Judging from the various body fat percentage meters I’ve used I’ve probably lost ~4%, likely going from ~20% to ~16%. But, I definitely have work to do. South Asians are “fatter” than their weight. This is clearly to a great extent genetic, or a gene-environment interaction relating to activity (or lack thereof), as I don’t eat a South Asian typical diet (“paleo-lite” is probably a good descriptor). That’s just how life is. (though these genetic issues probably don’t preclude a relatively high life expectancy, the Maldives for example has one of 77 years, while Kerala and Sri Lanka are at 74 years).

Neolithic farmers from Greece and Anatolia. ‘”I think it is time to declare the problem of “Neolithization of Europe” done.’ Basically. Onto the Bronze Age. And Asia.

What It’s Like to Grow Up as a Closeted Gay Extremist Muslim in East London. Unlike my white liberal friends I don’t think Islamophobia is a big issue in most of the West. I say this as someone who “looks Muslim” and has a “Muslim name” who also flies a lot. But what do I know about racism compared to my white liberal friends?

From Indonesia, a Muslim Challenge to the Ideology of the Islamic State. As I pointed out on Twitter, these sorts of articles were common before the 1998 Asian economic flu, though usually they had to do with Mahathir Mohammed and Malaysia at the time. And, as suggested in the article attempts to affect change in the Arab Islamic world from the demographically and economically powerful Asian Muslim periphery probably are not going to work because of ethno-racial chauvinism. Though one might not know this from the vantage point of post-colonial theory dominated academic departments, Arabs identify themselves as white, and have a fair amount of racial prejudice against East Asians, South Asians, and Africans. Though Persians historically had a huge influence on the shaping of Sunni Islam, today Iran is Shia, so they will have a difficult time getting heard. Turkey has its own recent colonial legacy with the Arab world to deal with, as well as Ataturk’s reforms forcing a cultural rupture despite recent attempts to close the gap. Islam’s ethnic valence is somewhere between that of Christianity, which has been re-appropriated multiple times in multiple contexts, and Judaism, which is both a religion and a nationality in its self-conception. I grew up marginally Muslim, insofar as my parents were involved in the Islamic community for the purpose of celebrating religious holidays, and the attitudes of Arabs, and a lesser extent Turks and Persians, in regards to the religion and South and Southeast Asians, as well as African Americans, tended toward condescension. They were happy to accept these groups as legitimately and authentically Muslim, but it was clear that they would never have brooked any lectures on proper practice and belief from these arrivistes.

The Near-Impossibility of Assimilation in Belgium. The headline is misleading. The substance of the article makes it clear that it is totally feasible to assimilate if you are white.

Tibetans Fight to Salvage Fading Culture in China. First, the issue is language. One can imagine that Tibetan identity would persist purely through religion, with the Tibetan language becoming a liturgical vehicle, as Coptic is among Coptic Christians, who all adopted Arabic by about 1800 (there were people speaking Coptic during the European Renaissance, since apparently some Europeans visited Egypt to learn the language during that time). A good model for Tibetans might be the Hui community, who speak Chinese but maintain a distinct Muslim religious identity. Second, there are >100 times more Han Chinese than Tibetans in China. The economic benefit of being able to speak Chinese is pretty clear. As occurred in Lithuania during the period of the Polish-Lithuanian Commonwealth I imagine it’s going to be hard for upper class Tibetans to not be linguistically assimilated by the more numerous Chinese.

Religion_Explained_by_Pascal_Boyer_book_cover‘To hell with their culture’ – Richard Dawkins in extraordinary blast at Muslims. I don’t agree with Dawkins on many things, and think some of his assertions are wrong and/or stupid. But, I do respect him for actually saying what he thinks rather than always testing the wind to stay on the right side of the norms of his “team.” It’s refreshing, rare, and it also adds to his genuine credibility, which is otherwise undermined by his tendency to be emotive and shoot-from-the-hip.

I should also add some specific issue in regards to my relationship to the “New Atheists,” and in particular Dawkins and Sam Harris. As a matter of analysis I disagree with their views of how religion as a phenomenon emerged and how it persists. In general my opinions are reflected most by cognitive anthropologists, such as Scott Atran and Pascal Boyer. But, when it comes to the political and normative debate, I have much more sympathy for Dawkins and Harris, because I think their attitude is a broadly liberal one which is hostile toward multiculturalism in a manner well aligned with a particular Western tradition which goes back to the Enlightenment, with which I have much sympathy (though not without reservations). More plainly, as much as I might disagree with Dawkins and Harris on the nature of religion, I totally reject the idea that they are racist in any way as some of their liberal (and sometimes conservative!) critics suggest. Perhaps some of their comments might have racist implications, or one might argue that the application of some of their policies are necessarily racist, but it is pretty obvious to anyone who knows their biographies that neither of them are racist in their intent or personal views. The accusation is basically just a rhetorical move to silence them. (I might add that I also dissent from some of Harris’ more interventionist foreign policy positions; but reasonable people can disagree on these things)

SciReader is great if you haven’t checked it out. One thing I would really like from these sorts of recommendation engines is the ability to tweak exactly how precise the results should be base on previous preferences. Or perhaps a way to add a “stochastic parameter” into the equation.

b127HB_lg For example, there are topics I’m interested in which I’m not working on in my current research, and are never showing up on these recommendation engines. E.g., Evolution of the additive genetic variance–covariance matrix under continuous directional selection on a complex behavioural phenotype. It’s open access. I recommend you read it! Check out the G-matrix page.

Donald Prothero has a new book, The Story of Life in 25 Fossils: Tales of Intrepid Fossil Hunters and the Wonders of Evolution. I’m not a big fan of the biographies of geologists and paleontologists that get interleaved into the science. I’m a computational biologist, so all I see is digging in dirt, digging in dirt, etc. etc. (obviously I feel differently about biographies about geneticists…but I’m a geneticist!)

But, I really liked Prothero’s previous book, Evolution: What the Fossils Say and Why It Matters. Earlier I said one of the things I like about Peter Turchin’s work is the balance between analytic framework and empirical data. Unfortunately many evolutionary genetics types get a little fixated on their model organism (often it’s Drosophila, let’s keep it real) and forget about the big picture of what evolution is. Sometimes it is useful to actually look at a survey of a lot of the fossils and see how all these evolutionary dynamics play out in terms of morphology.

Finally, I’m not open to debates on my comments policy. Trying to argue with me about it will probably get you banned. I know most of you know this, but some of you don’t, at least judging by the past week. So here I am stating it explicitly.

 
• Category: Miscellaneous • Tags: Open Thread

Bourbob_red_turkey_Tom-r2Most people know that animal breeding has a long history. At least since the Neolithic revolution, and probably in some fashion earlier if you consider that dog-human interaction/co-evolution dates to the Pleistocene. In some ways this is not always a good thing, when you consider flourishing from the perspective of the animal. It is a well known fact that when you keep selecting on one particular trait of an organism, there tend to be “correlated responses.” That’s because traits are interrelated, sometimes in a direct structural sense, and sometimes due to common genes. In nature these correlated responses often prevent excessive deviation from optimal fitness. E.g., if you make mice too big they can’t breed.

effetmaranelloBut outside of natural circumstances all sorts of things can happen under human tutelage. That’s how we get grotesquely large chickens with breasts so unwieldy that they can’t walk. And, it’s how we get “cute” cats like the Persian breed who are well known to have issues with conventional mastication. The point is that conventional quantitative genetic breeding methods can lead to “monsters,” because there are plenty of mutations floating around in natural populations. There’s nothing exotic, and even before understanding the genetic basis of inheritance humans were engaging in this sort of activity for thousands of years.

41ZhyEU5lGL._SY344_BO1,204,203,200_ All this is something you have to keep in mind when reading articles such as this in The New York Times, Open Season Is Seen in Gene Editing of Animals. Basically, probably triggered by the FDA approval of genetically modified salmon, there is now a lot of discussion around genetically modified organisms of the animal kind. The New York Times piece opens with an interesting twist:

Other than the few small luxuries afforded them, like private access to a large patch of grass, there was nothing to mark the two hornless dairy calves born last spring at a breeding facility here as early specimens in a new era of humanity’s dominion over nature.

But unlike a vast majority of their dairy brethren, these calves, both bulls, will never sprout horns. That means they will not need to undergo dehorning, routinely performed by farmers to prevent injuries and a procedure that the American Veterinary Medical Association says is “considered to be quite painful.”

If you read the whole article thought it is clear that what the new techniques are doing is supercharging the aims and methods of conventional breeding. In many cases there isn’t even going to be any transgene that moves between species. Rather, researchers may want to create specialized knock-outs, which lack gene function.

Bioethicists and animal rights organizations may suggest there are new ethical questions which are confronting us, but there really aren’t. Using traditional breeding techniques humans are already producing animals whose faces barely close in (many flat-faced cats basically have a hair-lip), or which need caesarian section to give birth. We’ve been confronting these questions for a while now, and better genetic modification techniques just amplify them, or, with greater precision allow ways to ameliorate some of the unfortunate side effects by offering more options.

 
• Category: Science • Tags: Genetics

151300203I haven’t talked much about the refugee crisis because at this point I’m in a “wait & see” mode. It seems almost fantastical that relatively small northern European countries should allow themselves to be demographically overwhelmed in less than a generation, but that isn’t a totally crazy proposition. But we should be cautious about extrapolations. Cultural norms can change rather fast, because most people are conformists (e.g., Sweden combines a very politically correct mainstream culture with a robust verging-on-volkisch minority party which is far outside of the bounds of anything you would see in the United States)

But an article in The New York Times, Emirates Secretly Sends Colombian Mercenaries to Fight in Yemen, does put into stark relief the sort of choices we’re facing in the modern world. On the one hand technology is advancing apace, but our social structures seem to recycle the same forms. The Gulf petro-state system is in some ways straight out of Dystopian science fiction, combining a modern capitalist economy with the a sort of commoditized attitude toward human life with a neo-feudal tincture. But it also reminds me of another model, that of the ancient Greek city-states. Dubai, Qatar, etc., are basically societies where the majority of individuals engage in production for the capital class, which also subsidizes the citizenry (“liturgies”), which is a minority. Though they are not democracies like Athens, this relationship between a notionally co-equal minority and a majority whose economic productivity allows for the life of the society to flourish isn’t particularly novel.

One thing that set the ancient Roman system apart from the Greek polities was that it was expansive, assimilating local elites. It is well known that many of the emperors were not made in Rome, but some of the patrician clans, such as the Claudii, were themselves of Etruscan or Sabine origin. Roman cosmopolitanism fused with an acknowledgment of the primacy of a core culture was a robust system that persisted for nearly 1,000 years, allowing for political scale. Additionally, it is a notable trend in history that when you reduce other humans purely to commodities, basically units of economic production, they have no loyalty to their contracts beyond self-interest. They’ll often try and take over through violence.

Another system is the Western democratic liberal one. This system presupposes citizens who are co-equal, without large groups of disenfranchised people. Even in the American case with slavery in most of the territory non-free males were a small minority. There is also often a rough cultural homogeneity which is presumed for a nation-state. Ergo, the carving up of the Austro-Hungarian polity after World War I followed ethno-linguistic lines. But these sorts of implicit understandings seem to be falling by the wayside. Not to be conspiratorial, but I think part of what’s happening is that cosmopolitan Western economic elites, the top 0.1% or so, have no real loyalty to the nation-state, and find them impediments to the free flow of their labor and their capital. Though few would explicitly admit this, I think that the Dubai model is quite appealing because it dispenses with the non-economic niceties. The main caution I would offer to this is that the Dubai model is probably a “high reward/high risk” play.

 
• Category: Foreign Policy • Tags: Economics

000e553e_medium In 2007 a friend told me of an encounter at a seminar where L. L. Cavalli-Sforza seem to offer agriculture almost reflexively as a solution to the conundrum of signals of positive selection in the genome of humans. Basically, all paths led to agriculture. I have to say that nearly ten years later Cavalli-Sforza’s deep intuition on these issues seems to be vindicated. Agriculture was an enormously big deal.

Carl Zimmer in The New York Times has a write up of Matheison et al. (it’s in Nature), Agriculture Linked to DNA Changes in Ancient Europe. There aren’t a whole lot of surprises, as the pre-print has been around for a year or so. But, having the work written up in a newspaper allows researchers to engage in some extemporaneous speculation. Ergo, you have:

Why? Scientists have long thought that light skin helped capture more vitamin D in sunlight at high latitudes. But early hunter-gatherers managed well with dark skin. Dr. Reich suggests that they got enough vitamin D in the meat they caught.

He hypothesizes that it was the shift to agriculture, which reduced the intake of vitamin D, that may have triggered a change in skin color.

This was to some extent Cavalli-Sforza’s idea, and I’ve proposed it as well. Then there is the model of sexual selection. These theories aren’t always exclusive, and pigmentation may have multi-causal underpinnings. It is very interesting that the best methods and ancient DNA seem to be suggesting lots of very recent change and likely adaptation. But ultimately, we still have no clear idea.

 
• Category: Science • Tags: Ancient DNA, Genetics

51DPT3AYDHL._SX321_BO1,204,203,200_ People like to quote Martin Luther King Jr., “The arc of the moral universe is long, but it bends towards justice.” This includes the president of the United States of America, arguably the most powerful non-plutocrat in the world. But after reading Frank McLynn’s biographies of Marcus Aurelius and Genghis Khan, I wonder if anyone actually bothers to read history when they say something that is so facile. Now, I agree that the trend does move toward one direction. Over the past 3,000 years the institution of slavery has gone from being a banal practice, to a necessary evil (e.g., as in Islam), to a taboo practice. But the phrase is often bandied about as if moral directionality is fine-grained on the scale of a generation or two, rather than on the scale of centuries or more. For all Marcus Aurelius’ strangeness in comparison to moderns, Genghis Khan was clearly more a figure who would fit in in a pre-Axial world.

In Genghis Khan: His Conquests, His Empire, His Legacy the author mentions legends that the “original” Mongols were a fair skinned and haired, eventually becoming more typically East Asian in appearance through admixture. There are some accounts where Temujin, who became Genghis Khan, had reddish hair. I note that Mongolian people seem to have a small proportion of West Eurasian admixture. My earlier assumption had been that this was recent (from Russians), but now I wonder if this is old. I note that if you look at the phylogeographic literature there is a lot of R1a1a in parts of East Asia. Among the Uyghurs, Altaic people, and to a lesser extent Mongolian groups. The Indo-Iranian modal R1a1a haplotype, Z93, is found among the Altaic people. My supposition at this point is that it may be that Christopher Beckwith’s argument in Empires of the Silk Road that Indo-Europeans were more influential on the eastern fringe of the Eurasian steppe than we may think.

Speaking of East Asia, and specifically China, a question came up on Twitter as to when it joined the rest of the World Island’s oikoumene. Though there were influences from the West at an early period (probably mediated by Indo-Europeans), I believe that the establishment of the Protectorate of the Western Regions around ~0 A.D. probably is a good early date. By the Tang dynasty China was clearly part of the “human web,” but by the first few centuries A.D. Buddhism and Roman merchants had already arrived through Central Asia.

The 2006 paper, Possible Ancestral Structure in Human Populations. Strange that it has only has 149 citations. I recently talked to Mike Hammer about the reception to these ideas in the mid-2000s, and he agrees with my recollection that they were totally marginalized and laugh out of the room back then.

Someone asked last week about a reader poll. I did one about a year ago. You can download and Excel file here of results.

galaxy-s6-edge_gallery_front_black In response to this question about writing, I don’t know if there is a most “complicated” writing system. I assume that Chinese is arguably more complicated since it takes longer for children to attain a high level of literacy. I don’t think it changes general fluid intelligence, though it probably has an effect on crystallized intelligence.

Response to this question, start here.

So I got a Samsung Galaxy S6 Edge. My previous phone decided that its sound was going to stop working while I was traveling on business. I don’t make regular phone calls often, but when I do, I like to be able to hear what the person on the other end says! This wasn’t a hardware issue, but a software problem, probably due to an app I downloaded. After wasting a few hours trying to get it working (it worked at one point, but then when I rebooted the problem cropped up again), I ended up just calling my provider to get a new phone for when I was back home.

As I’m a rebel from the hegemonic Apple ecosystem (now that I don’t use an iPod shuffle I don’t use any Apple products), I plunked down for the Edge. I have to say I’m pleased so far, though it does get annoying that some of these phones have so many features that I waste an hour or two just watching “tips & tricks” tutorials.

Recently I encountered the idea that the popularity of the “trans-Atlantic accent” in the 1930s and 1940s might have been due to the utility of this clipped and highly enunciated way of speaking when radio quality was low. Well, voice recognition today on these phones makes me wish I spoke with the trans-Atlantic accent….

Finally, Jerry Z Muller followed me on Twitter! It’s a personal “big deal” for me because his anthology, Conservatism: An Anthology of Social and Political Thought From David Hume to the Present, was very influential in my own thinking back in the late 1990s.

 
• Category: Miscellaneous • Tags: Open Thread

UltrasSoc_cover_epub A while back I promoted Joe Henrich’s The Secret of Our Success: How Culture Is Driving Human Evolution, Domesticating Our Species, and Making Us Smarter. I did finish Frank McLynn’s Genghis Khan book, and am re-reading his Marcus Aurelius biography. There will be a review of the first book coming out soon, but I will tease here that unlike Tyler Cowen I don’t think it would come close to being the best book of the year (in part, because unlike many readers I know a fair amount about the topic). I also have a copy of Mary Beard’s SPQR: A History of Rome, and someday really need to get to Dehaene’s Consciousness and the Brain: Deciphering How the Brain Codes Our Thoughts

But here’s another must read, Peter Turchin’s Ultrasociety: How 10,000 Years of War Made Humans the Greatest Cooperators on Earth. This seems like an excellent complement to Ian Morris’ War! What Is It Good For?: Conflict and the Progress of Civilization from Primates to Robots, which I have not managed to get to read, in part because I want to hit Foragers, Farmers, and Fossil Fuels: How Human Values Evolve. Yet I’ve read a fair number of Peter’s books (see my 10 questions for him), so I’ll probably be moving this up the stack.

Peter is a serious thinker, and human social complexity and cooperation is an important, and unresolved topic (I am not as sanguine or flip on this David Sloan Wilson). Currently only the Kindle edition is available, but Peter says that the “dead-tree” version should be available in the next few days.

(note, I have to read The Hive Mind!)

Addendum: Here’s Peter’s post on the book….

 

chg1

ncomms9912-f2 Over the past few years we have seen ancient DNA researchers “carve nature at its joints” when it comes to the paleohistory of Europe after the end of the last Ice Age. In relation to this historical reconstruction we aren’t at the end of the road, but I do think that the terminus is within sight. There are only so many populations one can sample, and so many statistical constructs one can posit, before one is on the plateau of diminishing marginal returns. For example, the model of Holocene Europe being a synthesis of two very distinctive populations which merged after the last Ice Age was too simple. A model with three populations is sufficient for the vast majority of European groups. Though in these sorts of situations more complex models may be consistent with the results, the bias is to go with parsimony, and attempt some alignment with linguistic and archaeological evidence.

A new paper in Nature Communications, Upper Palaeolithic genomes reveal deep roots of modern Eurasians, fills in some gaps in the broader picture. The figure at the top of this post illustrates the modification that these authors made to the schematic of Lazaridis et al. Iosif Lazaridis himself as weighed in on Twitter:

CHG = Caucasian hunter-gatherers. More specifically, the authors of this paper analyze two subfossils from Georgia dated to ~10 to ~13 thousand years, Kotias and Satsurblia. Kotias, at ~15x coverage (that is, each position is sampled ~15 times, so you have a good sense of variation at any given position), is particularly useful. What they found is as Lazaridis reports above: CHG seem one of the primordial groups to give rise to the extant variation of modern Europeans, and Western Eurasians writ large.

The rough stylized history of the non-African populations is as such: a “basal Eurasian” (bEu) population separates off first, and then west and east Eurasians diverge, and then in the west there is a divergence between the ancestors of western hunter-gatherers (WHG) and ancient north Eurasians (ANE). The early European farmers (EEF) are compounds between WHG and bEu, with a slight bias toward WHG. The Anatolian farmers were also admixed, though biased toward bEu. The eastern hunter-gatherers (EHG) are a balanced mix between WHG and ANE, and this group fused with the CHG to give rise to Yamnaya. This brings up the question: are CHG the basal Eurasians? I doubt it. The paleodemography of the ancient Near East has been barely elucidated. It seems likely that CHG, like the Anatolian farmers, are a compound of some sort. Basal Eurasians may manifest as an allele frequency spectrum across the Middle East during this period, the remnants of a back migration from west Eurasian groups mixing with the ur-Basal Eurasians, who were the first to split off from the Out of Africa migration. In the colder and drier world of the Last Glacial Maximum (LGM) it seems likely that some of the northern hunter-gatherer populations would move into territory occupied by basal Middle Eastern groups. In addition, the Sahara had periods of extreme dryness during the Ice Age, so the ur-basal Eurasians wouldn’t necessarily have been able to withdraw to Africa.

Using G-PhoCS they inferred separation dates between the various populations. I have two issues with this. First, their mutation rate seems likely, but there is still some debate about the exact value and whether it is constant across a lineage (for this level of phylogenetic distance the assumption of constancy seems valid). Second, the confidence intervals from these results are huge. The authors report the results, and tentatively attempt to relate separation to the LGM ~20 thousand years before the present, but know that they can’t assert anything robustly. It strikes me that we know the sequence of separations between the groups better than the period of separations.

ncomms9912-f4 But one definite result is the pattern of ancestry (or shared drift) which is derived from CHG. It is high in the Caucasus, as one would expect, but also in South Asia. This is not surprising. Several papers have suggested that the West Eurasian admixture into South Asians seems to have an affinity with northern West Asians. Agriculture in South Asia began at Mehrgarh with a traditional West Asian cultural toolkit, and likely the character of the ANI-ASI admixture took root here. In Europe many researchers believe that the replacement of the hunter-gather populations in most areas was rather complete after the initial admixture event that occurred when farmers initially entered the continent, and it seems possible that the same is true in South Asia as well. There are no “Ancestral South Indians” in pure form left, and the variation in ancestry between tribes and caste groups in many areas is not very large.

dstat When you into the supplements though it all becomes much clearer. To the left you see a table of D-statistics, where the left column are Indian populations, and in the right column are the top hits, X, for these groups in terms of inferred gene flow with the tree form (Yoruba, X; Onge, Indian population). The key thing to note is that while some Indian groups have the strongest hit from the Kotias CHG sample, others, and of note the North Indian Brahmin Tiwari community, the signal from the Afanasevo is strongest. The Afanasevo are genetically basically the eastern extension of the Yamnaya. In other words, the D-statistics are showing evidence of a migration from the steppe, and a migration from West Asia. This also makes sense of supplementary figure 3, which shows non-trivial shared drift among some South Asian groups with the Swiss Bichon WHG sample. The Afanasevo would have brought this via their EHG ancestry, which was about half similar to WGH.

The evidence from uniparental (Y and mtDNA) and functional genes is also interesting. CHG carry mtDNA haplogroups H13 and K3, and Y chromosomal groups J and J2. It seems likely that the prevalence of haplogroup in H is due to post-Neolithic population replacements. The CHG contribute about half the ancestry to Yamnaya, but these two did not have haplogroup R1a or R1b. Haplogroup J2 is particularly common among caste groups in South India. All this points to the likelihood that the Dravidian languages are probably derived from agriculturalists with West Asian roots, and gives a touch more plausibility to the idea that ancient Elamite in Khuzistan may have been a distant relative of Dravidian.

Additionally, the derived light-skin variant of SLC24A5 is found among the CHG, as it is among the Anatolian farmers. The haplotype is the common one found in West and South Eurasian populations. The variant for SLC45A2 in Kotias is definitely homozygous for the ancestral variant. On the whole most South Asians do not share European light-skin variants except for SLC24A5. The exceptions tend to be groups in the Northwest, and upper castes. Exactly the same groups which likely have the strongest Afanasevo stamp.

One thing the authors note is that the Caucasus themselves have been subject to great change. It is clear that a farmer group related to EEF has mixed with the CHG descended groups. And, today the Caucasus has very high fractions of ANE ancestry in some groups, but these samples did not at all. At ASHG a few years ago a prominent population geneticist offered to me that he thought ANE might not have been the best term, as there was no strong evidence that this group wasn’t more common elsewhere. But CHG did not have ANE ancestry, despite that being very salient in modern trans-Caucasian groups. This suggests a later expansion and mixing event. From what I know ANE drift is not evident in many Indian populations, pegging the arrival of ANE-bearing groups to a later period after agriculture. Gene flow into Amerindian groups, and high ANE fractions in Central Siberia and the Altai, do point to their locus of habitation in Northern Eurasia.

Finally, let’s remember that we’re constructing the past from the slim remains which we have on hand. Ten years ago we were using extant genetic variation, because that’s all we had, and that led us astray. In the broadest sketches the inferences were right, but in many details they were misleading. Similarly, we shouldn’t think that the ancient DNA yielding populations are necessarily the direct ancestors of any modern groups. We know, for example, that Ma’lta is actually not ancestral to the ANE population which contributed to both Europeans via the EHG and Native Americans. The ANE drift of these two groups has more in common than with Ma’lta. Like the ancient Ethiopian genome there are many interesting conclusions one can derive from novel results, but to the first carving of nature’s joints is not always the best.

 
• Category: History, Science • Tags: Ancient DNA, Genomics

I’ve been traveling on business this weekend.

 
• Category: Miscellaneous • Tags: Open Thread

51jFjmwJ3SL._SX317_BO1,204,203,200_ Several weeks ago I found out that the historian Lisa Jardine had died. This saddened me, as I have appreciated Jardine’s works. In particular two works stand out in my mind. Worldly Goods, which I read when I was 18, and which helped me to understand that there was a different sort of history from the standard one written by diplomats and taught in elementary schools, and Going Dutch: How England Plundered Holland’s Glory.

The subtitle for the second work is in my opinion somewhat misrepresentative of what the tone of the book is, from what I recall. That being said, Going Dutch does impart to one a sense of the menace which was threaded through the symbiotic and antagonistic relationship between these two similar Protestant North Sea nations. And, while the 17th century is recalled as the period when England rose and Holland fell as great imperial mercantile polities, Lisa Jardine’s narrative does highlight that the so called Glorious Revolution was implemented with more of a Dutch fist than is commonly recalled.

 
• Category: History • Tags: Lisa Jardine
Razib Khan
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