Geography of Genetic Variants Browser


Jonathan Novembre’s lab has released a new toy web 2.0 toy which you might find of interest. From an announcement on the lab’s website:

We have released a new teaching/research tool.  The Geography of Genetic Variants browser.  This is the hard work of our “programmer-at-large” Joe Marcus.  It’s also a pilot project for a grant we submitted earlier this summer to work on challenges that arise visualizing population structure in genomic-scale variation data.

This is very beta. E.g. “More features are on the way…scaled circles as alternates to pie charts, computing a bounding box for regional datasets, pdf export for publication quality figures, and search by rsID or tables of markers. Contact us with any ideas!” I’d like rsID in particular, since that’s what I know off the top of my head for variants of specific interest.

Why is this noteworthy? It seems that the group is trying to integrate disparate data sources and present the results in a comparable fashion. This is useful. The HGDP, HapMap, and 1000 Genome Browsers are great, but obviously they focused on a narrow subset of human genomic data (also, they’re from an older web era, when everything was synchronous GET/POST). Geography of Genetic Variants Browser is also displaying results from the POPRES data set, which is kind of them since only academic researchers who have duly inquired and obtained permissions can view this. Hopefully they won’t stop there, and the code is such that they can just integrate new data sets in a rolling fashion. And why limit it to humans? The fly people have enough geographic samples to browse pretty maps.

I found this via Pontus Skoglund, who asserts that you “get a feel for the stochasticity of human genetic variation” if you click the random option. That’s actually sort of true. It’s also evident that there’s geographic structure, and that structure starts to get consistent in a Gestalt sense if you click dozens of times. You can also see that the allele frequency difference in Africa vs. non-Africa is large, while that within Europe is modest (some sort of smoothed kernel density might be a nice complement to pinned-pie charts; there are many R packages which could handle render that).

Finally, this browser is a pilot project which might lead to a grant that is aimed at tackling visualization of population structure. That’s a big deal. Perhaps I’m wrong, but it strikes me that the 1000th PCA package that runs 10% faster than Eigensoft is probably more a CV-builder than anything else. There are lots of good analysis packages out there, though the PaintMyChromosomes project gives you an idea of where there’s still fruit to be picked. On the other hand tools to visualize and comprehend the analysis that’s bubbling up are few and far between. Not everyone is a “command-line fiend,” and it is in the GUI that you get purchase with the public. Genomic science needs that.

Addendum: Also, there is something called the Midwest Population Genetics conference being organized now. I’m sure it’s a coincidence that they used the term genetics rather than genomics, because when looking at their program it was rather heavy on -omics. Let the battle between freshwater and saltwater genomics conferences commence!

Facebook: being wrong

fb_icon_325x325Long time readers know that around 2010 I was a Facebook skeptic. I would periodically check Google Trends results, and post them, to illustrate that the phase of exponential growth was ending (you saw that in user base too). The Social Network film also seemed to herald the top of the cultural influence of Facebook. Well, whatever the search engine terms are, as a matter of business viability it seems that I was wrong, Facebook has not peaked. The fact that I stopped talking about Facebook is a clue to that, since I would no doubt be posting my vindication if I had been right. But I thought admitting I was wrong in public might be useful, in particular since others are.

Reality may not have your bias

nationsbookI’ve expressed a little disappointment in a book I recently read, Azar Gat’s Nations: The Long History and Deep Roots of Political Ethnicity and Nationalism. There are two primary reasons for this. Nations simply does not measure up to his previous work, War and Human Civilization. But that is perhaps not a fair assessment, since War and Human Civilization is quite possibly Gat’s magnum opus. A second issue is that the core assertion in Nations is quite modest, and not entirely at variance with conventional intuitions. Basically, Gat is refuting a modernist view, which has arguably gone from being revisionist to normative, that the concept and execution of a nation is a historically contingent construction of early modern Europe, and more precisely Revolutionary France of the 1790s. This is not an unfounded characterization of what the default position for many is, I myself have parroted the idea that the nation-state was “invented” by the French in the 1790s. This may be a vulgarization, but I’ve heard others express the same sentiment in the years since I first encountered this thesis in high school. It’s one of those “fun counter-intuitive facts” which has the beauty of simplicity, and the drawback of almost certainly being false on the face of it.

But note that I qualified the nation-state, rather than nation unadorned. When properly qualified and delineated one can perhaps defend the empirical validity of the idea that something unique emerged in early modern Europe after the Peace of Westphalia, and culminating in the Congress of Vienna. The problem is that the model being presented is usually not couched in modest terms. In hindsight the idea that nationalism is an invention of early modern Europe, and Revolutionary France, has as much plausibility as the idea that the Troubadours of the Provence invented romantic love. Yes, there are particular motifs and forms in the idea of love as it is culturally practiced in much of the world which may have its roots in this period and place, but I think it is totally misleading to assert that “love” is a cultural invention of the medieval West, as a common vulgarization goes.* Rather, love has a deep cognitive and evolutionary basis in our lineage, and manifests in a variety of ways in different social contexts. There isn’t a part of the brain which is our “love region,” rather, it is an emotion which synthesizes basic elements of human nature. It is not particularly surprising that romantic love is going to be more salient in an individualist society with consumer surplus, but that does not mean that subsistence level peasants lack the basic cognitive facilities because they had not been properly enculturated.**

Obviously there are differences between the phenomena of love and nationhood. The latter is a much more ‘high level’ phenomenon in terms of social complexity. Nationhood can not be understood except in the context of aggregates, while love is a phenomenon that can play out in dyads.*** Gat’s thesis is that given particular conditions nations are a primal unit of organization for humans. Those conditions obviously include a rate of primary economic productivity and elaborated social complexity which can support supra-tribal political units. Notice here that a state as we understand it is not necessary; the Greeks of the classical period were a nation, but they lacked a state. Nations supports Gat’s thesis with a literal flood of historical facts. Much of this is interesting. But, it presupposes that the readership can actually judge the selection and veracity of said facts. I can, because I know a lot of history. But I suspect that for readers with a weaker historical knowledge base a book of half its length would have sufficed. Second, throughout the narrative Gat refers to the modernist scholars who he is refuting extensively, but repeatedly suggests that even they don’t subscribe to the extremist caricatures of the origins and invention of nationhood (at least implicitly).

To state it in extremely plain language Nations argues that nations which are persistent have coherent cultural cores, which are more robust than states. To me this seems uncontroversial and obvious, but I do know that plenty of people find this surprising. Additionally, there is the problem that many lack the nuance to understand what this does, and doesn’t, mean. Consider for example the Byzantine Empire. As an empire one can immediately infer that it was multicultural, in that multiple nations were under its rule. It is a curiosity to note that until its last the Byzantines considered themselves Romans, and thought of their empire as the Roman Empire. Notwithstanding this peculiarity from the middle of the 7th century the core cultural identity of the Byzantine Empire was that of Greek speaking Christians. That Christianity varied in theology (e.g., see Monothelitism), but those within the Byzantine Empire and outside of it who adhered that position were consider orthodox and part of the imperial party.**** Additionally, Greek was obviously the language of the elite. In the classical Byzantine period between 650 and 1100 most of the emperors had ethnic origins which were clearly not Greek (e.g., Syrian and Armenian), and likely not orthodox (since certain ethnicities, such as Armenians, had national churches at variance with Byzantine orthodoxy). But nevertheless these individuals assimilated to the ethno-cultural identity which was hegemonic throughout the history of the Byzantine Empire.

Gat’s idea about nationhood is multi-textured, and gives due respect to the fact that the ancients held multiple ideas interleaved in their own minds. Nations were generally conceived in a manner which presupposed common descent and biological unity. That is, the population were descended from legendary founders. And yet they could also acknowledge composite origins. For example, the Romans were a Latin people, but they also had Sabine antecedents at the founding, including some of their most famous patrician families, such as the Claudii. Though the common Latin core persisted down to the fall of the Empire, it was integrative and assimilative. The Roman Empire was multicultural, but it was ruled by a Latin speaking elite. Gat points out that by the 5th century in much of the Roman Empire local languages and identities were fading, so that what had been an core ethno-cultural group was transforming into a majoritarian nation. The local populations conquered by Germanic tribes referred to themselves as “Romans,” in contrast to their rulers. And this illustrates the common sense model which is exposited in Gat’s work, nationality emerges and coalesces organically from loyalties and allegiances at a lower order of organization, and extends gradually upward and outward. The stylized contrast is the idea that nationhood is extruded ex nihilo from the minds of ruling elites in a specific period and place.

All of this is at the front of my mind while reading what’s going in the news right now. Consider two pieces in The New York Times, In a Syrian City, ISIS Puts Its Vision Into Practice and Report Cites ‘Aggressive’ Islamic Push in British City’s Schools. From the first piece:

…The traffic police are based in the First Shariah High School. Raqqa’s Credit Bank is now the tax authority, where employees collect $20 every two months from shop owners for electricity, water and security. Many said that they received official receipts stamped with the ISIS logo and that the fees were less than they used to pay in bribes to Mr. Assad’s government.

“I feel like I am dealing with a respected state, not thugs,” said a Raqqa goldsmith in his small shop as a woman shopped for gold pieces with cash sent from abroad by her husband.

From everything we read it seems that a shockingly high proportion of the front line troops of the Islamic State are psychopaths. By this, I don’t mean that they are normal people caught up in conforming to a cruel system, but that they are literally mentally unstable violent individuals. The fact that the Islamic State can organize a less venal system of political order than what came before in regions under its rule despite the human capital it has to work with tells you something both about the Islamic State and its enemies. It is cliche to suggest that the “nation-states” of the Middle East are all artificial kleptocracies derived from the imaginations of Europeans. What is less palatable is to admit that the Islamic State is presenting a positive vision which can impose order upon its subjects as well its less than mentally normal foot soldiers. I don’t think this is scalable or sustainable, but it is something we have to admit as truth. The Islamic State has Asabiyyah.

The second article is about the fears over Islamic fundamentalism taking over state sponsored faith schools in Britain. Here the back-story is that Britain has long mixed state and religion, ergo, education and religion. So with a large Muslim minority, and in some regions a majority, it is reasonable to expect that Islamic faith schools would emerge. The problem is that modern Britain also demands these schools adhere to particular Western liberal norms. There are debates aired within the article whether the British government’s reports on Islamic fundamentalism within these specific schools are exaggerated or not. That’s not my focus or concern in this post. Rather:

One public high school at the heart of the Trojan Horse controversy, Park View Academy, was ranked as one of the worst schools in Birmingham in the 1990s, with most students failing their final exams. But by 2012 it had received top marks from school inspectors, and nearly four in every five of its students now go on to university.

The dominant element in the Muslim population in the United Kingdom is from Pakistan, with the majority overall being from South Asia. These Muslims are likely Europe’s most socially conservative, and the dominant British ethos of multiculturalism is such that they are given free rein to develop their own identity (which is something somewhat different from that of their South Asian lands of origin). The fact that “British nationals” are prominent in overseas jihadi movements should be a tell that a substantial element within this population has an identification with worldwide Islam that is inimical to their integration into broader British society, which is post-Christian and liberal. Would it be entirely surprising if a population which has a conservative Muslim ethos would have more “buy in” to public education if they felt that that education reflected their deeply held values?

The New York Times piece quotes the British education secretary as saying ‘These people had “a restricted and narrow interpretation of their faith,” and had failed to promote fundamental British values and to challenge.’ Two points. First, where does the British education secretary get off critiquing how British Muslims interpret their faith when there’s been generations of hands off multiculturalism? As a person of no faith I don’t particularly privilege faith in any way, but Western liberals have been playing an inchoate game for several generations about the nature of religious liberty. There is no free lunch. If religious liberty is a fundamental right, then you should expect some religious people to cry foul when you constrain that right. Second, what exactly are British values? Tolerance, diversity, and respect for the Queen? British Muslims isolated in their ethnic ghettos have a clear and crisp voice from conservative and fundamentalist Islamic theorists in terms of what their appropriate standards of behavior and belief should be. I don’t see any such clarity from the British state, so as a matter of description it is entirely predictable that bringing a large population with such a different historical experience would result in a culture clash.

The problem is that Western liberals want to have their cake and eat it too. They want to tolerate diversity, but that diversity is constrained by the fact that their own vision of what is a “fundamental human right” is peculiarly isomorphic with the social consensus of their societies’ elites at a particular time and point. The current focus on LGBT rights is perfectly illustrative of this dynamic. Social and political thinkers who have only recently “evolved” on this issue, within the last 20 years, now wish to promote tolerance for LGBT individuals in a world where broad swaths reject that proposition. The reality is that this is Western cultural imperialism. Of the humane and good sort, just as the British campaign against suttee, but that is what it is. People whose ethos is non-Western see clearly that this is the specific and historically contingent ethos of a Western global elite, while Western thought leaders continue to speak of “universal human rights,” out of time and history, eternal.

Human social existence is thick. It is multi-textured and threaded with diverse strands, some at cross-purposes. When we attempt to model this complexity with thin abstract stylized models, we often fail. In the 19th and early 20th centuries a particular sort of biological model arose of nationality which conceived of the English and German races, where nations were inevitable and primordial expressions of genetic relatedness. After World War II such views fell into disrepute, and ideas of civic nationalism arose which seemed to presume that the nation-state could arise out of the will of elites within a single generation. Both of these are thin models which fail to predict the organic waxing and waning of nations, because they elide causal complexity. With simple models in hand it is hard to understand history and current events, because human behavior can confound in its riotous unpredictably. There are no short cuts here. The maxim to make models as complex as needs be, but no more, is easier to follow in the physical sciences where the models are actually not that complex!

* There are other non-Western candidates proffered for the inventors of love, so this need not be an issue of Eurocentrism.

** Even if romantic love did not loom large in the life of a peasant family in medieval Germany, to give an example, love as a generalized emotion surely existed between mother and child, and so on. I doubt the cognitive competencies here are separable, so humans likely retain a capacity for romantic love even if it is not culturally prominent.

*** Or in the case of narcissists, one suffices.

**** Ergo, even in Muslim lands those Christians who adhered to the Byzantine formula were “Melkites”, “imperial.”

Psychiatric genomics…or psycho-genomics?

Citation: Nature (2014) doi:10.1038/nature13595
Citation: Nature (2014) doi:10.1038/nature13595

Biological insights from 108 schizophrenia-associated genetic loci:

Schizophrenia is a highly heritable disorder. Genetic risk is conferred by a large number of alleles, including common alleles of small effect that might be detected by genome-wide association studies. Here we report a multi-stage schizophrenia genome-wide association study of up to 36,989 cases and 113,075 controls. We identify 128 independent associations spanning 108 conservatively defined loci that meet genome-wide significance, 83 of which have not been previously reported. Associations were enriched among genes expressed in brain, providing biological plausibility for the findings. Many findings have the potential to provide entirely new insights into aetiology, but associations at DRD2 and several genes involved in glutamatergic neurotransmission highlight molecules of known and potential therapeutic relevance to schizophrenia, and are consistent with leading pathophysiological hypotheses. Independent of genes expressed in brain, associations were enriched among genes expressed in tissues that have important roles in immunity, providing support for the speculated link between the immune system and schizophrenia.

This publication is accompanied by a massive grant to the Broad Institute for the purposes of making discoveries in the field of psychiatric genomics. Eric Lander is a brilliant scientist, but boy can he bring in the dollars. Psychiatric genetics has been around for a while, from the days of linkage studies to association analysis. But it’s been plagued by inability to replicate positive findings, strongly suggestive of issues of sample sizes too small to have the power to answer the questions being posed robustly. The people associated with the Broad Institute are smart. Hopefully they don’t have to worry about adding a line to their CVs with studies they’re not totally sure of. With these sorts of sample sizes there is a chance that they can brute force their way past some of the expected problems of finding genuine novel genetic associations when a trait his highly polygenic.

Finally, perhaps with some of the $650 million allocated to this research they could publish in journals that are open access or pay Nature/Science/Cell to have them open access? If you look at the author list it’s enormous. These projects in the future are going to involve many different research groups, and a substantial portion of peoples’ careers. It is probably optimal that this research is widely distributed partly to stimulate interest from those who are thinking about a career in science.

Addendum: I can see why they don’t call it ‘psycho-genomics.’ But it would be fun.

Because Science…Maybe…Sometimes

I am a child of the 1980s and early 1990s. Therefore I remember many things which I would perhaps like to forget. One of those things is the monomaniacal fixation on “low fat” which permeated our culture during the decade before the internet became mainstream. My mother used to buy us boxes and boxes of SnackWells fat-free cookies, which it turns out are almost a pure concoction of white flour and sugar. In The Big Fat Surprise: Why Butter, Meat and Cheese Belong in a Healthy Diet Nina Teicholz recounts that this brand of cookie was so popular that the manufacturer had to ration it across the distribution chain, they just couldn’t keep up with demand. Teicholz’s book basically seems an update of Gary Taubes’ Good Calories, Bad Calories. Many of my friends live and die by Taubes’ body of work, mostly because it produces results which are sustainable for them. The revolution in our perceptions of nutrition over the past generation can be summarized by the fact that The New York Times is willing to publish an article with this title: Study Questions Fat and Heart Disease Link.

What to think if you are a “well informed” person when the information changes so often and quickly? Melinda Wenner Moyer’s article in Aeon, Against Grain, is a good place to start. She observes:

In the midst of all the claims and counterclaims, there is a single clear piece of common ground. Experts of every stripe ask dieters to avoid refined sugars and grains. ‘Losing body weight on a plant-based diet is much less likely to occur if the diet includes too many refined carbohydrates,’ writes Cornell’s T. Colin Campbell in his book, The China Study, based in part on his Cornell-Oxford-China study research. Esselstyn instructs his dieters to consume only whole-grain products and avoid fruit juice. And McDougall urges his readers to eat complex carbohydrates instead of refined sugars and flours.

So where does all this leave us, other than confused and wondering if we should stop eating cupcakes? On the health side, the science does collectively suggest, but not prove, that a calorie is not always just a calorie, and that carbohydrates – particularly refined ones – might have unique metabolic effects that increase risk for chronic disease. Indeed, the notion that sugar and refined carbs are dangerous seems to be the one point on which nutrition scientists at either end of the carb-fat spectrum agree. I suspect that my weight-loss success a decade ago had something to do with the fact that, by cutting out wheat, I was replacing some refined carbohydrates with other macronutrients.

The problem here is what Jim Manzi in Uncontrolled terms “high causal density.” The most famous researchers, such as Dean Ornish and Robert Atkins, tend to present you with one-size-fits-all strident solutions. But the fact is that there are people who remain thin, who do not exercise, and consume processed carb and sugar.* I know them, and you probably know them. There are many factors which go into the end product of a person’s physical appearance and overall morbidity risk. On an aggregate scale of societies a few significant variables changing can result in enormous differences in outcomes, but people need to see efficacy on the individual level, and the causal signals can be confusing (in particular if efficacy varies from person to person for the same regime!).

A bigger issue has been institutional health’s monomaniacal focus on fat and a few biomarkers has left many not trusting scientific recommendations. That focus is shifting, as science does update. Unfortunately the generation of new robust inferences is noisy and prone to dead ends in domains of high causal density. This is not always the case in public health. It turns out that the model of germ theory is not too subtle; it describes the world in pretty uncomplicated terms. Similarly, why and how vaccines work is tractable because the etiology of how you get polio is much easier to tackle than how you get type 2 diabetes. In all likelihood there are many ways to get type 2 diabetes, and multiple factors impact different people at different weights (e.g., there are people with a greater genetic disposition to type 2 diabetes given the same exercise and nutritional regimes, though one might be able to explain this with something like the nature of fat deposition).

This reality of science as a messy and iterative process is obvious to anyone who practices science. A year ago I had a conversation with a friend who happens to be a professor of biology at a university, and we were talking about the problems with convincing the public about the efficacy of vaccination. He admitted that he had a bit of guilt in this area because when it came to his own health he took a very critically-rational perspective as to what his physicians told him. As someone who was aware of the protean nature of scientific literature he had no great confidence that the recommendations from on high were definitive or the “final answer.” Another friend who is a medical doctor did admit to me that for him patients who had a good science background were a pleasure to work with because for them healthcare was a collaborative process in which they were active participants, instead of being recipients of his commands ex cathedra. This reality is why I am somewhat uncomfortable with the “Because Science” meme. It attributes to science almost Solomonic powers of judgment, and in actuality is wielded to reinforce the prior conceptions of interlocutors.

Where does that leave us? Describing a problem is not a solution, and due to the nature of the reality here there isn’t an easy answer. But it does imply to me that we should be cautious about engineering aspects of human life when the scientific basis for that engineering is less than certain. The war on fat and salt over the past few generations have been due to putting science forward as the basis of policy which turned out to not be robust. In the case of salt the establishment has even done an about face, “the government says there is no good reason based on health outcomes for many Americans to drive their sodium consumption down to the very low levels recommended in national dietary guidelines.” Salt tastes good, so one can imagine just how much utility was left on the table because people changed their diet to become more insipid. Policies have consequences.

cupcake-red-velvetIncreasingly new way of thinking about diet has been to focus less on the latest science, and fall back on cultural culinary history. “Eat like your grandmother cooked” is trendy advice proffered by influential writers such as Mark Bittman and Michael Pollan. But by removing heavily processed foods it might be a major upgrade from modern diets, which are designed to sustain the profits of the food industry, not our own health (that’s a negative externality, the cost of which they don’t have to eat). Whether you go mostly plant-based or carnivorous, you’re probably going to be fitter in either direction, even if one is superior to the other at the end of the day.** Instead of deduction from what we know, anengineering an appropriate nutritional outcome, in the best course of action in the near future is probably “hipster nutrition.” Artisan hand-crafted diets which look back to the past, though in a non-ironic fashion, might be the best way to go because they’re the outcome of hundreds of years of innovation and experimentation. If you don’t have randomized control trials, go with the next best thing. History.

* Whether they are healthy is a different question obviously.

** One issue is that the different options might be superior for different people.

Open Thread, 7/20/2014

Natures-God-The-Heretical-Origins-of-the-AMERICAN-REPUBLIC-book-coverAlmost done with Azar Gat’s Nations. But I’m violating my preference for reading books serially by simultaneously going through Matthew Stewart’s Nature’s God: The Heretical Origins of the American Republic. It’s actually a hardcover book, as Stewart sent me a review copy. That makes it feel a little different when it comes to switching between Nations and Nature’s God. I’ve been a fan of Stewart’s books for a while, and did a 10 questions with him in 2006. There’s a lot in this book that I knew from more conventional history about the founding (see Jay Winik’s Great Upheaval), but I’m enjoying the interleaving of ancient philosophy. Stewart does a great of intellectual detective work from what I can tell. If you don’t know much about philosophy, but are curious to peruse a non-academic survey, the author’s previous work The Truth About Everything: An Irreverent History of Philosophy will be worth it.

Also, I’ve been a little disappointed by Nations. It’s good, but not nearly at the same level as War and Human Civilization. In that book the author had greater command of the material and clarity of presentation, so he didn’t try to keep hitting you over with the same point over and over. I’d still recommend the book, but readers should focus on the factual yield rather than the coherent thesis, since the basics of the latter are obvious early on.

Domestication due to the neural crest

"Domestic fox"
“Domestic fox”
The latest issue of Genetics has an interesting hypothesis paper, The “Domestication Syndrome” in Mammals: A Unified Explanation Based on Neural Crest Cell Behavior and Genetics. It sounds grand, but if you read the details it makes a lot of sense that changing the developmental pathway of neural crest cells has perturbed a great many traits. The target of selection in this case is “tameness,” the exact parameters of which they elucidate in the text. But there are numerous other phenotypic side effects which are hallmarks of domestication. Basically these are likely the outcome of the genetic correlation, as a given genetic alteration can have multiple downstream consequences. The paper is open access, so I invite you to read it yourself and make up your own mind.

For me the most interesting point is the argument that across mammals (and perhaps other vertebrates!) the disruption of development is due singularly to changes in neural crest cells, but on the genetic level the evolutionary process is polygenic and diverse. In other words the developmental pathway will exhibit similarities, ergo, similar correlated side effect traits. But the genetic architecture of the change across species may vary, because there are many genes which are effected by the phenotypic target of selection. Another way to state this is that there is no gene for domestication in the lineages under consideration, but rather many genes which have significant, but not overwhelming, effect. Of course there’s polygenic, and then there’s polygenic. One of the common side effects of domestication is depigmentation of the pelage of mammals, but this is one case where the number of genes effecting the trait is relatively low, on the order of ten genes account for more than half the variation. In contrast you have polygenic traits like height where you’re lucky to find one locus which can explain one percent of the variation. If domestication is like the latter then the role of standing variation in the evolutionary story is going to be large, nearly total. In contrast if pigmentation is representative than classical selection on new mutations of large effect unique to particular lineages may still be important. Not to be lame, but the answer is probably going to be in the middle, on average.

Second, there are broader questions about contingency, the genetic architecture of salient traits, and selection as a driver for adaptation, which come to mind after reading this paper. It seems hard to deny that if you constrain the phylogenetic space enough then there are many instances where evolutionary forces will basically result in broadly similar phenotypic and genetic outcomes. Though there are some differences in traits and genetic variations, there is a great deal of overlap across mammalian taxa which have been targeted by artificial selection. Though the authors don’t address this directly it, seems clear that many of the phenomena which revolve around domestication also apply to humans. If they do, and if “domestication” occurs through gradual selection upon standing variation, then the search for the gene which makes us uniquely human (e.g., “the language gene”) may be futile. Rather than a gene, our humanity may have emerged out of gradual change as the underlying frequency of alleles is shifted. This is not a sexy answer which will result in genomic fame for a researcher who discovers the gene-which-makes-us-human. Finally, there is the issue where we bracket artificial selection and domestication as if they are unique processes which derive from human agency. My own position is that though for semantic purposes we may speak of ‘artificial selection’,’ sexual selection’, and ‘natural selection,’ there’s really no fundamental difference at the root for these phenomena. Selection is selection, and the rest is commentary. To me that implies that attempting to understanding domestication may actually allow us to understand evolution more broadly (and Charles Darwin would agree with that point I suspect).

Social-political sectarianism swallowing public reason

Jacques Derrida
Jacques Derrida
Jargon is important. But it must be used judiciously. The term “allopatric speciation” may seem daunting, but it’s basically a pointer to a clear, distinct, and coherent idea. Too often scientists, and scholars more generally, get lazy in using jargon when they needn’t. But the original intent and roots of jargon and technical terminology is to condense complex and subtle ideas into one term which can serve as shorthand for specialists.

But there is another use of jargon, and that is to impress, intimidate, and signal that you are one of the initiates. Ideally jargon should facilitate faster and more transparent communication among specialists in a given topic. But in some cases jargon becomes a tool for intra-group argument, posturing, and maneuvering. It’s a stylistic flourish which connotes, rather than a substantive pointer which denotes. For example, I’ve been a bystander to arguments among conservative Christians who debate whether a particular political position is “glorifying Christ.” I have no clear idea what “glorifying Christ” means, but all the principals to the argument agree that it is a good thing, so it seems to me that this sort of utilization of the term in is mostly tactical and stylistic.

Recently I’ve been noticing a similar phenomenon in online discussions to which I’m am observer. Many on the cultural Left have started to engage in a seepage of jargon from critical theory into political arguments. The problem here is that politics is a public discussion, not discourse among specialists, so falling back on jargon narrows the horizons of engagement. To me the proliferation of terms such as ‘cultural appropriation’, as if everyone knows what that means (and if you don’t, your opinion is irrelevant), signals that the discussants are attempting to score points in their own social and political circles. Similarly, when Neoreactionaries using terms like the Cathedral they’re closing off the conversation to outsiders, and creating a group with initiate-like dynamics. Often American conservatives will talk about “liberty” and “freedom” in a manner which is more symbolic than literal (most people who are not conservatives also think liberty and freedom are good things). And libertarians have their own internal group language which points to divisions which are perceived to be significant within their own circles, but are totally opaque to outsiders.

The proliferation of this tendency across the political spectrum argues that our society is fracturing in a deep manner, as shared public lexicon is less important than winning internal battles within each faction. To some extent I think it also correlates with the decline in arguments over material-economic concerns, and the rise of cultural politics. Yes, there are populist noises across the political spectrum, but the status quo is rarely altered when it comes our economic politics today. For the social elites the cultural battles is what concerns them.

Why I’m not signing up for Kindle Unlimited

O2-slate-04-lg-appsMy household has three Kindle Fire tablets (two of them HD). Obviously they are used for things besides reading books, but the main reason for their purchase was as text delivery devices. If I an extra house to store physical books and a manservant of some sort to manage the collection, I would be very happy with “dead tree.” I had a professor years ago who admitted he had an extra house which he ended up filling with his enormous book collection, to the annoyance of his wife. I can’t imagine being in that situation, but my “book habit” was getting out of control by the middle years of the 2000s. Moving was starting to become a major chore which I dreaded because of the boxes of books. And I don’t miss lugging around large numbers of books when I’m going on a road trip. I am well aware that there are unintended downsides to signing on to the e-book revolution, and Amazon in particular. But the convenience factor is just too high. And yes, I’m a pretty big user of Amazon Prime; I never liked physical shopping.

So I was curious when Amazon launched a subscription book service. The New York Times reviews the pro’s and con’s, Amazon Unveils E-Book Subscription Service, With Some Notable Absences. Some people are calling it a glorified library card. If that was the case I would probably sign up. But looking at the collection of books I don’t see many recent academic press publications, which is the largest proportion of my reading. So as it it happens it isn’t a glorified library card. So I’m not signing up, even though the price point isn’t high at all.

Caste system probably does increase load of recessive diseases

Runs of homozygosity in North Indian Punjabi Brahmins, non-Brahmin Tamils, and Northwest Europeans (left to right)
Runs of homozygosity in North Indian Punjabi Brahmins, non-Brahmin Tamils, and Northwest Europeans (left to right)

The above figure is from Population and genomic lessons from genetic analysis of two Indian populations. What you see here is that two Indian Hindu populations from the north and south of the subcontinent have clearly elevated stretches of genomic homozygosity in comparison to the classic Northwest European population of whites from Utah. This is interesting because the social practices of the two groups here are quite different. Some South Indian Hindus practice consanguineous marriage; e.g., first cousins or uncle-niece. This is evident in some individuals in the data set. But North Indian Hindus traditionally enforce significant exogamy among relations via the gotra system and seeking partners outside natal villages. And yet the genomic evidence indicates a relatively small effective population. That’s because though North Indian Hindus practice exogamy on the scale of families, they nevertheless usually marry within a local caste. The effect of this genomically was one of the less trumpeted findings of the 2009 paper Reconstructing Indian Population History. India may have a very large population, but the genealogical history of many of its people is sharply delimited. This recent paper uses exomes, and I think clinches the finding.

Second, two data sets that I stumbled upon in case you don’t know which are in VCF and phased Beagle format (though the newest release of Beagle uses VCF anyhow):

Singapore Sequencing Malay, 100 Malays.

Singapore Sequencing Indian. 36 individuals. Mostly South Indian Tamil.