Another article, More scientists doubt salt is as bad for you as the government says, in the respectable Washington Post, arguing that the salt dietary guidelines in vogue for the last generation were not based on strong science. The problem here is that bureaucratic organizations are making decisions about the health of hundreds of millions on correlational science. The incentives are skewed, and the decisions are not without cost. In the piece the journalist reports on studies which suggest that excessively low sodium content might be associated with health problems, but perhaps more important than that is that most people love salty food. Withholding salt is another way to diminish the simple pleasures of life from the populace at large.
An interesting twist on this public health issue is that it turns out that some of the original scholars argued against salt on “Paleo” grounds. That is, the small-scale and Pleistocene societies likely had very low salt intake, suggesting we were not well adapted for it. But the fact that until recently the salt guidelines for African Americans and those over 50 were more stringent implies that even then there are individual differences. Populations likely vary on “optimal” salt (or fat or sugar) intake.
A few days ago I mentioned bioRxiv to a friend of mine who is a graduate student. She didn’t know of what I spoke, so I enlightened her. Since many of the readers of this weblog don’t have academic access, and pay journals like Nature come after you if you upload PDFs (though the open access via link option is now obviating that), it is often very nice when people originally post preprints on bioRxiv. Sometimes I even link to the bioRxiv version (or the latest) because believe it or not VPN’s can be kind of annoying even if you have access.
On one of the e-lists that I am on there was a conversation about the scientific literature that one reads (see a blog post on the topic). Because the scientific literature in an area like “evolutionary genetics” is an eternal tsunami now you need various filters and aids. PubChase, SciReader and Genomics-Twitter are pretty essential. Recently on bioRxiv I noticed an alerts page. So I am now subscribed to this on my RSS:
Just change the parameters, and you get different subject areas.
Update: Also, I should mention Haldane’s Sieve. I think one major argument for how success that site is is that many people have no idea who is actually running the site, even if they are at the same institution. The message has become bigger than the messengers. And also a mention for Dmitri Petrov, who pushed for the Bay Area Population Genomics meetings, which is another way that scholars push friction costs down and continue the process of disintermediation.
God knows I would sleep more if it weren’t for bioRxiv. A new single author preprint debuts a new method, 3P-CLR, which extends XP-CLR, as a method to detect natural selection. The key is that it uses an explicit three-population tree to pick up selection events after the most recent, and second most recent, divergence events. So in the tree of ((Eurasians , Africans)Archaic Humans), this method can pick up perturbations which suggest selection after the emergence of a coherent anatomically modern population, but before it differentiated into its gorgeous mosaic.
A powerful way to detect selection in a population is by modeling local allele frequency changes in a particular region of the genome under scenarios of selection and neutrality, and finding which model is most compatible with the data. Chen et al. (2010) developed a composite likelihood method called XP-CLR that uses an outgroup population to detect departures from neutrality which could be compatible with hard or soft sweeps, at linked sites near a beneficial allele. However, this method is most sensitive to recent selection and may miss selective events that happened a long time ago. To overcome this, we developed an extension of XP-CLR that jointly models the behavior of a selected allele in a three-population tree. Our method – called 3P-CLR – outperforms XP-CLR when testing for selection that occurred before two populations split from each other, and can distinguish between those events and events that occurred specifically in each of the populations after the split. We applied our new test to population genomic data from the 1000 Genomes Project, to search for selective sweeps that occurred before the split of Africans and Eurasians, but after their split from Neanderthals, and that could have presumably led to the fixation of modern-human-specific phenotypes. We also searched for sweep events that occurred in East Asians, Europeans and the ancestors of both populations, after their split from Africans.
The software will be posted on the author’s github when the manuscript is accepted somewhere.
A minor note is that the data set used was from the 1000 Genomes. The Sub-Saharan Africans then are not from the hunter-gatherer populations, the Khoisan and the Pygmy, who seem to have the largest reservoir of genetic variation. The figure above is from a major signal of selection which is specific to modern humans, but excluded from the Neandertal populations. That is, fixed in us for a derived mutation, fixed in our cousins for the ancestral type (ancestral as judged by reference to the chimpanzee outgroup). My main curiosity is to push the three-population model so that it is ((Khoisan, non-Khoisan)Archaic Humans). I know from ASHG that there are now a fair amount of good quality whole genomes from African hunter-gatherers, so no doubt people are looking for these signatures.
The holy grail here for some geneticists (e.g., Svante Paabo) is to find that gene or genes which changed in us to make us sui generis. I no longer believe that this will ever be found. Assuming tens of millions of polymorphisms floating around in the genome no doubt candidate genes will emerge, just like FOXP2 did all those years ago. But I no longer believe that there is a necessary or sufficient genetic variant for our humanity. It’s a quantitative trait, and many of the hominin lineages were actually stumbling in the same direction.
On a more optimistic note, those of us who work on non-human genomes will also have data sets to rival those who are savants of humanics in the near future, so these methods are generally useful.
Citation: Testing for ancient selection using cross-population allele frequency differentiation, Fernando Racimo, bioRxiv doi: http://dx.doi.org/10.1101/017566
Years ago I recall a reader (perhaps Ikram or Conrad Barwa?) quip that I was basically Magid Iqbal from the novel White Teeth. Probably the biggest similarities are the fact that Magid is an atheist with a pro-Western outlook, and, he’s a geneticist. But a major difference is that the Magid depicted in White Teeth strikes me as a prig. And, there are obvious biographical discrepancies. Despite my parents threatening to send me back to Bangladesh periodically for impudence, they never did. I grew up in the United States, and have the citizenship of that country, as well as Bangladesh. And I’m quite glad to be an American right now, because of articles such as this: Atheists are being hacked to death in Bangladesh, and soon there will be none left. The sad conclusion:
This weekend I arrived in Bangladesh with the naïve hope of writing about wide-eyed idealists fighting the fight no matter what, fuelled with the zeal of Je Suis Charlie. The reality on the ground is much harsher: atheists are being hunted down for both religious retribution and political gain. Washiqur Rahman was right: words cannot be killed. But a struggling movement can only take so much battering, and Bangladeshi atheism is fighting to survive.
I’m not much interested in a “movement” of atheists. Bangladesh has other problems, and in some ways it is making progress. As I may have mentioned my mother was impressed and confused by the rapid economic development she saw across the country when visiting a few months ago (my parents left Bangladesh when the nation was only about a decade old). But these recent developments sadden me greatly, because when basic liberty of thought is an offense, then we see a society regressing. Mind you, I am not much the Whig, so this does not surprise me, nor does it strike me as unnatural. I think organized Islamism is atavistic in only a rhetorical sense. The reality is that it is a feature of modernity, or at least a reaction to modernity.
Words are cheap. And “solidarity” across the oceans is pretty much worthless. But I think it is something to at least say that there, but for the grace of God go I, ironically in this particular case. To me a measure of the worth of a society is its ability to tolerate heretics. That is why I sympathize with the ancient Hellenists, and not the waxing homogeneity of Christendom über alles. And that is why I think the world of Islam is today by and large an inferior vessel for human possibility. Not to sound too much a Spenglerian, but I do hope that this flare-up of Islamic violence is simply a reaction to the inevitable liberalism which is being ushered in by the demographic transition and economic growth evident across Bangladeshi society.
It seems strikingly obvious that modern humans are a pretty big deal. In Pat Shipman’s The Invaders she argues that H. sapiens can be thought of as a top predator which is so efficient that it rearranges the whole ecosystem, wreaking havoc with the conventional trophic cascades. We can see this in the archaeological record. Humans arrive in Australia, and all sorts of cool marsupial species disappear. A similar phenomenon is attested for the New World. The more recent extinctions on islands such as Madagascar and New Zealand are well attested.
Examination of an under-exploited source of ancient DNA—small-mammal remains—identified previously unreported and unprecedented temporal population structuring of a species within Europe during the end-Pleistocene. That we identify a series of population extinctions throughout the Pleistocene from a small-mammal species demonstrates an extensive and prolonged diversity loss and suggests a nonsize-biased reduction in ecological stability during the last glaciation, a pattern consistent with climatic and environmental change as key drivers for changes in Late Pleistocene biodiversity.
You can find similar arguments for other particular regions and areas. For example, in North America. The mysterious hand of climate is everywhere. To some extent it reminds me of arguments about the Indo-European languages, and their origin. “Out of India” proponents make points which would be just as valid for the Greeks, e.g. the early Indians and Greeks did not have a memory of being from anywhere else. Obviously the Indo-European languages are unlikely to both originate in India and Greece, but when examining just one area the arguments can seem persuasive. What needs to happen when assessing probabilities though is to get a sense of the broader framework of prior information. The same applies to the mass extinctions of the past few hundred thousand years. A new preprint on bioRxiv tries to do this, Historic and prehistoric human-driven extinctions have reshaped global mammal diversity patterns:
…Results: We find that current diversity patterns have been drastically modified by humans, mostly due to global extinctions and regional to local extirpations. Current and natural diversities exhibit marked deviations virtually everywhere outside sub-Saharan Africa. These differences are strongest for terrestrial megafauna, but also important for all mammals combined. The human-induced changes led to biases in estimates of environmental diversity drivers, especially for terrestrial megafauna, but also for all mammals combined. Main conclusions: Our results show that fundamental diversity patterns have been reshaped by human-driven extinctions and extirpations, highlighting humans as a major force in the Earth system. We thereby emphasize that estimating natural distributions and diversities is important to improve our understanding of the evolutionary and ecologically drivers of diversity as well as for providing a benchmark for conservation.
It’s a preprint, you can read the whole thing. Of course I’m broadly persuaded, since it only confirms rigorously what I already believed impressionistically.
Citation: Sexual selection drives evolution and rapid turnover of male gene expression
Charles Darwin’s sequel to was The Origin of Species is often known popularly as The Descent of Man. But of course the full title was The Descent of Man, and Selection in Relation to Sex. Darwin was then an early expositor of sexual selection theory, though R. A. Fisher also made his contribution. My own interest in the topic has been partly motivated by the fact that I perceive many people seem use sexual selection as a deus ex machina to explain variation or change where no plausible mechanism can otherwise be provided (recall that this has come up with EDAR). Over a decade ago Geoffrey Miller wrote a book, The Mating Mind, which attempted to take Charles Darwin’s original ideas to heart. I’m not sure how much of the original arguments Miller would stand by today, but it was an entertaining read. My own first encounter with the idea of sexual selection was in the work of Jared Diamond in the early 1990s. In particular, in The Third Chimpanzee he offered that racial variation in human types might be due to sexual selection for aesthetic characters, as opposed to ecological adaptation (see also Peter Frost’s model of the origin of European complexion). But all this conjecture of human variation often strikes me as a touch too speculative. Ultimately what does the theory and the patterns on the tree of life say? More substantively, as a genomicist I’m curious as to the sequence wide signals which one might see presuming a species is subject to sexual selection. Ergo, two weeks ago I blogged The Once and Future Genomics of Sexual Selection.
So naturally I was very interested when this came into my PNAS feed: Sexual selection drives evolution and rapid turnover of male gene expression. Basically the authors looked at differential gene expression and sequence level evolution across a lineage of birds to see if there were patterns correlated with presumed intensity of sexual selection. The figure above illustrates several such trends. Species which were subject to stronger sexual selection on males showed a higher proportion of male-biased genes. I’m not usually very interested in work on transcriptomes, but it strikes me that this is going to be a really big deal in the near future if sexual selection is common and it operates primarily through modifying patterns of gene expression. With only six species the p-values above aren’t the greatest. Perhaps the results won’t stick, but, they open a window toward examining evolutionary processes in a comparative manner which allows us to gauge just how pervasive sexual selection is as a force in driving phenotypic variation.
I’ll finish with this conclusion from the authors:
Taken together, our results indicate that the focus of sexual selection shifts rapidly across lineages. Our results also suggest that sexual selection acts primarily on expression, which may be more labile and less functionally constrained than coding sequence and therefore more likely to be influenced by short-term mating system dynamics among related species. The lability of gene expression evolution is illustrated in recent experimental evolution approaches that found an association between sex-biased gene expression and variations in sex-specific selection (11, 13). Gene expression lability is also clearly illustrated by the rapid turnover of sex-biased genes in our phylogeny (Fig. 2), which has also been observed in other animal clades (6, 46). Furthermore, rank order correlations show that gene expression divergence increases with evolutionary time across the Galloanserae (Fig. 3), again illustrating the lability of gene expression.
Citation: Sexual selection drives evolution and rapid turnover of male gene expression.
What’s going on? Pretty busy with life right now. Cleaning up the house for Easter.
I checked out The Anglo-Saxon World, and to my confusion it turns out be a “coffee table book.” Its scholarly standards are high, but the illustrations and the nature of the paper makes it heavy and cumbersome. I have no idea what the motivations here were, though I suppose the authors were aiming at a non-academic audience.
Update: Public service announcement. If your name is not Ron Unz and you are telling me what I should and shouldn’t post about, you will probably be banned from commenting. I’ve pretty much ignored reader advice in this area for 15 years (here’s looking at you Ikram) and will continue to do so.
One of the most influential books for me in trying to understand how the American system has operated in relation to “religious freedom” is Winnifred Fallers Sullivan’s The Impossibility of Religious Freedom. A lawyer, she recounts how the legal framework of balancing religious freedom and the conformity to law expected by the state arose in the United States in the context of a particular Protestant confessional framework. More precisely, the exact purview of religion was delimited in such a way as to be congenial with the cultural expectations of Anglo-American Protestantism, and what that implied as to the shape of what a “religion” was. Religious traditions in earlier centuries which did not conform to these outlines were subject to cultural censure, or even repression (for example, see Catholicism and American Freedom: A History). Once religious traditions such as Judaism and Catholicism conformed to the normative template of American Protestantism (e.g., self-identity as a congregation of individuals rather than an expression of corporate collective consciousness), tolerance and religious freedom were provided on a liberal basis. In The Impossibility of Religious Freedom the author argues that the emergence of religious groups which have a different conception of what it means to be religious, for example, emphasizing particular practices rather than creeds, is again challenging the ability of authorities to balance the need for conformity to universal laws and the particularities of religious identity.
It strikes me that the period between 1990 and 2010 was peculiar in the history of the United States. Though the nation was atypical in that its founding lacked the explicit imprimatur of a religious tradition, the culture of the United States and its elite was fundamentally derived from that of Anglo-Protestantism. In the 20th century Catholicism and Judaism were both absorbed into this framework (on the terms of Protestantism), reflected in Will Herberg’s post-World War II thesis in Protestant, Catholic, Jew. By the 1990s this consensus had collapsed, and a variety of religious denominations and liberals of a multiculturalist bent aligned together to pass the Religious Freedom Restoration Act. I am old enough and conscious enough of these issues to recall this piece of legislation. The old order may have collapsed, but religious belief was still normative, to the point that Bill Clinton was recommending everyone read Stephen Carter’s Culture of Disbelief. As an atheist it struck me as peculiar that religious beliefs were given special latitude in comparison to other beliefs. After all, all religious beliefs were founded on human fictions from where I stood. But, as an observer of human nature it did not strike me as strange, because it is simply a fact that religious beliefs are precious and emotionally fraught for individuals and communities, and have been for much of human history. Even if accommodation was not entailed by the principles of our governance (and it arguably is), it was a prudent action to mollify democratic sentiment.
But what’s happened in the past generation is that a massive wave of secularization swept through the culture. In American Grace: How Religion Divides and Unites Us the authors report on data which suggests that many people on the cultural Left have abandoned even nominal affinity to religious denominations and identity. Since the 1970s religious conservatives have been talking about “secular humanists,” but as someone who remembers being an atheist in the 1990s it was always obvious that this was a bogeyman with little substance. Only in the past few years have the warnings about secular humanism started to seem plausible, as a large minority of young Americans are actually unabashed secular humanists, with no fond memories of a religious upbringing. The old consensus is collapsing, and where the Left has won on the culture wars, such as gay rights, the lack of affinity with religious sentiments makes them very unfriendly to the arguments of religious conservatives that their sincere views deserve consideration.
This brings me to a post by Rod Dreher, Christians ‘Must Be Made’ to Bow, where he notes that some liberal commentators seem to be suggesting that religious truths should be updated in light of the Zeitgeist. As a religious believer of intellectual predilections Dreher believes that some truths are eternal, so changing them would be craven. As I am not religious I don’t think that this is true. Rather, religious sensitivities will eventually abate as older beliefs will be “contextualized.” In fact many American conservatives agree with this idea , except they agree with it for Islam, not Christianity. They assume that Muslims should reinterpret their religion to be more in keeping with liberal democratic norms of a plural and secular society, just as secular liberals do. The problem is that what is good for thee is not so congenial for me, even if Christianity in the previous hundred years was broken multiple times by the ascendant liberal democratic order.
If you’ve ever read The Origin of Species, and perused Charles Darwin’s multiform thoughts, you will note one major area of muddle: an incoherent theory of inheritance. More formally Darwin’s theory of evolutionary change via adaptation had within it the assumption that there was heritable variation upon which natural selection could operate. If you have no heritable variation, then natural selection operating on populations has no power to affect changes which persist over the generations. In the 19th century there was no consensus as to the nature of inheritance. The ideas of Jean-Baptiste Lamarck were still influential, and had an impact on Darwin’s early thought. Though some thinkers, such as Francis Galton in an inchoate manner, put forward models of discrete inheritance, by and large the assumption was that traits were passed down from parents in sexual species through blending of the characteristics of the parents. This is an eminently intuitive thesis, and persists down to the present. It is why there the incorrect perception that admixture between light and dark skinned populations will lead to a uniform brown hued future. By analogy to mixing between buckets of paint it is clear that blending eliminates the variation which is the raw material of evolutionary process via natural selection. More formally the variance of the trait decreases by a factor of two every generation under a blending inheritance model.
How did Darwin address this issue? “Provisionally”, in his own words. The fact was that until the discovery of the significance of Gregor Mendel’s work in the early 20th century evolutionary biology had no persuasive mechanism for how the variation which it was dependent upon could be maintained. But the situation was worse than even that. Over at arXivAlan Rogers has put up a short note, Rate of Adaptive Evolution under Blending Inheritance. He concludes:
Late in the 19th century, two misconceptions undermined the debate about evolutionary time. One of these—the age of the earth—has been widely discussed. Yet by comparison, its effect was minor. Victorians underestimated the age of the earth by 1 or 2 orders of magnitude. Their theory of heredity implied a far larger error. Had they worked this out, they would have had good reason for skepticism about evolution
Using some straightforward algebraic manipulations Rogers concludes that for a new beneficial mutation the rate of mean increase within the population under a Mendelian model as opposed to a blending scenario is 2N times greater, where N is the population size. He observes that ” In a population of 10,000 individuals, adaptive evolution would be 20,000 times slower under blending than under Mendelian inheritance, given equal mutational inputs.”
Another article, More scientists doubt salt is as bad for you as the government says, in the respectable Washington Post, arguing that the salt dietary guidelines in vogue for the last generation were not based on strong science. The problem here is that bureaucratic organizations are making decisions about the health of hundreds of millions on correlational science. The incentives are skewed, and the decisions are not without cost. In the piece the journalist reports on studies which suggest that excessively low sodium content might be associated with health problems, but perhaps more important than that is that most people love salty food. Withholding salt is another way to diminish the simple pleasures of life from the populace at large.
It seems strikingly obvious that modern humans are a pretty big deal. In Pat Shipman’s 
