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71qnces9omL._SX450_ Over a year ago at my friend David Mittleman’s recommendation I got a Fitbit Aria Wi-Fi Smart Scale. The reason was two-fold. First, I’d been monitoring my weight since 2010 by using a spreadsheet, but I liked the idea of just jumping on the scale, and having it automatically record the weight. Yes, definitely a “First World Problem”, but it reduces even the need to think about recording my weight. Second, the scale also purports to measure body fat percentage. I say purports because many people are skeptical of the results because it utilizes bioelectrical impedance. But I still thought it was worth it because as long as it was precise, even if not accurate, I could see a possible trendline. Over the past year my body fat percentage has declined from ~20% to ~18%. This seems validated by the fact that my waist has also gone down an inch, as I can easily fit into 29 inches instead of 30 (my target is 28, which is where I’m at when I’m genuinely lean).

Obviously what you look like and what you can fit into is the best measure of your body fat. But I’m a bit of a quant nerd, so when a reader suggested that the Omron Body Fat Loss Monitor was better than the Aria, I purchased it. It uses the same method, but while the Aria is a scale, the Omron is a device which you grip two-handed. Yesterday I tested the Omron three times. The results came back in the 17 to 18 percent range. Perfectly in line with the Aria. I also had a few friends of various sizes and male and female use the Omron, and it seemed to make sense. My friend who came back at 7%, is totally believable at 7%. And the women always came back with higher proportions for their build than the men.

webpreview_htm_be9c6222 So how do I measure up? Below is the data from the CDC drawn from a survey of American males in the early 2000s. I’m definitely below average in my age class, but the curve here is not particularly strenuous (in fact, I might just fall into the “ideal” range for my age, though that’s contingent on the reading being accurate and population typicality). My ultimate goal is get below 15%. At that point I’ll stop caring much besides maintenance. Most of the guidelines seem to suggest that the border between fit and average body type is 17%, but I’m of South Asian ancestry, so I’m at higher risk for metabolic diseases. I suspect I’ll have to reduce my body fat percentage down further than the population wide guidelines to obtain the same risk value as the average person. Contrary to Aaron Lewis’ song a few extra pounds could hurt. I still have too much fat around my mid-section.

• Category: Science • Tags: Health 

A-Game-of-Thrones-Bantam-Spectra On January 23rd of 1999 I had just finished Paul Gottfried and Thomas Fleming’s The Conservative Movement. My roommate was pretty high, as usual (it was a Saturday). A few weeks earlier I’d gotten a paperback of a fantasy novel, Game of Thrones. I read a few pages, and then went to sleep. The next morning, Sunday, I began to read more. I did not finish until very late Sunday evening/Monday morning. I happened to have had a midterm in a biochemistry course the next day. I did not do so well. In a month the first edition of the sequel, Clash of Kings, came out. Satisfaction! In the year 2000 the British edition of the third book, A Storm of Swords, was published a few months earlier than the American one. I special ordered it from England so I could read it ahead of time. After I read Game of Thrones I emailed George R. R. Martin, and he actually responded, though it took about a year. He apologized for being responsible for my difficult midterm. He also confirmed that Bernard Cornwell’s Warlord Chronciles were similar in feel, if not directly influential, to his series.

Like many I was patient, though frustrated, by the delays after A Storm of Swords. Like many readers I also believe that A Dance with Dragons and A Feast for Crows were somewhat inferior to his first three books. But I understand that the “middle books” of such an expansive series are often the least interesting. Bridges between the past and future. I am patient. When I first encountered Martin’s series I was a callow youth. I am now a father. Much has changed.

But now I read this post at FiveThirtyEight, We’re Going To Learn How The ‘Game Of Thrones’ Books End On HBO. I haven’t much paid attention to the show because I do not watch television, and film or television of science fiction and fantasy are usually inferior and compromised products. But the math is compelling. I had assumed that A Song of Ice and Fire would conclude in the early 2020s. But if the television show has nearly caught up with the books, and is already through 4 years of its run, it seems implausible that it won’t race ahead. I’m at a loss for what I can even say to this. Is our patience and forbearance for naught? Apparently.

I agree with the suggestion o some: the HBO series and the books should explicitly “fork.”

• Category: Miscellaneous • Tags: Fiction 

41BlNMFJqNL._SY344_BO1,204,203,200_ A few separate pieces that I read today came together thematically for me in an odd confluence. First, an article in The Straits Times repeats the shocking statistics about the nature of modern academic intellectual production, Prof, no one is reading you, that you may be aware of. Here’s the important data:

Even debates among scholars do not seem to function properly. Up to 1.5 million peer-reviewed articles are published annually. However, many are ignored even within scientific communities – 82 per cent of articles published in humanities are not even cited once. No one ever refers to 32 per cent of the peer-reviewed articles in the social and 27 per cent in the natural sciences.

If a paper is cited, this does not imply it has actually been read. According to one estimate, only 20 per cent of papers cited have actually been read. We estimate that an average paper in a peer-reviewed journal is read completely by no more than 10 people. Hence, impacts of most peer-reviewed publications even within the scientific community are minuscule.

What ever happened to the “republic of letters”? Are humanists reading, but not citing, each other? Or is it that humanistic production has basically become a matter of adding a line to one’s c.v.? So the scholar writes the monograph which is read by their editor, and then published to collect dust somewhere in the back recesses of an academic library.

Second, an article in The New York Times, Philosophy Returns to the Real World, declares the bright new world in the wake of the Dark Ages of post-modernism. Through a personal intellectual biography the piece charts the turn away from the hyper-solipsistic tendencies in philosophy exemplified by Stanley Fish in the 1980s, down to the modern post-post-modern age. Operationally I believe that Fish is a human who reconstitutes the characteristics of the tyrannical pig Napoleon in Animal Farm. Despite all the grand talk about subjectivism and a skepticism about reality which would make Pyrrho blanch, Fish did very well for himself personally in terms of power, status, and fame by promoting his de facto nihilism. Money and fame are not social constructs for him, they are concrete realities. Like a eunuch in the Forbidden City ignoring the exigencies of the outside world, all Fish and his fellow travelers truly care about are clever turns of the phrase, verbal gymnastics, and social influence and power. As the walls of the city collapse all around them they sit atop their golden thrones, declaring that they are the Emperors of the World, but like Jean-Bédel Bokassa are clearly only addled fools to all the world outside of the circle of their sycophants. After all, in their world if they say it is, is it not so? Their empire is but one of naked illusions.

Finally, via Rod Dreher, a profile of David Brooks in The Guardian. He has a new book out, The Road To Character. I doubt I’ll read it, because from what I can tell and have seen in the domain of personal self-cultivation of the contemplative sort our species basically hit upon some innovations in the centuries around 500 B.C., and has been repackaging those insights through progressively more exotic marketing ploys ever since. Xunzi and Marcus Aurelius have said what needs to be said. No more needed for me.

But this section jumped out:

“I started out as a writer, fresh out of college, thinking that if I could make my living at it – write for an airline magazine – I’d be happy,” says Brooks over coffee in downtown Washington, DC; at 53, he is ageing into the amiably fogeyish appearance he has cultivated since his youth. “I’ve far exceeded my expectations. But then you learn the elemental truth that every college student should know: career success doesn’t make you happy.” In midlife, it struck him that he’d spent too much time cultivating what he calls “the résumé virtues” – racking up impressive accomplishments – and too little on “the eulogy virtues”, the character strengths for which we’d like to be remembered. Brooks builds a convincing case that this isn’t just his personal problem but a societal one: that our market-driven meritocracy, even when functioning at its fairest, rewards outer success while discouraging the development of the soul. Though this is inevitably a conservative argument – we have lost a “moral vocabulary” we once possessed, he says – many of the exemplary figures around whom Brooks builds the book were leftists: labour activists, civil rights leaders, anti-poverty campaigners. (St Augustine and George Eliot feature prominently, too.) What unites them, in his telling, is the inner confrontation they had to endure, setting aside whatever plans they had for life when it became clear that life had other plans for them.

Many of the ancients argued for the importance of inner reflection and mindful introspection. Arguably, the strand of Indian philosophical thought represented by the Bhagavad Gita was swallowed up by this cognitive involution, as one folds in upon one’s own mind.

But let me tell a different story, one of the outer world, but not one of social engagement, but sensory experience of the material domain in an analytic sense. Science. A friend of mine happens to be the first using next-generation sequencing technologies to study a particularly charismatic mammal. I reflected to her recently that she was the first person in the history of the world to gaze upon this particular sequence, to analyze it, to reflect upon the natural historical insights that were yielded up for her by the intersection of biology and computation. It is highly unlikely that my friend will ever become a person of such eminence, such prominence, as David Brooks or Stanley Fish. Feted by her fellow man. But my friend will know truth in a manner innocent of aspirational esteem totally alien to the meritocratic professionals David Brooks references. On the day that you expire, would you rather be remembered for a law review article, or discovering something real, shedding light on some deep truth (as opposed to “truth”)?

This perhaps offers up a possibility for why humanists don’t cite each other. Too many have been poisoned by the nihilism of the likes of Stanley Fish. They do not see any purpose in the scholarship of their peers, because humanistic scholarship of the solipsistic sort is primarily an interior monologue with oneself. The experiments of English professors always support their hypotheses. Their struggle is to feed their egos, they wrestle with themselves, Jacob’s own angel as a distillation of their self-essence. The limits of their minds are the limits of their world.

Finally, this filament threaded through, of a reality out there, the possibility of being made aware of it, even through the mirror darkly, is why I continue to do what I do, and aspire to what I aspire to. The truth is out there. It does not give consideration to our preferences. But it is, and we can grasp it in our comprehension. Over the past ten years in the domain of my personal interest, and now professional focus, genomics, we’ve seen a sea change. That which we did not even imagine has become naked to us. Before the next ten years is out who knows what else we’ll discover?

• Category: Ideology • Tags: Epistemology, Philosophy 

330px-KeiraKnightleyByAndreaRaffin2011 In the comments below someone asked if the model Bryan Sykes’ outlined in Seven Daughters of Eve (and later Saxons, Vikings, and Celts), that modern Britons descend predominantly from the Paleolithic stock which repopulated the island in the wake of the end of the last Ice Age (or fled Doggerland), is still tenable. I don’t think so much. First, the tripartite origin of modern Northern Europeans probably puts more of an emphasis on migration in the Western regions of the continent. Yes, in many groups the ancestry which derives from the small populations which followed as the glaciers retreated is overall predominant (that is, somewhat more than 50%). But that is distinct from the idea that the proportion of ancestry from hunter-gatherers in any given area, such as Britain, is from indigenous hunter-gatherers long resident. What I’m getting at is that socio-cultural groups, such as “Early European Farmers” (EFF) and the Yamna, which contributed a great deal of ancestry to modern people are themselves in origin compounds of disparate elements. Because of the seeming homogeneity of European hunter-gatherers, likely due to a Pleistocene bottleneck and then a rapid range expansion from small founder groups, earlier methods of aligning mtDNA and Y haplogroups may have misled because of the lack of power to distinguish between extremely close lineages (European hunter-gatherers are almost all mtDNA group U and predominantly Y group I). Therefore the predominant Paleolithic ancestry across Northern Europe may actually be a function of a few discrete pulse admixture events. Subsequently demographically successful groups then carried this ancestry where they went, possibly replacing natives in totality.

I grant that this is speculative and not certain. For example, one assumption I’m making is that the density of hunter-gatherers was rather low across Europe. But clearly there were marine environments where they seem to have been thicker on the ground, particular zones where agriculturalists seem to simply stop their advance abruptly The ultimate answer will probably be through ancestry deconvolution methods. Basically, looking at the distribution of lengths of distinct ancestral elements, and seeing which model the empirical patterns fit. If I’m correct, then the distribution of lengths for hunter-gatherer ancestry in Northern Europe will be narrower than if you had a scenario of continuous regional expansion. It’s certain that someone is working on this.

Genetically the two scenarios don’t make that much of a difference, because European hunter-gatherers were probably a very homogeneous bunch (though this might be generally true for Eurasian hominins, as Neandertals and the Denisovan sample also exhibit low genetic diversity in comparison to modern populations). But anthropologically it is critical, because it fleshes out the processes of potential cultural change and turnover in the transition between societies and modes of production.

• Category: Science • Tags: European Genetics, Genetics 

41v0RwMV8OL._SY344_BO1,204,203,200_ I have an old friend from college who I’m in touch with via Facebook. He looks great. In fact, he looks like how I’d like to look. After a year of running and lifting I’m noticeably more muscular. I’m 150-155 pounds at 5’8, and according to my Aria I’ve lost about ~3% body fat (I’m not reporting the absolute value because it’s not that accurate, though the readings seem consistent day to day). But, since I’m South Asian and tend toward a “baby face” mien I’m not where I want to be in terms of definition. In contrast my friend is very toned. I asked him how he had changed his physique so much over the years, since in college he was rather “soft” looking. His response? Gay peer pressure.

This is why articles like this in Salon drive me crazy, You should never diet again: The science and genetics of weight loss. It’s excerpted from the book Secrets From the Eating Lab: The Science of Weight Loss, the Myth of Willpower, and Why You Should Never Diet Again. The author, Traci Mann, is a professor at the University of Minnesota, as she proudly notes:

To tease apart the effects of genes from the effects of the shared environment, researchers located identical twins that were raised in separate homes without knowing each other. It may seem surprising that there are enough sets of twins that meet this criteria, but there are. This type of twin research was partly pioneered in the very psychology department in which I work, at the University of Minnesota (coincidentally located in the twin cities of Minneapolis and St. Paul). If you go up to the fifth floor, the walls are covered with photographs of identical twins that were separated at the age of five months (on average) and had been apart for about thirty years before being reunited as adults. The visible similarities are remarkable, as are the many documented behavioral similarities.

The crucial twin study of body weight (which comes from the Swedish Adoption/Twin Study of Aging) included 93 pairs of identical twins raised apart (and 154 pairs of identical twins raised together). Sure enough, the weights of identical twins, whether they were raised together or apart, were highly correlated. That study, along with several others, led scientists to conclude that genes account for 70 percent of the variation in people’s weight. Seventy percent! What is truly remarkable is that this is only slightly lower than the role genes play in height (about 80 percent of the variation). Don’t get me wrong. I’m not saying you can’t influence your weight at all, just that the amount of influence you have is fairly limited, and you’ll generally end up within your genetically determined set weight range.

41nk1RoCEWL._SY344_BO1,204,203,200_ Many readers will be familiar with twin studies. If you aren’t, read Born that Way by William Wright. The strange thing about this reference to this scientific project is that it’s incongruous to see it in a Left-wing publication like Salon. The more moderate Slate trashed twin studies about four years ago, even though cutting edge genomic methods are now validating their results. Why all the hostility? Mostly it has to do with non-trivial heritabilities for intelligence and personality which come out of this type of research, which are not congenial to a particular sort of Left-wing mentality (see Steven Pinker’s The Blank Slate). I suspect the issue here is that the political valence is not alarming to the readers of Salon, who are very open arguments about “thin privilege”, and the idea that the heavy might be considered another protected class. The analogy then in terms of heritability and a biological basis for this trait is with homosexuality, where the Left favors genetic determinism. The same studies also come with high heritabilities for traits such as weight in developed world populations. The quoted results above are correct, but the implications that the public takes from them are misleading.

I’m pretty sure that Traci Mann knows the technical definition of heritability by the way she writes. That is, the proportion of phenotypic variation that can be explained by genetic variation within the population. The problem is that the general public is going to see “70 percent heritable” and think “70 percent genetic,” when that’s not even wrong. The way the piece is written also misleads in this fashion. One thing to note is that even though height is 80 to 90 percent heritable, the correlation between full siblings for this trait is only 0.50. I suspect this would surprise people since it is such a heritable trait, but that goes to show that a population wide heritability statistic has only modest utility on the individual scale. More importantly by analogy to height the norm of reaction matters a great deal. We know empirically that genetically similar populations vary in mean and variance of weight and height over time and in different environments.

Which goes back to social context. My friend now works out a lot and watches what he eats. It’s something that he does every day, and something that is enabled by the social environment in which he is embedded (see this music video about “Mean Gays”). Weight varies in the United States by class and region, and from what I recall this remains after you control for demographic variables. What this probably means is that it takes a village to sustain weight loss. So in a way those who argue that dieting is useless are correct. But they’re being misleading when they imply that your weight is ultimately “genetic.” It’s social.

Update: A friend emailed me and pointed out figure 2 in a recent Nature paper. It gets at what’s producing the heritability statistic:

nature14177-f2 (1)

• Category: Science • Tags: Heritability 

22522805 I listened to an interview with Kazuo Ishiguro over at Wired with the title “Why Are So Many People Snobby About Fantasy Fiction?” After hearing what Ishiguro had to say I decided to check out reviews for his new novel, The Buried Giant, and noticed it was $5.99 in the Kindle version. So of course I bought it.

I’m not sure if I’ll be satisfied. The premise somewhat reminds me of Gene Wolfe’s Soldier of Arete, though obviously most of the major elements differ. I don’t know if I’ll get to reading The Buried Giant anytime soon, as I’m behind on various projects relating to my real professional life and will be rather busy for a while. Additionally, I have other books that I’d like to get through, such as Inventing the Individual, a work that I’m pretty sure I’m not going to much like if the first 20% or so is a guide. The author basically asserts a lot of things about the antique past with support from literary references that I’m often not personally deeply knowledgeable about (to be clear, there are factual issues I know about, such as comparisons between Greeks and Romans, where I think the author is basically wrong in eliding important distinctions among these cultures before Christianity). Additionally, the conclusions grate a bit on my priors. I really dislike works of the form, such as “How Love was Invented in 13th Century Provence.” Giving something a label does not something make (i.e., defensible to say love as we understand it). But I am the type of person who reads things he disagrees with, because new arguments are often informative. So I’ll finish it.

In other news, I’ve been using SciReader for a while now and I like it quite a lot. It’s a nice complement to PubChase. For nonacademic readers PubChase is pretty handy for trying to locate copies of PDFs that you can access. If you are a regularly reader of this weblog you should try them out.

One of the major ways I find scientific literature is Twitter (which SciReader has a pretty tight integration with right now). My old rule-of-thumb was that I’d maintain a 10:1 follower-to-follow ratio. I’m nearing 6,000 followers (thanks The New York Times, sort of!), and until recently I kept the follow count to around ~300. The past few days though I’ve been following people who look interesting, and will continue to do so until I hit 600. Mostly I follow individuals who work in genomics and evolution, because when it comes to “big Twitter” those all get re-tweeted anyhow if they are interesting. But I’m curious if readers have particular suggestions for whom I should follow. In particular, data Tweeters like Conrad Hackett, I really appreciate. I’m also curious about scholars in fields like history, philosophy, and economics. Also, please note that I’m looking for Twitter users who actually post somewhat frequently.

Going back to fantasy and science fiction, I have no idea why the haters hate. One of my pet theories is that less intelligent liberal arts majors are not very intellectually curious outside of the prosaic. They’re just not creative types, and don’t have the requisite imagination to process speculative fiction. But that’s probably not generous (in any case, some serious hard science fiction writers, such as Greg Bear and C. J. Cherryh, come out of liberal arts backgrounds), not to mention self-serving. Though I do admit that that a lot of science fiction and fantasy is crap, that’s true of fiction more generally. For some reason the crap sticks to the whole genre. Or genres, as the same disdain is aimed at mysteries or romance novels, neither of which I care for, but neither of which I go out of my way to dismiss since I don’t read them. My identity isn’t bound up in the idea of the Book and Literature.

• Category: Miscellaneous • Tags: Open Thread 

journal.pbio.1002112.g003

$_35 Very important paper in PLOS BIOLOGY just out, Natural Selection Constrains Neutral Diversity across A Wide Range of Species. Important enough that the journal commissioned this article: Lewontin’s Paradox Resolved? In Larger Populations, Stronger Selection Erases More Diversity. The paradox is pretty straightforward. Assuming the neutral theory of molecular evolution you’d expect that you’d have more genetic diversity in species with larger population sizes, because the larger the population size the longer it would take for mutations to transition from novelty to fixation. More formally the time until fixation of a neutral polymorphism is ~4N e, with N e being the effective population size. In small populations mutations will emerge and fix rather quickly due to the generation to generation volatility of drift being so powerful, and therefore keeping down the total diversity. In large populations mutations will take a long time to traverse the frequency range from 0 to 100% because of the weakness of inter-generational random drift. The paradox was a big deal because for the past 30 years or so the neutral (or nearly neutral) has been the implicit null model, and I’d argue broadly supported as such, albeit with strong dissents.

41TCN6WTB4L._SY344_BO1,204,203,200_ The “controversies” that occurred from the 1970s onward about the role of selection and and its enemies are somewhat notorious. Some of the figures are well known to the public. Richard Dawkins and Stephen Jay Gould both had cameos because of their differing views about the pervasiveness of adaptation in evolutionary process more generally. But the geneticists at the heart of the major disagreements are more obscure to the general public, though in the early 1990s the Sacramento Bee reported on the beef between John Gillespie and Motoo Kimura (Gillespie was based out of UC Davis, near Sacramento). From what I can tell, and who I know, it strikes me that genomics has now somewhat mitigated the role of rhetoric in the debate, and at the same time fostered an abating of the extremism of some of the anti-selectionists. Leibniz’s stance of “let us calculate” has now become more important than a turn of the phrase or evocative metaphor. With data there is less of a role for posturing. Additionally, the fact is that many researchers did not follow mathematical theoretical proofs very closely or with genuine comprehension, so empirical results are really what is changing the terms of the debate. The Drosophila world has long been a redoubt for selectionism, but now you see papers such as Genome-wide signals of positive selection in human evolution, which argue for the importance of that population genetic parameter even for small effective population size organisms such as humans.

187874 What the authors did in the above paper was leverage the fact that with genome-wide data they could test the theoretical propositions empirically. In particular, they looked at regions with reduced recombination,* and therefore should be subject more strongly to selection (whether selective sweeps, which allow for the hitchhiking of regions around the target of selection and generate long haplotypes, or background selection, which constrains genomic variation due to negative pressures against mutation). As the figure above shows there is a correlation between the power of selection on the genome and inferred effective population size. I say inferred because they had to use species range and size as proxies. Obviously this isn’t perfect, but I suspect that the utilization of these proxy variables only diminishes the correlation. The authors admit that there is a lot of work to be done, but this is just the first step. Perhaps the results will change somewhat with a different selection of organisms (N = 40), but I’m moderately skeptical. Probably the most important line in the paper is “it seems clear that, in most cases, BGS [background selection] is a more appropriate null model for tests of natural selection than strict neutrality.”

* Recombination shuffles the association of variants across the genome, and so separates their destiny, whether good (positive selection) or bad (negative selection).

• Category: Science • Tags: Evolutionary Genetics, Genetic Draft, Selection 
miscarriage

Blue variant derived, correlated with higher anueploidy rates

A quick follow up to my previous post. To recap, a new paper in Science reports high (20-40%) derived frequencies for an allele which seems correlated with higher rates of aneuploidy. Anueploidy is bad, because often it results in nonviable offspring (individuals with Down syndrome have a viable anueploidy). The strange thing about this region of the genome is that it looks like modern humans have harbored this variant since the divergence from Neandertals. But, it has not gone to fixation. Its frequency in the intermediate range all this time, segregating in pretty much all populations from what it looks like, suggests balancing selection.

41ePHetk1dL._SY344_BO1,204,203,200_ Most of the paper is focused on medical genetics and the genome-wide association. The evolutionary aspect is interesting, but struck me as something of an afterthought. I made some chit-chat with the first author at the Bay Area Population Genomics meeting last December, and he didn’t let on that he had any good idea for why this allele was persisting. So I doubt that the group is wedded to the idea that miscarriage is a strategy for masking paternity and encouraging male investment. I’ve asked around people who work in behavioral ecology and they’re skeptical too. There’s a mystery here, and it’s kind of a big deal in my opinion, but there’s not much clarity.

On Twitter Vincent Lynch pointed out that the locus in question, PLK4, has been implicated in testes development. So one possible answer that crops up is that it is some form of sexually anatongistic selection. Meanwhile, Greg Cochran posits that we’re seeing some sort of meiotic drive, where there is selection pressure operating on the level of the genome itself (e.g., “selfish genetic elements” type dynamics). These are both plausible to me, and suggest that there needn’t be an explanation rooted in our human uniqueness to answer this particular genomic mystery.

hominids A common tendency among genomicists, who are modern humans, is to always highlight variants which have been selected in our lineage in comparison to nearby lineages. Before ancient DNA this usually meant chimpanzees, but now we’re talking Neandertals and Denisovans. Humans are a pretty big deal, and intuitively we think that our genomics are also a pretty big deal. There must be a key that unlocks our uniqueness, so searching through the 3 billion base pairs in our genome we stumble upon distinctive evolutionary histories, and think “eureka, this is It, the ultimate locus of our genius!” In pre-modern language, our souls. But the fact is that over tens of millions of polymorphisms in the genome you are naturally going to find regions where we are unique in relation to our relatives, and the broader mammalian family tree, just as a matter of chance. If we lived in the world of the Neanderthal Parallex no doubt Neandertal genomicists would be engaging in the same search for the uniqueness of their lineage, and discover regions where they are sui generis in relation to other hominins and mammals more broadly. The few times I’ve been to ASHG I stumble onto talks where the authors present evidence of genomic regions which are unique in our species, the implication being that this might be somehow responsible for the nature of who we are. Of course the researchers in question are usually not interested in that topic that much, rather, it is an interesting side element that adds to the sexiness of their results, and the glamour usually fades over time.

There is the quest for the the gene for everything. It’s a major problem with media representations of behavior genetics. But a lot of interesting traits are polygenic. We’ve long known this from classical genetics, and genomics is confirming this. There’s not a gene for anything, but a host of genes. Quantitative genetics is banal, but it is powerful. We need to be more open to the possibility that humanity as we understand it isn’t a clear and distinct thing, but the end of a distribution of possibilities long pregnant in our lineage of apes.

• Category: Science • Tags: Genetics, Human Evolution 

defect

The above figure is from Common variants spanning PLK4 are associated with mitotic-origin aneuploidy in human embryos. The author has presented this work at meetings, so I knew it was pending. One of major angles here is that you now have an actionable genotype whereby one can make calculations of likelihood of aneuploidy.. If you are female, and have a 23andMe account, just click here. In accord with the results above the risk for aneuploidy is as follows AA > AG > GG. If you don’t have access, the supplements have a lot of interesting stuff. There you can see that there’s no discernible geographical distribution of the minor allele, which is present in ranges from 20 to 40 percent (here it is at the 1000 Genomes Browser).

From an evolutionary perspective the strange thing is that the derived allele seems to reduce reproductive potential. Neandertals don’t carry the derived variant. But the presence of this derived allele isn’t a coincidence, the authors detect an ancient selection event around this region. So either the variant is beneficial in some way, or, aneuploidy as a trait has hitchhiked. I’ll post the explanation in the paper here, because I honestly don’t even know what to say:

The fact that the haplotype bearing the derived allele did not sweep to fixation and is present at similar frequencies across human populations is consistent with the action of long-term balancing selection. We speculate that the mitotic-error phenotype may be maintained by conferring both a deleterious effect on maternal fecundity and a possible beneficial effect of obscured paternity via a reduction in the probability of successful pregnancy per intercourse. This hypothesis is based on the fact that humans possess a suite of traits (such as concealed ovulation and constant receptivity) that obscure paternity and may have evolved to increase paternal investment in offspring (24). Such a scenario could result in balancing selection by rewarding evolutionary “free riders” who do not possess the risk allele—and thus do not suffer fecundity costs—but benefit from paternity confusion in the population as a whole

Whatever is happening is very strange. The authors make the case that there ascertainment bias is such that they’re underestimating effect of the derived variant. All things equal the selection coefficient should be strongly negative.

• Category: Science • Tags: Genetics, Human Evolution 

height

The above figure is from a paper in Proceedings B which shows a Dutch data set from right after World War 2. Controlling for several variables taller men and average height women have maximal fertility. The authors contrast the results from the United States, where it seems that shorter women and average height men have maximal fertility. This is kind of a big deal. The reasons for why the Dutch, who were the shortest Europeans two centuries ago, are the tallest nation in the world today, have been a matter of public discussion for over ten years (see this article in The New Yorker).

In the 19th century American whites were far taller than Europeans. European elites who toured the United States were reputedly shocked by the fact that American yeoman farmers were no shorter than them, as was the norm among the peasant classes in their lands of origin. This lack of size differential due to surplus of land in the early American republic was often compared with the relative social egalitarianism of the United States, along with its broader democratic ethos.

Obviously things have changed since the 19th century. The Malthusian conditions which ground down Dutch peasants in the 18th century no longer applied in the 20th century, and definitely not in the 21st century. Modern agricultural techniques mean that Northern Europeans are no longer nutritionally constrained. Not only that, but one could argue that today Northern European societies are more egalitarian than the the United States. Naturally there has been a focus on the environmental factors which might have shaped this difference in the distribution of heights between Northern Europeans and American whites of Northern European heritage.

But there are some biological issues which are likely relevant. Average human size, including height, actually peaked in the wake of the Last Glacial Maximum, ~20,000 years ago. Some of this is likely due to the nutritional changes enforced by the Neolithic Revolution, but the decrease in sizes predate that. Likely standard dynamics common to mammals, such as Bergmann’s rule, have also affected humans. The recent increases in height across the developed world have still not produced a population as imposing as that of late Pleistocene humans. Second, over the past few years plenty of genomic work has now argued for selection on height in Europe, explaining why there are small but persistent differences between populations in the north and south. Ancient DNA analysis has now confirmed this broadly result, as populations diverged in size due to local ecological pressures.

These new results suggest that selection is driving change in allele frequencies which control for height even today among the Dutch. The methods were pre-genomic. Basically they tracked fertility of individuals along with a bunch of variables, including height. There was no need to go into genomic details because there is a wide body of research which indicates that 80-90% of the variation in height in developed societies is controlled by variation in genes. In other words, height is a highly heritable trait. As per the breeder’s equation all you need to change a trait value for a highly heritable trait is selection:

Selection × Heritability = Response to selection

If there is selection but no heritability, then there is no response. If there is heritability but not selection, then there is no response. In this case the heritability is well known, and now they have shown selection in the Dutch population as an implication of differential fertility that tracks this heritable variation.

This framework is true for quantitative traits more generally. I wouldn’t be surprised to see that there is a fair amount of evolution going on in modern human populations, which large and robust data sets might be able to capture in the near future.

Citation: Does natural selection favour taller stature among the tallest people on earth? Gert Stulp, Louise Barrett, Felix C. Tropf, Melinda Mills, Proc. R. Soc. B: 2015 282 20150211; DOI: 10.1098/rspb.2015.0211. Published 8 April 2015

• Category: Science • Tags: Quantitative Genetics 

41o2X6mtArL._SY344_BO1,204,203,200_ 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.

• Category: Science • Tags: Health 

Print 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:

http://connect.biorxiv.org/biorxiv_xml.php?subject=genomics+genetics+evolutionary_biology.

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.

• Category: Science • Tags: bioRxiv 
SELECTION

Is ADSL the locus of human genius?

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.

In any case, the most recent version of the preprint, Testing for ancient selection using cross-population allele frequency differentiation:

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

• Category: Science • Tags: 3P-CLR, Human Evolution, Selection 

razib 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.

• Category: Foreign Policy • Tags: Bangladesh 

mammothIt 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.

Nevertheless, many people still argue that the pattern of extinctions which we see over the Pleistocene and Holocene is not the outcome of human expansion, but climate change. In other words, they are not anthropogenic. Don’t believe me? Here’s a paper from a few years ago, Serial population extinctions in a small mammal indicate Late Pleistocene ecosystem instability:

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: Historic and prehistoric human-driven extinctions have reshaped global mammal diversity patterns, Søren Faurby , Jens-Christian Svenning, doi: http://dx.doi.org/10.1101/017368

• Category: Science • Tags: Ecology, Extinction 
sex

Citation: Sexual selection drives evolution and rapid turnover of male gene expression

cover150x250 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.

mating-mind-193x300 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.

• Category: Science • Tags: Genomics, Sexual Selection, Transcriptome 

Screenshot from 2015-04-05 13:27:53

Also, Mexico has a population on the order of 50% of the United States. Saudi Arabia and Yemen have about the same population.

• Category: Foreign Policy • Tags: Saudi Arabia, Yemen 

9780300125344 What’s going on? Pretty busy with life right now. Cleaning up the house for Easter.

51fFtmA2D5L._SX258_BO1,204,203,200_ 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.

Also, Derek Roff’s Modeling Evolution: An Introduction to Numerical Methods arrived in the mail. It is nota coffee table book.

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.

• Category: Miscellaneous • Tags: Open Thread 

41Nob9EJOOL._SY344_BO1,204,203,200_ 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.

agcover165.jpg 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.

• Category: Ideology • Tags: Religion 

ontheoriginofspecies 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 arXiv Alan 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 2 N 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.”

Lord Kelvin had nothing on that.

• Category: Science • Tags: Genetics 
Razib Khan
About Razib Khan

"I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. If you want to know more, see the links at http://www.razib.com"