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deleterious

F5.medium A common model of the range expansion of modern humans out of Africa ~50,000 year ago forces us to conceptualize it is as a tree with successive bifurcations. Each of these bifurcations often is accompanied by a bottleneck in one of the daughter populations, with the sum totality of the demographic events producing a “serial bottleneck” model of the origin of modern human lineages around the world. Though this paradigm has been around in various forms for decades, most influential among geneticists has been the 2005 paper, Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa. In the paper the authors show persuasively that heterozygosity declines as a function of distance from Addis Ababa, near the likely point-of-departure out of Africa.

But there’s minor problem with this model. Most extant populations may in fact be compounds of highly diverged late Pleistocene lineages. That is, after an initial serial founder expansion ~50,000 years ago there may have been many local extinctions and admixture events overlaying it. That is the model that Joe Pickrell and David Reich argue for in Towards a new history and geography of human genes informed by ancient DNA. While in a serial founder conceptualization of an out of Africa migration modern populations are the tips of the phylogenetic tree, in the Pickrell and Reich framework they’re syntheses of divergent evolutionary histories. As Towards a new history and geography of human genes informed by ancient DNA shows older genetic techniques and data, not informed by ancient DNA, may not have had the power to differentiate between the serial bottleneck model, and one of reticulation and fusion.

41h+3YmTZRL._SY344_BO1,204,203,200_ It seems likely that the serial founder model has some utility. One can still hold defensibly that everyone outside of Africa, excluding recent admixture from within Sub-Saharan Africa, sits within their own phylogenetic clade. That is, all non-Africans are equally related to Sub-Saharan Africans, because all of them descend from an ancient population of ~1,000 breeding individuals. But, you have populations such as South Asians who are both numerous, and, fusions of two very distinct branches of out of Africa humanity. The stylized model of a tree subject to bifurcations fundamentally misleads in this case.

All this came to mind reading a new preprint that’s on biorxiv, Distance from Sub-Saharan Africa Predicts Mutational Load in Diverse Human Genomes. Theory and intuition should suggest to us that out of Africa populations will have higher genetic load of deleterious mutations than within Africa populations. The reasoning is straightforward: the power of selection to remove deleterious mutations is hampered the smaller the effective population size, as random genetic drift becomes more determinative in generation to generation changes in allele frequency. More formally if 4 N es << 1, where N e is effective population and s is the selection coefficient, then even deleterious alleles behave as if they are neutral. From neutral theory we know that the rate of substitution in this model is simply the rate of mutation. That is, molecular evolution is determined by new mutational input, rather than being constrained or diversified by selection. In small populations which are drift dominated N e can get very small. I’ve seen assertions that the original group of humans who settled North America and South America may have had an effective population in the first generation on the order of ~100. In their history they also had the out of Africa effective population of ~1,000. In addition, there were likely bottlenecks between Berengia and the out of Africa event.

download You can see in the figure above from the preprint that the number of deleterious mutations does seem to increase with further distance from Africa. Their genomic coverage was good, ~80x on the exome. That is, when they found variants that differed from the reference sequence they could be confident that it was not in error. On the other hand their population coverage struck me as less than ideal, though I am willing to accept that their result is probably true (and obvious with finite resources they selected their individuals and populations to be informative). They admit for example in the text that the Mozabite population has higher heterozygosity due to a back-to-Africa migration, which has had successive admixtures of Sub-Saharan ancestry. In addition, it is also rather inbred. Its demographic history bears no correspondence to the serial founder bottleneck model which spans 50 to 15 thousand years (i.e., from the out of Africa to the settlement of the NewWorld). The Pathan and Cambodian populations also are actually the product of Holocene fusions between distinct groups with very different histories. The PSMC results in the bottom left panel can be thought of as collapsing distinct population histories, and, from what I am to understand may then inflate the effective population trajectories of individuals who descend from admixture events.

As one might expect from this sort of title the authors refer back to the 2005 paper that I mention above. I don’t want to belabor this point, as I think the authors’ results are probably robust, and, important, population history aside. But, much of the audience will not know that the serial founder bottleneck model is now being challenged. The 2005 paper has 588 citations as of this writing. The Pickrell and Reich paper, which was published in 2014, has 5 citations. I just want to mention this since it’s a preprint and presumably the authors are taking in any critiques.

When it comes to burden of deleterious mutations in human populations there have been some conflicting results, reviewed in the preprint, about mutational load. The authors argue that results which suggested that non-Africans did not exhibit higher load were subject to a bias which did not have power to detect non-common variants, and also modeled mutations as additive, as opposed to across the full range of dominance (h). It turns out that non-Africans, and those populations which are more drifted, exhibit higher recessive deleterious loads. This is what you would expect intuitively, as you need large populations to purify this class of deleterious alleles (since they are only exposed to selection in homozygotes). This matters when it comes to expectations of the number of recessive diseases one might expect in populations which practice consanguinity. I would, though, have liked to see more typical populations in the mix. For example, instead of just African hunter-gatherers it would be nice to see the Yoruba, as well as Han Chinese, and a northern European population. I doubt it would be very surprising, but it would give one a better baseline.

Finally, I want to note that many ancient DNA results, from “archaics” to modern human Mesolithic hunter-gatherer groups, have very low effective population sizes due to inbreeding. Genetic load may be more important in the history of the human species, especially on the edge of the range in the far north, than we may now understand, because of its tendency to reduce fitness of groups due to the drag of recessive disease.

Citation: Distance from Sub-Saharan Africa Predicts Mutational Load in Diverse Human Genomes, Brenna M. Henn, Laura R Botigue, Stephan Peischl, Isabelle Dupanloup, MikhailLipatov, Brian K Maples, Alicia R Martin, Shaila Musharoff, Howard Cann,Michael Snyder, Laurent Excoffier, Jeffrey Kidd, Carlos D Bustamante,

• Category: Science • Tags: Genomics, Human Genetics 

51QrNyN0KzL._SY344_BO1,204,203,200_ In 2002 I read Stanislas Dehaene’s The Number Sense: How the Mind Creates Mathematics. Though it’s not at the same level as Steven Pinker’s The Language Instinct*, it’s not that far below it. There was a time when I read a fair amount of cognitive neuroscience. Not so much now. So I’m finally trying to get through Reading in the Brain: The New Science of How We Read, again, by Stanislas Dehaene. This is partly an exercise of narcissism, since I want to do what I can to understand myself.

CoverReadingInTheBrain Speaking of which, Bryan Caplan, a big fan of Judith Rich Harris’ The Nurture Assumption, reports that reading is kind of a big deal in developing a child, and impacting their ultimate life outcomes. The effect is modest, but robust. Though also please read Will Ambrosini’s cautionary comments about interpretation of this result.

So what else is going on? I apologize to those whose comments I don’t respond to who are asking me a direct question. Time is finite and it often slips my mind, even though responding to questions is on a “TO-DO”. Also, the new book about Elon Musk, Elon Musk: Tesla, SpaceX, and the Quest for a Fantastic Future, looks interesting. But I doubt the whole of the text is worth purchasing. I care a lot less about Musk’s family background and personal life than I do about his vision for the human race. But really the latter could be outlined on a napkin.

Finally, BAPG XII @Stanford in Palo Alto. May 30th, a Saturday. Looking forward in particular to Michael McLaren’s talk on fitness landscapes.

* The Blank Slate is probably more well known, and Pinker’s most successful book in terms of broad cultural impact. But I think The Language Instinct is his best science book aimed at a general audience.

• Category: Miscellaneous • Tags: Open Thread 

51fQMbh-NnL._SY344_BO1,204,203,200_ A few months ago the anthropologist Pat Shipman published a book, The Invaders: How Humans and Their Dogs Drove Neanderthals to Extinction. I’ve read Shipman before, and because of my interest in domestication it’s been on my radar, but I haven’t gotten around to purchasing it. The major reason is that as I understand it the title is somewhat misleading, in that there’s a lot less in the text on human-dog cooperation than one might think. Which is reasonable, it’s a speculative hypothesis at best.

Perhaps the biggest problem is that there’s no strong evidence that dogs were domesticated or distinct as early as ~35 thousand years ago, when modern humans replaced Neandertals in Europe. This comes up in a very highly rated comment on Amazon in fact. The best genetic work, Genome Sequencing Highlights the Dynamic Early History of Dogs, implies a date of ~15,000 years before the present, at the earliest.

But now it looks like it’s time to update our priors on this. Shipman’s speculative theory, still unlikely in opinion, is no longer extremely unlikely. The reason is ancient DNA. Ancient Wolf Genome Reveals an Early Divergence of Domestic Dog Ancestors and Admixture into High-Latitude Breeds:

The origin of domestic dogs is poorly understood…with suggested evidence of dog-like features in fossils that predate the Last Glacial Maximum…conflicting with genetic estimates of a more recent divergence between dogs and worldwide wolf populations…Here, we present a draft genome sequence from a 35,000-year-old wolf from the Taimyr Peninsula in northern Siberia. We find that this individual belonged to a population that diverged from the common ancestor of present-day wolves and dogs very close in time to the appearance of the domestic dog lineage. We use the directly dated ancient wolf genome to recalibrate the molecular timescale of wolves and dogs and find that the mutation rate is substantially slower than assumed by most previous studies, suggesting that the ancestors of dogs were separated from present-day wolves before the Last Glacial Maximum. We also find evidence of introgression from the archaic Taimyr wolf lineage into present-day dog breeds from northeast Siberia and Greenland, contributing between 1.4% and 27.3% of their ancestry. This demonstrates that the ancestry of present-day dogs is derived from multiple regional wolf populations.

gr2_lrg As you can see from the figure to the left the Taymyr sample diverges at about the same time as the common ancestor of wolves and modern dogs. In other words, you have a polytomy. Not only that, but there has been introgression from the Taymyr lineage into particular northern dog populations.

Genetics and genomics are big deals. But at this point I have to point out that archaeologists have really been here the whole time. Archaeologists reported that the Amerindians brought dogs with them over through Berengia. Historians know that the indigenous people had dogs. Yet in 2010 geneticists published, in Nature, Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication, who put the focus on the Middle East and the Neolithic revolution. There was basically no way this really made sense. Then you had a 2011 paper in PLOS ONE, A 33,000-Year-Old Incipient Dog from the Altai Mountains of Siberia: Evidence of the Earliest Domestication Disrupted by the Last Glacial Maximum. Even the authors themselves assumed that this was a “false dawn.” That this dog-like canid probably did not give rise to later dog lineages. But if the results above are correct, then in fact this 33,000 year old individual may actually be part of the extant proto-dog population.

Let’s let this sink in: if the results above hold, then the arrival of modern humans to northern Eurasia may have been coincident with the emergence of a distinct dog lineage. The term “man’s best friend” takes on a whole new meaning. The relationship between man and dog may be nearly as ancient as modern humans as we understand them, that is, populations capable of copious and protean symbolic cultural production which explode out in the archaeological record over the past ~40.000 years. In addition, I also believe we now need to totally reconceptualize how we view the relationship of wolves and dogs. Rather than an ancestral and derived set of populations, whose “species” status is only semantic convenience, they are actually sister clades. The results in this paper confirm other findings that the wolves of North America and Eurasia seem to share a post Last Glacial Maximum origin. Wolves as we understand them today may have emerged simultaneously with dogs, both descending from the melange of canid lineages which flourished during the Pleistocene. There’s a reason that feral dogs, such as dingos, do not “revert” to wolves. The ancestor may not have even been a wolf!

Additionally, the authors also note that the features of the dog which are hallmarks of domestication may themselves be derived within the dog lineage. That is, the separation of the ancestors of dogs and wolves predates the Last Glacial Maximum, ~20,000 years ago. But the evolution of dogs so that they exhibit particular derived traits may have occurred far later in time. In fact, I would hold that perhaps the true story is one of co-evolution between dogs and humans.

The ultimate moral of this true story to me is that many Pleistocene mega-fauna with wide ranges in Eurasia were subject to similar evolutionary dynamics. Extinction of distinct local lineages was the rule, not the exception. Recolonization from populations which dodged extinction was also inevitable. The phylogenetic tree was pruned repeatedly, but tempered somewhat in the ferocity of clipping by admixture and introgression, as branches fused together.

• Category: Science • Tags: Evolution, Human Genetics, Science 

ncomms8152-f1

Large-scale recent expansion of European patrilineages shown by population resequencing:

The proportion of Europeans descending from Neolithic farmers ~10 thousand years ago (KYA) or Palaeolithic hunter-gatherers has been much debated. The male-specific region of the Y chromosome (MSY) has been widely applied to this question, but unbiased estimates of diversity and time depth have been lacking. Here we show that European patrilineages underwent a recent continent-wide expansion. Resequencing of 3.7 Mb of MSY DNA in 334 males, comprising 17 European and Middle Eastern populations, defines a phylogeny containing 5,996 single-nucleotide polymorphisms. Dating indicates that three major lineages (I1, R1a and R1b), accounting for 64% of our sample, have very recent coalescent times, ranging between 3.5 and 7.3 KYA. A continuous swathe of 13/17 populations share similar histories featuring a demographic expansion starting ~2.1–4.2 KYA. Our results are compatible with ancient MSY DNA data, and contrast with data on mitochondrial DNA, indicating a widespread male-specific phenomenon that focuses interest on the social structure of Bronze Age Europe.

Looking at this paper, it basically confirms what we know from ancient DNA, and other large scale sequencing projects. Until recently much Y chromosomal phylogenetic analyses were done utilizing highly mutable regions, microsatellites. This had a major upside, in that variation was copious. But, it wasn’t as precise as more slow mutating regions of the genome would have been. But without next generation sequencing the Y chromosome is just hard to work with due to its paucity of SNP variants. So that’s why we’re seeing some gains here.

The relatively homogeneity in Northern Europe in particular is attributed to a few lineages which have gone through “star-like” expansions. That aligns rather well with the idea that the arrival of populations from the steppe was demographically an earthquake.

• Category: Science • Tags: Y Chromosome 

nature13810-f6

A few years ago a paper was published, Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins, in PNAS, which argued that ancient population structure within Africa might be the reason that non-African populations are genetically closer to Neandertals. The basic logic is simple. If within Africa there was variation in relatedness to Neandertals, and modern non-Africans are derived from the group that was closer to Neandertals, then one might infer that there was recent admixture between the groups even though any connection was very distant in the past. This objection actually popped up immediately when the Neandertal admixture Science paper was published. Over time many people have been convinced by various ingenuous and abstruse arguments.

The problem is that not everyone is a statistical geneticist, nor do they think about these issues very often. When it comes to the media they have to rely on what’s being published in prominent journals. The PNAS paper above has haunted the field in my opinion, because reporters have had to take the researchers at their word, when frankly most statistical geneticists that I know did not find their arguments very persuasive in the first place. Today we have even less reason to believe them. A few hours ago I saw this in my feed from the Genetic Literacy Project, More mystery about Neanderthal and modern humans: How reliable is ancient DNA analysis? The answer is very reliable. There’s no controversy.

The figure at the top of this post is from Genome sequence of a 45,000-year-old modern human from western Siberia. What you see is that the markers diagnostic of Neandertal ancestry are clustered together in segments to a far greater extent in the ancient sample than among modern peoples. This sort of pattern of decaying tract length is a hallmark of pulse admixtures. Each generation recombination breaks apart associations until the tract lengths are very small (or, they are not detectable). There are now at least two ancient samples which show that Neandertal-modern human admixture occurred in the relatively recent past in relation to their own period in comparison to modern individuals. That in itself reduces the probability of ancient structure being the dominant explanation for the Neandertal affinities of non-Africans, as ancient structure would not exhibit this tract length bias. And, this result has the utility of being amenable to common sense comprehension.

• Category: Science • Tags: Neandertal 

Olivia Munn

Olivia Munn

Periodically rather than offering up original thoughts it is needful to engage defensive warfare against pernicious memes. For example, one thesis that is commonly bandied about today is that racial admixture will result in the blending away of all differences, toward a homogeneous beige future without end. This is false. It is false for several reasons, genetic, and sociological. But, it is persistent for ideological reasons.

Here’s the latest instance, Future Humans Will All Look Brazilian, Researcher Says:

Meanwhile, many other physical traits will simply blend together. “Most of the traits that we think of as distinguishing different groups (hair colour, skin colour, hair curliness, facial features, eye shape) are controlled by multiple genes, so they don’t follow a simple dominant/recessive pattern,” McDonald explained. “In those cases, blending will make people look more similar over time.”

Hazara

Hazara

The recourse to a blending analogy is unfortunate. Genetics is not a blending process, it is a discrete one, which reconfigures variation every generation. The underlying variation in the form of alleles is maintained, even if the genotype frequencies shift. This insight is implied in the article with talk about recessive phenotypes and nods to Hardy-Weinberg equilibrium. One of the key problems with Charles Darwin’s original theory of evolutionary process is that it did not account for how heritable variation could be maintained. If that variation melted away every generation through blending processes then the world would rapid equilibrate toward homogenization. Roughly half the variation would disappear per generation in an exponential decay process.

41PHSZN6AEL And yet variation remains! Though the phenotypes, the traits, may exhibit blending between parents, the underlying genetic variation is governed by Mendelian dynamics. This is why in populations where alleles for traits like pigmentation segregate in a polymorphic fashion, such as in India, it is not uncommon for complexion to vary within families. Though on the population wide scale there is some tendency toward clustering about the mean, variance remains within a random mating group at equilibrium.

Another major issue is that these discussions too often focus on single traits. When evaluated across loci the variation and range in possibilities due to admixture in fact results in greater diversity than is possible today. Mendel’s law of independent assortment implies that traits and variation will not be co-inherited. Before international travel and migration the possibility of someone with blue eyes, an epicanthic fold, and tightly curled hair, was a theoretical affair. Today there are almost certainly people who exhibit all these traits.

By coincidence these people are likely to be Brazilian, as this is a nation where there are large populations of African, Japanese, and Northern European (German) ancestry. And the example of Brazil itself illustrates empirically why homogenization will not proceed in the manner which intuition tells us. Brazil may be modally a brown nation, but its physical types run the gamut, expressing the underlying genetic variation. Among populations such as the Uygurs, who are fusion of eastern and western streams, individuals arise who reflect in near totality the physical types of only one of their ancestral populations, even if most individuals exhibit configurations in equipoise.

And so it was, and so it will be. The reality is that today is not the age of amalgamation, that age has passed. The most recent work in human genomics actually brings us to the conclusion that in fact most of the “pure” populations we see around us today are fusions of deeply diverged human evolutionary threads. The ancestors of Europeans in the Pleistocene were as differentiated as modern continental races (i.e., Fst on the order of 0.05 to 0.15 depending on the pairwise comparison). The same is true of South Asians, and most other groups you can think of. The “Great Mixing” after the retreat of the ice and collision of peoples may explain why there is so little evidence for hybrid inviability today in cross-racial pairings; it may have been purged from the genomes of modern groups through selection during that period.

The admixture of this age will be but a shadow of the past. The reality is that for centuries into the future huge numbers of people will persist who we might recognize as European, African, and East Asian, in totality of their form and genetic heritage. The amalgamation of the early Holocene probably occurred through the fusion of groups in the early stages of demographic expansion. They were tribal affairs, parochial in their scope, born out of desperation and chaos, even if the consequences were continental in their implications. The clans of yore became the mothers of nations, but those nations are mature and endless in their number now. The existence of Brazil as we understand it is exceptional, the product of racial slavery on a massive scale during a time of tumult. It is the exception, rather than the norm.

Rahul Gandhi

Rahul Gandhi

In the next few decades international elites will no doubt enter into a period of intermarriage as old barriers fall, and new commonalities of class transcend ethnicity. But for the majority of the citizenry of the old nations such considerations will be theoretical. The initial period of synthesis and cross-fertilization will give way to stasis as all those open to the new possibilities of finding mates across old racial categories will have done so. Those who remain, the majority, will be more conservative in their preferences and tastes. The Holocene ushered in races which are extant across the world today through admixture; the anthropocene will usher in the post-national international race of global elite. Rather than twining a few threads of the human lineage, this new population will twist all the threads together in a radical new conformation. And it will be anything but homogeneous and uniform in its expression!

• Category: Race/Ethnicity, Science • Tags: Genetics, Race 

1280px-Testudo_formation

12918295 Sometimes it is useful to enter into the record what you think, even if it is not fully formed, or even not strongly held. After reading a review on mutational load in human populations, which lingered long over demographic inferences of our species’ fluctuations in population size, as well as conversations with Gregory Cochran and Ian Mathieson, I have come to the conclusion that cultural group selection is a very important, perhaps dominant, dynamic in explaining the ubiquity of anatomically modern humans over the past ~50,000 years.

This is not a novel position. A group of evolutionary theorists, most prominently today David Sloan Wilson, have argued for the primacy of group level collective dynamics for human societies which allow for a plausible organismic metaphor in their action and behavior for the past 40 years. Peter Richerson and Robert Boyd have developed an extensive body of theoretical work outlining precise models (see Not by Genes Alone) which extend this framework. Importantly, I want to be careful and qualify that I am being precise when I limit my conjecture to humans, and, cultural phenotypes. For empirical and theoretical reasons I believe that humans may be sui generis.

My intuition here is tied in to what I have stated earlier about Aurignacian populations, and their likely extinction in Europe due to the arrival of Gravettian populations. The ancient DNA results are yielding to the conclusion that the human past has been subject to a great deal of local population replacement. To me this is peculiar, because even in the course of inter-group competition one would expect a fair amount of admixture, as is assumed in a demic ‘wave of advance,’ where populations push forward their range through natural increase. In fact the replacements don’t strike me as typically genetical in their fluctuations. Rather, they’re cultural. Punctuated. Alternating between stasis and rapid switches in state and character. The genetic data may simply be witness to the outcomes of winner-take-all outcomes.

Of course there has long been speculation that the social organizations of anatomically modern humans was the key for why they replaced their cousins. Many of these models though were derived from conjecture, and extrapolation. The new twist for me is that the historical population genetics is now aligning with this possibility. These are real concrete data and results.

• Category: Science • Tags: Human Evolution 

51aBlSPDX8L._SY344_BO1,204,203,200_ I’ve been reading The Making of Modern Japan. Tokugawa Ieyasu is a pretty big deal, and I’ve long been intrigued by him as an individual after reading about him and his contemporaries in the novel Taiko. Also, Japan seems a good way to investigate the possibilities of how one becomes modern without being fully Western.

Stanford is hosting BAPG XII in two weeks. Unless something intervenes I’ll be attending as usual. I also assume that the excessive population genomics tweeting will lose me some followers, as is the norm.

Had a good chat with Iain Mathieson today, as I swung through Berkeley (had Peking duck for lunch and Texas barbecue for dinner!). It’s a good time to be alive and be interested in human evolutionary genomics.

Lots of comments below on my post on Asian Americans and university admissions. I don’t really have a strong opinion as to how admissions should be handled. As usual my sentiment is to make a plea for honesty and candor. But I’m probably being naive and hopeless about it all.

Update: I’m in the third & fourth segments.

• Category: Miscellaneous • Tags: Open Thread 

The Wall Street Journal is reporting on a suit brought by Asian American organizations, Harvard Accused of Bias Against Asian-Americans:

The complaint, filed by a coalition of 64 organizations, says the university has set quotas to keep the numbers of Asian-American students significantly lower than the quality of their applications merits. It cites third-party academic research on the SAT exam showing that Asian-Americans have to score on average about 140 points higher than white students, 270 points higher than Hispanic students and 450 points higher than African-American students to equal their chances of gaining admission to Harvard. The exam is scored on a 2400-point scale.

Ron Unz, among others, has written about this, before. So not a big surprise as to the underlying empirical trends. Liberal commentator and Harvard grad Matt Yglesias has talked about the patterns for years. It’s an open secret. The question is whether anyone cares, and whether the legal system will do anything about.

But let me note something, a lawyer defending Harvard notes:

Robert Iuliano, Harvard’s general counsel, said the school’s admissions policies are “fully compliant with the law.” The school says its admissions process takes into account a variety of factors besides academics, including applicants’ extracurricular activities and leadership qualities.

This is what a leader looks like

This is what a leader looks like

It strikes me as unlikely that Asian American applicants lack extracurricular activities. Though first generation immigrants may come from societies where academic achievement is the summum bonum, they know that in American admissions criteria that non-academic strengths matter. But, you can’t manufacture leadership and charisma. Harvard’s role is to educate and inculcate the leaders of the next generation of Americans. It is the training ground for our natural aristocracy. Can American society actually conceive of a situation where 40% of those leaders are Asian? I doubt it. Asian Americans are not seen as plausible leaders. Especially by the established oligarchs, who would prefer their own offspring to inherit the mantles of power. Asian males in particular exhibit a “penalty” in the dating game. White females perceive them to be sexually impotent (on average), and for better or worse the opinions of white females as to who is a plausible leader in our society is very telling. If American women won’t want have to have sex with them, then why would the broader society see them as creditable leaders?

This is related to something Josh Harkinson at Mother Jones pointed out recently: Asians are far underrepresented in top management in relation to their representation among rank and file workers, especially in technical positions, in Silicon Valley. This is well known. People make all sorts of excuses for this. For example, a large number of the Asians are immigrants to the children of immigrants, who may not have the “social capital” to be successful in management at an American firm.

For me, here’s the upshot: we just need to be honest. Perhaps the cultural skills and dispositions that Asian Americans bring to the labor force are naturally more amenable to technical positions and professions like medicine than they are to management. It may not be as much discrimination, even of the implicit sort, as opposed to the natural sorting of personality types. This is an option we may need to entertain, rather than assuming that it is all invidious discrimination. It does strike me as obvious that Harvard and other Ivy League schools are attempting to racially balance by putting their fingers on the admission knobs in just the perfect manner. Though I’m not particularly happy about this, being transparent and honest would at least allow us to address what’s going on, and wonder whether we should do something about it. The fact is that Asian Americans are doing relatively well, even if their proportion at Harvard is 20% instead of 40%. Do we as a society need to abolish all discrimination by any means necessary? I’d say no.

• Category: Race/Ethnicity • Tags: Asian Americans 

Phylogenetic tree of mtDNA lineages, with 40 K B.P Aurignacian "Fumane 2"

Phylogenetic tree of mtDNA lineages, with 40 K B.P Aurignacian “Fumane 2″


220px-Cro-Magnon A new paper in Science, The makers of the Protoaurignacian and implications for Neandertal extinction, seems to establish definitively that the Aurignacian culture, often identified as the first modern human society within Europe, was in fact of modern humans. The part that is of interest to me is the DNA evidence from this paper. In particular, they got a good quality mtDNA sequence, and put it on a phylogenetic tree with other humans. As you can see, it is clearly within the clade of modern humans, and in particular non-African modern humans. More precisely, this individual is a basal branch of haplogroup R, which is common across western Eurasia, and ancestral to many common lineages. The fact that it’s basal isn’t too surprising, this individual is ~40,000 years in the past. Because of the rapid turnover of mtDNA lineages it isn’t surprising if past lineages have gone extinct in a given region, even if total genome content is passed down.

But, I do want to enter into the record that in concert with rumors I’ve been hearing as well as the broad picture of what ancient DNA is telling us about genetic turnover that I doubt that modern Europeans in any way descend from the Cro-Magnon populations of the first settlement of the continent by moderns. Rather, I’d bet that the “hunter-gatherer” ancestry of the Europeans of today goes no further back than the post-Gravettian cultures, and perhaps later. The genetic makeup of ancient populations seems to have been more complex than we’d have imagined, and there were meta-population dynamics which we’re only getting a good grasp of. With low population densities and a fragmented Pleistocene landscape it strikes me as plausible that Palearctic mammals in particular may be characterized by repeated resettlement of the frontier of the range from core source populations after local extinctions and retrenchments.

• Category: Science • Tags: Paleoanthropology 

51GD7A9F3WL._SY344_BO1,204,203,200_ Recently I reread War Before Civilization: The Myth of the Peaceful Savage, with a particular focus on the transition in Europe during the Mesolithic/Neolithic. Today with ancient DNA we know that in western Europe there were two distinct populations which came together with the arrival of agriculture. One population, which is very similar to modern southern Europeans, was a synthesis of Ice Age indigenes and an intrusive group from the Middle East. The other population, Mesolithic hunter-gatherers, were related to, or in part ancestral to, much of the heritage of modern northern Europeans. An interesting aspect of the division between these two populations is that their genetic distance was very high, on the order of 0.05 to 0.10. Or that between continental races. Additionally, the hunter-gatherers may have been a fearsome sight to behold, large robust people with dark skin and hair and piercing blue eyes. A novelistic treatment of the meeting between hunter and farmer invites itself naturally (Ted Kosmatka?).

WillianGolding_TheInheritors Further back in time you have the meetings between our own lineage and Neandertals and other assorted hominins. No doubt some of the same discordances that characterized the interface of farmer and hunter would have applied in these situations, though even more starkly. I’ve read a fair number of novelistic takes on this “first contact.” Clan of the Cave Bear of course. But also Bjorn Kurten’s Dance of the Tiger. I’m finally getting to reading William Golding’s The Inheritors. And Robert J. Sawyer’s Neanderthal Parallax series, which is a strange twist on the theme, deploys many of the same tropes as prehistorical fantasy despite its science fiction setting.

Orientalism But a major problem with these books is that they turn the Neandertals into reflections of some aspect of our own dreams and nightmares about ourselves. Jean Auel’s Neandertals in Clan of the Cave Bear were patriarchal brutes, as opposed to the matrifocal Cro-Magnons. Ayla’s nemesis Broud is a nightmare inversion of dreamy Jondalar. In contrast Sawyer and Kurten depict Neandertals as a more gentle folk, more or less, in comparison to the rapacity of modern humans (Golding also goes in this direction). This is the same problem that Keeley observes in War Before Civilization, and that Steven Pinker explored in depth in The Blank Slate, though applied to our own species, with Europeans tellingly substituted for modern humans. Against this reference the Other is a noble savage, with different weights to nobility and savagery contingent upon cultural fashion.

cover_passing Contemporary American discourse about social justice is marinated in this intellectual framework, the heir of the age of white supremacy and scientism which crested in the early 20th century. Left-liberals who espouse strident progressive social justice views ascribe regressive practices among non-whites purely to extraneous Western colonial influences, as if non-white peoples were innocents in the garden before the arrival of Europeans, lacking agency for good or will. Whereas a previous generation of white supremacists perceived in the non-Western the inferior and primitive, a modern generation of Westerners sees the authentic and pristine. Though the moral valence differs, the underlying structural framework is invariant. To truly carve nature about its joints in a manner which exhibits appropriate fidelity we need to go beyond this reflex. Hopefully in such a manner we can also begin to probe our own past without fewer illusions which are haunted by the present.

• Category: Ideology • Tags: Human Nature 

By now you are aware that another blogger who happened to be an atheist was killed. The modus operandi is pretty familiar. It looks like there are now “hits” going up against these individuals as a way for Islamic radicals to target an easy to scapegoat minority in Bangladesh. Atheists are now caught in a crossfire between religious nationalists and secularists, a divide which goes back to the Pakistan days. How vulnerable are the atheists? Well:

“The culture of impunity that has spread over the last few years clearly has very damning results,” Arifur Rahman told IHEU after Washiqur Rahman was killed. “… The word ‘Nastik’ (atheist) has been vilified in Bangladesh (and the rest of the Muslim world); they are seen as sub-human, it is OK to kill them.”

All cultures are not the same. In most of the Islamic world sufferance would be enough for many minorities. While craven Leftists wring their hands over insults to Islamic minorities in their midst, Islamic civilization is wrecking havoc upon the liberties of millions. That being said, there is a continuum. Saudi Arabia, Iran, Turkey, Malaysia, and Azerbaijan are not interchangeable. There are some analogies being made to Pakistan right now (like being analogized to Mississippi in the United States this is never good). That’s apposite at this particular moment because 45 Ismaili Muslims have been gunned down in Karachi. It strikes me that Pakistani sectarianism is now proceeding down a Bonhoefferian Niemöllerian gangplank, first dehumanizing non-Muslims, and then progressively narrowing the set acceptable. The nation is on the way to being a literal circular firing squad.

Bangladesh is a different case. I won’t rehash it. I will point out though that when I posted about my own identity, as an atheist of Bangladeshi origin, that when put that on reddit the response by one individual was “Who cares”? Obviously there are many things in Bangladesh that warrant attention, but, targeted killing of a reviled minority is apparently not worth notice by some. Fair enough, I suppose.

But I’m not here to emote and reflect. Rather, what does the data say? The World Values Survey has data from Bangaldesh for 1999 to 2004. One of the questions asks: Politicians who don’t believe in God unfit for public office. It seems a rough gauge for attitudes toward atheists. The results are below.

Atheist_htm_4ce6039

As you can see Bangladesh is roughly in the middle of the list. Observe the contrast with Pakistan. Hostility toward atheism is the majority position in all likelihood, but protests of people in the face of Islamist terror, as well as the persistence of atheists in Bangladeshi culture, indicates that there is a sufficient groundswell of liberal religious civil society that there’s a shot. In contrast in Pakistan you have a society which is now at total conformity when it comes to toleration for free thought.

Raw data:

Question: “Politicians who don´t believe in God unfit for public office”

Country Agree strongly Agree Neither agree or disagree Disagree Strongly disagree No answer Don’t know
Sweden 1.7 2.3 11.4 36.8 47.3 0 0.4
Spain 1.8 8.7 17 40.2 23.7 0 8.7
South Korea 2.6 6.7 27.3 37.5 15.4 0 10.5
Vietnam 4.5 11.9 16.9 47.4 5.8 0 13.5
Bosnia 5.1 10 30.2 25.5 22.2 0 7
Serbia 8.7 16.2 14 34.7 17.2 0 9.2
Canada 6.6 12 21.8 35.9 21.2 0 2.5
India 14.5 18.2 11.3 26.6 8.1 0 21.3
Chile 14 18.3 10 20.6 31.4 0 5.6
Japan 2.2 5.4 49.6 25.5 14.9 0 2.5
Mexico 14.9 21.5 9.2 27.3 16.2 0 10.9
Macedonia 17.7 14.7 16.8 27.5 16.6 0 6.8
Argentina 13.7 20.5 17 31.1 12.3 0 5.4
Kyrgyzstan 10.5 25 19.1 35.2 9.6 0 0.6
Moldova 11.7 28.9 21 24.1 5 0 9.2
Albania 16.1 24.8 24.7 19.2 7.2 0 8
United States 17.6 20.3 25.8 27.1 8.4 0 0.8
Zimbabwe 14.9 36.4 8.3 31.8 3.6 0 5.1
South Africa 22.9 24.6 19 19.9 7.1 0 6.5
Turkey 28.7 28.2 11.5 16.9 9.1 0.1 5.6
Venezuela 35.5 15.8 15.1 18.8 12.7 0 2.2
Uganda 25.2 36.2 14.3 17 4.3 0 3
Bangladesh 30.2 37 5.2 20 2.3 0 5.3
Puerto Rico 36.5 26.9 11.7 19.3 3.6 0.4 1.5
Tanzania 53.4 11.2 11 13.9 8.1 1 1.4
Philippines 26.8 44.4 14.7 11.9 1.9 0 0.2
Algeria 51.7 20.7 8 8.7 3.3 0 7.6
Jordan 66.6 11.1 2.1 6.8 9.3 0 4.1
Iraq 66.1 15.1 0 5.5 6.9 2.2 4.2
Nigeria 56.8 24.2 7.6 6.8 3.6 0 1
Indonesia 59.4 27.9 1.9 7.2 2 0 1.6
Morocco 72.4 14.2 2.7 4.3 1.2 0 5.1
Egypt 70.1 17.6 2.4 4.9 4.9 0 0
Pakistan 82.4 12.5 4 0.9 0.2 0 0
• Category: Foreign Policy, Ideology • Tags: Bangladesh, Religion 

The_Clan_of_the_Cave_Bear_cover By now you have heard of the recent ancient DNA finding dating from ~40,000 years ago in Southeastern Europe. The individual is a representative of one of the first anatomically modern groups to arrive in Europe…sort of. It exhibits robust characteristics, and may have had some admixture from Neandertals. Now, thanks to ancient DNA, that’s confirmed:

Qiaomei Fu, a palaeogenomicist at Harvard Medical School in Boston, Massachusetts, told the meeting how she and her colleagues had sequenced DNA from a 40,000-year-old jawbone that represents some of the earliest modern-human remains in Europe. They estimate that 5–11% of the bone’s genome is Neanderthal, including large chunks of several chromosomes. (The genetic analysis also shows that the individual was a man). By analysing how lengths of DNA inherited from any one ancestor shorten with each generation, the team estimated that the man had a Neanderthal ancestor in the previous 4–6 generations. (The researchers declined to comment on the work because it has not yet been published in a journal).

Two major points. First, the admixture fraction is way higher than any modern population. This isn’t a fluke. Second, they must be seeing ancestry tract lengths to make this inference. Basically the Neandertal ancestry blocks have been chopped up, but only a finite number of times. This really one-ups talk of “Cherokee great-grandmothers”, that’s for sure.

So what about the earlier results that most of the admixture must have happened in the Middle East? There have been revisions to this model, with many researchers now suggesting that a second pulse might have occurred in eastern Eurasia. But, another possibility is that very little of the ancestry of the first modern Europeans remains in modern Europeans. That is, the later Paleolithic populations of Europe may have replaced the first settlers, just as they in their turn were replaced or assimilated. The landscape of Mesolithic/Neolithic Europe seems demographically complex, so I see no reason not to suspect that the same was the case for the period before the Last Glacial Maximum. There may have been several admixture events with Neandertals, but the “outriders” may have been left no traces in the modern human lineages. It may be that the human “phylogenetic bush” has been extremely pruned many times over, so that most “fossil ancestors” are simply dead ends.

Addendum: As usual, great piece in Nature too.

• Category: Science • Tags: Paleoanthropology 

Screenshot from 2015-05-13 07:47:30 In a review for the new installment of Mad Max Dana Stevens in Slate writes:

The way the world ends, for Miller, is not in overpopulated high-tech megacities slicked with film-noir rain, but in something like the polar opposite. Miller’s nightmare of the future posits the planet as a parched desert landscape against which the world’s few remaining humans scratch out a meager, violent existence, equipped only with the salvaged remains of mid-20th-century technology. It’s that future that, 36 years after Mel Gibson first put the pedal to the metal as Max Rockatansy, is looking more like the one we may be leaving to our own survivors….

I understand this is a movie review, and that line was probably thrown in there for artistic effect. But facts matter, and there is no way that you justify the position that the world is more like that of Mad Max today than 40 years ago. Paul Ehrlich has definitely lost his bet, and even the peak oil worry has abated. The data show that a smaller proportion of the world’s population is undernourished and and poor. The total fertility rate is declining and life expectancy is increasing. Yes, the situation of the middle class in much of the developed world has been in relative stagnation by many metrics, but enormous increases in human well being have occurred throughout what was once termed the Third World.

The Right and Left have particular hobbyhorses. Young people today are more secular and tolerant of sexual diversity in lifestyles, but they are also less sexually promiscuous (we were blogging about this at Gene Expression seven years ago by the way). Similarly, despite worries about income inequality in the developed world, billions are rising out of poverty in places like China and India. Yes. Billions. Though environmental threats exist, the world is healthier and wealthier than it was a generation ago.

It’s not very important that Dana Stevens’ editor didn’t remove a rhetorical flourish which was just factually unfounded (though I it’s insulting to the people of places like the Sahel who suffered through privation a generation ago, and no longer do so). But, it does suggest a mental weakness that these sorts of slips get through, to influence the public, and continue to distort the perceptions of the way the world is. To prepare for the exigencies of the future we need to see the present clearly.

• Category: Ideology • Tags: Environmentalism 

god-is-back Long-time readers of my content know that about 10 years back I used to make fun of a book by two writers for The Economist, God Is Back: How the Global Revival of Faith Is Changing the World. It was a sexy thesis, but really it was meant to appeal to paranoid liberals who were scared, as well as reassure religious conservatives worried about “a secular age.” The basic idea was that religious views and values were ascendant again, not a totally crazy thesis on the face of it. The problem is that the data in some regions were already suggesting major changes in the direction of secularism, in particular in the United States. This change took most people by surprise unless they were looking closely. Samuel Huntington’s last book, Who Are We?, was written unfortunately in the late 1990s just before the release of multiple academic surveys which chronicled the rapid de-Christianization of vast swaths of the American populace. In it Huntington took for granted the thesis that America would become more, not less, Christian, as more Asian Americans converted to Christianity, and the Hispanic Catholic fraction increased (contrary to visible evangelical Asian-American Christians, this is the least religious of America’s ethnic groups, and Hispanics are secularizing very fast).

Even though the data are pretty clear, and were for a long time, people tend not to update. And timing is always an issue. For example, the last major wave of secularization in the USA happened in the late 1960s, before which Time Magazine published Religion: Revival’s Crest in 1963. In the early years of my blog I kept having to remind people of facts when they relied on impressions. In 2009 I corrected The New York Times’ John Tierny, who stated that “As an agnostic myself, I’ve tended to see the European trend as a harbinger of a general move toward secularism as societies become richer and more educated. But you don’t see that trend in the United States, where church attendance is still robust….” I happen to know his email address and I sent him my post. He wasn’t convinced that I was right even then. I bet now he would admit that the data were robust.

PF_15.05.05_RLS2_1_310px I suspect that a new survey from Pew (very large sample sizes) is going to change resistance even from holdouts who don’t want to read the writing on the wall, America’s Changing Religious Landscape. The major “shock result”, which has been prefigured elsewhere, is that huge numbers of younger Americans are not religiously affiliated, and larger fractions are now admitting to being atheists and agnostics. The change over the generations has been enormous, going from a nation that’s over 85 percent Christian, to 70 percent Christian, mostly driven by defection. Before the 1990s religious adherence was a matter of social conformity. Far less today when 25 percent of the population does not have an affiliation, and even less so in regions where religious adherence may even be a subculture, rather than a norm. The fraction of the unaffiliated who are atheists and agnostics is also increasing, suggesting that the taboos around these terms are declining (I doubt I’d get as many shocked expressions saying I’m an atheist today in Red America as I did in the early 1990s).

agcover165.jpg What does this portend for the future? Over 1/3 of those born in the 1980s and 1990s have no religion. These are people who will be retiring in the 2040s and 2050s, the grandparents of that era. The trends, which are not guaranteed, mind you, indicate then that future generations may be even more secular, so that the electorate of that period may be extremely polarized in terms of religious culture (as the fractions of evangelicals is holding its own better than other Protestants and Catholics). This result was already evident in Robert D. Putnam’s American Grace: How Religion Divides and Unites Us, which received far less attention than Bowling Alone. But it was an important finding. Basically, the association of religion and right-wing politics has been having a secularizing effect on non-right wing Americans, and making ostensibly right-wing individuals more religiously identified. In other words, socially binding cross-cutting institutions are unraveling.

I believe this is more important than the coming “white” minority of 2050. The reasons are manifold. In the early 2000s some Democratic strategists saw an emerging majority from the coalition of minorities. On the other side many on the Right feared the rising tides of color, implicitly or explicitly. Nearing the end of the Obama era we now see how this story did not turn out to be so neat, with one of the proponents of demography-as-Democratic-density now recanting. Obviously we need to be cautious about over-reaction. The white Protestant conservative demographic core of the modern Republican party, and American conservatism, is going to decline somewhat over the generations. But the basic thesis that all non-white populations will vote Democratic indefinitely for generations seems unfounded. And definitions matter. Many Americans of mixed backgrounds may be assumed by Left-liberals to take the black tack of hypodescent, but they may actually simply exhibit more flexible self-identities which do not disassociate them so much from the mainstream (people who are visibly white, but have non-white ancestry, do not react well to racism against non-whites for obvious reasons, but neither are they anti-white, and often identify as white).

In an America where racial boundaries are fuzzier and more malleable, the strictness enforced by social-cultural categories in theory may actually be appealing and bracing. This goes to the heart of genetic vs. cultural distance in variation. Genetic variation rapidly diminishes due to the constraints and conditions of biological inheritance. Cultural inheritance is theoretically more powerful and airtight. As the ethno-biological categories melt on the edges, religious-cultural ones may emerge to more fully demarcate various tribal-political coalitions. And this is part of the reason why religion may increase in salience, despite the rapid expansion of a non-religious population. Confessional politics may come to the United States in an explicit fashion with the decline of implicit normative convention.

Postscript:

51KXqRwj+gL._SY344_BO1,204,203,200_ Some of you may wonder as the Americo-centric focus of this post, especially light of another recent Pew survey which highlights religion’s international robustness, The Future of World Religions: Population Growth Projections, 2010-2050 (as well as books I’ve blogged such as The Next Christendom: The Coming of Global Christianity and Shall the Religious Inherit the Earth?). First, international projections are dicier than national ones. More variables are on the move. You can’t predict easily the rapid secularization you saw in Quebec in the 1960s, in the United States in the past 15 years, or, the glimmers of change on the horizon in the Arab world. Second, what happens in the developed world matters more. The huge numbers of African Christians will result in change. But, Catholicism will still be based out of Rome, and intellectual currents out of Western Christianity will likely shape Sub-Saharan African Christianity more than the reverse. Philip Jenkins in his work celebrating African Christianity nonetheless observes that over time indigenous religious traditions begin to align themselves with world-normative practices, often to standards established in Western societies.

• Category: Race/Ethnicity • Tags: Religion 

Silver Fox

Silver Fox

Update: Preview clip is online. Click “domesticating animals”. End update

There are different opinions on whether domestication as a process can give you insight into evolutionary processes. The divergence goes back to the beginning of evolutionary biology. Charles Darwin was an optimist, a country gentlemen who spent much of is life in rural England. Alfred Wallace on the other hand seemed to focus more on natural selection in the wild, raw and unconstrained. A week ago at the Biology of Genomes Conference Alex Cagan presented research on broad convergences of the evolutionary genomics of tame and domestic lineages in mammals, Tameness is in the genes:

Cagan and colleagues examined DNA in Norway rats (Rattus norvegicus) that had been bred for 70 generations to be either tame or aggressive toward humans. Docility was associated with genetic changes in 1,880 genes in the rats. American minks (Neovison vison) bred for tameness over 15 generations had tameness-associated variants in 525 genes, including 82 that were also changed in the rats.

Some people on Twitter joked that this was a trivial finding, as we’ve long known that domestication is a heritable process mediated via quantitative genetics. But the interesting aspect of this research is that it seems that the same pathways lead back to the same broad set of genetic families. In other words, selection does not operate over an infinitely malleable and plastic genome over the medium-term evolutionary time scale. Not world-shaking, but critical to get a fix upon (definitely not surprising in light of how Hox genes and opsins have been known to evolve over and over).

MV5BMTc2Mzc0MDM4OV5BMl5BanBnXkFtZTcwNDg1MzczNQ@@._V1_SY317_CR29,0,214,317_AL_ I bring this up now because on tonight’s episode of Through the Wormhome, titled Are We Here for a Reason?, I’m interviewed in the third segment, where I give my opinions on domestication and its relevance toward evolution and the human future. This follows up my small role in the PNAS paper from last fall, Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication. As my current professional interests are still fixed upon this area of evolutionary genomics, expect to hear more from me!

As for the logistics of the show, it’s on The Science Channel, a Discovery cable property. For those without a television it seems that you’ll find it online soon enough. I have seen a preview, and it’s pretty good. I’m flattered to be on after Richard Lenski. The production values are good, I’m hoping that people will learn something. Please do remember that a lot of filming was reduced down to 5-10 minutes. It is amusing to see where they inserted graphs; that’s usually where I got a little too nerdy and technical, even though the director kept trying to get me under control.

P.S. I had a cold that day, for the record.

• Category: Science • Tags: Through the Wormhole 

516JD1M3N5L Been pretty busy around here. But I want to point out that our old friend Armand Leroi, author of Mutants and The Lagoon, is out with a new paper, The evolution of popular music: USA 1960–2010. It’s open access, and has gotten a lot of press already, but I do think it’s an important result to ruminate upon. I give a CEfKf4OUgAAZipL lot of thought to theoretical models of cultural evolution derived from evolutionary theory, but it’s obviously important to bridge these with empirical patterns as well.

In other news, a few people in the comments below are asking about my post in regards to Julia Galef’s comment about Dawkins. One thing some readers may not know is that I’m personally pretty well acquainted with many of the “rationalist” crowd who live around Berkeley. As in, they are my personal friends more or less. That should give you some sense how open minded these people are to heterodox ideas. It’s hard to escape the bounds of group conformity, but my experience is that for various reasons (often innate) these are people who are generally bound less to that tendency than is the norm in the broader culture. Take that how you want to take it.

Finally, any interesting papers and books would be appreciated. This is an open thread, but it seems that unless I make an explicit call people don’t think to contribute.

• Category: Miscellaneous • Tags: Open Thread 

The below is ~2 minutes from Julia Galef. Not really about Richard Dawkins per se. I’m thinking on this. Strikes me as important.

• Category: Ideology • Tags: Psychology 
Citation:,/b> Tree of life reveals clock-like speciation and diversification

Citation: Tree of life reveals clock-like speciation and diversification

speciation Perhaps Charles Darwin was wrong about how species originated? This shouldn’t be so surprising. If you read The Origin of Species you’ll be struck by how much Darwin got wrong, and, how much he got right. As a fully grown adult with some knowledge of evolution re-reading Darwin in the original confirmed for me what a genius he was. The man was writing over 150 years ago in a pre-genetic era. Not only did he not have molecular phylogenetics, but he didn’t even have a proper theory of inheritance! It’s a miracle Charles Darwin got so much right. It’s no sin that he missed the mark even on the big questions.

simonconway05_16 With that I have to admit it’s awkward when people ask me about big picture evolutionary questions (as opposed to, for example, the rate of new mutations in humans), as unfortunately I’m not very well versed in macroevolution. Much of what I know about speciation in particular I know from Jerry Coyne and H. Allen Orr’s mid-2000s book Speciation. It’s true that both are population geneticists by training, so that might give me a biased view, so I’ve also read Stephen Jay Gould’s books (e.g, The Structure of Evolutionary Theory). But with Gould it’s hard to tell when he’s transmitting consensus, and when’s presenting his own heterodox views, unless you engage in very close reading. Simon Conway Morris wrote The Crucible of Creation specifically to rebut what he felt were Gould’s misrepresentation of his research in Wonderful Life (by the way, I feel that Gould’s literary style is best suited to essay format; in books he’s interminable).

A new open access paper in MBE, Tree of Life Reveals Clock-Like Speciation and Diversification, concludes that speciation is a clocklike and neutral process. As you can see from the figure above it looks as if ~2 million years is some major peak when it comes to the point at which lineages which are species converge in terms of their last ancestral populations. First, it seems clear that they’re using the biological species concept. Second, their mechanism is totally unoriginal. Rather than positive selection due to exogenous natural pressures (think Darwin’s finches, though he himself gave a lot of thought to sexual selection as the driver of speciation) the authors indicate that neutral mutational differences between diverged populations eventually lead to genetic incompabilities. This was an idea that was part of the neo-Darwinian Synthesis, so we’re talking about modulating weights, not overturning of the established order. This is an active area of research in population genetics today, see Emergent speciation by multiple Dobzhansky-Muller incompatibilities. It’s not crazy on the face of it as a hypothesis.

But it’s a whole different thing to generalize about the tree of life. Quanta Magazine has a collection of responses from researchers in the field, A Surprise for Evolution in Giant Tree of Life: Researchers build the world’s largest evolutionary tree and conclude that species arise because of chance mutations — not natural selection. I think the title is misleading for the general audience, as this isn’t a novel thesis at all, but the piece itself is more evenhanded. As noted within phylogenetics is a highly statistical enterprise. Leibniz’s famous injunction “let us calculate” is a bit more complicated when you have biased data to put into your inference generation machine. Obviously the authors couldn’t sample extinct lineages, as noted by some in the Quanta piece. They try to account for this, but the devil is in the details. Overall a ~2 million year figure invariant across arthropods and vertebrates strikes me as strange, and likely a statistical artifact if I had to put money on it (or perhaps low effective population size lineages exhibit more build up of neutral alleles producing genetic incompabilities, while large Ne groups are more impacted by positive diversifying selection, when it comes to speciation?).

Time will tell. This is not the final answer, and my passing acquaintance with this field suggests that a “first look” often does not hold up because people are missing part of this very big picture. The whole tree of life is a big thing to tackle when it comes to generalization. But, I am optimistic that this generation shall not pass before we have enough sequence across the tips of the tree and computational power to analyze it to come to more robust conclusions.

Citation: S. Blair Hedges, Julie Marin, Michael Suleski, Madeline Paymer, and Sudhir Kumar, Tree of Life Reveals Clock-Like Speciation and Diversification, Mol Biol Evol (2015) 32 (4): 835-845 first published online March 3, 2015 doi:10.1093/molbev/msv037

Addendum: I should note also that natural selection itself is somewhat stochastic over short enough time intervals. Don’t know if that would produce neutrality in speciation over the long term.

• Category: Science • Tags: Evolution 

On-Liberty In the wake of the events in Garland a few days ago the above tweet by a reporter at The New York Times has garnered a fair amount of attention. It’s really hard for some (including me frankly) to not see this as “victim-blaming.” Free speech is a very special and distinctive liberty, in particular the liberty to speak in public without censure in a manner which assaults the basis of what is holy and sacred. In much of the world this particular absolutism, neigh, idolatry, of freedom of thought even unto the bounds of blasphemy and hatred that is adhered to in the United States thanks to our Bill of Rights is viewed as strange and offensive. The insights of classical liberal thinkers were strange and novel in their time, but they captured our imagination. We put freedom of conscience first and foremost not because that is how it has always been, but it is how we believe it should be. Conscience even for the devil himself!

To some extent there are aspects of incommensurability here. The right to blaspheme is relatively new in the history of the world, and especially in a multicultural world. Many Muslims who don’t understand how one could insult their religion often get confused when it’s pointed to them that their own religion is based in large part on invective against other faiths (e.g., ‘idolaters’). One person’s insult is another person’s fact. This rational critical position “outside” of society is abnormal in human psychology, which is embedded in all sorts of cultural and social presuppositions.

But in any case, with all that in mind, I was curious about attitudes toward speech in the GSS. There are a series of questions which exhibit the form:

If such a person wanted to make a speech in your community preaching hatred of the United States, should he be allowed to speak, or not?

In this case, a Muslim cleric who preaches hatred of the United States. Other questions refer to racists, atheists, militarists, homosexuals, and communists. Basically, these questions get at whether respondents would tolerate public expression of views which they might personally find objectionable. Look at the trend line over the years it is generally heartening:

speech_htm_8ee3688

The question about Muslim clerics only began to be asked in 2008, so I didn’t put it above. But, I was curious about how it related to a question about whether to let a racist speak in your community. Below are some demographic cross-tabs:

Demographic Allow Muslim cleric to speak Allow racist to speak
Extremely liberal 62 66
Liberal 52 64
Slightly liberal 49 58
Moderate 39 57
Slightly conservative 44 61
Conservative 40 61
Extremely conservative 34 60
Strong Democrat 42 57
Democrat 38 56
Lean Democrat 50 57
Independent 37 56
Lean Republican 46 66
Republican 41 62
Strong Republican 40 62
No HS diploma 18 41
HS diploma 37 56
Junior college 45 61
Bachelor 60 72
Graduate 65 74
Wordsum 0 11 31
Wordsum 1 20 43
Wordsum 2 19 37
Wordsum 3 23 49
Wordsum 4 28 56
Wordsum 5 31 54
Wordsum 6 39 54
Wordsum 7 48 62
Wordsum 8 60 70
Wordsum 9 68 81
Wordsum 10 85 88

correlation

Click to enlarge

In case you are curious the correlation between the two trends across these demographics is 0.95. To the left is a scatter plot which shows the pattern (click to enlarge). I was pretty shocked how nearly monotonic the tendency for the more intelligent (Wordsum is the score on a 0 to 10 vocab test which has a 0.71 correlation with general intelligence) to be more supportive of free speech is. Note that extreme liberals are more supportive of free speech even for racists than conservatives, though there isn’t much social difference at this point (I’m not surprised by the lack of partisan differences, which are much less segregated by social values than ideological identification).

Next I wanted to relate how the two attitudes toward speech related. Below you see the first two set of cross-tabs with marginals on the rows and columns. So the first set shows what percentage of those who would allow a Muslim cleric to speak would also allow a racist to speak. The second set shows what percentage of those who would allow a racist to speak would also allow a Muslim cleric to speak. In both cases the top left and bottom right are the “consistent” positions. Finally, I decided to look at attitudes by demographic again, this time broken down by both positions on speech with the marginals for the column. That means that every row shows the percentage of those who would allow a racist to speak who would also allow a Muslim cleric to speak, and those who wouldn’t allow a racist to speak who would also allow a Muslim cleric to speak.

Allow racist Don’t allow racist Total
Allow Muslim cleric 88 12 100
Don’t allow Muslim cleric 38 62 100
Allow racist Don’t allow racist
Allow Muslim cleric 63 13
Don’t allow Muslim cleric 37 87
Total 100 100
Allow racist Don’t allow racist
Allow Muslim cleric to speak Extremely liberal 81 27
Liberal 71 17
Slightly liberal 70 21
Moderate 60 12
Slightly conservative 63 15
Conservative 61 8
Extremely conservative 53 3
Wordsum 0-4 40 10
Wordsum 5 48 13
Wordsum 6 63 9
Wordsum 7 70 12
Wordsum 8 79 17
Wordsum 9 77 27
Wordsum 10 92 32

 

The consistent free speech position gets stronger as you get more liberal, and, as you get more intelligent. But it is interesting that the position where you won’t allow a racist to speak but you will allow a Muslim cleric to speak gets more frequent among liberals and the very intelligent. This, I believe, explains some of the rumblings and equivocation about free speech absolutism. These are a minority, but they are vocal. In contrast, though there are hardcore civil libertarians on the Right, it is almost certainly true that many conservatives who support the right to blaspheme Islam are less willing to stand up for the right to blaspheme the flag of the United States (e.g., allow someone to defecate on it, for example).

One major caveat that needs to placed here is that traditionally the elites of this country have been more defensive about free speech than the populace as a whole. That’s probably because the elites are worried more about power plays by their rivals. Ultimately politically oriented free speech is important for those with ambition and aspirations.

• Category: Ideology • Tags: Free Speech 
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"