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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:


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


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 

The New York Times has a painful write-up of what a humanities conference is like, The Conference Manifesto. My question is pretty straightforward: is this really representative? E.g., reading line-by-line from papers? Readers with experience as asked to weight in.

• Category: Miscellaneous • Tags: Humanities 

i-e0ed6daf62985b09716b019fe85fdc0e-invisible-gorilla A few years ago when I reviewed The Invisible Gorilla: And Other Ways Our Intuitions Deceive Us, I joked that it was the anti-Malcolm Gladwell manifesto. The joke was only half serious. Chris Chabris and Daniel Simons presented in their book serious arguments which weren’t sexy and offered no easy shortcuts. As such it is no surprise that Gladwell is still rolling in the money, while Chabris and Simons are respected academics, though not public intellectuals on the same magnitude (the irony is that arguably they are intellectuals in a more substantive way than their famous bête noire). A more egregious individual when it comes to science popularizing than Gladwell was Jonah Lehrer (not surprising that Jonah was somewhat of a protege of Gladwell). Aside from the admitted fabrications, Chabris has been long pointing out that Lehrer seems to purposely misrepresent or misunderstand the process of science, taking isolated studies and stitching them together to support novel and counter-intuitive theses which might sell copies of books (it was ironic that he wrote a long piece for The New Yorker on problems with replication).

The fact that you shouldn’t hinge your perception about the validity of a hypothesis on one study isn’t an issue for most scientists. They know how science works. It’s a noisy process, with lots of fits and starts, and consensus emerges slowly, and is periodically overturned or extended. There’s a reason that John Ioannidis’ Why Most Published Research Findings Are False is highly cited. There are thousands and thousands of studies published every year. If you want, you can search through the stack and find “peer reviewed research” to support nearly any proposition. The issue isn’t whether there are scholars willing to support your position, but what the scholarly consensus is, if there is one.

thinking-fast-and-slow All this came to mind when I saw this blog post, A Trick For Higher SAT scores? Unfortunately no. The short of it is that a few years ago the author read Thinking, Fast and Slow, from Daniel Kahneman, a Nobel Prize winner. He reported with excitement results from a study which primed individuals to focus more with less clear fonts, and therefore increased their cognitive performance substantially. The reason why this study’s results are important is obvious to anyone, increasing median cognitive performance is a social good (this is why we put iodine in salt to combat cretinism).

Though Kanheman is a great scholar, most people are not going to know about this study from him. Rather, Malcolm Gladwell used the study in David and Goliath: Underdogs, Misfits, and the Art of Battling Giants to illustrate one of his points. Unfortunately Gladwell is a big deal for many people. Though I quite liked The Tipping Point when it came out, over the years I’ve come to see that Gladwell is less a communicator of scholarship than a storyteller who sells intellectually-themed yarns. Gladwall hasn’t seen a sample size that dissuades him from reporting enthusiastically on a result with a marginally significant p-value, so long as it supports one of his story arcs.

Three years on the author of the blog post, and one of the original authors of the paper, have a follow up publication where they report that there is no effect at all from the priming with less clear fonts. The sample size of the original study was 40. The follow up, 7,000 total (they pooled multiple studies). The author of the blog post ends on a down note:

I expect that the false story as presented by Professor Kahneman and Malcolm Gladwell will persist for decades. Millions of people have read these false accounts. The message is simple, powerful, and important. Thus, even though the message is wrong, I expect it will have considerable momentum (or meme-mentum to paraphrase Richard Dawkins).

Probably descriptively correct. But you can do something about it. Be the asshole at the party to point out that the “latest research” your friend has read in the current issue of The New Yorker is most likely to be crap, especially if it is both counter-intuitive and supports your group’s normative priors. (yes, I am usually that asshole in real life too)

Note: the reason I say irrelevant, rather than false or wrong, is that a lot of research is trivial improvement on an already established consensus if when the results are robust.

• Category: Science • Tags: Psychology, Science 

41ncnodwApL._SY344_BO1204203200_ Just a reminder to people leaving comments, I’m not the typical laissez faire moderator. Obviously you are immediately going to be banned if you go full-snark from the get-go (yes, some commenters are under the illusion that they are brilliant and wise, and unmoderated comment threads allow them to continue with that delusion indefinitely), but repeated stupidity also is going to result in abolition of commenting. Sure some commenters who I have banned are angry, but the reality is that you are probably less intelligent and informative than you’ve been led to think. Better you passively read than contribute to the discussion.

Second, I finished Inventing the Individual: The Origins of Western Liberalism, and have been thinking about why the book rubbed me the wrong way. One, the author often writes beautifully.. So whatever qualms I had with the thesis it wasn’t difficult to push myself to finish it. Second, he has a thorough mastery of the material. There was lots of data to extract and assimilate. And I don’t object to the thesis itself, so I’m skeptical. There are plenty of arguments which I don’t agree with beforehand, and which I remain skeptical of, but are worth engaging in.

But here’s a relatively random passage which illustrates my problem:

Why did Ockham insist, above all, on God’s freedom? The biblical argument that freedom reveals the way humans are made ‘in the image of God’ suggests one possible answer. The nominalists were reasserting the Jewish sources of Christian thought against Greek influences. But there is another possibility. The canonist conversion of natural law into a theory of natural rights, founded on the assumption of moral equality, was feeding back into the conception of divinity itself. Emphasizing the claims of the will in human agency led Ockham to emphasize the same trait in divine agency. Human freedom and God’s freedom were becoming mutually reinforcing characteristics. This is why contingency and choice, rather than eternal ideas and a priori knowledge, loomed so large in this thinking. Ockham denied that the kind of a prior knowledge of the universe required by the doctrine of eternal ideas or ‘essences’ is possible. Exaggerating the capabilities of human reason, it compromises God’s freedom and power, his ‘sovereignty’. [page 308, Inventing the Individual]

This section is part of a broader section which seems to suggest that the medieval nomimalism opened up the way for empiricism and liberalism. This is not an original thought. But, I find it ironic because the problem with much of Inventing the Individual: The Origins of Western Liberalism is that it plays out as a logical explication of its own thesis, rather than supporting it with empirical data. In other words, Inventing the Individual oftentimes reminds me of beautifully written scholasticism. Larry Siedentop, the author, believes in the power of ideas to change the human soul. His argument is not a particularly original one, suggesting that the synthesis of Greek philosophy and Hebrew religion which manifested in the form of St. Paul laid the seedbed for the core assumptions of liberal individualism, which came to maturity over a millennium later. But the argument is rather thin on empirical examples of how individuals themselves conceived of themselves as liberal individuals, rather focusing on the 50,000 foot view from the organic development of social institutions, or the abstruse details of canon law.

51YU-l46UbL._SY344_BO1,204,203,200_ In Nature’s God: The Heretical Origins of the American Republic Matthew Stewart makes a similar sort of argument, though the details obviously differ. Like Siedentop Stewart is a very good writer. His prose is not a drag to work through. Arguably he took a more novelistic tack, focusing more on personality and lives than Siedentop did (Stewart is focused I think on a more general audience). In addition, Stewart took a much softer touch in arguing for this thesis than Siedentop.* That probably is the key in being able to appreciate the work without being annoyed by the author’s agenda. Like Siedentop Stewart marshaled intellectual history to support his argument, but the explicit details of the argument served more of a coda, allowing the reader to come to their own conclusion. In contrast, in Inventing the Individual the author always talks about how the individual was invented! Yes, we get it. The individual was invented, rather than always being there.

Overall I can see why those who agree with the thesis proffered are enthusiastic about this book. It’s very well written, and it is dense with quite a bit of erudition. And, if you agree with the thesis, the relatively heavy-handed manner in which all roads lead to the invented individual won’t come off as so annoying. Rather, it’s probably just part of the backdrop which you barely notice. It’s rather different if you’re trying to convince someone, and you keep waving about the big hammer, threatening to nail the truth into their heads. For much of the text Siedentop almost takes for granted that the readers already accept the thesis, and enters into long sequences of propositions which beautifully outline how it all came to be, except for the fact that those who are unconvinced will object to every inference made in the sequence from beginning to end. It’s kind of like reading Alvin Plantiga.

* For what it’s worth I’m skeptical of Stewart’s thesis too. But it’s much more modest, and I think I can say with more assurance that there is something real there. Tracing intellectual pedigrees from the 17th century down to the 18th is a far easier haul than traversing the 1st to the 15th.

• Category: Miscellaneous • Tags: Open Thread 


Kalash girl

Kalash girl

A new paper in The American Journal of Human Genetics, The Kalash Genetic Isolate: Ancient Divergence, Drift, and Selection, illuminates and obscures the history of this enigmatic people. Some framing is necessary here for why the Kalash are important. The Kalash are a “pagan” people who live in the uplands of Pakistan. By pagan, I mean to say that they preserve the primal religious traditions of a strand of the Indo-Iranian peoples, untouched by Islam, or, later developments which led to “higher religions” which arose directly out of Indo-European religion, Zoroastrianism and Hinduism (Sanatana Dharma). It would perhaps be defensible to depict the Kalash as the pagans of yore, a fierce people unbowed by philosophical monotheism or the quietism which explodes out of aspects of the gita.

902168-M Which brings us to another peculiarity of the Kalash: they are white. By white I do not mean white Europeans. They are not. The genetics is not in dispute, the Kalash are distantly related to the other peoples of South Asia. Some South Asians remind white Europeans (and also white West Asians) of themselves when they look at them face to face. But this tendency is heightened in isolated mountain peoples, such as the people of the Chitral valley. Among the Kalash it is more the norm the exception, ergo, legends of descent from the armies of Alexander the Great. In a previous age this paradox of an exotic and pagan barbarian people whose external appearance was white was utilized in fiction. Rudyard Kipling’s novel The Man Who Would Be King is set among the people of “Kafiristan,” what is today called Nuristan. Eight years after the publication of Kipling’s book the people of this region were forcibly converted to Islam by the king of Afghanistan. Even today if a Westerner wants to “pass” as an Afghan it is mostly plausibly as a Nuristani, because some among these people look to be Western in their outward appearance. The Kalash people were under British rule, and so were shielded from conversion to the religion of peace. Today the Kalash are surrounded by territories infested with Pakistani Taliban. Though protected by the state of Pakistan and vigilant against interlopers, it still seems unlikely that they’ll pass through the next generation unconverted.

ma1The Kalash Genetic Isolate is open access, so I invite you to read it. I saw part of the above figure at ASHG 2014. The important aspect of this paper is that it confirms that the Kalash have a great deal of “shared drift” with MA-1, the canonical individual which represents the ancient North Eurasian people who contribute ~10-20% of the ancestry of Northern Europeans and 30-40% of that of Native Americans (and nearly as much as some Caucasian peoples). Unfortunately the tables don’t show f3 statistics of each population, so we aren’t totally clear which population is which in the ternary graphs. But we can make some guesses. The outlier South Asian group is almost certainly the Sino-Tibetan Sherpa group. The South Asian groups include the Gujarati sample from the 1000 Genomes, as well as HGDP populations such as the Sindhis. The West Asians are Iranians, Palestinians, Turks. etc. if this is correct it seems to depict South Asians as sharing a great deal of drift with MA-1. There is also a second plot which shows that Kalash share a great deal of drift with La Brana, the Mesolithic hunter-gatherer from Spain. In contrast to the result from MA-1 it does not seem that other South Asian groups share this drift. To me this is tentative support for the contention in last year’s Science paper that there was some gene flow from Europe to the Kalash over the past few thousand years.

treeBut I need to end here on a down note. Though a lot of the results in this paper are fine, the interpretation strikes me as totally out of kilter with their own citations! They say:

LD decay showed that the Kalash were the first population to split from the other Central and South Asian cluster around 11,800 (95% CI = 10,600−12,600) years ago. This estimate remained constant even after the addition of an African (YRI) population or when the Kalash were compared with different subsets of non-African populations. The pairwise times of divergence with other Pakistani populations ranged from 8,800 years ago with the Burusho to 12,200 years ago with the Hazara.

Most of the populations and clusters that they are speaking of here did not exist when the divergence has been adduced. The Hazara for example are a compound population which emerged in the last 1,000 years due to the admixture of Mongols upon a Persianate substrate. The Uygurs are similar. The “Central” and “South Asian” population genetic clusters are refications of admixed groups which have emerged in the past ~4,000 years. That is, thousands of years after they purportedly diverged from the Kalash. The problem here is that the authors keep forcing their interpretations into a tree, when population genetic history for humans in the Holocene has not been a tree at all. As outlined in Towards a new history and geography of human genes informed by ancient DNA it is plausible that every major group of humans today (major = numerous) is the product of fusions of branches of the human race which were sharply diverged during the Pleistocene. The genomes of individuals and peoples then represent a complex and reticulated graph of interlaced histories. Reducing them to branching trees obscures rather than illuminates.

The deep divergences being inferred here strike me as likely a function of the fact that the authors do not take into account that South Asian populations are themselves a compound of two very distinct groups. One of these, the “Ancestral South Indians” (ASI) are very diverged from the groups of western Eurasia (and, the “Ancestral North Indians”, the ANI). The peoples to the south and east of the Kalash have much higher fractions of ASI, so the calculation of a divergence that is >10,000 years before the present is simply reflecting the very deep divergence of the ASI ancestry from the West Eurasian heritage of the Kalash (note, it is important to remember that the Kalash also have ASI, but just at lower levels).

Overall, this is an interesting paper. There are notable nuggets in it. For example, phenotypically the Kalash are lactose tolerant, but they lack the common Eurasian variant in totality. That implies that there is another variant in the LCT region unique to the Kalash. This also implies that the Eurasian variant has spread relatively recently into Northwest South Asia, perhaps post-dating the arrival of the Indo-Aryans! But the discussion is marred by the straightjacket of tree-thinking, imported from macroevolutionary contexts into a population genetic one, where it is less useful.

• Category: Science • Tags: Kalash 

I get sad when I read things like this in Slate, Twitter at the Crossroads: The company knows it’s in trouble. And its options are bleak. That’s because in areas such as genomics so much of the cutting-edge discussion has moved to Twitter that you can be privy to information which was previously the purview of the “scientific 1%.” Today for example I see the above from Pontus Skoglund.

I’ve discussed this issue before, Miscarriage as a behavioral strategy and Human uniqueness is not unique. Basically a derived mutational variant is found in PLK4 which is correlated with higher miscarriage rates, and seems to be maintained at appreciable frequencies by balancing selection. Derived because Neandertals carry the ancestral variant. Balancing selection because 1000 Genomes results make it pretty clear that it’s not fixed or absent all across Africa, Eurasia, and the New World. If it increases miscarriage rates, why isn’t it extinct yet? If it is beneficial, why isn’t it fixed somewhere? Ergo, balancing selection presents itself as an option.

But above Skoglund reports that it does seem nearly absent among the Bushmen. Or at least among the Ju’/hoansi. What about that 1 copy among the 38? Well, the Bushmen are admixed somewhat with newcomers to the region, so it could be a recent introduction. I asked Skoglund about the Pygmies, and he reported that it is at low frequencies in the Mbuti. It may be that this variant differentiates African hunter-gatherers from the rest of humanity. Remember that the latest genomic data implies that Bushmen diverged from the main lineage leading to other human groups about ~1/3 of the time back to the divergence the ancestors of Neandertals from those of modern humans. Depending on the measure and genetic data the agriculturist Sub-Saharan Africans may actually be closer to the rest of non-African humanity than they are to extant hunter-gatherers, at least the non-admixed ones.*

Addendum: Years ago Greg Cochran told me that Pygmies are reported to have very low miscarriage rates.

* Main qualifier is that human genetic history seems to be highly reticulate, as opposed to tree-like.

• Category: Science • Tags: PLK4 

warLike slavery war has a long history in our species, but it does have a history, a beginning, and perhaps an end. That is the sort of message you can take away from a paper such as Zefferman and Mathew’s An Evolutionary Theory of Large-Scale Human Warfare: Group-Structured Cultural Selection. War is a culturally mediated human phenotype, and one which requires particular contingent conditions to flourish, and others to diminish. Perhaps the best survey I’ve read on this topic is Azar Gat’s War in Human Civilization (which is $9.99 on the Kindle, so I just got a copy even though I already read this book!). But Gat doesn’t seem to come to any definitive conclusion as to the nature of war from what I could tell (the book is long and meandering). And that makes sense, because war is complicated, and the behavioral phenotype isn’t clear and distinct. What exactly qualifies as war? World War II clearly does. But how about the feud between the Hatfields and McCoys? Obviously there is a continuum, and we have to draw lines. The phenomenon which Zefferman and Mathew focus on is the paradox of mass intergroup conflicts which are defined by clashes between coalitions of unrelated males. More concretely, in wars between nation-states you have old men sending young men to their deaths in large numbers. Why do these young men put themselves in harm’s way?

The authors focus on two species as a contrast with humans, common chimpanzees and social insects, Argentine ants, which have been known to engage in war. War here can be thought of as coalitional intergroup conflict. Chimpanzees are informative toward any discussion of human evolution because they are phylogenetically close to our own lineage, while social insects are not, but like humans are highly complex in their organization (they even farm!). But, there are important contrasts between the wars of chimpanzees and social insects, and those of humans. Chimpanzee wars are of small scale, on the level of the band, and always opportunistic. That is, they occur in a manner which could be modeled as competing firms acting in their own rational interests. When two bands interact, and one of them is much larger, then the larger band proceeds to attack the smaller. Chimpanzees do not engage in conflict by and large when there is parity between two bands. The attackers take on little risk, to the point where there hasn’t been a documented instance of casualty on the part of attacking bands in field observation. Social insects are very different. The scale of their warfare is on the same order of that of humans, millions of ants for example may be party to conflict. But, unlike humans the coefficient of relatedness of the opposing coalitions are such that it can be explained via traditional inclusive fitness theory.

warbefore The figure above, from the paper, illustrates how humans are different. Humans engage in high intensity conflict despite most of the genetic variation being partitioned within the groups. In other words, unrelated individuals (almost always, but not exclusively, men) are fighting and dying for each other. In the examples above over ~20% of the genetic variation across Argentine ants is partitioned across the groups. You may know that across geographical populations a similar order of magnitude of human variation is partitioned across groups; for example, ~10% of the variation between Chinese and English populations is between the two groups. But for the ants we’re talking about adjacent groups, not those geographically distinct. As the figure above makes clear in the vast majority of cases where conflict might arise because of competition over resources or simple opportunity the genetic distance between the groups is very small. That is because a small amount of gene flow can quickly equilibrate differences between populations (1 migrant per generation across groups is sufficient to prevent genetic divergence if they separate). ~7,000 years ago the amount of variation partitioned in Europe between Mesolithic hunter-gatherers and the first farmers in parts of Central Europe which were co-resident was ~10%. Today, the average difference between national groups (e.g., Czech vs. Portuguese) is on the order of ~1%. Gene flow quickly removes variation, which is important, because without variation natural selection can not operate. Heritable variation is its raw material. morris Evolutionary pressures can maintain intergroup conflict on a massive scale among social insects because of the high degree of relatedness within colonies and supercolonies. In other words, they’re superorganisms. Similarly, moderately social behavior among chimpanzees manifests in a manner such that elegant individual level evolutionary dynamics such as inclusive fitness and reciprocal altruism are sufficient to explain interactions, in addition to the close relatedness of the males because of patrilocality. Larger groups of chimpanzees attack smaller groups of chimpanzees because it is the rational behavior in the context of minimal risk to self. Higher level group explanations are not really necessary.

Cultural_Evolution__How_Darwin_2_28_2013_10_16_35_PMThe answer to the question for why humans often, but not always, engage in warfare from Zefferman and Mathew is “group-structured cultural selection.” Often this phenomenon goes by labels such as “cultural group selection” or “multi-level selection,” but the authors assert that these terms are somewhat fraught, so they seem to be presenting their own so that there is a precise and distinctive understanding of what they are getting at without old baggage. As you can see above the Fst between cultural groupings is far higher than that for genetics. Why? Intuition can lead us to the answer easy enough: genetics is a straightjacket in terms of the nature of inheritance, while cultural is more flexible. If, for example, one group defeats another in war and kills all the males and older females, but takes the younger females as slaves, then the genes of the defeated may persist. But often the culture will go totally extinct. Conversely, a group victorious in war may increase demographically through amalgamation, while preserving to a great extent its cultural distinctiveness and identity. As an example, the Zulu were two centuries ago simply one clan among the Nguni. Today, they are one of the major tribes of South Africa thanks to the victories of Shaka and his successors. The recent genetic results coming out of Britain, which suggest that Anglo-Saxons had an impact, but a secondary one genetically, illustrates how a demographic minority can drive a cultural rupture among a conquered populace. The language of the people of Devon, which was once Dumnonia, is a sibling to that of the Germans across the North Sea, with no relationship to the Brythonic Celtic of their ancestors (I choose Devon because this is a region of the British Isles with very little Anglo-Saxon genetic footprint; Dumonia was even conquered after the Anglo-Saxons had become Christian, and so postdates the sub-Roman era).

0226712842 If war as a behavioral pattern is selected on the level of a culture, a group, what does that imply for its innateness? Probably that there is not a “war instinct,” and, that war may not be primal as an ancestral character for our lineage. Rather, war is a social phenomenon which emerges out of the constellation of other cognitive traits which we have as part of our ancestral heritage. In that way, it may be like organized religion or representational sculpture, aspects of evoked culture. Given particular conditions war may bubble up out of the possibilities for human behavior “naturally,” and then be selected upon as Zefferman and Mathews imply (its benefits are made explicit in works such as Ian Morris’ War! What is It Good For?). The reason that there are hundreds of millions of people who are the cultural descendants of Romans and their Latin allies, rather than Etruscans, is that the latter were defeated in war and absorbed by the Romans. Clearly there was a benefit to the Romans as a culture for developing social institutions which made them incredibly effective as a nation at arms. Some of the glory of victory was likely demographic, insofar s Roman colonies spread far and wide, but most of it was in terms of posterity and memory. Though the French may conceptualize themselves today as the descendants of Gauls (genetically this is probably correct), their language and religion come down to them because of the Romans.*

If memes, rather than genes, are the targets of selection, and groups are the units, how is it then that the genes for males who engage in highly risky behaviors persist? Shouldn’t cheaters have a higher fitness? Some of this is likely explained by the benefits to the group. Even though risk is entailed in war, the fitness benefits can be quite great for successful males. But there’s something else going on too. Zefferman and Mathew refer to the tendency toward conformity. This is an innate psychological bias which humans exhibit, and it allows for rapid change in cultural norms and expectations. Twenty years ago Bill Clinton did not hesitate to sign the Defense of Marriage Act in the interests of his political ambition, while today he wouldn’t hesitate to term someone opposed to gay marriage/marriage equality a “bigot.” In Daniel Schacter’s The Seven Sins of Memory he recounts how white American Southerners who came of age from the 1960s to 1980s often remember themselves as being ahead of the times when it came to segregation and race relations, a recollection belied by longitudinal studies. Psychological conformity as an individual level trait allows for rapid homogenization of cultural norms very fast and across wide swaths of the population. in relation to warfare it can explain why the Japanese can shift their national consciousness from that of being very militaristic on the whole to being opposed to the existence of a standing army which engages in force projection. Culture is protean because of a fixed aspect of human nature, social intelligence which fosters group conformity. Those who lack the tendency toward conformity exist, but they are often ostracized, and are considered disagreeable. Though cheating may be beneficial, it may be that the same psychological trait which allows for conformity and agreeableness means that few will wish to betray their “little platoon” for self-interest. War’s raw material exists because it is highly beneficial at a lower level of organization in terms of human social interaction. Humans sacrifice as a consequence of being human as we understand it, embedded in a network of trust, friendship, and affinity.

End_of_War_lores20130205-2-1ovxa4r Human psychology also means that John Horgan’s hope in The End of War that this phenomenon may have a “sell by” date is not futile. Perhaps the best analogy here is to slavery, an institution which arose during the Neolithic in a mass form which many thinkers across time took as a given, whether it was for the good or bad (Aristotle believed there were natural slaves, while other thinkers accepted it as an inevitable evil). And yet a cultural shift, enabled likely by economic and social forces, occurred over the past few centuries, and de jureslavery is now all but abolished, and de facto chattel slavery exists only furtively in the hidden places beyond the reach of modern human norms. Like war the institution of slavery was universal among complex societies, though its magnitude and manifestation varied in detail. With the emergence of radical stratification, with some individuals deified, it stands to reason that the lowest form of abasement within a society would be to utterly dehumanize. Mind you, the anthropological evidence seems clear that dehumanization is common among humans, even in the primal condition, but this was of the Other, those outside of the tribe. Though slavery often had a tribal connotation (e.g., blacks or non-Muslims could be enslaved), the key difference between it and dehumanization in the generality is that slaves became human tools integrated into the body of society, part and parcel of the fabric of human cultures. The abolition of slavery was the revenge of the dignity of the individual, as the circle of human empathy was expanded outward and totality. Hierarchy and inequality persist, but they are dampened by novel cultural institutions and ancient intuitions.**

The_Better_Angels_of_Our_Nature I do not know how war will end exactly, or, if it will end. History is not filled with many inevitable end points. But, the evidence in Steven Pinker’s The Better Angels of Our Nature is moderately compelling to me. Humans do have a nature, and it explains why war emerges so often in our history. But that nature also holds the keys for why it may diminish into irrelevance. If psychological conformity can be aligned with non-zero sum interactions then we may see an opportunity to avoid the conflicts that arise because of disputes over finite resources and opportunities.

* The French self-conception has gone through several iterations, some of which are much more philo-Roman than others.

** Do unto others as you would have done unto to you is simply a formalization of an iterated game.

Citation: Zefferman, Matthew R., and Sarah Mathew. “An evolutionary theory of large‐scale human warfare: Group‐structured cultural selection.” Evolutionary Anthropology: Issues, News, and Reviews 24.2 (2015): 50-61.

• Category: History, Science • Tags: End of War, War 

41rxx-UtsWL._SY344_BO1,204,203,200_ Genetically modified organisms (GMO) are a topic I have some interest in, even though I don’t talk about it much. That’s partly because I’m a genetically modified organism; on the order of 8% of my genome was inserted by viruses. More importantly a moral panic about GMO is currently an obstacle to their utilization in full. Yes, GMO are in corn and soybean, but their application is constrained by explicit and implicit bars. Of course these constraints are quite popular. This is why Chipotle is removing GMO from their food. It’s a matter of capitalism, not science or health.

Often when you drill down to it fear of GMO come down to two issues. First, there is the “wisdom of repugnance.” People who are not aware of how common horizontal gene transfer in the natural world is are frightened by the idea of “fish genes in tomatoes.” How about snake genomes in cow? That is not something man hath wrought. Then there is the issue of corporations and monoculture. But this is not a necessary function of GMOs. Organics are very popular with corporations because they can charge a premium through price discrimination (the poor can’t afford organics, while the upper middle class will pay more for them). And monocultures in food production has been an issue which goes back at the latest to the Irish potato famine. Well before transgenics of the scientific sort.

I was curious about opinions about GMO in the General Social Survey. I found the variable TOMATOES. It states: “Ordinary tomatoes do not contain genes, while genetically modified tomatoes do. (Is that true or false?)”

The correct answer is obviously false. But I was curious what proportion of the population would answer “true.” Here are some demographics….

True %
Sex Male 28.3
Female 31.9
Highest level of education Less than HS 48.6
High School 33.4
Junior College 36.3
Bachelor 18.1
Graduate 17.6
Political ideology Liberal 26.8
Moderate 33.3
Conservative 28.3
Belief about nature of God Atheist 25.2
Agnostic 23.2
Believe in higher power 20.5
Believe in God sometimes 30.1
Believe with some doubts 34.6
Know God exists 31.8
Belief about nature of Bible Word of God 38
Inspired word of God 31.3
Book of fables 18.2
Age 35 and under 34.5
35 to 64 24.7
65 and over 40.8
Correct number on vocab test 0 to 4 59.1
5 41.5
6 40.7
7 28.6
8 13.6
9 to 10 7.1

I decided to check these variables against a logit regression. The results are as so:

Logit Coefficients Test That Each Coefficient = 0
B SE(B) Exp(B) T-statistic Probability
WORDSUM 0.413 0.099 1.511 4.173 0
DEGREE 0.226 0.15 1.254 1.504 0.134
SEX -0.841 0.367 0.431 -2.291 0.023
POLVIEWS 0.063 0.127 1.065 0.491 0.624
BIBLE -0.068 0.242 0.934 -0.28 0.779
GOD -0.076 0.145 0.926 -0.525 0.6
AGE -0.003 0.01 0.997 -0.258 0.796
Constant -0.433 1.406 0.649 -0.308 0.759

The big variable here that remains very significant is WORDSUM. The score on a vocabulary test from 0 to 10 which has a correlation with general intelligence of 0.71. Perhaps only the intelligent can really comprehend or understand this question? Looking at the descriptive results above it shouldn’t be surprising. The educational gap turns out to mostly be explained by WORDSUM. If your remove WORDSUM then DEGREE becomes a very big deal.

Note: the question was asked in 2010, and the sample size was on the order of 1,000 (depends on the crossing variable). Also, I understand some people will claim that the question is priming respondents and confusing people with minimal science understanding. I would suggest you’d get confused if you aren’t very smart or thoughtful. Or, you think “genes” are unnatural and the reason we can’t have nice things.

• Category: Ideology • Tags: Genetically Modified Foods, GMO 

51fjBuOLFnL._SY344_BO1,204,203,200_Robert Trivers is one of the giants of modern evolutionary biology, with a diverse portfolio of interests. Apparently he has an autobiography coming out in the near future, and his editors did not think it was prudent to include a chapter where he launched salvos against enemies, while praising his friends. Ron Unz has published it in unexpurgated form, Vignettes of Famous Evolutionary Biologists, Large and Small. It’s fascinating, though probably on the whole not surprising to those who have followed Trivers’ career.

I can’t help but note that much of the reflection here seems to be an elaboration of observations you can find in Natural Selection and Social Theory: Selected Papers of Robert Trivers. If you haven’t read this, do so. It’s important, and Trivers is always an interesting writer. W. D. Hamilton and George C. Williams are gone (not to mention John Maynard Smith and George R. Price). Trivers is one of the witnesses to a major revolution in our understanding of the evolution of behavior, so I’m definitely curious as to his reflections on the life he’s led.

• Category: Science • Tags: Robert Trivers 

51Odj8gZIeL._SY344_BO1,204,203,200_ Gerard Russell’s Heirs to Forgotten Kingdoms is a somewhat uneven work with a surprisingly broad thematic coverage. The subhead is “Journeys Into the Disappearing Religions of the Middle East.” But one of the groups covered, the pagan Kalash, are not Middle Eastern. A group like the Mandaeans, who have disappeared from the region due to the 2003 invasion of Iraq, are not in any way comparable to the Coptic Christians of Egypt, who number in the millions.

Rather, the bigger issue that is being put into focus is how religious minorities are faring in the Islamic world. The short answer is not very well. The recent events on Mount Sinjar, where the Yezidi were targeted for what seems a classical case of genocide by the Islamic State, illustrates that. The issue though is less that the Islamic State is eliminationist in its intent, but that the Muslim majorities are quite apathetic or uninterested in how religious minorities fair. Russell relates how non-Muslim Kalash children were converted to Islam by teachers who made them recite the shahada, after which they were barred from identifying as non-Muslim due to the punishments enforced upon apostates. In this way a whole generation of Kalash were extracted from their broader family networks and cultural heritage individual by individual. This is in complement to the mass expulsion of peoples in the aftermath of the late lamented Iraq invasion, which sent ripples throughout the region. It is ironic that George W. Bush, an evangelical Christian, was instrumental in the eventual disappearance of Christian traditions which are nearly 2,000 years old from their ancestral homelands.

download A more interesting, and less depressing, aspect of Heirs to Forgotten Kingdoms, is the historical speculation by the author that many heterodox groups such as the Druze, Yezidi, Alawites, and Mandeans, preserve elements of Middle Eastern religious thought derived from antiquity. In particular, the influence of the Sabians of Harran looms large. This was a clearly pagan group which persisted down through the early Muslim centuries by asserting that they were the Sabians mentioned in the Koran, ergo, deserving of protection as People of the Book. The true religious identity of the Sabian seems to have been a synthesis of the ancient traditions of the Fertile Crescent, as well as Hellenistic Neo-Platonism. Sabians such as Thābit ibn Qurra were instrumental in the dissemination of Greek philosophy in the Baghdad created by Harun al-Rashid. Russell documents how threads of these beliefs have persisted among groups as disparate as the Yezidi, Alawites, Druze, and Mandaeans.

But these may be the last generations of these religious sects, who are grappling with the consequences and implications of modernity. The collective/corporate identities which insulated them in the past are fading, and dislocation and migration to the individualistic societies of the West are rendering them vulnerable to deracination. Heirs to Forgotten Kingdoms is then perhaps useful as it records a world which will fade into memory before this generation shall expires.

Addendum: One of the more fascinating aspects in the narrative are references to a book with the title The Nabataean Agriculture. The aim of the work is mostly utilitarian. But, in an offhand manner the author, who lived in the first few centuries of Islam, recounts ethnographic detail which is strongly suggestive of the likelihood that in many rural areas of unmodified rural paganism dating to antiquity persisted in the Fertile Crescent. This, in contrast to the organized and “high culture” paganism of Harran. This is not entirely surprising, and is perhaps analogous to the survival of the Kalash into modern times. The “high religions” were dominant in urban areas among elites, but often took a laissez faire attitude toward the peasantry.

• Category: History • Tags: Middle East, Minorities 

51Odj8gZIeL._SY344_BO1,204,203,200_ On a plane trip I finally finished Heirs to Forgotten Kingdoms: Journeys Into the Disappearing Religions of the Middle East. It’s about equal parts travelogue, ethnography, and historical speculation. Though not a scholarly work there’s a lot of peculiar and fascinating data. I’d recommend the book, and will probably have a longer review up at some point. NPR had an interview with the author a while back, in part because he has a chapter about the Yezidis, who were in the news at the time because of the attack of ISIS on Sinjar.

So I have determined that I’m going to go to ASHG 2015 and PAG as far as conferences go in the near future, though I’m a little confused why ASHG decided to pick Baltimore rather than D.C.. I assume there’ll be a Bay Area Population Genomics meeting before that of course.

It’s strange, but I’ve noticed something about Twitter for me. I’ve been on since April of 2009. I finally topped 6,000 followers. That’s fine, but it’s literally ~1,000 followers per year. Below you can see the Twitter analytics, which dates to August of 2012. It’s basically a linear progression, except for a kink here and there.

Screenshot from 2015-04-25 22:51:21

Also, I’ll be on the third episode of Through the Wormhole. Premiers mid-May.

• Category: Miscellaneous • Tags: Open Thread 


51IZQjMbVlL._SY344_BO1,204,203,200_ I am often asked by people online to give an “elevator pitch” as to the genetic history of the Indian subcontinent. At this point we’ve got ~90 percent of the story I think. Modern humans arrived in the Indian subcontinent ~50,000 years ago, and pushed onward to East Asia, but over the past ~10,000 years massive changes have occurred genetically due to the intrusion of populations form the northwest and northeast, with likely total cultural turnover. What do I mean by this? First, it’s highly probable that all of the extant language families of the Indian subcontinent are rooted in lineages which were present outside of the Indian subcontinent before the Holocene. In other words, during the Ice Age the ancestral linguistic entities which gave rise to Indo-European, Dravidian, and Austro-Asiatic, were present outside of confines of India, Pakistan, Bangladesh, Sri Lanka, Nepal, and Bhutan. The only exception here are the languages of the indigenous peoples of the Andaman Islanders.*

516ma6FzHPL._SY344_BO1,204,203,200_ Older historical works on South Asia often have a preface which suggests that the Austro-Asiatic Munda languages, and those of the Dravidians, were deeply indigenous to the region, to be marginalized in the north and west of the subcontinent by Indo-Aryan dialects which arrived relatively recently. This strikes me as likely wrong in terms of broad brush impressions. I now believe that Peter Bellwood was probably correct to argue in First Farmers that the arrival of Dravidian languages to the subcontinent was mediated through the arrival of agriculturalists, and perhaps may not have predated the Indo-Aryans by very much time at all in most of the subcontinent. I am even more confident that the Munda people are descended from a group with relatively recent origins on Southeast Asia, approximately contemporaneous with, though likely marginally preceding, the arrival of Indo-Aryans. What you see in South Asia today when it comes to linguistic-cultural agglomerations is the jostling of groups whose origins are all exogenous and date to the post-Neolithic period. Though the Pleistocene genetic heritage of South Asia persists to a great extent, as culturally coherent units I doubt there is much of the Pleistocene left in the region (with the exception again of the Andaman Islands).

51MGYd330tL._SY344_BO1,204,203,200_ Let’s talk about the Munda people first. Most of South Asian social-demographic analysis focuses on a divide between two disparate elements. Culturally, Indo-Aryan vs. Dravidian. Religiously, Hindu vs. Muslim. Genetically, Ancestral North Indian (ANI) vs. Ancestral South Indian (ASI). These dyads are useful analytically, but they elide the more richly textured diversity of the subcontinent (in the case of Muslim vs. Hindu, neither groups, especially the “Hindu” category, are very homogeneous). According to a new paper, A late Neolithic expansion of Y chromosomal haplogroup O2a1-M95 from east to west, as much as ~15% of the Y chromosomal lineages of South Asia may be attributed to these populations. This group uses quite old-fashioned methods. That is, they’re about 10-15 years old, an eon in modern genetics! Basically the focus is on fast evolving microsatellite lineages, and the patterns of variation thereof. But, the power of the paper is the massive data set, which has strong representation of many populations. By looking at thousands of individuals from some regions they were able to observe patterns with a very high degree of confidence as to their representativeness of a given group.

The following table illustrates what I’m talking about:


The cultural-historical debate is whether the Austro-Asiatic languages are indigenous to South Asia or not. The balance of the evidence now seems to be that they are not. What likely occurred is that the Austro-Asiatic languages waxed with the rise of an agricultural Diaspora, whose locus of origin was in what is today the southern regions of China proper. More precisely, the Austro-Asiatic languages may have spread with rice farming across Southeast Asia and eastern South Asia. Likely they were the first on the scene in Southeast Asia, as Bellwood reports in First Farmers and First Migrants that archaeology and anthropometrics can detect admixture between the farmers arriving from the north and native hunter-gatherers in places like the Red river valley in northern Vietnam ~4,000 years ago. The frequency of O2a1-M95 for regions and populations is subdivided very precisely in the above paper, and it is clear that in island Southeast Asia its proportions match those in an earlier paper on autosomal inferences of Austro-Asiatic ancestry. Populations in eastern Indonesia and in the Philippines have minimal numbers of males carrying lineages of O2a1-M95, while the densely populated island land of Java has frequencies of ~50%.

The clincher for why O2a1-M95, and therefore Austro-Asiatic populations, are likely exogenous to India genetically would be the genetic diversity of the lineages. In short, there is tentative information from the variation on the microsatellites that the coalescence of the diverse lineages in Laos are the deepest by a few thousand years. But there was another paper from a few years back which makes my confidence in these results higher, Population Genetic Structure in Indian Austroasiatic speakers: The Role of Landscape Barriers and Sex-specific Admixture, which presented autosomal data which was very persuasive to me. In particular, the derived variation of EDAR which is present in very high frequencies among Northeast Asians and Amerindian populations, is present at about ~5% frequency among Munda groups. Among Dravidian populations in South India according to the 1000 Genomes Browser the frequency is less than 1%, while it is absent among populations in Northwest India, aside from those with clear East Asian admixture.

Next we address the issue of the Dravidian languages. A new paper in Human Genetics, West Eurasian mtDNA lineages in India: an insight into the spread of the Dravidian language and the origins of the caste system, points to an association between particular mtDNA lineages in South India and southern Iran, in particular the region which was once inhabited by the Elamites, who have been posited to have an association with the Dravidian languages. I don’t put particular stock in the philological association between Dravidian langauges today and Elamite; I can’t judge it with any degree of certainty or competency. But the genetic data is certainly suggestive. Here’s the portion which is relevant:

The autochthonous subhaplogroups—HV14a1 and U1a1a4 uniquely found in contemporary Dravidian speakers share their ancestry primarily with the Near East-Iran populations (Derenko et al. 2013). The coalescence times of HV14a1 and U1a1a4 were estimated to be ~10.5–17.9 kya. The shared ancestry of the Dravidian of South India and Iranian of Near East populations has been shown in the HV14 and U1a1 phylogeny (Fig. 1a) and their time estimates are consistent with the proto-Elamo-Dravidian language diffusion. hypothesis which emphasized that the proto-Dravidian language evolved over 15 kya, specifically in western Asia before the beginning of agricultural development ~11 kya. This language was introduced by Neolithic pastoralists, and was thought to be associated with the spread of these west Eurasian-specific mtDNAs to peninsular India (Pagel et al. 2013). The Y-chromosome haplogroup L1a has added a further dimension to this hypothesis. The subclades of haplogroup L such as L1a, L1b, and L1c were found predominantly in Iranian populations of western Asia (Grugni et al. 2012). In India, only the L1a lineage was observed and was largely restricted to the Dravidian-speaking populations of south India (Sahoo et al. 2006; Sengupta et al. 2006). The coalescence time (~9.1 kya) (Sengupta et al. 2006) and the virtual absence in Indo-Aryan speakers in north indicate that the L1a lineage arrived from western Asia during the Neolithic period and perhaps was associated with the spread of the Dravidian language to India

There has long been a presumption to assume that the Dravidian languages are primal to South Asia. But that was before modern genomics revolutionized our understanding of Indian genetic history. More or less all South Asian populations are a fusion between a deeply indigenous strain which distant affinities to the peoples of eastern Eurasia (ASI), and a group very close to the ones typically found in Western Eurasia (ANI). There are no pure indigenes. South Indian tribal populations, who are presumed to be the closest to indigenous groups are at least ~25% ANI, if not more. To presume that the Dravidian languages are indigenous to South Asia one would have to assume that this exogenous element was absorbed by the cultural substrate, something I find implausible on cross-cultural grounds (more dominant South Asian social elites, even ones of pure Dravidian extraction, such as the Reddy group, have higher fractions of ANI). Additionally, Dravidian languages themselves are not particularly variegated, as one might expect if there was deep local structure, as is the case in inland Papua and pre-Columbian America.

Of course the title of this post has to do with males, so with that, let’s look back to a paper which was first posted on the web last year (though finally “published” this March), The phylogenetic and geographic structure of Y-chromosome haplogroup R1a. Here’s the important part:

…Using the 8 R1a lineages, with an average length of 48 SNPs accumulated since the common ancestor, we estimate the splintering of R1a-M417 to have occurred rather recently, ~5800 years ago (95% CI: 4800–6800). The slowest mutation rate estimate would inflate these time estimates by one-third, and the fastest would deflate them by 17%.

With reference to Figure 1, all fully sequenced R1a individuals share SNPs from M420 to M417. Below branch 23 in Figure 5, we see a split between Europeans, defined by Z282 (branch 22), and Asians, defined by Z93 and M746 (branch 19; Z95, which was used in the population survey, would also map to branch 19, but it falls just outside an inclusion boundary for the sequencing data4). Star-like branching near the root of the Asian subtree suggests rapid growth and dispersal. The four subhaplogroups of Z93 (branches 9-M582, 10-M560, 12-Z2125, and 17-M780, L657) constitute a multifurcation unresolved by 10 Mb of sequencing; it is likely that no further resolution of this part of the tree will be possible with current technology. Similarly, the shared European branch has just three SNPs.

The authors emphasize that the TMRCA has a wide confidence interval. I don’t think so. There’s now a fair amount of work on sequencing R1b and R1a lineages which are very common across Eurasia, and one thing is xclear: they’re star-shaped phylogenies which are likely reflecting massive population expansions relatively recently (see A recent bottleneck of Y chromosome diversity coincides with a global change in culture). Additionally, they note that the “Asian” (which includes South, Central, Southwest Asia) and the European branches of R1a1a are relatively well separated, and, the greatest diversity of R1a1a can be found in Iran.

I doubt that R1a1a was associated with one ethno-linguistic group at the end of the last Ice Age. It is present at relatively high frequencies in low caste and tribal populations in South India, so I am skeptical of an exclusive association with Indo-Europeans, though in Europe it may actually be that it arrived only with Indo-Europeans. But, the fact that R1a1a is so common all across Eurasia points to a genetic-cultural revolution. Just as Haplogroup O2a1 is almost certainly rooted in populations outside of South Asia before the Holocene, so is the case with R1a1a. They came with groups of men who brought a new dominant lifestyle. From the west came wheat and cattle. From the east, rice.

The latest research suggests about half the ancestry of modern South Asians dates to the Pleistocene. That is, it predates 10,000 BC. The majority of the mtDNA lineages are from this ancestral element. But culturally this group likely had minimal influence. One question which comes to mind is whether the ASI ancestry is from many groups, or, from only a few which were assimilated into an expanding group of agriculturalists. If the former, then one expects that the ASI ancestral segments which exhibit a tendency toward regional structure. I suspect thought that this is not the case, that the genetic landscape of modern India is characterized by overlapping populations which are all hybrids of different regional groups which only recently expanded. The pattern of Munda groups in South Asia, surrounded by Dravidian and Indo-European speaking groups, points one to the possibility that these groups were pioneers of some sort, but eventually lost.

* Language isolates like Kusunda and Nihali may date to the era before the Holocene, but without relatives we can’t really make a good guess. Possible relationships of Kusunda to Andaman or Papuan languages strike me as implausible due to the time depth of separation.

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

Drakas_cover Everyone and their mother has heard of the story about the CRISPRed embryos by now. If you haven’t, the original paper is open access. Second, Carl Zimmer’s primer is excellent, Editing Human Embryos: So This Happened. For those who are overly alarmed by the non-ethical aspects, I think this is key:

Just because this experiment came out poorly doesn’t mean that future experiments will. There’s nothing in this study that’s a conceptual deal-breaker for CRISPR. It’s worth recalling the early days of cloning research. Cloned embryos often failed to develop, and animals that were born successfully often ended up with serious health problems. Cloning is much better now, and it’s even getting to be a business in the world of livestock and pets. We still don’t clone people, though–not because we can’t, but because we choose not to. We may need to make the same choice about editing embryos before too long.

Livestock and pets. And plants. I think CRISPR is going to be a big deal. It already is a big deal. But some people are worried now about a profusion of designer babies. We need to get calm here. For something to become a consumer product it needs to get much better in terms of probability of outcomes, and we’re a long long way from that. As Ramez Naam pointed out people are very risk averse with their children.

Rather, the real danger is more one of ethics. Something out of S. M. Stirling’s Draka series where a government or society isn’t bound by normal human ethical standards, and begins to basically treat their population like livestock. As is usually the case the major issues looming are not scientific, but have to do with human volition.

• Category: Science • Tags: Crispr 

41ncnodwApL._SY344_BO1,204,203,200_ Beauty can lie all too easily, while oftentimes truth is ugly on first inspection. I’ve been reading Inventing the Individual: The Origins of Western Liberalism, and it is a beautiful book, full of style and erudition, and paragraph after paragraph of mellifluous argumentation. It is far more gossamer than Victor Lieberman’s Strange Parallels, which is weighted down by turgid prose. But where Lieberman’s narrative is dense in unique and distinctive data, Larry Siedentop’s Inventing the Individual circles around the same big facts. Siedentop promotes a bold, if not original, thesis, that the Hebrew-Hellenic synthesis which became Christianity was the seed for the invention of liberal individualism, which reigns ascendant today, at least in name if not reality. Lieberman makes an observation about the parallel development of societies across Eurasia, even in its isolated and far-flung regions in the protected peninsulas and archipelagos of Southeast Asia, and gropes confusedly at overarching explanations. And yet it is the “ugly duckling” of Strange Parallels that is more satisfying than the crisp and elegant theses of Inventing the Individual. The latter is a joy to read, but if you know a fair amount of 61LXo6U7a4L._SY344_BO1,204,203,200_ history, and cross-cultural history at that (I do), a lot of it comes off as hot air and naked assertion. It’s a great read, but will only persuade the persuaded, and unfortunately is a little thinner on “dense description” than I would have liked for a work which I knew I was going to look at skeptically (that is, even if you find a work uncongenial on the whole, there are often great gains to be made in extracting nuggets of information).

The ultimate problem that confronts me when entertaining the core contention of Inventing the Individual is sentences such as the following on page 77: “But texts are facts. And the facts remain.” The question is whether they are non-trivial facts, and that is debatable. There is a school of thought that ideas are the drivers of history, and Inventing the Individual takes that position as a premise. If one is wobbly on that premise, the force of the argument falls flat.

Second, do readers have any particular papers/books on domestication that they think are particularly good? My professional research focus is in this area and I need to do a thorough survey of the literature.

Third, I am not an “adaptationist” as Larry Moran has asserted. I’m “dynamic agnostic,” and am wary of null hypotheses of what drives variation in organisms as a whole (i.e., I think neutrality may be more justified for some branches of the tree of life than others).

Fourth, I should mention again that if you are following an RSS feed for my content, is preferred. The reason is that it bundles all my content, and I don’t like to cross-post notifications across blogs. E.g., if I write for The Guardian again or something it will show up in that feed, and I’m liable not to mention it on this blog (though it will show up in Twitter since that pushes the above feed).

• Category: Miscellaneous • Tags: Open Thread 

22522805 Amazon believes that e-books are price-elastic. That is, the lower the price, the more units sell. The print list price for Kazuo Ishiguro’s The Buried Giant is $26.95. I noticed it was $5.99 in the Kindle version, so I purchased it on a whim. It’s basically cheaper than lunch. I can say with some confidence that if it was priced at “normal” e-book rates, which are still discounted, I probably wouldn’t have purchased it. I don’t read much fiction, and when I do I tend to shy away from material with too many mainstream plaudits because the mainstream often strikes me as banal in their preoccupations.

I stated last week I probably wouldn’t get to finishing The Buried Giant very soon. I was wrong. It’s a quick read, and I was just on an airplane, so the book is done. Overall I’d say it was worth the money. Ishiguro writes well and evocatively threads through his broader themes, while still allowing the narrative itself to have some drive to it.

The Buried Giant operates in the area between the literary allusive opacity of Gene Wolfe’s The Book of the New Son and the sort of sincere and transparent high fantasy you see in Brandon Sanderson’s The Way of Kings. Because it is notionally set in post-Roman but pre-Anglo-Saxon Britain you might think The Buried Giant exhibits some of the historical fantasy flavor you see in works such as Guy Gavriel Kay’s Sarantine Mosaic (or quasi-scholarship about this period, such as Nikolai Tolstoy’s The Coming of the King). But it does not.

Though the Saxons and the Britons are real people who coexisted in a real time, the world is anachronistic and laced through with fantastical elements. There are dragons and ogres, but also Norsemen and knights. The latter are features of periods centuries after the late 5th century. One aspect that is difficult to not acknowledge in a book about this time period is the foreshadowing of the Saxon conquest of lowland Britain, what became England. But, I do think as a point of historical fact one should note that as late as the early 7th century Celtic British kings such as Cadwallon ap Cadfan were conquering eastern areas of England, with armies reaching the North Sea. Though the Germanization of Britain seems inevitable now, it is possible to imagine a scenario where the late 6th century marked the low point from which Britons reconquered the islands, in a manner that the Christians in Spain reconquered their peninsula. But The Buried Giant operates under the assumption of Saxon inevitability, with the Britons being portrayed faintly as if they are a feckless and complacent people, with more civilized refinement than genuine honor.

68520 Finally, one aspect of this book that many readers of traditional fantasy will find disappointing is that its description of the world and the people within it is very understated. Ishiguro exhibits an admirable economy of prose, but at the sacrifice of a rich and deep color of character and landscape. For example, I can not tell you what the main characters looked like aside from the thinnest of generalities (e.g., two characters were aged, one was a strong warrior, etc.). Obviously this makes it difficult to conceptualize them in one’s mind’s eye, but perhaps the point was to identify with the character and their life rather than their embodiment. The fact that concrete aspects of character and landscape were put into the background probably allowed the broader themes to be more clearly obvious.

I can see why mainstream audiences might find The Buried Giant appealing, as it doesn’t push them too far. The fantastical elements are unobtrusive background furniture. But if you want real a real “Dark Age” Arthur, I highly recommend Bernard Cornwell’s Warlord Chronicles.

• Category: Miscellaneous • Tags: The Buried Giant 


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 
Razib Khan
About Razib Khan

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