Open Thread, 4/17/2016

41yT8hhOZJL._SX339_BO1,204,203,200_A day may come when the courage of men fails, when we forsake our work and break all bonds of employment. But it is not this day. And yet it shall come to pass that I’ll make room for finishing The Shape of Ancient Thought. Say what you will about e-books, but that you can have someone’s magnum opus for $20 is a good thing.

My daughter improvised a song about me. It begins: “I’m a brown guy.” But there is a line where she says “I work a lot.” Obviously having issues with work-life balance. People always say that at the end of their life they wish they had spent more time with their loved ones.

Estimating Basal Eurasian. Remember, some of the devisors of “Basal Eurasian” admit it may just be a useful construct….

A lot of people are talking about The Green Room. I grew up in Oregon. And not Portland (rather, the eastern parts). I know that the Pacific Northwest makes for a good setting for these sorts of films because of the gloomy ambience and the real presence of white nationalists, but really their presence is all but invisible. Don’t get the wrong impression from these sorts of films.

This study 40 years ago could have reshaped the American diet. But it was never fully published.

Here is an intro video from the company I’m working for:

Still trying to get used to humidity again. There’s a reason people live in California. In Cramped and Costly Bay Area, Cries to Build, Baby, Build.

McDonald’s of the future coming to St. Joseph. The owner says that the high tech features won’t eliminate labor, but it’s pretty clear that this is where it’s going (and not a moment too soon in light of minimum wage hikes!).

I’m excited to be going to the Evolution Meeting in June in Austin. Should be a change-up from ASHG.

The Aerogram uses an illustration which depicts a woman in a niqab, presumably as a Muslim. I’ve noticed this pattern on other progressive websites. This strikes me as really strange because even many practicing and believing Muslims of a non-liberal religious persuasion (e.g., my parents) find the niqab to be extreme and somewhat disturbing. The difference from the hijab is simple: not being able to see someone’s face in a public situation is alarming, especially when they can see you. All part of the weirdness of the tight embrace between Islam and political liberalism/progressivism in the West. Sometimes my (liberal) friends are curious why I’m conservative. One answer is that I can’t align with people who align with people who would look the other way while I was killed. It’s pretty simple. I’d rather be #problematic than dead.

Mounting evidence suggests antibacterial soaps do more harm than good.

macbookpro-select-intheboxI’ve started to work on a Macbook Pro…now my friends can stop making fun of me. Kind of confusing going between Mac and Ubuntu at home, but perhaps I will finally get an iPhone instead of the next Edge.

Gene-edited CRISPR mushroom escapes US regulation.

Country Star Zac Brown Busted With Pot, Strippers, Cold Beer, Trucks, Freedom.

The Great Ordeal

611jQLzlbwL._SX338_BO1,204,203,200_I notice that R. Scott Bakker is finally coming out with a sort-of conclusion to his second trilogy, with The Great Ordeal. I say sort-of because it seems that his final book in the second trilogy of this planned three trilogy series is going to be one of two, as Bakker submitted a manuscript that was far too long.

Presumably there were issues in relation to the logistics of publishing, because it’s been nearly five years since The White Luck Warrior. That’s unfortunate, because Bakker’s series really has no parallel in the epic fantasy genre from what I can tell. It leverages standard genre tropes, but introduces a dark philosophic undertone set against the foreground of an incredibly rich and finely crafted world. Much of the brutality in The Prince of Nothing seems almost gratuitous, but if you want a more antiseptic narrative, there’s always Brandon Sanderson.

Bakker’s descriptions of the antagonists threaded throughout his series are chilling, and communicate both menace and mystery. The Inchoroi are like no other villains I’ve read of in fantasy….

DNA.Land and new ancestry inference

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DNA.Land has a new ancestry report. Above is my own. I’m pretty aware that designing these consumer-oriented services/applications isn’t easy. But I want to express a little skepticism that two of the three South Asian populations which they used for their “Dravidian” reference are not Dravidian speaking. In fact, geography and ethno-linguistic affinity in South Asia is only modestly correlated with genetic variation because of caste. Something more generic, such as “South Indian” is what I would have gone with.

Neanderthal Y chromosomes, a tale of loss?

445px-Neanderthal-2D-MJCThere’s a new paper in AJHG (open access), The Divergence of Neandertal and Modern Human Y Chromosomes. From the discussion:

The fact that the Neandertal Y-chromosome lineage we describe has never been observed in modern humans suggests that the lineage is most likely extinct. Although the Neandertal Y chromosome (and mtDNA) might have simply drifted out of the modern human gene pool…it is also possible that genetic incompatibilities contributed to their loss. In comparing the Neandertal lineage to those of modern humans, we identified four coding differences with predicted functional impacts, three missense and one nonsense….

For obvious reasons the media has found the argument of functional differences compelling. E.g., Anne Gibbons in Science, Modern human females and male Neandertals had trouble making babies. Here’s why. That’s fine. But I think it is important to note that for many people the loss of ancient Y chromosomes is actually a pretty strong null model. Basically, Y and mtDNA are tree phylogenetic trees (no reticulation), and as you traverse up the tree you note that there is consistent gene loss as surviving lineages coalesce together. Additionally, the rate of extinction will be higher because of higher drift in uniparental lineages (Y and mtDNA effective population sizes are constrained to one sex).

As far back the mid-2000s John Hawks was arguing that lack of high diverged mtDNA and Y lineages, which would suggest archaic admixture, was not evidence for lack of admixture, because of the high likelihood of extinction. In other words, lack of evidence in this case tells us far less than evidence itself.

Peak pr0n, the massive social experiment

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The Washington Post posted an op-ed about a week ago with the title Is porn immoral? That doesn’t matter: It’s a public health crisis. The author is listed as follows: Gail Dines is a professor of sociology at Wheelock College in Boston and author of “Pornland: How Porn has Hijacked our Sexuality.” To not put too fine a point on it sociologists are generally full of shit. Sometimes they are correct. Oftentimes they are wrong. But they are always full of shit. The “reproducibility crisis” means we need to look at a lot of science with a skeptical eye, from the sexy findings of social psychology, to the medical studies which clinicians rely upon. Out of all these scholarly endeavors sociology may be the most insulated from concerns of reproducibility since it is such a brazen prostitute of a discipline, beholden to political considerations Über Alles.

41WL2k2+47L._SY344_BO1,204,203,200_Dines uses the words “association” and “correlation” several times. Here is the only reference to cause in the piece: “Pornography can cause lifelong problems if young people are not taught to distinguish between exploitative porn sex and healthy, safe sex.” They rest on associations and correlations.

If you’ve read Jim Manzi’s Uncontrolled you know that you need to be very wary of modest correlations in social science. I would not be surprised if Brazilian fart porn was associated with sexually deviant behavior. But my own supposition is that it is more likely that Brazilian fart porn is an indicator of serious underlying problems, rather than the cause of those problems.

But, we do have a massive social experiment going on today in relation to the impact of porn on society. Starting around 1995, and at various points of initialization over the next ten years in various locales, the internet became ubiquitous enough in the developed world that the tight constraint on “supply” of porn was removed, so that it met “demand.” This is pushing porn in more perverse and kinky directions. It also means youth over the past generation have had incredibly easy access to very hardcore pornography.

As you can see above in the early 1990s the FBI began receiving fewer reports of rape, concomitant with the decline in violent crime generally. The decline in rape has continued through the age of porn. I doubt there is a causal relationship. But it goes to show that there is no macrosocial evidence that porn results in increased rapes in the aggregate.

Early and rapid settlement of the New World

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The above model of the settlement of the Americas is from a new paper which utilized ancient mtDNA, Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas (open access):

The exact timing, route, and process of the initial peopling of the Americas remains uncertain despite much research. Archaeological evidence indicates the presence of humans as far as southern Chile by 14.6 thousand years ago (ka), shortly after the Pleistocene ice sheets blocking access from eastern Beringia began to retreat. Genetic estimates of the timing and route of entry have been constrained by the lack of suitable calibration points and low genetic diversity of Native Americans. We sequenced 92 whole mitochondrial genomes from pre-Columbian South American skeletons dating from 8.6 to 0.5 ka, allowing a detailed, temporally calibrated reconstruction of the peopling of the Americas in a Bayesian coalescent analysis. The data suggest that a small population entered the Americas via a coastal route around 16.0 ka, following previous isolation in eastern Beringia for ~2.4 to 9 thousand years after separation from eastern Siberian populations. Following a rapid movement throughout the Americas, limited gene flow in South America resulted in a marked phylogeographic structure of populations, which persisted through time. All of the ancient mitochondrial lineages detected in this study were absent from modern data sets, suggesting a high extinction rate. To investigate this further, we applied a novel principal components multiple logistic regression test to Bayesian serial coalescent simulations. The analysis supported a scenario in which European colonization caused a substantial loss of pre-Columbian lineages.

The key here is that looked at whole mitochondrial genomes, which gives them more information to work with. Earlier work often focused on a particular variable region of the mitochondrial genome. And, mtDNA is copious, so they got good quality data from all of their samples (really 5x is decent for population genomic work, and that was the worst). Combined with the fact that they had ancient genomes, which allow them to investigate the phylogeny in a more precise manner temporally, and have you the potential to make some really strong inferences.

F3.largeFigure 3 in the paper makes everything really clear. The last common ancestors between Native American mtDNA lineages and those of Siberians is >20,000 years before the present. That is, before the Last Glacial Maximum. The next major feature you see is an explosion of lineages aroun ~15-16 thousand years ago. This is the hallmark of a rapid population expansion. But after the initial period of diversification you see the persistence of a lot of deeply divergent lineages. Additionally, further population genomic modeling indicate that there was a major extinction event ~500 years ago, no doubt due to the Columbian Exchange and the arrival of Old World populations and their diseases.

This paper is fundamentally about Native American historical genetics. It is another nail in the coffin of the “Clovis first” model of Amerindian origins. Basically, that the Clovis group of megafaunal hunters were the First Americans. No, it does seem likely now that modern humans were present in portions of the New World thousands of years before Clovis. The Monte Verde site’s occupation on the Chilean coast less than two thousand years after the opening of a coastal route from Beringia indicates that perhaps there was a strong focus on marine environments for a significant period of time. Once the New World was settled there seems to have been a lot of persistent population structure, until the arrival of Europeans, at least in comparison to what ancient DNA has told us about Europe. Additionally, the long isolation of the Beringians is also significant in my opinion.

In a world of billions of humans it may be that we lack proper intuition for how little gene flow may have occurred between populations in a sparsely populated globe. The Beringians were separated from Siberians for on the order of ~5,000 years. It only takes ~1 migrant between two populations per generation to prevent them from drifting apart in allele frequencies, so the gene flow was very low (this is mtDNA, so not strictly applicable, but the same logic holds). But it is possible that in much of northern Eurasia during the Last Glacial Maximum humans retreated to zones of survival, and vast swaths of territory became empty. This would result in islands of human habitation diverging and become very different over several thousands of years. In sharp contrast, the world over the past 4,000 years or so has been characterized by the ability of humans to travel long distances over inclement territory, and settle amongst strangers, usually through conquest. Partially this is due to the domestication of the horse, but partially it is probably due to the emergence of high density complex societies which can incubate specialist castes whose role arose initially as defense, but who often engage in offense whenever the opportunity arises.