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December 30, 2017

Predictions for 2018

Filed under: Open Thread — Razib Khan @ 10:31 pm

I don’t normally do year-end stuff. But I figured, why not? After all, I put up a post at my work blog about the major things that happened in historical human pop gen this year.

Indian population genomics will move forward notably. The ancient DNA work really feels like vaporware sometimes. Some of the researchers involved reach out to journalists (people of my acquaintance) and leave tantalizing clues, but they disappear off the face of the earth. I assume that some sort of Indo-Aryan intrusion from Central Asia will seem clear from the data and results, though the Indian media and intellectual class will claim the opposite (in this way they are just like the American media and intellectual class; if the evidence does not fit just say that the evidence says the opposite of what it does).

The current protests in Iran won’t go anywhere. Someone with guns needs to be on the side of the protestors. That’s it. Also, if a group with guns ends up favoring them, the West will find that anti-clerical Iranians are quite nationalistic and not necessarily liberal democrats.

The Democrats will win the House of Representatives. I think there’s about a 50/50 chance that they’ll get the Senate.

The United States will be in a recession by the last quarter of 2018. We’re overdue. All OECD countries are growing, to the point where Brent crude prices are going up. This isn’t sustainable, especially since many developed nations have been kicking the bucket down the line.

Personal genomics is going to be more of a presence as the year progresses. I was surprised by all the attacks from the tech-press on direct to consumer genomics over the past few months. That indicates to me that the industry is getting big enough to be a click-bait target.

George R. R. Martin will publish Winds of Winter.

More ancient DNA from the New World. This has been in the works for a while. I’m really skeptical that they won’t be able to push it out in 2018.

Twitter will continue to not be able to find its way. Basically, it can’t win, and won’t win.

Preparing for Nero

Filed under: History,Intellectual history,jahiliyya — Razib Khan @ 12:18 am

Richard Elliott Friedman’s The Hidden Face of God grapples with the reality that over time in the Biblical narrative the deity becomes less and less a direct presence. In Genesis, humankind has conversations with the divine, and arguably even wrestles with God himself. This is not what we see in later books. Or more precisely, we don’t see.

For a nonbeliever, this is an issue of intellectual curiosity (I’d be one of those). But if you are a believer in the God of Abraham, the God of Isaac, and the God of Jacob, then these are serious and important questions. God is, after all, the most important truth of them all.*

The “hiding” away of a great truth or truths is not simply of relevance to God or the supernatural. Whigs believe that modernity converges toward truth. But Whigs may not get to define the truth of matters on this question.

Let’s posit, hypothetically, that the notionally open Enlightenment republic of letters, which plumbs the depths of nature and society for Truth, is beyond its hide tide. That over the next decade or so intellectuals, seekers of the truth in a notional objective reality, slowly withdraw from visibility or at least begin to engage in explicit and self-conscious opacity. In public speaking on code or dog-whistles. But private intellectual communities will persist.

The question is how will they persist? Face-to-face salons and meet-ups are one option. Then there are private e-lists and slack channels, as well as direct message communities on Twitter and Facebook groups (these have all emerged in the last few years as public discourse on social media has gotten nastier).

The major problem I see here is that you trade-off scale for security. Consider what happened with JournoList. Any “exclusive” group will become infested with moles over time, and private conversations will be made public. People will anticipate this as a group becomes popular and become less candid. As a group scales, it loses its utility.

In contrast, in-person meetings are generally totally free from these worries (unless someone is recording you). Unfortunately, these do not scale well. Adding and removing people from in-person meet-ups and semi-regular salons take a lot of work, and from what I’ve seen often that work is done by a few individuals who eventually get burned out. At which point the social group dissolves or breaks up into smaller more socially-focused units. If a group can not scale, its utility is constrained and limited.

What we need are technological tools which will allow for surreptitious private candid freethought in a public world dominated by social credit and conformity due to authoritarianism. Demagogues may persecute those who speak uncomfortable truths for the sake of the body politic, but if these people are discreet they surely have a role in to play in the great game of mass manipulation that will probably become much more advanced as this century proceeds. Truth is a tool which even the princes of lies can use to win their battles. When Nero comes all will make peace with the new brutality no doubt.

The reality is that many of our institutions are already quite corrupt. And yet it is also true that privately many people who lie in public exhibit virtue and common sense. They are constrained by the system, they do not create it. Of course, they are craven and one has to understand that they will make the denunciations necessary when the time comes for them to do so. But it’s all just business. This seems the human norm.  Technology has to work with our nature, not against it.

From what I am to understand Snapchat’s feature of messages which disappear was created so that teens could exchange nudes. The aim here was to share an intimacy, titillate, not create a permanent record. Similarly, any technological system to foster intellectual discussion has to take into account considerations of privacy, trust, and permanency. In a way, the peer-review system has some of these features, but it is rather slow and calcified at this point.

We need better things….

* Christians reverse the disappearance of God through the incarnation, but that’s a different thing altogether.

 

December 29, 2017

The iPhone killed commenting

Filed under: Technology — Razib Khan @ 12:41 am

Back when this domain received about 15 or 20 percent of the traffic it now receives there were many more commenters. What happened? One of the reasons the Sepia Mutiny weblog was shutdown was that as the commentariat withered after 2007 there was less motivation to keep a community going (there was none).

The explanation at the time was that people were moving conversations to Facebook. Today we would add Twitter and Reddit to the list of “culprits.”

But there’s another thing that is hard to ignore: about half the traffic that comes to this website is now on iOS or Android. That is, half the traffic to this domain is mobile.

I’m pretty sure that the nature of browsing content on a phone is such that it discourages the sorts of intense back & forth exchanges which were at one point the bread & butter of comments sections of weblogs in the ancient days of yore.

December 28, 2017

Why Darwinian metaphors work for start-ups

Filed under: Cultural Evolution — Razib Khan @ 11:46 pm

Peter Thiel is a deep thinker. I say that because some of my friends in the Bay Area who I respect for being punctilious practitioners of cognitive hygiene nevertheless exhibit awe in relation to their conversations with him (for what it’s worth, most do not agree with his politics). Though Thiel has the standard educational qualifications and cognitive abilities of America’s ruling class, I think the key aspect is that people perceive in him a deep cunning which is very unnerving. This cunning is why he is a successful entrepreneur, and not an affluent lawyer on staff at a major tech firm.

Zero To One has many insights for the typical reader, though perhaps less so for those steeped in economic history, endogenous growth theory, or evolutionary biology. The novelty is in a situation of scientific ways of viewing in the world in the business and tech landscape of Silicon Valley.

But one way of talking that Thiel expresses skepticism of is the “Darwinian” language of competition employed by many people in business. I think here he misses the mark because he conceives of Darwinian processes in purely biological terms. As it is, a lot of the ideas in the field of cultural evolution, which models inter-group human dynamics, dovetails with recommendations in Zero To One.

Probably the biggest takeaway for me was the importance of asabiyyah in the likelihood of the long-term success of a firm. But anyone who has worked at a start-up knows this intuitively. Financial alignment of interests are necessary, but not sufficient. Culture matters.

Against Thomas Jefferson!

Filed under: American History — Razib Khan @ 11:01 pm

I was unexpectedly traveling on an airplane recently, so I had some time to read Michael Lind’s Land of Promise (I had just finished Peter Thiel’s Zero to One). Though with the subtitle “An Economic History of the United States,” it’s not a dispassionate, or frankly scholarly, take. Lind marshals a great deal of evidence, but it’s in the service of promoting a Hamiltonian or “developmentalist” view of American history, as opposed to a Jeffersonian or “producerist” perspective.

As such, Land of Promise steps into a debate that goes back to the early days of the republic, though modern interpretations are colored by own peculiar perspectives. One of the major problems with this debate is that it transcends contemporary political alignments. Today Lind is broadly to the Left (he was originally a neoconservative), but he stands strongly against the sort of arguments promoted by Matt Stoller in How Democrats Killed Their Populist Soul. Stoller is an heir to the populist tradition in the Democratic party which goes back to Thomas Jefferson, but famously crystalized under Andrew Jackson. In contrast, Michae Lind and the developmentalists are heirs to Henry Clay’s American System.

In What Hath God Wrought Daniel Walker Howe suggests that though Jacksonian populism was politically ascendant in the first half of the 19th century, with the battle over the Second Bank of the United States symbolic of the reputation of Alexander Hamilton’s vision, ultimately Hamilton and Clay’s ideas ultimately won the day. As Lind and others have pointed out Abraham Lincoln was explicitly an heir of Henry Clay, and the high-tariff Republican party of the 19th and early 20th century maintained the germ of developmentalism, even during the height of Gilded Age laissez-faire.

The “problem” is that today these differences between developmentalists and producerists are hard to map onto modern configurations, though the impulses remain with us. The post-World War II American consensus favored a gradual deemphasize on industrial policy and free trade, in line with producerist thinking, but also public investment in national projects, such as the interstate highway system or the internet, in line with developmentalist thinking.

I haven’t finished  Land of Promise, but it was written in the wake of the 2008 financial crisis, and before the chaotic Trump revolution of 2016. Lind’s argument seems to be that government and large private actors should act in partnership, with the former restraining the worst impulses of the latter. In ways the method here is not that different from what “business Republicans”/”donor class Republicans” would prefer. In contrast, someone like Matt Stoller is suspicious of bigness, oligopoly, and concentration of power, in classic Jeffersonian fashion. In this manner he actually shares a rhetorical pose with some populist conservatives.

As a modern person, I don’t know where I fall. The America of my youth, the Reagan-Clinton era, was dominated by a Jeffersonian-producerist rhetoric, if not always action. On the other hand, history generally suggests to me that a Hamiltonian-developmentalist paradigm is friendly to the facts of how the world is, as opposed to how it should be.

December 26, 2017

Why the Democratic wave may be bigger because of gerrymandering

Filed under: 2018,Politics — Razib Khan @ 10:38 pm

I’ve been saying for a while that I think the Democrats will probably retake the House in 2018. More recently the probability seems to be getting higher and higher if you look at the generic ballot.

But I noticed something on Twitter and made an observation which I think perhaps I should put here: the conscious Republican gerrymandering after 2010 opens the possibility for greater Democratic gains because of tail risk. I was prompted to this comment after seeing a distribution of likely outcomes of the November 2018 election. The shape of the likely number of Republican/Democratic representatives wasn’t Gaussian. Rather, there was a much longer Democratic tail to the distribution. I hypothesized that this was the outcome of massive Democratic gains if the wave was high enough, and gerrymandering districts begin to overtop and flip.

The logic is pretty straightforward. Republican gerrymandering involves packing Democrats into some districts and dividing others between very Republican districts. The packing decreases the proportions of Democrats in some Republican districts. But the dilution of Democrats across very Republican districts, leaving somewhat less Republican, but still reliably Republican, districts, is where my point comes in.

If the national generic ballot swing toward Democrats is large enough, then some safe Republican seats come into play. Distribution of Democrats across these districts in a normal year does not entail anything more than a trivial shift in probabilities. But in a wave election, the standard operating procedure might not hold. If the Democratic votes were in a single district, then the Republican districts that remained would be more robust to a wave. As it is, removing these safe Democratic districts and distributing them across Republican districts made these districts a little less robust to a wave.

December 24, 2017

Open Thread, 12/24/2017

Filed under: Open Thread — Razib Khan @ 12:26 am


Well, Merry Christmas Eve!

I’ve been rereading Zero to One: Notes on Startups, or How to Build the Future. Recommended. A little different now that I’ve been involved in start-ups.

I would say that a lot of it is a pretty straightforward application of stuff you’ll encounter in economics and economic history to Silicon Valley (e.g., economic growth through technology vs. Smithian growth through globalization).

Haven’t had time to work on the South Asian Genotype Project much since I’ve burned a lot of hours on the margin moving websites. I’ll get back to it in the next few days.

Just a reminder, two days now to get $80 off Helix products (say early hours of December 26th), including Neanderthal, Metabolism and Regional Ancestry.

A friend asked about which podcasts I listen to. Here are the ones I listen to habitually:

In Our Time. I’ve been listening to this podcast for 10 years now. The Glenn Show on bloggingheads.tv. Probably listen to 75% of these discussions. Planet Money and Tides of History.

Secular Jihadists. One of the cohosts pointed out on the last episode that Stalin and Mao killed more people than Hitler. Oh, and that white people are the “least racist.” We live in a predictable world, and this podcast always surprises me with the originality of the hosts (though I demur from their New Atheism).

Chap Trap House. I don’t really get it, but the bro-banter is pretty amusing to me.

Stuff You Missed In History Class.

Politics Podcast from FiveThirtyEight.

Also, my podcast with Spencer Wells is going well (if downloads are any measure). We have some stuff coming up on Neanderthals (two episodes), as well as the Aryan invasion of India. You can find it on iTunes, Stitcher, and Google Play too (Spotify hasn’t gotten back to me).

I’ll be taking some time off from this weblog and my day job spending some time with my kids the week after Christmas. I’ll probably post stuff if I really have to, but otherwise might be a little quieter….

December 22, 2017

“Rakhigarhi paper” out in January 2018?

Filed under: Indian Genetics,Rakhigarhi — Razib Khan @ 10:01 pm

Tony Joseph has an interesting piece up, Who built the Indus Valley civilisation?, which people are asking me about via email. First, I don’t have any inside information. Last I heard in September was that the Rakhigarhi results were “one or two months away,” like they have been for a year or so. So I put it out of mind.

In any case, here are the important points:

All this could now change thanks to the science of genetics and four ancient skeletons excavated from a village called Rakhigarhi in Haryana. The four people to whom these bones once belonged — a couple, a boy and a man — lived roughly 4,600 years ago when the Indus Valley civilisation was in full bloom.

In the three-and-a-half years since its excavation, Shinde has brought together scientists from Indian and international institutions like the Centre for Cellular and Molecular Biology, Hyderabad (CCMB), Harvard Medical School, Seoul National University, and the University of Cambridge to work on different parts of the project, including extracting and analysing DNA from these ancient people, reconstructing their faces, and studying the remains of their habitation to understand their daily habits and ways of life.

The DNA analysis will also help figure out their height, body features, and even the colour of their eyes….

Joseph also asserts that the publication will happen in a “leading international journal” in a month or so. If I had to bet, I’d say Nature.

Harvard Medical School suggests to me they finally got David Reich’s group involved. As for Cambridge University, Eske Willerslev now has an appointment there.

The piece talks a lot about Y and mtDNA. But if they are talking about height, body features, and color of eyes, they must have gotten genome-wide data. If Eske Willerslev is involved they may have sequenced the whole genome at some coverage of at least one of the samples.

If I had to bet I think the Rakhigarhi samples will be Y haplogroups J2 or the Indian branch of L, and the mtDNA will be an Indian branch of M. In terms of genome-wide patterns they will exhibit a mixture between West Eurasian ancestry, with strong affinities to Near Eastern farmers from the Zagros, and what we now term “Ancestral South Indians” (AS), who descend from the aboriginal peoples of the subcontinent, and are genetically somewhat closer to East Eurasians than West Eurasians (to be fair, I think it is not implausible that much of ASI heritage is the product of westward migration out of Southeast Asia during the Pleistocene and early Holocene).

December 21, 2017

The general social complexity factor is a thing

Filed under: Cliodynamics,History,Seshat — Razib Khan @ 11:35 pm

The above is the Inglehart–Welzel cultural map of the world, derived from responses to the World Values Survey which are subject to principal component analysis. Basically, you take all the variation and pull out the biggest independent dimensions which can explain the variation. You’ve seen this with genetic data, but the method is pretty common in the social sciences.

When you do this with genetic data and human populations and use adequate sample representation PC1 is almost always African vs. non-African and PC2 is West Eurasia/North Africa vs. the rest of the world that’s not Africa. Though one can quibble with the details the reality is that these patterns are easy to reconcile with evolutionary history. Humans first split between Africans and non-Africans, and the west vs. east division in Eurasia is arguably the next major bifurcation (and gene flow barrier).

For the above map, the first two principal components explain 70 percent of the variance in the data. So what are they? You can see above that they labeled the x-axis as survival to self-expression, and the y-axis tradition to secular-rational. I’m not hung up on what this means and am not going to explore that. Rather, notice the geographic clustering.  These dimensions pass the smell test in terms of their clustering.

If you look at the distributions pretty much none of them should be surprising to you historically.  Protestant Northern Europe was very different in 1700 from today, but it was already a coherent socio-cultural phenomenon. Similarly, Russia has been historically distinct from Western Europe culturally for nearly the whole of its existence as a coherent polity (from ~1000 AD on). In fact, the marriage of Ann of Kiev into the French royal family in the 11th century may be indicative of the closest relationship of what became Russia to the West before the early modern period.* On this map, Russia and other Eastern European nations are quite distant from Northern Europe, and to some extent from Catholic Europe.

But this map isn’t just a reflection of geography. You see that Serbia, Bosnia, Croatia, and Slovenia occupy positions in relationship to Russia and Western Europe exactly where you would predict from their history. Serbia has a much stronger affinity with Russia, Croatia is in Catholic Europe, while Slovenia seems more like Northern European nations than Croatia. Bosnia occupies a position between Croatia and Serbia. These variations are important because ethno-linguistically the divisions between Serbians, Croatians and Bosnians (and lesser extent Slovenians) are minor. They originate from groups of Slavs who settled among the native Pannonians, whether Latin or Illyrian speaking, only in the centuries before 1000 AD.

What you are seeing here quantitatively are the historical fissures that occurred during to division between Western and Eastern Europe through theological conflict, and later the shock of the Tatar Yoke for the Russians, and Ottoman domination in the Balkans. If you know some history the reality that Croatia is Catholic, and oriented toward the West, and long been under Austrian and Hungarian hegemony, explains why it is where it is culturally. Similarly, Serbia is Orthodox, was oriented toward Byzantium, and later subjugated for centuries under the Ottomans.

But most people don’t know much history. This is why visual representations of quantitative social science data are quite useful. It’s almost impossible to convince the ignorant of historical truths when they don’t know any history because they can’t tell if you are making things up. Usually they trust you if you are part of their in-group, and distrust you if you are of an out-group.

For example, over the years a few times I’ve had really strange conversations about whether Russia is a Western nation or not on Twitter. There are roughly two groups that assert Russia is a Western nation: 1) white nationalists, for whom whiteness is necessary and sufficient for being Western 2) historically naive public intellectuals who can’t evaluate competing hypotheses, and implicitly impute Western identity to Russia because Russians are white and Christian (at least culturally). With white nationalists obviously there isn’t going to be a major argument. Their framework is just so different.

But historically naive public intellectuals are a different case. They simply don’t know enough facts to make even the weakest judgement, and so default back to the heuristic of racial and cultural categorization at the coarsest levels (this also explains their need to transform white-skinned and often blue-eyed Turkish and Balkan Muslims into “people of color”). At this point one can point out a lot of facts, including the reality that for centuries Russian intellectuals themselves debated about whether to become Western or retain their own distinctive identity as separate. And yet at the end of it all how would someone who doesn’t know much history know whether to give credibility to my contentions? If I stated that much of late medieval Russian statecraft owed much to experience of princes who grew up under the Tatar Yoke as well as the creation of a frontier culture which assimilated aspects of the Tatar lifestyle (as well as some Tatar nobility, who converted to Christianity and became part of the boyar class), how would they easily figure out if I’m bullshitting them? (yes, they could go read-up, but by the fact they don’t know relatively introductory history well into adulthood indicates no deep interest in doing this).

Quantitative and formal measures give us a simple language that even the naive can navigate. One can define Russia as within the West, or without, but one can not deny that socio-culturally it is quite distinct from Western and Northern European cultures. The data say it is so!

This brings me to a new paper in PNAS (OA), Quantitative historical analysis uncovers a single dimension of complexity that structures global variation in human social organization. It’s one of the first results from the Seshat: Global History Databank. Peter Turchin is heavily involved in this, but I notice the above paper also includes Harvey Whitehouse on the author list. I’ve long admired his work on the cognitive dimension of cultural production and variation.

Here’s the abstract:

Do human societies from around the world exhibit similarities in the way that they are structured, and show commonalities in the ways that they have evolved? These are long-standing questions that have proven difficult to answer. To test between competing hypotheses, we constructed a massive repository of historical and archaeological information known as “Seshat: Global History Databank.” We systematically coded data on 414 societies from 30 regions around the world spanning the last 10,000 years. We were able to capture information on 51 variables reflecting nine characteristics of human societies, such as social scale, economy, features of governance, and information systems. Our analyses revealed that these different characteristics show strong relationships with each other and that a single principal component captures around three-quarters of the observed variation. Furthermore, we found that different characteristics of social complexity are highly predictable across different world regions. These results suggest that key aspects of social organization are functionally related and do indeed coevolve in predictable ways. Our findings highlight the power of the sciences and humanities working together to rigorously test hypotheses about general rules that may have shaped human history.

Intuitively most people would have guessed this. Social complexity is a thing. Human cultural evolution has exhibited some directionality or at least a general secular trend. If you have read a lot of history and thought about these things you’d come to these conclusions intuitively.

I could also assert that northern France in the 12th century AD was a more socially complex society than the one the Romans conquered in the 1st century BC. Why? I could give plenty of reasons. But it is at this point that a fashionable viewpoint in some academic circles would problematize this assertion, and argue that characterizing High Medieval France as more complex than pre-Roman Gaul exposes one’s own assumptions and beliefs, as opposed to facts about the world.

You know the type. One problem one often encounters with this line of argument is that the individuals making the argument really don’t know enough in terms of facts to know what they’re refuting. Rather, they’ve been caught along on a current academic fashion.

This is why figures like the one to the left are important. It shows values on the social complexity factor, PC1, for Latium (red), the Paris basin (blue) and Iceland (green). What you see is that the Paris basin lags Latium up until around 0 AD. At this point there is catch-up. Though Gallic social complexity was already increasing in the centuries up to the Roman conquest (one reason the Romans found conquest of Gaul useful was that it was wealthy enough to steal from), it was only around the time of assimilation into the Roman state that it caught up to Latium.

Latium and the Paris basin both decrease in social complexity after the fall of the Roman Empire. But after 1000 AD the Paris basin outstrips Latium. In the 12th century it does seem that the Paris basin was more socially complex than it was in the pre-Roman period.

It is much easier to point an ignorant person to a chart than go through a laundry list of facts. Facts without context and background knowledge are not useful. But visualizations of data are much more easily digestible.

The authors show that the nine complexity characteristics are highly correlated with each other. Some of these make sense (those related to polity scale). But others are not as straightforward, though the verbal arguments present themselves (e.g., polities with lots of people are more likely to need written scripts for bureaucratic record keeping; the data show this to be true). Additionally, the models that are general can predict patterns in individual regions. That implies that the same dynamics are occurring cross-culturally. Each society is not sui generis for the purposes of analysis.

Of course a standard retort will be that the selection and coding of criteria of complexity itself is biased. That’s fine. But with formal methods we can actually hash out disagreements and points of interpretation in a much simple and clear manner than before. Ultimately I think those who object to this sort of analysis actually object to analysis driven by data and formal methods, as opposed to their own intuitions and personal preference. After all, it’s not a great discovery to find that there is a common cross-cultural dynamic which underpins social complexity.

But in the future Seshat and the researchers who utilize it will smoke out counter-intuitive or surprising results. The data and methods are there.

* Ann herself seems to have been mostly of Scandinavian ancestry as was the norm for the early Kievan nobility. Her mother was a Swedish-born princess, while her father was a Slavicized Rurikid.

Finland to sequence 10% of its population in 6 years

Filed under: Medical Genomics — Razib Khan @ 12:07 am

As you may have heard, Finland is starting a major genomics initiative. Basically , hey’re going to try and sequence 500,000 Finns over the next 6 years. Obviously, these are goals, and sometimes efforts fall short. But sequencing is only going to get cheaper, so I think they’ll get it done.

After the UK Biobank, honestly I’m starting to wonder if European countries with robust socialized medical sectors are really going to start shining because of their ability to ramp up scale and coordination fast. In the late 2000s, a few friends predicted this might happen, and that seems right.

And it is true because of their low effective population size and therefore genetic homogeneity sequencing and analyzing Finns is useful. Also, it might be some sort of bias in the discovery but they do seem to have a lot of recessive diseases. But ultimately I’m hoping a non-European nation besides an East Asian can get it together to do this sort of effort so we get some more genomic diversity into the system. The Gulf states are my best bet, as they have major issues with recessive diseases and some money to pump into the system.

December 20, 2017

Natural selection in humans (OK, 375,000 British people)

Filed under: Natural Selection,Population genetics,Population genomics,Selection — Razib Khan @ 10:41 pm

 


The above figure is from Evidence of directional and stabilizing selection in contemporary humans. I’ll be entirely honest with you: I don’t read every UK Biobank paper, but I do read those where Peter Visscher is a co-author. It’s in PNAS, and a draft which is not open access. But it’s a pretty interesting read. Nothing too revolutionary, but confirms some intuitions one might have.

The abstract:

Modern molecular genetic datasets, primarily collected to study the biology of human health and disease, can be used to directly measure the action of natural selection and reveal important features of contemporary human evolution. Here we leverage the UK Biobank data to test for the presence of linear and nonlinear natural selection in a contemporary population of the United Kingdom. We obtain phenotypic and genetic evidence consistent with the action of linear/directional selection. Phenotypic evidence suggests that stabilizing selection, which acts to reduce variance in the population without necessarily modifying the population mean, is widespread and relatively weak in comparison with estimates from other species.

The stabilizing selection part is probably the most interesting part for me. But let’s hold up for a moment, and review some of the major findings. The authors focused on ~375,000 which matched their sample criteria (white British individuals old enough that they are well past their reproductive peak), and the genotyping platforms had 500,000 markers. The dependent variable they’re focusing on is reproductive fitness. In this case specifically, “rRLS”, or relative reproductive lifetime success.

With these huge data sets and the large number of measured phenotypes they first used the classical Lande and Arnold method, which leveraged regression to measure directional and stabilizing selection. Basically, how does change in the phenotype impact reproductive fitness? So, it is notable that shorter women have higher reproductive fitness than taller women (shorter than the median). This seems like a robust result.

The results using phenotypic correlations for direction (β) and stabilizing (γ) selection are shown below. The abbreviations are the same as above.

 

There are many cases where directional selection seems to operate in females, but not in males. But they note that that is often due to near zero non-significant results in males, not because there were opposing directions in selection. Height was the exception, with regression coefficients in opposite directions. For stabilizing selection there was no antagonistic trait.

A major finding was that compared to other organisms stabilizing selection was very weak in humans. There’s just not that that much pressure against extreme phenotypes. This isn’t entirely surprising. First, you have the issue of the weirdness of a lot of studies in animal models, with inbred lines, or wild populations selected for their salience. Second, prior theory suggests that a trait with lots of heritable quantitative variation, like height, shouldn’t be subject to that much selection. If it had, the genetic variation which was the raw material of the trait’s distribution wouldn’t be there.

Using more complex regression methods that take into account confounds, they pruned the list of significant hits. But, it is important to note that even at ~375,000, this sample size might be underpowered to detect really subtle dynamics. Additionally, the beauty of this study is that it added modern genomic analysis to the mix. Detecting selection through phenotypic analysis goes back decades, but interrogating the genetic basis of complex traits and their evolutionary dynamics is new.

To a first approximation, the results were broadly consonant across the two methods. But, there are interesting details where they differ. There is selection on height in females, but not in males. This implies that though empirically you see taller males with higher rLSR, the genetic variance that is affecting height isn’t correlated with rLSR, so selection isn’t occurring.

~375,000 may seem like a lot, but from talking to people who work in polygenic selection there is still statistical power to be gained by going into the millions (perhaps tens of millions?). These sorts of results are very preliminary but show the power of synthesizing classical quantitative genetic models and ways of thinking with modern genomics. And, it does have me wondering about how these methods will align with the sort of stuff I wrote about last year which detects recent selection on time depths of a few thousand years. The SDS method for example seems to be detecting selection for increasing height the world over…which I wonder is some artifact, because there’s a robust pattern of shorter women having higher fertilty in studies going back decades.

December 19, 2017

Pick the right team, not the right answer (most of the time)

Filed under: Cognitive Science,Cultural Evolution,Group Think — Razib Khan @ 7:07 pm

Often you will hear people say “why do people always engage in ‘group-think'”? As if group-think is always a bad thing! The reality is that group-think is often highly adaptive. That’s why people engage in it. You’re outsourcing expensive cognition to the collective, tradition, or in some cases to someone with expertise.

Of course, there are whole domains of heuristics and biases that developed out of exposing how humans do not reason appropriately, but other researchers have argued that our species’ irrationality is often quite useful in our ancestral evolutionary environment. In other words, a lot of what frustrates is us not a bug, but a feature.

For example, in an ancient pre-modern environment where culture and environment were generally stable reasoning to everything basically consists of reinventing the wheel constantly. The contemplative life may have been the starving life. The “way things have been done” may not always seem perfectly optimal, but they were sufficient.

To give an empirical example of this that I’ve always found sad, the Irish were exceptional among European peasants peoples in taking to a potato monoculture without must hesitation. Believe it or not the Russians were tardy at adoption. This resulted in a massive demographic expansion which saw Ireland’s population peak at around 8,000,000. But the cost of this was the Great Famine, which illustrated how the wholesale adoption of practices which were optimal in the short-term were not optimal evaluated over the long-term (Ireland’s population today is less than 5,000,000, though some of this is due to the culture of emigration which emerged during the Great Famine). Evolution is evaluated over the long-term, so universal cognitive ticks which we see across our species are probably there for a reason, whether as a direct cause, or a side-effect.

Finally, intellectuals who enjoin the masses to not engage in group-think have no difficulty in falling into the same practices when operating outside their own domains of expertise. What this suggests is that “critical-rationalism” is not something that emerges in a vacuum. Rather, it is a cognitive method that develops in a particular cultural context, and individually is often the outcome of confidence and experience gained through years of education and mental practice within a narrow topic.

Getting yourself out of the cave and not misinterpreting the shadows can be hard. And truthfully, it probably wasn’t even optimal. The roaches will inherit the earth long after we’re gone, and they likely never even reflect upon their own selfhood.

Motivated reasoning in “science journalism.”

Filed under: Psychology,Psychometrics — Razib Khan @ 6:09 pm

The “reproducibility crisis” has really benefited some sectors of science journalism, as there is less credulous amplification of spurious results. That being said, motivated reasoning is powerful. They “want to believe.”

So when I saw this piece in Quartz, Highly motivated kids have a greater advantage in life than kids with a high IQ, I immediately scanned for what I usually look for, and found it:

Over the next four decades, the Gottfrieds and several colleagues collected a staggering trove of data on the study participants, yielding important insights into working parents, temperament, and other topics. Researchers collected information about participants from parents, teachers and transcripts, tested their IQ and motivation levels,and even visited their homes. In all, the Fullerton Longitudinal Study has amassed an estimated 18,000 pieces of information on each of the remaining 107 participants. “It’s our life’s work,” says Allen cheerfully. “We’ll take it to our grave.”

107 participants. Lots of information huh? Things that make you go hm….. Also, 19% of the children had IQs of 130 or above. About 2% of the population has an IQ at this level. The sample size was relatively small, and the sample was very unrepresentative.

This doesn’t mean that there aren’t real results in these data. But I don’t think they warrant the fanfare in the title, except for the fact that people want a silver bullet that will abolish social inequality.

Even the text itself doesn’t justify the title at all (to be fair, usually headline writers differ from the persons writing the text of a piece): “[Motivation] in itself is accounting for a certain amount of variance in achievement that goes above and beyond IQ….” That is, they don’t even say it accounts for more of the variance, only that there is variance that isn’t accounted for by IQ (which everyone already agreed upon).

Finally, I’ve spent my life around highly educated and intelligence people a bit perplexed and befuddled by my diverse interests. This includes in academia. So I can see that there is difference between people for whom learning is a means to a professional and social ends, and for those whom learning is the ends. I suspect the ancients could have told you this!

Samsung Galaxy S8 is pretty good

Filed under: Technology — Razib Khan @ 5:35 pm

One of the more convenient things with having a blog that has more than a few readers is that you can ask questions and get some answers.

Recently I was figuring out whether I’d go full-Apple, and get an iPhone. I got a lot of feedback, but ultimately I decided to to be boring and get a Samsung Galaxy S8.

The verdict? Bixby sucks. Everything else is pretty good. Would recommend.

A living fossil, back to GNXP.COM

Filed under: Blog — Razib Khan @ 4:29 pm

Just a note. I am moving back to the original Gene Expression domain. If you consume my content through my Twitter auto feed (not my main Twitter account) or my Total Content Feed, it’s pretty irrelevant, since all the places I post content to push to them (I still post to Brown Pundits and Secular Right now and then). If you use bookmarks, here is the page:

https://www.gnxp.com

There’s not much to say about why I’m moving. My “side-hustle” energies have shifted to DNA Geeks, while I’m cranking out content for Insitome as well. Speaking of which, our second podcast is up for The Insight.

You can get it at iTunes, Stitcher, and Google Play right now (just search “The Insight” and “Insitome”). Submitted to Spotify too! (though to be honest, I have a paid subscription to Spotify and it seems weird to listen to podcasts through that app).

We’ve got two Neanderthal-related conversations being edited right now, including one where we have John Hawks on as a guest. And we have plenty of ideas for what we’ll be talking about come 2017.

One thing we’ve floated is a “Journey of Man Redux.” Basically, it’s a review of the topics that Spencer Wells, my boss, covered in his early 2000s book The Journey of Man. What stood the test of time? What new things do we now know?

Finally, moving back to the old domain has me thinking about blogging and my own location in the ecosystem. In the 2000s someone like me wasn’t exceptional. Generalist bloggers with a few primary foci. Today, in 2017, I think that’s pretty rare. A lot of what would have been blogging in the 2000s is now on Twitter or Facebook. Many bloggers have become highly professionalized, and where blogging stops and journalism begins is very blurred (many now are journalists!).

And yet I also feel that outside of a few fields, such as economics, independent academic blogging has also withered. They either got swallowed up by a journal or field-specific publication or, their purview is very narrow and specific to the output of their scholarship. There’s a place for that. But that naturally narrows the space of topics which they explore.

As for what I’m doing, I still don’t really know. There isn’t a “purpose” or “end” to all of this. This is just something I’ve been doing since 2002, and I’ll probably keep doing it until professional or family obligations (or both) get in the way.

The main thing I would observe is that I suspect that we might see platform disaggregation soon. I suspect it will be technology driven. The dominant trend of acquiring information through social media has already removed the personal relationship between producers and consumers of content.

Addendum: I’ll probably do a URL redirection for the archives here, but I’ve now copied over the whole of everything from 2002 to 2017 on GNXP.COM except for this one post.

December 14, 2017

Three books to understand the “Dark Matter” of American History

Grand theories of history often have less utility than the claims they make for themselves. Marxism is a classic example.

But that does not mean that theories of history are useless. And arguably, Marxism is a classic example in this case too. Material forces and class conflicts can’t explain all of history, but they do explain some of history. Chris Wickham’s magisterial Framing the Early Middle Ages: Europe and the Mediterranean, 400-800 suffers from its excessive materialist and economistic thesis, but it also benefits from this perspective, because it captures part of the answer.

Moderation in all things, and due consideration to the importance of viewpoints in coloring perceptions, are the keys to comprehension in my opinion..

Today in some quarters it is fashionable to reduce all of history to the interplay between white supremacy and nonwhite peoples, who are depicted implicitly as nearly supine “noble savages,” existing in an Edenic state of nature before the intrusion of European peoples. This is a silly viewpoint from a scholarly perspective, and some of the ideological implications are ones which I object to most strongly.

And yet that begs the question, how does one understand the forces of history? In the American context, I think it is critical to understand the elementary regional folkways which congealed into these United States, and whose “cultural DNA” echoes down through the generations. Much of this is implicit and invisible culture because it is the culture of white English -speaking peoples of British provenance (though not all were Anglo, such as the French Canadians or Hispanos of the southwest).

Recently, Colin Woodward’s American Nations: A History of the Eleven Rival Regional Cultures of North America is the best example of this sort of work, which attempts to trace the historical dark matter the skeleton beneath the flesh. A more scholarly and narrow treatment can be found in David Hackett Fisher’s expansive Albion’s Seed: Four British Folkways in America. Finally, perhaps the most underrated and overlooked offering in this genre is Kevin Phillips’ The Cousins’ Wars: Religion, Politics, Civil Warfare, And The Triumph Of Anglo-America.

While Woodward focuses on all of North America, and Fisher more narrowly on the four folkways which extend from New England to the Deep South, Phillips’ integrates an American history with a broader narrative that shows the connections to events and processes occurring in the British Isles, and in particular England. The peculiarities of New England culture and economics, and their love-hate relationship to the British elites of the late 18th and 19th century, are critical pieces of the puzzle in explaining how the United States diverged from the United Kingdom, and, how the United Kingdom diverged from the United States.

If an understanding of population genetics allows one to decompose evolution and broadly biological phenomena into tractable analytic units, so an understanding of the elementary units of American culture, and their historical antecedents, shines a whole new light upon contemporary developments.

Three books to understand the “Dark Matter” of American History

Grand theories of history often have less utility than the claims they make for themselves. Marxism is a classic example.

But that does not mean that theories of history are useless. And arguably, Marxism is a classic example in this case too. Material forces and class conflicts can’t explain all of history, but they do explain some of history. Chris Wickham’s magisterial Framing the Early Middle Ages: Europe and the Mediterranean, 400-800 suffers from its excessive materialist and economistic thesis, but it also benefits from this perspective, because it captures part of the answer.

Moderation in all things, and due consideration to the importance of viewpoints in coloring perceptions, are the keys to comprehension in my opinion..

Today in some quarters it is fashionable to reduce all of history to the interplay between white supremacy and nonwhite peoples, who are depicted implicitly as nearly supine “noble savages,” existing in an Edenic state of nature before the intrusion of European peoples. This is a silly viewpoint from a scholarly perspective, and some of the ideological implications are ones which I object to most strongly.

And yet that begs the question, how does one understand the forces of history? In the American context, I think it is critical to understand the elementary regional folkways which congealed into these United States, and whose “cultural DNA” echoes down through the generations. Much of this is implicit and invisible culture because it is the culture of white English -speaking peoples of British provenance (though not all were Anglo, such as the French Canadians or Hispanos of the southwest).

Recently, Colin Woodward’s American Nations: A History of the Eleven Rival Regional Cultures of North America is the best example of this sort of work, which attempts to trace the historical dark matter the skeleton beneath the flesh. A more scholarly and narrow treatment can be found in David Hackett Fisher’s expansive Albion’s Seed: Four British Folkways in America. Finally, perhaps the most underrated and overlooked offering in this genre is Kevin Phillips’ The Cousins’ Wars: Religion, Politics, Civil Warfare, And The Triumph Of Anglo-America.

While Woodward focuses on all of North America, and Fisher more narrowly on the four folkways which extend from New England to the Deep South, Phillips’ integrates an American history with a broader narrative that shows the connections to events and processes occurring in the British Isles, and in particular England. The peculiarities of New England culture and economics, and their love-hate relationship to the British elites of the late 18th and 19th century, are critical pieces of the puzzle in explaining how the United States diverged from the United Kingdom, and, how the United Kingdom diverged from the United States.

If an understanding of population genetics allows one to decompose evolution and broadly biological phenomena into tractable analytic units, so an understanding of the elementary units of American culture, and their historical antecedents, shines a whole new light upon contemporary developments.

A genetic map of the world

Filed under: Population genetics — Razib Khan @ 4:46 pm


The above map is from a new preprint on the patterns of genetic variation as a function of geography for humans, Genetic landscapes reveal how human genetic diversity aligns with geography. The authors assemble an incredibly large dataset to generate these figures. The orange zones are “troughs” of gene flow. Basically barriers to gene flow.  It is no great surprise that so many of the barriers correlate with rivers, mountains, and deserts. But the aim of this sort of work seems to be to make precise and quantitative intuitions which are normally expressed verbally.

To me, it is curious how the borders of the Peoples’ Republic of China is evident on this map (an artifact of sampling?). Additionally, one can see Weber’s line in Indonesia. There are the usual important caveats of sampling, and caution about interpreting present variation and dynamics back to the past. But I believe that these sorts of models and visualizations are important nulls against which we can judge perturbations.

As I said, these methods can confirm rigorously what is already clear intuitively. For example:

Several large-scale corridors are inferred that represent long-range genetic similarity, for example: India is connected by two corridors to Europe (a southern one through Anatolia and Persia ‘SC’, and
a northern one through the Eurasian Steppe ‘NC’)

We still don’t have enough ancient DNA to be totally sure, but it’s hard to ignore the likelihood that “Ancestral North Indians” (AN) actually represent two different migrations.

India also illustrates contingency of these barriers. Before the ANI migration, driven by the rise in agricultural lifestyles, there would likely have been a major trough of gene flow on India’s western border. In fact a deeper one than the one on the eastern border. And if the high genetic structure statistics from ancient DNA are further confirmed then the rate of gene flow was possibly much lower between demes in the past. Perhaps that would simply re-standardize equally so that the map itself would not be changed, but I suspect that we’d see many more “troughs” during the Pleistocene and early Holocene.

Because there are so many geographically distributed samples for humans, and frankly some of the best methods developers work with human data (thank you NIH), it is no surprise that our species would be mapped first. But I think some of the biggest insights may be with understanding the dynamics of gene flow of non-human species, and perhaps the nature and origin of speciation as it relates to isolation (or lack thereof).

A genetic map of the world

Filed under: Population genetics — Razib Khan @ 4:46 pm


The above map is from a new preprint on the patterns of genetic variation as a function of geography for humans, Genetic landscapes reveal how human genetic diversity aligns with geography. The authors assemble an incredibly large dataset to generate these figures. The orange zones are “troughs” of gene flow. Basically barriers to gene flow.  It is no great surprise that so many of the barriers correlate with rivers, mountains, and deserts. But the aim of this sort of work seems to be to make precise and quantitative intuitions which are normally expressed verbally.

To me, it is curious how the borders of the Peoples’ Republic of China is evident on this map (an artifact of sampling?). Additionally, one can see Weber’s line in Indonesia. There are the usual important caveats of sampling, and caution about interpreting present variation and dynamics back to the past. But I believe that these sorts of models and visualizations are important nulls against which we can judge perturbations.

As I said, these methods can confirm rigorously what is already clear intuitively. For example:

Several large-scale corridors are inferred that represent long-range genetic similarity, for example: India is connected by two corridors to Europe (a southern one through Anatolia and Persia ‘SC’, and
a northern one through the Eurasian Steppe ‘NC’)

We still don’t have enough ancient DNA to be totally sure, but it’s hard to ignore the likelihood that “Ancestral North Indians” (AN) actually represent two different migrations.

India also illustrates contingency of these barriers. Before the ANI migration, driven by the rise in agricultural lifestyles, there would likely have been a major trough of gene flow on India’s western border. In fact a deeper one than the one on the eastern border. And if the high genetic structure statistics from ancient DNA are further confirmed then the rate of gene flow was possibly much lower between demes in the past. Perhaps that would simply re-standardize equally so that the map itself would not be changed, but I suspect that we’d see many more “troughs” during the Pleistocene and early Holocene.

Because there are so many geographically distributed samples for humans, and frankly some of the best methods developers work with human data (thank you NIH), it is no surprise that our species would be mapped first. But I think some of the biggest insights may be with understanding the dynamics of gene flow of non-human species, and perhaps the nature and origin of speciation as it relates to isolation (or lack thereof).

December 13, 2017

My new podcast with Spencer Wells

Filed under: Podcast — Razib Khan @ 9:42 am

Spencer Wells and I have a new podcast, The Insight. On the first episode, we’ll be talking about the Neolithic revolution.

We’ve already got several more in the pipeline that will come out in the next few weeks (being edited), including one with John Hawks. This will be a regular thing, so please subscribe!

Update: Also see: http://insitome.libsyn.com/website.

Update: Here is the podcast embedded:

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