Bringing back street kids

Just spent some time with a friend. He lives in a safe neighborhood, so I asked if there were any kids for his kids (they’re young) to play with. Apparently not really.

In this country today we have problems with racial and wealth inequality. There are huge debates about how we address these issues. And they don’t seem like they are going away any time soon.

But huge numbers of Americans adults grew up on the mean streets of the 1980s. We know there is a solution to childhood social isolation, because many of us grew up playing on streets, rather than being shepherded on ‘play dates.’ This is also an issue which most people agree on as a problem. We can solve this.

Totality, 2017

We saw totality in Independence, Missouri. It was a pretty long car trip with the kids, all of whom are under school age (though just barely in the case of the eldest). We had a big fright because there was a massive thunderstorm in the morning…but it cleared out for a few hours. And that was when the total eclipse occurred.

Really words don’t do the experience justice.

Chase a total eclipse if you get a chance.

Open Thread, 08/20/27

I’ve been off the map for a bit because I’m eclipse chasing. #TotalityOrBust as they say. The whole family has been converging on zone of totality, and now we’re there. Obviously I’m excited.

There are lots of things going on in the world. One thing though that I’m beginning to think is that people would benefit reading more cognition science. I know I certainly did years ago. The main issue is that we’re not rational in the way we think we’re rational, and that leads to a lot of confusions why other people behave the way they do. Check out Enigma of Reason (I came upon a lot of this literature through the study of the cognition of religion).

Complex Patterns of Admixture across the Indonesian Archipelago. Someone who knows archaeology should read this….

The genetic history of Ice Age Europe. This was published last year. But it should be re-read. Closely.

Blogging on an island as opposed to an archipelago

On a Twitter conversation it came up yesterday that a lot of people know each other from blogging in the 2000s. It was a different world back then, and the pond was much smaller. To my knowledge Derek Lowe is the only continuously active science blogger who has been at this longer than me (there are some, such as Dave Appell, who began blogging before me, but stopped for a while before starting up again). I’ve seen a lot of changes. Some good. Some perhaps not so good.

One major aspect is that blogging is no longer a conversation with many nodes. Rather, it’s a platform for individuals or networks to speak to their particular audience. I’m obviously part of this. I don’t subscribe to many blogs in my RSS feed. Basically I use Twitter to find blog posts. There are a few blogs I subscribe to, like Why Evolution Is True, but mostly I just wait until content shows up in my timeline.

And I’m not the only one. I have Google Analytics that go back very far. Below are referrals by site for equivalent periods in 2007, 2012, and 2017. I’ve standardized the top referral source (in pageviews) to 100.

2017, June – Aug
1 twitter 100
2 mobile facebook 38
3 unz.com 36
4 facebook 33
5 feedly.com 20
6 slatestarcodex.com 19
7 razib.com 11
8 brownpundits.com 9
9 eurogenes.blogspot.com 9
10 vox.com 6
2012, June – Aug
1 reddit.com 100
2 stumbleupon.com 60
3 facebook.com 49
4 scienceblogs.com 34
5 gnxp.com 31
6 fark.com 31
7 pulsenews 21
8 twitter 13
9 digg.com 12
10 isteve.blogspot.com 10
2007, June – Aug
1 digg.com 100
2 reddit.com 38
3 slashdot.org 20
4 isteve.com 19
5 stumbleupon.com 17
6 scienceblogs.com 11
7 dilbertblog.typepad.com 6
8 instapundit.com 4
9 del.icio.us 4
10 buzzfeed.com 3

I removed stuff like organic Google search, which I get a fair amount of. Additionally, I bolded all the sites where I am somehow involved in driving the traffic. So in 2017 I bolded Twitter because I have a big Twitter footprint that drives a lot of the traffic. I did not bold Facebook because I don’t use Facebook much to promote this website. Other people are sharing my posts. I separated mobile and non-mobile Facebook to show you that in 2017 mobile really matters.

You can see that over the years I’ve had to drive more and more of the traffic. I never posted my posts to Reddit. But for Twitter I push all my own content.

Roman cultural history has almost no demographic imprint


Several friends have asked that I weigh in the recent dust-up between Nassim Nicholas Taleb and Mary Beard. I haven’t for a few reasons. First, I can’t really be bothered to go incognito and see every detail of Taleb’s argument, as he has me blocked on Twitter (he called me a fucking idiot or something at some point). Second, the passion around this topic has little to do with genetics or ancient history from what I can see, two topics which I am actually interested in. Rather, it’s more about contemporary geopolitics. This is interesting too, and I have opinions on that, but I try really hard to keep history and politics in separate silos unless I am explicit about the connections and relevance. That’s because I don’t see classical history as simply something instrumentally important for modern times, but interesting in and of itself (the same goes for population genetics).

And for what it’s worth, Mary Beard says the same in her conclusion to SPQR. The ancients were ancients. Let them be what they were.

That being said, as someone with knowledge sets in ancient history and historical population genetics, I will make a few statements and let others interpret them however they wish (to be frank, I’m not going to cede ground to any of the experts I’ve seen who have spoken on the intersection of these two knowledge sets, so I figured it was time to put something somewhere beside Twitter).

* The prior probability that a Roman officer of the period in Britain would have visible black African ancestry (as seems clear by the cartoon, though no one has asked the cartoonists what their intent was) probability seems rather low. But it is non-zero, because a small minority of Roman subjects and citizens would have been defined as black by their physical appearance if they were alive today (they are mentioned passingly in the literature and texts from the period). Including in Britain.

* The probability conditional that he was based on an officer in Britain who was a native of Tidis is low, but higher. Several historians have pointed out in defense of the cartoon’s plausibility that there were many North Africans in Roman service, as well as prominent North Africans in Roman history (to name three of note, Septimius Severus, Tertullian, and St. Augustine). Whole tribes of what we’d today term Berbers enrolled in the Roman military a federates.

There are several separate issues to note. First, of the many North African genotypes I’ve seen detectable Sub-Saharan ancestry is found in almost all of them. But, many (most?) North Africans do not look visibly of Sub-Saharan African ancestry (see list of heads of states of Algeria). Second, both historical and genetic evidence indicates that this admixture from Sub-Saharan Africa is overwhelmingly (though not exclusively) from the period after Islam and the rise of a much bigger trans-Saharan trade (see Genomic Ancestry of North Africans Supports Back-to-Africa Migrations). Modern North Africa does have a large population today of people who are black or of obvious part-black ancestry, but this is due to the slave trade under Islam, and not antiquity.

* As evidence of the lack of non-European ancestry the paper The fine-scale genetic structure of the British population has been submitted. This is a great paper with best-of-breed methods and a massive data set of native English, with regional data. How do we resolve textual and archaeological evidence of people born outside of Britain during the Roman period in Britain with their lack of long-term genetic footprint among native modern Britains?

These sorts of questions need to be integrated in a broader context of the demography and genetics of antiquity that we have. On the whole looking at papers on modern and ancient DNA I am surprised by the lack of perturbation on the genetic structure attributable to the Roman period across Western Eurasia. I will offer two likely reasons that are related.

First, Classical civilization was an urban one, and the textual evidence we have is going to be highly skewed culturally in terms of our perception. The Roman world was predominantly written in cultured Latin and Greek (from what I have read the early translations of the Bible are indicative of a more pedestrian background of Christians due to the class markers of their lexical choices and idioms). But it was not necessarily spoken in cultured Latin and Greek across vast swaths of its territory. Even in St. Augustine’s time Punic was still spoken in the North African countryside, while the persistence and resurgence of Basque and Berber, and perhaps Brythonic Celtic in Britain, attest to vast reservoirs of people who were under the Roman peace, but not of it (also, the persistence of Albanian from a native Illyrian substrate). Because of the resources historians have on hand, text, there is going to be a major lacunae in our understanding and perception of the past. We hear the urban elites speaking to us. Not the rural majority.

Second, Classical civilization was an urban one, and this might have a major impact on the demographic consequences of migration. At any given size the effective breeding population is smaller than the census population, and the breeding population may not be representative of the overall population in terms of their genetic character. More specifically, it seems highly possible that the cosmopolitan urban Roman cities were massive demographic sinks. Rome before the Gothic Wars was a very populous city, not too far on the path of decline from its early imperial peak. But by the year 600 it had decreased its population to the point that vast swaths of the city were abandoned. Where did these people go? No doubt some of the elites scattered. Cassiodorus simply moved when barbarism came to his front step. But this was less possible for the urban proletariat. There is strong evidence that slaves in the ancient world were not replacing themselves reproductively due to brutality under which they lived. Some of the same was likely true of the urban proletariat.

* There is a difference between the inheritance pattern of culture and genes. In The Geography of Recent Genetic Ancestry across Europe this passage has always stuck out for me: “There is relatively little common ancestry shared between the Italian peninsula and other locations, and what there is seems to derive mostly from longer ago than 2,500 ya…The rate of genetic common ancestry between pairs of Italian individuals seems to have been fairly constant for the past 2,500 years, which combined with significant structure within Italy suggests a constant exchange of migrants between coherent subpopulations.”

The straightforward conclusion from this is that the Latinization of the Italian tribes and Magna Graecia occurred with no great demographic transformation. Modern Italy has within it the ghost of tribes long gone. This is notable because if you read the historical records of the Roman period you see evidence of trade, transport, and migration. But the genetic data would not lead you to this conclusion outside of Sicily and a few parts of Southern Italy.*

Above I have presented my reasoning for why this might be. But I think what it tells us that genetic data can informs us when there is a demographic turnover, and therefore a cultural turnover, but it will miss cultural turnovers which don’t have demographic impacts. These are many. To give a few examples, the rise of Islam in South Asia and Southeast Asia, the Latinization of the Western Mediterranean, the de-Latinization of Britain after the withdrawal of Roman legion and before the mass arrival of Saxons, and arrival of Buddhism in East Asia. All these are massive historical and cultural events, but they would not be visible in the genetic record.

If you want to learn about Roman history there are many books you could read. But I do recommend you try Bryan Ward-Perkins’ The Fall of Rome: And the End of Civilization. It’s a nice materialist take, and I think it gets to the underlying dynamics of institutional fragility of ancient civilization which was so easily wiped away by barbarism.

Addendum: The migration of the Slavs, Anglo-Saxons, and the Islamic Empires, all seem to differ from antiquity in having a major demographic impact. Why? In the case of massive institutional collapse, as in the first two cases, very old dynamics of inter-group competition arise, and famine probably does the rest of the trick. For Islam, it was a genuinely cosmopolitan civilization, with a more complex gradation between free and slave than in antiquity. Though it was quite brutal, African and Turkish slaves became free, and their genetic impact can be seen throughout the Islamic world.

* Like Spain, a substantial proportion of the Sicilian gene flow exchange is almost certainly due to the Islamic period. There are segments of North African and Sub-Saharan ancestry in Sicilians, albeit to a smaller extent than in Spain (in keeping with the shorter time period as part of the Islamic world).

Open Thread, 08/13/2017

Busy with kids and life. But perhaps time to read Peter Turchin’s Ages of Discord: A Structural-Demographic Analysis of American History. I was skeptical when Peter presented this idea years ago. Less so now.

I’m on the eclipse train. The whole family will be chasing it soon.

Paul Thompson is on Twitter. If you read this blog in the early/middle 2000s it will be a familiar name. Paul had thought I had stopped blogging! Moving platforms every few years does that.

So a friend of mine was advising that I should push sign-ups to my newsletter, as he too believes that Twitter’s days in its current form are numbered. I’ve only sent out one mailing so far, but may increase the frequency to once a month or so. Mostly I’m a little worried that without Twitter people like me who produce content, but aren’t affiliated with a media distribution channel, are going to get lost in the din.

Anyway, please sign up if you don’t follow me on Twitter (or if you do).

The revolution which came to archaeology without archaeologists?

The recent letter to Nature, Genetic origins of the Minoans and Mycenaeans, has elicited some response from those outside of genetics. The first author of the paper linked to these two, Who are you calling Mycenaean? and On genetics and the Aegean Bronze Age.

One of the common elements to both reactions was that the paper’s definition, or reification, of Mycenaean and Minoan constructs was naive. From one of the posts:

In a press interview following the publication of the study, one of the main authors claimed that ‘there is no doubt that our findings reflect historical events in the Greek lands’: ‘the picture of historical continuity is crystal clear, as is very clear the fact that through the centuries Greeks evolved receiving genetic influences from other populations.’ The category of ‘Greekness’ here appears more or less given and stable, despite the ‘influences’, from the Early Bronze Age to the present. It sounds like a version of the 19th-century national narrative of the power of eternal Hellenism to absorb external influences.

Context is important here. The last ten years have seen a massive updating of our assumptions about the nature of demographic change in the pre-modern world. Geneticists using ancient DNA have been central to this process. They’ve overturned a lot of archaeological orthodoxies.

One of the major assumptions seemingly at the heart of the two critical posts is that modern ideas of nationhood were a recent construction. The stylized assertion is that modern nationalism begins with the French Revolution. To me this is like the assertion that the troubadours invented romantic love during the High Middle Ages. While it is true that the troubadours popularized a particular form of romantic love, the core emotional impulses are primal, and didn’t need “inventing.” Similarly, ideas of nationality are clearly primal, because they derive from the tribal structures of prehistoric humanity. Tribes are an evoked part of human culture. That is, given similar cognitive hardware, the same software seems to get installed for the same tasks (group cohesion and inter-group competition).

Ironically, the period between the “rise of civilization” and the modern era may have been one defined by the regression of nationalistic thinking, because tribalism had to be suppressed with the rise of multiethnic agricultural states. Only with early modern information technology, and the spread of a literate middle class culture united by common mores and touchstones, could primal tribalism be transformed into modern nationalism (to this way of thinking it is not a coincidence that German nationalism with the Lutheran Reformation was supercharged by the arrival of the printing press).

Peter Heather in Empires and Barbarians and Azar Gat in Nations outline the revisionist views I’m alluding to in regards to the ancient origins of nationalism. But from a perspective of a geneticist the very high differentiation between nearby groups that persist for hundreds and even thousands of years is indicative of high levels of cultural distinction and consciousness (because only small amounts of gene flow between groups is enough to eliminate differences very rapidly). Genetics can’t maintain these sorts of differences, only strong cultural ideologies can.

Finally, quoting from the same post:

First, there’s not much new here. I mean, the data are new, but the conclusions are largely consistent with the archaeological consensus: there’s no big genetic difference between “Minoans” (Late Bronze Age Cretans) and “Mycenaeans” (Late Bronze Age inhabitants of the Greek mainland), and both are pretty close genetically to Late Bronze Age southwestern Anatolians….

The archaeological consensus was correct here to a great extent. But in other areas it has not been right of late. That’s why it is not so ho-hum. In The Beaker Phenomenon And The Genomic Transformation Of Northwest Europe the authors show that:

1) the spread of Beaker culture from Southwest Europe to Central Europe was one of cultural transmission (archaeologists would not be surprised).

2) the spread of Beaker culture to England from Central Europe was one of demographic replacement on the order of 90% over a few hundred years (archaeologists would be surprised).

It’s easy for archaeologists to be surprised that geneticists are presenting ideas that they “refuted” in the 1960s. But it turns out that the predictions on a demographic scale are easily refuted in many places and times by genetics. The issue isn’t whether it’s pots or peoples, but what the mix of pots and people are. This research is part of a broad program of nailing down the values in these parameters, as opposed to simply going along with archaeological orthodoxy.

Addendum: The title is somewhat unfair now that I think about it. Many archaeologists have been instrumental in the revolution triggered by ancient DNA. But, the vast majority of archaeologist and historians who are outside of these collaborations, I’m not so sure they are aware of the recent developments.

Empires of the Word: A Language History of the World is a monthly deal

Just a heads up to readers, Amazon Empires of the Word: A Language History of the World is $1.99 right now. I’d highly recommend you get this book if you are interested in this general topic.

Here is my review from about seven years ago.

But evolution converges!

Stephen Jay Gould became famous in part for his book Wonderful Life: The Burgess Shale and the Nature of History. By examining the strange creatures in the Burgess Shale formation Gould makes the case that evolution is a highly contingent process, and that if you reran the experiment of life what we’d see might be very different from what we have now.

But the scientist whose study of the formation that inspired Gould’s interpretation, Simon Conway Morris, had very different views. Though it can sometimes be churlish, his rebuttal can be found in The Crucible of Creation: The Burgess Shale and the Rise of Animals. Simony Conway Morris does not believe that contingency is nearly as powerful a force as Gould would have you believe. And his viewpoints are influential. Richard Dawkins leaned on him to make the case for convergence in evolution in The Ancestor’s Tale.

This crossed my mind when reading Carl Zimmer’s new column, When Dinosaurs Ruled the Earth, Mammals Took to the Skies:

Today, placental mammals like flying squirrels and marsupials like sugar gliders travel through the air from tree to tree. But Volaticotherium belonged to a different lineage and independently evolved the ability to glide.

They were not the only mammals to do so, it turns out. Dr. Luo and his colleagues have now discovered at least two other species of gliding mammals from China, which they described in the journal Nature.

Dr. Meng said that the growing number of fossil gliders showed that many different kinds of mammals followed the same evolutionary path. “They did their own experiments,” he said.

This ultimately comes down to physics. There are only so many ways you can make an organize that flies or glides. Mammals come to the table with a general body plan, and that can be modified only so many different ways.

This is not a foolproof point of datum in favor of convergence as opposed to contingency. Frankly these are often vague verbal arguments which are hard to refute or confirm. And even molecular evolutionary analyses come to different conclusions. It may be that we are asking the wrong question. But, it does suggest that evolution may work in a much narrower range of parameters as time progresses because of the winnowing power of selection.

Jon Snow + Daenerys Targaryen far creepier genetically than you know

Screenshot 2016-06-14 22.09.51
Credit: poly-m (deviantART)

If you have been following Game of Thrones you have been noticing that there is a brewing romance between Jon Snow, King in the North, and Daenerys Targaryen, the aspiring claimant to her father’s Iron Throne.

Of course there is a twist to all of this: unbenknownst to either, Jon Snow’s biological father is Daenerys’ dead brother, Rhaegar. This means that Daenery’s is Jon Snow’s aunt.

Long-time followers of the world of Game of Thrones are aware that incest between near relations is neither unknown nor shocking. But there is a non-trivial detail which it is important to note. Jon and Daenerys are far more closely related than typical aunts and nephews.

The reason is simple, Daenerys and her brother were the products of two generations of sibling incest. Incest results in inbreeding, and inbreeding as you know results in loss of genetic diversity. By Daenerys’s generation the coefficient of relationship between herself and her brothers was much higher than normal.

To be concrete, the coefficient of relationship of full-siblings is 0.50. That of half-siblings 0.25. Identical twins? Obviously 1.0. Another way to think about this is how much of the genome do any two pairs of individuals share in terms of long tracts of inheritance from recent ancestors. On the whole siblings share about half of their genomes in such a fashion. After two generations of inbreeding Daenerys and Rhaegar have a coefficient of relationship of 0.727 (using Wright’s method). They’re not identical twins, obviously, but their genetic relationship is far closer than full-siblings!

Don’t let the mother of dragons ride you Jon!

Dividing  this in half gives 0.36 as the coefficient of relationship between Jon and Daenerys, as opposed to 0.50 for full-siblings and 0.25 for a conventional aunt-nephew. Jon and Daenerys have almost the same genetic relationship as 3/4 siblings; two individuals who share a common parent, like half-siblings, but whose unshared parents are first order relatives (full-siblings or parent-child).

Not Jaime & Cersei creepy, but still creepy.

Addendum: Though Daenerys is quite inbred, Jon is not at all. One generation of outbreeding can eliminate all inbreeding.