Beyond visualization of data in genetics

totalvarHopefully by now the image to the left is familiar to you. It’s from a paper in Human Genetics, Self-reported ethnicity, genetic structure and the impact of population stratification in a multiethnic study. The paper is interesting in and of itself, as it combines a wide set of populations and puts the focus on the extent of disjunction between self-identified ethnic identity, and the population clusters which fall out of patterns of genetic variation. In particular, the authors note that the “Native Hawaiian” identification in Hawaii is characterized by a great deal of admixture, and within their sample only ~50% of the ancestral contribution within this population was Polynesian (the balance split between European and Asian). The figure suggests that subjective self assessment of ancestral quanta is generally accurate, though there are a non-trivial number of outliers. Dienekes points out that the same dynamic holds (less dramatically) for Europeans and Japanese populations within their data set.

All well and good. And I like these sorts of charts because they’re pithy summations of a lot of relationships in a comprehensible geometrical fashion. But they’re not reality, they’re a stylized representation of a slice of reality, abstractions which distill the shape and processes of reality. More precisely the x-axis is an independent dimension of correlations of variation across genes which can account for ~7% of the total population variance. This is the dimension with the largest magnitude. The y-axis is the second largest dimension, accounting for ~4%. The magnitudes decline precipitously as you descend down the rank orders of the principle components. The 5th component accounts for ~0.2% of the variance.

The first two components in these sorts of studies usually conform to our intuitions, and add a degree of precision to various population scale relations. Consider this supplement chart from a 2008 paper (I’ve rotated and reedited for clarity):


pcamyers

The first component separates Africans from non-Africans, the latter being a derived population from a subset of the former. The second component distinguishes West Eurasians from East Eurasians & Amerindians. These two dimensions and the distribution of individuals from the Human Genome Diversity Project reiterates what we know about the evolutionary history of our species.

And yet I wonder if we should be careful about the power of these two-dimensional representation’s in constraining us excessively when we think about genetic variation and dynamics. Naturally there is the sensitivity of the character of dimensions upon the nature of the underlying data set upon which they rely. But consider this thought experiment,

Father = Japanese
Mother = Norwegian
Child = Half Japanese & Half Norwegian

If you projected these three individuals upon the two-dimensional representation above of the worldwide populations the father would cluster with East Asians, the mother with Europeans, and the child with the groups who span the divide, Uyhgurs and Hazaras. So on the plot the child would be far closer to these Central Asian populations than to the groups from which its parents derive. And here’s a limitation of focusing too much on two-dimensional plots derived from population level data: is the child interchangeable with a Uyghur or Hazara genetically in relation to their parents? Of course not! If the child was a female, and the father impregnated her, the consequence (or probability of a negative consequence) would be very different than if he impregnated a Uyghur or Hazara woman.

The reason for this difference is obvious (if not, ask in the comments, many readers of this weblog know the ins & outs at an expert level). Abstractions which summarize and condense reality are essential, but they have their uses and limitations. Unlike physics biology can not rely too long on elegance, beauty, and formal clarity. Rather, it always has to dance back between rough & ready heuristics informed by the empirics and theoretical systems which emerge from axioms. Usually a picture has its own sense. But the key is to be precise in understanding what sense it makes to you.

The Chinese Muslims

The post is titled the Chinese Muslims, not the Muslims of China. One may make a semantic distinction here in that the latter connotes the residence of a Muslim community within Chinese society, while the former indicates members of Chinese society who happen to be Muslim. Such black and white dichotomies are naturally artificial, but to a large extent the Uyghurs of Xinjiang fall into the category of a group of Muslims (of Turkish language) who happen to fall within the boundaries of the modern Chinese state (thanks to that inheritance of the Chinese state of the full expanse of the Manchu Empire of the 18th century). On the other hand, the Hui people are arguably more a Chinese people who happen to be Muslim.

For more on the topic, please see my blog post at the Islam in China website. It was submitted a while back, but it only went up recently.

Doing evolution’s sums

PLoS Biology has a review of Elements of Evolutionary Genetics up, Evolution Is a Quantitative Science:

But why has evolutionary genetics stood apart from biology’s resolutely qualitative, rather than quantitative, tradition? Most remarkably, while biomechanics employs the laws of physics, and biochemistry is founded on the quantitative science of chemistry, evolutionary genetics is based on axiomatic foundations that are entirely biological, and yet are capable of precise mathematical formulation. The rules of Mendelian genetics, encapsulated by unbiased inheritance and random mating in a diploid genetic system, predict Hardy-Weinberg frequencies, the binomial sampling of gametes in finite populations determines the properties of genetic drift, and, with a Poisson process of mutation, the complex theory of neutral genetic variation can be established on the basis of very simple assumptions.

A few books to get a historical perspective of the origins of modern evolutionary genetics (albeit with a pop gen focus), The Origins of Theoretical Population Genetics, Sewall Wright and Evolutionary Biology and R.A. Fisher: The Life of a Scientist.

The genes in Spain fall rather evenly

A new paper is out which drills down a bit on the genetic substructure in Spain. Genetic Structure of the Spanish Population:

Background
Genetic admixture is a common caveat for genetic association analysis. Therefore, it is important to characterize the genetic structure of the population under study to control for this kind of potential bias.

Results
In this study we have sampled over 800 unrelated individuals from the population of Spain, and have genotyped them with a genome-wide coverage. We have carried out linkage disequilibrium, haplotype, population structure and copy-number variation (CNV) analyses, and have compared these estimates of the Spanish population with existing data from similar efforts.

Conclusions
In general, the Spanish population is similar to the Western and Northern Europeans, but has a more diverse haplotypic structure. Moreover, the Spanish population is also largely homogeneous within itself, although patterns of micro-structure may be able to predict locations of origin from distant regions. Finally, we also present the first characterization of a CNV map of the Spanish population. These results and original data are made available to the scientific community.


They used a 160 K SNP-chip for this, though for the PC charts below they were constrained to ~100,000 SNPs. Nothing too revolutionary in the paper. The fact that Spaniards have more haplotype diversity vis-a-vis the “CEU” sample in the HapMap, which consists of Utah Mormons, isn’t too surprising, since those individuals are Northern European and Northern Europeans tend to be a touch less diverse than Southern Europeans (more heterozygosity in Southern Europe than in the North). A common explanation for this is that Northern European populations emerged as subsets of Southern populations which expanded out of Ice Age “refugia” within the last ~10,000 years or so, and this migratory process would have induced some bottlenecks and so reduced their diversity. The findings in this paper are broadly consistent with the idea that Spain was a refugium, and so one of the sources of the population of Northern Europe. But, note that there are lots of controversies about recent European demographic history right now, so I wouldn’t take the aforementioned model as a given. Also, one major issue which sticks out is the lack of Basque populations in the sample, since that’s a group which has long been of interest, and some aspects of many demographic scenarios hinge on their nature. No surprise that Visigoths, Berbers and Arabs didn’t perturb these results too much. I believe that these groups did arrive in Iberia in large numbers, but on a relative scale their proportions were small and they probably didn’t alter Spain’s basically genetic character.

Below are some charts of note.

First, dimensions of genetic variation in the Spanish population using 100,000 SNPs by locality where the sample was collected.

spain1

If some of the localities were as obscure to you as me, here is the PC chart with a subset of them rotated and superimposed upon a map of Spain.

spain2

Finally, here are the Spanish samples plotted in relation to two HapMap populations, the CEU (American whites of Northern European ancestry) and TSI (Tuscans from Italy).

spain3

There are a few outliers here in relation to their putative population cluster, but in general the three groups are nicely separated as expected. Spain is bounded by water and a rather imposing mountain range. These serve as natural barriers to gene flow. But within the peninsula it’s dominated by a high plateau. I really don’t have an intuitive understanding of whether the spatial distribution of Spain’s people (which for ecological reasons probably can be extrapolated back to antiquity) should homogenize it through a circular pattern of gene flow, but perhaps that’s what these data are showing. I am a bit wary of saying that Spain is internally homogeneous without referencing other European populations of the same scale in detail. Perhaps what this group found is what you’d find on this scale with this chip; not much.

Cite: BMC Genomics 2010, 11:326doi:10.1186/1471-2164-11-326

H/T Dienekes

ResearchBlogCast #7

Here. The paper is Coordinated Punishment of Defectors Sustains Cooperation and Can Proliferate When Rare. The blog post highlighted is Punishing Cheaters Promotes the Evolution of Cooperation.

It is probably obvious that I’m not on the internet as much right now. But I’ve been thinking on the topic of this paper for a few days, and plan on putting together a post when I have something interesting to say, and nothing interesting to do off-net.

P.S. We decided to bring Kevin Zelnio back on.

How the Swedes became white

vikingsA few weeks ago I read Peter Heather’s Empires an Barbarians, but I had another book waiting in the wings which I had planned to tackle as a companion volume, Robert Ferguson’s The Vikings: A History. Heather covered the period of one thousand years between Arminius and the close of the Viking Age, but his real focus was on the three centuries between 300 and 600. It is telling that he spent more time on the rise and expansion of the domains of the Slavic speaking peoples than he did on the Viking assaults on Western civilization; an idiosyncratic take from the perspective of someone writing to an audience of English speakers. But within the larger narrative arc of Empires and Barbarians this was logical, the Slavs were far closer to the relevant action in terms of time and space than the Scandinavians who ravaged early medieval rather than post-Roman societies (where the latter bleeds into the former is up for debate). In Heather’s narrative the Viking invasions were a coda to the epoch of migration, the last efflorescence of the barbarian Europe beyond the gates of Rome before the emergence of a unified medieval Christian commonwealth. And these are the very reasons that Robert Ferguson’s narrative is a suitable complement to Peter Heather’s. Ferguson’s story begins after the central body of Heather’s, and most of its dramatic action is outside of the geographical purview of Empires and Barbarians. In The Vikings the post-Roman world has already congealed into the seeds of what we would term the Middle Ages, and it is this world which serves as the canvas upon which the Viking invasions are painted. Aside from what was Gaul the world of old Rome is on the peripheries of Ferguson’s narrative.


It was refreshing to me that the author of The Vikings makes a concerted effort toward balance (despite what I perceive to be his clear identification as a scholar of the Vikings with the Scandinavian peoples of the period in a broadly sympathetic sense). He explicitly lays out the tendency of previous scholars and commentators to lean excessively toward the Vikings or their victims in weighing the veracity of narratives, or ascribing a moral high ground to one particular vantage point. More common perhaps of the two is the tendency toward depicting the Vikings in the manner that Christians of the time viewed them, as an avaricious force of nature whose role was to punish civilization for its sins (in our era we may secularize the events, but the tendency toward viewing barbarians as deterministic elements operating upon civilized agents often remains). As a reaction against such a one-sided classic framing some scholars have reinterpreted the Vikings as well-armed traders who were simply misunderstood and libeled by their Christian antagonists. In this telling the Vikings sacked the monasteries because they were locked out of trade networks due to their status as cultural outsiders. Raiding was simply a substitute for trading. Both of these normative and simplified frames really belong in a “First Book” for children; individual humans are more complex than that, and history is more complex than individual humans. When it comes to history true objectivity is probably impossible, but admitting that past workers have had strong biases is probably a good place to start.

In The Vikings Robert Ferguson regales us with in large part is an ancient “Clash of Civilizations.” He notes that the sources invariably distinguish between Christians and Heathens as opposed to English and Norse (or Franks and Norse), and in keeping with this he lays out a dichotomy between Christian civilization and “Heathendom.” Our view of the past is colored by the reality of the victory of the former against the latter, but the slow and inexorable expansion of the arc of Christian civilization among the Scandinavians which we view in hindsight as a process which has a clear terminus actually took nearly five centuries, with most of the Christian success at the expense of the Heathens occurring within the last one hundred and fifty years (despite missionary endeavors across the whole period, mostly out of Bremen and Hamburg). Ferguson convincingly argues the Heathens had a sense of their own identity, distinctiveness, and even superiority, in relation to the Christians during this period when Scandinavia was outside of the boundaries of the West. This is actually most evident in Muslim sources, who had more distance from the pagan Scandinavian culture and so could view it with more ethnographic third party objectivity (the Muslim sources were often engaging in trade or diplomacy). They report for example the argument of one Scandinavian that his peoples’ practice of burning was far superior to the inhumation that was the norm among Christians, Muslims and Jews, because the transition to the afterlife is far faster with the rapid disintegration of the body, as opposed to decomposition and later consumption by “worms” (this critique is almost a trope from what I can tell when it comes to the perception of peoples who burn the bodies of their dead of the customs of those who bury). What we see here is not some deep philosophical sense of superiority, but the native chauvinism and ethnocentrism which most peoples have in regards to their own mores and traditions. Heathens were not simply a negation of Christian civilization, in contemporary parlance they were an indigenous folk of northern Europe resisting the expansion of an international and globalist Christian culture.

A more historically grounded rationale for Heathen sense of distinction from Christians, and their hostility toward Christian civilization generally, is the real history of forced conversion which they experienced at the hands of Christian powers. In particular the author points to the conquest and conversion of the Saxons by Charlemagne as a turning point. These German tribes were on the margins of the Scandinavian world, so word of their oppression, and ultimate destruction of their native traditions at the hands of outsiders, must have percolated to the north (Saxon warriors took refuge among the Danes). In The Vikings the author explicitly suggests that the savagery of the Norse in their assaults on Christian monasteries may be connected to the fear and hostility engendered toward the Christian religion by these instances of mass forced conversion and aggression. The analogy here may be the Boxer Rebellion, where indigenous anger at the expansion of foreign powers and their cultural mores exploded in targeted violence. The brutal nature of Christian conversion is highlighted vividly by the anecdote of Olaf Tryggvason, Norway’s first explicitly Christian king, threating to kill the three year old son of a British Norse warlord in front of his father unless he and his people submitted to immediate baptism. Ferguson observes that the Christian chronicler records this action approvingly, but certainly this sort of behavior on the part of Christians against the Heathen Scandinavians integrated over centuries may account for some of the motive for the violence of the Vikings against Christian holy sites and institutions. For the Heathen the Christian was the threatening Other, and so thoroughly dehumanized.

But the relationship of Heathendom to Christian civilization, and the local and indigenous Scandinavian tradition to global cultures, was not simply one of hostility and mutual exploitation and brutality. One of the interesting aspects of the Scandinavian expansion of the 8th to 10th centuries is its geographic range. Their presence on the northwestern fringes of Europe as Vikings is well known in the English speaking world. But Scandinavian raiders were prominent in Muslim Spain, and even broke into the Mediterranean. Of more permanence was the influence and power of a group known as the Rus across the vast swaths of land from the Baltic to the Caspian. It seems probably that Slavicized Rus were the core of the early polities of Novgorod and Kiev, which later gave rise to Russian identity. In the generation of the grandfather of Vladimir I of Kiev, credited with bringing the Russians to Christianity, the elite of the Kiev seemed invariably to possess Scandinavian names. This was an empire of war, trade and colonization along the fringe of early medieval Christendom, and sweeping down toward the margins of the world of Islam on the Caspian.

Why the expansion? A conventional explanation has been overpopulation. This doesn’t hold water, in pre-modern societies Malthusian dynamics were always at play. That is, growth was very slow because high fertility was counterbalanced by high mortality. In the event of an epidemic there may be a period when demographic expansion is possible, but these would be transient phases. There is evidence that across northern Europe in the first millennium there was underway a transition toward more productive forms of agriculture which allowed for a larger basal population, but this was a general feature of European societies, not one restricted to Scandinavia. In fact the increase in population was probably most pronounced in two regions to which the Vikings were most drawn to plunder: northern France and the Low Countries. And this may explain a cause for the Viking expansion, they sought wealth, and more wealth was to be gotten in the Christian lands than within Heathendom.

Ferguson seems to posit both push and pull dynamics. The push dynamics had to do with a restructuring of Scandinavian society in the centuries before 1000. This involved the emergence of more powerful apex leaders who marginalized the numerous figures lower down on the status hierarchy. A shift toward a more centralized political order would have concentrated power and wealth in the hands of few at the expense of the many. In this case the many in fact is going to be a minority of the population, free males who are part of the political and military class, and who collect rents from peasants and extract labor out of their human property (thralls). This dynamic is not conjecture, the migration of warlords to the British Isles in the wake of the rise of Harald I of Norway is apparently documented. The rise of a Great Man seems to invariably come at the expense of many less great men in a zero sum world. Similarly, the arrival of the reputed sons of Ragnar Lodbrok to British Isles may have had to do with political events in Denmark in the decades before the reemergence of the Jelling dynasty. But this push process can not be decoupled from wider social and historical events. In other words, the parameter is not purely endogenous. Rather, the events within Scandinavia were strongly shaped by the emergence of a global political and economic order which Heathendom was a participant, if at times a reluctant and belligerent party. Scandinavia’s political connection to other parts of Europe was clear even in the Late Antique period; Scandinavian warriors and kings were a presence at the courts of post-Roman figures such as Theodoric the Great of the Ostrogoths. Conversely, German peoples who were on the losing side in the post-Roman scramble would on occasion exercise an exit option of migration back to their homelands, which sometimes included southern Scandinavia.

So the elites of Scandinavia were aware of the wider world well before the Viking Age, and certainly had a sense of the possibilities of unitary political systems as far back as Classical Antiquity. There is also a great deal of circumstantial evidence that the elaborated nature of late Scandinavian paganism has much do with the model which Christianity presented as a complex institutional religion. The mythos around Balder has often be assumed to have been influenced by the Christian mythos around Jesus, but we need not hinge our inference on literary recollections which may have been influenced by later generations who were Christian. There is a great deal of evidence from the Wends and Lithuanians, who persisted in their paganism even longer than the Scandinavians, of the development of a pagan “anti-Christianity” around which their ethnically based polities could coalesce (there are references to a shadowy pagan equivalent to the pope among the later Lithuanians during the apogee of their empire in the 14th century). In Empires and Barbarians and Empires of the Silk Road the authors argue that the emergence of more complex and large scale political and social orders beyond the limes of settled agricultural civilizations dominated by literate elites was a reaction to developments within the ecumene. For the nomadic confederations of the east Eurasian steppe it was the unification of China under Qin Shi Huangdi. For the Germanic tribes beyond the Roman limes it was Rome itself, which periodically erupted beyond its borders to engage in punitive expeditions (archaeology has been uncovering unrecorded Roman expeditions into Germania in the century following the defeat of Varus’ legions). For the Scandinavians it seems to have been the rise of the Frankish political order, and particular the Carolingian dynasty, which annexed and Christianized the lands of the Saxons just to the south of Scandinavia which served as a spur to their social and political revolution.

With the rise of a powerful Christian state to its south bent on cultural, political and economic conquest and assimilation, there would naturally have been greater self-consciousness of the peoples of Scandinavia in regards to their indigenous traditions. Despite periodic attempts by powerful aristocrats and kings from the 9th century on there was stubborn resistance from sub-elites in acceding to the shift from their customary cults to the Christian religion. I think a little bit of Homo economicus in terms of rational behavior might allow us to explain this disjunction between the apex elites in the form of kings, and sub-elites. In societies without a tradition of autocracy under a singular individual a broad level of consent from numerous sub-elites of modest means was necessary for an individual to rise to kingship. But these sub-elites may not have been economically advanced enough to see any gains in integration into a globalized political order where their nations were part of a commonwealth of Christian monarchies. Rather, they perceived a dispossession of their traditional cultic roles under the aegis of a transnational church apparatus (albeit, one which operationally co-opted local elites rather rapidly after Christianization by assimilating them into the clerical superstructure). Put more simply, there was great gain to monarch in becoming part of the international order, but little for the population as a whole, even among the lesser nobility, who were dependent on local rents, not international trade or conquest.* In the world of the Malthusian trap the lives of the peasantry would be little changed by an ideological shift on high, so they were of no consequence (in fact, Protestant Reformers routinely complained that the Church had left the peasantry of many nations barely Christian in anything but name).

Of course there was a way for sub-elites to become wealthy rather rapidly: steal from wealthier societies instead of depending on protection money (rent) from your poor peasants. It is notable that the Viking Age spans the period which saw the decline of Charlemagne’s political system, but before the emergence of the medieval antecedents of the nation-states which would crystallize in the early modern period. It was also during this time that northern France and the Low Countries, and to a lesser extent England, saw an expansion of aggregate wealth because of improved agricultural techniques and tools such as the three field system and the mould-board plough as well as the beginning of the Medieval Climatic Optimum. The idea that one could steal wealth was not an innovation of the Vikings, Charlemagne’s campaigns were in part motivated by the need to generate plunder to satisfy his vassals. Similarly the Roman wars of conquest were magnificently lucrative for the Republic’s aristocracy, and it can be argued that the wealth stolen from the early conquests were critical in maintaining Roman dynamism. It is possible that no imperial conquest after that of Dacia in the early second century was profitable, and it is this period which saw the high water mark of the Roman civilization, the century of the Good Emperors.

Shifting back to the Vikings, the model then is rather easy to summarize. Step 1, Western civilization in the form of the Christian Frankish polities push north and east, toward the fringes of Scandinavia. Step 2, this results in a coalescence of counter-identities among the populations which are being impinged upon and destabilized. In the case of the Saxons under Widukind and his confederates resistance was futile, and they were absorbed into the new Christian order (in fact, Saxon Christian monarchs in the 10th century placed so much pressure on pagan Denmark that it probably facilitated the final absorption of the Jelling monarchy into the Christian state system as another lever to maintain their independence). But for populations further out, as in Scandinavia, or in the eastern marches which were inhabited by the West Slavs, the Frankish expansion lost its steam before it could fully absorb them. This left these populations in a stronger position in terms of the ability to engage in coordinated action than before, because they now had a common identity in the face of Christian expansion as well as more powerful military leaders who had come to the fore in the face of the threat from the alien superpower. Step 3, the collapse of the Frankish Empire into sub-states leaves the margins of Christian civilization more vulnerable as none of these polities now can bring to the fore overwhelming force against small groups of raiders. Step 4, the integrative phase within the cultures outside of Christian civilization combined with wealth differentials across civilizational boundaries produce the convulsions which result in the out-migration of militarized sub-elites. They are well aware enough of wealthier societies to understand the cost vs. benefit for them, and they lack ideological affinity with those wealthier societies, so their actions are unencumbered by any moral or ethical framework. In other words, Heathens and Christians exhibited a much less robust sense of empathy toward each other than they did those from within their own culture, so the depredation of one upon the other was particularly savage and utility maximizing (in the Middle Ages the paganism of many Baltic populations was somewhat convenient because Christians were allowed to enslave pagans, making them extremely economically profitable as tenants since they lacked human rights). Step 5, the military assault upon civilization by the barbarians eventually peters out and results in the assimilation to a great extent of the barbarians into the civilized order. Once the windfall wealth is spent the inevitable consequence is the absorption of the less numerous and organized society into the more numerous and organized one.

These steps in general seem broadly applicable to the post-Roman and post-Han dynasty periods in Europe and China as well. In the end the barbarian societies which initially have a strong aversion to the civilized societies whom they oppose, are oppressed by, and often conquer, became ideologically identified with those societies. This generally occurs through religion, but also often through other aspects of assimilation in identity (e.g., the Franks became the Latinate French, the barbarian groups in China often became Chinese speaking and switch their ethnic identity to Han). The main exception to this general trend which I can think of is the case of the Arab Muslim conquest, and in this case the barbarians brought with them an ideology which was robust and in large part mimicked that of civilized societies.**

We do not live in the world of the Vikings, where Malthusian parameters reign supreme, elites live off the toil of peasants, and religion is a matter of life and death (excepting parts of the Muslim world like Sudan or the Communist world like North Korea). But cultural identity still matters. Today when we speak of “indigenous people” we allude to relics of a bygone age, small-scale cultures on the margins. But as recently as one thousand years ago vast swaths of Europe, in particular its north and east, were populated by indigenous peoples, attempting to preserve their ancient traditions and customs in the face of Christian globalization. More broadly, in the period between 500 and 1000 numerous peoples outside of the Eurasian Rimland, to the north, east and west, contingent upon the point of reference, were affected by the expansion of ideological systems from the Rimland civilizations, which arrived through military, demographic and economic means. The Gauls of France lost almost all unique aspects of their identity, their language, their religion, even their name for themselves. Other populations, such as the Germans and the Turks retained much of their identity, and profited through integration into a broader civilization through which they channeled their cultural influence. But this process took centuries, and was not without tumult. The Viking Age was not an act of God, it was not an isolated case. It was rather an instance of a general process whereby the cultural configurations of the World Island were assigned in a manner which we would recognize today, with civilizational boundaries hardening into forms which were robust to exogenous shocks.

One interesting aesthetic observation which I will take away from The Vikings: A History is that the peoples of the north were generally tattooed and made recourse to eye shadow and other such body adornment. Christian sources point to this only in a negative fashion, that is, the practice is explicitly banned for Christians in the north, presumably because this was previously a common practice (as well as the consumption of horseflesh, which had cultic significance). But the Muslim sources describe the obsession of the northern people with aesthetic detail thoroughly, and it notable to me that Otzi the Iceman was also tattooed. These sorts of markings have obvious functional purposes, in identifying a member of one tribe from another in an indelible fashion, but they also are perhaps reflective of societies where aesthetic expression was personalized and small scale. Their Pantheons were their bodies. This is familiar to us today from small-scale societies and small indigenous groups, who maintain these traditions and this outlook. It was only 1,000 years ago that many European peoples were still vigorously adhering to these folkways, before they became Christian, and therefore white.

Note: I have avoided discussing the likely brisk trade between Scandinavia and the pre-Muslim and post-Muslim Middle East, which is vividly documented in coinage. The blockage of this trade by steppe powers such as the Khazars has been argued to be one of the major motives for the Rus exploration of the Dnieper and Volga river systems. It’s an interesting story, but takes us a bit afar, though illustrates another economic motive in the barbarian expansion.

Additionally, in keeping with the tone of the book I have exhibited some broad empathy to the Viking societies transformed beyond recognition by assimilation into European society around 1000. But I will add into the record that as a personal normative preference I believe that cultural homogeneity, in particular in language and religion, can often be beneficial in generating economic and ethical economies of scale. Though I believe that there are diminishing returns on the margin here (there is harm when police states attempt to impose one language and one religion on the whole populace through extreme tactics).

* In the late Roman Empire the aristocratic nobility remained pagan far longer than the Emperors and the service nobility dependent upon the Empire, as opposed their personal wealth.

** There is a great deal of debate as to how Islam arose, and some scholars argue that Islam is actually a relatively late development out of a sect of Arab Christians. If this is true the Islamic exception is no exception at all, but serves as an alternative history where the Goths remain Arian and assimilate their Roman subjects to their religion and language.

Chickens are like people

In that their demographic history is complicated. The Origin and Genetic Variation of Domestic Chickens with Special Reference to Junglefowls Gallus g. gallus and G. varius:

… domestic chickens diverged from red junglefowl 58,000±16,000 years ago, well before the archeological dating of domestication, and that their common ancestor in turn diverged from green junglefowl 3.6 million years ago. Several shared haplotypes nonetheless found between green junglefowl and chickens are attributed to recent unidirectional introgression of chickens into green junglefowl. Shared haplotypes are more frequently found between red junglefowl and chickens, which are attributed to both introgression and ancestral polymorphisms. Within each chicken breed, there is an excess of homozygosity, but there is no significant reduction in the nucleotide diversity. Phenotypic modifications of chicken breeds as a result of artificial selection appear to stem from ancestral polymorphisms at a limited number of genetic loci.

I wonder if domesticates in particular exhibit these more complex reticulated patterns in their phylogenies because they spread along human trade routes.

Daily Data Dump (Wednesday)

Insulin Signaling and Dietary Restriction Differentially Influence the Decline of Learning and Memory with Age. I’d be curious what people who practice dietary restriction would say (I know many scientists do this, so it isn’t just quacks).

Spicing the Meat Also Cuts the Cancer Risk, Research Suggests. Spicy foods have antioxidants.

Punishing Cheaters Promotes the Evolution of Cooperation. The big long-term issue is how to explain complex societies from their basic atomic units and elementary dynamics.

Why Science Journals Need to Move to Online Only Publishing. Fair enough, but sometimes the constraints of a print format do impose some discipline.

Massachusetts: Student Accused of Faking His Way Into Harvard. Sounds like a sociopath, though perhaps a touch on the arrogant and dumb side.