Razib Khan One-stop-shopping for all of my content

May 31, 2010

Beyond visualization of data in genetics

Filed under: Genetics,Genomics,Population genetics — Razib Khan @ 6:08 am

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.

May 29, 2010

The Chinese Muslims

Filed under: China,Hui,Islam,Religion,Uyghur — Razib Khan @ 1:04 pm

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.

May 28, 2010

Katz

Filed under: Blog,Katz — Razib Khan @ 10:53 am

babygirl3

lazydude
lazysunday1

May 27, 2010

Doing evolution’s sums

Filed under: Evolution,Evolutionary Genetics — Razib Khan @ 3:10 pm

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

Filed under: Genetics,Genomics,Spain — Razib Khan @ 3:23 am

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

May 25, 2010

ResearchBlogCast #7

Filed under: Blog,ResearchBlogCast — Razib Khan @ 1:19 pm

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.

May 24, 2010

How the Swedes became white

Filed under: Anthroplogy,History,Norse,Scandinavia,Vikings — Razib Khan @ 6:15 am

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.

May 21, 2010

Katz

Filed under: Blog,Culture,Katz — Razib Khan @ 11:51 am

alertgirl

babygirlbabygirl2

May 20, 2010

Chickens are like people

Filed under: Genetics,Genomics,phylogenetics — Razib Khan @ 3:17 am

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.

May 19, 2010

Daily Data Dump (Wednesday)

Filed under: Blog,Daily Data Dump — Razib Khan @ 2:23 pm

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.

Fundamentalists have a smaller vocabulary

Filed under: data,Data Analysis,Fundamentalism,GSS,Religion — Razib Khan @ 1:15 pm

In the comments below a question was asked in regards to “fundamentalist” vs. agnostic Jews. I put the quotations around fundamentalist because the term means different things in different religions. As for the idea of an agnostic Jew, remember that Jews are a nation (ethnicity) as well as a religion, and that religious belief has traditionally been less explicitly emphasized than religious practice.

It wasn’t too hard to find some answers in the GSS. I used the somewhat crude “BIBLE” variable again. Remember that BIBLE asks if the respondent believes that the Bible is the literal and inerrant Word of God, the inspired Word of God, or a book of fables. I reclassified these as Fundamentalist, Moderate, and Liberal, respectively. There are two variables I used in the first chart, JEW and RELIG. The former looks just as Jews, and breaks down by Orthodox, Conservative and Reform. The latter I combined with BIBLE to bracket out Fundamentalists, Moderates and Liberals of each religious group. The vocabulary test scores are from WORDSUM. Remember that they correlate 0.71 with adult IQ. Because the sample size for Jews was so small I included 95% intervals so you can modulate confidence appropriately. I limited the sample to whites.


fundwords1

Jewish readers can correct me if I’m wrong, but I am to understand that the gap between Conservative and Reform is actually not very large in terms of belief and practice today, as it may have been in earlier decades. In fact the two movements emerge as much from cultural differences between earlier German Jewish immigrants and the later Eastern European migration. And Orthodoxy and a Protestant understanding of “fundamentalism” do not necessarily overlap. It is notable that for the other groups the Fundamentalist segment had smaller vocabularies. This probably aligns with our intuition. But I was curious, is the pattern among Protestants a regional effect? It isn’t. When I controlled for region the same pattern exists. So rather than plotting that chart, I decided to look at the combination of educational attainment and Fundamentalist orientation for white Protestants only (the sample sizes here are large).

fundwords2

To some extent the pattern is as you’d expect. Those with less education have smaller vocabularies. But notice the step-wise pattern. Fundamentalists with a greater level of education than religious liberals do not necessarily have much larger vocabularies. That’s interesting to know.

The trajectory of American Jews, lessons from history

Filed under: Culture,Jews — Razib Khan @ 7:07 am

I notice that a peculiar piece of datum from First Things contributor David Goldman is being passed around, repeated by Ross Douthat no less. Goldman states:

Beinart offers a condescending glance at the “warmth” and “learning” of Orthodox Jews, but neglects to mention the most startling factoid in Jewish demographics: a third of Jews aged 18 to 34 self-identify as Orthodox. “Secular Jew” is not quite an oxymoron–the Jews are a nation as well as a religion–but in the United States, at least, secular Jews have a fertility barely above 1 and an intermarriage rate of 50 percent, which means their numbers will decline by 75 percent per generation. It is tragic that the Jewish people stand to lose such a large proportion of their numbers, but they are lost to Judaism in general, not only to Zionism. That puts a different light on the matter.


A reader of Goldman’s who happens not to be stupid and can actually read observes that 34% of Orthodox Jews are 18 to 24 according to the original source Goldman was citing. No surprise that Goldman makes such an error, he has a way with faux erudition which amazes the dull and dumb. In fact, the American Jewish Survey reports that 16% of Jews between the ages of 18 to 29 self-identify as Orthodox.

With that small error out of the way, in regards to the future of the American Jewry I think the story outlined in Amos Elon’s The Pity of It All: A Portrait of the German-Jewish Epoch, 1743-1933 may serve as a possible vision of the future. Elon notes that almost the whole of the German Jewish elite of the late 18th and early 19th century converted to Christianity. Moses Mendelssohn’s last Jewish descendant died before the 20th century; the rest of his descendants had become Christians. Karl Marx and Heinrich Heine were not atypical. But there was a large German Jewish community in the early 20th century, though even that was being eroded by intermarriage and conversion. If Elon is correct that the bulk of the 19th century Jewry became Christian, where did the Jews of the 20th century come from? It seems that as the German Jewish burghers abandoned the Reform temples for Lutheran churches, their spots were filled by assimilating Eastern European Jews who were immigrating into Germany and taking over the institutions which the earlier community had built. They were heirs in spirit, if not blood, to Moses Mendelssohn. In other words, a large bumper crop of Orthodox youth may be the salvation for the Reform and Conservative movements. There may be no third generation Reform, but not all third generations beyond Orthodoxy remain Orthodox either.

We live in Utopia!

Filed under: Culture,Futurism,Matt Ridley,Optimism — Razib Khan @ 6:40 am

Rod Dreher mulls his bias toward declinism while evaluating Matt Ridley’s new book The Rational Optimist. Here’s a portion of Ridley’s argument:

But with new hubs of innovation emerging elsewhere, and with ideas spreading faster than ever on the Internet, Dr. Ridley expects bottom-up innovators to prevail. His prediction for the rest of the century: “Prosperity spreads, technology progresses, poverty declines, disease retreats, fecundity falls, happiness increases, violence atrophies, freedom grows, knowledge flourishes, the environment improves and wilderness expands.”

Dreher gloomily observes:

Well, I would certainly love to be wrong; neither I nor my descendants gain anything out of a world of decline. But it would be useful to go back and look at how 19th-century progressives expected the 20th century to be a wonderland of peace, prosperity and progress. Didn’t quite work out that way. I suspect the truth is that nobody knows anything about tomorrow, and that we can only make our best educated guesses based on history and the wisdom of experience.

Looking at the imaginings of past futurists is often pretty amusing. And Ridley’s projections of plentitude and prosperity seem to involve an extrapolation of the conditions of the past 200 years, whereby a greater and greater proportion of humanity has broken the shackles of the Malthusian trap. The reality is that for most of human history innovation was always immediately counter-balanced by population growth so that median wealth never increased. Only in the 19th century did a new social pattern and demographic dynamic emerge whereby prosperous individuals did not reproduce to a greater extent in keeping with their greater wealth. Rather, societies went through the “demographic transition”, and greater wealth for future generations became the new norm. There’s no reason that this doesn’t have to be a transient state between long epochs of Malthusianism, so I think assuming that the new normal is the normal forever more is a step too far.

That being said, it seems to me that we do truly live in a utopia in any objective terms when viewed from the 19th or early 20th centuries. The Dickensian lot of the poor no longer characterize the lower classes of the developed world, and obesity is actually a feature of the lives of the poor, as opposed to starvation. The period between 1800 and 1970 witnessed a massive shift in earning power to the working classes, and a closing of the wage gap between skilled and unskilled workers. Infection has not been abolished, but it is no longer so deadly. Violence has decreased, despite the periodic outbreaks of industrialized genocide. And so on.

Utopia is always over the hill, and the new normal was the aspiration of the past, not the bliss of the present. But the past and the present and the future are actually instantiated simultaneously. Consider three airports which I have sharp experiences of. Dhaka airport is the past. John F Kennedy airport is the present. And Munich airport is the future. If you took a flight from Dhaka to Munich you would have thought that you’d been transported to utopia.

I don’t take these utopian dreams as an injunction toward complacency. Rather, we should appreciate all that modern science, technology and government has achieved, and be vigilant. Before we despair at all which might be lost, remember this famous chart:

sala-fig-1-1

May 18, 2010

Fecundity vs. lesbianism; what’s more atypical?

Filed under: Anthroplogy,antonin scalia,Culture,lesbianism,natalism — Razib Khan @ 9:52 pm

Sex Lives of Supreme Court Justices:

Now that the sex lives of Supreme Court justices have become grist for commentators, we are finally free to discuss a question formerly only whispered about in the shadows: Why does Justice Antonin Scalia, by common consent the leading intellectual force on the Court, have nine children? Is this normal? Or should I say “normal,” as some people choose to define it? Can he represent the views of ordinary Americans when he practices such a minority lifestyle? After all, having nine children is far more unusual in this country than, say, being a lesbian.

The GSS can answer this question. Sort of. It turns out that the highest number of children it asks about are “8 or more.” Limiting the sample to 1998-2008 so it has some contemporary relevance, ~1% of respondents in the GSS has 8 or more children. But that’s not quite fair, since many respondents are young adults, or just starting their families. Limiting the sample to those who are 60 years or older you have ~3.5%. Limiting to 70 and above it goes up to ~4.5%. Scalia is 74 years old, so I think it might be appropriate to judge him by his generation, though the relative gerontocracy of the Supreme Court, and American politics in general, might warrant examination. In 2008 in the GSS asked about sexual orientation, and ~2% of women stated they were lesbian, gay or homosexual. So whether Scalia is more abnormal than a lesbian measured against the general population depends on the reference population you use. For his generation, probably not, but for this generation, perhaps.

On the personal genomics turning point

Filed under: Genetics,Genomics,Medicine,Personal genomics — Razib Khan @ 3:09 pm

From fantasy to fact? Personal Genomics, tipping points and a personal perspective:

But now I think we’ve turned a corner. It feels, to mix metaphors, that we’ve hit a tipping point. The Human genome project, the mapping and sequencing of the/a human genome from 1990 to 2003, cost approximately 2,700,000,000 dollars (that’s 2.7 billion, I wanted to get all the zeros in). Celera did the genome for 300,000,000. The cost of sequencing an entire human genome has been plummeting ever since. In 2007, the cost of sequencing the genome of James Watson (co-discoverer of DNA) was about 2,000,000. The today cost is about 10,000. Complete Genomics and other companies are on the march to quickly reducing the cost of sequencing a genome under 1,000.

So, within a year, the cost of sequencing your, my, genome will reach 1,000. If not less. We’ve seen this coming for years now, and it’s upon us. But what does it mean? A lot of data. But data means nothing without context and analysis. Sequencing my genome would be a waste of 1,000 dollars if I gleaned nothing from it.

I can believe that we’ll be able to get a tarball with our own full sequence for a reasonable price in a few years. Cheaper than orthodontia and cosmetic surgery even. Though the utility in prevention and treatment is a different matter. Most people already have a treasure trove of data through family history, and that doesn’t seem to change behavior for many in the short-term. Once the magical power of genomics wears off I suspect that knowing you have variant X with risk Y will be less transformative than not.

Betting on prediction and hypotheses

Filed under: Culture,Journalism — Razib Khan @ 2:18 pm

Felix Salmon points to someone who asks, Is the European crisis good for America? A piece at Politico suggests that Midterm fury might leave Nancy Pelosi safe. Journalism of this sort would get very boring, very soon, if the journalists actually had to place any money on their musings, either directly by changing their investment portfolio, or getting involved in betting markets like Intrade.

Daily Data Dump (Tuesday)

Filed under: Blog,Daily Data Dump — Razib Khan @ 2:02 pm

Gene Tests For Everyone. Probably not much value in most of these tests for most people right now. Also, many of these common variants have been found in subject populations which are European, so if you are Colored it might not tell you anything relevant (i.e., the SNP which is identified as a risk has only been shown to have an effect in Europeans, or, you know you have a trait but it turns out you don’t have any of the “common” variants, perhaps because your population has different variants which are common).

Return of the Neanderchimps. Complex demographic history for one and all! I do find the genetic isolation between Bonobos and Common Chimpanzees interesting. Apparently the Congo river was an imposing enough barrier to allow for allopatric speciation. I wonder if this can tell us about the fear our own ancestors might have had in traversing water barriers.

A New Clue to Explain Existence. Physicists can always make themselves look the non-devilish scientists by inserting a reference to God.

Only Processed Meat Boosts Diabetes And Heart Disease. Medicine was quackery until the 20th century. Nutritional science seems to be quackery into the 21st.

The Microcephalin Ancestral Allele in a Neanderthal Individual. No evidence for introgression/admixture at this locus.

An umbrella against the mutational showers

Filed under: Biology,Genetics,Good Genes,Selection,Sex — Razib Khan @ 2:41 am

Mutations are as you know a double-edged sword. On the one hand mutations are the stuff of evolution; neutral changes on the molecular or phenotypic level are the result of from mutations, as are changes which enhance fitness and so are driven to fixation by positive selection. On the other hand mutations also tend to cause problems. In fact, mutations which are deleterious far outnumber those which are positive. It is much easier to break complex systems which are near a fitness optimum than it is to improve upon them through random chance. In fact a Fisherian geometric analogy of the affect of genes on fitness implies that once a genetic configuration nears an optimum mutations of larger effect have a tendency to decrease fitness. Sometimes environments and selection pressures change radically, and large effect mutations may become needful. But despite their short term necessity these mutations still cause major problems because they disrupt many phenotypes due to pleiotropy.

But much of the playing out of evolutionary dynamics is not so dramatic. Instead of very costly mutations for good or ill, most mutations may be of only minimal negative effect, especially if they are masked because of recessive expression patterns. That is, only when two copies of the mutation are present does all hell break loose. And yet even mutations which exhibit recessive expression tend to generate some drag on the fitness of heterozygotes. And if you sum small values together you can obtain a larger value. This gentle rain of small negative effect mutations can be balanced by natural selection, which weeds does not smile upon less fit individuals who have a higher mutational load. Presumably those with “good genes,” fewer deleterious mutations, will have more offspring than those with “bad genes.” Because mutations accrue from one generation to the next, and, there is sampling variance of deleterious alleles, a certain set of offspring will always be gifted with fewer deleterious mutations than their siblings. This is a genetics of chance. And so the mutation-selection balance is maintained over time, the latter rising to the fore if the former comes to greater prominence.

The above has been a set of logic inferences from premises. Evolution is about the logic of life’s process, but as a natural science its beauty is that it is testable through empirical means. A short report in Science explores mutational load and fitness, and connects it with the ever popular topic of sexual selection, Additive Genetic Breeding Values Correlate with the Load of Partially Deleterious Mutations:

The mutation-selection–balance model predicts most additive genetic variation to arise from numerous mildly deleterious mutations of small effect. Correspondingly, “good genes” models of sexual selection and recent models for the evolution of sex are built on the assumption that mutational loads and breeding values for fitness-related traits are correlated. In support of this concept, inbreeding depression was negatively genetically correlated with breeding values for traits under natural and sexual selection in the weevil Callosobruchus maculatus. The correlations were stronger in males and strongest for condition. These results confirm the role of existing, partially recessive mutations in maintaining additive genetic variation in outbred populations, reveal the nature of good genes under sexual selection, and show how sexual selection can offset the cost of sex.

mutAdditive genetic variance just refers to the variation of genes which affect the phenotype by independent and usually small effects which sum together to produce the range of variation of the trait. Imagine for example that the range of variation in height within the population was 10 inches, and that there were 10 genes which varied, and that each gene exhibited co-dominance. One could construct a model where every gene pair could add 0, 0.5 or 1 inch to the height independently, so that the maximum height could be constructed by adding 10 inches to the baseline and 1 inch per locus, and the minimum height by adding no inches to the baseline when each locus is homozygous for null alleles.

Mutations can be conceived of in the same manner, with each mutation being a new variant which changes trait value. Even if most of the impact of a mutation is masked there is a small effect in the heterozygote state, and this may serve as a fitness drag. The range in mutational load can then naturally be analogized to additive genetic variance, in this case the trait under consideration ultimately being fitness, mediated through life history and morphological phenotypes.

In this report they focused primarily on the weevil’s ability to obtain resources and transform those resources into size, which correlates with greater sexual access for males and fecundity for females (ergo, greater fitness). They bred various outbred and inbred lineages across families of these weevils, because these sorts of crosses gauge the impact of masked deleterious alleles, which will manifest in homozygote state more often between related pairs who share mutations than unrelated ones. They found a correlation of -0.24 between inbreeding and breeding value; in other words the more inbred the pair the fewer offspring. The impact of these recessively expressed alleles is mitigated in heterozygous individuals, but because of the non-trivial impact the number of these alleles within an individual will determine its fitness all things equal.

328_892_F1Interestingly when background variables were controlled males tended to show the greatest fitness drag due to inbreeding depression. This would comport with models of sexual selection where males justify their expense (because they can not bear offspring) within the population by serving as the perishable dumping grounds of bad genes. In particular in a polygynous population a few healthy males with good genes could give rise to most of the next generation, and so providing the balance of selection to the background mutational rate.

Of course mating patterns vary between taxa. The more reproductive skew there is, in particular for males, the more recourse selection has every generation to dump deleterious alleles via selection. In contrast monogamous populations will have less power to expunge mutations in this fashion because there is more genetic equality across males, the bad will reproduce along with the good, more or less. Therefore a breeding experiment of weevils may have more limited insight than these authors may wish to admit. Geoffrey Miller’s The Mating Mind attempted to take the insights of sexual selection and develop a model of human evolutionary history, but it does not seem that this theory has swept all before it. Only time will tell, but until then more breeding experiments can’t help but clarify where theory goes wrong or right.

Citation: Tomkins, J., Penrose, M., Greeff, J., & LeBas, N. (2010). Additive Genetic Breeding Values Correlate with the Load of Partially Deleterious Mutations Science, 328 (5980), 892-894 DOI: 10.1126/science.1188013

May 17, 2010

Links of note for today

Filed under: Blog,Links — Razib Khan @ 6:34 pm

Didn’t spend enough time on the internet today for a Daily Data Dump. But,

1) ResearchBlogCast #6, sans Kevin Zelnio.

2) Noah Millman is on Bloggingheads.tv.

Evolution is false, the Bible tells me so

Filed under: creationism,Culture,Data Analysis,GSS — Razib Khan @ 2:04 pm

In the post below I pointed to various differences in regards to acceptance of evolution by demographic. One of the issues is that just because X correlates with Y, does not entail that X causes Y (and of course, if X correlates with Y, and Y correlates with Z, that does not entail that X correlates with Z). You can use the GSS to run some regressions and see what the strongest predictive variables. Because of this I know that the variable BIBLE is very predictive of skepticism of evolution. Additionally, even smart people with college educations who have a literal inerrant view of the Bible are skeptical of evolution. To show the power of Biblical fundamentalism I thought it would be useful to plot differences in regards to the Index of Creationism by various demographics for both Fundamentalists and non-Fundamentalists. So below I have a set of charts which have two series, one for Fundamentalists, and one for non-Fundamentalists, of a given demographic. So for example one chart has Fundamentalists and non-Fundamentalists separated by attainment or non-attainment of college educations.

The primary variables are BIBLE & SCITEST4.

BIBLE is:

Which of these statements comes closest to describing your feelings about teh Bible? 1. The Bible is the actual word of God and is to be taken literally, word for word. 2. The Bible is the inspired word of God but not everything in it should be taken literally, word for word. 3. The Bible is an ancient book of fables, legends, history, and moral precepts recorded by men.

I recoded so that responses 2 and 3 are classed as non-Fundamentalist.

SCITEST4:

For each statement below, just check the box that comes closest to your opinion of how true it is. In your opinion, how true is this? d. Human beings developed from earlier species of animals.

I created the Index of Creationism = (% “definitely not true”) X 3 + (% “probably not true”) X 2 + (% “probably true”) X 1, from three of the four responses to SCITEST4.

In the charts below the blue squares = Fundamentalists. The red diamonds = non-Fundamentalists. I rescaled so that 1 is the minimum for the Index of Creationism on all charts.


evowordsum

evocollege

evoincome

evoregion

evoreligion

Reminder: blue squares = Fundamentalists, red diamonds = non-Fundamentalists. A few notes. For stupid, average and smart, I simply recoded the WORDSUM vocabulary test. Stupid = 0-4, Average = 5-7 and Smart = 8-10. For region, it’s pretty self-explanatory, though do note that I placed Texas and such in the South, not the West. The West are the Pacific & Mountain regions only. Those with no college degree includes all those without bachelor’s degrees (non-four year degrees).

Do you notice the counterintuitive pattern when it comes to intelligence and Creationism, and income and Creationism? The sample size for SCITEST4 isn’t that hot, so you could chalk it up to noise, but I’ve done enough poking around the GSS to trust this. There is a pattern where very intelligent and/or high socioeconomic status Fundamentalists adhere to the viewpoint which in the general population is correlated with lower intelligence and socioeconomic status. I think the dynamic here is partly the same one when it comes to political polarization: stupid and lower status people tend to be less ideologically coherent because they don’t spend much time thinking about abstract questions. From what little field investigation I’ve performed dull human tends to fixate on sensory or interpersonal questions, not intellectual ones. In other words, very stupid Fundamentalists may not even understand what they’re being asked. Very stupid people also tend to agree that they’re political moderates more often than the intelligent; moderate seems like a good thing to say for someone who never thinks about politics. I think this issue to some extent explains the lack of effect among Roman Catholics. Unlike Protestants views about the Bible are less emphasized in Roman Catholicism traditionally, so many Catholics may not have well thought out opinions on the topic.  Those who answer that they believe the Bible is the literal and inerrant Word of God may not really even know what this really should mean. The question is geared toward those with Protestant presuppositions.

There may also be the secondary effect of self-selection when it comes to intelligence and income for Fundamentalists. Fundamentalism tends to correlate with lower intelligence and income, and those who choose to remain Fundamentalists despite higher intelligence and income may self-select for the most extreme and rigorous subset of this class. More theologically liberal and lax Protestant denominations tend to be biased toward wealthy and well-educated individuals, some of whom have switched denominations as they go up the class hierarchy. Those who refuse to switch as they ascend the class ladder may be a peculiar subset. By contrast, lower class status denominations may include more lax individuals in relation to belief or practice who would not feel comfortable in a liberal denomination because of their class status.

This pattern of social sorting probably explains the fact that region still has a significant predictive power even controlling for Fundamentalism. Northeastern Fundamentalists are equivalent in skepticism toward evolution as Southern non-Fundamentalists. I have seen similar tendencies among black Americans in relation to social issues and religion; secular individuals who are black are invariably more socially conservative that secular individuals who are white. I think this is a function of the fact that secular blacks are embedded in a more socially conservative cultural milieu. Similarly, non-Fundamentalist Southerners are embedded in a more Creationist culture, as Fundamentalists are numerically more preponderant in the South than non-Fundamentalists. New Englanders exhibit the inverted tendency. Someone who is a conservative, Fundamentalist or Republican in New England may actually be liberal, theologically moderate and a Democrat in the South.

Variables: Region, Wordsum, Relig, Income, Degree, Scitest4

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