Today I took some time out to see Cave of Forgotten Dreams. My main reaction is that I really would have appreciated less verbal exposition from Werner Herzog. The most gripping portions of the film were invariably those which focused on the cave art with no commentary. These were the scenes where Herzog also seems to have leveraged 3D technology the most seamlessly. In contrast many of the outdoor shots were really disorienting, especially where were trees in the background. There was shot near the end where a person was approaching the camera  with branches framing the background, and it was so jarring that I just looked away.

Not surprisingly all of the standard “talking heads” exposition really didn’t benefit at all from the 3D; it just distracted you while people were trying to explain various archaeological details. Speaking of which, I wish there was more of the scientific background here. Obviously that’s going to be my bias. Herzog naturally provide a spiritual rationale for why the original artists did what they did. That seems more plausible than anything else, but I still assume that the probability of any given hypothesis we offer being correct is going to be low. We just don’t know enough about the human past, and what might have motivated Paleolithic peoples.

If you do go to see Cave of Forgotten Dreams, don’t get discouraged in the middle section when the director allows the researchers to talk at length. The best scenes, with the least verbal and visual clutter within the cave, are near the end of the film. If you can, it might be most rational to purchase the ticket, go do something else, and show up for the last 30 minutes.

Epigenetics is making it “big time,” Slate has a review up of the new book Epigenetics: The Ultimate Mystery of Inheritance. In case you don’t know epigenetics in terms of “what it means/why it matters” holds out the promise to break out of the genes → trait conveyor belt. Instead positing genes → trait → experience → genes, and so forth. Or perhaps more accurately  genes → trait × experience → genes. Epigenetics has obviously long been overlooked as a biological phenomenon. But, I think the same could be said for the ubiquity of asexual reproduction and unicellularity! Life science exhibits anthropocentrism. That’s why there’s human genetics, and biological anthropology. My own concern is that epigenetics will give some a license to posit that the old models have been overthrown, when in fact in many cases they have been modified on the margin. Especially at the level of organisms which we’re concerned about; human-scaled eukaryotes. Humans most of all.

The last paragraph in the review highlights the hope, promise, and perils of epigenetics in regards to social relevance:

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Some of you may have read Oliver Miller’s AOL Hell: An AOL Content Slave Speaks Out. If you haven’t read it, please do! This section is important:

“LADY GAGA PANTLESS IN PARIS” is the example given in “The AOL Way” internal documents. That’s the best possible title. A buzz-worthy topic, a sexy result. It mattered little if Lady Gaga was actually pantless in Paris; it only had to relate somehow to the article as a whole. The entire title could be a come-on, a tease. It might well turn out that Lady Gaga was neither pantless, nor in Paris at the time. The important part was that the reader would click on those words to read the rest, thereby producing ad revenue for the websites. Words didn’t matter; stealing other people’s work also didn’t matter.

I still have a saved IM conversation with my boss, written after 10 months of employment, when I was reaching the breaking point:

“Do you guys even CARE what I write? Does it make any difference if it’s good or bad?” I said.

“Not really,” was the reply.

A lot of Miller’s piece focuses on the fact that he was overworked and underpaid. That’s not optimal, but lots of people are overworked and underpaid. If AOL content slaves were producing valuable content then someone would benefit: the public. One person’s cheap skilled labor is another person’s cheap quality product. But there’s no redeeming aspect to this. The sweat and anxiety of the content slave is in the service of…search engine optimization. That’s it. Their goal is to swamp your pop-culture Google News queries.

I don’t think there’s anything necessarily bad about throwing content at “trend topics,” but most of it is just crap. This is the sort of thing which will drive people to get their information from twitter and Facebook. At least there it is harder to “game” the system because there are regular people doing the filtering for you.

Content farms and their ilk remind me of the salt which builds up in the most fertile irrigated fields. Pretty soon Google will become barren if they don’t start aggressively pruning these offal generators.

In the image to the left you see three human males. You can generate three pairings of these individuals. When comparing these pairs which would you presume are more closely related than the other pairs? Now let me give you some more information. The rightmost image is of the president of Tanzania. The middle image is of the president of Taiwan (Republic of China). And finally, the leftmost image is of the prime minister of Papua New Guinea. With this information you should now know with certainty that the prime minister of Papua New Guinea and the president of Taiwan are much more closely related than either are to the president of Tanzania. But some of you may not have guessed that initially. Why? I suspect that physical inspection may have misled you. One of the most salient visible human characteristics is of the complexion of our largest organ, the skin. Its prominence naturally leads many to mistakenly infer relationships where they do not exist.

This was certainly an issue when European explorers encountered the peoples of Melanesia. An older term for Melanesians is “Oceanic Negro,” and some sources suggest that the Spaniards who named the island New Guinea did so with an eye to the old Guinea on the coast of West Africa. To the left is an unrooted tree which illustrates the relationships between Papuans, Bantu from Kenya, and Han Chinese. Since the font is small I’ve underlined the focal populations in red. Africans are always the “outgroup” to any two non-African populations. This is a robust pattern whenever you look at averaged total genome phylogenies. In other words, when you don’t privilege particular genes in a phylogeny humanity can be divided into African and non-African branches.

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As a follow up to the previous post I’ve spent some of this weekend looking for the results which might shed some more light on the genetic impact of Germans on the British landscape between ~500-600 A.D. There are some problems here even assuming all other conditions are met: Northwest Europeans are already genetically rather close. This does not mean you can not distinguish an Irishmen from a German, but, once you take into account the clinal variation in gene frequencies due to isolation-by-distance models it becomes somewhat difficult to ascertain admixture in the spaces in between. After all, populations spatially between northern Germany and Ireland, the Brythonic Celts, are presumably going to be genetically between these two populations as well. That being said, space is not the only variable. Culture is another. The Celtic dialects spoken in Ireland and Britain are extremely distinctive, being of two branches of the broader language family, but there was still a clear resemblance between the two cultures (e.g., druids and other aspects of religion). In other words, the Celtiberians of Spain, the Galatians of Anatolia, the Gauls, and the various peoples of Britain in Ireland, all traded in a common cultural currency. Not only are they likely to have had some common ancestors, but there is going to be a dialect continuum across much of this cultural zone, facilitating continuous gene flow. And speaking of continuity, the fact that Britain is separated by water from the European mainland and Ireland is at least something that works in favor of genetic inferences, as that is a structural constant which mitigates in favor of distinctions and between group variation.

As I stated below, the ideal case would be a data set where you compare genetic variation as a function of geography within the British Isles (with linguistic information intact, so that Welsh speakers are labeled) against a north German reference. The problem with a pooled Northern European reference is that there’s also a “Finnic dimension,” which is pretty much irrelevant when you’re comparing Germans to British. And usually there isn’t the fine-grain that you’d want. Irish are not the ideal proxies for Brythonic Celts. Welsh, or perhaps Cornish or individuals from Devon, might be.

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I just finished reading a review of the literature since 1984 on the bioarchaeology of the transition to agriculture. Stature and robusticity during the agricultural transition: Evidence from the bioarchaeological record:

The population explosion that followed the Neolithic revolution was initially explained by improved health experiences for agriculturalists. However, empirical studies of societies shifting subsistence from foraging to primary food production have found evidence for deteriorating health from an increase in infectious and dental disease and a rise in nutritional deficiencies. In Paleopathology at the Origins of Agriculture (Cohen and Armelagos, 1984), this trend towards declining health was observed for 19 of 21 societies undergoing the agricultural transformation. The counterintuitive increase in nutritional diseases resulted from seasonal hunger, reliance on single crops deficient in essential nutrients, crop blights, social inequalities, and trade. In this study, we examined the evidence of stature reduction in studies since 1984 to evaluate if the trend towards decreased health after agricultural transitions remains. The trend towards a decrease in adult height and a general reduction of overall health during times of subsistence change remains valid, with the majority of studies finding stature to decline as the reliance on agriculture increased. The impact of agriculture, accompanied by increasing population density and a rise in infectious disease, was observed to decrease stature in populations from across the entire globe and regardless of the temporal period during which agriculture was adopted, including Europe, Africa, the Middle East, Asia, South America, and North America.

The abstract makes the conclusion more cut & dried than it is. It’s the result of aggregating their literature review and arriving at a net conclusion. Yes, on the balance agriculture did result in the deterioration of health. The old truism that farmers are a small and ill lot in comparison to hunter-gatherers seem to be correct in the generality. But the literature review also makes it clear that when it comes to something like stature there are often periodic reversals of the trend toward decrease in size. There may be spottiness of the record, and sampling error, but I began to wonder if we might not be seeing evidence of evolution & innovation in action!

Consider the checkered history of the potato in Ireland. In the 18th century the Irish shifted toward the potato faster than most other European peoples, and so entered into a phase of massive population expansion. On a per unit basis the potato was nutritional gold. Unfortunately we all know that the blight of the 19th century triggered a series of social and demographic catastrophes.

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Quite often rather amusing articles which operate in the malleable zone between genetics and nationalism pop into my RSS feed (thanks to google query alerts). But this piece from Spiegel Online article, Britain Is More Germanic than It Thinks, actually appeals to some legitimate research in making a tongue-in-cheek nationalistic argument that the affinity between the Germans and the English is stronger than the latter would wish to admit. The article starts out with the interesting nationalist back story:

Until now, the so-called Minimalists have set the tone in British archeology. They believe in what they call an “elite transfer”, in which a small caste of Germanic noble warriors, perhaps a few thousand, placed themselves at the top of society in a coup of sorts, and eventually even displaced the Celtic language with their own. Many contemporary Britons, not overly keen on having such a close kinship with the Continent, like this scenario.

Thomas Sheppard, a museum curator, discovered this sentiment almost a century ago. In 1919, officers asked for his assistance after they accidentally discovered the roughly 1,500-year-old grave of an Anglo-Saxon woman while digging trenches in eastern England.

Sheppard concluded that the woman’s bleached bones came from “conquerors from Germany” and announced: “These are our ancestors!” But the soldiers were thunderstruck. At first they cursed and refused to believe that they were related to the “Huns.” But then the mood darkened. The trip back to the barracks “was like a funeral procession,” Sheppard wrote.

It is a coincidence which must be acknowledged that the vogue for Germanophilia amongst the English corresponds neatly to the decades when Irish nationalism waxed in the face of British imperial domination. And that Germanophilia naturally abated with the two World Wars. In lieu of the vision of Saxons, Angles, and Jutes, driving the Celtic British into the sea, Germanization was conceived as a process where an elite band of warriors imposed their culture atop a fundamentally pre-German substrate. This model is reflected in the historical scholarship, for example Norman Davies’ The Isles, as well as the genetics treatments, most prominently Bryan Sykes’ The Blood of the Isles.

In terms of the history, we have to make due with archaeology and the rather thin texts of the Celts. From what I can gather the archaeology does imply a rapid shift in material technology and symbolic aspects of culture such as burial customs on the Saxon Shore. Linguistically the modern English language owes very little to the Celtic dialects. Finally, the Christian Church seems to have disappeared across much of the zone of expanding German territory, only to be re-planted in the early 7th century by Irish & Scottish missionaries, followed up by those from the European mainland. In the Spiegel Online piece an archaeologist quotes a number of “200,000” for total migration for about a century, presumably inferring from the quantity of material remains, and what that implies about the numbers within the settlements which are indubitably German.

There are a few objections which crop up. Some scholars, such as Stephen Oppenheimer, argue that German speech was already common before the Roman conquest within the boundaries of England. Very few accept this position. A more mainstream argument is that like Gaul and Iberia much of Britain had been Latinized by the time of the German conquest. Because of their geographic isolation Cornwall, Scotland, and Wales, were the areas most insulated from both the German expansion and the dynamic of Latinization. Finally, some scholars have suggested that the outsiders get too much of the credit for the resurrection of the Christian Church in 7th century England, that an indigenous Christian culture persisted over the century of the British “Dark Ages” before the conversion of the Saxons.

The problem with each of these arguments is that they don’t cohere together very well. If Latin was the dominant language in Britain proper (i.e., outside of the “Celtic Fringe”) that begs the question why the Germans were not assimilated in Britain as they were in France and Iberia. Unlike the Saxons, Angles, and Jutes, the Frankish Empire was explicitly bicultural in that it spanned both Latinate Gaul and Germania. And yet the Franks who settled in Francia invariably adopted Latin and what later became French as their language. Additionally, Britain was one of only two regions of the Roman Empire where both the imperial languages (Latin and Greek) and the Christian Church disappeared with the barbarian invasion. The Balkans was the other zone.

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1) Post from the past: The biological bases of behavioral variation.

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At The Intersection Chris Mooney points to new research which reiterates that 1) political ideology exhibits some heritability, 2) and, there are associations between political ideology and specific genes. I’ll set #2 aside for now, because this is a classic “more research needed” area at this point. But as I mentioned in the comments the heritability of political ideology is well known and robust. From what I can gather most people assume it’s mediated through personality traits. In the comments Chris asks:

That sounds sensible. What i find amazing is that if the heritability of politics is so robust–and I agree, it would happen via personality–why is this so widely ignored?

There are I think several issues at work. First, many people are not comfortable within imagining that beliefs which they attribute to their conscious rational choice are not only subject to social inculcation, but that may also have an element of genetic disposition. Second, most people have a poor grasp of what heritability implies. Take a look at some of Chris’ commenters. The response is generally in the “not even wrong” class. Finally, what’s the actionable component to this? In other words, what are people going to do with this sort of information?

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Update: John Hawks’ lab is working in the same area, and he disagrees with the specific results presented here. Always reminds you to be careful about sexy results presented at conference! (someone should do a study!)

So claimed Peter Parham at a Royal Society meeting last week, Human evolution, migration and history revealed by genetics, immunity and infection. You can actually listen to the talk by pulling down the mp3 file. To get the part about human evolution and introgression, jump to 24 minutes in.

Here is the general sketch: It looks like ~50 percent of the HLA Class I alleles in Europeans derive from Neandertals, ~70-80 percent of HLA Class I alleles in East Asians derive from Denisovans, and that and ~90-95 percent of HLA Class I alleles in Papuans derive from Denisovans. If you recall, ~2.5% of the total genome content of non-Africans seems to be Neandertal, while ~5% of the total genome content of Papuans seems to be Denisovan. The total genome content proportions are rough estimates, there may be some wiggle room in there. But you can see that the HLA allele admixture estimates from these ancient Eurasian lineages is greater by an order of magnitude. Why?

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