After my last post on inevitable nature of the shift of the book toward electronic formats, I revisited the data which highlights the decline in sales of e-readers. Some of this is probably competition with tablets. But I’ve had the same Kindle for two and a half years. I got a newer version of the Kindle for my wife, but have seen no need for me to upgrade (and, I got a Kindle Fire for my daughter). Why? The point of e-readers is the content, not the delivery. This reiterates that “e-books” aren’t revolutionary, they’re evolutionary, and the fixation on technology is going to be transient. A true revolution in information transmission and delivery would be a direct data port, which would transform “publishing” in a much deeper fashion than the digitization of type and script.

The Estonian Biocentre has put up lots of data in Plink pedigree format. Format is important because now many of you can manipulate these data. This the source of some of the data in PHYLO, so I need to double check the IDs or rebuild the data set (though for basic exploration I think PHYLO is still sufficient). This data set, combined with my ADMIXTURE tutorial should give everyone the tools to replicate results of the sort of papers which were cutting edge from 2006-2010 (i.e., model-based clustering with bar plots + PCA/MDS visualization).

Props to Mait Metspalu and company for release these data.

Unfortunately history is a discipline where we can not run experiments. From my earlier posts it should be clear that I have a keen interest in Western antiquity. But another passion of mine is Chinese history. A frustrating experience I have is that many people feel confident in making cross-cultural generalizations despite having deep familiarity with only one civilizational tradition. A comparative perspective is highly illuminating, but only if you stand on a solid ground of factual bases from which to actually make comparisons.  The existence of complex societies at both ends of Eurasia over the past 2,500 years are fascinating parallel “natural experiments.” But to compare and contrast you need to know a great deal about both civilizations.

Increased knowledge enriches discussion, and in the near future this weblog will once again have vibrant comments sections. With that in mind here are some books on Chinese civilization which I have found informative and useful:

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Earlier editions:

Using your 23andMe data: exploring with MDS
Using your 23andMe data in Plink

From Reconstructing Indian Population History:

…We hypothesize that founder effects are responsible for an even higher burden of recessive diseases in India than consanguinity. To test this hypothesis, we used our data to estimate the probability that two alleles from a group share a common ancestor more recently than that group’s divergence from other Indians, and compared this to the probability that an individual’s two alleles share an ancestor in the last few generations due to consanguinity…Nine of the 15 Indian groups for which we could make this assessment had a higher probability of recessive disease due to founder events than to consanguinity, including all the Indo-European speaking groups (Table 2). It is important to systematically survey Indian groups to identify those with the strongest founder effects, and to prioritize them for studies to identify recessive diseases and map genes.

South Asian populations exhibit a lot of between population genetic distance, and not simply as a function of geography. With more markers and an expansive data set Dan MacArthur will be able to assess exactly which South Asian caste his ancestry is from.

But this is an issue where I have fancied myself an outlier. My own background is moderately heterogeneous, and I’ve always explained to people that I’m not inbred like most South Asians, only half in jest (from what I can tell Muslims in the subcontinent have castes too, though they may somewhat different terminology). I know that my paternal grandmother came from a Brahmin family (clear by the customs preserved in the family even in her generation), while my maternal grandfather was almost certainly from a group with a Kayastha origin (going by surname, and who my mother actually clusters with). My maternal grandmother had considerable non-Bengali ancestry, which does show up in Middle Eastern signatures in my mother.

But this is talk. Am I truly not as inbred as the average brown? Leveraging methods which I discussed earlier (see posts above) I can very quickly check this.

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Note: please read the the earlier post on this topic if you haven’t.

The above image is from 23andMe. It’s from a feature which seems to have been marginalized a bit with their ancestry composition. Basically it is projecting 23andMe customers on a visualization of genetic variation from the HGDP data set. This is actually a rather informative sort of representation of variation. But there has always been an issue with the 23andMe representation: you are projected onto their invariant data set. In other words, you can’t mix & match the populations so as to explore different relationships. The nature of the algorithm and representation produces strange results, so varying the population sets is often useful in smoking out the true shape of things.

With the MDS feature I wrote about yesterday you can now compute positions with different weights of populations and mixes. This post will focus on how to manipulate the overall data set. You should have PHYLO from the the earlier post. Open up the .fam file. It should look like this:

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With the recent $99 price point for 23andMe many of my friends have purchased kits (finally!). 23andMe’s interpretive results are pretty rich now, but there are still things missing. There are plenty of third party tools you can use, but I know some people might want to do their own data analysis. There are many ways you could go about this, but I want to put up some posts on DIY genomic data analysis to making the learning curve a little less steep, and get people started. Motivation to actually begin going down this road is a big issue, but I think once you get over the hump it gets a lot easier.

First, you need Plink. It is really preferable that you work on a Mac or in Linux to engage in heavy duty analysis, but in this post I’ll assume you are working on the Windows platform. Again, the point here is to make this accessible. Download Plink if you don’t have it, and extract it where ever you like.

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Bryan Ward-Perkins in The Fall of Rome: And the End of Civilization spends a great deal of time on the archaeology of the Classical and post-Classical world. But, he also devotes only somewhat less space to the historiography of the study of the Roman Empire, and Late Antiquity. That is because the study of the past is not just the study of the past, but it is the study of the concerns and values of the present. We look through the dark mirror to the past, and in it we see our own outlines. Similarly, science fiction which purports to be a projection of the future is often nothing much more than a retelling of the present in shinier garb. This reality of history, its reflection of the prescription of the present despite the conceit that it is a description of the past, needs to be kept in mind. It is not a failing which pollutes the whole enterprise, it is a reality which must inform our interpretation of it. The study of Rome is a study of what humanity was, but it can not help but also reflect and define what we wish to be, by comparison and contrast.

But before I go on, a minor mea culpa. After further research and correspondence I believe that I extrapolated too far from lead concentrations in Greenland ice caps in a previous post. Though I still believe that it is a good reflection of the decline in proto-industrial vigor in the Western world, I do think that distance from China means that we do not have a good gauge on any comparisons between 0 AD and 750 AD (the later date being the apogee of the Tang). Though I do note that world population estimates seem to be somewhat lower for 700 than 0. But these are not precise estimates, so they need to be taken with a grain of salt. Chinese census records indicate that Tang population was higher than that of the Han, while it seems plausible that the Arab Imperium of the 8th century resulted in a higher population for the regions under its purview than during antiquity. Therefore to make the “math work” one can reasonably assume that the population in Europe was far lower.

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A week ago Keith Kloor had a post up, What Science, Environmentalism and the GOP Have in Common, where he bemoaned the lack of representation of non-whites in these categories. As a matter of fact I think Keith is wrong about science. Even constraining the data set to American citizens and permanent residents people of Asian ancestry are well represented in many areas of science. But not all sciences are created equal. In 2011 there were 158 doctorates which were awarded within the category of ‘evolutionary biology’ for American citizens or permanent residents. Of these 135 were non-Hispanic white, and 5 were Asian. In ‘neuroscience’ the respective figures were 742, 535, and 96. In ‘zoology’ 55, 49, and 0. In ‘bioinformatics’ they were 80, 51, and 17. Finally, in ‘ecology’ the breakdown was 330, 300, and 11. If you are involved in academic biology I’m rather sure that these numbers won’t surprise you too much, even if you’d never thought about it. You can even infer these by walking through the posters at ASHG 2012, and seeing how the demographics of the crowds shift.

We can look at this issue another way. In 2010 US News & World Report listed the top 10 ecology & evolution graduate programs. I went to the faculty websites after typing the university and ‘ecology,’ and then ‘neuroscience.’ Looking at names, and sometimes head shots, I classified everyone as ‘Asian’ (as defined by the US Census) and ‘Not Asian.’ You can find the data here. Please note that the left columns are ecology faculty, and the right are neuroscience.

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While reading The Founders of Evolutionary Genetics I encountered a chapter where the late James F. Crow admitted that he had a new insight every time he reread R. A. Fisher’s The Genetical Theory of Natural Selection. This prompted me to put down The Founders of Evolutionary Genetics after finishing Crow’s chapter and pick up my copy of The Genetical Theory of Natural Selection. I’ve read it before, but this is as good a time as any to give it another crack.

Almost immediately Fisher aims at one of the major conundrums of 19th century theory of Darwinian evolution: how was variation maintained? The logic and conclusions strike you like a hammer. Charles Darwin and most of his contemporaries held to a blending model of inheritance, where offspring reflect a synthesis of their parental values. As it happens this aligns well with human intuition. Across their traits offspring are a synthesis of their parents. But blending presents a major problem for Darwin’s theory of adaptation via natural selection, because it erodes the variation which is the raw material upon which selection must act. It is a famously peculiar fact that the abstraction of the gene was formulated over 50 years before the concrete physical embodiment of the gene, DNA, was ascertained with any confidence. In the first chapter of The Genetical Theory R. A. Fisher suggests that the logical reality of persistent copious heritable variation all around us should have forced scholars to the inference that inheritance proceeded via particulate and discrete means, as these processes do not diminish variation indefinitely in the manner which is entailed by blending.

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Nicholas G. Carr, purveyor of high-brow neo-ludditism and archeo-utopianism, has a piece out in The Wall Street Journal, Don’t Burn Your Books—Print Is Here to Stay. The subtitle is “The e-book had its moment, but sales are slowing. Readers still want to turn those crisp, bound pages.” Here are some of his rancid chestnuts of un-wisdom:

… Hardcover books are displaying surprising resiliency. The growth in e-book sales is slowing markedly. And purchases of e-readers are actually shrinking, as consumers opt instead for multipurpose tablets. It may be that e-books, rather than replacing printed books, will ultimately serve a role more like that of audio books—a complement to traditional reading, not a substitute.

What’s more, the Association of American Publishers reported that the annual growth rate for e-book sales fell abruptly during 2012, to about 34%. That’s still a healthy clip, but it is a sharp decline from the triple-digit growth rates of the preceding four years.

…

The initial e-book explosion is starting to look like an aberration… 2012 survey by Bowker Market Research revealed that just 16% of Americans have actually purchased an e-book and that a whopping 59% say they have “no interest” in buying one.

…

From the start, e-book purchases have skewed disproportionately toward fiction, with novels representing close to two-thirds of sales…Screen reading seems particularly well-suited to the kind of light entertainments that have traditionally been sold in supermarkets and airports as mass-market paperbacks.

…

Readers of weightier fare, including literary fiction and narrative nonfiction, have been less inclined to go digital. They seem to prefer the heft and durability, the tactile pleasures, of what we still call “real books”—the kind you can set on a shelf.

…In fact, according to Pew, nearly 90% of e-book readers continue to read physical volumes. The two forms seem to serve different purposes.

Having survived 500 years of technological upheaval, Gutenberg’s invention may withstand the digital onslaught as well. There’s something about a crisply printed, tightly bound book that we don’t seem eager to let go of.

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