Archive for May, 2012

Cain, Where is Abel thy brother?

By Razib Khan | May 30, 2012 4:06 am

Community differentiation and kinship among Europe’s first farmers (via Dienekes):

Community differentiation is a fundamental topic of the social sciences, and its prehistoric origins in Europe are typically assumed to lie among the complex, densely populated societies that developed millennia after their Neolithic predecessors. Here we present the earliest, statistically significant evidence for such differentiation among the first farmers of Neolithic Europe. By using strontium isotopic data from more than 300 early Neolithic human skeletons, we find significantly less variance in geographic signatures among males than we find among females, and less variance among burials with ground stone adzes than burials without such adzes. From this, in context with other available evidence, we infer differential land use in early Neolithic central Europe within a patrilocal kinship system.

I have already stated on this weblog that we will probably begin to discern a rather strong pattern soon of an interleaved genetic pattern across Eurasia and Africa where we can infer that populations in an expansionary demographic phase absorbed a host of other groups (more, or less). The exact details are to be worked out, but I’m moderately confident in this sort of pattern.

But these results align with another of my expectations, which I have rather stronger confidence in: that in parts of Eurasia the emergence of agriculture was correlated with the rise of powerful patrilineal kinship groups, which served as the cores of pre-historic polities. I no longer believe that demographic expansion due to cultural innovation can be separated from the likely political and social consequences of these changes. No, rather what we saw with the rise of agriculture was another powerful social innovation, collective units of large numbers of males who operated as one in the quest for land, women, and material self-enrichment. I do not mean to imply here that violence began with the Neolithic. Rather, I simply believe that the numbers enabled by agriculture allowed for specialization and scalability to fundamentally change the game. This was a high stakes “winner-take-all” bet.

As these males spread across the landscape, enabled by their culture (agriculture) and propagating their culture (language), in many cases their genetic-demographic signal may have been diluted across the wave of advance. But their cultural cohesion remained, and I believe that the patterns of Y chromsomal patterns evident across the modern world are an echo of their elimination of rivals. A tree of many Abels was pruned, as a few Cains proliferated like weeds.

CATEGORIZED UNDER: Uncategorized
MORE ABOUT: Agriculture

H. Allen Orr, most influential evolutionary biologist of all time?

By Razib Khan | May 29, 2012 8:51 pm

A reader reminded me of an amusing paper, Who Likes Evolution? Dissociation Of Human Evolution Versus Evolutionary Psychology. The gist of the results are below (I added some clarification):

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CATEGORIZED UNDER: Evolutionary Psychology

The current bias in genealogical databases

By Razib Khan | May 29, 2012 7:13 pm

As a follow up to my post below on the thick coverage of European information in genealogical and genomic databases, here are the “Ancestry Finder” matches from 23andMe for my daughter using the default settings:

If I increase sensitivity India does come up, at 0.1%, second to last in a very long list of European nations. I’m pointing this peculiarity out because my daughter is 50 percent South Asian, but this element of her ancestry doesn’t find many matches because there aren’t many people out there in the database to match. In contrast, because she is 1/8th Norwegian (her great-great grandparents were immigrants from the Olso area; thanks Ancestry.com!) this “block” jumps out, and aligns up with many people in their database.

This isn’t just an exceptional case. Here’s the result for a friend who is 50 percent East Asian (Chinese) and 50 percent American white:

The old warning rears its ugly head: the tool is just a tool, and must be used with and understanding of what it can and can’t do. If you decrease sensitivity many South Asians actually match people from European nations before they do people from India. Why? Part of it is probably that many South Asian groups are highly endogamous, which dampens intra-South Asian segment sharing. And the other part is that the sample size of Europeans is so large that random matches with this population are just as, or more, likely than genuine matches with the smaller number of South Asians.

CATEGORIZED UNDER: Personal Genomics

Reason: the God that fails, but we keep socially promoting….

By Razib Khan | May 29, 2012 1:03 pm

One point which I’ve made on this weblog several times is that on a whole range of issues and behaviors people simply follow the consensus of their self-identified group. This group conformity probably has deep evolutionary origins. It is often much cognitively “cheaper” to simply utilize a heuristic “do what my peers do” than reason from first principles. The “wisdom of the crowds” and “irrational herds” both arise from this dynamic, positive and negative manifestations. The interesting point is that from a proximate (game-theoretic rational actor) and ultimate (evolutionary fitness) perspective ditching reason is often quite reasonable (in fact, it may be the only feasible option if you want to “understand,” for example, celestial mechanics).

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CATEGORIZED UNDER: Anthroplogy, Psychology
MORE ABOUT: Cognitive Science

Science, the genealogical leveler?

By Razib Khan | May 29, 2012 2:15 am

I follow CeCe Moore’s blog posts on scientific genealogy pretty closely. But it’s more because of my interest in personal genomics broadly, rather than scientific genealogy as such. My own knowledge of my family’s past beyond the level of grandparents is very sketchy. This despite the fact that I know I have two very well documented lines of ancestry which I could follow up on, my paternal lineage, and the paternal lineage of my mother’s maternal grandfather. I don’t have a great interest in this beyond the barest generalities, and my parents tend to have a rather disinterested stance as well. Why? I can’t help but wonder if part of the issue is that unlike many South Asians my family has a relatively diverse background, so it isn’t as if we are sustained by a coherent self-identity as members of a sub-ethnicity (Bengalis are not tribal, so lineage groups are more ad hoc and informal). Additionally, there is probably some self-selection in the type of personalities who would transplant themselves across continents and are willing to spend the majority of their lives in a nation not of their birth.

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CATEGORIZED UNDER: Personal Genomics
MORE ABOUT: Personal genomics

A day late, but still….

By Razib Khan | May 28, 2012 1:49 am

Brings back some memories.

And the original….

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CATEGORIZED UNDER: Uncategorized

Space & the beginning of summer

By Razib Khan | May 27, 2012 11:51 am

It’s been a big few weeks for space, with the success of Dragon. I don’t have anything to add in a descriptive or analytic sense, I know as much (or likely less) as you on this issue (this is why should read Bad Astronomy). Needless to say I’ve been rooting for Elon Musk’s enterprise, so to speak. I’m not old enough to remember the “space race,” which put a man on the moon. Rather, for my generation space and NASA had become rather pedestrian, with the shuttle being a sky ferry par excellence. Space is important not because of what it will do for us in concrete terms (e.g., Tang), but what will do for us on a deeper level. Otherwise we may fall prey to the sort of ennui one reads about in science fiction universes such as the city of Diaspar. Remember, we’re the species which made it to the New World and Oceania. This sort of crazy and irrational endeavor is part of who we are.

On a different note, hope people are enjoying the de facto start of the summer (Memorial Day weekend in the USA).

CATEGORIZED UNDER: Space
MORE ABOUT: Space

Genetics' random truths

By Razib Khan | May 27, 2012 1:05 am

Update: Please do not take the labels below (e.g., “Baloch”) as literal ancestral elements. The most informative way to read them is that they indicate populations where this element is common, and, the relationship of proportions can tell us something. The literal proportion does not usually tell us much.

End Update

I was browsing the Harappa results, and two new things jumped out at me. Zack now has enough St. Thomas Christian samples from Kerala that I think we need to accept as the likely model that this community does not derive from the Brahmins of Kerala, as some of them claim. Their genetic profile is rather like many non-Brahmin South Indians, except the Nair, who have a peculiar attested  history with the Brahmins of their region.

But that’s not the really interesting finding. Below is a table I constructed from Zack’s data.

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CATEGORIZED UNDER: Anthroplogy
MORE ABOUT: India, Indian

The Dao of Learning

By Razib Khan | May 26, 2012 12:17 am

Accidental Blogger points me to a rather funny event, the yearly victory of some brown kid in the National Spelling Bee. ‘I was nervous': Texas whiz kid beats teens in 2012 National Geographic Bee. This Texas whiz kid, Rahul Nagvekar, beat a prodigy from Wisconsin, Vansh Jain. Here were the 10 finalists for the GeoBee:

– Raghav Ranga, Arizona
– Varun Mahadevan, California
– Anthony Stoner, Louisiana
– Adam Rusak, Maryland
– Karthik Karnik, Massachusetts
– Gopi Ramanathan, Minnesota
– Neelam Sandhu, New Hampshire
– Rahul Nagvekar, Texas
– Anthony Cheng, Utah
– Vansh Jain, Wisconsin

Speaking of bees, the National Spelling Bee is coming up. Here are the contestants (page down). And here’s a list of the 2012 Intel Science Contest finalists. And winners of the American Mathematics Competition.

I think it’s great that kids from certain demographics do so well at these academic competitions. But I have to be honest and wonder if sometimes we aren’t seeing individuals who are so focused on the measure, that they forget what we’re trying to measure. God knows I think metrics are very important, but the pursuit of knowledge ultimately has nothing to do with a panel of judges or selection of correct answers. South Korea already exists, it’s a fine enough country, we don’t need to replicate it.

CATEGORIZED UNDER: Culture
MORE ABOUT: Bees

Genes in space

By Razib Khan | May 25, 2012 11:38 pm

From some of the same people who brought you the genetic map of Europe, a very important paper, A model-based approach for analysis of spatial structure in genetic data. Here’s the abstract:

Characterizing genetic diversity within and between populations has broad applications in studies of human disease and evolution. We propose a new approach, spatial ancestry analysis, for the modeling of genotypes in two- or three-dimensional space. In spatial ancestry analysis (SPA), we explicitly model the spatial distribution of each SNP by assigning an allele frequency as a continuous function in geographic space. We show that the explicit modeling of the allele frequency allows individuals to be localized on the map on the basis of their genetic information alone. We apply our SPA method to a European and a worldwide population genetic variation data set and identify SNPs showing large gradients in allele frequency, and we suggest these as candidate regions under selection. These regions include SNPs in the well-characterized LCT region, as well as at loci including FOXP2, OCA2 and LRP1B.

Within the guts of this paper they make an important observation: constructing a set of populations and then generating pairwise statistics of differentiation across those populations has an element of arbitrariness. Rather than going in that direction the authors here are evaluating variation of genes as a function of continuous space, rather than binning them into discrete populations. In this way they can use patterns of genes to back infer the likely geographic origin of an individual, and more intriguingly pinpoint genetic loci which exhibit sharp gradients across space, and so may be targets of natural selection. The adaptive story for LCT is straightforward. But what of OCA2, which is mostly well known as a pigmentation locus which has been implicated in blue vs. brown eye variation in Europeans? As I like to say, interesting times….

And of course, they have released the software.

Credit: Wikipedia

CATEGORIZED UNDER: Human Genetics, Human Genomics
MORE ABOUT: Human Genomics

Fear of a black past

By Razib Khan | May 25, 2012 10:35 pm

I notice that the media has started reporting that scientific genealogy has now established to a great extent the likely origin of the Melungeons. You can find the original paper online. The gist is that the Melungeons seem to exhibit a large proportion of Sub-Saharan African origin Y chromosomal lineages, and European mtDNA lineages. The lack of Amerindian ancestry in the generality is also notable. But, this does not entail that the origins of the Melungeons is from the union of free black males and white women necessarily, at least on purely genetic grounds (the paper itself has a wealth of genealogical evidence pointing to this likelihood). The Melungeons are an endogamous community, and so have a low effective population. African or Amerindian mtDNA lineages may simply have been lost by chance over the past few hundred years.

But I point to the story of the Melungeons because it is a nice counter-point to that of the Hispanos of the Southwest. This is a case where historians and anthropologists who made the case for the false construction of a mythical Middle Eastern ancestry for the Melungeons as a way in which to escape the bounds of the American racial caste system were correct. In contrast, this model was not totally supported for the Hispanos, who do seem to have some grounds to argue for genuine connection to Jewishness. In other words, genetic evidence is an important complement to other methodologies.

CATEGORIZED UNDER: Race
MORE ABOUT: Melungeon

A quick note on comments policy

By Razib Khan | May 25, 2012 5:43 pm

Happy Memorial Day weekend to Americans. In light of my various time pressures which are going to be operationally indefinite in their temporal scope for me I need to consider various options about optimizing the comments. I generally do rather well on reading comprehension tests, so I’ve decided that if your comment strikes me as incoherent or irrelevant on first inspection I’m likely to simply remove it without warning. This means that there will be false positives, and those of you who have unfortunately been caught in the spam filter may worry, but I think in the interests of useful comments which address the substance of the posts and time management this is probably for the best. Those of you who are caught in the spam filter can email me as is the usual case; this seems to be a sporadic issue. There are of course a whole host of comments/comment styles which will result in banning, but these transgressions are usually one-off affairs by “newbies.” But again in the interests of optimal use of time I’m probably going to not bother warning people anymore, aside from directly engaging with individuals as I usually do to clarify any points made.

CATEGORIZED UNDER: Administration

An Orientalist fantasy

By Razib Khan | May 25, 2012 12:31 am

A few months ago I had a post up about Game of Thrones, where I argued that to a great extent the book and the world that George R. R. Martin created was racist because that’s true to how pre-modern worlds generally are constructed structurally. When fantasists create a ‘secondary world’ they are almost always using our own universe as a prototype, often shading or refashioning some aspect here and there to taste. A true fantasy which is totally counter-intuitive and lacks familiar coherency is without any anchor for a reader, and so lacks narrative power. Fantasy stripped away of injustice or oppression would be without dramatic tension. Utopia does not sell. Additionally, the speculative element in this literature is sharply bounded by precedent. Modern fantasy in its origins is simply an elaboration of the epic literature which is often at the root of contemporary civilizations. J. R. R. Tolkien attempted to create in his own works a simulacrum of a rich epic folk past for the Anglo-Saxon peoples analogous to what the Scandinavians had thanks to Snorri Sturluson’s efforts.

My post on Martin’s work was prompted by the ruminations of one Saladin Ahmed, whose piece in Salon manifested all the stale standard post-colonial inflected drivel which riddles much of popular literary criticism. Ahmed popped up in the thread of my post, but actually misunderstood the intent! The reason is pretty straightforward I think: our “paradigms” are so different that he had a hard time hearing me correctly initially. I responded to Ahmed, but weirdly enough though he hung around the comment thread he never really engaged with me after I made my own stance clearer to him. Whether it disturbed him, or did not interest him, I will never know.

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CATEGORIZED UNDER: Culture
MORE ABOUT: Fantasy

Vaccination as heterodoxy

By Razib Khan | May 24, 2012 11:00 pm

Apparently Mayim Bialik, Ph.D. neuroscience, is skeptical of vaccination. This just goes to show you that “science education” itself is no guarantee of immunity against acceptance of false propositions. Rather than reason from one proposition to another independently humans operate in an ecology of ideas. Bialik’s general suite of beliefs about mothering and her social milieu make her stance on vaccination rather unsurprising, notwithstanding that she has a doctorate in neuroscience.

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CATEGORIZED UNDER: Uncategorized
MORE ABOUT: Vaccination

Hispanos and Sephardic ancestry

By Razib Khan | May 24, 2012 12:06 pm

A correspondent emailed me to tell me that Linda Chavez, whose father was a New Mexican Hispano, was found to have Sephardic Jewish ancestry in Henry Louise Gates Jr’s Finding your Roots series. This brings me to point to a recent paper, The impact of Converso Jews on the genomes of modern Latin Americans:

Modern day Latin America resulted from the encounter of Europeans with the indigenous peoples of the Americas in 1492, followed by waves of migration from Europe and Africa. As a result, the genomic structure of present day Latin Americans was determined both by the genetic structure of the founding populations and the numbers of migrants from these different populations. Here, we analyzed DNA collected from two well-established communities in Colorado (33 unrelated individuals) and Ecuador (20 unrelated individuals) with a measurable prevalence of the BRCA1 c.185delAG and the GHR c.E180 mutations, respectively, using Affymetrix Genome-wide Human SNP 6.0 arrays to identify their ancestry. These mutations are thought to have been brought to these communities by Sephardic Jewish progenitors. Principal component analysis and clustering methods were employed to determine the genome-wide patterns of continental ancestry within both populations using single nucleotide polymorphisms, complemented by determination of Y-chromosomal and mitochondrial DNA haplotypes. When examining the presumed European component of these two communities, we demonstrate enrichment for Sephardic Jewish ancestry not only for these mutations, but also for other segments as well. Although comparison of both groups to a reference Hispanic/Latino population of Mexicans demonstrated proximity and similarity to other modern day communities derived from a European and Native American two-way admixture, identity-by-descent and Y-chromosome mapping demonstrated signatures of Sephardim in both communities. These findings are consistent with historical accounts of Jewish migration from the realms that comprise modern Spain and Portugal during the Age of Discovery. More importantly, they provide a rationale for the occurrence of mutations typically associated with the Jewish Diaspora in Latin American communities.

The evidence for the Lojano community is stronger in the paper than the Hispano samples. Nevertheless, it is interesting to view this in light of the 2000 piece in The Atlantic, Mistaken Identity? The Case of New Mexico’s Hidden Jews”. Long story short, cultural anthropologists posited in the late 1990s that the Jewish cultural features of Hispanos were distortions of the beliefs of Protestant missionaries. Thank god for genetics.

CATEGORIZED UNDER: Anthroplogy, History
MORE ABOUT: Hispanos

Are Hispanics that socially conservative?

By Razib Khan | May 24, 2012 11:35 am

I often hear in the media that Hispanics are “socially conservative.” For that sort of thing you do need “quick & dirty” rules-of-thumb, and the assertion seems broadly plausible. On the other hand, the Hispanic attitude toward gay marriage isn’t really that different from non-Hispanic white (see GSS MARHOMO variable). So I decided to query non-Hispanic white and Hispanic attitudes to a range of “hot-button” social issues in the GSS. I also broke it down by college vs. non-college educated cohorts. All results are from the year 2000 and later.

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CATEGORIZED UNDER: Data Analysis
MORE ABOUT: Politics

The utility and reality of species

By Razib Khan | May 24, 2012 10:16 am

Of all the taxonomic ranks species is the most clear, distinct, and concrete. More practically, it is the level which most naturally falls out of the patterns of life’s tree. Or does it? If the term “species concept” does not ring a bell, please see this entry. If it does, how do you define species in a non-arbitrary manner?

CATEGORIZED UNDER: philosophy
MORE ABOUT: Species concepts

The American Community Survey: mend it, don't end it!

By Razib Khan | May 22, 2012 10:13 pm

To my surprise there is apparently a move on the part of the Republicans in the House of Representatives to curtail funding for The American Community Survey. I am not too excited by the idea that you could get fined for not filling out a government survey form, but neither do I think that abolishing social statistics is the correct solution to this problem. Rather, better surveys which compensate for biases in response rates are the direction we need to go. The reality is that a government of our scope and continuing responsibilities needs the best social statistics that money can buy. I understand that many believe that some of the functions of our government are illegitimate or unwarranted, but destroying the government’s general ability to function is counter-productive unless you want to total social collapse to trigger a revolution.

Second, government data collection is a public good with positive externalities. If we abolish endeavors such as the American Community Survey than social data will be the domain only of corporations, who are not always keen on sharing that data.

CATEGORIZED UNDER: Data Analysis

GEDmatch

By Razib Khan | May 22, 2012 9:28 pm

For genetic genealogy buffs, I highly recommend Gedmatch. It’s been rolling out a lot of new features, including ancestry inference tools from the major genome bloggers. Here is my “chromosome paining” using Zack Ajmal’s reference populations:

CATEGORIZED UNDER: Personal Genomics
MORE ABOUT: Gedmatch

The Atlantic has competition

By Razib Khan | May 20, 2012 12:50 pm

Foer Returns to New Republic as Editor:

Two months after buying a majority stake in The New Republic, the technology entrepreneur Chris Hughes has lured one of its former stars, Franklin Foer, back to the magazine as its editor.

The print magazine and Web site will be redesigned and the page count of the print edition will be expanded, Mr. Hughes said. He added that when he was researching whether to buy the New Republic, he had to read through old editions on microfilm in the archives at the New York Public Library.

Mr. Hughes’s goal is to guide The New Republic out of the category he called “little magazines” in Washington like The National Review and into a category that includes magazines he sees as more natural competitors, like The New Yorker, the Economist and New York Magazine.

I don’t add much value in a lot of areas, so I don’t say much. But this piece seems to make a major omission: the analogous model to what Chris Hughes is aiming to do with The New Republic is what David Bradley did with The Atlantic, down to the robust web strategy. The New Yorker, the Economist, and New York are all really different beasts, aside from being relatively prominent.

CATEGORIZED UNDER: Uncategorized
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This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!
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