Archive for October, 2012

Most mtDNA lineages expanded before the Neolithic?

By Razib Khan | October 18, 2012 9:00 pm

A new short communication in Scientific Reports suggests that most demographic expansion as ascertained using mtDNA occurred before the Neolithic. MtDNA analysis of global populations support that major population expansions began before Neolithic Time:

Agriculture resulted in extensive population growths and human activities. However, whether major human expansions started after Neolithic Time still remained controversial. With the benefit of 1000 Genome Project, we were able to analyze a total of 910 samples from 11 populations in Africa, Europe and Americas. From these random samples, we identified the expansion lineages and reconstructed the historical demographic variations. In all the three continents, we found that most major lineage expansions (11 out of 15 star lineages in Africa, all autochthonous lineages in Europe and America) coalesced before the first appearance of agriculture. Furthermore, major population expansions were estimated after Last Glacial Maximum but before Neolithic Time, also corresponding to the result of major lineage expansions. Considering results in current and previous study, global mtDNA evidence showed that rising temperature after Last Glacial Maximum offered amiable environments and might be the most important factor for prehistorical human expansions.

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CATEGORIZED UNDER: Human Genetics, Human Genomics

The original Africans are Neandertals (in part)

By Razib Khan | October 18, 2012 2:10 am

In antiquity what we term Tunisia and Tripolitania were part of “African province.” Just as “Asia” originally referred to the margins of what we now term Asia (regions of Anatolia), so “Africa” originally denoted a subset of the northwest fringe of the continent which became Africa. In biogeography this segment of the continent is actually not part of Africa (it is part of the Palearctic ecozone). And yet the vicissitudes of early modern cartography are such that continent had to be bounded by water on as many sides as possible, and today we clumsily make recourse to the term “Sub-Saharan Africa” to distinguish that region from the northern littoral, which is really part of the Mediterranean world.

This context is somewhat relevant when we evaluate a new PLoS ONE paper, North African Populations Carry the Signature of Admixture with Neandertals. This paper makes little sense unless you’ve read an earlier one, Genomic Ancestry of North Africans Supports Back-to-Africa Migrations. In that paper authors make the case that a majority of the ancestry of modern Maghrebis seems to date back to before the Neolithic, from a late Pleistocene migration of Eurasians. Though the indigenous North African element is naturally somewhat diverged from other West Eurasian components, it nevertheless comes out of the West Eurasian milieu, on the order of 10-40,000 years before the present.

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MORE ABOUT: Neanderthal

The unpredictability of cultural norms

By Razib Khan | October 18, 2012 12:28 am

I do pay for The New York Times, but as you may know I get frustrated with the lack of context for international stories. Most Americans are not particularly informed about world affairs, so fact without frame can confuse. For example today a story came into my feed, Uruguay Senate Approves First-Trimester Abortions. Naturally the article alludes to Latin America’s Roman Catholicism, but I also happen to know that aside from Cuba Uruguay has long been Latin America’s most secular nation. The chart from the left is from Uruguay’s household survey. I don’t know Spanish, but even to me it’s clear that 17.2 percent of Uruguay’s population identifies as atheist or agnostic, about three times the similar number in the United States (being generous). Fully 42 percent of the nation’s population is non-Christian, with 40 percent disavowing any religion.

This is all relevant because most readers of The New York Times are going to see Uruguay, a Latin American country where the Catholic religion is the dominant confession, and make some inferences of the weakening of the power of the church. But in Uruguay the church has been weak for 100 years! So why has Uruguay had strict abortion laws like its more religious neighbors? Because it is a small nation surrounded by influential neighbors, who no doubt effect its mores and norms. It reminds us of the power of cultural inertia and peer effects.


Open thread, 10-17-2012

By Razib Khan | October 17, 2012 5:29 pm


MORE ABOUT: Open Thread

Neandertal one stop shopping

By Razib Khan | October 17, 2012 12:46 am

If you have a hard time following all the Neandertal genomics findings from the last few years, and their implications, National Geographic has a really thorough piece up. It’s a good digest of all the news you can use. One thing I would like to add: from what I can tell the probability of the signals of admixture in non-Africans being genuinely Neandertal seem to be increasing as we progress. In other words, you should weight the “other side” (ancient population structure, where some African populations were closer to Neandertals before they left Africa) less than you did in 2010.

Of course one of the more inevitable aspects of the admixture story has been the humanization of Neandertals. I don’t know how I feel about this. Should our own affinity to Neandertals alter our view of their behavior or anatomy? Plenty of behaviorally anatomically modern humans were beastly after all.

MORE ABOUT: Neandertals

Atheist conservatives and libertarians are not rare

By Razib Khan | October 16, 2012 11:45 pm

A generous definition of rare I would think is 10% or less (you might argue for a more stringent threshold, but let’s work with 10%). So what are the politics of atheists? I bring this up because someone named Bridget Gaudette is looking for conservative and libertarian atheists to ask them about their views (so naturally I came up), but prefaced her inquiry to me by the assertion that “conservative/Republican” and “Libertarian” individuals in the “Atheist community” are rare. I don’t think this is empirically valid, depending on how you define the atheist community (e.g., atheist activists are probably to the Left of the median atheist). But even among the types who are motivated enough to attend secularist conferences, a substantial minority are non-liberals. I know because many people approached me after I spoke about my conservatism at the Moving Secularism Forward event last spring, and expressed their libertarianism, or specific conservative heterodoxies. Many of the young male atheists who I encountered in particular tended to be libertarians. Genuine self-identified conservatives are moderately rare, to be fair.

Nevertheless, to probe this question let’s look at the GSS. The variable GOD has a category which includes those who frankly state they “don’t believe” in God. These are by any definition atheists. I limited the data set to 1992 and later so as to take into account the reality that American politics have become more polarized over the past generation along religious lines (I would have used 2000, but the sample sizes started to get small for atheists).

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Twitter is not declining

By Razib Khan | October 16, 2012 12:09 am

The Decline and Fall of Twitter?:

Even Twitter? Can Twitter be declining? Over at the Atlantic‘s Technology Channel I note that my own Twitter conversations are not quite as dynamic as they once were, and speculate about why that might be. I didn’t say this in the post, but I wonder whether it might have something to do with people who enjoy online conversations also enjoying new tools and toys: perhaps we get tired of Twitter not because it has a deficiency, but just because it’s been around a while. I’m not suggesting this in lieu of the explanations I offer there, but in addition to them.

I think this is an artifact of the fact that Alan Jacobs seems to have been a very early Twitter adopter. Here’s Google Trends for the USA for searches for Twitter:

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MORE ABOUT: twitter

Singularity Summit 2012: the lion doesn’t sleep tonight

By Razib Khan | October 15, 2012 10:07 pm

Last weekend I was at the Singularity Summit for a few days. There were interesting speakers, but the reality is that quite often a talk given at a conference has been given elsewhere, and there isn’t going to be much “value-add” in the Q & A, which is often limited and constrained. No, the point of the conference is to meet interesting people, and there were some conference goers who didn’t go to any talks at all, but simply milled around the lobby, talking to whoever they chanced upon.

I spent a lot of the conference talking about genomics, and answering questions about genomics, if I thought could give a precise, accurate, and competent answer (e.g., I dodged any microbiome related questions because I don’t know much about that). Perhaps more curiously, in the course of talking about personal genomics issues relating to my daughter’s genotype came to the fore, and I would ask if my interlocutor had seen “the lion.” By the end of the conference a substantial proportion of the attendees had seen the lion.

This included a polite Estonian physicist. I spent about 20 minutes talking to him and his wife about personal genomics (since he was a physicist he grokked abstract and complex explanations rather quickly), and eventually I had to show him the lion. But during the course of the whole conference he was the only one who had a counter-response: he pulled up a photo of his 5 children! Touché! Only as I was leaving did I realize that I’d been talking the ear off of Jaan Tallinn, the lead developer of Skype . For much of the conference Tallinn stood like an impassive Nordic sentinel, engaging in discussions with half a dozen individuals in a circle (often his wife was at his side, though she often engaged people by herself). Some extremely successful and wealthy people manifest a certain reticence, rightly suspicious that others may attempt to cultivate them for personal advantage. Tallinn seems to be immune to this syndrome. His manner and affect resemble that of a graduate student. He was there to learn, listen, and was exceedingly patient even with the sort of monomaniacal personality which dominated conference attendees (I plead guilty!).

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Don’t trust an archaeologist about genetics, don’t trust a geneticist about archaeology

By Razib Khan | October 15, 2012 2:38 pm

Who to trust? That is the question when you don’t know very much (all of us). Trust is precious, and to some extent sacred. That’s why I can flip out when I realize after the fact that someone more informed than me in field X sampled biased their argument in a way they knew was shady to support a proposition they were forwarding. What’s the point of that? Who cares if you win at a particular bull-session? You’re burning through cultural capital. And not that most of my interlocutors care, but I’m likely to never trust them again on anything.

In any case, this came to mind when I ran across a James Fallows’ post at The Atlantic. Here’s a screenshot of the appropriate section, with my underlines:

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MORE ABOUT: Human Evolution

AncestryDNA is now accepting the necessity of raw data downloads

By Razib Khan | October 15, 2012 1:02 am

The Legal Genealogist points me to the fact that AncestryDNA is now going to work on allowing users to download their data. Here’s the specific section:

AncestryDNA believes that our customers have the right to their own genetic data. It is your DNA, after all. So we’re working to provide access to your raw DNA data in early 2013, which includes related security enhancements to ensure its safety during every step of the process. Moving forward, we plan to add even more tools and improvements for our customers, and any new features will be available to all AncestryDNA members.

If the rights of the customers to own their own data were so important to them they should have front-loaded this feature. As it is, they didn’t, and as many bloggers noted the firm had stated they didn’t have plans to unroll this feature in the near future. What changed? I don’t know the details, but I suspect they realized that many of us who complained in the past were going to continue to complain constantly. Combined with the contrast with its competitors, like 23andMe, and I assume they realized this just wasn’t going to solve itself if they ignored it. The key here is follow up. I’ll assume “early 2013″ is no later than March 31st (the first 1/4th of the year). If AncestryDNA doesn’t have the feature out by then I’ll assume they’re not serious, and will begin trying to make sure that their deficits come up high on Google searches again.

Blogs and word of mouth matter a lot in this domain. I convinced James Miller, author of Singularity Surviving, to get his parents genotyped this weekend. Also, after more than two years of harassment a friend who works at Google finally got typed, and will be sending me his data.

CATEGORIZED UNDER: Personal Genomics
MORE ABOUT: Personal genomics

I believe in the blank slate!

By Razib Khan | October 12, 2012 12:21 pm

Well, not really…but in some ways close enough judged against the initial reference point of where I started on certain questions. Dienekes contends:

This will help us understand both: the ancestors of non-Africans did not come forth fully formed, like Athena from Zeus’s head, having spent millennia of perfecting their craft and honing their minds by perforating shells and scratching lines in some South African cave. Instead, they may been plain old-style hunter-gatherers who stumbled into Asia by doing what they always did: following the food. At the same time, the UP/LSA revolution may not have been effected by a new and improved type of human bursting into the scene and replacing Neandertals and assorted dummies, but rather as a cultural revolution that spread across a species that already had the genetic potential for it, and was already firmly established in both Africa and Asia.

The former position, that the Out-of-Africa population were genetically endowed supermen who blitzkrieged other humans ~50,000 years ago was probably the most common position ~10 years ago. It’s outlined by Richard Klein in The Dawn of Human Culture. A contrasting argument was put forth at about the same time by Stephen Oppenheimer in The Real Eve. With 10 years of hindsight much of Oppenheimer’s model leaves much to be desired, but the one aspect which I laughed at at the time, but now give much more credit to, is the proposition that the Out-of-Africa migration was an expression of a cultural revolution in a proximate sense, rather than a biological revolution.

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CATEGORIZED UNDER: Anthroplogy, Human Evolution
MORE ABOUT: Human Evolution

You don’t need “genes” for genetics

By Razib Khan | October 12, 2012 2:04 am

After yesterday’s post I feel it is important again to reiterate that there is an unfortunate tyranny of the gene-as-physical-entity when it comes to our understanding of human heredity. To clarify what I mean, I think it is useful to borrow a framework from Andrew Brown. On the one hand you have a conventional modern mainstream understanding of the gene as a molecular biological entity, fundamentally derived from DNA and its role as envisaged by Francis Crick and James Watson, but with roots deeper back into the physiological genetic tradition which Sewall Wright was embedded within. In contrast to this concrete and biophysical conception of the gene there are those who conceive of the gene as an abstract unity of analysis. Richard Dawkins is the primary proponent of this viewpoint on the public intellectual scene, though men such as William D. Hamilton self-consciously understood the difference between their own genetics, and that which arose out of the insights of Crick and Watson.

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MORE ABOUT: Human Genetics

A dangerous man

By Razib Khan | October 11, 2012 3:32 am

I was a little sad when I heard my friend Steve Hsu had accepted a position at Michigan State some months back. My reasons were two-fold. First, I swing by Eugene now and then, and I wouldn’t have the opportunity to drop in on his office. Second, it seemed that Steve was becoming an Administrator. To some extent I feel like that’s going over to the dark side. But ultimately it’s his decision, and Steve has a lot of things going on at any given moment, and I’m hopeful he’ll continue to be involved in the production of scholarship in some form (he’s more of a scholar than most as it is).

Now apparently his move has resulted in submerged tensions coming to the fore. You can read the article in The Lansing Journal, New director’s experience a plus for MSU, but his controversial views concern some. Let’s qualify who these “some” are:

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There may be no gene which is essential for our humanity

By Razib Khan | October 11, 2012 12:39 am

The always informative Ann Gibbons has a piece in Slate, The Neanderthal in My Family Tree. There is almost nothing new for regular readers of this weblog, but it’s rather awesome that Slate is now publishing stuff like this. Many people are simply unaware of the new paleogenomics. Case in point, a good friend who has a doctorate in chemical physics, and was totally unaware a year after the seminal Science paper on Neandertal admixture of the likelihood of Neandertal admixture!

Nevertheless, I think it is important for me to be repetitive and highlight a disagreement I have with the Gibbons’ piece. She says:

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CATEGORIZED UNDER: Anthroplogy, Human Evolution
MORE ABOUT: Human Evolution

A plea for population genetics

By Razib Khan | October 10, 2012 10:31 pm

The title here is somewhat misleading. This is not just a plea for population genetics, but for quantitative genetics as well. Genetics is a big field. But today it is defined by and large by DNA, the concrete entity in which the abstraction of the gene is embedded. Look at the header of this website, or the background to my Twitter account. Mind you, I’m pathetically informed about molecular genetics, and don’t have a strong interest in the topic! I did consider using the H.W.E. or the breeder’s equation for the header, but in the end I judged it too abstruse and unfamiliar to most readers. DNA dominates when it comes to the modern mental conception of genetics, and we have to live with it to some extent.
But there is also great value in the genetics which has intellectual roots in the pre-DNA Mendelians and biometricians. This genetics exhibits a symbiotic, but not necessary, association with genetics as a branch of biophysics. Yet I come here not to insult or impugn my friends who toil in the trenches of the molecular wars. Rather, I simply want to point out that our world needs balance, and the systematic aerial perspective of population, evolutionary, and quantitative genetics can provide a different kind of intellectual ballast. More importantly, for the mnemonically lazy in the audience pop, evo, and quant gives you information for free. By this, I mean that these are highly theoretical fields, and theory can predict and allow you to infer facts about the world. You don’t need immerse yourself in every scrap of data if you can derive the likely probable pattern from theory.

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CATEGORIZED UNDER: Population Genetics

More atheists in the Age of New Atheism

By Razib Khan | October 9, 2012 1:14 am

Pew has an important new report out, “Nones” on the Rise: One-in-Five Adults Have No Religious Affiliation. Here is the bottom line in terms of numbers: over the past generation the proportion of Americans who explicitly reject a religious affiliation has doubled, from ~10 percent, to ~20 percent. In addition, the, the proportion who hold to Christian fundamentalist religious views has also declined. The United States of America is still a very religious nation in the context of the Western world, but 1990-2012 has been as second period of secularization after the “pause” of the 1970s and 1980s (after the initial wave of defections in the 1960s).

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MORE ABOUT: Religion

Dienekes and ADMIXTOOLS

By Razib Khan | October 8, 2012 7:55 pm

Less than a month ago I pointed to the release of ADMIXTOOLS. Unfortunately, though I have a desktop at home devoted purely to my personal genomic hobbies I haven’t been able to free up the time on weekends to start doing my own analysis. This is pretty pathetic, and sometimes I get a little depressed at how little usage there is of all the great scientific software released into the public domain. But in case you haven’t seen it, I want to point you to Dienekes Pontikos’ posts using ADMIXTOOLS. Frankly, my personal experience with this sort of thing tells me to hold off on any judgement until I’ve used the software package and gotten a feel for its tendencies. But until those of us with aspirations manage to get some blocks of time together Dienekes has the field all to himself.

CATEGORIZED UNDER: Personal Genomics

Ancient DNA and Sumerians

By Razib Khan | October 8, 2012 7:49 pm

A few months ago someone asked me (via email) which populations I would love to get typed (genetically that is). There is one population which did not come to mind at the time: the Sumerians. Why? Because these are arguably the first historic nation. The first self-conscious ethnic group which operated by the rules which we define as the fundamentals of literate civilization. Strangely, they are an ethno-linguistic isolate. My own assumption until lately has been that this is not too surprising, in that prior to the rise of expansive civilizations (Sargon of Akkad) there was much more linguistic and ethnic diversity than we currently see around us. Or, was evident even in the early Iron Age. In other words, the ancient Fertile Crescent may have resembled the highlands of Papua, with Hurrians, Akkadians, Gutians, Elamites, Sumerians, etc., all speaking mutually unintelligible dialects which diverged very far back in the mists of antiquity.

I am no longer quite so sure about this model. That is largely due to the possibility that there was a great deal of demographic change between the Mesolithic and the Bronze Age, with successive waves of layering and replacement. My rough model is that a few groups of farmers may have expanded to swallow up thousands of hunter-gatherer groups. These homogeneous farmer societies eventually would diversify, because they were not united by the institutional forces which cemented later imperial regimes, in particular, literate elites which had a sense of consciousness which extended deep into the past because of written records. Therefore, the diversification would presumably have been similar to what we see with Romance languages, or Indo-Aryan, branching out from an common root language which replaced many competitors rapidly. Without writing and large scale polities the divergence would be more rapid, and there would be many more tips on the phylogenetic tree.

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MORE ABOUT: Sumerians

The end of phylogenetic controversies

By Razib Khan | October 7, 2012 11:10 pm

I put up kind of a ridiculous title. But I do hope that at some point in the near future we’ll have some of the same flavor of debates on the macroevolutionary time scale that we have on the human microevolutionary time scale. There’ll be a surfeit of sequence at nearly every node of interest on the tree of life, and computational power galore devoted to analyzing variation and reconstructing any phylogeny we can conceive of. To be fair, one could argue we aren’t there even with human phylogenetics either. But it is rather strange we’re debating the origin of mammals and the nature of the lineage’s phylogenetic tree at this time. This is the kind of thing that I hope a more robust and assertive molecular phylogenetics can resolve (and paleontology as well, but I’m not up on the latest in computational analysis of morphological characters).

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MORE ABOUT: phylogenetics

The relative decline of New York

By Razib Khan | October 7, 2012 10:38 pm

Despite the real estate bubble bursting, it looks as if Florida will surpass New York in population by the next Census. I once made some quick money by betting an older gentleman that Texas had a larger population than New York. I suspect there’s even more money to be made by betting people that Florida has a larger population than New York in a few years. The reality is that most people don’t check statistics in their free time, so some “facts” get frozen in their minds. A great number of adults alive today were told in elementary or secondary school that New York was the second largest state in population. They are unlikely to update their views as they age. Unfortunately, I suspect these confusions are going to lead to public policy problems as well. I am not confident that our elected officials are any more aware of statistics than their constituents.

MORE ABOUT: Florida, New York

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