Archive for September, 2012

I am free of rare homozygous recessives! (well, perhaps)

By Razib Khan | September 30, 2012 4:11 pm

I got a notification today from Ian Logan that he set up a page on my genotype using a method which detects rare homozygous SNPs in the ~1 million markers I put up from my 23andMe results. My raw data is online, so anyone can analyze it. Here is the summary of my results:

The program finds about 50 ‘rare/uncommon’ SNPs from the 900,000+ tested by 23andMe.

The are no ‘homozygous-recessive’ results (surprisingly, as 1-2 might be expected).

There are a list other individuals, and sure enough most of them do have a rare recessive homozygous locus or two. I assume that ascertainment bias (the technology finding variation in Europeans better than non-Europeans in most cases) wouldn’t result in my case, because I should have less variation, not more (less variation would presumably result in more homozygous recessives). So I am thinking it may simply be that because I’m from a population with greater genetic variation (South Asians) I am less likely to yield a homozygous recessive.

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CATEGORIZED UNDER: Personal Genomics
MORE ABOUT: Personal genomics

The moral measure of bad teeth

By Razib Khan | September 29, 2012 9:57 pm

Recently I was at the dentist and I was told that because I did not have any caries at this age, I would probably not have to worry about that in the future (in contrast, I do have some issues with gingivitis). I wasn’t surprised that I didn’t have caries, I have no great love of sweet confections. I had chalked up my evasion of this dental ailment to my behavior. To make a long story short my dentist disabused me of the notion that dental pathologies are purely a function of dental hygiene and diet. Rather, he explained that many of these ailments exhibit strong family and ethnic patterns, and are substantially heritable. My mother did suffer from periodontal disease a few years back, and that has made me much more proactive of my own dental health.

As someone who is quite conscious of the power of genetics, I was quite taken aback by this blind spot. I realized that not only did I attribute my own rather fortunate dental health (so far) to my personal behaviors, but, I had long suspected those with dental issues of less than optimal habits. Obviously environment (e.g., high sugar diet) does matter. But apparently a great deal of the variation in the trait is heritable. If you are still curious, here’s a paper which might interest you, Heritable patterns of tooth decay in the permanent dentition: principal components and factor analyses.

MORE ABOUT: Heritability

Free speech Über Alles!

By Razib Khan | September 29, 2012 2:45 am

Will Saletan has has published a piece making a traditionalist American absolutist case for free speech. He points out that in most Western nations there are in fact curbs on speech which is considered offensive, disturbing, and perhaps dangerous. Therefore, Muslims who point to Western hypocrisy have a point. I agree with this argument without reservation. But, I do want to reiterate the putative targets of offense are illustrative of a divergence of values in and of themselves. Though I wouldn’t criticize non-Western Muslims for pointing out the existence of laws banning denial of the Holocaust, I do have issues when Western Muslims bring this point up even innocuously. The reason is simple: the Holocaust concerns the systematic state-sponsored murder of millions of human beings. This is a far more serious issue than the reputation of the prophet Muhammad. Of course that statement reflects my particular values. And, whether you accept the idea of hate speech or not I suspect most Westerners would accept the validity of this proposition.

More generally a major thread running through conflicts about speech is globalization and technology. Today communication and propagation is nearly frictionless, and government curbs on speech either have to be very robust (e.g., Saudi Arabia or China), or, they have to be nominal and selective. The great thing about American free speech absolutism is that the implementation is relatively easy and clear. The problem with speech laws in other nations is that it seems that they are enforced sporadically and at the pleasure of the authorities. This may seem coherent in nations with heavy censorship, but it seems peculiar and out of place in those nations where censorship in the exception and not the rule.


The Others, in black and white

By Razib Khan | September 29, 2012 1:18 am

New Scientist has a piece up, Europeans did not inherit pale skins from Neanderthals, based on a paper I blogged last month. One thing that I hadn’t though about in detail…how did anatomically modern humans of various shades perceive Neandertals of various shades? For example, it seems highly likely that there were swarthy Neandertals and pale Neandertals. Similarly, there were swarthy modern humans, and soon enough pale ones. Skin color is a very salient trait. Very different populations phylogenetically, Sub-Saharan Africans, Melanesians, and South Asians, have been defined as “black.” Did modern humans perceive Middle Eastern Neandertals, who may have been relatively dark, as much closer to humanlike status because of their similar complexion to anatomically modern Middle Eastern humans? Did they perceive European Neandertals, who may on average have been much lighter, as fundamentally different?

When doing physical reconstructions it seems to me that the gross morphology of Neandertals has been more emphasized. Their brow ridges, large prominent noses, and stocky body plans. But in this manner perhaps they’re like our imaginings of ancient Greek temples as alabaster white. In reality the temples of antiquity and many public buildings were festooned with color. Similarly, Neandertals came in all shades.

MORE ABOUT: Human Evolution

Signal of Indo-Aryan admixture in South Indian Brahmins

By Razib Khan | September 29, 2012 12:59 am

I’ve mentioned a few times that the Reich lab has been finding suggestive evidence for admixture between indigenous South Asians and a West Eurasian group on the order of ~3,000 years before the present. The modal explanation is probably an Indo-Aryan intrusion. Dienekes used rolloff in ADMIXTOOLS to repeat these general findings. Specifically, he found signal for an admixture event analogous to one between non-Brahmin South Indians and Northern Europeans. I say analogous because I do not mean to imply that the admixture was exactly of this form. Rather, there are general resemblances in the genetic profiles across the four groups (i.e., Orcadian & North Kannadi, and population X and Y which merged to form South Indian Brahmins).

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

Skewing my winnings

By Razib Khan | September 29, 2012 12:42 am

Last spring I made a bet with a friend that Mitt Romney would win. He gave me 5:1 odds, and I assumed a 40% chance that Romney would win. So I expected to lose, but if I won I’d win big. At this point I assume I’m out that money, because I’d put Romney’s chances at less than 40% (though I think people underweight uncertainty, so I believe there’s a lot of variation in this prediction). But now I’m hearing/reading that many Republicans are under the impression that the polls are skewed. If you believe that the polls are skewed would you be willing to bet money that the polls are skewed? Specifically, I want to wager that “unskewed polls” turn out to be further off the mark than the regular polls in reference to the final election results. I’m not 100% sure that the pollsters are correct, and I don’t know more than a superficial amount as to the weighting methodologies, but the track record of skew-skeptics is suspect enough that I think this is a way I can make money off people who I perceive to be suckers. Of course, the people who I perceive to be suckers think I’m the sucker, which is fair enough. Take my money! Please speak up in the comments if you want to make a bet. I’d want it to be public, and you have to put your real name out there. Also, I want to know if you’ll give me some odds, because I assume you are moderately confident in your assessment that the polls are skewed.

MORE ABOUT: Politics

Paleopopulation Genetics

By Razib Khan | September 27, 2012 10:57 pm

It seems a new field is being born! Jeff Wall & Monty Slatkin have a pretty thorough review out, Paleopopulation Genetics:

Paleopopulation genetics is a new field that focuses on the population genetics of extinct groups and ancestral populations (i.e., populations ancestral to extant groups). With recent advances in DNA sequencing technologies, we now have unprecedented ability to directly assay genetic variation from fossils. This allows us to address issues, such as past population structure, changes in population size, and evolutionary relationships between taxa, at a much greater resolution than can traditional population genetics studies. In this review, we discuss recent developments in this emerging field as well as prospects for the future.

Nothing very new for close readers of this weblog, but the references are useful for later mining.


A zoom in on Western Eurasia

By Razib Khan | September 27, 2012 2:00 am


That one thing

By Razib Khan | September 26, 2012 11:40 pm
MORE ABOUT: Human Nature

Open thread, 9-26-2012

By Razib Khan | September 26, 2012 11:00 pm

Be heard!


Paying for pop gen a thing of the past?

By Razib Khan | September 26, 2012 8:40 pm

Via Haldane’s Sieve, Genetics has a new preprint policy:


GENETICS allows authors to deposit manuscripts (currently under review or those for intended submission to GENETICS) in non-commercial, pre-print servers such as ArXiv. Upon final publication in GENETICS, authors should insert a journal reference (including DOI), and link to the published article on the GENETICS website, and include the acknowledgment: “The published article is available at” See for details.

Here’s a more thorough list of preprint guidelines by journal. For all practical purposes this means that population genetics can now percolate more freely among the masses. Many of the differences between “draft” preprints and the final manuscript have to do with formatting, etc., from what I have seen. So the content shall flow!


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MORE ABOUT: Open Access

Re-imagining genetic variation

By Razib Khan | September 26, 2012 12:39 am

To the left is a PCA from The History and Geography of Human Genes. If you click it you will see a two dimensional plot with population labels. How were these plots generated? In short what these really are are visual representations of a matrix of genetic distances (those distances being general FST), which L. L. Cavalli-Sforza and colleagues computed from classical autosomal markers. Basically what the distances measure are the differences across populations in regards to their genetics. The unwieldy matrix tables can be visualized as a neighbor-joining tree, or a two dimensional plot as you see here. But that’s not the end of the story.

In the past ten years with high density SNP-chip arrays instead of just representing the relationship of populations, these plots often can now illustrate the position of an individual (the methods differ, from components analysis or coordinate analysis, to multi-dimensional scaling, but the outcomes are the same).


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CATEGORIZED UNDER: Genetics, Genomics

Singularity Summit 2012 – be there!

By Razib Khan | September 25, 2012 12:48 am

As regular readers know I have been to two previous Singularity Summits (2008 and 2010), and will be at the 2012 event. The speakers look particularly interesting to me this year. I may finally be stupid enough to blurt out to Vernor Vinge how awesome the adolescent me thought Fire Upon the Deep was (I downed a beer with Vinge in 2008, but didn’t say a word to him). Carl will be there again, and we’ll definitely catch up in the “meat-space.” More importantly I have a lot of socializing to do, since I haven’t seen any of my friends from the Berkeley LW community since I left the Bay Area in the summer of 2011. But I hope to meet new & interesting people, as I always have at these events (the social circle overlaps a great deal with BIL). So if you read this weblog and are going to the Singularity Summit and think I’m worth talking to in person just come on up, I’m not very shy. With the prior that you’re actually at the Summit my assumption is that you’re interesting, unless proven otherwise!

Addendum: Some people are curious if I am a “believer” in the Singularity. I’ll be honest and say I don’t think that the idea is necessarily crazy, but I spend my days thinking about genetics far too much to really be a hardcore A.I.-obsessive, which is what is needed to entertain the concept with any seriousness. Rather, my interest is rather in the social milieu where I can temporarily dispense with niceties and get down to the type of verbal blood-sport which I truly relish: engagement with intent not to thrash your opponent, but to wrestle with reality and perhaps squeeze out a few points against it.

MORE ABOUT: Singularity Summit

The First Men and the Last Men

By Razib Khan | September 24, 2012 11:59 pm

In the comments below there is a discussion about whether personhood is a continuous or categorical trait. I lean toward the former proposition as a matter of fact, but let’s entertain the second. What if personhood, and in particular consciousness and moral agency, emerged repeatedly over the past two million years in singular individuals? A model I propose is that the reason that ‘behavioral modernity’ exhibited such a long lag behind ‘anatomical modernity’ is that the first conscious human kept killing themselves. After all, imagine that you come to awareness and all your peers are…well, ‘dirty apes.’ You are literally the sane man in the asylum. This is similar the idea proposed, reasonably enough, that a demographic ‘critical mass’ was required for cultural evolution to truly enter into ‘lift-off.’ In any case, perhaps ~50,000 year ago a psychopath was born who could live with the knowledge that their days were to be spent copulating with and eliminating with animals. Animals whom said psychopath could congenially manipulate to increase their own fitness. No sensitive soul, he.

Ultimately obviously my hypothesis is far more science fiction than serious model. But it does get to the heart of something critical: the essence of humanity is not our rational reflective individual faculties, but our powerful social awareness and need for embeddedness. Even a misanthrope like me can recognize this. By our negation of it we recognize that which is the standard. Consciousness and self-awareness did not explode into the world like a shot in the dark in the form of the original human. Rather, groups of proto-humans through their collective actions stumbled upon the configuration of characteristics which connote to us humanity. There was no sentinel, only the passage of countless generations, melting unto each other.

MORE ABOUT: Philosophy

The great Malagasy leap into the unknown

By Razib Khan | September 24, 2012 11:33 pm

Today there was a short article in Discover on a paper published last spring on the models for the settling of Madagascar. I didn’t pay too much attention when the paper came out for two reasons. First, it focused on Y and mtDNA, and I’ve been playing with Malagasy autosomes. Second, it seemed a ridiculously brutal computational attack on a question which seems to have a straightforward intuitive explanation: yes, Madagascar was settled by a small founding group. With hindsight I may have spoken too soon, or passed judgement too hastily. Looking at the paper the explicit model building of demography does still seem like overkill, but they obtain some important precision here. The phylogenetics and the archaeology align nicely.

Though the authors of the article talk about future directions, I think we will find that the Malagasy originate from a small group of Malayo-Polynesians who did find themselves stranded on Madagascar (later to absorb African admixture). This is not controversial. Rather, when I came to this position with enough solidity I began to look at the cultural anthropology of Madagascar. In particular, what do the Malagasy remember of about their own past in Southeast Asia? From what I could tell (the literature on Madagascar is not too rich in English) the Malagasy don’t recall much. This is important, because it tells us just how fragile oral memory can be when you have a major geographical and demographic rupture. The influence of Sanskrit is apparently evident within Malagasy, attesting to the early period if Indic influence in Southeast Asia. But the Malagasy are not part of Dharmic or Islamic civilization. They are the people forgotten by time. I think what little we know about the Malagasy can shed on light memories and legends preserved by peoples who we suspect were migrants into the only homelands they knew (e.g., how could the Aryans be exogenous if they didn’t record any memory of lands before India?).

CATEGORIZED UNDER: Genetics, Genomics

The delta quadrant of American politics & culture

By Razib Khan | September 24, 2012 10:43 pm

Apparently when he was a consultant Mitt Romney would praise the merits of ‘wallowing in data.’ I agree with this, you can’t get more data than you need. Therefore I highly commend Public Religion Research Institute‘s survey of the “white working class.” More specifically, do read the full PDF. It’ll take you some time, but just trade that in for commenting on a weblog! Of course the results are strongly contingent upon the definition of what the white working class is. In this survey they fix upon the white population which does not have a college education (though may have some college) and is not employed in salaried labor. This seems like serviceable definition. The incomes range from low to lower upper middle class, with a mode in the lower middle class, so you get a broader cross-section of non-elite white America than Honey Boo Boo, which is to working class white America what the “ghetto life” is to working class black America.

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Quartz, kind of a big deal?

By Razib Khan | September 24, 2012 4:12 am

A site called Quartz is going to go live today. I have been hearing a lot about it in the media (e.g., The New York Times). One of the people who launched ScienceBlogs, Chris Mims, is involved. I’ve seen a guideline for its freelance writers, and I have to say that I’m impressed by the flexibility and openness to variation and personalization that it communicates. Not sure if it is revolutionary, but I suspect that it will be quite the content machine. And the emphasis on tablets and mobile access via a browser, rather than an app, is probably the best way to optimize readership.


Humanity isn't, it becomes

By Razib Khan | September 23, 2012 7:55 pm

John Hawks prompts to reemphasize an aspect of my thinking which has undergone a revolution over the past 10 years. I pointed to it in my post on the Khoe-San. In short, the common anatomically modern human ancestors of Khoe-San and non-Khoe-San may not have been people. Rather, people may have evolved over the past 100-200,000 years ago. Of course the term “people” is not quite as scientific as you might like. In philosophy and law you have debates about “personhood”. Granting the utility of these debates I am basically saying that the common ancestor of Khoe-San and non-Khoe-San may not have been persons, as well understand them. Though, as a person myself, I do think they were persons. At this point I am willing to push the class “person” rather far back in time.

As I suggested earlier there is an implicit assumption that personhood is a shared derived trait of our species. Or at least it is a consensus today that all extant members of H. sapiens are persons. Since Khoe-San are persons, the common ancestor of Khoe-San and non-Khoe-San must also be persons if personhood is a shared derived trait. But, we also know that there are many aspects of realized personhood on a sociological or cultural scale which seem to diminish the further back in time you go. For example, the Oldowan lithic technology persisted for ~1 million years. A common modern conception of persons is that persons in the aggregate are simply never so static. Persons have culture, and culture is protean. Therefore, one might infer from the nature of Oldowan technological torpor that the producers of that technology were not persons.

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CATEGORIZED UNDER: Anthroplogy, Human Evolution

Reader survey results, biologists vs. non-scientists

By Razib Khan | September 23, 2012 3:54 pm

There are now over 400 responses to the survey. Here is a link to the responses in CSV format. If you import this into R, an extra parameter in regards to encoding may be necessary:

responses=read.csv("responses.csv",sep="t",header=TRUE,fileEncoding = "UCS-2LE")

I decided to separate the respondents into two categories, biologists and non-scientists (therefore, excluding other types of scientists from further analysis). You can see the filtered responses for biologists and non-scientists yourself. Below are some comments on interesting differences.

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MORE ABOUT: Reader Survey

Further survey results

By Razib Khan | September 21, 2012 1:36 am

I have now reformatted the responses into a csv file. So you can do something boring like create a scatterplot with Excel, as above. Or, you can import into R and dig for more interesting patterns. Here is an updated to the PDF which shows you the simple non-crossed results.

Also, out of curiosity I separated respondents into geneticists vs. non-biologists (so I exclude biologists who are not geneticists from this analysis). First, here are the non-biologists on race:

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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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