Archive for December, 2006

Convergent evolution in skin color – part n

By Razib Khan | December 31, 2006 4:43 pm

Genetic Evidence for the Convergent Evolution of Light Skin in Europeans and East Asians:

…these results point to the importance of several genes in shaping the pigmentation phenotype and a complex evolutionary history involving strong selection. Polymorphisms in two genes, ASIP and OCA2, may play a shared role in shaping light and dark pigmentation across the globe while SLC24A5, MATP, and TYR have a predominant role in the evolution of light skin in Europeans but not in East Asians. These findings support a case for the recent convergent evolution of a lighter pigmentation phenotype in Europeans and East Asians.

Related: A post on SLC24A5 and one on OCA2. Earlier commentary on the lead author’s work (a correction from her). Convergent evolution on skin color.
Skin color is a very salient trait, we notice it pretty easily. So I believe it is a very good thing in terms of public understanding of the postgenomic era that this character is now being elucidated on a fine grained scale. Within 5-10 years I predict this will be a rather uninteresting trait because we’ll have a good grip on 95% of the variation between and within populations.
Via Dienekes.
Addendum: After I initially drafted this post I found this paper which isolates the DCT locus as implicated in light skin in East Asias, but not Europeans. The science here is pretty fast, loci build up as I write!



By Razib Khan | December 29, 2006 12:01 pm

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The reality of epistasis

By Razib Khan | December 29, 2006 11:31 am

Earlier this week I sketched out the general theoretical basis for not denying unexpected deviations from expectation, so to speak, when it comes to quantitatve traits. The main issue is that varying genetic backgrounds leave unaccounted for gene-gene interactions, and so our predictions when two populations are crossed maybe confounded (within a population ceteris paribus is far more likely to hold). In any case, I thought I’d give you two obvious examples from humans.
First, in 2005 Helgadottir et. al. found that African Americans are at greater risk for myocardial infarction vis-a-vis their parental populatons, Africans and Europeans, because of a combination of alleles of one population against the genetic background of the other (genetic and historial studies tend to converge upon a median admixture proportion of 20-25% European and 75-80% African in black Americans, with variance of course between subpopulations and families). Since genomic data suggest that the Out of Africa event and expansion into Eurasia induced multiple selective sweeps in populations which left the ur-heimat I would not be surprised if more studies like this emerge which suggest decreases in fitness because of problematic genetic combinations. As I’ve said before, racial admixture increases variation and genetic diversity, and I see no reason why this would not result in an increase in the proportion of those who are far more and less fit than is in the norm in major racial groups (corrected for some possible masking of deleterious recessives and so hybrid vigor). The Neandertal-modern introgression story was in part an illustration of how novel genetic combinations may have unexpected positive benefits. Though on average I think racial admixture is probably a wash for most populations I do believe that the likelihood for the arrival of a genuine Übermensch will increase as powerful assortative mating across a few valued characters proceeds apace.
A second example of epistasis is the Pakistani family that can’t feel pain. Note:

The SCN9A gene is active both in nerves that mediate pain and in those of the sympathetic nervous system, which controls vital bodily functions like heart rate. But for reasons that are not yet understood, the affected members of the Pakistani families had no symptoms of a disordered sympathetic nervous system, such as irregular heart rate, and seemed entirely normal apart from the occasional self-inflicted damage caused by their inability to feel pain.

Though we don’t know the precise genetic reason for this family’s insulation from the normal debilitations which follow from their condition, theoretically I think it is very likely to be a modifier gene which lurks in the clan’s genetic background and is not generally present in others who exhibit this mutation. If individual X carries mutation Y which should result in a decrement in fitness Z, but does not, I think an a priori plausible hypothesis is that there are other loci which mask the deleterious affects. Many single locus Mendelian diseases with moderate or low penetrance may simply be polygenic in nature and exhibit variation which is cryptic because those without the ailment aren’t tested for the mutation.


Evolutionary genetics going down

By Razib Khan | December 28, 2006 10:44 pm

Life has been occupying me, why, between good wine (I prefer mild Chardonnay), work, books and beautiful women who detest science fiction I haven’t been able to resume my survey of Evolutionary Genetics: Concepts & Case Studies. Nevertheless, I’d like to point you to Jason Rosenhouse’s Evolution Blog which has been putting the Science in ScienceBlogs. I especially enjoyed Chance, Stochasticity, Probability and Evolution, though I am of the opinion that these sort of disagreements are often more semantical than substantial. Terms like “adaptationism” and “punctuated equilibria” allude to a central tendency which emerges out of an extremely rugged conceptual topography. Once you agree on scale (molecular or morphological?) or taxon (mammaliam vs. drosophilid?) many of these “disputes” fade into the distance and science rises to the fore, sweeping aside petty egos. Or that’s the story that some would tell!
Strange fact of the day: Anastasius I, a Roman Emperor of the East who flourished in the late 5th century, was the last to be deified. This was one century after outright persecution of paganism began in the Empire, and nearly two centuries after Christianity became the the privileged faith of the Empire. I was induced to search out this fact because as I read The Fall of the Roman Empire by Peter Heather, the author recounted a mid-5th century incident when a Roman diplomat rebuked a colleague for comparing Attila the Hun to the Emperor Theodosius II, on the grounds that Theodosius was a god while Attila was a man. I will frankly admit that I expressed great surprise, seeing as how it was the family of Theodosius which managed to impose Christianity as the official religion of the Empire in a manner which served as a model for later relations between Church and State in Europe (e.g., Theodosius the Great’s tacit submission to Ambrose after the massacre at Thessalonika serves as a model for Henry at Canossa). It just goes to show that what might be blasphemy to later Christians was nothing of note to the early Imperial Christians who still carried forward their pagan ancestors’ sensibilities.


Yahoo Mail "Beta" sucks

By Razib Khan | December 28, 2006 2:12 am

I work on two machines in the mid-to-high 2 Ghz range with 1 gig of RAM on a regular basis. And yet the new YAHOO MAIL “Beta” has consistently crashed and throttled Firefox multiple times within the last few days. If your AJAX app does this you’re worse than Microsoft.
Client: Is my app Web 2.0TM©® ready???
Me: Oh yeah baby, you won’t be able to find a desktop it won’t crash!


Dawkins & theological sophistication

By Razib Khan | December 28, 2006 1:25 am

John Lynch has a post up about Richard Dawkins’ lack of theological sophistication in The God Delusion. John is basically reiterating the point that Dawkins did not truly engage theological arguments for theism on a very high or sophisticated level. In fact, John levels the implicit charge that Dawkins’ engagement of theology mirrors the level of good faith that Creationists render toward evolutionary science. Though I am a Neville Chamberlain atheist I am ambivalent about the theological tack. I’ve told Chris that I think that making a stand on theology isn’t the best strategic choice, and though it is tactically sound (i.e., Dawkins is almost proudly ignorant and dismissive of theology in his work) I believe it will lead to long term problems. The short of it is that I believe that the coherency of theology is implicitly presuppositionalist. By this, I mean that Christian theology is coherent and persuasive when one presupposes a Christian set of axioms. I believe theology can assuage and aid in belief, but in the vast majority of cases I doubt it is necessary or sufficient. One could say that science is also presuppositionalist, one must assume a coherency and rationality about the world around us, and generally reject excessive solipsism.
But, there is a difference: science is testable via the world around us, and, it leads to engineering. No matter its manifold flaws, it works. In contrast, theology must remain at remove from the world. Some arguments (e.g., the teleological argument) are informed by the world around us, but fundamentally they operate via a chain of propositions derived from axioms and observations in a rather abstract domain. Mathematics is similar, but I hold that its formalism renders it objectively transparent. In contrast theology’s verbal logic is more opaque and must be mediated by social consensus. The truths of theology are arrived via consensus as opposed to an independent cognitive process.1 The historical record suggests that theology explores a sample space of ideas etched out by contingencies which are derived from human sociology. By an large theology is what cognitive anthropologist Scott Atran would term a “quasi-propositional” system. It has the general form of logic, but its overall direction is dictated by extra-analytical parameters (theologians may get to God in different ways, but in the end, they know that God exists and that the concept is sensible).

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More complex than simple addition

By Razib Khan | December 26, 2006 11:29 am

additiveindependent.jpgA few months ago I posted Discrete continuity in genetics to show how the granular nature of genetic inheritance may still manifest to our perception as continuous variation (i.e., quantitative traits). I used skin color as a model trait because it is easy to relate to, and we are beginning to understand its genetics in detail as I write. To recap, it seems that 3-5 genetic loci control more than 90% of the intergroup variation across populations in complexion. That is, you have a small number of genes which generate the range between black and white skin. These genes come in various flavors, alleles, which in concert sum up to one phenotype. I used a biallelic model which posited 4 loci of independent and additive effect. If a genotype on locus 1 was Aa, I assumed that the quantitative impact would be 1/2 of AA vs. 0 for aa. And so on for each successive locus, resulting in a biological binomial distribution. But, I do not believe that additivity and independence need to be perfect.
I won’t address developmental and environmental variance too much because they are pretty straightforward. In industrialized societies 90% of the variation in height is genetically specified because environmental variation in regards to nutrition is not particularly important, malnutrition has been rendered rather irrelevant (obesity is a problem though). Nevertheless, there is still some environmental component of variation. An acquaintance of mine was rather short in comparison to her sisters and she attributed it to her competitive gymnastics. Additionally, there might be an element of stochasticity introduced during development as a fetus prior to birth. How does this explain skin color? Well, there is still wiggle room even outside the genes of large effect, particularly on the individual level.

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The season needs no reason

By Razib Khan | December 24, 2006 4:29 pm

Below I spoke of historical perspective, while earlier I referred to Christmas as “universal pagan wine poured into a particular Christian chalice.” I thought I might elaborate upon this.
First, the cultural and historical origins of Christmas are multi-textured. Though Christians assert “Jesus is the reason for the season,” a more precise formulation might be that “Jesus became the reason for the season in the minds of some.” This is important. It is not without rationale that Christian groups like the Jehovah Witnesses reject Christmas, it is not a scriptural festival. Its emergence in the 4th century coincided with the synthesis of Christianity with Roman Imperial culture as the latter took upon the former as the state religion. In 274 the Roman Emperor Aurelian dedicated a temple to the sun god, Sol Invictus, on the 25th of December, Natalis Sol Invictus, “the birth of the invincible sun.” Interestingly, many early depictions of Jesus Christ co-opted solar imagery (e.g., the halo around the Christ). It seems that the thrusting forward of December 25th as the birth of Christ was strongly motivated by co-option of a pre-existing festival. Additionally, holiday merry-making seems to have its classical antecedants in Saturnalia. But this tendency of a mid-winter festival is not limited to Southern Europe. Yule and its cousins play an even greater role in the north than they do in the sunny Mediterranean. The darkness of the mid-winter solstice festivals bloom to usher in the season of hope and lengthening days. Customs like the Yule Log, Christmas cookies and gift exchange all emerge out of this pre-Christian substratum. This is was not unknown to the Christian Church, during the medieval period there were futile attempts to suppress some of these practices. A great enough frustration broke out during the Reformation that groups like the Puritans banned the celebration of Christmas, which was after all a minor holiday next to Easter.
Today the Christmas season has become capitalism’s handmaid. And yet nevertheless there is an economic case against Christmas. But such arguments will, I suspect, be as successful as Christian attempts to co-opt or abolish a fundamentally primal holiday. So long as winter’s darkness passes over us in the Northern Hemisphere our minds will demand a luxury to usher in the new year. It may not be economically optimal, but the human psychology naturally introduces inefficiencies and ‘irrationality’ into the action of Homo economicus. And so in some ways the battle between those who would “defend” Christmas, and those who promote a more inclusive Holidays, is somewhat beside the point, the name is less than the substance that persists. The tendency toward mid-winter holiday is, I believe, evoked from the natural interaction of our cognitive machinery and the seasonal flux of the world around us. The emergence and perpetuation of mid-winter festivals in agricultural societies in the north isn’t a coincidence or an act of cultural diffusion, it is a tendency which our minds are canalized toward. I believe that in general it is best to make the best of our eternal instincts in this matter. Our nature does not insist that we engage in a gross orgy of consumption after all, but neither can we truly honor the Puritan intent to root all acts in scriptural reason, or the economically optimal behavior which would deny the darkening skies above which finally cede ground to the sun. In the end, such exuberant “inefficiencies” are the ends toward which efficient means aim….


Historical perspective

By Razib Khan | December 24, 2006 12:57 pm

I’m reading The Fall of the Roman Empire by Peter Heather. Most people know I’m a classical history buff (e.g., I’ve read a fair number of the late Michael Grant’s works). Now, one thing that always strikes is this: 2,000 years ago a political organization existed which stretched from Scotland to Iraq, from Hungary to Morocco. How wild is that?


And a Merry Christmas to you!

By Razib Khan | December 22, 2006 10:58 pm

Steinn Sigurðsson has an has an amusing post up about his multicultural Christmas. Here is the “American Infidel,” Robert Ingersoll, on Christmas (1892):

This is the festival of the sun-god, and as such let its observance be universal.
This is the great day of the first religion, the mother of all religions — the worship of the sun.
Sun worship is not only the first, but the most natural and most reasonable of all. And not only the most natural and the most reasonable, but by far the most poetic, the most beautiful.
The sun is the god of benefits, of growth, of life, of warmth, of happiness, of joy. The sun is the all-seeing, the all-pitying, the all-loving.
This bright God knew no hatred, no malice, never sought for revenge.
All evil qualities were in the breast of the God of darkness, of shadow, of night. And so I say again, this is the festival of Light. This is the anniversary of the triumph of the Sun over the hosts of Darkness.
Let us all hope for the triumph of Light — of Right and Reason — for the victory of Fact over Falsehood, of Science over Superstition.
And so hoping, let us celebrate the venerable festival of the Sun.

When it comes to Christmas I’m a Post-Modernist, the “reason for the season” is a matter of social debate and interpersonal discourse. To be pithy about it Christmas is universal pagan wine poured into a particular Christian chalice. I choose not to reject the drink no matter the vessel of its deliverance to our modern age.



By Razib Khan | December 22, 2006 12:41 pm

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Brown people are all the same (perhaps)

By Razib Khan | December 22, 2006 11:59 am

New paper in PLOS Genetics, Low Levels of Genetic Divergence across Geographically and Linguistically Diverse Populations from India. Here’s the conclusion:

Populations from India, and groups from South Asia more generally, form a genetic cluster, so that individuals placed within this cluster are more genetically similar to each other than to individuals outside the cluster. However, the amount of genetic differentiation among Indian populations is relatively small. The authors conclude that genetic variation in India is distinctive with respect to the rest of the world, but that the level of genetic divergence is smaller in Indians than might be expected for such a geographically and linguistically diverse group.

It’s in PLOS, so you can read the whole thing. This figure is pretty illustrative.
a) Brown people form a distinct genetic cluster. South Asians that is. This shouldn’t surprise.
b) South Asians are more related to other South Asians than non-South Asians. Punjabis (Northwestern India) might resemble Iranians and Arabs more than other South Asians, but they are still more like other South Asians than Iranians or Arabs.
c) This study showed very little internal population substructure within South Asia. I think the caveats are important, the study looks at American South Asians. This isn’t going to be as rich a sample space as all South Asians, there are caste, regional and socioeconomic biases. Within the next 5 years you’ll see a paper on South Asia just like this: European Population Substructure: Clustering of Northern and Southern Populations.
d) Please be cautious about taking comments like this literally:

The correlations are increased by using a linear combination of allele frequencies with ∼2/3 contribution from Europe/Middle East and ∼1/3 contribution from East Asia. At the same time, however, the separate cluster for India in population structure analysis indicates that allele frequencies in India are distinctive, so that predictions obtained based on European and East Asian groups cannot fully explain allele frequencies in Indian populations.

The “take home” message some get is that this means South Asians are 2/3 group A and 1/3 group B. That’s probably not what’s going on. It wasn’t the case that 10,000 years ago a Ur-European race and an Ur-Asian race got together in India and mated. Rather, South Asia is a crossroads in Eurasia, and it makes sense that the flow of genes would reflect influences from both the west and the east. You notice that populations in Eastern India show the biggest influence from East Asia, and populations from Western India show the biggest influence from West Asia. Geography matters!


Pre-implantation genetic diagnosis

By Razib Khan | December 22, 2006 4:19 am

Via Genetics and Health, Many Clinics Use Genetic Diagnosis to Choose Sex (on NPR radio feed). Of course, the couple profiled are brown.
Related: To breed a better human – we have the technology.


Bruce Lahn, gene thug strikes again

By Razib Khan | December 22, 2006 2:07 am

150Bruce_1.jpgOver at GNXP p-ter posts two profiles from Science on Bruce Lahn.


4 Stone Hearth #5

By Razib Khan | December 21, 2006 10:39 am

4 Stone Hearth #5 is up! Via Bora.


Book review – The Gecko's Foot: Bio-inspiration: Engineering New Materials From Nature

By Razib Khan | December 20, 2006 9:20 pm

My review of The Gecko’s Foot is out in Science & Spirit. I’ll be honest, I’m not happy with the review since I was on a time crunch (I was a back up reviewer and the piece needed to be sent in on a short deadline) & very busy with other things. Nevertheless, the take home message is about right.


I, coolie

By Razib Khan | December 20, 2006 12:18 pm

Well, as many of you know I have been criticized quite a bit by some fellow ScienceBloggers (this query will take you where you need to go if you are a virgin to this incident). I haven’t really responded for a few reasons
1) I’ve been very busy with week at work
2) I’ve been reading a great book when I’ve not been busy
3) I don’t really see the need to address arguments which don’t relate at all to what I said or intended
But, two comments piqued my interest and I feel I have to say something. They deal with my racial identity. Seeing as I’m known in some quarters as “cinnamon love, you can intuit that I’m not a pale-face. Ed says:

If we are to use the terms of Razib’s argument, one must then ask why a brown-skinned man like Razib was doing in a wine bar, clearly the exclusive province of Caucasians! I know this, because Ann Coulter told me that racist antebellum times represented “a chivalric, honor-based culture that was driven down by the brute force of crass Yankee capitalism.” I therefore must believe her when she says that this is so! And we all know that the Confederacy meant rewarding the true winner: the glorious white male! So what business does Razib have drinking wine among the elite? It lacks honor and chivalry and respect for the white man. I’m shocked (shocked!) that any brown-skinned man would be doing this. Am I a freak to think this is freaky? I haven’t had a sip of wine, so it isn’t the alcohol. Guess it has to be my specious and outdated logic!

Now, this comment over at Madame Zuska’s:

razib shouldn’t worry too much, because like many south-east asian males, his parents will probably ship him over a bride from the home country who will wash his clothes and have his babies and keep her mouth shut. so all us pesky women aren’t really going to be a part of his blessed future, unless he gets saddled with a real ass-kicker of a mother-in-law. he just needs to get good grades and do well in school and get enough money for him to be worth a good bride, one with enough education to be worth her dowry and to not embarass the family, and maybe bring in some extra money, but not actually think too hard for herself. meantime he can just wear his older brother’s clothing and eat his mom’s food. oh, and keep that screwing around with us slutty local white women under wraps, so we can all pretend you’re a virgin too, which of course you’re not. and if god forbid you marry a female scientist, it will all be ok, because she can still run your household and ship your babies and all of you over to your parents house every weekend because hey, what mother needs a break when you have an extended indian family to cater to. and all of this will just support, in the end, your bottomless idea of your own self-worth and just how lucky the world is to have you.
like being stereotyped, razib? like how it feels? oh, but i wasn’t been explicitly negative about your culture, was i, because, you know, it’s all true, so it’s just a statement of fact and you should just get over it. you’re just another whiny brown man with a sense of entitlement.
get it yet?

My italics and bolding.

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Top 10 Myths About Evolution

By Razib Khan | December 19, 2006 1:31 pm

Check out the list (upon which a book is based). Food for thought, some of the “myths” are actually starting points for philosophical debates (e.g., Dawkins vs. Gould).


Firefox gripe

By Razib Khan | December 19, 2006 12:08 pm

I upgraded to Firefox 2.0 almost immediately, but am feeling user’s remorse. Perhaps 2.0 was a non-trivial improvement over 1.5, but the lack of familiarity with its options and preferences because things were changed (I’m sure there was a UI rationale) really means that I took a short-term step back. Anyway, this is my first irritation with Firefox, the “release” seemed timed to one-up IE 7.0, it really should have been a bug fix and the switcheroo in the UI seems to be the main reason to stick it with a 2.0, even though as I offer above I think the UI changes mean a loss of short term productivity.


John Hawks on introgression

By Razib Khan | December 18, 2006 9:49 pm

The whole post is worth reading, but the money shot:

The central point of the paper is exceedingly simple. Haldane demostrated in 1927 that the fixation probability of a single copy of a new adaptive allele is 2s. This means that if archaic humans had any alleles that would have been adaptive for modern humans, it would take only a very small amount of interbreeding for modern humans to pick up these alleles, with a near-100 percent likelihood.

Greg Cochran has more. Obviously this work builds upon the Lahn introgression paper. Instead of crude species typologies the data is now pointing to a more complex set of relations between gene lineages.


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