Archive for December, 2007

Gay heads of state (as in, obligate homosexuals)

By Razib Khan | December 31, 2007 7:14 pm

So, I just found out that Sayyed Qaboos bin Sa’id Al ‘Bu Sa’id, the Sultan and autocrat of Oman, is a homosexual. Not that there’s anything wrong with that! But that got me thinking, are there any other homosexual heads of state* out there? Please post a reference if you submit a candidate.
* Prime Ministers count in a parliamentary democracy.


Formalization & process

By Razib Khan | December 31, 2007 6:22 pm

Rich Lawler has an insightful comment:

It’s interesting to note that a few of the most insightful observations about the evolutionary process were first promulgated verbally, then later proven mathematically (unlike H-W equilibrium). These include runaway sexual selection (first adumbrated by Fisher, then shown mathematically possible by Lande and Kirkpatrick), the handicap principle (first adumbrated by Zahavi, then–finally–shown to be mathematically possible by Grafen), and, of course, natural selection (first adumbrated by what’s-his-face, then formalized by Wright, Fisher, and later Price, among others). And of course, all of these topics were debated back-n-forth until the math made them more clear.

I think the key here is the reference to evolutionary process, dynamics which span time and space beyond intuitive conceptualization. Verbal “lock & key” models are often sufficient to communicate the biophysical processes at work when an enzyme and substrate interact. A graphical illustration of a biophysical process is clear as the visual mapping is can be precise and accurate; the primary actors here are material. Not so for something as abstract as “fitness.” Verbal descriptions of moments about distributions of abstract concepts are not sufficiently precise to allow for fruitful theoretical inference beyond the most elementary level. Of course, a non-mathematical idea can, and usually does, serve as the seed for future growth of formal theory. But when the subject is by its nature complex formalism is often simplest route.


Sex ratio & migration via X & Y

By Razib Khan | December 31, 2007 9:56 am

Looking for Nm* values for humans I stumbled across an interesting paper, Estimating sex-specific processes in human populations: Are XY-homologous markers an effective tool?:

…To test this idea, we analyzed XY-homologous microsatellite diversity in 33 human populations from Africa, Asia and Europe. Interpopulation comparisons suggest that the generally discordant pattern of genetic variation observed for X- and Y-linked markers could be an outcome of sex-specific migration processes (mfemales/mmales ~ 3) or sex-specific demographic processes (Nfemales/Nmales ~ 11) or a combination of both….

Basically the authors were looking at diversity on homologous markers on the X & Y chromosomes. Previously researchers had compared mtDNA (female) and Y (male) lineages, but the authors point out that the comparison using these two regions of the genome might be problematic (e.g., mtDNA is subject to its own peculiarities such as high mutational rate, and might not be as neutral as we assume). The diversity across the markers that they focused on implied two general dynamics:
1) female biased migration or 2) female biased sex ratios
The authors do note data which is locally contradictory, but the overall trends fit our expectations from other data, males usually exhibit more reproductive skew which drives their effective population down vis-a-vis females. Additionally, both common chimpanzees and H. sapiens seem to exhibit a tendency toward patrilocality & patrilineality which is somewhat anomalous among mammals (think of the matrilineages which are focus of social life among whales and elephants). But what is the balance between the two? The models above were presented as extreme cases, holding sex ratio or male and female migration even. It seems that a skew of 1 to 11 is a bit high for most populations, so likely the female migration rate is somewhat higher than the male one. But if history is a guide it may also be that male and female migration tend to follow different tracks, the former being rarer long distance movements and the latter much more common deme-to-deme exchanges. The Arab enslavement of women from black Africa is the main example I can think of long distance migration of females as opposed to males (black males in much of the Arab world were castrated). In contrast, we have many cases of groups of males founding new hybrid populations. The mestizo populations of the New World and the peoples of Madagascar are two prominent cases where males traveled over long distances and left a dominant genetic imprint (in the case of Madagascar the female lineages tend to be from the adjacent African continent).
* N = population size and m migration rate between populations.


p's & q's vs. verbs

By Razib Khan | December 30, 2007 7:28 pm

icedancing.jpgEvolgen and Popgen Ramblings have put up posts where they criticize a parameter of the acceleration paper. John Hawks responds in the comments. But I thought this line was priceless:

Nah, you’re not a dirty anti-adaptationist! All these labels are nonsense; all that is important is understanding the math involved — something Gould never really seemed very interested in. The problem with purely verbal arguments is that there is no scorekeeper.: it’s like Olympic ice dancing, or something.

A lot of the formalism in population genetics isn’t that mentally taxing (although the derivations may be!). For example, the famous (or infamous) Hardy-Weinberg Equilibrium, p2 + 2pq + q2 = 1, requires about a middle school level of mathematical knowledge (grade 7 or 8). And one can describe it in words, but by doing so one removes its algebraic utility and clear precision of communication. A non-formal Hardy-Weinberg Equilibrium could never have become one of the pillars upon which population genetic theory was built, to use programming terminology, verbal arguments are often far less extensible than mathematical ones. In the short term verbal description of population genetic theory is much clearer to those who are not used to thinking in terms of variables, but over the long term they leave a lot to be desired in generating a contingent & systematic model. I also think that when scientists communicate and debate it wastes a lot of time when you argue in words because without any magnitude placed upon the implicit variables people easily talk past each other and generate mountains of repetitive prose.
Update: See comments for a clarification.


It's about inevitability….

By Razib Khan | December 30, 2007 4:08 pm

Laelaps has an excellent post up, Evolution’s Arrow, which you should read. Set some time aside, it is long. I don’t know enough about paleontology to comment with great insight on the many of the topics which Laelaps alludes to, and some of them get a bit philosophical for my own taste (that is, issues turn on the interpretation of words), but there is one point which I might assert is somewhat muddy:

…Looking at the hominid evolutionary bush pictured below [see here, it’s clear that we are but a single surviving twig of a group that once had a much greater diversity, australopithecines (including the “robust” forms in Paranthropus) seeming to be a much more successful type of hominid even if they are presently extinct. Given that our own species has only been in its modern form for little more than 200,000 years and we are daily poisoning our own well in terms of the global environment, I don’t know if we can rightly say that we are any better or worse than any of the related forms that came before. The extinction of so many different hominids begs the question of why they are no longer around to join us if their forms were so good. If so many hominids so close to us could go extinct, doesn’t that reflect that evolution is more contingent than directed towards a certain number of forms?

First, regarding the other hominid groups. Certainly some of them had some longevity on their side, but, it is important to note we are considerably more numerous. One could integrate across the time period that these species flourished and sum up total numbers to compare a raw count and use this as an estimator of “success.” But as I said, much hinges on words such as successful. But the second point is that I think there is a strong likelihood that other hominids no longer exist because we marginalized them (or absorbed them) through direct competition or destruction of their habitat. Look at what we are doing the other extant homonoids. We are co-opting their ecosystems for our own use, and on occasion we even hunt and consume them. It seems likely that they have been saved so far because they tend to inhabit biomes which our species has exploited to a lesser degree until recently. This emphasizes the fact that adaptation and response to other organisms, evolution’s arms race, is a critical parameter which expands the scope of the discussion beyond the interface of the environment and the phenotype of a given species.



By Razib Khan | December 28, 2007 9:59 am

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Obesity is heritable, not genetic

By Razib Khan | December 27, 2007 1:27 pm

Genome Wide Association (GWA) Study for Early Onset Extreme Obesity Supports the Role of Fat Mass and Obesity Associated Gene (FTO) Variants. Even if this is true, these correlations between particular alleles and obesity hold for the modern German lifestyle. I guarantee you that population level diversity in weight correcting for height was sharply attenuated when all Germans were basically farmers and laborers. It seems possible to me that in pre-modern times “obesity alleles” might have been selected for something different in an environment where gaining a lot of weight and becoming subject to higher risk of various chronic diseases was not a plausible outcome. With the change in environment the whole phenotypic landscape shifted as the environment in which the genes expressed was radically altered.
Note: I’m skeptical that obesity alleles mark a much more efficient metabolism. After all, if LCT can nearly fix in northern Europe why not genes which allow you to more efficiently convert food into energy would not have been swept to fixation long ago? I suppose this could be balancing selection, but there’s only so much of that a genetic architecture can support.


Vitamin D: why evolution may matter

By Razib Khan | December 27, 2007 9:47 am

Mark of Denialism left a comment below re: Vitamin D deficiency:

I wouldn’t call that evidence thin biff. The role of vitamin D in tuberculosis was actually pretty well nailed by studies of immigrants in the UK which demonstrate that latent TB infections will reactivate in the sunless climate. The demonstration of the role of Vit D in making defensins seems the likely physiological explanation.
I am wary though of some of the more hyperbolic claims I’ve seen about vitamin D lately. It’s fascinating stuff, sure. But until replicated in RCT rather than epidemiologically I think it’s too early to recommend universal supplementation with a vitamin that does have a toxic syndrome. Many vitamins have appeared similarly astounding in such studies and the benefits failed to pan out. This is likely due to certain epidemiologic biases that tend to show people who actively take care of themselves (take supplements, exercise, etc.) are generally wealthier, and healthier

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The Elders of Ron Paul

By Razib Khan | December 27, 2007 5:11 am

Ed and Mark are asking what’s up with Ron Paul and the Neo-Nazis? I think…it’s complicated. Colugo sketches out the general lay of the land pretty well, Ron Paul is a “paleo,” specifically a paleolibertarian. He derives his ideology from the Old Right, and promotes a personal bourgeoise ethic. Three points:
* Ron Paul’s intellectual mentor was a Jew, Murray Rothbard, and the greatest intellectual in his firmament was a Jew, Ludwig von Mises. If Ron Paul is a closet Neo-Nazi he is a strange sort indeed. I think we can dismiss the idea that Ron Paul is a closet white nationalist. In his spare time he tends to obsess over the Gold Standard monomaniacally. That’s his passion, not the race.
* But there are white nationalists in the broader “paleo” movement. That is, though they do not personally avow racialist views they also do not necessarily view it is illegitimate prima facie. Joe Sobran is a man who mixes these various streams in on person, a convert to anarcho-capitalism through the writings of Murray Rothbard, this former editor of National Review was purged for his anti-Israel stances during the early 1990s, and now flirts with white nationalism and Holocaust Revisionism. But this isn’t to show that all paleos are racialist, after all, the conservative Bob Taft Club is headed by an individual who is half-Korean and half-Jewish. But note that the same individual was interviewed (as a fellow traveler) on a Neo-Confederate radio show with a strong racialist and non-trivial anti-Semitic tinge (the show also interviewed David Duke and a host of other white nationalist luminaries). Most of you will also know of Ron Paul’s famous newsletter from the mid-1990s. I would be willing to bet that if Ron Paul did not write the text, he was probably aware of its general outline. Again, I think this is not evidence of a convinced and principled racialist, but it reflects a man who does not reject white nationalist viewpoints as a matter of course. This should not shock some of the more liberal readers of this weblog, after all, I suspect many of you would find some of the milder and more hinged critiques of Jewish and/or Zionist1 power in shaping American attitudes toward the Israeli-Arab conflict quite cogent. Just because someone is crazy doesn’t mean all their utterances are crazy. That is, in my assessment, Ron Paul’s attitude toward white nationalists (many of you would probably hold though that the views Paul accepts as non-crazy from white nationalists are crazy!).

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The Ascetic Style in American Atheism

By Razib Khan | December 25, 2007 12:52 pm

On this Sunday’s Weekend Edition on NPR there was a piece titled Removing Religion from the Holidays a Tall Order. Much of the story focuses upon Greg Epstein, a Humanist Chaplain at Harvard, and his attempt to forge a new more humane secular cultural sensibility which does not reject all that that is religious because it is religious. On the other side there are others who say that the trends Epstein is promoting “sounds like religion and smells like religion.” As I noted in earlier, these sorts of issues are not so cut & dried, and common sense is often a better guide to the “right decision” than inferences from axiomatic doctrine. Shouldn’t we be as concerned about if it smells good as the provenance of the smell?
I’m assuming that on this day many of your are celebrating Christmas right now. This was written earlier and scheduled to post now, so I am eating, drinking and socializing. Many of you will likely read this a day or two later. As a culture we exhibit a synchronicity in our behaviors and rituals, we are not creatures who engage in social Brownian motion. This is not a matter of right or wrong, it is a matter of what we are.

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Fun Christmas music

By Razib Khan | December 24, 2007 9:56 am

Indigenous European paganism

By Razib Khan | December 24, 2007 4:57 am

Found out something interesting today. In the Russian republic of Mari El there exists an indigenous pagan tradition which is not a reconstruction. That is, the pagans of Mari El trace their practice in an unbroken line back to their ancestors, as the Christianization during the period of Ivan the Terrible (the 16th century) was only partial. Other European pagans are by necessity neo- and must reconstruct their system of beliefs and rituals from extant records and folk traditions. The Saami were pagan until the 18th century, and with that I had assumed that all pre-Christian traditions had died. This falsifies that, though some might quibble that the European nature of the cult of Mari El is a matter of geographical technicality (that is, Orthodox Russia’s status as a European nation are somewhat ambiguous to begin with). Here is an article about the pagan revival:

Unlike in western Europe, paganism among the Mari constitutes an unbroken tradition rather than a New Age construction. Mari anthropologist Nikandr Popov points out that pagan prayer meetings were permitted by decree during the Second World War – with collections being made for the front – and survived subsequent Soviet attempts to suppress them. Today Mari pagans gather together for approximately 20 festivals annually, at which they offer animal sacrifices in specially designated sacred groves. There are now 360 such groves in the republic and around 120 karts (pagan priests), according to one of the claimants to the title of head kart, Aleksei Yakimov.

We forget that Russia is one of the most ethnically diverse nations in the world. Much of this is simply due to the fact that the settlement of Siberia by Slavs is a relatively recent and half-measured affair, and the indigenous tribes have no been absorbed into the national identity. But even in European Russia to the west of the Urals the Slavic speaking farmers who expanded into the forests of the hunting & fishing peoples to the north and east did not sweep away all before them. In contrast such relics are rare in central and western Europe; one case may be the Sorbs in eastern Germany, who are what remains of the Slavic people who once dominated the lands on the eastern side of the Elbe. Another are the Vlachs of the Balkans, Romance speaking herders who are probably the remains of the peasants of Pannonia & Illyircum who once sent Emperors to Rome (e.g., Diocletian). In this case Russia is more like China or India than the rest of Europe. The dominant cultural dispensation is numerically preponderant and can assert hegemony within the bounds of the geographic extent of the civilization, but numerous residual peoples with distinct identities remain “undigested.”


She be mighty fly

By Razib Khan | December 23, 2007 3:42 pm

M. Yglesias seems to be dissing Rihanna’s “Umbrella.” Well, I’ll raise him “Pon de Replay”….

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Jamie Lynn Spears: it runs in the family?

By Razib Khan | December 23, 2007 12:58 pm

Hometown Reacts: Residents Respond To Pregnancy News in relation to Jamie Lynn Spears & Casey Aldridge’s impending parenthood:

But we did manage to talk to a few locals, who, quite honestly, weren’t too shocked to learn that Britney’s little sister was pregnant, either because teen pregnancies aren’t all that uncommon in Kentwood, or because, after all, she is Britney’s little sister.
“They tried to keep it secret, I don’t know why. In Kentwood, everything gets out. You got kids who are 13 or 14 and pregnant in Kentwood, we’re about used to it around here,” Donald Church said. “But it seems like a big deal around here. … A lot of people can’t believe it. I used to work with her dad, and I couldn’t believe it. You know, little Jamie … it’s kind of freaky.”
“I heard about it on the radio, they were talking about it. It’s real popular down there. Everybody knows about them,” Raynard Norman laughed. “It’s embarrassing, kind of. If it’s not her, it’s Britney, so at least it’s not Britney this time. But I’m not surprised, not really. … Nobody’s surprised because it’s not uncommon with her family. Next time, use a condom.”

In The Genetical Theory of Natural Selection R.A. Fisher offered up a reason why long term decreased fertility was never going to be an evolutionary problem for the human race: if any fertility was in any way heritable the proportion of the population which exhibited traits resulting in relative fecundity would slowly increase and replace those disinclined toward reproduction. Evolution is often characterized as “Survival of the Fittest.” First, that is actually simply even metaphorically corrected in regards to evolution driven by natural selection. But second, it is probably more accurate to say it is survival of the fertile. Physiological fitness may not correlate with reproductive output. Remember antagonistic pleiotropy?
Note: It could of course be cultural heritability. Fisher elucidates that argument as well, arguing that pro-natalist religions will promote the increase of their flock. In Rodney Stark’s The Rise of Christianity he makes the argument that the sects opposition to infanticide and communal support networks were critical in allowing it to marginalize paganism in part through procreation.


Tocharians within the last 6,000 years?

By Razib Khan | December 23, 2007 6:11 am

From Different Matrilineal Contributions to Genetic Structure of Ethnic Groups in the Silk Road Region in China:

Although our samples were from the same geographic location, a decreasing tendency of the western Eurasian-specific haplogroup frequency was observed, with the highest frequency present in Uygur (42.6%) and Uzbek (41.4%) samples, followed by Kazak (30.2%), Mongolian (14.3%), and Hui (6.7%).

The paper supports the idea that Uyghurs are an admixed population from Western and Eastern sources. But is this just an ancient cline of allele frequencies? In other words, are Uyghur lineage frequencies simply a function of their geographical position between East and West?

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Most Canadian Non-whites have Vitamin D deficiency

By Razib Khan | December 23, 2007 1:21 am

Are you getting enough vitamin D?:

The research, which is awaiting publication in a medical journal, found that 100 per cent of those of African origin were short of vitamin D, as were 93 per cent of South Asians (those of Indian or Pakistani origin), and 85 per cent of East Asians (those of Chinese, Indochinese or Filipino origin, among other countries).

Insufficient vitamin D amounts were also found among those of European ancestry, but were less widespread, at 34 per cent of those surveyed.

This is in Canada, very far north. That being said, if 93 percent of South Asians in Canada have Vitamin D deficiency I doubt it is that much lower in the United States, we aren’t that far south. Additionally, a greater proportion of Canadian South Asians are light skinned Punjabis, while more American South Asians are darker skinned Gujaratis. My doctor had me tested because she knew I didn’t drink milk, and her own olive skin had resulted in her having a deficiency. As for as other groups, blacks and East Asians are generally not lactose tolerant, so it is more likely that these groups won’t be drinking fortified milk. That’s a problem.
Why should you care? There are probably some long term consequences in terms of chronic diseases of old age, but the biggest issue is probably it makes you more susceptible to flu and other low grade ailments. It’s a quality of life issue.


Whither the adaptive hypersphere?

By Razib Khan | December 22, 2007 9:26 am

No, this should not be in the “Physical Science” category. By hypersphere I’m thinking of the model that R.A. Fisher popularized as opposed to Sewall Wright’s conception of the adaptive landscape, a multidimensional sphere within which was located a position which was the adaptive optimum. While Wright’s landscapes were rugged, and so opened up the possibility that gene-gene interactions and some level of stochasticity and meta-population dynamics were critical factors in evolution over the long term, Fisher’s more symmetrical model focuses on the power of selection operating on loci of independent effect in driving inevitable frequency changes. The image to the left is simply a 2-dimensional rendering of Fisher’s idea, as a population converges upon the adaptive peak the mutations should be of smaller and smaller effect so that they do not result in an “overshoot” and a decrease in fitness. The implication clear: initial mutations may be of large effect, but over time as selection for a trait affects change across the genome subsequent mutations should be of smaller fitness effect. Additionally, if the ecological pressures remain the same it seems plausible that the selection coefficient of the initial mutant which drives the population toward the optimal phenotype will be greater than the selection coefficients of subsequent mutations, which after all arise in a situation where other mutants already exist.
That’s the theory. Why do I bring this up? It’s about the evolution of skin color. I’ve posted quite a bit on this topic, and have read many of the recent papers coming out of genomics labs. In short over the past 5 years a lot has come into clearer focus and we seem to know the half a dozen or so genes of large effect which control most of the world wide variation in pigmentation. These genes and their allelic variants come in many flavors and combinations which result in the range of phenotypes we see around us, a continuous variable controlled by discrete genetic components. There are many of these genes. SLC24A5, SLC45A2/MAPT/AIM1 (yes, it has three names that I can tell), KITLG, OCA2, MC1R and ATRN, these are just some of the candidates which have been fingered so far. Note that some genes seem to be responsible for between population variation in some comparisons but not in others (e.g., SLC24A5 can account for about 1/3 of the difference between Europeans and Africans, it can account for none of the difference between East Asians and Africans). Additionally note that some of these genes are definitely responsible for other traits. OCA2 and KITLG seem to have associations with variation on eye color and hair color, while some MC1R alleles cause red hair.

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Why adaptive evolution is not evolution

By Razib Khan | December 22, 2007 3:58 am

Specifically, as evolgen points out the acceleration paper was focused on adaptive evolution, the subset of allele frequency changes driven predominantly by the force of natural selection. What’s the rest? Read the post.
Why does this matter? Evolution is a science, and in science this sort of pedantic precision in definition, terminology and meaning matters a great deal because it is embedded in a contingent system. One of the most frustrating things about the necessity of the rearguard action against Creationists is that the “controversy” swamps this reality, that evolution is a science which is the process of refinement and change due to theoretical & empirical developments. Instead evolution is only discussed in the broadest generalities, which is an insight with might spark the imagination in the 19th century, but is now simply a background assumption which serves as the framework for the real action. Books such as this one are a necessary evil. Why evil? Because the time invested in the production of that prose could have been time devoted to research and (alas) grant writing.



By Razib Khan | December 21, 2007 3:41 pm

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Why phenotypic races may not disappear

By Razib Khan | December 21, 2007 5:46 am

In response to my post Mixed-race but homogeneous appearance? several individuals mooted the possibility that admixture may result in the vanishing of race as a social construct. Actually, I don’t think this is the true. To the left is a photo from my post Can you tell if you’re black or white? where I explored the genetics of a case where two black-white biracial parents produced fraternal twin daughters of disparate appearance. While one sister seemed to favor her African ancestors in look, another sister seemed to resemble her European forebears. Across the full sample space of their genome it seems likely that both these girls are about half European and half African in ancestry, but on the finite loci which are salient in the production of the features which we use to code for “races” they most certainly favor one ancestral group over the other. The basic point is that a population, and individuals, can exhibit great admixture and yet still realize the full phenotypic range of the ancestral types. This is because genetics is not blending, admixture will not result in a homogenization toward a mean unbounded by a distribution characterized by variance.

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