Gene Expression

Evolutionary history reversible  permlink

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At least in this case, Troglomorphism, trichobothriotaxy and typhlochactid phylogeny (Scorpiones, Chactoidea): more evidence that troglobitism is not an evolutionary dead-end:

The scorpion family Typhlochactidae Mitchell, 1971 is endemic to eastern Mexico and exclusively troglomorphic. Six of the nine species in the family are hypogean (troglobitic), morphologically specialized for life in the cave environment, whereas three are endogean (humicolous) and comparably less specialized. The family therefore provides a model for testing the hypotheses that ecological specialists (stenotopes) evolve from generalist ancestors (eurytopes) and that specialization (in this case to the cavernicolous habitat) is an irreversible, evolutionary dead-end that ultimately leads to extinction. Due to their cryptic ecology, inaccessible habitat, and apparently low population density, Typhlochactidae are very poorly known. The monophyly of these troglomorphic scorpions has never been rigorously tested, nor has their phylogeny been investigated in a quantitative analysis. We test and confirm their monophyly with a cladistic analysis of 195 morphological characters (142 phylogenetically informative), the first for a group of scorpions in which primary homology of pedipalp trichobothria was determined strictly according to topographical identity (the "placeholder approach"). The phylogeny of Typhlochactidae challenges the conventional wisdom that ecological specialization (stenotopy) is unidirectional and irreversible, falsifying Cope's Law of the unspecialized and Dollo's Law of evolutionary irreversibility. Troglobitism is not an evolutionary dead-end: endogean scorpions evolved from hypogean ancestors on more than one occasion.

More at ScienceDaily. Those with broader knowledge of different species can weigh in, but for some reason I always felt skeptical of the idea that specialization was a dead end...though I suppose it could be analogized to an asexual clonal lineage which is at some adaptive peak. A naive idea I had in mind is that specializations are at least as likely to be gain of function mutations as loss of function mutations, and it is easier to go from functional variants to non-functional ones. But in any case, biological generalizations almost always have a lot of exceptions, the question is the extent of the exceptions, and whether that makes the generalization useful or not.

Citation: Cladistics, 26:2, doi:10.1111/j.1096-0031.2009.00277.x

Posted by Razib Khan at 1:13 AM • 0 Comments

Small dogs & wolves in The New York Times  permlink

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A few weeks ago I commented on the paper about the origin of the small dog phenotype in the Middle East. Now The New York Times has an article on a newer paper, New Finding Puts Origins Of Dogs in Middle East. Here's the conclusion:

Dog domestication and human settlement occurred at the same time, some 15,000 years ago, raising the possibility that dogs may have had a complex impact on the structure of human society. Dogs could have been the sentries that let hunter gatherers settle without fear of surprise attack. They may also have been the first major item of inherited wealth, preceding cattle, and so could have laid the foundations for the gradations of wealth and social hierarchy that differentiated settled groups from the egalitarianism of their hunter-gatherer predecessors. Notions of inheritance and ownership, Dr. Driscoll said, may have been prompted by the first dogs to permeate human society, laying an unexpected track from wolf to wealth.

Humans are often conceived of as the selection pressure on our domesticates, but clearly this is a two-way street. Cows have strongly shaped the human genome in the form of lactase persistence. And of course there have been many pathogens which have jumped from domesticates to humans, including ones which might change human behavior. The evolutionary process in this conception is a complex series of interactive feedback loops, and the task of reconstruction is going to be a laborious, but fascinating one. And luckily, we have "control" populations who have been little impacted by domesticated animals.

Here's the letter in Nature.

Posted by Razib Khan at 7:45 PM • 5 Comments

The continuing "death of comments"  permlink

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A week ago I observed that commenting was being transformed with the spread of Disqus and Echo. The Big Money has now introduced Echo:

The comments themselves are also more interactive. Any of your postings can be shared with your friends on Facebook, followers on Twitter, or any of your connections on the other supported services. You can also reply to fellow commenters, tell them you like their posts, or flag any inappropriate or spam messages that you see. All commenters have their own profiles, which you can find by clicking on their profile names and viewing their details. There you'll be able to find all the comments they've recently left, allowing you to develop commenter-crushes on the smartest TBM readers.

Since no biomedical firm has developed a drug which allows you to become "sleepless" as in Nancy Kress' Beggars series comments and comment structure has to be value-added. As I made clear earlier, I don't generally see much value-added in comments on many websites, but that's just me. I depends on what you want to get out of comments, and how much marginal time you have in your life I guess. Flagging/comment rating systems are probably good though. I like Less Wrong's system for what it's worth, even though I've gotten voted down for kind of being a dick over there. It's better than nothing.

The readership of my weblogs are rather select, so I have to delete very few transparently stupid comments (that is, stupid because of the endogenous stupidity of the commenter, not because someone is being a jackass for fun or spite). Consider the highest educational attainment of the readership of this weblog for American readers:

84% have at least a bachelor's degree
19% have a master's degree
13.5% have a professional graduate degree (JD, MD, etc.)
20.5% have a non-professional doctorate*

I assume that a substantial number who haver only a bachelor's degree are likely graduate school drop-pouts, or currently pursuing graduate degrees (going by the age distribution, which is skewed toward those in their twenties and thirties). Additionally, 83% of readers have taken calculus. These variables should argue against stupid comments (I have a friend who is a quantitative social scientist who can't blog about quantitative social science because his readers on his popular weblog are simply too stupid to really understand distributions, so the comment threads devolve from the get-go).

On the other hand, 86% of readers are male, and 12% are virgins. These are two demographics more likely to engage in what I might term "Usenet" behavior.

Note: ~25% of Americans aged 25 or older have bachelor's degrees, for point of comparison.

* Of those with non-professional doctorates, 60% are in math, science and engineering. 23% are in social science, such as psychology and economics. The balance are in other fields, with a little over half of those in the humanities.

Posted by Razib Khan at 6:51 PM • 3 Comments

South Park  permlink

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14th season begins tonight. The website. You can usually get the episode a bit earlier at Allabout-SP.net.

Posted by Razib Khan at 5:13 AM • 0 Comments

A little bit of the Others in Us  permlink

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Dienekes has reposted some of the abstracts from the meeting of the American Association of Physical Anthropologists. This one caught my eye, Genetic analyses reveal a history of serial founder effects, admixture between long separated founding populations in Oceania, and interbreeding with archaic humans:

Genetic anthropologists continue to debate whether human neutral genetic variation primarily reflects a continuum of demes connected by local gene flow or colonization and serial founder effects. A second unresolved issue concerns the genetic contribution of archaic species to the modern human gene pool. Some studies suggest that this contribution was substantial and that it played an important role in human adaptation. These issues remain unresolved because of inadequacies and biases in datasets, problems in statistical methodology, and the failure to recognize that different evolutionary processes may produce similar outcomes. This study redresses these limitations by analyzing gene identity within and between populations in a dataset comprised of 614 STRs assayed in 1,983 people from 99 widespread populations. Our strategy is to fit hierarchical models to these data and examine residual deviations from the models. Each model involves nesting smaller units such as populations into larger units such as continental regions. It is possible to restate many of these models as either expansions or reductions of each other and thereby identify aspects of population structure that have had a major impact on the overall pattern of diversity. The strong fit of a model estimated using the Neighbor Joining algorithm indicates that human genetic diversity primarily reflects a history of successive founder effects associated with our exodus from Africa, not a continuum of demes connected by gene flow. Residual deviations from the model suggest: 1) the genomes of Oceanic peoples are the product of two independent waves of migration to the region and admixture, and 2) genetic exchange occurred between archaic and modern humans after their initial divergence.

Would be nice if they found a gene which was likely differentiated between archaic and modern alleles, but it doesn't look like that. But the number of populations seems rather large.

Posted by Razib Khan at 3:51 AM • 1 Comments

Diversity in the tech world  permlink

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A few weeks ago I had dinner and drinks with an old friend who works for the firm which invented the x86 series of microprocessors. He's doing well financially right now, and was very bullish on his firm. More specifically it seems that they're on a hiring binge (he knows because he's been on hiring committees). So a while back he forwarded a resume of a graduate school acquaintance to human resources. His boss came up to him later and told him that there were remunerative benefits to forwarding resumes. If the individual gets hired:

- There is a entry-level $2,000 bonus to the referrer

- But, if the hire is female, there is a $6,000 bonus to the referrer

- But, if the hire is an underrepresented minority, there is a $12,000 bonus to the referrer

All well and good. But my friend was curious: "How about if the hire is a female from an underrepresented minority?" Apparently his boss was at a loss for words, and admitted that he didn't really know. That situation had simply never occurred.

The NSF has data from 2008 on doctoral recipients. 28% of recipients in the physical sciences were female, multiplying that out by the number of blacks, Hispanics and American Indians, I get 84 physical science doctorates to women who were are underrepresented minorities in 2008.

Context: My friend is a European American, his boss is Southeast Asian. Additionally, in general the engineering jobs referred to here require a doctorate in the physical sciences.

Posted by Razib Khan at 11:34 PM • 4 Comments

You have no privacy  permlink

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How Privacy Vanishes Online. Pretty banal actually. Social networking has really changed things. As I've said before I'm fascinated by the large number of people who, even those who want to be anonymous, enter in their real email addresses when leaving a comment. There seems a default "trust unless you shouldn't trust" setting, so we naively input our information assuming it isn't being mined by someone. In any case, a bigger issue in the future I think will be stupid government officials who scan up documents which they shouldn't scan up. It's happened a few times so far, but I think it'll get worse in this decade.

Posted by Razib Khan at 11:07 PM • 7 Comments

The Genius in All of Us: Why Everything You've Been Told About Genetics, Talent, and IQ Is Wrong  permlink

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Over the past week I've been asked via email and on message boards about about David Shenk's new book, The Genius in All of Us: Why Everything You've Been Told About Genetics, Talent, and IQ Is Wrong. Since I haven't read the book I can't really comment, but I did finally listen to Will Wilkinson's interview with Shenk on bloggingheads.tv. It seems to me that Will exhibited more clarity and precision in one sentence in relation to the term heritability than Shenk did in 10 minutes. It is true there are many people who don't understand that 80% heritable does not mean that a trait is "80% genetic." In fact, I really don't know what a trait being "80% genetic" means in a precise sense, but I also know that long time readers of this weblog do fall into this trap.

Instead of reading Shenk's book I strongly suspect that people might gain some more genuine insight about heritability and the genetics of complex traits by looking at what we know about height. We don't know much in terms of the underlying genes; height seems to be controlled by many genes of small effect. But, we do know that in the developed world, where nutritional intakes have saturated, height is about ~80% heritable. That is, most of the variation in the population can be accounted for by variation in genes. There are probably gene-environment interactions in regards to the trait of height. For example, there may be individuals whose genotypes are more sensitive to nutritional deprivation than others, so that changing uniform nutritional intakes across a population may not change just the median of the distribution, but also the general shape. But those interaction effects are obviously not as important today in the developed world where malnutrition is very rare.

At least judging by the conversation with Wilkinson, and the title of the book, Shenk seems to want to spotlight people who are many standard deviations from the norm. For example, Mozart and Michael Jordan are arguably not 1 in 100, or even 1 in 1,000, in regards to their domains of virtuosity. I think that focusing this far out to the tails is interesting, and makes for good narrative as one can populate it with illustrative anecdotes, but on any given quantitative trait most people are going to be much closer to the median. Variation on the margins of the normal are very significant, and all too often ignored. In here that I think that the simplest models have the most utility. So you want to complexify, just focus on the outliers....

Note: Using Amazon's search inside feature I see that Shenk mentions gene-environment interaction quite a bit, but not gene-environment correlation.

Posted by Razib Khan at 6:58 PM • 7 Comments

I see white people (in China)  permlink

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There's an article in The New York Times on the recent paper which extracted genetic material from remains in Xinjiang dated to 4,000 years ago. Remember that these remains exhibited male lineages which were west Eurasian, specifically R1a1, while the female lineages (mtDNA) were more heterogeneous, both eastern and western. This particular twist in history is of very strong interest. I think there are three reasons for this. First, it is counter-intuitive, as we don't have a good grasp of how mobile ancient nomadic populations were. Most of their history is unaccessible because they were often not literate. We know of them by and large by the shadows that they cast upon the literate civilizations. Our map of the past is strongly skewed toward civilized sedentary groups, where lack of mobility was the norm. Second, there has been a strong attempt by the Chinese government to control and massage these findings for a generation, in large part because of concerns about separatist movements in western China. The Uyghurs of Xinjiang are almost certainly in part descended from these ancient Europoid populations. Finally, there is sublimated race pride on the part of white people.* Since white people created the modern world as we know it, it may seem rather trivial to exhibit interest in lost white civilizations. But the Chinese are apparently proud of a partly fictitious 5,000 year history based on descent from the Yellow Emperor,** while black nationalists have long ludicrously grappled onto continuity with Carthaginians and Egyptians. The fame of peoples long gone seems to have a stronger proportional weight than more recent contributions.***

One of the major points in regards to the Indo-European peoples of ancient Xinjiang are their strange affinities to populations on the western rim of Eurasia, the textile patterns which seem almost Celtic for example. But you have to be careful how you frame data. Consider this from The New York Times article:

The language spoken by the people of the Small River Cemetery is unknown, but Dr. Mair believes it could have been Tokharian, an ancient member of the Indo-European family of languages. Manuscripts written in Tokharian have been discovered in the Tarim Basin, where the language was spoken from about A.D. 500 to 900. Despite its presence in the east, Tokharian seems more closely related to the "centum" languages of Europe than to the "satem" languages of India and Iran. The division is based on the words for hundred in Latin (centum) and in Sanskrit (satam).

There is actually some dispute as to significance of the centum-satum division as phylogenetically informative, but here's a map which shows the modern 3,000 year old distributions of the two groups (pretty close to modern distributions as some groups, like Celtic, were replaced by languages in the same category, Romance):

Read on »

Posted by Razib Khan at 3:15 PM • 13 Comments

Tickle Partay  permlink

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Posted by Razib Khan at 1:31 AM • 0 Comments

Apartheid of Iberian Neandertals & modern humans  permlink

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The Middle-to-Upper Palaeolithic transition in Cova Gran (Catalunya, Spain) and the extinction of Neanderthals in the Iberian Peninsula:

The excavations carried out in Cova Gran de Santa Linya (Southeastern PrePyrenees, Catalunya, Spain) have unearthed a new archaeological sequence attributable to the Middle Palaeoloithic/Upper Palaeolithic (MP/UP) transition. This article presents data on the stratigraphy, archaeology, and 14C AMS dates of three Early Upper Palaeolithic and four Late Middle Palaeolithic levels excavated in Cova Gran. All these archaeological levels fall within the 34-32 ka time span, the temporal frame in which major events of Neanderthal extinction took place. The earliest Early Upper Palaeolithic (497D) and the latest Middle Palaeolithic (S1B) levels in Cova Gran are separated by a sterile gap and permit pinpointing the time period in which the Mousterian disappeared from Northeastern Spain. Technological differences between the Early Upper Palaeolithic and Late Middle Palaeolithic industries in Cova Gran support a cultural rupture between the two periods. A series of 12 14C AMS dates prompts reflections on the validity of reconstructions based on radiocarbon data. Thus, results from excavations in Cova Gran lead us to discuss the scenarios relating the MP/UP transition in the Iberian Peninsula, a region considered a refuge of late Neanderthal populations.

ScienceDaily has a lot more. Here's the important point I think:

The samples obtained at Cova Gran using Carbon 14 dating refer to a period of between 34,000 and 32,000 years in which this biological replacement in the Western Mediterranean can be located in time, although the study regards as relative the use of Carbon 14 for dating materials from the period of transition of the Middle to Upper Palaeolithic period( 40,000 and 30,000).

The results also support the hypothesis that there was neither interaction nor coexistence between the two species.

There's long been a model that modern humans replaced Neandertals without coming into direct conflict with them. The model would be that modern humans simply disrupted the ecology which the Neandertals depended upon. It seems a bit too pat for me, but considering the very low population densities of hunter-gatherers, and in particular Neandertals, perhaps it is possible.

Citation: The Middle-to-Upper Palaeolithic transition in Cova Gran (Catalunya, Spain) and the extinction of Neanderthals in the Iberian Peninsula, doi:10.1016/j.jhevol.2009.09.002

Posted by Razib Khan at 12:44 AM • 1 Comments

Twins in Kerala  permlink

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The strange case of the twins of Kodinji:

The latest survey, from December 2009, counted 265 pairs of twins in the village, which is home to about 3,000 families and 13,000 inhabitants. This equates to a twinning rate of about 30 to 35 per 1,000 live births within a radius of about 500 metres. The average in the rest of the country is 8.1 per 1,000 live births.

...

Unlike in Cândido Godói, consanguineous (blood-related) marriages are not a factor in the Kodinji twin phenomenon. "The majority of the population is Muslim, but the incidences of twinning are present even among the small minority of Hindu families," Sribiju explains. "More importantly, brides who are not originally from Kodinji are giving birth to twins after they move to the village."

Posted by Razib Khan at 12:21 AM • 3 Comments

Vitamin D & influenza - randomized trial  permlink

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Randomized trial of vitamin D supplementation to prevent seasonal influenza A in schoolchildren:

Design: From December 2008 through March 2009, we conducted a randomized, double-blind, placebo-controlled trial comparing vitamin D3 supplements (1200 IU/d) with placebo in schoolchildren. The primary outcome was the incidence of influenza A, diagnosed with influenza antigen testing with a nasopharyngeal swab specimen.

Results: Influenza A occurred in 18 of 167 (10.8%) children in the vitamin D3 group compared with 31 of 167 (18.6%) children in the placebo group [relative risk (RR), 0.58; 95% CI: 0.34, 0.99; P = 0.04]. The reduction in influenza A was more prominent in children who had not been taking other vitamin D supplements (RR: 0.36; 95% CI: 0.17, 0.79; P = 0.006) and who started nursery school after age 3 y (RR: 0.36; 95% CI: 0.17, 0.78; P = 0.005). In children with a previous diagnosis of asthma, asthma attacks as a secondary outcome occurred in 2 children receiving vitamin D3 compared with 12 children receiving placebo (RR: 0.17; 95% CI: 0.04, 0.73; P = 0.006).

I will attest to improvement in my own respiratory health since I began taking vitamin D supplements in 2007, but more studies need to be done to confirm that this is a robust finding.

Citation: Am J Clin Nutr (March 10, 2010). doi:10.3945/ajcn.2009.29094

Posted by Razib Khan at 5:56 AM • 6 Comments

God is too cute to be a literalist  permlink

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And God Said: How Translations Conceal the Bible's Original Meaning is a litany of how the mapping from Hebrew to other languages has resulted in a distortion of the precise idiom of the original. I actually thought the best example of this given was a non-Biblical one, the fact that English-speakers are totally clueless as to the implication of the title of the Mexican film Like Water for Chocolate, which sends a rather clear message only intelligible in a Spanish speaking context. English speakers have tended to generate novel meanings from the cryptic title at total variance with the original intent and clarity in Spanish (I actually recall spending some time trying to figure out the deeper meaning of the title when I first watched this film).

This all got me to thinking: what exactly was God thinking in delivering his revelation in verbal form? It seems clear that formal logic would have been much more precise, or even some form of ancient mathematics. The fact that God delivered his revelation in the flexible form of language seems to weigh in on the side of those Christians who are not Biblical literalists, since literalism is pretty much a joke. This sort of assertion by me is a rejection of a position I held several years back whereby non-literalist Christians were slippery types who always attempted to fit the scripture to the context of their times. That may be true, but it is likely true for self-described Fundamentalists as well, except they don't admit it. Some atheists, myself in the past, are wont to declare that the Fundamentalist despite the falsity of his beliefs at least adheres to an honest "plain" reading of the text of the Bible. The reality is that there is no "plain" reading, for believer and non-believer alike.

Posted by Razib Khan at 5:38 AM • 18 Comments

Small dogs guide  permlink

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Via a comment, a site which you will love, or which will drive you insane, Complete Small Dogs Guide. I found this story about a chihuahua carried away by a large bird, only to return to its owner.

Posted by Razib Khan at 5:16 AM • 3 Comments