Archive for March, 2010

Others in Siberia

By Razib Khan | March 24, 2010 3:04 pm

The complete mitochondrial DNA genome of an unknown hominin from southern Siberia:

With the exception of Neanderthals, from which DNA sequences of numerous individuals have now been determined…the number and genetic relationships of other hominin lineages are largely unknown. Here we report a complete mitochondrial (mt) DNA sequence retrieved from a bone excavated in 2008 in Denisova Cave in the Altai Mountains in southern Siberia. It represents a hitherto unknown type of hominin mtDNA that shares a common ancestor with anatomically modern human and Neanderthal mtDNAs about 1.0 million years ago. This indicates that it derives from a hominin migration out of Africa distinct from that of the ancestors of Neanderthals and of modern humans. The stratigraphy of the cave where the bone was found suggests that the Denisova hominin lived close in time and space with Neanderthals as well as with modern humans….

The tree gets bushier? Just see John Hawks and Carl Zimmer.

CATEGORIZED UNDER: Evolution, Genetics

The biophysical limits of cognitive computation

By Razib Khan | March 23, 2010 8:26 pm

In this diavlog with Glenn Loury the behavioral economist Sendhil Mullainathan recounts the results of an experiment.
– If given the option of paying $100 for an item vs. $80 for an item, but in the second case having to go across town for the item, respondents choose $80 and going across town
– If given the option of paying $1000 for an item vs. $980 for an item, but in the second case having to go across town for the item, respondents choose $1000 and not going across town

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CATEGORIZED UNDER: Economics

Fructose, bad in rats

By Razib Khan | March 23, 2010 7:45 pm

You’ve probably heard about the research in the press, but please see Derek Lowe for perspective. The difference between high fructose corn syrup and sugar as an additive may, or may not, be problematic. But the uncertainty in this area is why I try and avoid excessively processed foods*, there’s just so much we don’t know. If you’re poor and short on cash perhaps the high ratio of calories per cent of processed foods are simply necessary, but for people of even modest means I don’t think it is that difficult to cut most consumables which come out of boxes from your diet.
Again, I want to reiterate that I don’t necessarily have an atavistic fear of food science and industry. Or think that “nature always knows right.” The human state of nature is Malthusian and characterized by high mortality. But I think some trends in the modern food industry driven by demand side pressures result in medium-to-long term gains in morbidity in return for short-term spikes in pleasure.
* If something has fewer than six ingredients, and you know what the ingredients are (i.e., they’re not obscure chemicals), I don’t know if I would avoid that. After all, cooking is in many ways a form of processing too. As are cheeses and pickling.

CATEGORIZED UNDER: Culture

Research blogger of the year is….

By Razib Khan | March 23, 2010 7:36 pm

Not Exactly Rocket Science, authored by a certain Edmund Yong. Congratulations Mr. Yong, but I will admit being less than surprised.
Update: And also, congratulations to all the other winners, several of whom are in my “regular reads.”

CATEGORIZED UNDER: Culture

The evolution of morals

By Razib Khan | March 21, 2010 11:09 pm

I have a short piece up at Comment is Free at The Guardian, The origins of morality do not matter. Its flavor is a bit different from my typical blog posts because the format enforces more brevity, so I decided to try and leverage some analogies. I conclude:

… Our moral consensus is a river whose course shifts across the plain, constrained by the hills thrust upward by biology. Only history knows where the river will flow next, though evolution can hint at the range of possibilities.

On a note related to this piece, I will be posting a review of The Price of Altruism: George Price and the Search for the Origins of Kindness in a few months.

CATEGORIZED UNDER: Anthroplogy, Evolution

Personal genomics is dead, long live personal genomics

By Razib Khan | March 21, 2010 8:21 pm

The Andrew Pollack piece which I hinted at came out a few days ago: Consumers Slow to Embrace the Age of Genomics. For what it’s worth, I think this chart from Dr. Daniel MacArthur is right on:

This too will pass. I believe that like the internet the knowledge and analysis of our genetic information is going to be ubiquitous after a rough period when most of the dreams of grandeur from the first generation entrepreneurs fade.

CATEGORIZED UNDER: Genetics

Katz

By Razib Khan | March 19, 2010 11:19 am

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CATEGORIZED UNDER: Blog

The luck of the Irish

By Razib Khan | March 18, 2010 2:12 pm

Henry Louis Gates Jr. is looking for his male Irish forebear using genetics:

Well, it turns out that the men sharing that Ui Neill haplotype tended to have certain surnames. If we use those surnames, we narrow the number of possibilities in Allegany and Hampshire counties to 178 men born between 1800 and 1830 bearing 22 surnames.
What’s so exciting about this? Well, it turns out that the men in the Gates family line have a particular mutation, a slight variation, in our Ui Neill haplotype. And we inherited that slight mutation, a spelling variant in that DNA signature, through one of those 178 guys. If the father of Jane’s children, my Irish great-great grandfather, has any other male descendants walking around on the planet, he will have exactly the same y-DNA signature, with this particular variant, as my father, brother and I do.
And so, we are advertising for any male descendant of one of these 178 men to contact us and take the DNA test. With a (wee) bit of luck, one of the millions of unsolved genealogical mysteries facing African Americans today can be solved.

Descendants of slaves naturally have less of a paper trail than most people (Chinese clans often trace descent on the order of one thousand years, though some of this may be fictive). This is where even simple uniparental lineages can offer some psychic utility.

CATEGORIZED UNDER: Genetics

We be symbolic

By Razib Khan | March 18, 2010 4:25 am

The Evolution Of Symbolic Language by Terrence Deacon and Ursula Goodenough. Deacon’s The Symbolic Species: The Co-Evolution of Language and the Brain is a book I liked a great deal, though in hindsight I don’t think I had the background to appreciate it in any depth (nor do I now).

CATEGORIZED UNDER: Cognitive Science

Evolutionary history reversible

By Razib Khan | March 18, 2010 1:13 am

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

CATEGORIZED UNDER: Evolution

Small dogs & wolves in The New York Times

By Razib Khan | March 17, 2010 7:45 pm

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.

CATEGORIZED UNDER: Evolution, Genetics

The continuing "death of comments"

By Razib Khan | March 17, 2010 6:51 pm

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.

CATEGORIZED UNDER: Blog, Culture

South Park

By Razib Khan | March 17, 2010 5:13 am

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

CATEGORIZED UNDER: Blog

A little bit of the Others in Us

By Razib Khan | March 17, 2010 3:51 am

Dienekes has reposted some of the abstracts from the meeting of the American Association of Physical Anthropologists. This one caught my eye, <bGenetic 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.

CATEGORIZED UNDER: Evolution, Genetics

Diversity in the tech world

By Razib Khan | March 16, 2010 11:34 pm

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.

CATEGORIZED UNDER: Culture

You have no privacy

By Razib Khan | March 16, 2010 11:07 pm

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.

CATEGORIZED UNDER: Culture, Technology

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

By Razib Khan | March 16, 2010 6:58 pm

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.

CATEGORIZED UNDER: Genetics

I see white people (in China)

By Razib Khan | March 16, 2010 3:15 pm

Central_Asian_Buddhist_Monks.jpegThere’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):

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CATEGORIZED UNDER: Genetics, History

Tickle Partay

By Razib Khan | March 16, 2010 1:31 am
CATEGORIZED UNDER: Blog, Culture

Apartheid of Iberian Neandertals & modern humans

By Razib Khan | March 16, 2010 12:44 am

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

CATEGORIZED UNDER: Ecology, Evolution
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