Friday, February 29, 2008

Neurogenomics and genetic interactions   posted by Razib @ 2/29/2008 01:18:00 PM

Two PNAS papers today that caught my eye, going to read for later, Distinct genomic signatures of adaptation in pre- and postnatal environments during human evolution and Defining genetic interaction. Both Open Access.


Snorg Tees Girl   posted by Razib @ 2/29/2008 02:23:00 AM

A story about Alice Fraasa the Snorg Tees girl. I've been bombarded on The New York Times website with the ads all week and I clicked. I assume that it has ads all the time, but hell if I could tell you what they were about, I don't notice them. Until this week. Other people must have clicked too, the Snorg Tees link was down. Assume this is a new ad buy and their network engineers weren't ready for the increase in traffic....

Thursday, February 28, 2008

A Spanish coincidence?   posted by Razib @ 2/28/2008 11:39:00 PM

Empire: How Spain Became a World Power, 1492-1763 is an excellent narrative history which focuses on the period of time when Spanish history was a substantial subset of world history. The author, Henry Kamen, is a British historian who happens to be a resident of Barcelona, and he's gotten into trouble with Spanish nationalists for not framing the facts in a manner befitting Castilian triumphalism. All for the good I would think. In any case, Kamen does a good job balancing the standard kings & battles narration with thick social history. I checked out the book for two reasons. First, I was interested in the treatment given to the impact of disease in its relation to the New World, and secondarily, a better understanding of the role of the Hapsburg dynasty in early modern European history (I'm working through another book focusing on the Austrian Hapsburgs). Though the author was more interested in the social and economic parameters which drove the Spanish conquest of the New World, he really couldn't dodge the critical necessary precondition of disease, so I found out what I needed to know. Imagine that the sepoys who fought for the East India Company and the maharajas who aligned with the British were extinct a generation or two after the aid that they rendered the new sahibs. That's a pretty good analogy. On the second issue, there was a lot of detail which was illuminating; who knew that Phillip the II was a connoisseur of Dutch culture? I didn't (though I did know that Charles V was a Netherlander, I suspect that my Anglo-Saxon cultural background has inculcated me thoroughly with the Black Legend). But there some other more surprising points which I hadn't thought of.

First, I did know of one dynamic which plays a large role in explaining various events in Spanish history: during this whole period the Spanish Empire, and even the core kingdom of Spain, was actually a dynastic union which was relatively unintegrated politically. In fact, the Carlist Wars of the 19th centuries were fought over in part by the regions to preserve their customary laws and traditions against the centralizing tendency of the crown (or one lineage of it), which was attempting to create a modern nation-state. In an ironic but unsurprising twist, the same regions, such as the Basque provinces and Catalonia, which had served as centers of traditionalist-reactionary factions switched to supporting Leftish movements when those political configurations supported their autonomy from the centralizing pressures of Madrid. So in the 19th century the regions of Spain supported reaction and tradition because that reaction and tradition overlapped with their independence. In the 20th century conservatives had become reconciled with the nation-state and so it was to the Left that these regions looked to to support their aspirations for freedom from Castilian imperialism. But I had not been aware of the extent to which regions such as Aragon, which was a separate kingdom from Castile under the same monarchy, were definitively independent. Not only would the assemblies of Aragon refuse to be taxed to support wars on behalf of the Spanish Empire (e.g., the attempt to suppress rebellion in the Netherlands), but they also might refuse to send troops! This was not an isolated incident, it seems that the New World was Castile's responsibility, while Aragon looked towards its own possessions in Italy. Speaking of which, Kamen points to the fact that these Italian possessions, in particular Genoa, provided much of the capital and financial talent which kept the Empire afloat. Christopher Columbus was not the only Genoese in the service of the Spanish crown, the trade with the New World based out of Seville was backed in large part by non-Castilian capital, whether it be Italian, Portuguese or German.

I only emphasize the international aspect to the Spanish Empire (which was Kamen's sin in the eyes of Spanish historians who wanted to highlight Castile's overwhelming agency in all events) because the text is also littered with references to a particular parochialism of Castilian culture and society which is all too familiar. Kamen notes that, for example, in the 16th century Castilian literature was relatively popular in translation in other parts of Europe. But the Castilians rarely translated works in other languages into the their own! Additionally, even Castilian works were usually printed abroad because of the relative shoddiness of local artisans and technology; often in the possessions which later became Belgium or in Italy. Finally, Kamen observes that the Spanish foreign service had difficulties because of the lack of polyglots in Castile; generally diplomats would make recourse to translators, or, they would recruit from Italy, Flanders or Wallonia, because many in those regions would know Castilian as well as their own native tongue and possibly other languages. There are numerous other examples given the text. Assuming this is correct, it reminds me a great deal of aspects of the Ottoman or Chinese interaction with the West when these societies were in relative decline, down to the lack of interest in foreign arts & literature as well as the need for middlemen to translate because of linguistic ignorance. Of course, a one-dimensional picture of these societies is going to be incorrect, there were attempts to modernize from within and influences from without. But a strong overall sense pervades that these cultures were inwards looking by conscious preference and their elites were very satisfied with their station in the world and saw no need to measure themselves against outsiders.

One could chalk this up to Muslim influence in Spain. But resemblances to the last century of the Chinese Empire suggest to me that this is a repeated pattern in many societies which have reached an equilibrium which can be broken only by powerful exogenous shocks. One could imagine for example something very similar to what happened to the Ottomans and Ching (Manchus) if a Slavophile faction had succeeded in keeping the Russian aristocracy insulated from Western European influences (as one was, one could make the case that something like this did happen because of the inability to shift from the outmoded absolutism which the Tsars perpetuated). I don't have a real answer to what was going on in Spain, but I had to comment on the correspondences with the trajectory of the Ottoman Empire at the other end of the Mediterranean. After a vigorous expansion under a warrior caste both these polities seemed to have just decided to take a few centuries long nap, spelled by occasional attempts to modernize and catch-up, but only in terms of specific ends as opposed to general techniques.


Gene expression differences between populations   posted by Razib @ 2/28/2008 09:36:00 PM

Evaluation of Genetic Variation Contributing to Differences in Gene Expression between Populations (Open Access):
Gene expression is a complex quantitative trait partially regulated by genetic variation in DNA sequence. Population differences in gene expression could contribute to some of the observed differences in susceptibility to common diseases and response to drug treatments. We characterized gene expression in the full set of HapMap lymphoblastoid cell lines derived from individuals of European and African ancestry for 9156 transcript clusters...Gene expression was found to differ significantly between these samples for 383 transcript clusters. Biological processes including ribosome biogenesis and antimicrobial humoral response were found to be enriched in these differential genes, suggesting their possible roles in contributing to the population differences at a higher level than that of mRNA expression and in response to environmental information. Genome-wide association studies for local or distant genetic variants that correlate with the differentially expressed genes enabled identification of significant associations with one or more single-nucleotide polymorphisms (SNPs), consistent with the hypothesis that genetic factors and not simply population identity or other characteristics (age of cell lines, length of culture, etc.) contribute to differences in gene expression in these samples. Our results provide a comprehensive view of the genes differentially expressed between populations and the enriched biological processes involved in these genes. We also provide an evaluation of the contributions of genetic variation and nongenetic factors to the population differences in gene expression.

ScienceDaily has the digest.


Wednesday, February 27, 2008

Mitty Romney is hyper-typical for a Mormon   posted by Razib @ 2/27/2008 11:01:00 PM

The Audacious Epigone crunches the Pew Religion Survey and comes up with some more insights....


More pathogens means more collectivism?   posted by Razib @ 2/27/2008 07:07:00 PM

Pathogen prevalence predicts human cross-cultural variability in individualism/collectivism (Open Access):
...We suggest that specific behavioural manifestations of collectivism (e.g. ethnocentrism, conformity) can inhibit the transmission of pathogens; and so we hypothesize that collectivism (compared with individualism) will more often characterize cultures in regions that have historically had higher prevalence of pathogens. Drawing on epidemiological data and the findings of worldwide cross-national surveys of individualism/collectivism, our results support this hypothesis: the regional prevalence of pathogens has a strong positive correlation with cultural indicators of collectivism and a strong negative correlation with individualism. The correlations remain significant even when controlling for potential confounding variables. These results help to explain the origin of a paradigmatic cross-cultural difference, and reveal previously undocumented consequences of pathogenic diseases on the variable nature of human societies.

The, r = -0.69 at p-value 0.001 and n = 68. You can find the raw data here. It would be cool to see trends within nations/societies. For example, variation in altitude.

Related: Toxoplasma gondii & human culture.

Labels: , ,

SLC24A5, the molecular genetics?   posted by Razib @ 2/27/2008 01:55:00 AM

How Skin Color Is Determined:
In 2005 researchers identified a gene called SLC24A5 as a key determinant of skin color. Rebecca Ginger and colleagues now confirm that the protein product of this gene (NCKX5) is an ion exchanger; it exchanges sodium for calcium across a membrane, regulated by potassium. But unlike other NCKX proteins, they found that NCKX5 is not present on the cell surface, but internally in a compartment known as the trans-Golgi network. This compartment is where new proteins and vesicles are processed, modified and sorted.

When the researchers knocked out NCKX5 in melanocytes (the skin cells that manufacture the melanin pigment), melanin production decreased dramatically. They also demonstrated that changing the ancestral amino acid (alanine) at position 111 to the European form associated with lighter skintone (threonine) reduced NCKX5's exchanger activity.

Related: SLC24A5 and skin color.

Labels: ,

Tuesday, February 26, 2008

The economic basis of cultural creativity?   posted by Razib @ 2/26/2008 05:32:00 PM

Reading Power and Plenty: Trade, War, and the World Economy in the Second Millennium by by Ronald Findlay and Kevin H. O'Rourke. So far somewhat like A Farewell to Alms, except painted on a much broader palette. I've read The Moral Consequences of Economic Growth, and though I wasn't convinced by all the specific examples the general thrust of that work makes sense. Nevertheless, I was still surprised when Findlay and O'Rourke connected the introduction of Champa rice strains and the cultural efflorescence of the Sung period. Say what? OK, this the logic, the new rice strains resulted in far greater productivity, and so China's population doubled in about 200 years, from 50 to 100 million. This 200 year period can be thought of as a transient between stationary states around the Malthusian limit. Findlay & O'Rourke don't focus much on the specific expressions of creativity during this period, but if you read much Chinese history you note that there was a lot of stuff going on during this period which set the tone for the next 1,000 years, from Neo-Confucianism to styles of landscape painting.


Monday, February 25, 2008

Pew Religion in America   posted by Razib @ 2/25/2008 07:02:00 PM

Pew is out with a new survey of religion in America. I've only skimmed it so far, but it has lots of interesting stuff. Note for example that this survey suggests that are marginally more self-identified Buddhists in America than Muslims (this is probably a function of the fact that Buddhism, and generally Buddhist ideas and concepts, have a much wider appeal to white Americans than Islam, whose "product" is less strong differentiated from forms of Christianity).

Check the methodology.

Via Rod Dreher.


Sunday, February 24, 2008

Podcastiness   posted by amnestic @ 2/24/2008 09:38:00 PM

I've been going into podcast overload lately, mainly because of this boing boing post. Wanted to alert you all to the high quality and interesting sound engineering of Radio Lab if you didn't know about it already. I've jammed the Memory, Placebo, and Stress episodes so far and was pleased overall with the level of informativeness, though I always prefer for brain regions to have names rather than descriptions. The Memory episode features Joe Ledoux and Karim Nader discussing the reconsolidation revival that occurred a few years ago.

In other news, The Sound of Young America has cool guests and The Rub has been doing a History of Hip Hop series that is worth your time.


Emotional fragility as a sexually selected trait   posted by agnostic @ 2/24/2008 03:02:00 PM

Roissy recently drew up a list of female skills for attracting males, and although it is clearly weighted toward succeeding in short-term relationships, the rank order seems about right for getting married too. One quick way to see what has mattered to men is to look for sexually dimorphic traits. As Darwin noted, such traits can have the flavor of "armaments," used to shove same-sex rivals out of the mating competition (such as deer antlers), or "ornaments" which attract mates (such as the peacock's tail), or both. I'll review some evidence that emotional vulnerability has been sexually selected in human females due to its attractiveness to males, rather than its use in female vs. female competition.

First, let's use YouTube to convince ourselves that emotional fragility makes a female more attractive, regardless of her physical appearance. Consider Emmylou Harris, Karen O, Elizabeth Fraser, or Hope Sandoval -- each is more desirable as a mate than if she were more tough-minded. In males, the attractiveness of fragility is conditional. If he can honestly signal manliness in dominating other males (however he does that), then emotional fragility around women may convince them that he's the best of both worlds. But if he lacks drive or ambition, then fragility will only make him appear needy and pathetic. Males who succeed here include Johnny Cash, Mike Ness, LL Cool J, and Joey Ramone.

Next, let me clarify the term "emotional fragility." It's a tendency to cry easily about something that would upset a caring person, a trait that will move men to protect and comfort her. More concretely, I'll treat it as a combination of the Big Five personality traits Neuroticism and Agreeableness, with more weight given to the former. A graph will help to illustrate [1]:

As for sex differences in these traits, see this previous post for a review of a meta-analysis by Costa et al. (2001). In brief, across all cultures of the world, females score higher than males on average for both Neuroticism and Agreeablness, though the magnitude depends on the physical and social environment that the population is adapted to: Europeans show huge sex differences, while Africans and East Asians show less pronounced differences. Among Europeans, the female mean is between 0.5 and 0.6 SD above the male mean for both Agreeableness and Neuroticism. A new cross-cultural survey by Schmitt et al. (2008) confirms this, although they find a slightly lower difference between means in Agreeableness. Both of these articles also provide good overviews of previous research.

While other personality traits show sex differences, Neuroticism and Agreeableness are by far the most dimorphic. Interestingly, in the first large-scale study designed to test changes in personality during adolescence, using a personality measure very comparable to an adult measure, McCrae et al. (2002) found a significant Time x Gender interaction effect for Neuroticism. During adolescence, females were much more likely to increase in Neuroticism than were males, in both the US and Belgium. Neuroticism declines for both sexes in the mid-20s, and drops even further by age 40. So, we observe a pattern of dimorphism that emerges just after puberty and gradually switches off beginning at the age when females would have had their first child. It is similar to physical attractiveness in females or muscularity in males, suggesting it has been sexually selected.

It is clear that fragility is unlikely to count as an "armament" used for same-sex competition, since it makes one more vulnerable to intimidation, teasing, and other forms of pushing one's same-sex rivals out of the mating market. We would expect it to be more of an "ornmament" that attracts mates, then. It may not make a female appear sexier, but when a girl starts to cry because she feels that she's become a burden to her friends and family, it may be nonsense, but a guy can't help but want to comfort her and protect her. Once she inevitably feels a little better, the guy will feel like he's performed his service as a man. And, modern malarkey aside, guys feel good when they do chivalrous and manly deeds, so that they would seek out women who offered the greatest opportunity to do so, and girls feel good when these acts are done for them. [2]

Moreover, comforting a female in need often involves close physical contact, such as holding her hand, holding her close and rubbing the upper part of her back, brushing the hair off of her face, or wiping the tears from her eyes. Physical bonding like this strengthens the relationship two people have, and also signals to her that the guy is a "protector of loved ones" (to borrow a phrase from the Mystery Method) -- a quality she is interested in during the years leading up to motherhood. It also tells her that he would take care of her if she became sick. So, it serves the dual purpose of attracting mates and detecting who among them is worth hanging onto.

[1] The fact that the Big Five uses the axes of low Neuroticism - high Neuroticism and low Agreeableness - high Agreeableness doesn't mean anything deep about how the traits are realized physiologically, or about how genes influence personality. We could rotate the old axes by, say, 45 degrees and come up a new set of two axes: a Tough-minded - Fragile dimension and a Cordial - Irascible dimension. The old traits of high A, low A, high N, and low N would lie in the quadrants of the new graph. In short, like a physicist, I'm perfectly free to chose my coordinate system to make life easy; I'm not claiming that things are different from how they're typically described.

[2] Of course, there is variation too -- some women succeed in the tough-minded niche and feel belittled when men try to do romantic things for them, and thus around whom men feel little motivation to behave in a chivalrous way. Roissy's many remarks about female lawyers serve as a good example of this.

Labels: ,

Saturday, February 23, 2008

Group Selection and the Wrinkly Spreader   posted by DavidB @ 2/23/2008 06:28:00 AM

A recent article by D. S. and E. O. Wilson [1] has been acclaimed by some as reviving the fortunes of group selection. It must for a time have been available on the web (since I downloaded a pdf of the published version a month or so ago), but the closest thing I can find at present is this slightly different version submitted to (and presumably rejected by) Science in 2006. [Added: I should perhaps have mentioned that the two Wilsons are not related. No kin selection here!]

As gnxp's resident critic of group selection I feel an obligation to say something about the article, but I find the task dispiriting. Much of the Wilsons' article is a re-working of issues which have been debated many times before. (See e.g. my discussion here.) The debate has been largely about the most useful way of describing and classifying the phenomena, rather than about the biological facts. Hostility to group selectionism is provoked in part by the tendency of its advocates to claim for group selection a range of phenomena that other biologists regard as more usefully described in terms of inclusive fitness (kin selection). This hostility will not be allayed by such prominent assertions as:

During evolution by natural selection, a heritable trait that increases the fitness of others in the group (or the group as a whole) at the expense of the individual possessing the trait will decline in frequency within the group.

If the 'group' contains local concentrations of relatives (as it very often will), or if the trait preferentially affects relatives, this assertion is simply not correct. Did the Wilsons not notice this, or were they deliberately loading the dice against interpretations in terms of kin selection? Another potential confusion of the issues comes later in the article, where the Wilsons discuss insect eusociality. They argue strongly that between-colony selection is important in the evolution of eusocial insects, for example in traits such as nest construction. But whoever doubted it? Once eusociality (specialisation of reproduction) has been established, of course genetic variation and selection will often be between different colonies. The difficult question is how eusociality itself becomes established. The important insights into this have come from inclusive fitness theory, not group selectionism. (See for example chapter 11 of [2].)

Rather than spend more time on arid and abstract theoretical issues, I think it will be more rewarding to focus on a single empirical case, which the Wilsons themselves offer as a good example of the benefits of a multi-level approach. It can therefore serve as a test case of the benefits of that approach. The example I have chosen is the Wrinkly Spreader...

As the Wilsons describe this case,

the "wrinkly spreader" (WS) strain of Pseudomonas fluorescens evolves in response to anoxic conditions in unmixed liquid medium, by producing a cellulosic polymer that forms a mat on the surface. The polymer is expensive to produce, which means that non-producing 'cheaters' have the highest relative fitness within the group. As they spread, the mat deteriorates and eventually sinks to the bottom. WS is maintained in the total population by between-group selection, despite its selective disadvantage within groups, exactly as envisioned by multi-level selection theory.

I have followed up the Wilsons' reference for this case, and then some other citations. [Refs. 3, 4, and 5]

The facts of the WS case (stripped of theoretical baggage) seem to be as follows.

Pseudomonas fluorescens is a rod-shaped flagellated aerobic bacterium. It is found widely in the soil and in fresh water. In nature it is normally found as a single free-moving cell. In laboratory cultures, on the other hand, it often develops mutant strains which stick together rather than living singly. One of these is the Wrinkly Spreader strain, so-called because on slides of nutrient jelly it spreads out in sheets with a distinctive wrinkly appearance. In open containers (e.g. test tubes) of nutrient fluid the WS bacteria form a mat on the surface. Within about 10 days the mat becomes too heavy and sinks to the bottom. If the supply of nutrient is adequate, the process may be repeated, with new WS mats forming and eventually sinking.

Rainey and colleagues have studied the genetics of the WS strain.[3, 4 and 5] They have found that WS bacteria produce an excess of a cellulosic polymer which causes them to stick to each other and to surfaces. A side-effect of this is that they form a scum at the liquid-air interface (I presume this is a surface-tension effect, but the precise mechanism does not matter.) The production of the polymer uses scarce resources, so WS bacteria reproduce more slowly than non-WS bacteria in the same circumstances. However, this is offset by the advantage of being able to colonise the surface layer, with its better access to oxygen.

The description so far assumes that the mats on the surface contain only WS bacteria, usually derived from a single mutant individual. WS bacteria within the mat may however mutate in various ways which stop them overproducing the polymer, so that they revert to the ancestral phenotype. These mutants reproduce more quickly than the WS strain. They therefore tend to spread within the mats. But this weakens the structural integrity of the mats, which causes them to break up and sink more rapidly than the pure WS mats.

So what has this to do with group selection? What are the 'groups', and where is the 'selection'?

I think it will help to divide the cycle into two stages: before and after the emergence of non-WS mutants within the mats. At the beginning of the process, there are only single bacteria. Some of these mutate to the WS form, and literally stick together. Within the broth culture as a whole, WS mutants have lower fitness than the ancestral form, but the mutation gives them characteristics which enable them to predominate in a particular part of the ecosystem, i.e. the surface layer. Rainey et al. describe this as a form of 'cooperation', in which 'cooperation is costly to individuals, but beneficial to the group'. They note that the WS individuals are closely related (since they are descended from the same mutant individual) and describe the trait as spreading by 'kin selection'. This seems to me an unnecessary interpretation. The WS individuals in the surface layer are not sacrificing any fitness for the benefit of other individuals: they are simply using resources in a way that enables them to occupy this part of the environment. In a heterogeneous environment it can be misleading to average fitness over the entire range of sub-environments. For analogy, suppose a species of sheep ranges over a variety of altitudes. At higher altitudes the climate is colder, and the sheep need thicker fleece to live there in the winter. Sheep with mutations causing them to grow thicker fleece may have lower fitness than the average sheep, because it is costly to grow thick fleece, but at high altitudes the thick-fleeced variant may predominate because it is better adapted to that particular environment. Similarly, the WS strain is better-adapted to the surface layer. It is merely a coincidence that the adaptation involves the formation of 'groups'. We could imagine that instead of producing a polymer, and sticking together, the mutants produced little bubbles of gas which enabled them to float at the surface. In this case, no-one would dream of describing the process as either kin or group selection.

There is a more plausible case for appealing to group selection in the later stage of the process, when non-WS individuals have emerged within the WS mats. These individuals obtain the advantage of living in the surface layer without paying the cost. It is therefore reasonable to describe them as 'cheaters' or 'defectors'. They reproduce more rapidly, for a while, but in the longer term destroy the mats, to the detriment of all. According to the Wilsons, 'WS is maintained in the total population by between-group selection, despite its selective disadvantage within groups, exactly as envisioned by multi-level selection theory.' This is one possible interpretation of the facts, but it seems to me to go beyond the evidence presented by Rainey et al. We should note (as the Wilsons do not) that all surface mats collapse within a few days, whether or not they contain defectors. The regeneration of surface mats then depends on the establishment of a new population of WS individuals at the surface. These could emerge either by new mutations from the ancestral form, or from fragments of the collapsing WS mats. (It is not clear from the papers I have seen which of these usually occurs.) Either way, the Wilsons' description is incomplete. It implies that some WS 'groups' (the ones without defectors) survive indefinitely, while others fail. This is not the case. Even if a description in terms of group selection is formally valid, it does not (in my opinion) add much of value to the understanding of the phenomena. And if this is one of the best examples of group selection that its advocates can find, one cannot have much confidence in the others. (And indeed, some of the others, like the Wilsons' reference to the territorial behaviour of female lions, seem even worse. How can anyone sensibly discuss this without mentioning that the lionesses of a pride are usually closely related? [6, p. 37])

This is not to say that an account in terms of group selection will never provide useful insights into evolutionary processes. The evolution of disease organisms such as Myxomatosis seems to be one very plausible example. But the Wilsons' article does not persuade me that group selection, as distinct from inclusive fitness, is more than a minor wrinkle on the face of evolutionary theory.


[1] D. S. and E. O. Wilson: 'Rethinking the Theoretical Foundation of Sociobiology', Quarterly Review of Biology, December 2007, vol. 82. No.4, 327-348.

[2] J. Maynard Smith and E. Szathmary: The Origins of Life: from the birth of life to the origins of language, 1999

[3] P. B. and K. Rainey: 'Evolution of cooperation and conflict in experimental bacterial populations', Nature, 425, 2003, 72-4.

[4 P. B. and K. Rainey: 'Adaptive radiation in a heterogeneous environment', Nature, 394, 1998, 69-72.

[5] A. J. Spiers et al.: 'Adaptive divergence in experimental populations of Pseudomonas fluorescens. I: Genetic and phenotypic bases of Wrinkly Spreader fitness', Genetics, 161, 2002, 33-46.

[6] G. B. Schaller: The Serengeti Lion, 1972.

Labels: , ,

New kind of diavlog   posted by Razib @ 2/23/2008 02:58:00 AM

The other day I was wondering whatever happened to A New Kind of Science. Well, Stephen Wolfrom is on the latest

Friday, February 22, 2008

NPR on human variation   posted by Razib @ 2/22/2008 12:44:00 PM

An In-Depth Look at Genetic Variation, covers Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation (about ~15 minutes long, interview with Rick Myers). Also, Wired blogs the most recent spate of papers (and gets a sound-bite from Marcus Feldman)....

Update: Readers might appreciate this from the Science paper:
However, the between-population variance is sufficient to reveal consistent population structure because subtle but nonrandom differences between populations accumulate over a large number of loci and yield principal components that can account for a major portion of the variation (21).

What's reference "21"? A. W. Edwards, Bioessays 25, 798 (2003). Human Genetic Diversity: Lewontin's Fallacy. Ding, dong....

(A figure from the Science paper below the fold)


Thursday, February 21, 2008

Where be the bugs?   posted by Razib @ 2/21/2008 03:28:00 AM

Cool paper in Nature, Global trends in emerging infectious diseases. Not cool because infectious diseases are great, but I believe they've been (and are) major evolutionary pressures on our species. Great map too. From the legend:

a) zoonotic pathogens from wildlife
b) zoonotic pathogens from non-wildlife
c) drug-resistant pathogens
d) vector-borne pathogens

Not surprised about the intersection with world population density. Just by inspection, the Indo-Gangetic plain looks to be the "winner" here! Though it does seem that Sub-Saharan Africa holds its own in terms of representing above its population-weight class in the wild-life derived and vector-born pathogen categories. Might we be able to chalk that up to a long history of coevolution between the African ecosystem and hominid species? Domesticated animals seem to be more of an issue in the old Eurasian Oikumene as you would expect. For more precision on the global trends and correlates, check out their regressions.


Robert J. Samuelson is not an economist (Paul A. Samuelson is)   posted by Razib @ 2/21/2008 01:42:00 AM

This is a post for Google. A post I wish had been there for me during my periods of confusion on this topic. I notice that Chris Roach recently referred to Robert J. Samuelson as a "Respected economist." He isn't. Robert J. Samuelson is a financial and economic journalist. He has bachelor's degree in government from Harvard, so one assumes he has taken an economics course or two or three. Samuelson has a column in Newsweek which often focuses on economics; this means that he is a major public figure in this area. I had assumed that Robert J. Samuelson was a prominent economist who was moonlighting as a journalist until a few years ago when I was curious if he was related to Larry Summers. I knew Summers was related to an economist with the last name Samuelson. I think this is a reason that people assume that Robert J. Samuelson is an economist. Paul A. Samuelson is obviously an economist, to some extent the economist of the 20th century (along with Kenneth Arrow and a few others). When I didn't know anything about economics I too believed that Robert J. Samuelson was an economist partly because I vaguely knew Paul A. Samuelson was the economist, which says a lot about how eminent Paul A. Samuelson must be if I had any awareness of the man!


Wednesday, February 20, 2008

Economic history is so clean   posted by Razib @ 2/20/2008 06:48:00 PM

I've been reading a fair amount of economic history and political economy recent (e.g., A Concise Economic History of the World, The Moral Consequences of Economic Growth and Angus Maddison's substantial body of work). I've read a few micro & macro texts so I come into this with some vague theoretical understanding of the framework which economists are marinated in, and of course I know about comparative advantage and am broadly sympathetic to globalization. The analytic sharpness that economics brings to broad historical questions is illuminating. That being said, on occasion there are comments which make me wonder about the excessive simplicity of the economic narrative.

Consider the case of two nations which trade with each other. One nation starts out far wealthier. Businesses in the wealthier nation relocate some factories to the poorer nation. This increases aggregate utility, consumers in the wealthy nation can now purchase cheaper products, while a substantial number of workers in the poorer nation are more well off than they otherwise would be. But, there's an issue here, inequality is likely to increase within the nations. Overall inequality in the aggregate has decreased, the poorer nation is now far wealthier and so the income gap is not as stark across national boundaries. But a minority of those who had factory jobs in the wealthy nation now might have to shift to lower paying service sector employment. Additionally, income inequality might initially also increase in the poorer nation as some are left behind (though as economic development proceeds one might suppose that the lower orders would catch up).

As someone who lives in a relatively wealthy nation let's just consider that case. I'm not sure if I'm particularly reassured that aggregate utility has increased across the world while a bunch of factory workers now go unemployed or are marginally employed. It's not that I'm a particularly empathetic person, I'm not, but perhaps I'll run into these people in the subway or at the shopping mall. It's great that people in a far off country are now wealthier and also increase my own access to more baskets of goods; but I can't but help be a little worried about idle hands and potential riots in the streets from the "victims" of the redistribution of economic activity. More immediately, what's the point in my being able to purchase more bling if it only invites a mugging at hands of the victims of globalization?

I have Joseph Stiglitz's Making Globalization Work on my "to read" list, so perhaps my qualms will be addressed at some point. So far I'm not reassured that economists truly internalize the structural biases in human psychology when talking about these macro-level issues. It seems that in universal suffrage democracies the political class always has to pretend as if comparative advantage doesn't exist and mouth populist slogans, but they always favor globalization when it comes to implementing policy (at least over the long term). At this point most humans understand that the the earth is not at the center of the solar system; but it seems to me that that is an easier concept to grasp than the logic of economics, in part because human intuitions about social facts and dynamics are very strong and persistent in the face of intellectual persuasion.

Note: Feel free to recommend books on economic history in the comments. Douglass North is also on my "to read."


Tuesday, February 19, 2008

Natural selection and cultural rates of change   posted by Razib @ 2/19/2008 12:26:00 PM

Natural selection and cultural rates of change (Open Access).

Monday, February 18, 2008

Interracial marriage and Asian Americans   posted by Razib @ 2/18/2008 09:55:00 PM

As a follow up to Assman's last post I was thinking I should link to this article from Asian-Nation which parses Census 2000 data on interracial marriage of various Asian American groups. Do read the article (caveats appropriate to identity politics organs), but I just took their data and placed it below the fold. Also, I modified it a little and added the ratios of men to women who marry whites by generation and immigration status. That is, the Census broke up individuals according to whether they were immigrants, or US-raised or born. There are some caveats with analyzing the data in that way; Asian Indians and Vietnamese have only 1 US-raised or born generation which is actually marrying right now. These groups are post-1965, in contrast to Japanese Americans, who are predominantly US-raised or born, with many 3rd, 4th and 5th generation individuals. With that stated, I was surprised at the relatively moderate sex ratios when you constrain marriages only to those where both partners are non-immigrants; i.e., pretty much acculturated as Americans. Arguably the most assimilated Asian American group on this list, the Japanese, have the second most balanced sex ratio, 0.829 between males and females in outmarriage to whites. Why the most second balanced? Asian Indians are tops in terms of balance. In fact, when you look at all marriages men outmarry somewhat more than women in this group. But Asian Indians are a bit different than the others on the list in a whole lot of ways. Look at the very low marriage rates to "Other Asians" for example. These might even include Pakistanis, Bangladeshis, etc., overstating intermarriage with the other groups on the list. The full table below the fold....

Marriage Patterns for Six Largest Asian American Ethnic Groups (Oct. 2007), Source Asian-Nation

All spouses US born/raised X US born or foreign born US born/raised X US born/raised

Asian Indians

Men(All) Male : female outmarriage ratio - 1.28
(All US born) Male : female outmarriage - 0.862
Asian Indian91.973.356.7
Other Asian0.92.72.8
Multiracial & All Others0.41.62.7
Asian Indian93.677.554.2
Other Asian0.71.72.0
Multiracial & All Others0.50.91.9


Men(All) Male : female outmarriage ratio - 0.381
(All US born) Male : female outmarriage - 0.735
Other Asian4.511.511.6
Multiracial & All Others0.41.42.0
Other Asian2.77.37.8
Multiracial & All Others0.62.12.6


Men(All) Male : female outmarriage ratio - 0.338
(All US born) Male : female outmarriage - 0.779
Other Asian2.86.97.3
Multiracial & All Others2.36.38.4
Other Asian2.86.46.9
Multiracial & All Others2.54.05.7


Men(All) Male : female outmarriage ratio - 0.516
(All US born) Male : female outmarriage - 0.829
Other Asian9.912.49.4
Multiracial & All Others3.24.44.9
Other Asian6.48.07.7
Multiracial & All Others3.74.84.9


Men(All) Male : female outmarriage ratio - 0.232
(All US born) Male : female outmarriage - 0.663
Other Asian2.69.612.5
Multiracial & All Others0.41.72.7
Other Asian3.79.48.9
Multiracial & All Others1.11.82.3


Men(All) Male : female outmarriage ratio - 0.257
(All US born) Male : female outmarriage - 0.530
Other Asian2.97.05.8
Multiracial & All Others0.31.01.4
Other Asian3.58.27.8
Multiracial & All Others0.71.21.6


The mediocrity of local peaks   posted by Razib @ 2/18/2008 12:38:00 AM

Steve on Extended families and materialism:
Anyway, I have a theory about why West Asian materialism runs in such narrow ruts. If you are Ed Begley, you want to impress other people who share your tastes and values, so you socialize primarily with other environmental fanatics who will be impressed that your house is off the power grid. But if you are from a West Asian group, there's much pressure on you to socialize mostly within your extended family and their in-laws and in-laws' in-laws. And because extended families are pretty average on average, specialized interests don't cut much ice. Instead, the common denominators are the surest road to approbation.

You just bought a state-of-the-art kayak? Ho-hum. Sure, your kayak-nut friends will be wowed, but your family? Yawn. In contrast, your cousin Aram just bought the most expensive BMW. Now, that's something that everybody in the family can be floored by!

I think he's on to something here. When I visited Bangladesh in 2004 I found myself seeking out my uncle who is a religious fundamentalist for conversation. Trained as a geologist he spends all his marginal time engaging in dawah and harassing less strident Muslims about following all the picayune details of shariah. Why did I seek his company? It wasn't because I enjoyed chit-chatting about the inanity of Islamic law, or that I agreed with him about the negative implications of Muslim immigration to the West because of inevitable assimilation. No, when a critical mass of Bengali women come together the constant talk about the family-matters makes you want to commit seppuku. I really didn't give a shit that my second cousin was going to marry some random loser who was from across-the-river and spoke-Bengali-with-a-weird-accent; or whatever banal chatter that they were obsessing over.

There were two ways to escape this sort of mind-asphyxiating conversation. First, seek out people not interested in mundane topics. Despite my secularity my uncle's rationales and preoccupations were interesting from an academic perspective; his relative admiration of Buddhism for example was not something one might expect from a Sunni fundamentalist (he had traveled to Australia and Southeast Asia with his religious order multiple times). Even better conversation was my cousin who had a master's degree in math, an interest in cosmology and was employed as a systems administrator. She was much more like the sort of person I would proactively associate with in my natural environment, and despite the fact that we shared relatives in common she didn't have a great need to review every last incident of gossip that she'd stumbled upon. But there was another way to dampen family-gossip: don't hang out with family! One of my father's best friends from college was an engineer, and we went to have dinner at his house one day. His brother, a physics professor at Dhaka university was there, and much of the conversation hinged upon whether the current excitement within the biological sciences compensated enough for the fact that it lacked the elegance and beauty which physics could offer. Now there's a conversation I could bite into! Of course we weren't going to talk much family gossip because they weren't family.

As family sizes shrink within a society I assume that the mind-numbing chatter which emerges from the social-networking of families will slowly diminish. People will associate based on shared-traits instead of shared lineages, mostly because lower fertility means that there's less lineage to go around. I have on the order of half a dozen aunts and uncles on each side of my family (paternal and maternal). But in my own generation the average number children is about 2 (some have 1, some have 3, etc.). There simply won't be hordes of cousins in the next generation because the sibling groups are too small (and some of them won't reproduce, as a few in my parents' generation have not).

Values, norms and ideas float on a social surface. If one's local network is saturated with family values will be preeminent. Eccentric interests are not likely to be shared across the family network unless one is totally inbred. So there is a strong selection for banal conversation topics which everyone can participate in, or signalers that everyone can appreciate. There's a local fitness peak of mediocrity around which a family gathers in terms of topic and creative expression; everyone knows uncle-so-and-so or the terrible thing that happened to that particular cousin. Remove the close relations and the landscape is no longer so regular and coalescence around a local fitness peak no longer as inevitable. An isolated individual you move to a new location and float in and out of social circles based on common affinity. In other words, the non-family world is one of a shifting balance of ideas and an exploration of a more rugged topography. The sample space of possibilities is larger, the risks greater, the comfort zone less incestuous. Depending on your values, that might be a good thing....

Addendum: The point can be generalized. Even shared affinity groups can become too incestuous, to the point where all creativity is removed. As an example, consider that William D. Hamilton believed that the George Price's formalism, which was far superior and more general than that which he had introduced earlier, was a product in large part of the Price's ignorance of what had come before in the field of evolutionary biology. Because of his ignorance George Price started in a very strange part of gene land and stumbled upon very startling vistas unknown to mainstream theoreticians who were constrained by the precedents of their elders.

Update: I do want to be clear, the dangers of family conversation isn't even that family members are that mediocre. It's that you have so much in common with family that the topics tend to be pretty banal. Even if your brother has a Ph.D. you might be more likely to talk about figuring out how to handle the fact that your parent is succumbing to dementia. These are needful conversations, but if your socialization experience is strong skewed toward family members they start swallowing up all your marginal time. The same dangers are applicable to the tendency for many Americans to spend all their marginal time with their significant other. Diversity is good.

Related: Theresa's cousin on cousin marriage & corruption. And the famous profile of the Syrian Jews of Brooklyn.


Sunday, February 17, 2008

Arms races and interracial encounters   posted by agnostic @ 2/17/2008 08:19:00 PM

After YouTubing VH1's The Pickup Artist (a contest reality show where guys learn how to pick up girls), something struck me about how the bar and nightclub scene so thoroughly devastated the East Asian contestant. Sure, every guy gets rejection anxiety and experiences rejection, including the occasional antarctic stare and turn-away response that the Asian guy received. But he looked like he was about to commit suicide, which he ended up doing symbolically by electing himself to be kicked off the show. You see the same stewing-in-rage pattern among Angry Asian Male websites, where they barely contain their bitterness about how White females show no interest in them. * Why is it that Asian guys seem to experience shell-shock in the bar and nightclub scene?

The answer may lie in the arms race between the sexes, whereby males become better and better at showing off or charming and seducing females, which makes females evolve higher standards for the showing-off trait or greater skepticism and iciness when they sense they're being hit on. It's clear that this arms race has escalated much farther in sub-Saharan Africa and other places of similar latitude, compared to more extreme latitudes (although latitude is not the primary cause -- probably pathogen load, ease of female farming, and so on, that correlate with it). So, when an Asian male is dropped into the lion's den of the Western bar and nightclub scene, he is not dealing with a merely unfamiliar group of females -- a large proportion of Europeans and Latin Americans -- but one that has evolved to defeat a far tougher opponent than he.

If European, Latin American, and African females have evolved levels of skepticism and strategies for rejecting an unwelcome suitor that reflect the levels of male seduction skill in their own populations, then when they use these against the far less threatening Asian male, he will perceive it not as a woman's natural self-defense, but as malicious overkill, as though a first-world superpower dropped bombs on a hunter-gatherer tribe that had picked off some of its members with crude arrows. **

Because there has been very little contact -- cultural or genetic -- between Europe, East Asia, sub-Saharan Africa, and the Americas for most of the time after these groups went their own way, it is not surprising that this pattern is pervasive when they meet for the first time. A well known example is the devastation of American groups when European colonists introduced pathogens that were not just unfamiliar but the outcome of thousands of years of arms-race evolution against the human immune system. Similarly, Europeans never managed to colonize sub-Saharan Africa: they dropped like flies in the even harsher pathogen-load areas there. There is no reason to expect the pattern would not show up in social arms races.

Steve Sailer has collected data on who marries who interracially: African male with White female is far more common than White male with African female. While plenty of causes have been given -- for example, dark skin is more attractive on males than on females -- I don't know of anyone mentioning the seduction arms race. African males would have an easier time charming over White females than African females, other things equal, since Whites are more naive to high-level seduction skills. *** Conversely, White males are underprepared in the charm department to evade the African female's more sensitive bullshit-detector, and their show-off skills are unlikely to meet her higher standards (in dancing ability, for example).

In general, it appears that females will date males of other groups if the latter are higher in seduction skills, and so males will date females of other groups if the latter are more naive to seduction than same-group females. I don't claim this accounts for all of the variation, since it would suggest East Asian female with African male would be the most common pattern -- but this datum is a thorn in the side of all other explanations too, such as differing levels of masculinity and femininity between groups.

* The rant linked to contains the following:

"I'd be willing to bet that you could scan entire racks of trashy romances at your local supermarket and not find a single one that depicts an Asian man seducing and romancing a white woman."

Well, the novelists have to keep the plot somewhat believable, and they have to supply a real rather than non-existent demand. The stereotype, probably true, is that East Asians are more pragmatic, tough-minded, and call-it-like-it-is compared to the more idealistic Europeans. But this example shows that the male contest for mates can fog up anyone's clear mind.

** Finnish males may also count here as honorary East Asians.

*** Maybe not so true for Italian females -- any female who's been to Rome or Staten Island knows how relentless Italian males are.

Labels: ,

Religion & loneliness   posted by Razib @ 2/17/2008 02:08:00 PM

God (and Gadgets) of the Lonely?:
I've been hanging out with fellow atheists for a while now, and one of the more common discussions I've had when the topic of religion comes up is, why are people religious? The two most common answers I've heard from atheist friends and acquaintances are that religion is a fantasy designed to explain the mysterious and otherwise unexplainable, and that religion is a fantasy designed to make people feel less alone in the universe. As those of you who've been reading Mixing Memory for a while may have noticed, these discussions have led me to be somewhat obsessed with understanding the psychological origins of religion. While the final answer to why people are religious is a long, long way off, I can say with some confidence that the first of the two answers above is almost certainly wrong. People's religious impulses stem from much more mundane sources than the mysteriousness of the world around us. That's not to say that religion can't serve to help explain the otherwise inexplicable, or that this isn't an important purpose of religion, but it doesn't seem to be one of the fundamental or original purposes of it. Instead, it seems that religion's social functions are actually more foundational. This leads to the second answer above -- the one that says religion is around to make us feel less lonely -- seeming plausible. Most of the research on the social aspects of religion to date, however, has been on its function in communities. A paper in this month's issue of Psychological Science, however, takes a more direct look at the role of loneliness in religion.


A revival of functionalism?   posted by Razib @ 2/17/2008 12:11:00 AM

Human Culture Subject To Natural Selection, Study Shows:
The Stanford team studied reports of canoe designs from 11 Oceanic island cultures. They evaluated 96 functional features (such as how the hull was constructed or the way outriggers were attached) that could contribute to the seaworthiness of the canoes and thus have a bearing on fishing success or survival during migration or warfare.

They also evaluated 38 decorative or symbolic features (such as the types of carved or painted designs). They analyzed mathematically the rates of change for the two groups of canoe design traits from island group to island group. Statistical test results showed clearly that the functional canoe design elements changed more slowly over time, indicating that natural selection could be weeding out inferior new designs. This cultural analysis is similar to analyses of the human genome that have been successful in finding which genes are under selection.

The study is coming out on the 19th in PNAS (so that means it will show up on the website at some time after that date). As most of you know in the 1960s the neutral theory of molecular evolution emerged in response to the finding that there was a great deal of extant genetic variation on allozyme loci (OK, to be fair neutralist ideas predate the empirical results; but I think it is clear that those results made the model intellectually far more compelling). Prior to this there were two broad schools of evolutionary genetic thought; one group accepted that there would be low levels of polymorphism due to balancing selection, and another assumed that there would be little to no polymorphism because of selective constraint. No matter the rearguard attempts by the likes of Richard Dawkins to argue that molecular variation "doesn't count," I think the neutralist (or nearly neutralist) insights are important in giving us a better understanding of the nature of evolutionary dynamics on the genomic scale. In The Origins of Genome Architecture Mike Lynch argues that low effective population sizes have had a strong role in shaping the character of genomic variation in more complex organisms. In other words, we are all non-adaptationists now!

What does any of that have to do with the paper above? Peter Richerson & Robert Boyd, L. L. Cavalli-Sforza and Marcus Feldman and E. O. Wilson & Charles Lumsden have all attempted to show how evolutionary processes are relevant to our understanding of human soceties. Unfortunately, as L. L. Cavalli-Sforza observes, cultural anthropologists are less interested in understanding humans as opposed to interpreting them. Formal frameworks to accompany the mass of empirical observations are simply neglected or seen as unnecessary. This is an unfortunate overreaction to the hubris of earlier generations of anthropologists who attempted to shoehorn all human variety into a set of functional adaptations. Instead of a happy medium where skepticism is balanced with empiricism and rationalism, anthropology has swung from a total lack of critical analysis toward one where positive assertions are eschewed on principle (unless, of course, those assertions are directed toward Western culture).

In Darwin's Cathedral David Sloan Wilson tries to make an argument for resurrecting a functional understanding of cultural traits as adaptations. I think that this sort of work is hard-going, at least beyond the level of triviality (e.g., the rationales for why the Inuit dress the way they do is rather straightforward). That is because "culture" is a very broad and ill-defined term and the selective pressures are myriad; the environment, the social matrix and the correlations with other traits are all critical. Wilson's methodology in Darwin's Cathedral was to use case studies; I don't think that that will cut it. Rather, massive surveys of collected data tested via statistical methods are probably more useful in extracting out the adaptive trends as a function of time and space. I do not, for example, think it is a coincidence that over the last 2,500 years all the complex cultural traditions on the World Island became associated with what we would call "Higher Religions," roughly, the fusion of supernaturalism with philosophy and institutional structures. But were these parallel developments a function of the specific adaptive needs of these complex societies? Or where they perhaps inevitable byproducts of the sufficient intersections of modal human psychology with the rise of the novelties of mass post-tribal society?

These are big complex questions. I think that are certainly functionally significant cultural adaptations. That being said, I am not sure sure that they are responsible for the preponderance of between cultural variation. To go back to the example of Higher Religions, I think one can plausibly argue that some sort of synthesis between intuitively appealing extant supernaturalism with the intellectual & institutional abstracting tendencies of complex societies made them inevitable, necessary perhaps. Societies which were united by a common religious ethos may very well have been more fit than societies still characterized by a welter of tribal gods uncomfortably corralled under one political dispensation (though the dynamic might usually have been played out within an intrasocietal context; e.g., the introduction of Buddhism to Tibet and Japan by a particular faction at court and the subsequent nativist reaction with failed). But the specific nature of the Higher Religions may very well be arbitrary, neutral so to speak, because like a synonymous substitution they have no functional significance.

Obviously the paper above targets the law hanging fruit. Engineering is not contingent upon the caprice of human social dynamics; it works, or it doesn't, by the grace of Mother Nature. But it's a start, as it is a reality check upon those who would argue that the full sample space of cultural possibilities are theoretically at play, and equally likely. The next step is to start examining traits not so strongly constrained by physical conditions.

Labels: ,

Saturday, February 16, 2008

As obscure as ATP   posted by Razib @ 2/16/2008 01:11:00 AM

By the good graces of google I stumbled upon this ranking system.

Thursday, February 14, 2008

The Structure of Evolutionary Theory blogging   posted by Razib @ 2/14/2008 10:16:00 PM

As you probably know at my other weblog I've been going through Stephen Jay Gould's The Structure of Evolutionary Theory chapter by chapter. I just finished the first part of the work, which is a history of science as opposed to a discussion of contemporary science. I've blogged chapter 1, 2, 3, 4, 5, 6 and 7 so far. If you're interested in the topics covered by Gould so far I recommend Peter J. Bowler and Will Provine. Bowler is a lot more concise about 19th century evolutionary theory, in part because that's his academic specialty. Provine offers a Sewall Wright-centric perspective, but that's a good starting point to get a sense of the arc of 20th century evolutionary biology.


Andrew Gelman on Steve Sailer's Dirt-Gap   posted by Razib @ 2/14/2008 09:09:00 PM

Red states, blue states, and affordable family formation is a commentary on new article by Steve about his Affordable Family Formation theory. I don't have much to add, except a note on this:
To get back to the main point, Sailer is making a geographic argument, that Democrats do better in coastal states because families are less likely to live in coastal metropolitan areas, because housing there is so expensive, because of the geography: less nearby land for suburbs. This makes a lot of sense, although it doesn't really explain why the people without kids want to vote for Democrats and people with kids want to vote for Republicans. I can see that more culturally conservative people are voting Republican, and these people are more likely to marry and have kids at younger ages--but in that sense the key driving variable is the conservatism, not the marriage or the kids.

I think that Steve's response would be that a family and kids tend to make you more inclined toward social conservatism. Specifically, full-throated principled defenses of lifestyle libertarianism are less attractive to people who aren't going to be indulging in that in any case because of the constraints of family life.


The lamentations of their women - the movie?   posted by Razib @ 2/14/2008 02:40:00 AM

Roger L. Simon reviews a new Russian film, Mongol, which is a biopic of Genghis Khan. See the trailer. If you want a fictionalized, but relatively accurate, narrative of Genghis Khan's tale I suggest Pamela Sargent's Ruler Of The Sky (Sargent extrapolates into the blank spaces of his life to fill out the story, as opposed to making things up to add "spice" in contradiction to the spirit of what we know). Why post about this on a weblog generally science-focused? The Genetic Legacy of the Mongols:
We have identified a Y-chromosomal lineage with several unusual features. It was found in 16 populations throughout a large region of Asia, stretching from the Pacific to the Caspian Sea, and was present at high frequency: ∼8% of the men in this region carry it, and it thus makes up ∼0.5% of the world total. The pattern of variation within the lineage suggested that it originated in Mongolia ∼1,000 years ago. Such a rapid spread cannot have occurred by chance; it must have been a result of selection. The lineage is carried by likely male-line descendants of Genghis Khan, and we therefore propose that it has spread by a novel form of social selection resulting from their behavior.

Certainly a way to make population genetics interesting to a particular subset. In Genghis Khan and the Making of the Modern World the author argues that the world conqueror's success was in large part owed to the fact that he marginalized his extended family and promoted an inner circle of loyalists on the merit of their talents (e.g., Subutai). But subsequently to this first generation direct line descent from Genghis Khan became the "gold standard" across much of Eurasia for who could ascend to power; ergo, the inference by some population geneticists that the Mongolian modal haplotype derives from Genghis Khan.


Wednesday, February 13, 2008

What people say, and what they do   posted by Razib @ 2/13/2008 10:08:00 PM

What Men And Women Say And Do In Choosing Romantic Partners Are Two Different Matters:
When it comes to romantic attraction men primarily are motivated by good looks and women by earning power. At least that's what men and women have been saying for a long time. Based on research that dates back several decades, the widely accepted notion permeates popular culture today.

But those sex differences didn't hold up in a new in-depth study of romantic attraction undertaken by two Northwestern University psychologists. In short, the data suggest that whether you're a man or a woman, being attractive is just as good for your romantic prospects and, to a lesser extent, so is being a good earner.

You can read the full preprint yourself. The standard caveats about taking one social psychological study of 20 year old college students tracked for 30 days and generalizing apply here; the point isn't that this punctures all of the trends which we observe (I doubt it does), rather, it refines our understanding of the pattern of variation and the central tendencies as a function of particular parameters. Additionally, instead of just trusting what people say, and their own self-conceptions, you need to actually study how people behave. With something like sexual preferences inferring that one's avowed preferences don't match one's revealed preferences isn't that difficult; psychologists have to use more tricky techniques when it comes to something like fleshing out how people really conceptualize the God they say they believe in. But the general lesson holds.

Update: See this comment. Hey, it's social psychology....


Deletions and autism   posted by p-ter @ 2/13/2008 08:09:00 PM

A recent paper in NEJM is worth a read; it suggests a deletion on chromosome 16 predisposes to autism. The phenotype appears to be highly variable, though:
[I]n a study of the same population by investigators at deCODE Genetics, this deletion was observed at a markedly increased rate in subjects with a psychiatric or language disorder. This study showed that the deletion was present in 1 of 648 patients with schizophrenia, 1 of 420 patients with bipolar disorder, 1 of 203 patients with ADHD (the father of a child with autism, as noted above), and 1 of 3000 patients with panic disorder, anxiety, depression, or addiction. In addition, 1 of 748 patients with dyslexia carried the deletion. Overall, in the Icelandic samples, the carrier frequency among patients with autism was 1%; the frequency was approximately 0.1% among patients with a psychiatric or language disorder and 0.01% in the general population.
All these disease phenotypes can probably be thought of as extremes of some distribution of an underlying trait; I wonder how much variation in the "normal" range can be explained by de novo or rare copy number variants like this one.

Labels: ,

Tuesday, February 12, 2008

What's in a name?   posted by Razib @ 2/12/2008 12:39:00 AM

A few weeks I read a The Great Encounter of China and the West, 1500-1800. A fair proportion of the book discussed the introduction of Roman Catholicism into China during the late Ming period (early 17th century) down to the denouement of the rites controversy. Because China and the West had developed on different intellectual tracks for 2,000 years before this meeting of the minds, so to speak, the Jesuits had to grapple with the fact that details of translation were of great import. For example, they introduced the neologism Lord of Heaven to distinguish their monotheistic god from the traditional Chinese concepts of Lord on High and Heaven (the personal and impersonal forms of the divine respectively). The missionaries were worried about conflations within the Chinese mind between the new religion and their preexistent supernatural beliefs; an issue emphasized by the repeated lack of distinction by locals between the exoteric aspects of Roman Catholicism and Pure Land Buddhism. Speaking of which, the Jesuits regularly utilized realistic European paintings of religious scenes, individuals and events, in their attempt to impress & imprint upon the natives the sensory pageantry of Counter-Reformation Catholicism. But they had to cease displays of the Madonna with the infant Jesus because Mary was often assumed to be a rendering of Guan Yin, a bodhisattva of compassion. Now reading T'ang China I stumble upon a passage where the author points to scholars who suggest that the evolution of the male bodhisattva Avalokitesvara into Guan Yin and the associated imagery was influenced by Nestorian Christianity's depiction of Mary! It is not surprising that crypto-Christians in Japan cloaked their Mary veneration within devotions to the Japanese variant of Guan Yin.

The possibility that Guan Yin might be phylogenetically related to Mary mother of Jesus is only that, a possibility. Alternatively, it seems plausible that both serve as a specific focus for relatively universal cognitive reflexes easily evoked in most contexts. Nevertheless, it would be richly ironic if the Jesuits turned away from excessive attention to Mary because of a confusion with Guan Yin because the latter had integrated aspects of Mary into her persona and presentation in the first place! From the outside as an irreligious person the often vacuous assertions of religious liberals that all faiths manifest the same truths actually makes some sense; but whereas the religious would interpret the truth as a transcendent supernatural one the materialist would simply give the nod to universal human psychological propensities intersecting with generic exogenous inputs (e.g., you look upon the star filled sky and feel a sense of awe). All that being said, to many religious people the specific name given to these cognitive constructs is very, very, important. In the days of yore when religion was simply an extension of tribal custom & tradition adherence to the name of a god was a cultural marker. All men are fundamentally human, variations upon the theme, but in a patrilineage which specific man you are descended from (at least notionally) determine all aspects of your social relations. Similarly, which god to which you bend the knee is critical in determining your circle of kin and fictive kin. The basic building blocks are psychologically universal, but the specific twists are socially functional, leveraging other cognitive tendencies in the process (conformity and xenophobia). Remember, the last of the pagan philosophers quipped that the Christians of the time were killing each other over one letter, i, whether one adhered to the doctrine of homoiousia or homoousia. Though to be fair, the difference was over the weighty matter of whether the three aspects of the Trinity were of similar or same substance...whatever that means.


Monday, February 11, 2008

The many dimensions of history   posted by Razib @ 2/11/2008 06:02:00 PM

T'ang China - The Rise of the East in World History:
Interconnections, one may agree, are both old and wide. Initially there was the genetic connection. Although the new alliance between genetics and history is in its infancy, it has already established that, at least since sapiens replaced Neanderthal, habilis and erectus, there have been no true human races. The human genome is unitary and the genetic differences within it are not that large. Cavalli-Sforza states: 'According to that first estimate, the woman from whom all modern human mitochondria descend lived about 190,000 years ago', adding 'this first attempt was not so bad'. Subsequently, Bryan Sykes of the Oxford Institute of Molecular Medicine has concluded that 'almost all native Europeans belong to one of seven distinct clans each with a founding mother ... But there is virtually no consistent pattern to the way the clans are distributed in modern Europe: in the thousands of years of European history they have become thorough mixed. Since Europe was originally populated from Asia, and to a lesser degree from Africa, similar continuities are likely to be traceable there. As Teilhard de Chardin saw, the absence of human branching is striking. The continued convergence rather than divergence is not easily explained by the first three principles of evolution - mutation, natural selection and drift - but only by the fourth, flow, especially the mobility of women, which in turn implies contact between groups....

I've read a great deal of Samuel Adshead's work; though perhaps overly ambitious, like William McNeill he approaches big questions in a with a wide and diverse toolkit. It's thinly populated territory, but one which needs to be explored. Unlike some humanists Adshead has no problem with including the natural sciences as part of his toolkit; the reference to population genetic parameters such as selection, drift, mutation and gene flow imply a level of familiarity far beyond the ken of expectation. That being said, I would obviously object to many of Adshead's characterizations. Biology is it not physics, and like history sentences such as "The human genome is unitary and the genetic differences within it are not that large" need to be placed in their proper context. And within an area such as human genetics one needs to be cautious about citing works and opinion from even the 1990s; one needs to read the journals as opposed to paying attention what L. L. Cavall-Sforza or Bryan Sykes reported as to the state of consensus a decade ago.

A truly synthetic take on the history of our species needs to consider all population genetic parameters. The necessary subtly and depth of understanding is, I believe, properly modeled in the sort of dynamic system which is illustrated in William McNeill's Plagues and Peoples, though even more so in terms of its complexity. The lactase persistence story over the past two years illustrates the power of gene-culture coevolution; but too often it is framed in terms of the power culture has in shaping genetics, but what about the impact that genetic revolutions may have upon history? The Out-of-Africa movement itself may be a more viable template than we could have imagined, after all, a common hypothesis is that evolutionary/genetic changes gave our African predecessors a fitness advantage over other archaic hominid species. The LCT region is the largest portion of the European genome cleaned of genetic variation because of powerful selection; and it all occurred within the last 7,000 years! History as traditionally understood by cothe rise of Sumer is 5,000 years ago, so on the scale of populations the domain of evolutionary genetics does impinge upon that of other humane studies.

Much of Ashdead and McNeill's work hinges upon networks and flow of information. I would hold that one of the great stories soon to be told about human history over the last 10,000 years are the changes in the nature and extent of gene flow due to the rapid increase in population (triggered by the agricultural revolution). A change in density may have had a natural affect on the weighting of various alternative population genetic parameters. Here you have a case where a cultural innovation, agriculture, results in necessary shifts in evolutionary dynamics, which themselves may set in motion historical processes!

But to understand and infer historical processes, I do believe that the insights and knowledge of scholars of promiscuous inclinations such as Samuel Adshead will be essential in putting the pieces in place.

This is a map of the distribution of two alleles of SLC24A5. In case you don't know, this locus has an ancestral and derived variant on one SNP. A few years ago one group noted that Africans & Asians were nearly fixed for the ancestral variation, while Europeans were fixed for the derived on. Through an admixture study on an African American population they determined that the variation on SLC24A5 was responsible for 1/4 to 2/5 of the trait value different between Africans & Europeans. A recent study with South Asians shows that this locus is responsible for about the same proportion of the within population variance among this group. The frequency of the derived variant is still high in South Asia as you can see on this map...but since it is sampled from the northwest one can't get a fix on the cline within South Asia. Another paper tells us more, among a sample of Tamils in Sri Lanka the derived variant is extant at frequencies around 25%, while the Sinhalese the frequency was 50%. I've seen other samples which suggest that among central Indian populations the frequency could be as high as 80%. The point is that though the frequency of the derived variant drops as you go south it remains rather high. Population number 30 on the map are the Uighers. Historical and other genetic studies suggest that the Uighers are a recent hybrid population; a pre-Turkic, likely Indo-European speaking, substrate seems to have been absorbed over the last 1,000 years. I point this out because Uighers have about equal measures of the ancestral and derived variants of SLC24A5; one might posit that this is natural noting the location of Xinjiang, but the Uighers as they are today are a new population which did not exist during the distant past. In fact, the earliest "European" mummies which have been found in Xinjiang date to 4,000 years ago. The circumstantial evidence is that for several thousand years a population of West Eurasian provenance was numerically dominant along the oases around the edge of the Tarim Basin. A late date for the initiation of the sweep which resulted in the high frequencies of SLC24A5 across Western Eurasia is 6,000 years in the past; that doesn't leave much time. To make a long story short it seems like at some point within the last 10,000 years the derived variant of SLC24A5 was strongly selected from Norway to Kerala to Morocco, but it stopped at the Himalayas and Altai.

Why was SLC24A5 selected? I've asked many, many, people. Geneticists who are studying this locus. No one seems to really know! Yes, it causes a change in skin color...but the people of South India are very dark-skinned for a reason. I have a few ideas, as some of you may have gathered, but, to generate these ideas I'm having to do a lot of reading. Men like William McNeill and Samuel Adshead have done a lifetime's worth of reading and become collectors of odd facts and obscure trends. If a great deal of the evolution over the past 10,000 years was due to adaptation to cultural change, then human scientists whose bread & butter are these topics need to join the conversation. History and Geography of Human Genes needs to become more than just a footnote, it needs to turn into a window onto another domain of knowledge which they must become fluent in so that they can help generate a better picture of the past.


Richard Dawkins retires   posted by Razib @ 2/11/2008 05:34:00 PM

Richard Dawkins is retiring from his position at Oxford. They are now looking for someone to fill the spot as Charles Simonyi Professorship in the Public Understanding of Science. I nominate Armand Leroi. He's young, charismatic, and a very engaging writer.

Apes or Angels?   posted by Razib @ 2/11/2008 01:08:00 AM

Imagine a brief which is aimed at both Christianity Today and The Humanist; Cornelius J. Troost's Apes or Angels does just that. Synthesizing the latest research coming out of modern genomics with ideas first mooted by Charles Darwin 150 years ago Troost launches an extended broadside at the pieties of the modern age and the cult of equality. He wields the 'universal acid' of evolutionary thinking and makes a case for a post-supernatural world view which fulfills its promise by making peace with nature; as opposed to pretending as if our dreams of the good and should reflect the truth of a world. Troost asks us to consider the implications of a world wrought in blood, red in tooth and claw. In short, fraternity does not depend upon the reality of equality; at least if fraternity as such already exists while the equality never did. Confronting a many-headed hydra Apes or Angels makes recourse to a wide array of tools to cut its antagonista down to size. In the process Troost surveys the grand arc of the history of evolution, naturalistic philosophy as well as the latest insights from neuroscience. Evolutionary science serves as the sinew, but the bone and flesh of the argument are variegated and diverse.

In The Blank Slate Steve Pinker observed curiously that even into the 21st century we take as our philosophical sages in the domain of human affairs to be men who lived in the 17th and 18th century. Hobbes, Locke, Montesquieu and Hume to name names. All them lived before evolution, before psychology, before even the fissuring of natural philosophy into its manifold faces that we know today as science. It is perhaps a reflection upon our species that decisions we make as to how we order our affairs as a social organism are influenced by the ideas of men who lived before the great flowering of scientific thought; common sense ideas from an a priori world. In Apes or Angels the full arc of the hammer-blow that Darwin's common sense idea about natural selection and descent with modification had upon traditional religion is detailed; from the outraged Victorians to the Scopes Monkey Trial to the Dover fiasco. This is a well known tale and many an enlightened liberal would chuckle at the travails of the yokels who populate the broad expanses of the heartland of this nation. The ignorati who refuse to make their peace with the truths unearthed by science.

But interlaced with this familiar story is a less well known one which suggests that the reality that humans are different in nature, capacity and propensity is being established by the more cutting edge of the human sciences. It is commonly observable that as humans we vary, but the causal factors underlying that variation have long been subject to dispute, and to be frank, the fashions of the day. During the high tide of the blank slate men such as Leon Kamin could claim in polite company that the heritability of IQ was about zero. No more. The waters are retreating and exposing what was once obscured; we need to rapidly prepare ourselves for the new and the surprising. Troost's book is chock-full of research from every cutting edge field relevant to the human sciences. On occasion I would submit that his enthusiasm gets the better of him; results reported do not necessarily imply facts established. Theories propounded are a dime a dozen. Science as a process is riddled with error and noise; its genius is in its rigorous corrective mechanisms. But those mechanisms need time to work so as to shape a better picture of reality. That being said, the tentative findings of one generation are the background assumptions of the next. It is the job of scientists to engage in the process of hypothesis generation and subsequent falsification. It is the job of those who follow science, which should be every broadly educated individual, to determine how science fits into our view of how the world is, should be, and how we can make it be what we believe it should be.


Sunday, February 10, 2008

Time to take another look at your (third) cousin?   posted by p-ter @ 2/10/2008 02:25:00 PM

I'll admit it: I'm fully baffled by the recent report by the cats at Decode that marriages between third and fourth cousins tend to be more fertile than other relationships. But it's a pretty fascinating observation--using their extensive Icelandic genealogies, they compile the figure on the right: on the x-axis is a measure of the relatedness of a couple, and the y-axis various measures of fertility. For the most relevant measures--the number of children that reproduce and the number of grandchildren--you see a sort of n-shaped curve, such that very closely-related and very distantly-related couples are less fertile than couples related at the level of third or fourth cousins.

Given the amount of data that they have, they're able to see this pattern is robust across historical periods, during which average relatedness of couples has decreased by an order of magnitude. And since Iceland is relatively socially homogeneous, the authors suggest there really is biology underlying this phenomenon. But how? I've no idea.

(See also John Hawks).


The Archbishop Speaks   posted by DavidB @ 2/10/2008 03:01:00 AM

The Archbishop of Canterbury, Dr Rowan Williams, has stirred up a hornets' nest this week by suggesting that some aspects of Sharia (Islamic law) are bound to be applied in Britain. Much of the commentary has been wildly inaccurate, so as a public information service here is a link to what he actually said. Congratulations to anyone who reads it all the way through. I certainly haven't. But of course he is not suggesting that Sharia should be applied to non-Muslims, or that it should override the law of the land in criminal matters. How far it should be recognised by the Courts in civil cases (such as matrimonial disputes) is a complex matter which I will leave to others to discuss. I would however mention that in a wide range of commercial practice it is common for the parties to agree to arbitration instead of legal action, and the findings of arbitration are not only accepted but enforced by the ordinary courts, both nationally and internationally under the New York Convention. Arbitration is commonly based on the 'custom and practice' of particular trades or professions, so the idea that that there is only one 'law of the land' is oversimplified.


Saturday, February 09, 2008

Lordi monster film   posted by Razib @ 2/09/2008 11:40:00 PM

Lordi hopes for monster hit with horror film debut. A Finnish horror film? What, is it going to feature a mutant which makes eye contact with strangers while fully sober? Might this result in a reign of prosocial terror as the eye-contact-making-monsters eat the brains of Finns and transforming them into mutants as well; turning a quiet nation into a horde of demonic Neaopolitans?


Japanese Giant Hornet blitzkrieg   posted by Razib @ 2/09/2008 11:10:00 AM

If you like bees, perhaps you don't want to click this video....

The native honey bees have evolved defensive tactics. Guess it goes to show that kin selectively driven altruism doesn't matter for jack shit unless you actually have some proximate tactics to go along with the strategic good intentions. Sometimes we could learn from nature's lessons....

Update: Counter-attack! Bee-day!


William D. Hamilton & Narrow Roads of Gene Land week   posted by Razib @ 2/09/2008 10:42:00 AM

If you don't know, I've been reviewing William D. Hamilton's Narrow Roads of Gene Land the past week over at my other blog. The papers I blogged were The genetical evolution of social behaviour - I & II, The moulding of senescence by natural selection, Extraordinary sex ratios and Innate social aptitudes of man. In The Altruism Equation Lee Alan Dugatkin notes that it's rather obvious that in the scientific literature the citation for many of Hamilton's two papers where he outlined the nature of inclusive fitness were blindly based on the verbal summary in Sociobiology and The Selfish Gene; errors in the bibliographies of both books are replicated in a substantial portion of the cites after 1975. That's pretty sad; we're not talking quantum gravity theory here. I encourage all readers interested in evolution & behavior to check out Hamilton's work in the original.


Friday, February 08, 2008

Retroviruses & Evolution   posted by Matt McIntosh @ 2/08/2008 09:15:00 AM

Our adaptive immune system (thought to have evolved around the time of the earliest jawed vertebrates) functions by recognizing things in our bodies that aren't us and attacking them, which is why transplants and grafts of tissues that are different from our own tend to get rejected by our bodies. But this poses an interesting problem for the evolution of placental mammals (first pointed out by Peter Medawar in 1953): The fetus is genetically different from the mother, so before she can start carrying her progeny around inside her for long stretches of time there would have to be some mechanism in place to prevent her immune system from going into attack mode on it.

There are a few different ways this could plausibly be accomplished, but the one that evolution actually seems to have hit on is pretty neat, I think. One way we know it doesn't happen is by the mother somehow recognizing that the fetus carries half her genes, because otherwise IVF blastocysts implanted into surrogate mothers would spontaneously abort. So whatever is going on here is a "kin-blind" adaptation.

A significant chunk of our DNA had its origins as retroviral DNA. Most of these are now inactive, but a tiny portion actually appear to still code proteins. It's been found in mice, sheep and humans (and presumably generalizes to all placental mammals) that a particular kind of endogenous retrovirus is highly expressed in the outermost layer of the blastocyst (see e.g. Venables et al. 1995 for the human example). Furthermore, when you inhibit the expression of these genes the result is uniform spontaneous abortion immediately following implantation (Dunlap et al. 2006).

Most retroviruses are immunosuppressive, the most infamous example being HIV. Connecting the dots, it's quite plausible that these particular ancient retroviruses have been recruited into the mammalian genome and serve as local immunosuppressors in the uterus during development. In fact, we already know that syncytin, a protein crucial in placenta formation, is the product of a retroviral gene (Knerr et al. 2004), so there's nothing at all far-fetched about this. (In fact talking about these genes as if they were viruses just clouds the issue: The fact that they're now propagated in exactly the same way as the rest of your nuclear genome means that they're just as much your genes as any other bit of your DNA.)

The idea that viruses played a crucial role in the evolution of placental mammals is pretty nifty, but this is just the best-investigated case and there's circumstantial evidence suggesting that retroviruses have been involved in other major evolutionary innovations too. For instance, it turns out that eukaryotic DNA polymerases bear a closer structural resemblance to viral DNA polymerases than they do to those of eubacteria, suggesting that perhaps the genes of DNA viruses were recruited in the evolution of eukaryotic cellular machinery (Villarreal & Filippis 2000).

But around here we're more interested in human evolution, and there's some suggestive data on that score: Turns out human endogenous retroviruses are expressed in a wide range of tissues during development (Andersson et al. 2002; Muir, Lever & Moffett 2004); that retroviral promoters, enhancers & silencers inserted near genes can alter gene expression (Thornburg, Gotea & Makalowski 2006; Dunn, Medstrand & Mager 2003; Ting et al. 1992); and that sequence & phylogenetic analysis suggests they may be responsible for a significant portion of large-scale deletions and insertions on the genome (Huges & Coffin 2001). We're used to thinking of predators and parasites as indirect drivers of evolutionary change in organisms, but when the parasites can obtain direct access to their host's DNA this gets taken to a whole deeper level that's only recently been appreciated.

Labels: ,

Thursday, February 07, 2008

Resonance and plasticity   posted by amnestic @ 2/07/2008 09:14:00 AM

Did you know that neurons have resonant properties? I didn't know that until I read this paper from the Johnston lab down in Austin, TX. Usually I think of synaptic transmission in terms of a single action potential or other event that releases neurotransmitter, so I don't end up in the frequency domain. But, of course, the pattern of release is just as important as the magnitude. Neurons can fire in rhythmic patterns that have additive effects downstream because of the principle of temporal summation. Neurons are continuously deciding whether to fire or not. In a simple view, they do this by summing the 'aye' and 'nay' votes across all inputs. Aye votes move the voltage potential across the neuronal membrane in a positive direction by allowing positive ions to flow into the cell. There is a time window in which an input can cast its vote and still be counted based on how long it takes the receiver neuron to respond to inputs and how long it takes to return to a clean slate after responding. This allows the same input to vote several times if it does so at just the right frequency. If it tries to go too fast it will run up against the membrane capacitance. You see, the membrane potential isn't exactly a count of the number of positive and negative charges inside and outside the cell. Rather, the ions have to be lined up right next to the membrane producing a capacitive current for the period of time it takes to push positive charges off the outside of the cell and line other ions up on the inside. People familiar with basic principles of electrical circuits know that charging a capacitor adds a time dimension. So if an input votes too fast, say, at a frequency of more that 10 to 20 Hz (I'm not sure of the exact number) the effect will be attenuated as the receiver simply can't add that fast.

On the other hand, firing too slow simply won't do either. Neurons have components that react to any change in membrane potential and push back toward baseline. Of particular interest is the H-conductance. The H-conductance is an ion channel in the membrane that allows positive ions to flow into the neuron (as long as the membrane potential is more negative than -30ish mV). Curses. I didn't want to, but I think I have to explain reversal vs. activation potential. Reversal: Ions want to flow to places where there is a lower concentration. They want room to spread out and have a nice big yard with a swingset for the kids and all that, but they also want to get away from other ions with the same type of charge. So if there were a bunch of K+ ions sitting inside a cell and only a few outside and a channel opened up they would want to go out, but if there are already a bunch of Na+ ions outside then they might think twice because there is too much positivity out there already. In other words, potential and concentration gradients are taken into consideration. SInce there is a lot of Na+ outside the cell, it wants to flow into the cell and drive the potential up. There is a lot of K+ inside a neuron, so it wants to flow out of the cell and drive the potential down. If you open a channel that allows both ions through they will arrive at a consensus (equilibrium, reversal) potential that accommodates everyone's needs. The H-conductance does just that and arrives at around -30 mV. If the membrane was at -30 mV, no net ion flow would occur. If it strays, the driving forces will push back towards -30. Normally, due to other considerations, a neuron sits near -55 to -60 mV, so activating the H-conductance will push the neuron toward a more positive potential. Now Activation: Ion channels respond to changes in membrane potential by opening and closing. The H-conductance is closed at positive potentials and becomes activated when the potential moves more negative than about -60 mV. This has the effect of opposing hyperpolarization, the increased difference in voltage across the membrane, because when the membrane tries to move more negative the channel opens and pushes positive. Since the activation potential for H-conductance is near the resting membrane potential, it can also oppose depolarization by shutting portion of channels and reducing the push towards positive. Finally, channel activation and inactivation takes time. It takes more time than charging the membrane capacitance. If an input wants to make a difference, it has to get its votes in before the H-conductance comes into play and brings everybody back to baseline. In this way, the H-conductance acts as a high-pass filter, only allowing speedy inputs to have a say.

Now we have a window of input frequencies that can really strongly affect the cell. If they are too fast, they are filtered out by the membrane capacitance. If they are too slow, they are filtered out by the H-conductance. Really the H-conductance is just one type of conductance that might do the job. Any conductance that is activated near resting membrane potential and opposes change would work fine. You can measure how this plays out in a real cell using something called an impedance amplitude profile (ZAP). You measure the voltage change in a neuron as you inject current at different frequencies but constant amplitude. In practice, this is done really quickly as a sweep across the frequencies. The result is a peak voltage change that corresponds to the resonant frequency of the cell. Like so:

Narayanan and Johnston already knew that you could measure resonant properties of neurons. What we didn't know was that these properties varied in space and time. They measured resonance in CA1 pyramidal neurons. These are the major excitatory cells in an important region of the hippocampus, a brain structure responsible for memory encoding and spatial navigation. CA1 neurons are some of the best characterized neurons available because the CA1 region is highly accesible for in vivo recording and easily delineated for slice electrophysiology, and much is known about its specific inputs and outputs. Imagine an Egyptian pyramid. Now imagine a giant tree growing up through the center of it to about 10 times its height. That is what a pyramidal neuron looks like. The roots of the tree are basilar dendrites and the branches are apical dendrites. Dendrites are specialized structures for receiving input. One giant root will run out of the bottom of the pyramid and send output to some downstream cell. This is the axon. One of the first things that Narayanan and Johnston showed was that the resonant frequency of a CA1 neuron varies along the apical extent of the dendritic tree. The frequency increases as you get further toward the top of the tree, from 3 Hz to 8 Hz at the top. This correlates with the quantity of the channels responsible for H-conductance which also increases toward the tippy-tops of the tree. Input into CA1 neurons is spatially organized such that the entorhinal cortex inputs at the very tip of the apical extent while the CA3 region of the hippocampus inputs at sites more proximal to the cell body. One hypothesis that the authors put forward is that the resonant properties may be tuned to the specific types of inputs. Unfortunately, I can't tell you whether entorhinal neurons fire at 8 Hz vs 3 Hz. I think this is an interesting avenue, but I wonder why you would need to filter the inputs by frequency if you already have them filtered by space. I suppose if the entorhinal cortex naturally fires around 8 Hz and you want the maximal downstream effect then its not so much a matter of filtering out bad frequencies as enhancing the good ones.

The most interesting thing to me though was that certain excitation patterns could alter the resonant frequency. If, by direct stimulation, they caused the neuron to fire in bursts separated by about 100 ms, they could later observe a upward shift in the resonant frequency. They used several stimulation protocols. Of highest interest was the effect of inducing LTP. LTP (Long-Term Potentiation) is a cellular model for learning in memory. It involves the seleective strengthening of synapses between two coincidentally active neurons. There are various LTP inducing stimulation protocols. The one these folks used requires stimulating axons headed for the apical dendrites of the CA1 neuron while depolarizing the CA1 neuron's cell body to cause it to fire. Thus input activity is paired with downstream firing and that particular input is strengthened. Coincident firing is detected by a special receptor (the NMDA receptor) that is activated only when post-synaptic (dendritic, receiving end) membrane depolarization is paired with neurotransmitter release (from an axon of another neuron). After LTP induction, that input now has a bigger say in the overall activation election of the downstream neuron. The analogy between LTP and learning has been argued for decades now and some good evidence exists that this is a legitimate model. Early attempts to show this involved blocking the NMDA receptor in LTP and in learning and showing that both were impaired. Here is the key interesting thing for me about Narayanan and Johnston's paper. Blocking the NMDA receptor not only blocked LTP, but also blocked a global, non-input specific, upward shift in the resonant frequency of CA1 neurons. Now we have two physiological phenomena that you are manipulating when you inject an animal with an NMDA receptor antagonist. Is learning disrupted because of failed LTP or failed resonance shifts?

Why would a resonance shift matter? Here's one reason. Neurons don't work alone. Thousands of neurons have to send input to one downstream neuron to get any reaction. They need to do this in a temporally coordinated fashion. One of the best methods for temporal coordination is oscillatory firing. Watch a tug of war sometime and note the effectiveness of "1,2,3 PULL!" compared to everybody struggling on their own time. This coordinated group of neurons is referred to as an ensemble. If members of the ensemble are connected to each other, they can settle on a frequency of oscillation that best excites everyone at once. If anyone gets out of line and starts going faster or slower, the big PULL will drag them back in, unless they are so far out that they simply can't get down with a certain tempo. If a CA1 neurons is part of some larger ensemble that really loves to fire at 3 Hz and then its resonant frequency jumps up to 5 Hz, it will be that much less responsive to its former buddies. Instead, some other more enticing fast-paced ensemble might recruit that dude into their little 5 Hz cult. The implication is that NMDA receptor-dependent learning could be caused by changes in ensemble size and strength rather than or in addition to strengthening or weakening of specific synapses. A good place to begin on testing this implication would be to record from CA1 neurons in live, behaving animals (this is routine) during a learning task and note whether their preferential firing pattern shifts in frequency and whether this is coordinated across multiple neurons.

The H-conductance has more effects than just determining the resonant frequency. The Narayanan and Johnston paper was published alongside an article describing their effect on active properties of dendrites (dendritic calcium spikes) and third paper featuring the H-conductance prominently.

Labels: , , ,

Monday, February 04, 2008

What makes human populations different?   posted by p-ter @ 2/04/2008 05:25:00 PM

I and others at this site have written much about recent human evolution, with a particular emphasis on papers that have used large-scale genotyping data on individuals from diverse populations to make inferences about regions of the genome that appear to be under natural selection. The sources of information used by these papers vary, and the logical chain from the observation to the inference of selection might be difficult for a non-specialist to follow.

So it's nice to be able to clearly state the logic behind a new paper scanning the genome for evidence of the action of natural selection: if an allele is at really high frequency in one population and really low frequency in another, that's interesting.

To go into a slight bit more detail, the authors use the HapMap, a database of genotypes at >3 million SNPs individuals of East Asian, African, and European descent, and calculate Fst, a measure of how different allele frequencies are between the three broad continental groups. They hypothesize that, assuming population differentiation is driven by natural selection and not genetic drift, the most extreme SNPs should then be enriched for genic regions (as opposed to non-genic regions) and non-synonymous SNPs (as opposed to synonymous SNPs).

On the right is the moneymaker, showing exactly that--high Fst SNPs (ie. towards the right of the graphs) are enriched for both genic and non-synonymous SNPs. Interestingly, SNPs in the 5' untranslated region of genes are also highly differentiated, suggesting perhaps some role for gene regulation through microRNAs in recent human adaptations.

The authors compile a list of the genes most highly differentiated between the three human populations included in their study (also on the right), including many of the known suspects, including EDAR and SLC24A5. To me, the striking thing is the huge list of genes of unknown function--it's always humbling to realize how little is known about human biology. Humbling and of course exciting--someone's going to figure out what these genes do, and this study suggests at least some of the them play large roles in determining what makes human populations so diverse. Something to watch for...

Labels: ,

Sunday, February 03, 2008

Just Science 2008 feed   posted by Razib @ 2/03/2008 08:36:00 PM

Subscribe here.


Saturday, February 02, 2008

Super Tuesday   posted by Razib @ 2/02/2008 09:55:00 PM


HERC2/OCA2, can you spare an h?   posted by Razib @ 2/02/2008 03:38:00 PM

I've been blogging the HERC2/OCA2 story a fair amount. It seems this genomic region is the locus of main effect for variation of eye color in Europeans, in particular blue vs. non-blue eyes. But I also pointed out that this locus has also been connected to variation in skin color, and while that variation is additive in effect, the variation on eye color exhibits strong dominance/recessive dynamics. My inference here is that it is more plausible that selection occurred on skin color, while eye color was a tissue specific expression pattern which emerged as a byproduct. Peter Frost has an objection to this:
The correlation between eye color and skin color may simply be an artefact of geographic origin. Europeans vary clinally for both eye color and skin color along a north-south and west-east gradient, so if the pool of subjects is geographically heterogeneous you will almost certainly get a correlation between eye and skin color. But this doesn't prove a cause and effect relationship.

Fair enough. Spurious associations driven by cryptic population substructure is one of the main reasons Structure was developed. I responded to Peter here, here and here. The short of is that I don't know of any analysis within an admixed population like African Africans, which would settle the matter, but there are plenty of other points which would suggest that we should look at the skin color trait (and, to be fair, if substructure exists at the level of British Isles origin samples we really need Strucure!).

But there was something that has been bothering me: eye color difference exhibits a lot of dominance/recessive dynamics in expression. The skin color data here does not, and aside from KITLG (which is dominant for light skin) all the other loci seem additive and independent (the report of epistatic effects here & there don't seem reproduced very often). One of the main reasons that I am favoring a skin color model as the phenotype driving selection is that if it is additive it is exposed to selection immediately at low frequencies. In contrast, recessive traits at low frequencies have the problem that most copies of the allele which increases fitness are still in heterozygotes which mask them from selection. It came to my mind that the different assumptions about dominance would matter in terms of long term evolutionary dynamics and how that would be realized in terms of results from tests for selection. So I found this paper, Directional Positive Selection on an Allele of Arbitrary Dominance. It says:

...fixation of a beneficial allele leaves a signature in patterns of genetic variation at linked neutral sites. If this signature is well characterized, it can be used to identify recent adaptations from polymorphism data. To date, most models developed to characterize the effects of positive directional selection (termed "selective sweep") have assumed that the favored allele is codominant. In other words, if the fitnesses of the three genotypes are given by 1, 1 + sh, and 1 + s (where s is the selection coefficient), then h = 1/2....

For skin color h would be 1/2 for HERC2/OCA2, it has half the effect on the trait value. Assuming proportional selection based on the character value two copies would be better than one copy which would be better than no copies. In contrast, for eye color the h would be between 0 and 1/2, and probably closer to 0 because of predominant recessivity in expression for blue eyes. That means the fitness of those with one blue eye copy would be much closer to those with no blue eye copies than those with two; to the homozygote recessives would go all the benefit. On to the results:
...when h is small, most of the sojourn time is when the allele is at low frequency in the population. During this phase, the allele will have the opportunity to recombine onto other backgrounds. In other words, the favored allele will tend to increase in frequency on multiple backgrounds, preserving more of the diversity that existed when it first arose. In contrast, for dominant alleles, most of the sojourn time is spent at higher frequency, when there is less opportunity for the favored allele to recombine onto other backgrounds. This results in a wider signature of a fixation event for larger h-values.

...presents the two statistics as a function of distance from the selected site for different h-values. As can be seen, both reach 0 faster for smaller h. For example, for these parameters, the means of these statistics 18 kb from the selected site are ~0 when h = 0.1, but they are still negative 40 kb away for h = 0.9. This finding suggests that, all else being equal, it will be more difficult to detect a selective sweep if the beneficial allele was recessive.

...This difference produces distinct genealogies and hence distinct patterns of polymorphism after the fixation of a beneficial mutation. In particular, our simulations show that the fixation of dominant alleles influences a larger genomic region, suggesting that this type of favorable substitution may be easiest to detect from polymorphism data.

Why the bolded parts? From A Map of Recent Positive Selection in the Human Genome:
Some of the strongest signals of recent selection appear in various types of genes related to morphology. For example, four genes involved in skin pigmentation show clear evidence of selection in Europeans (OCA2, MYO5A, DTNBP1, TYRP1). All four genes are associated with Mendelian disorders that cause lighter pigmentation or albinism, and all are in different genomic locations, indicating the action of separate selective events. One of these genes, OCA2, is associated with the third longest haplotype on a high frequency SNP anywhere in the genome for Europeans....

I don't know if my connection of inferences here is valid, and the paper I originally referenced makes clear that it is important to frame these sorts of assumptions within their statistical context; just because something is less likely does not mean it is impossible. I've sent out emails about OCA2 and skin color, and will report back, but at this point I suspect that the final proof in the pudding will have to be admixture analysis in a group like African Americans. But I think the above makes it more likely that whatever was going on 10,000 years ago did not express as a recessive phenotype.

Labels: ,

Friday, February 01, 2008

Social Explorer gets religion   posted by Razib @ 2/01/2008 08:36:00 PM

Via Andrew Gelman, check out the Social Explorer geographic interface for distributions of religious denominations and all the major census data parameters. One gripe, I do notice that their prices aren't public. I assume that this is because they negotiate different price points for different subscribers, so it must be really spendy to justify the time. Maybe I just have a messed up perception of the costs here, the time & effort it takes to program the application, and the hardware it takes to run it, but I think there are a lot of data nerds out there who would pony up a non-trivial fee for access to this sort of service. There are benefits to having a huge subscriber base....


Blue eyes correlate with lighter skin, OCA2 & HERC2   posted by Razib @ 2/01/2008 06:18:00 PM

The story about HERC2 & OCA2 is getting a lot of press; that is, the genetics behind how people have blue eyes. But see this in ScienceNow:
There are still large questions, though. Why did blue eyes persist? Scientists say it is difficult to see how eye color would have an environmental advantage, as skin color does. Some theories suggest that women may have played a role in driving the selection. Perhaps, Kayser says, "the females thought it more exciting to have a male with blue eyes."

I already posted this before: the SNPs which are used to predict blue eyes also track skin color variation. In other words, pleiotropy. This shouldn't be a surprise, OCA2 is a pigmentation locus which in many cases doesn't exhibit tissue specific expression patterns; its name derives from the fact that some forms of albinism are associated with mutants on it. In any case, some concrete data about skin color and the OCA2 SNPs can be found in a previous paper from a research group behind one of the current publications, A Three-Single-Nucleotide Polymorphism Haplotype in Intron 1 of OCA2 Explains Most Human Eye-Color Variation. Look at table 1, and you find these data:

Fair skin Medium skin Olive skin
Blue/Blue 46.5 46.1 7.4
Blue/Brown 31.3 52.2 16.6
Brown/Brown 25.6 37.9 37.0

Let's do something with the numbers. Give fair skin a trait value of 1, medium skin 2, and olive skin 3. Then generate an average value for each genotype by weighting appropriately, and divide by the number associated with heterozygotes. This is what I get:

GenotypeAverage Value

Looks additive for skin color, doesn't it? Since blue eyes as a trait seems to exhibit strong recessivity HERC2/OCA2 derived variants are unlikely to have initially been selected for that phenotype. It could be something besides skin color, but that is the most plausible abduction at this point from where I stand (we know that selection was powerful on the locus).

Related: Genome-wide associations, HERC2 and eye color, 1 SNP to rule them & in the darkness bind them?, Why do you have blue eyes?, HERC2 & blue eye color & Danes and OCA2, blue eyes and skin color.

Labels: ,