Friday, August 31, 2007

10 Questions for Greg Clark   posted by Herrick @ 8/31/2007 02:04:00 PM

In his new book A Farewell to Alms, Greg Clark, an economic historian at the University of California, Davis, contends that "[t]he New World after the Neolithic Revolution offered economic success to a different kind of agent than had been typical in hunter-gatherer society: Those with patience, who could wait to enjoy greater consumption in the future. Those who liked to work long hours. And those who could perform formal calculations in a world of many types of inputs and outputs...."

Clark also provides archival evidence that in medieval Britain (and to a lesser extent in China and Japan) the wealthy-who presumably had those "middle class" skills in abundance-raised more children than the average person. If you put these pieces together-a system that rewards a new set of abilities, plus greater reproductive success for those who have those abilities-then all you need to get some form of selection is one more link: A transmission mechanism. On the nature of the mechanism, Clark leaves the door wide open. Could be parent-to-child cultural transmission, could be genes, could be both.

While much of the discussion of Clark's book has focused on his "survival of the richest" hypothesis, Clark himself appears to be equally devoted to demolishing the widely-held view that economic institutions are the key to modern economic growth. He notes that the British people had solid property rights, limited government, and sound currency for centuries before they had their Industrial Revolution. Drawing on early work by Nobel Prize-winner Douglass North, he argues that economic institutions are largely endogenous and relatively efficient, at least when we're talking about time horizons lasting a century or more. If institutional change wasn't the driving force behind modern economic growth, then what was? In Clark's view, the driving force was change within human beings themselves.

1. In some early work, you wondered why workers in British cotton mills were so much more productive than workers in Indian cotton mills. You discuss this in the last chapter of A Farewell to Alms. You looked at a lot of the usual explanations-incentives, management, quality of the machines-and none of them really seemed to explain the big gap in productivity. Finally, you seemed to turn to the idea that it's differences between the British and Indian workers themselves-maybe their culture, maybe their genes-that explained the difference. How did you come to that conclusion?

Clark: I came to economics as an undergraduate expecting, as is the central view of economics, that the explanation for wealth and poverty would ultimately be located in social institutions and that people everywhere have basically the same aspirations and abilities.

But unlike most of my colleagues in economics I have always been interested in the mechanisms, and the fine details, of how things actually function. Much of modern economics is entirely theoretical, and even most empirical work in economics involves just looking at very high level correlations between variables such as income per person and education, or democracy, or the openness of trade.

When I set out in my PhD thesis to try and explain differences in income internationally in 1910 I found that asking simple questions like "Why could Indian textile mills not make much profit even though they were in a free trade association with England which had wages five times as high?" led to completely unexpected conclusions. You could show that the standard institutional explanation made no sense when you assembled detailed evidence from trade journals, factory reports, and the accounts of observers. Instead it was the puzzling behavior of the workers inside the factories that was the key.

2. Your book is clearly a call for a new research agenda in the fields of economic growth and economic history, one focusing less on institutions and more on what we might broadly call "labor quality." But your key hypotheses seem to turn on the question of how and why entire workforces change across the centuries, and involve questions of culture, child-rearing methods, and perhaps human genetics-fields quite outside the expertise of most economists. If you could command an army of, say, biologists, anthropologists, and neuroscientists to test your hypotheses about long-term changes in labor quality, what would you have them work on?

Clark: That is a great question. If, as is possible, the pre-industrial era changed people genetically to be better adapted to market economies, then a systematic comparison of the DNA of societies should find correlations between gene frequencies and the histories of these societies. If genetic change was also occurring in historical time, as opposed to the pre-historic era, then we would expect these changes to be incomplete even in societies with a long history of settled agriculture. In that case we would actually predict class differences genetically! The rich in these societies would differ genetically from the poor in certain systematic ways! All this should be testable at some point.

If the change was purely cultural, then we still might be able to discover systematic behavioral differences between poor and rich in modern capitalist society, such as over time preference rates, that correlate with differences between rich and poor societies.

3. What do you think are the weakest links in the now-conventional "Institutions Matter" chain of reasoning?

Clark: The book challenges the modern orthodoxy of economics - that people are essentially the same everywhere, and with the right set of institutions, growth is inevitable - in three ways. First by showing that there were societies like medieval England where the institutional structure provided every incentive for growth, yet there was no growth. Second by pointing out that by objective measures the institutions of many highly successful modern economies, such as in Scandinavia, provide much poorer incentives to individuals than those of very poor economies. And lastly by showing that in the long run economic institutions that would prevent growth tend to get replaced endogenously by ones that are pro-growth.

4. You provide a variety of evidence that interest rates have fallen over the centuries; this is a fascinating set of data that we've discussed before at Gene Expression. Should economic historians still be searching for transaction cost stories to explain this fall in interest rates-e.g., lenders needed a high return in ancient Rome to compensate them for the high cost of searching for safe borrowers-or is that search likely to hit a dead end?

Clark: Interest rates on safe assets like houses and land fell from 25% or more in Ancient Babylon, to 10% in Ancient Greece, Roman Egypt and medieval Western Europe, to 4% in the eighteenth century in the Netherlands and England. Most economic historians assume this just represents transaction costs. But I can show in cases such as medieval England that transaction costs have nothing to do with this - the real return on investments as safe as modern Treasury Bonds was 10% or more. So I am confident that something much more fundamental was changing over these years.

5. You use data on British wills to argue that the British people of today are by and large the descendants not of peasants and not of the violent medieval aristocracy-both groups failed to reproduce themselves. Instead, the British people of today are largely the descendants of the bourgeoisie of the middle ages. Nowadays, that seems to be a testable hypothesis; have you run into genetic evidence bearing on what you call the "survival of the richest?"

Clark: I agree that, in principle, this is a completely testable hypothesis. If there was genetic change in the Malthusian era then we will find systematic differences in genes that influence behavior such as patience and propensity to violence between groups such as the British and those such as Australian Aboriginals that had no experience with settled agriculture.

However, as far as I am aware, the identification of genes that influence such behaviors is at a very early and tentative stage. The only such studies I have seen reported are those of differences across ethnic groups in variants of genes encoding monoamine oxidase enzymes.

6. How are economists reacting to the book? In particular, are there any misunderstandings that you'd like to address?

Clark: I expected a hostile and perhaps even dismissive reaction, given the controversy that the "survival of the richest" argument was bound to create, and given the attack on the modern orthodoxy amongst economists about institutions being the key to wealth and poverty. But economists who have read the book, even when they remain skeptical of the conclusions, have generally found it interesting and challenging. They have been surprised to learn in particular that the history of economies is not anything like the implicit assumptions they have, based on modern economic doctrine.

7. One implication of your model is that human populations that haven't been through the full Neolithic Revolution are going to fail miserably when they try to build a modern market-oriented society. If people turn out to as hard to change as they appear to be-if neither culture nor genes prove to be all that malleable in the medium-run-then how would you recommend improving the lives of these people? Do you think economists can design institutions that can help make these populations productive?

Clark: Anyone who reads history cannot fail to be impressed by the difficulties that hunter-gatherers, or societies with only limited experience of settled agriculture, have in successfully incorporating into the modern capitalist economy. I spent a week in Australia this summer, and the plight of Australian Aboriginals is very sad. The surviving Aboriginal communities have seen tremendous rates of poverty, alcoholism, drug use, violence and sexual assaults.

But an important point in the book is that while some of this cultural variation may be due to the long histories of societies, there is a lot of cultural variation within these constraints that produces dramatic differences in wealth in modern societies. So there is no ground for fatalism on the possibilities for any society. The problem is that measures to reform the cultures of societies seem difficult to devise. Look at the lack of success the Chinese Communist Party had in remaking Chinese Culture. China has emerged from a period of extreme ideological indoctrination seemingly with its pre-communist love of individual wealth and status completely intact.

8. You emphasize that "[t]he argument is not that agrarian life was making people smarter." But you also emphasize that agrarian life placed greater value on verbal and mathematical skills than hunter-gatherer life. Let's set aside for the moment the question of whether these skill changes were cultural, environmental, or genetic. Are you claiming that the rise in math and verbal skills was counterbalanced by an equal loss of some similarly valuable hunter-gatherer mental skills? In other words, were the mental effects of the Malthusian process zero-sum? If so, what process within your model would make that occur?

Clark: I wanted to emphasize in the book that I was not advocating any kind of Social Darwinism. The long Malthusian economy that preceded the Industrial Revolution changed people, but there is no evidence it made them "better" or "smarter." Indeed there is evidence that we did not become any happier as result of economic growth.

Anthropological accounts of forager societies suggest that people in these communities have strikingly developed powers of observation and memory (as well as an amazing ability to endure pain) - they are just not abilities that the modern market economy places much value upon.

9. Bowles, Camerer, and an interdisciplinary research team led a series of ultimatum-game studies in pre-modern societies; the found incredibly diverse outcomes. By contrast, across modern societies, ultimatum game play is much more similar, so it looks like the modern world really is a world of conformity, at least on this topic. How do you think their experimental evidence bears on your question of whether the "long Malthusian night," as you call it, selected for a certain set of behaviors and attitudes?

Clark: I have seen these results reported, but had not thought of relating them to the arguments of the book. I would have expected that pre-modern societies would have had a common response, but potentially a different response than in modern societies. So I do not think I could call this any kind of vindication of the hypothesis in the book.

10. What's the next project?

Clark: I always have several going at the same time. One is a follow up to the "survival of the richest" study for England reported in the book which will look more closely at the intergenerational transmission of economic success with a much larger set of data, and seek to show through examination of the effects of family size that the mechanism is indeed almost entirely the transmission of culture or genes. This study will also look over the whole period 1600-1914 and examine when and why richer men ceased to have more children than average and began to have less. I would love to use this data to try to tease out whether we have just cultural evolution as opposed to genetic - I just cannot think of any way to do that!

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Wednesday, August 29, 2007

Haldane and self-experimentation   posted by p-ter @ 8/29/2007 07:06:00 PM

No, not that Haldane. His father. Seth Roberts points to several reviews of a new biography of JS Haldane. He was apparently quite the self-experimenter:
He survived concentrations of carbon monoxide in the blood that would, as his biographer notes, have looked entirely plausible as the 'cause of death' on a death certificate. 'Dry air,' Goodman writes, 'he could withstand to an astounding high of 300F, though if he moved about too much his hair began to singe.' Working in 99F 'dry bulb' heat, on one occasion, a colleague gave up after half an hour with a rectal temperature of 102.4F; Haldane went on for another 30 minutes. He spent hours and hours breathing toxic air and taking careful, methodical notes of its effects. He gassed himself with chlorine, methane, carbon dioxide, carbon monoxide, pure oxygen, nitrogen, mustard gas and god knows what else in various combinations... you name it, he turned blue and passed out on it. And, typically, no sooner had he come back round than he returned to the chamber to have another go.
Related: various posts on lil' Haldane

Not So Sure   posted by DavidB @ 8/29/2007 08:04:00 AM

Over the last few years the British government has spent a good deal of taxpayers' money on educational activities for pre-school children, under the heading of 'Sure Start', aimed especially at those from 'disadvantaged backgrounds'.

If this sounds vaguely familiar to American readers, that should not be surprising, as the Sure Start scheme is partly inspired by the American Head Start scheme.

This week research by academics at the University of Durham has been published, showing that the Sure Start scheme has so far had no measurable effect on the abilities of children entering school.

In view of the Head Start precedent, this should not cause any great surprise. Even supporters of Head Start do not claim more than moderate benefits.

Predictably, parts of the educational establishment in Britain have jumped to the defence of Sure Start. According to Prof. Ted Melhuish, writing in the Guardian (where else?) "The effects won't show themselves for a couple of years yet and the really important effects won't show themselves until adolescence".

Are you sure, Ted? In most of the studies on the effects of Head Start, any educational benefits actually fade out after a year or two. Prof. Ted's optimism therefore seems to be a triumph of hope over experience.

Tuesday, August 28, 2007

Can you chuck your kännykkä   posted by Razib @ 8/28/2007 10:07:00 PM

Finns dominate mobile-chucking contest.


Dutch Height (again)   posted by DavidB @ 8/28/2007 05:04:00 AM

As I have several times discussed the height of the Dutch (and other peoples) I was interested to come across a reference to this article. Unfortunately I don't at present have access to the full article (without paying $30), but the abstract says:

In the late-Middle Ages and at the onset of the early modern period, the Dutch population was taller than in the first half of the 19th century. This inference is partially based on skeletal evidence, mainly collected by the Dutch physical anthropologist George Maat and his co-workers. A spectacular increase in Dutch heights began in the second half of the 19th century and accelerated in the second half of the 20th century. At the end of the 20th century, the Dutch became tallest in the world.


Monday, August 27, 2007

More howler monkey lovin'   posted by p-ter @ 8/27/2007 04:10:00 PM

John Hawks follows up the monkey hybridization story, providing some important ecological context:
[T]he primary difference between the two species is cold tolerance: A. pigra can and does live at higher altitudes than A. palliata, ranging high enough that it must tolerate freezing temperatures
Larger monkeys with larger, more complex molars, differences in throat anatomy, and greater cold tolerance, in contrast to a smaller, more cosmopolitan species, with the opportunity for gene flow during interglacials. They sound like Neanderhowlers.


Genomics & insurance   posted by Razib @ 8/27/2007 03:08:00 PM

The Economist has a long piece about the impact that ubiquitous genetic testing will have on health insurance, especially in the United States. This part is crucial:
...If that is the consequence, then other ways of paying will have to be devised. Carol McCall of Humana, a big American health-care provider, thinks a move toward some sort of compulsory, universal coverage is inevitable, even in America. That need not necessarily mean a scheme financed mainly out of taxation, of the sort found in most other rich countries. However, social outrage over a rising class of uninsurables may make the government an insurer of last resort-particularly, as Dr Cecchetti observes, when some rich and powerful people discover that they, too, are not immune from the genetic lottery. He reckons testing will lead to individuals receiving a health score akin to today's personal credit score. Those whose files come on screen to the accompaniment of flashing red lights will not find it easy to obtain cover for much less than the cost of paying for their treatment themselves.

Actually I think the key here is family. Just as surveys have found that having a friend or family member who is gay tends to change how one perceives attitudes toward gay rights, my own hunch is that genetic predispositions found among the circle of family and friends will tend have more of an impact than we might think. The distribution of mutational load being what it is it seems likely that uninsurables will be found across all classes and socioeconomic clusters, as opposed to the current population of uninsured which is disproportionately young, poor or marginalized in some way.


Against Open Access???   posted by Razib @ 8/27/2007 08:47:00 AM

It seems that a coalition of non-Open Access journals, Partnership in Research Integrity in Science & Medicine, is out to take down journals like PLOS. I know people have to put bread on the table, but really there isn't an open-ended guarantee that you can milk your business model forever. In any case, Blog Around the Clock has links to many comments around the web in regards to this issue.


Sunday, August 26, 2007

Redheads going extinct hoax   posted by Razib @ 8/26/2007 12:38:00 PM

Just wanted put a note here that I have two posts, here and here about a new incarnation of the "redheads are going to go extinct" meme. The current culprit is National Geographic Magazine. The only reason that I know about this is that there was a spike of traffic from message boards on my other blog attempting to debunk the story using some stuff I'd posted earlier.


News from Derbyshire   posted by DavidB @ 8/26/2007 07:10:00 AM

I tend to assume that all people of taste and intelligence (e.g. readers of Gene Expression) will regularly check out John Derbyshire's site, but in case they don't, here is his brilliant review of a book by Robert Spencer.

Saturday, August 25, 2007

New Steven Pinker interview   posted by Razib @ 8/25/2007 07:31:00 PM

Check out this new interview with Steven Pinker. It ostensibly focuses on his new book, The Stuff of Thought, though it covers a lot of ground. My own feeling is that the interviewer should have let the focus be more on Pinker than his own pet theories, but there's a lot of good stuff in there.


The Bailey article   posted by p-ter @ 8/25/2007 01:24:00 PM

Alice Dreger's account of the Bailey story is available here [pdf]. It's a dizzying trip through the looking glass-- there are plastic vulvas, Stalinist purges of the transexual ranks, and, of course, a neo-conservative conspiracy. If you don't want to read the whole thing, just imagine an Almodovar movie gone horribly, horribly wrong.

Drink as I say   posted by Razib @ 8/25/2007 01:07:00 PM

I'm reading When Baghdad Ruled the Muslim World: The Rise And Fall of Islam's Greatest Dynasty, a history of the Abbasids. This on page 169 caught my attention:
...the caliph called for wine. A golden goblet was brought and the drink was poured into it. Ma'mum drank and handed it to Hasan....Hasan, a good Muslim had never drunk wine, yet to refuse could be seen as an insult to the caliph...'Commander of the Faithful,' he said, 'I will drink it with your permission and following your order,' for if the caliph himself had commanded him to do it, how could it conflict with Islam? The caliph replied that if it had not been his order, he would not have held out the goblet to him. So the tension was relaxed and they drank together

There are many references in this book to the consumption of wine at the court of the Abbasids, and even the patronage of a genre of poetry focused upon wine. I knew the general outline of this, and amongst Muslim rulers alcohol consumption doesn't seem that rare. I recall that the Mughal ruler Jehangir was an alcoholic, as was Saud bin Abdul Aziz, the king of Saudi Arabia in the 1950s and early 1960s (his problems with alcohol were one of the reasons that he was forced to abdicate by his brothers). Of course, Islam prohibits the consumption of alcohol, and yet here you have the titular spiritual leaders of the Islamic world, the caliphs, making it a normal part of their lifestyle. What's going on here?

One of the main reasons that I have generally turned a skeptical eye toward explanations of religious constraint upon behavior are these sorts of examples. From an atheist perspective I had always tended to view religions as clear and distinct sets of axioms; but operationally the practice seems far more subject to social consensus and individual rationalization. This isn't only an issue with religions, I have known of environmentalists who drive SUVs, self-proclaimed social conservatives who are heavy users of drugs and indulge in non-standard sexual practices, and so on. I'm sure most people can repeat such examples. Years ago when I found out that George H.W. Bush had switched from being pro-choice to pro-life, as had Ronald Reagan to some extent (Reagan's pro-choice period was more that he simply signed laws decriminalizing abortion in California as governor), I assumed this was conscious political opportunism. The same for Al Gore or Jesse Jackson, who made the inverted transition. And surely some aspect of political calculation was at work here on the ultimate level, but what about the proximate cognitive processes? Humans are good at rationalization, and I'm not sure anymore that the elder Bush or Reagan were insincere in their rather fortuitous conversions. Or, at least part of their minds were pretty convinced that their change in opinion had more to do with reflective shifts in the underlying assumptions and values and not an exogenous push due to circumstance.

In short, humans beings perceive themselves to be reflective beings shaped by essential axioms open to conscious inspection. But the reality is that human behavior and psychology seems to exhibit a great deal of contextual contingency which shape a host of cognitive processes insulated from conscious inspection. We regularly seem to make up, and believe in, stories which reinforce our self-perception that we are rational beings with free will who make decisions and form beliefs by carefully taking into account data filtered via our avowed norms. But cognitive psychology shows that humans can be easily influenced by priming inputs which they are not conscious of in regards to the choices they make, all the while happily regaling researchers with their theories that sketch out the underlying causal factors behind their behavior. Yet it seems here that as in the case above the reason is posterior to the act; constructed post facto to give intellectual support to decisions made via other means.

Surely there is a method to the madness, and the outline of human behavior is constrained by a host of concrete parameters (biology, sociology, history, even rational calculation!). But, the biases which serve as weighted parameters in the function that generates the distribution of human behavior are likely more complex, contingent and opaque to the naked eye then we might have hoped for. Just as "friction," "bounded rationality" and "behavioral economics" are emerging as necessary and essential tools in economics, so broad brush histories and anthropologies must take into account the multi-dimensional nature of human psychology and the disjunction between the stories we tell and the dynamics which drive us.

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Inter-species monkey lovin'   posted by p-ter @ 8/25/2007 08:50:00 AM

From an article in Genetics:
Well-documented cases of natural hybridization among primates are not common. In New World primates, natural hybridization has been reported only for small-bodied species, but no genotypic data have ever been gathered that confirm these reports. Here we present genetic evidence of hybridization of two large-bodied species of neotropical primates that diverged ~3 MYA. We used species-diagnostic mitochondrial and microsatellite loci and the Y chromosome Sry gene to determine the hybrid status of 36 individuals collected from an area of sympatry in Tabasco, Mexico. Thirteen individuals were hybrids. We show that hybridization and subsequent backcrosses are directionally biased and that the only likely cross between parental species produces fertile hybrid females, but fails to produce viable or fertile males. This system can be used as a model to study gene interchange between primate species that have not achieved complete reproductive isolation.
The fact that the species (two species of howler monkey) diverged about 3 million years ago is pretty striking-- the divergence time of humans and chimps is "only" one or two million years more than that, but creating a humanzee doesn't seem to be possible. Humans and Neandertals, though, only split a few hundred thousand years ago.


Skull Shape-Shifters   posted by DavidB @ 8/25/2007 05:21:00 AM

The UK Times today has a short report into some surprising research findings. The main text is as follows:

A study into the mysterious changing skull shape of medieval man casts serious doubt on current theories.

The peculiar shift from long narrow heads to those of a rounder shape, and back again, which took place between the 11th and 13th centuries, has been noted at sites throughout western Europe. But a study of skulls found at the deserted village of Wharram Percy, near Malton, North Yorkshire, suggests that the anatomical blip was not down to an influx of Norman immigrants, or climate change, English Heritage has said.

It examined nearly 700 skeletons recovered from the village. Unlike other research, data from the Wharram site traces the change to a single, indigenous community which has been radiocarbon-dated.

Simon Mays, a skeletal biologist, said: "Our work has yielded few clues on why skulls changed, but we have cast serious doubt on some of the current theories. Despite the best efforts of science, we're still in the dark to explain why it happened."

Another report, in the Guardian, has more detail, including the important point that the changes are only found in male skulls.

And yet another report is here.

It's all very mysterious. I was aware that archeologists had found some changes in the shape of English skulls over the last thousand years, but I didn't know it was a change found elsewhere in Western Europe, or that skulls had changed in one direction and then back again in a few centuries.

And before anyone says 'Black Death', and has me chewing the carpet, I must point out that the change between the 11th and 13th centuries precedes the Black Death.

Friday, August 24, 2007

And so it starts   posted by Razib @ 8/24/2007 11:41:00 PM

John Hawks has put up an inaugural post in a series on natural selection. His background as an English major shows (in a good way). It is interesting to note that John alludes to the Malthusian background of natural selection, since Greg Clark's work presupposes exactly this dynamic up until the 19th century for our species (Clark notes we were subject to the same dynamics as any other animal, though I would add that more or less we still are).


In Germany Tyler Cowen blogs for Gene Expression!   posted by Razib @ 8/24/2007 10:46:00 PM

Read all about it in Spiegel Online (who knew that Yoda wrote for a German audience?). Here is the original post by "Tyler Cowen."


Parallels   posted by amnestic @ 8/24/2007 09:09:00 PM

Pardon the interruption, but if anyone has successfully used Parallels with a Windows XP partition in Boot Camp that is FAT 32 configured would you please drop a line (clicking the name "amnestic" above will result in a pop-up window with a contact box)? I have been combing through the knowledge bases, blog entries, and forums for a couple days and I am still stuck with "Unable to open disk image Boot Camp!" Frustration mounts.

The impulse to prefer now to then?   posted by Razib @ 8/24/2007 05:50:00 PM

There's a new paper which uses fMRI to localize an area of the brain which seems to be involved in preventing impulsive actions. I can't but help think that something like this, which might vary from person to person, could be one of the upstream factors which shapes individual time preference. This is on my mind because I just finished Farewell to Alms by Greg Clark, and change in mean time preference is at the root of a shift in behavior which he believes primed the English (among others) for their breakout from the Malthusian trap. But it is one thing to posit a behavior whose distribution is governed by selective forces of a quantitative genetic nature, the case for any such arguments gains a boost if one could tunnel down to the level of biophysical specificity so as to assess variation across individuals and populations.

In other news, watch this space. Our own Herrick has a "10 questions" with Clark pending, so keep an eye out (that means you Ambrosini Critique).


Thursday, August 23, 2007

RNA regulons   posted by amnestic @ 8/23/2007 10:59:00 PM

One of my favorite recent ideas wondering through the literature is that of an RNA regulon or post-transcriptional operon. Operons in prokaryotes are groups of genes whose protein products all function in the same biochemical pathway. The genes are coordinated by sticking them all next to each other and transcribing all when you transcribe one. The post-transcriptional operon idea is that RNA motifs allow proteins in the same biochemical pathway to be regulated at the translation step instead. If several proteins were needed, for instance, to build some new architecture sticking off a cell at a specific location far from the nucleus, it wouldn't do to have to coordinate them way back there. Instead, you just throw in an RNA motif, say AUUUA. Then produce an RNA binding protein that is specific for that motif. Now traffic that protein to the location of interest. All of the RNAs will be localized to the right spot.

Of course, localizaton is just one way this could work. Any process better controlled faster or farther away from the nucleus could use an RNA regulon. One notable case is that of the Pumilio family (Puf) RNA-binding proteins in yeast. Melissa J. Moore explains it here:
... each Puf protein exhibited a highly skewed distribution of bound mRNAs: Puf1p and Puf2p bound mostly mRNAs encoding membrane-associated proteins, Puf3p almost exclusively targeted messages for nuclear-encoded mitochondrial proteins, and Puf4p and Puf5p associated primarily with transcripts encoding proteins bound for the nucleus. In several cases, a majority of the subunits comprising a particular multiprotein machine, such as the mitochondrial ribosome and a number of nuclear chromatin modification complexes, were encoded by mRNAs "tagged" by a single Puf protein. Together with earlier data (12), these new results (16) strongly support the idea that the expression of proteins with common functional themes or subcellular distributions is coordinated by large-scale regulatory networks operating at the mRNP level.

Many other examples can be found in this review by Jack Keene. I don't think I've seen an example of this yet, but given the slight wobble in microRNA specificity, one could imagine a single microRNA regulating a whole set of genes. Also, most interesting for my neuro-tastes is the recent report from the Moore lab showing that the immediate-early gene implicated in neuronal homeostasis, Arc, may be part of a regulon defined by introns in the 3'UTR. The mechanism is just too clever but requires an explication on the "pioneer round" of translation. Basically the cell tricks itself into thinking it made a funky RNA and destroys it after one round of synthesis. The other RNAs regulated in this path in neurons must have opposing effects to Arc though because knocking down this negative regulation pathway led to increased excitability (increased Arc reduces neuronal excitability). This raises a more general question. The idea of RNA regulons is nice, but how much can you predict knowing that your gene of interest is part of one? RNAs associate with multiple complexes throughout their lifespan, and complexes gain and lose factors dynamically. Also, how promiscuous are RNA binding proteins for cellular processes? For instance, I originally became aware of the Hu proteins as positive regulators of the pre-synaptic calcium-buffering protein GAP-43, but it turns out that they also regulate proteins involved in immune function. Maybe I am just thinking at too high a level of cellular organization. Perhaps all of those proteins respond to calcium in some way. At any rate, I'm expecting that RNA regulons will be increasingly important in understanding the translational regulation that must take place in dendrites to produce persistent memories. Looking forward to more on that in the next year or so.

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A modern classic text   posted by p-ter @ 8/23/2007 08:16:00 PM

I recently finished Uri Alon's An Introduction to Systems Biology: Design Principles of Biological Circuits, which I concluded about halfway through was one of the greatest textbooks I've ever read. No joke. It's simply excellent. If you're a biologist with any interest in gene regulation, read this book. If you're a physicist or engineer with any interest in biology, read this book. If your eyes don't glaze over when you read my more technical posts, read this book. Here are a few reasons:

1. The organization of the book itself, and the narration within, is spectacular. Alon takes a classic reductionist look at biological networks-- the whole can be understood by considering the parts. Though the parts, in this case, are not individual genes themselves, but the recurring types of regulatory interactions-- "motifs"-- that are seen in different types of network, biological or otherwise. As he points out multiple times, it didn't have to be this way-- in principle, evolution could have stumbled on incredibly complex network architectures, but that isn't the case. A simple mathematical analysis of two or three node circuits reveals subtle behaviors that are seen over and over again-- it's truly sublime.

2. This is not a laundry list of experiments, tools, and results. Each example is fully explored, both using mathematical models and, where available, experimental results. This leads to a nice fully picture of a mathematical model and its application. And note the math itself is completely accessible to anyone with some exposure to calculus and differential equations.

3. Alon doesn't stop at describing biological networks and their architecture, though he could have stopped there and had an excellent text (the retrospectively obvious points he makes about the different time scales of reaction times in different networks, and the impact that has on network organization, was worth the price of the book alone). He goes on to ask the evolutionary questions: why are certain genes regulated by activators, and others by repressors? In what situations is a certain type of network motif favored, and in which situations is it disfavored or neutral? He closes the book with a quote from Michael Savagaeu that very much resonated with me:
Differences in biochemical details might be the result of historical accidents that are functionally neutral, or they might be governed by additional rules that have yet to be determined. One can always assume that certain differences are the result of historical accident, but such an explanation has no predictive power and tends to stifle the search for alternative hypotheses. It generally tends to be more productive if one starts with the working hypothesis that there are rules. One may end up attributing differences to historical accident, but in my opinion it is a mistake to start there.
Again, read this book.


Taboo questions and the internet   posted by p-ter @ 8/23/2007 05:53:00 PM

The New York Times has a piece on J. Michael Bailey, a psychologist best known for his rather controversial thoughts on sexual orientation. His book, The Man Who Would Be Queen, made him something of an internet celebrity (if that's the right word). A few paragraphs from the article pretty much sum it up:
In his book, he argued that some people born male who want to cross genders are driven primarily by an erotic fascination with themselves as women...Other scientists praised the book as a compelling explanation of the science. The Lambda Literary Foundation, an organization that promotes gay, bisexual and transgender literature, nominated the book for an award.

But days after the book appeared, Lynn Conway, a prominent computer scientist at the University of Michigan, sent out an e-mail message comparing Dr. Bailey's views to Nazi propaganda. [B]y the end of 2003, the controversy had a life of its own on the Internet. Dr. Conway, the computer scientist, kept a running chronicle of the accusations against Dr. Bailey on her Web site. Any Google search of Dr. Bailey's name brought up Dr. Conway's site near the top of the list.

The site also included a link to the Web page of another critic of Dr. Bailey's book, Andrea James, a Los Angeles-based transgender advocate and consultant. Ms. James downloaded images from Dr. Bailey's Web site of his children, taken when they were in middle and elementary school, and posted them on her own site, with sexually explicit captions that she provided. (Dr. Bailey is a divorced father of two.) Ms. James said in an e-mail message that Dr. Bailey's work exploited vulnerable people, especially children, and that her response echoed his disrespect.
These sorts of tactics are unsurprising (especially to some people here familiar with the One People's Project), but the juxtaposition of the fact that the book was nominated for an award by a group specializing in transgender literature with the following storm is particularly striking. The internet often acts as a echo chamber for people with similar views, which then tend to drift more extreme-- if a mob of people is insulted, somehow all-out character assassination becomes the obvious next step.

Wednesday, August 22, 2007

Demon rum   posted by Razib @ 8/22/2007 09:05:00 PM

Baltic neighbours face alcohol crisis:
The Estonian government plans to raise taxes on alcohol by 30% next year as the small Baltic nation of 1.3 million is struggling with a drink problem....

Finland has traditionally had very strict controls on alcohol. Strong drinks can only be bought in the state-controlled Alko shops - rather uninviting buildings which have few signs outside advertising their wares.

In related news, Evidence of positive selection on a class I ADH locus:

...Products of the three class I ADH genes that share 95% sequence identity are believed to play the major role in the first step of ethanol metabolism...we used genomic data to test the hypothesis...Both the F(st) statistic and the long-range haplotype (LRH) test provided positive evidence of selection in several East Asian populations...Interestingly, this haplotype is present at a high frequency in only some East Asian populations, whereas the specific allele also exists in other East Asian populations and in the Near East and Europe but does not show evidence of selection with use of the LRH test. Although the ADH1B*47His allele conveys a well-confirmed protection against alcoholism, that modern phenotypic manifestation does not easily translate into a positive selective force, and the nature of that selective force, in the past and/or currently, remains speculative.

What's going on here? As a great man once said, maybe it's agriculture?

Though seriously, I doubt that protection against alcoholism here is a major issue. So why is it being selected? Who knows. It seems likely that ADH1B is somehow involved in metabolization of various biochemicals which might have fitness implications. What are these populations consuming? And what aren't the other populations consuming? Or, perhaps they're consuming similar things (at least biochemically), but other (e.g., Near Eastern) populations have different selected alleles or functionally relevant loci which result in no great selection on the ADH1B allele in question.

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No comment needed   posted by Razib @ 8/22/2007 08:07:00 PM


Calcium-permeable AMPA receptors   posted by amnestic @ 8/22/2007 01:55:00 PM

AMPA receptors are the major receptors for excitatory neurotransmission. There is a firm basis for the hypothesis that synaptic plasticity and thus memory is based on the increase or decrease in the number of AMPA receptors in specific synapses. AMPA receptors are actually ligand-activated ion channels made up of subunits. Sodium passing through the AMPA channel depolarizes the membrane potential of the receiving neuron and pushes the cell toward firing. Calcium can also pass through AMPA channels, but there is one subunit, the GluR2 subunit, that can block calcium. AMPA receptors lacking GluR2 are relatively rare, so most AMPA receptors can't pass calcium.

Calcium has implications beyond membrane potential changes because calcium acts as a signaling molecule activating enzymes downstream. Plant et al published a report last year showing that GluR2-lacking AMPA receptors are incorporated into synapses for about 25 minutes after induction of plasticity at a synapse, after which they are replaced by GluR2-containing AMPA receptors. They were able to perform these experiments by checking the sensitivity of plasticity to a drug that should only affect GluR2-lacking AMPA receptors. This is an interesting idea because it allows for an increase in calcium signaling at specific synapses that outlasts the inducing event. This calcium signaling could serve as a mark to show the slower synapse-building machinery to find the favored synapses and get to work.

However, all is not well because Adesnik and Nicoll published pretty much the opposite result in April. I mean both labs used phillanthotoxin, the special GluR2 drug, and one got an effect and one didn't. I don't know why, but controversy is so exciting, right? John Isaac wrote a response to the Adesnik and Nicoll paper defending the Plant et al findings, but it doesn't really offer a concrete explanation for the differences. Anyone who can explain it to me gets a free hug if I ever see you.

Now, even more recently, Gray et al (TJ O'Dell's lab) seconded Adesnik and Nicoll's motion damaging the Plant/Isaac thesis. Very similar to the previous two publications but using a different drug and a different waterbath temperature, O'Dell and colleagues could find no indication that GluR2-lacking receptors were necessary for long-term plasticity. When two independent laboratories shoot down a high-profile finding, no matter how theoretically appealing, it is probably time to let it go. It is a shame that the null finding and its replication weren't published in quite as high-tier journals as the first.

Here are two recent reviews on AMPA receptors and GluR2:
Regulatory mechanisms of AMPA receptors in synaptic plasticity
The Role of the GluR2 Subunit in AMPA Receptor Function and Synaptic Plasticity
Keep an eye on the publication dates. The second review here addresses the Adesnik and Nicoll finding, but neither of them address Gray et al.

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Tuesday, August 21, 2007

Genetics and geography   posted by p-ter @ 8/21/2007 09:52:00 PM

There's a nice review in the most recent Trends in Genetics on the use of spatially explicit models in human population genetics. As everyone knows, classic population genetic theory generally makes very restrictive assumptions about the amount of structure in a population-- that is, that there is none. Or maybe a couple populations that exchange migrants. These are all nice assumptions for making the math less hairy, but the recent influx of data (largely generated for medical genetic purposes) on populations from around the globe has revived an interest in modeling variation in a more flexible manner. Along with every person comes their approximate latitude and longitude-- how does genetic data vary on those axes?

The review is a nice summary of recent work in the area, which has shown that a progressive two-dimensional stepping stone model is, for the moment, a decent approximation for human variation (the bottom part of the figure shows parts of the world shaded according to heterozygosity. The largest values are in Africa, where humans originated, and gradually go down, through the serial bottleneck, the further you go from the origin). But this field is ripe for new models and theory. And exploring new models, of course, leads to overturning old ones.

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Monday, August 20, 2007

The genetics of normality   posted by p-ter @ 8/20/2007 05:48:00 PM

I previously mentioned the Nature Genetics "Question of the Year":
What would you do if it became possible to sequence the equivalent of a full human genome for only $1,000?
A large number of responses have now been posted; most of them are actually pretty dull. I wonder if everyone really is that passionate about finding the genes involved in their favorite disease, or whether they've simply convinced themselves of that because that's where the money is.

Anyways, I did appreciate David Goldstein's answer (note he was the leader of the group that published the paper on the genetics of HIV infection I briefly mentioned):
Less appreciated, I think, is the role that inexpensive sequencing will play in basic biology. Today genomics is expensive and concentrated on disease endpoints, which are necessary to motivate the high price tags of these studies. As full representation of human genetic variation gets less expensive, these studies can move back into the study of human biology. We humans are different from one another not only in the diseases that we suffer, but in myriad other details, small and large. Many of those are the result of genetic differences that remain unknown and almost unstudied. It is finally time to study all the normal variation that enriches the human world and experience-memory, behavior and personality. In short, economical sequencing of human genomes will help us to understand who we are and how we got that way.


Sunday, August 19, 2007

Greek v. German philosophy   posted by Darth Quixote @ 8/19/2007 08:35:00 AM

Saturday, August 18, 2007

Evolution, a story told by the winners   posted by David Boxenhorn @ 8/18/2007 09:54:00 PM

I had what I seemed to me like an interesting thought when I read this, and I wanted to explore it further. But I have been very busy these days, and I just don't have the spare cycles, so I'm just going to throw it out there. My biggest question is: "What am I missing?" R. A. Fisher didn't think that epistasis was an important evolutionary force. I can't believe he would miss this, so the only alternative is that he considered it...

From the link:

Finally, that we failed to find a significant grandfather effect in our monogamous society in which we restricted our data to those men who married only once in their lifetimes (and hence could only gain fitness by grandfathering after the menopause of their wife) strongly suggests that the evolution of prolonged life in men cannot be explained by the selective benefits of grandfathering.

My thought, as I expressed in the comments of that post, was that average fitness is not particularly meaningful, since a relatively small number of males at the top of the social pyramid probably had a disproportionate evolutionary impact - what really counts is the grandfather effect among them. I can easily imagine a scenario where grandfathers decrease fertility of ordinary families (another mouth to feed...), but increase it among the rich. The long-term fitness impact of grandfathers could well be positive, even though the average impact is negative, since the rich have the biggest long-term evolutionary impact.

I can tell this same story on the gene level. Imagine a population which is 99% "aabb" and 1% "aabB", each of which have equal fitness. Now, imagine that there's a mutation "A" that reduces fitness by 10% in "bb" individuals, but raises fitness by 10% in "bB" individuals. Let's say by chance we get a "aAbB" individual before the "A" allele dies out. That "aAbB" individual will have the same fitness as a normal "aabb" individual, since its offspring will be 25% "aabb" (average fitness), 25% "aAbb" (10% lowered fitness), 25% "aAbB" (10% higher fitness), and 25% "aabB" (average fitness). Nevertheless, over time, the "A" allele will increase and eventually fix (together with the "B" allele). (Those of you who want to quibble about the percentages can adjust them accordingly.)

Now that seems like an interesting result to me! We talk a lot about average fitness here, but if I am not mistaken, average fitness can tell a story that's very different from what's really going on. Increasing the fitness of winners seems to count a lot more than decreasing the fitness of losers - and in evolution it's the winner's story that will eventually be told.

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Positive selection in regulatory sequences   posted by p-ter @ 8/18/2007 07:11:00 PM

As many of our readers are aware, humans and chimpanzees are rather different, and have diverged considerably since we last shared a common ancestor a few million years ago. An interesting question in evolutionary biology is: what the hell happened? What makes us so different? Comparing the consensus genome sequences of humans and chimps shows millions and millions of base pairs that have changed; which of those are functionally relevant?

One of the hypotheses that has been "rediscovered" in the last few years is that the important changes should be involved in gene regulation, rather than protein sequence itself (this is of course from the classic King and Wilson paper). A new paper takes a look at putative regulatory regions at a number of genes, and concludes that, yes, some of them have been under positive selection since the divergence of humans and chimps. Further, they run a quick and dirty analysis on the functions of the genes whose regulation appear to be under positive selection, and see some enrichment in neural and nutrition-related categories. From this, they conclude, "the present survey...suggests that human cognitive, behavioral and dietary adaptations have arisen primarily through changes in cis-regulatory sequences." Meh.

That could, of course, be true. But frankly, the input of this paper didn't really change the weight I put on that possibility at all (that is, I'd estimate the Bayes factor of this paper at about zero). Here's why:

1. I'm starting to become somewhat ill-at-ease with tests for selection that are based on estimating evolutionary substitution rates (in this paper, they compare rates at promoters with those in introns). What exactly do tests like these detect? Ultimately, this is a population genetics question-- how many new positively selected alleles have to arise and become fixed for this test to be significant? And why would you expect that many are necessary for phenotypic change (as opposed to, say, one really well-placed substitution)? For example, a recent paper showed that three regulatory substitutions completely accounted for a major morphological difference between two Drosophila species. Is that enough for a significant result in a test like this? If not, what kind of functional biases are being introduced into the results?

2. I'm always ill-at-ease with results based on enrichment in gene ontology categories. In this case, the most significant result is in "protein folding", which is neither a neural nor nutrition-related category. The next ones: 0.01 p-values for "other neuronal activity" and "neurogenesis", and a 0.02 p-value for "neuronal activities". The categories are non-disjoint (presumably "neuronal activities" and "other neuronal activity" share many of the same genes, for example), so are the enrichment results due to a few genes that fall in every neural-related category? And how can one conclude, based on this evidence, that "human cognitive, behavioral and dietary adaptations have arisen primarily through changes in cis-regulatory sequences" ? Given what we're working with, that's still pretty much speculation.

So yes, changes in regulatory sequences seem to be important in driving the divergence of humans from chimps (though not necessarily to the exclusion of other changes). But the precise changes, and the traits they involve, are certainly still up in the air.

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Gregory Clark in The Times   posted by DavidB @ 8/18/2007 06:00:00 AM

The (UK) Times seems to be getting frisky in its old age. A few days ago there was Matthew Syed's article on race and IQ (see a few posts down), and today the Times has an article by Gregory Clark, summarising the thesis of his book Farewell to Alms. I don't personally find the thesis very convincing (was England really so different from other European countries in its demographic patterns?) but it is certainly intriguing.

Friday, August 17, 2007

Neocortical olfactory memory erasure   posted by amnestic @ 8/17/2007 08:26:00 AM

Rapid Erasure of Long-Term Memory Associations in the Cortex by an Inhibitor of PKM{zeta}
Reut Shema, Todd Charlton Sacktor, Yadin Dudai

Little is known about the neuronal mechanisms that subserve long-term memory persistence in the brain. The components of the remodeled synaptic machinery, and how they sustain the new synaptic or cellwide configuration over time, are yet to be elucidated. In the rat cortex, long-term associative memories vanished rapidly after local application of an inhibitor of the protein kinase C isoform, protein kinase M zeta (PKM{zeta}). The effect was observed for at least several weeks after encoding and may be irreversible. In the neocortex, which is assumed to be the repository of multiple types of long-term memory, persistence of memory is thus dependent on ongoing activity of a protein kinase long after that memory is considered to have consolidated into a long-term stable form.

The authors used conditioned taste aversion (you may be familiar with this learning paradigm if you've ever made yourself sick off tequila). Injection of a peptide inhibitor of this enzyme (PKM zeta) completely removed the aversive association. This isn't a paper about how to erase memories for any clinical application because, for instance, injecting the drug erases multiple olfactory associations (i.e. we don't have a clue how to achieve specificity). It is a paper about how memory works, and it is pretty remarkable that a simple mechanism like persistent kinase activation may be central to this neural function.

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Thursday, August 16, 2007

Common disease, single gene?   posted by p-ter @ 8/16/2007 06:33:00 PM

The prevailing consensus on "common" or "complex" diseases is that they result from the interplay of multiple genetic and environmental inputs. This is assumed largely because results from linkage studies were discouraging, which rules out a single, highly-penetrant gene as a possibility. There are many disease models where linkage studies could fail, however; a model involving multiple factors just seems to make more sense than the alternatives (and has been confirmed for a growing number of diseases). But consider this paper on a certain type of glaucoma:
Glaucoma is a leading cause of irreversible blindness. A genome-wide search yielded multiple SNPs in the 15q24.1 region associated to glaucoma. Further investigation revealed that the association is confined to exfoliation glaucoma (XFG). Two non-synonymous SNPs in exon 1 of the gene LOXL1 explain the association and the data suggest that they confer risk to XFG mainly through exfoliation syndrome (XFS). Approximately 25% of the general population is homozygous for the highest risk haplotype and their risk of suffering XFG is over 100 times that of those only carrying low-risk haplotypes.
Crunching the numbers on the table in the publication suggests that, in the population over 60, people carrying the allele have a 22% chance of developing the disease, while people without it have about a 1.5% chance (the difference between my calculations and those in the abstract is that I'm considering presence or absence of the allele, rather than the genotype, and our numbers on the prevalence of the disease might be slightly different--I used 15%). That's a huge effect, and the authors claim that the population attributable risk of the risk haplotype is almost 100%-- that is, if the haplotype were to disappear from the population (which is obviously not a real possibility), the disease would as well.

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Rape and culture   posted by p-ter @ 8/16/2007 05:49:00 PM

Apropos of the post on sexual charity, I came across this in the "readings" section of Harper's, from a United Nations report called "The Dynamics of Honor Killings in Turkey" [pdf]:
The boy was seventeen at the time and the girl about eleven. He assaulted and raped her. Then, thinking he had killed her, he buried her. Her friends found her. The boy was sentenced to fourteen years in jail. After a while, the girl got well. The boy's family went to the girl's family and said, "We will accept your girl as a bride, but you have to withdraw your case against our son so he can get out of prison." The girl's family thought, Who will want to marry her when she gets older anyway? So they withdrew the case. Now the two of them are married. --female, twenty-two
An anecdote, yes (and possibly a second or third-hand one). But perhaps some evidence that the seriousness of rape is not a constant across cultures.

Times article   posted by DavidB @ 8/16/2007 06:37:00 AM

The UK Times today has an article by Matthew Syed with the heading Let's not cower from the hard truth about race and IQ.

The article itself is not very impressive - largely a tired rehash of arguments familiar from Gould, Lewontin, and Flynn - but it is unusual for the subject to be discussed at all.

Addendum from p-ter: The author of the article makes an appeal the authority of geneticists on race:
This will not come as a surprise to geneticists who have long understood that racial categories are social constructs lacking genetically rigorous boundaries. Most genetic variation exists within groups rather than between them and skin colour can be a highly misleading measure of the genetic distance between populations.
These are tired claims to hear for long-time readers, but I feel the need to link to my post on race and AWF Edwards's paper on Lewontin's fallacy.

Wednesday, August 15, 2007

EuIslamica   posted by Razib @ 8/15/2007 10:44:00 PM

For some readers, MSNBC has a nice map which shows the rough numbers of Muslims in each European country.


Not sexual charity   posted by Razib @ 8/15/2007 02:41:00 AM

Remember the post Sexual Charity? This is not sexual charity, Grooming of white girls for sex is exposed as two Asian men jailed. The root:
"At the point in their lives when they are ready for this sort of activity, Asians cannot go to Asian girls because it would be a terrible breach of the honour of the community and their family to have sex with an Asian girl before marriage." She said that the reason Asian men targeted very young white girls was because older white girls knew that a relationship with an Asian youth was unlikely to last as the community would seek an arranged marriage with someone from the Asian sub- continent....

However, Ms Cryer added: "I think there is a problem with the view Asian men generally have about white women. Their view about white women is generally fairly low. They do not seem to understand that there are white girls as moral and as good as Asian girls."

[Asian means Muslim here]

"Moral" is a loaded term. Are you less "moral" if you have 3 or 4 relationships before marriage and sexual relations with those individuals? What about if you are a virgin before marriage, but you don't see the person you are going to have sex with for the first time until a few days before you marry them? There is some talk that in the United States candor has made the perfect the enemy of the good, that a little bit of hypocrisy is necessary and beneficial. But then you see the other extreme.

Of course this isn't restricted to Muslims or "traditional" cultures. Most readers know that my adolescence was spent around many Mormons, and what passes for a socially conservative milieu in the United States. A particular subset of Mormon males, generally popular jocks, would date non-Mormon girls pretty explicitly for the purposes of sexual gratification. These men would subsequently go on to marry "good" Mormon girls. One of my friends told me quite frankly that he broke up with his Mormon girlfriend and dated a non-Mormon because he was so frustrated with having his sexual urges so constrained. After he got what he wanted he went back to his Mormon girlfriend (last I heard they were married and had several children). I'm assuming things would have been a little less relieved in Provo where everyone is a "good" girl....


Tuesday, August 14, 2007

Height and health   posted by Razib @ 8/14/2007 03:49:00 PM

Height, health, and development:
...This paper investigates the environmental determinants of height across 43 developing countries. Unlike in rich countries, where adult height is well predicted by mortality in infancy, there is no consistent relationship across and within countries between adult height on the one hand and childhood mortality or living conditions on the other. In particular, adult African women are taller than is warranted by their low incomes and high childhood mortality, not to mention their mothers' educational level and reported nutrition. High childhood mortality in Africa is associated with taller adults, which suggests that mortality selection dominates scarring, the opposite of what is found in the rest of the world. The relationship between population heights and income is inconsistent and unreliable, as is the relationship between income and health more generally.

From what I recall in modern countries height is about 80% heritable (the proportion of within population variation is controlled by genes). Obviously this is probably going to be lower in less developed nations.

Related: An article in The Washington Post talking about the tall Dutch again. Has anyone thought to check the height in the Dutch areas of southwest Michigan? Whites seem smaller in many east coast or southern cities than in the Pacific Northwest (e.g., Boston and New Orleans). I assume my perception has to do with the ethnic mix, since the Pacific Northwest has fewer "ethnic" whites than other parts of the country, and a disproportionate number of the ethnics are Scandinavian ("everyone in Ballard is Norwegian").

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David Warsh on Farewell to Alms   posted by Razib @ 8/14/2007 03:40:00 PM

David Warsh does not like A Farewell to Alms. Warsh is the author of Knowledge and Wealth of Nations (I have the book, haven't gotten to it, but will probably read it before Greg Clark's book). Here is a copy of Clark's Genetically Capitalist. Via Tyler Cowen, who is also hosting a Book Forum on the topic.

Update: The Ambrosini Critique keeps posting on Greg Clark's work. Also, Michael Stastny smacks up Warsh a bit.


Building a better tomato   posted by p-ter @ 8/14/2007 02:39:00 PM

Let's hope these guys come up with a better name than Flavr Savr.
We have modified the flavor and aroma of tomatoes by expressing the Ocimum basilicum geraniol synthase gene under the control of the tomato ripening-specific polygalacturonase promoter. A majority of untrained taste panelists preferred the transgenic fruits over controls. Monoterpene accumulation was at the expense of reduced lycopene accumulation. Similar approaches may be applicable for carotenoid-accumulating fruits and flowers of other species.


Math Test   posted by DavidB @ 8/14/2007 01:19:00 AM

I am planning some posts which will use a few mathematical symbols, but I suspect that some browsers will not be able to read them, and show them as nonsense symbols, blank spaces, or empty rectangles. Please let me know if you cannot read any or all of the following properly. (In each case the symbol itself should be between the double quote marks):

1. "∑" should be large Greek sigma, meaning 'sum of'

2. "σ" should be small Greek sigma, meaning 'standard deviation'

3. "β" should be Greek beta

4. x"²" should be x squared (x with superscript 2)

5. "√"x should be 'square root of x'

6. a"bc"d should be the letters abcd with the letters bc (and only these) shown as subscripts.

Monday, August 13, 2007

Religiosity and personality: How are they correlated?   posted by agnostic @ 8/13/2007 01:01:00 AM

Bad news for atheists: individuals low in religiosity are more likely to have a "slacker" personality. And worse news: this is true even among intellectually gifted people. First, a disclaimer that I consider myself an atheist, though I would never use that term.* So no guff about having an agenda. Also, though obvious, it needs to be said that correlations don't tell you about particular individuals -- if you're a nose-to-the-grindstone atheist, then great. My purpose here is to describe correlations of interest to students of psychology or religion, as well as to deflate some of the smug -- and in this case false -- stereotypes that some atheists have about religious people.

In the interest of time (that is, to save me time), I'll be quoting most of the results since the authors provide enough exposition already. Throughout, the quoted article is McCullough et al. (2003).

Beginning with a review of the Eysenckian work done:**

Cross-sectional studies using Eysenck's P-E-N model (e.g., Eysenck, 1991) indicate that religiousness, as measured by a variety of indicators including frequency of attendance at worship services, frequency of private prayer, and positive attitudes toward religion, is inversely related to Eysenckian Psychoticism (e.g., Francis, 1997; Francis & Bolger, 1997; Francis, Lewis, Brown, Philipchalk, & Lester, 1995; Lewis & Maltby, 1995, 1996; Maltby, 1997, 1999; Maltby, Talley, Cooper, & Leslie, 1995; Robinson, 1990; Smith, 1996; Svensen, White, & Caird, 1992; Wilde & Joseph, 1997) but essentially uncorrelated with Extraversion or Neuroticism. Indeed, the basic finding that religiousness is negatively related to Eysenckian Psychoticism (i.e., sex-adjusted correlations in the neighborhood of -.30) (e.g., Francis et al., 1995) and essentially uncorrelated with Eysenckian Neuroticism and Extraversion has been replicated with children, adolescents, adults, and older adults from around the world.

And then a review of the Big Five work done:

Several recent studies have employed measures of the constructs in the Big Five, or five-factor personality taxonomy (e.g., John & Srivastava, 1999; McCrae & Costa, 1999), to examine the association of religiousness and personality. Kosek (1999), MacDonald (2000), and Taylor and MacDonald (1999) found that measures of Agreeableness and Conscientiousness were positively associated with measures of religious involvement and intrinsic religious orientation. These results are not surprising in light of the robust link between Eysenckian Psychoticism and religiousness because Eysenckian Psychoticism appears to be a conflation of Big Five Conscientiousness and Agreeableness (Costa & McCrae, 1995).

The authors' original contribution used data from the Terman Longitudinal Study to examine the relationship between religiosity in early adulthood and personality traits in adolescence. The latter were judged by teachers and parents, not self-reported. It's also worth noting that the students in this study were selected to have an IQ of at least 135, a point to which we return. Of the 1528 students in the TLS, the authors looked at 492 of them (280 male) for whom the relevant data was obtainable. Their findings:

Conscientiousness (beta = .14) was also a significant predictor of [early adulthood] religiousness, suggesting that for each standard unit increase in adolescents' Conscientiousness, their religiousness in [early adulthood] increased by .14 standard units.

And although other personality traits did correlate with religiosity:

Table 1 shows that children who were rated as Open to Experience (r = .11), Conscientious (r = .20), and Agreeable (r = .15) in adolescence went on to be slightly more religious 19 years later, p less than .05. In addition, adolescents who became highly religious reported having had relatively strong religious upbringings, r = .43, p less than .001.

These did not remain after their correlation with Conscientiousness was accounted for:

In part, the Openness-religiousness association may simply reflect the variance that Openness shares with the rest of the Big Five -- and Conscientiousness in particular -- in this sample. Measures of Openness and Conscientiousness were related at r = .43, which is not surprising because participants' traits were being evaluated within an achievement setting (i.e., they were rated by their teachers as well as parents), which might cause children who are more conscientious about their studies and assignments also to appear more open to experience (i.e., higher in intellect). Indeed, when we controlled for the intercorrelations among the Big Five through multiple regression, Openness and Agreeableness did not retain significant unique associations with religiousness, but Conscientiousness did.

So that's the reality. Atheists like the author of the following comment will no longer be able to assume they are more conscientious (original emphasis):

Personally, I trust atheists the most. I think they're more likely to keep their word than some Christians who think they're automatically going to Heaven solely because they accept Jesus as their Lord and Savior. I think atheists, in general, are more conscientious about their actions because they don't want to face negative consequences in the here-and-now.

As anyone knows, that attitude is not exceptional among those who wear the atheist label. Nor can they move the goalposts and suggest that, yes, this may hold in general, but since atheists are smart, we don't need religion to make ourselves more conscientious -- "Only retards need a written rule system for how to behave," as brainiacs can rely on their superior common sense to behave diligently. But the TLS data contradict this self-satisfied pap as well: even among MENSA-level people, religiosity correlates positively with Conscientiousness. To be blunt, it's time for atheists to stop patting themselves on the back about how conscientious they are, since as a group they score lower than more religious people.

On a related note, I'm getting pretty sick of atheists congratulating themselves for having low divorce rates or infidelity rates. Steve Sailer has suggested that one reason why Massachussetts citizens have lower divorce rates is that they marry much later in life, so that would-be homewreckers take one look at their wrinkled, sagging skin and say, "Yeah, no thanks." Inductivist showed from GSS data that atheists commit less adultery, but I posited the same reason that Steve would have: for a variety of reasons, they're just not attractive enough to would-be homewreckers, sheer age being the most obvious one (just look at the putz in the article linked to in the beginning of this paragraph). And because infidelity correlates with Psychoticism or low Agreeableness and low Conscientiousness, we expect atheists to cheat more -- ceteris paribus, but in real life things aren't equal and thus most atheists are not put to the same tests of temptation.

In closing, although I'd like for religiosity to hold no relation to Conscientiousness, the real world does not care what I'd like. (On a side note, it's odd how frequently atheists fall victim to the moralistic fallacy in this way, given how many of them profess a belief in a universe indifferent to their desires.) Religious nutballs who paint atheists as deformed scoundrels are wrong, but merely not being a wretch hardly merits all the more-ethical-than-thou braggadocio coming from the other side. The data are in, and it's high time that some atheists lose the vainglory.

* "Atheist" understandably makes a person think of a permanent student activist who works in a used bookstore and argues with his co-workers over which progressive rock album is the best.

** If you want the full references to what McCullough et al. (2003) quote, it shouldn't be difficult to look it up on Google -- how many articles on religion and personality could the given authors publish in a given year? If that doesn't work, then email me. I just don't want to waste space listing out all their references.


McCullough, M., J. Tsang, & S. Brion (2003). Personality traits in adolescence as predictors of religiousness in early adulthood: Findings from the Terman Longitudinal Study. Pers Soc Psychol Bull, 29, 980-91.

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Sunday, August 12, 2007

Facebook ~ AOL?   posted by Razib @ 8/12/2007 03:31:00 PM

Facebook Grows Up:
What does Facebook get from this? If all goes well, much of what people do on the Internet will be accomplished within Facebook. Instead of eBay, you can buy in Facebook's marketplace. Instead of iTunes, there's iLike. In other words, Zuckerberg wants to keep you-student, graduate or graybeard-logged on to Facebook, organizing virtually everything you do via the social graph.

AOL, PointCast, the portal sites. I think the past 10 years has shown that you better focus on what you can do well before doing everything.


Cleaning up your nerdy appearance   posted by agnostic @ 8/12/2007 12:57:00 PM

This is apropos of the discussions about nerdiness and helping girls get math by appealing to conventional femininity, rather than fostering a counter-culture of female nerdiness. Obviously, encouraging girls to not care about their appearance is awful advice. [1] However, smart females are not deplorably inept at meeting standards, since their feminine instincts guide them to attend to such things. But the sartorial state of smart males couldn't be worse, excepting the ground zero of 20th Century slovenliness -- the counter-culture of the late 1960s and early 1970s. [2] An excerpt from bad-cop Udolpho's "Dressing like a retard isn't impressing anyone":

Ironically, people who dismiss clothes as a superficial indication of the person are the first to boast that their unconventional (or, more likely, sadly conventional) attire is a hint to their creative genius -- usually they cloak this boast by saying something like, "the smartest people I know wear…" as if I would give a damn. These people cannot face what they really are.

Rather than argue hypothetically over "creativity vs. conformity," let's just see if dressing like an adult hurt any of the great minds of the past. Now, I'm not arguing that dressing properly is a necessary or sufficient condition for greatness, only that it is neither here nor there in the matter. This deflates the protestation of "hindering creativity," leaving the underdressed with no excuse to reject growing up and showing your colleagues that you hold your relations with them in higher regard than stepping out to get the morning paper. It also inspires confidence in you among those below you at work, and it presents a good role model to your social inferiors. [3]

Gallery of geniuses in genteel garb

Look at how well the greats of the past dressed themselves, sticking just to mathematicians, since they are the prototypical anti-social, unkempt geek of the present day:

In the interest of space, I'll just link to pictures of Cauchy, Riemann, and Hilbert. And look how well Galois dressed, even though he was likely no older than 20. (And lest you think him a stuffy conservative, he was a radical Republican.) So c'mon, if Euler could find time to dress well during his busy schedule of churning out theorems and babies, much like Bach, then so can you.

Look at what a difference this makes, using the bodies of a geek and a gent, and the head of uber-nerd Brian Krakow from My So-Called Life:

What to do?

Now for the aspiring adults, here are some links to online guides and shopping sites. For starters, browse Clothes and the Man, or any of the similar books featured on the page. I haven't read any of them, so I can't say which is best, but they all have high ratings. You can also visit the men's section of Caveat: it tends to be more hip and trendy (though still good-looking), and if you need help, it's best to start with less transient styles.

For example, pick Valentino from the "Complete Collection" menu. Most of that you could copy and look great year after year. For the more conservative or traditional readers, visit the websites of Hickey Freeman or Ralph Lauren's Purple Label. Just get some ideas -- you don't have to buy anything yet.

When the time comes to purchase, unless you have lots of money, you'll need to go to a discount designer store in person or online. If you live in a large metro area, chances are there's at least one of the following nearby: Filene's Basement, Century 21 (NY area only), or any of The Mills or Premium Outlets malls, which typically house outlets for Saks Fifth Avenue, Neiman Marcus, Nordstrom's, etc.

The two best online stores are, in order, Yoox and Bluefly. They let you return items, so don't worry. Speaking of which, the clothes don't have to fit perfectly: you can always have them tailored, once and for all. Some things must fit, though, like the neck of a dress shirt, or the shoulders of a blazer. I'm sure the books I linked to spell out all of this in detail.

That should be plenty to get started. Obviously you're not going to dress like a prince every day, but big deal. No one will care if you don't dress impeccably, since no one's perfect; the point is to make a satisfactory effort. And don't be daunted: the process of change is quick like adaptive evolution, whereby large fitness gains come from the first handful of substitutions, not the myriad others that fine-tune things afterwards.

[1] It will slash their chances of landing a nice boyfriend, increasing the probability of having to settle for dopes. It says to potential employers that they won't cave in to minimal professional duties. And it shouts out, "I'm too smart / cool to have to impress you by looking presentable." Yeah right -- remind me again how many Nobel Prizes you've won? That's what I thought.

[2] Like most guys of today, I was pretty slobbish, but only up until my senior year of college. Take it from a nerd who's been there: dressing well will mark a drastic change in how others treat and view you, whether they're your peers, inferiors, or superiors.

[3] Your inferiors may not be in a financial position to dress as well as you, but if they look around and see an abandonment of standards, they will feel free to go around in sweatpants, holey "wife-beater" shirts, and chewed-up flip-flops. This situation, because of its pervasiveness, is a public nuisance more offensive than the occasional blaring of reggaeton from ghettofied car stereos.


Incarceration Nation   posted by DavidB @ 8/12/2007 07:42:00 AM

An interesting article here on American penal policy.

Friday, August 10, 2007

A new evolution textbook   posted by Razib @ 8/10/2007 10:19:00 AM

Evolution by Doug Futuyma & and Evolution by Mark Ridley are probably two the most common intro texts used by instructors. Well, there's an enormous new textbook out creatively titled Evolution. Here is the important bit from the website:
Evolution, to be published on June 27, 2007, is designed to serve as the primary text for undergraduate courses in evolution. It differs from currently available alternatives in containing more molecular biology than is traditionally the case. But this is not at the expense of traditional evolutionary theory. Indeed, a glance at the Table of Contents and the authors' interests reveals the range of material covered in this book. The authors are world-renowned in population genetics, bacterial genomics, paleontology, human genetics, and developmental biology. The integration of molecular biology and evolutionary biology reflects the current direction of much research among evolutionary scientists. Click here to read more.

The book is being published by Cold Spring Harbor Press.


Thursday, August 09, 2007

I like introgressed rice   posted by Razib @ 8/09/2007 05:40:00 PM

Neat article on the introgression of an allele for switching the red seeds of rice to white from the japonica to the indica subspecies. Basically the mutant arose in the japonica subspecies, "jumped" to the indica, and fixed. You can read the paper for why people prefer white to red varieties, but the important point that the authors offer is that a) rice is highly inbred and b) there are fertility barriers between the two varieties. That implies that the selective advantage was so great that people worked hard to hybridize the two even though it was something of an unnatural act.


Lactase persistence in Eurasia   posted by Razib @ 8/09/2007 11:40:00 AM

At my other blog I have a long post reviewing the new paper on lactase persistence in Eurasia. The authors conclude that the allele which confers most of the latcase persistence in Eurasia arose among "Caucasian" populations. The question is whether the authors meant Caucasian in the 1930s physical anthropological sense (i.e., Caucasoid-Mongoloid-Negroid), or in the more precise sense of peoples from the Caucasus. Here is the portion of the paper which might "clear" this up:
We also monitored the prevalence pattern of the less common LNP [lactase non-persistence -ed.] H87 haplotype that, on the basis of the MJ network, represents the immediate allelic haplotype on which the LP H98 mutation occurred. The highest frequencies of H87 alleles were observed among Daghestan Nogais (8%) and Hazara (7%). This allele was detected in Daghestan Nogais, Hazara, Baluch, Sindi, Brahui, Makrani Baluch, Iranians, Basques, individuals from Utah, and Finns (eastern region). From this distribution of H87, we were able to propose that the ancestral population in which the LP T-13910 H98 mutation occurred is of Caucasian origin.

The Daghestani Nogais are a Turkic group in the Caucasus. None of the rest are technically Caucasian groups. Here are the populations that exhibit H87 with the percentages and N's:

Hazara 7 28
Baluch 5 38
Iran 3 42
Kalash 3 60
Sindhi 2 56
Basque 2 170
Makrani Baluch 2 58
Utah 2 184
Pathan 2 56
Brahui 1 60

The N's aren't as big as you'd like (I know, this is like saying "I'm not as rich as I wish I were!"). H87 is a haplotype one mutational set away from H98, the modal variant associated with lactase persistence throughout Eurasia. The haplotype two mutational steps away from H98 (see the chart on my other blog), H84, has high frequencies throughout Eurasia, but its center of gravity is shifted toward the east (i.e., France has a far lower proportion than China). I think that this implies that H98 and the dominant LP genetic profile arose somewhere in the heart of Eurasia, probably the north-central regions.

Now, one thing that I am curious about are the non-modal alleles, some of which seem to be independent mutational events from a different genetic background than H84/H87. As noted before these variants are:

1) Very new (on the order of 2,000 instead of 8,000 years ago for the most recent common ancestor).

2) Rather rare. Here are the percentages in the populations which exhibit the haplotypes associated with the more recent mutational event. I've also included to the right the percentage in the older cluster, and finally the N's:

Udmarts 15 14 60
Mokshas 11 14 60
Erzas 5 20 60
Iranian 5 2 42
Parsi 4 6 58
Baluch 2 34 38
Somali 2 1 158
Arabs 1 5 102
Southern Italy 1 4 200
Basque 1 58 170
Morocco 1 13 180

What to say here? First, the highest frequencies are found in populations along the Urals. Iranians also seem to have high frequencies of the newer alleles. I am curious about the relative balance between the older and newer alleles in several of the higher frequency populations. If the older variant exists why would the newer one rise in frequency over the past few thousand years? If the older variant exists why did it not sweep to fixation? If the selection pressure was too weak (or various balancing forces maintained polymorphism) to fix the older variant why did the newer mutational event begin to rise in frequency in the first place? Here are some thoughts:

1) LP is weird. It has to come with some cost, probably metabolic. With the domestication of cattle any costs were overridden by the benefits of adult milk consumption. Perhaps the new mutational event has associated functional elements around T-13910 which make them a better solution? Perhaps there are regulatory elements which mask some of the negative correlated responses due to this mutation?

2) The populations which have the highest proportion of LP (northwest Europe) don't seem to exhibit the new variants. What gives? The selection pressure is obviously strong for anything that confers LP. We know that some African and Middle Eastern populations have other LP conferring SNPs besides T-13910, but the major groups above already had that, and, they were likely to be near the source of the rise of frequency of the mutant in the first place (judging by the distribution of H84/H87). Perhaps there is selection pressure for LP around the Urals (extant diary culture), but there are other forces which prevent its increase (maintain polymorphism). So the new mutant and associated haplotype might be a response to (counter) pressure #2. Pressure #2 might not be operative in western Eurasia so it is just another neutral allele because it doesn't have any fitness boost.

3) It seems suspicious to me that it seems likely that both clusters arose in central Eurasia. It isn't like there are more cosmic rays or enormous populations churning out mutations here. My own suspicion would have been that central Eurasia would just have a diversity of descendants from the original mutant from H87, but that doesn't seem like what's going on. A de novo mutational event occurred. Don't know what to make of that. There's other things lurking the background.


Wednesday, August 08, 2007

Sexual charity   posted by p-ter @ 8/08/2007 07:56:00 PM

I'm as much of a sucker for the flawed thought experiment as the next guy, so I'll pass on this one, via Robin Hanson:
Scott Aaronson asks a great question:

Consider two men, A and B. Man A steals food because he's starving to death, while Man B commits a rape because no woman will agree to have sex with him. From a Darwinian perspective, the two cases seem exactly analogous. In both we have a man on the brink of genetic oblivion, who commandeers something that isn't his in order to give his genes a chance of survival. And yet the two men strike just about everyone - including me - as inhabiting completely different moral universes. The first man earns only our pity. We ask: what was wrong with the society this poor fellow inhabited, such that he had no choice but to steal? The second man earns our withering contempt.

One problem with the question is that in our society giving enough sex to satisfy is expensive, while giving enough food to satisfy is cheap. So it might help to imagine a society where the person who lost the food was also in some, though less, danger of starving.

But even then food and sex seem to be treated differently. When we give food aid we don't just give rice and beans to keep folks from starving; we give them enough money to have a moderately tasty diet. We do nothing remotely similar for sex.

To me the obvious answer is that our concern about inequality is not very general - compared to inequality in access to food, humans are just not that concerned about sexual inequality, especially for men. Presumably for our ancestors, the gene pool of a tribe could benefit from equalizing food in ways that it could not benefit by equalizing sex.
Hanson's answer is far too simple a selective scenario. I'm even inclined to think that the evolution of sexual jealousy and the evolution of "justice" are less different than the question presupposes. It's easy to say "imagine a situation where stealing from an individual would lead to their starvation", but less easy to actually imagine it. How different were food and sexual access to our ancestors?

The answer, I'm inclined to think, is: not so different. Among chimpanzees, food and sex are both commodities to be traded:
Political coalitions were recognized early on as part of an elaborate 'marketplace of services' in which chimpanzees trade grooming, sex, food and support. The rules of reciprocity governing social exchange are only beginning to be understood, but evidence is accumulating that chimpanzees repay both positive acts (for example, sharing food preferentially with previous grooming partners) and negative acts (for example, squaring accounts with those who previously opposed them) [citation]
While it's difficult to study these sorts of exchanges, a specific instance of male chimpanzees exchanging sexual access to females for political support was recently documented [citation], suggesting that perhaps this moral instinct Hanson is ready to justify evolutionarily isn't quite so universal.

That's all in chimpanzees, of course, and it's true we live in a society where rape is certainly considered more reprehensible than stealing (of course, rape in wartime was considered par for the course until very recently). I'd be interested to see a study, however, comparing punishments for rape versus stealing across different societies, ranging from hunter/gatherer to our own. Is stricter condemnation of the forceful taking of sex as compared to the forceful taking of food a human universal?

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Brains and beauty: review of Math Doesn't Suck by McKellar   posted by agnostic @ 8/08/2007 12:03:00 PM

Barbie was right: math is hard. Most people find this out in middle school when algebra is introduced, and even the smarties become humbled in college. Danica McKellar, who some readers will remember as Winnie Cooper from The Wonder Years, recently published a book that's part math textbook, part motivational speech, and part "modern girl's guide to life" -- Math Doesn't Suck: How to Survive Middle-School Math Without Losing Your Mind or Breaking a Nail. Tara Smith, who runs the blog Aetiology, recently interviewed McKellar, and has hosted several general discussions about the book here and here. (Another favorable review from The Intersection.) I want to review Math Doesn't Suck in the context of these discussions, especially the one on whether math books that appeal to girls' interest in fashion are apt to turn them into "consumerist tools of the patriarchy". (The intersection of radical feminist ideology and activist pedagogy: where outside parody would be superfluous.)

I had to kill several hours after work tonight before going home, so I perused Math Doesn't Suck at Barnes & Noble, reading carefully just the parts that set it apart from other textbooks (I'm proud to say I already knew the middle school math). First, let me say that I'm not qualified to review its pedagogical strengths -- that's best left to controlled experiments with large sample sizes, an idea that's seldom raised whenever a new educational miracle arrives. Instead I'll focus first on the lessons to be learned, and then review the book's tone, use of examples, and appropriateness for various groups.

I. Lessons learned

The key lesson to take away from this book is that we are witnessing the twilight of the days when "women in science" activists browbeat girly girls into behaving more like Amazons in some imaginary war of the sexes within the academy. Let's look at those two ideas.

First, McKellar takes an unabashedly anti-Amazon approach, some aspects of which I'll discuss in the review. Briefly though, she emphasizes the following qualities throughout: humility, gracefulness, zeal or diligence, snuffing out envy, maintaining a pleasant appearance, and self-reliance but also seeking help when needed.

Second, and more importantly, McKellar bases her book on the assumption that girls are their own worst enemies, not that the patriarchal oppressors conspire to keep them down. I know, you must be falling out of your chair laughing when someone suggests that the physically unprepossessing and emotionally retarded nerds who tend to run university math departments are the incarnation of masculinity and power, but anything goes in rad-fem ideology. McKellar instead sees individual girls acting counter to their own best interests -- that's true of both sexes, since we're riddled to the core with flaws, not being blank slates or angels -- as well as being the targets of their same-sex competitors.

It is telling that the only two anecdotes in which a girl is made to feel awful about her math skills involve female adversaries. One woman tells the story of another girl making fun of her as a nerd for scoring highly on a math test. And McKellar herself relates an instance when her science teacher pulled her aside to ask how she'd managed to score so highly, given how pretty and stylish she was. No, this wasn't a male chauvinist from the 1950s but rather a female girl-hater from the late 1980s. Rather than shaming her into downplaying her girliness, this incident emboldened McKellar to stick it to The Woman -- she didn't have to "dress like a dork" just to be good at math. (And guys, lest you think you're going to get off easily, I have a post in the works on improving your personal appearance, as befits a mature and responsible professional.)

That the true sources of present-day female underachievement have little to do with patriarchal oppression could only be a surprise to someone who just landed here from Mars. Last year there was a WSJ article on how women in the workplace tend not to treat each other well, to such an extent that a majority feel their male bosses treat them better than do their female bosses! And as far as popular fiction goes, the three greatest teen movies of the past 20 years all share the theme of female-female sabotage, and none of it due to the machinations of male manipulators: Heathers, Clueless, and Mean Girls.

Incidentally, why on Earth does Hollywood choose actresses like Denise Richards and Lindsay Lohan to play nuclear physicists and mathletes, given how dopey they are? McKellar, just to pick the most convenient example, would have made a much more convincing protagonist of Mean Girls, and is a superior role model to Lohan. OK, so that's true of anyone who isn't incarcerated or walking the streets, but you know what I meant.

II. Review

Tone. McKellar uses a very informal and conversational tone throughout, which aside from making the exposition clearer to beginning students, also has a disarming effect, since suspicious readers will probably expect a stern, lecturing tone since the book is about practicing math. One thing I learned if I need to write a popular book for teenage girls: ask lots of personal questions to the reader and use exclamation points frequently. And mention boys in every other sentence.

Moreover, the tone is always one of encouragement, like that of a cheerleader getting the student body fired up during a pep ralley. There is no condescension toward their concerns and no trace of male-bashing. And what McKellar is encouraging them to do is not to try to one-up the boys -- like, "go show those boys you can take them on in math!" -- since that "something to prove" mindset will only exacerbate their existing insecurities. Rather, she appeals to their desire for personal accomplishment. Individuals differ in their levels of achievement striving, so this appeal will not resonate with all readers, but it is worth noting that, even though there are pronounced sex differences in the means of almost all personality traits, the facet of Conscientiousness called "Achievement striving" shows no such differences in the US. [1]

Examples. McKellar has received some flak for her choice of examples: looking cute, boys, and looking cute for boys (with the occasional baking example). For instance, the ratio of lipglosses that one sister has to the lipglosses her sister has, or having girls list all the traits that each of their crushes has had and circling the ones in common ("their type") to introduce common factors. Even though the women featured in the book's testimonials talk about how they use math to speculate on foreign currencies for Wall St. firms, McKellar is not so clueless as to think that serious finance would appeal to girls who aren't even in high school. If their biology programs them to only have a few top priorities at that age, you're just going to have to deal with that constraint when trying to reach them.

However, the author does not take such a cynical attitude toward young girls' concerns: she is glad that they are enthusiastic about femininity, and the examples show McKellar's unashamedly pro-girly stance where many a "women in science" activist would have treated young girls' priorities at best as outdated and in need of social re-engineering, and at worst as something the girls should feel embarrassed about. It's worth noting that all of the testimonials include pictures of the women: all are clearly above-average in physical attractiveness and enjoy dressing stylishly and making themselves up.

Appropriateness. Well, obviously the book will bore and turn off the half of the teenage population that has a Y chromosome. Still, looking just at girls, McKellar has clearly written a book to benefit bright girls, and this should be kept in mind when recommending it for use. The author herself graduated summa cum laude from UCLA, co-authored a proof in mathematical physics, and though she is too modest to blab how high her SAT score was, she mentions that her sister got a "near perfect" score on the LSAT, attended Harvard Law School, and is a "high-powered lawyer" in New York City. Before UCLA, the author attended the elite Harvard-Westlake High School in Los Angeles. It shouldn't be any surprise that two sisters should correlate so highly in intelligence, given its moderate-to-strong heritability. Also, sprinkled throughout the book are testimonials from women who felt queazy about math in secondary school but who now use math every day at, for example, Manhattan investment banks.

Conservatively, we may estimate the mean IQ of these women at 130, and more likely around 145 (or 2 to 3 standard deviations above the population mean of 100). These are the girls who will effortlessly assimilate the myriad tricks and strategies that McKellar provides -- anyone who thinks that merely expounding on a neat trick, and even walking the student through the trick using many examples, will cause them to learn it has never taught students of average or below-average IQ. Due to regression toward the mean and just chance, some children of bright parents end up mediocre in intelligence, and having tutored some of them, I can say that their parents' wealth and power can't do squat to make their kid smarter. Of course, if there is a proven IQ-booster (aside from, e.g., providing better nutrition to deprived children), it is a very well-guarded secret.

To her credit, though, McKellar does not drape her work in the frippery of quixotic egalitarianism. Again, most of the testimonials are from very smart women, who we know were very smart to begin with, and who just needed to get over their mathphobia if they wanted a career in investment banking. I didn't keep score, but I believe that bourgeois professionals vastly outnumbered academics in these testimonials [2], something that McKellar does not feel apologetic about -- rightly, as most smart girls don't want to grow up to be nerds but "high-powered" professionals.

As an aside, this freedom of choice for smart girls certainly accounts for some of the variance in the percentage of Nobel Prizes won by women in the pre- and post-women's liberation periods. Once women were allowed to enter the professions, they won fewer "hard" Nobel Prizes, indicating that some of the female scientists and mathematicians of the past would likely have preferred to practice medicine or law, but had no other choice than to conduct research. McKellar, her sister, and most of the women from the testimonials are cases-in-point: they are all great at math, yet only one has chosen a career as a research scientist.

The author herself majored in math at a prestigious university, graduated summa cum laude, and shares credit for a math/physics proof -- how much more positive encouragement could she need if she truly wanted to be a research mathematician? She just prefers what more women than men prefer to do with their lives: to work more with people than objects, and to help and nurture more than to figure out how things work. Hence her career as an actress and tutor / life coach.

One gripe I do have is that, even bearing in mind that only smart girls will benefit from the book, the very first topic treated is the prime factorization of integers -- something that would frighten away most smart adults who haven't seen math in awhile. Later she shows how to tease the greatest common factor of two integers out of their prime factorizations. Here I think McKellar's math nerdiness got the better of her: the most boring branch of math for most people, even math and science nerds, is number theory, and prime factorization offers little practical use in secondary school math to compensate. This could have the effect of scaring away some girls who would otherwise have pounded through the remainder of the book, which focuses appropriately on the basics of pre-algebra.

In sum, don't take this book at face-value -- it's not going to solve an educational crisis, attract more than a handful of girls into research-based careers, and so on. Indeed, no book will be a philosopher's stone that alters human nature in that way. On the other hand, for what such a book is capable of, Math Doesn't Suck passes with flying colors. It is best suited to bright young girls who simply need a good kick in the rear to get them over their mathphobia. The tone and use of examples are excellent, bearing in mind who the real target audience is. And most importantly, for all of her outward feminism, McKellar -- as well as Tara Smith, a former cheerleader -- has laid the first stone along a route away from orthodox "women in science" activism. You can disagree with some of what they'd say, but you feel you are interacting with good-faith, rational human beings instead of someone whose emotions so overwhelm her thought processes that she would get nauseous and nearly faint upon hearing contrary viewpoints in a dispassionate discussion.

So, who out there is going to write the companion volume for young boys?

[1] See my review of the relevant meta-analysis here, appropriately enough in the context of women in science.

[2] There was one student of neuroscience, and I think that was it. There was also a petroleum analyst.

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Tuesday, August 07, 2007

The genetics of tone deafness   posted by p-ter @ 8/07/2007 03:03:00 PM

There's an "old-school" article in the most recent American Journal of Human Genetics on familial aggregation in tone deafness:
Congenital amusia (commonly known as "tone deafness") is a lifelong impairment of music perception that affects 4% of the population. To estimate whether congenital amusia can be genetically transmitted, its prevalence was quantified by direct auditory testing of 71 members of 9 large families of amusic probands, as well as of 75 members of 10 control families. The results confirm that congenital amusia is expressed by a deficit in processing musical pitch but not musical time and also show that the pitch disorder has a hereditary component. In amusic families, 39% of first-degree relatives have the same cognitive disorder, whereas only 3% have it in the control families. The identification of multiplex families with a high relative risk of experiencing a musical pitch deficit (lambda_s = 10.8; 95% confidence interval 8-13.5) enables the mapping of genetic loci for hereditary amusia.
I imagine it's difficult to get money to study this sort of phenotype, but eventually the technology will be cheap enough. I wonder, though, if any sort of "genetic counseling" company (if such a thing exists) would pony up the cash to find genes involved in tone deafness. Offering the ability to test for and select non-tone deaf embryos for IVF could be a lucrative niche market.

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ADHD & DRD4   posted by Razib @ 8/07/2007 10:45:00 AM

Polymorphisms of the Dopamine D4 Receptor, Clinical Outcome, and Cortical Structure in Attention-Deficit/Hyperactivity Disorder:
Possession of the DRD4 7-repeat allele was associated with a thinner right orbitofrontal/inferior prefrontal and posterior parietal cortex. This overlapped with regions that were generally thinner in subjects with ADHD compared with controls. Participants with ADHD carrying the DRD4 7-repeat allele had a better clinical outcome and a distinct trajectory of cortical development. This group showed normalization of the right parietal cortical region, a pattern that we have previously linked with better clinical outcome. By contrast, there were no significant effects of the DRD1 or DAT1 polymorphisms on clinical outcome or cortical development.

A correlation between the 7-repeat allele, which exhibits variation in frequency between populations, and ADHD is interesting and important. But it is nice to get some more functional specificity to clarify the chain of causation responsible for the correlation we see.

Related: In Our Genes.


Monday, August 06, 2007

Nick Wade on A Farwell to Alms   posted by Razib @ 8/06/2007 10:11:00 PM

Nick Wade of The New York Times has an article up on Greg Clark's A Farewell to Alms: A Brief Economic History of the World. I haven't gotten to Clark's book because I've set myself the goal of reading Hal Varian's Intermediate Microeconomics (halfway through) before I touch another pop or historical econ book, but I'll get to it (population genetics textbooks are are good prep for microeconomics!). I'm cautiously skeptical, though I think Clark's ambitious but heterodox ideas are a good thing (ambitious but orthodox I am less interested in).

Related: Clark's Survival of the Richest meets Mokyr's Industrial Enlightenment, The British: More patient than the Greeks?.


Mating minds?   posted by p-ter @ 8/06/2007 08:38:00 PM

The Economist has a review of a paper briefly mentioned here on "conspicuous altruism" and signaling. It's a good account of the research, but I feel like some of the ideas are getting mixed up. The Economist sums up Geoff Miller's "mating mind" theory thusly:
Dr Miller, who works at the University of New Mexico, thinks that mental processes which are uniquely human, such as language and the ability to make complicated artefacts, evolved originally for sexual display.
The experiments then described don't really have much to do with that theory, as far as I can tell. Here's the summary of the results:
The sexes do, indeed, have different strategies for showing off. Moreover, they do not waste their resources by behaving like that all the time. Only when it counts sexually are men profligate and women helpful...Romantically primed men wanted to buy items that they could wear or drive, rather than things to be kept at home. Their motive, therefore, was not mere acquisitiveness. Similarly, romantically primed women volunteered for activities such as working in a shelter for the homeless, rather than spending an afternoon alone picking up rubbish in a park. For both sexes, however, those in an unromantic mood were indifferent to the public visibility of their choices.
This is an interesting result, but what does it have to do with the evolution of language or "human-ness"?


Sky academics   posted by Razib @ 8/06/2007 07:15:00 PM

In light of the previous post, Climate and civilization follow-up, I have to post a link to this article, Inner-city smarts honed in Rockies.


Template changes   posted by Razib @ 8/06/2007 02:47:00 PM

Some of you may have noticed that I've been tweaking with the template a bit. The goal is to make the site look less ghetto and maximize ease of use for regulars and new readers. Using the site for the past day I have noticed that I had been using the big ScienceBlogs image to check my other weblog, so I added a small link to the right with a link to the other Gene Expression. The main other difference is that I added links to the various categories ("labels") that we've been using for a while now. It's messy as there are inconsistencies with spelling and casing, and I'll fix that later, but if you are interested in category views, well, they're back after a 3 year hiatus (I deleted the MT templates for categories years ago during one of the "server over usage" crises we used to have back when we weren't being hosted by Rick & Liz. I never reinstalled them because it didn't look like it was easy and I didn't want to spend the time on that, but people have long wanted to have category archives).

Update: You can now send an email immediately to the author of any post by simply clicking their name (see above to the right of the post). There has been a contact link to the right for a while, but I just figured this would be easier for a lot of people, especially if (for example) the author of a study critiqued found a post via google and wanted to respond directly instead of in comments (which would likely be long dead).


Dayananda Saraswati, and Hindu 'fundamentalism'   posted by Razib @ 8/06/2007 12:51:00 PM

I've been reading about Hinduism recently, a few textbook introductions + some of the canonical scriptures. Mostly this is in the interest of trying to place it within a greater framework of my understanding of how cultures evolve and relate to one another. One of the books I'm going through deals with seminal early thinkers in Hindu nationalism (or proto-nationalism). Of these is Dayananda Saraswati, a Gujarati Brahmin who founded the reformist Hindu sect Arya Samaj. I have long known of the general ideas of Saraswati, but it is different seeing quotations where he elaborates upon his beliefs. The radical, almost "Salafist" character of his thoughts, jumps out at you.

I have posted before about how some religious people, usually the more systematically inclined, have a tendency of reducing the whole universe to a collection of phenomena which can be explained by their religious texts. Saraswati illustrates this, he seems to prefigure modern Hindutva thinkers in reinterpreting the sacred Hindu texts so as to show how they anticipate and describe the whole world. For example, he points to just where in the Hindu canon Europe and the New World are described. Naturally they had to be there, the Vedas are perfect and timeless descriptions of the universe. I could not but help recall the exact same tendency of Christians in terms of mapping real geography to Biblical geography. Additionally, though Saraswati is contemptuous of Islam and Christianity and views Vedic Hinduism as the One True Religion, it is jarring to see him take some pleasure in the iconoclasm of Muslims as they engaged in cultural assault on a massive scale, destroying idols and temple complexes. This reminded me much of many fundamentalists who seem to exhibit more animus toward their notional co-religionists than the enemy far away. The Salafist "reformers" in Saudi Arabia were responsible for the destruction of much of Arabia's older religious architecture (dating from the Caliphate down to the Ottoman period) during the 18th century, exemplified by their attack upon the tomb of the prophet Muhammad. Saraswati's minimalist and notionally reconstructionist (that is, back to first principles) world view will be familiar to anyone who takes an interest in Christian or Muslim fundamentalism. For example, on the one hand he discards post-Vedic Hinduism, the use of images, polytheism (incarnation), philosophical monism, and so on. And yet he also promotes radical planks based on his reading of the Vedas. He accepts the utility of caste and the submission of the lower orders to the higher (a duopoly of Brahmin and Kshatriya dominance aided by economically productive Vaishyas served by humble Sudras). But, he rejects that this hierarchy is one of birth, rather, Saraswati promotes a nobility of attainment and accepts that as some rise from their station of origin others shall fall. It is clearly simply a reinstatement of the Platonic system, the people of gold shall rule over the lower orders. Additionally, Saraswati notes positively the European custom of individuals choosing their own spouses, which was something that really jumped out at me knowing the normative traditions within South Asia. But in my own family it turns out that the religious fundamentalists are also the ones most open to these sorts of modes so long as they can be justified and affixed within their understanding of the religious order. In other words, custom & tradition are secondary in relation to revealed axioms.

Dayananda Saraswati lived during the 19th century, the heyday of British rule. He did not speak a Western language, so his reading of the Koran and Bible were in translations. Therefore, I am struck by the question: what proportion of the ideas that he elaborates upon are 'native' and what proportion 'foreign'? A definitive answer is difficult and ultimately impossible, we can't do a phylogenetic analysis using a coalescent model here. But it does strike me as interesting that a whole host of reformist movements arose in various world religions during the late 18th to early 20th centuries. Salafism in Arabia, the Deobandi movement in South Asia, the Buddhist revival in Sri Lanka (where a substantial portion of nominal Christians converted to Buddhism), muscular Christianity and later fundamentalism in the West. One the one hand one could assert that minimalist fundamentalist (for lack of a better word) is a natural outcome of diffusion from the center of European culture. That is, the success of Europe and its Christian religion resulted in conscious (Brahmo Samaj) and unconscious (Arya Samaj) imitators throughout the world. Another argument could be that given particular parameters concomitant with the rise of the modern world and the transition from the mass society to the middle class one the "higher religions" which arose in mass societies characterized by a pyramid shaped stratification will naturally be canalized toward specific convergent evolutionary paths. A form of cultural selection, so to speak. For example, mass literacy and wealth outside of the rentier classes and castes might almost always lead to a reinterpretation of texts and customs which had been the dictatorial preserve of aristocratic elites. Finally, one could also hold that both factors noted above are at play, though there are particular natural developmental pathways elicited by the same parameters, the magnitude of the directional movement might be shaped by emulation and precedent from one particular source. The Buddhist revival in Sri Lanka for example was aided in large part by Westerners from Christian backgrounds who defected toward non-Christian religious traditions. The Theosophical Society played a large role in promoting Indian nationalism and was even associated with Saraswati's Arya Samaj for a period. These sorts of questions can only be answered by someone with a larger database than I currently have, but I don't think that they are intractable given enough time and full access to theoretical tools.

Note: Many ideas are common throughout all "higher" cultures. For example, philosophical monism & and dualism existed in both the West and India at different periods, though in the West the latter was victorious, while in India the former was. Similarly, the atheist critiques of the Carvaka school in relation to many aspects of Hinduism can be found in Islam and Christianity, though obviously they would add one God to the universe.


Sunday, August 05, 2007

Climate and civilization follow-up   posted by agnostic @ 8/05/2007 07:12:00 PM

Recently I suggested that civilization flourishes in some areas of the world more than others, in part, because winged insects thrive more in environments that are lower in elevation and latitude. These insects are a key source of chronic infectious disease in humans, and having to deal with the recurring symptoms must sap some of your body's resources that could be used for "luxury" processes involved in societal innovation. I neglected to mention that what likely makes wingedness more common in such environments -- a higher degree of environmental heterogeneity -- likely selects for an increase in migratory features more broadly, not just in insects. So some small animal may be more migratory, and it could be carrying parasites or pathogens itself, or be harboring insects that carry pathogens. It's just a lot easier for disease vectors to make their way to you in such environments. And of course, it may be that the fatigue caused by hot, humid weather makes you less productive.

Since then, I looked again at Inductivist's analyses on White IQ in various regions of the US, based on GSS data. In the first two posts (here and here), he showed that adults in the Mountain (MTN) region score better than average on mean IQ and percentage of holders of college degrees. More interesting, though, is the post on IQ and geographical mobility. Although New England and the Mid-Atlantic far and away attract the smartest Whites, the smartest of all are the NE transplants who were raised in MTN. Moreover, none of the bottom 10 pairs consisted of a group that was raised in MTN. By contrast, even though 2nd place goes to those raised in East South Central and who moved to NE, those raised in ESC also occupy 4 of the bottom 10 spots.

Why does growing up in MTN appear to boost your IQ? Probably because the climate is less favorable to the spread of pathogens by vectors that are migratory. And that, again, is probably due to less environmental heterogeneity in that area -- the Rockies are cold, dry, and very high in elevation, all tied to greater environmental stability. That's surely one reason why Colorado in particular performs so well, and its state government should publicize the hell out of Inductivist's findings to draw in wealthy parents who want the best environment for their kids. "Baby Einstein" pre-schools won't accomplish squat, but being raised in the salubrious climate of the Rockies sure will. Even the hot areas in the southern part of MTN, which are less impressive than the northern areas, are not humid or sub-tropical but desert, which is characterized by little environmental change over time or across space.

You might think that the lower population density is also a factor, and that could be, but people raised in regions with high density make a good showing in Inductivist's ranking. Population density is more critical in influencing acute, contagious diseases like the flu or perhaps rarer and wilder stuff like schizophrenia. But it could be that adult IQ is more influenced by the presence of chronic infections that continually disturb the development process. As before, knowledge of which pathogens and which vectors are the culprit is not necessary to believe this idea: just knowing that the local ecology in region X favors such things far more so than in region Y is enough to suspect that diminished IQ in region X is at least partly due to infection.

Moving on to larger concerns, one puzzle that I admitted in the original post was South Asian civilization -- isn't that one of the nastiest places to be climate-wise? I should've investigated further, because the answer is "yes and no." The climates in the Subcontinent vary a lot more than I thought, as you can see in this climate map of India and this climate map of the world. But does climate correlate with degree of civilization in South Asia? Beats me, since I couldn't say which areas over the long-haul show more development than which others. However, I have catalogued below a list of the climates for the capitals of South Asian civilizations beginning in the Neolithic. I used the chronology of Wikipedia's History of India article for convenience, and looked up the capitals there as well.

I'll leave it up to the more historically informed to say whether the hypothesis is supported or not My rough impression is that the North has shown greater development over the past several thousand years, even though the civilizations of the South and Bengal have been no slouches, but that may be wrong in general or perhaps correct broadly but wrong in finer detail. One interesting exception to the rule of Southern climates being more tropical, though, is that of Bangalore -- the "Silicon Valley of India" -- which enjoys a semi-arid climate, lies higher above sea level than Madrid (920 m vs. 667 m), and is known as a "Garden City."

And yes, I know that the current climates where the earliest civilizations flourished might not be identical to what they were at the time, but Iran and the modern countries occupying the Fertile Crescent also have mostly arid or semi-arid climates nowadays. The point is that they didn't consist of tropical wet & dry climates like you find in Sub-Saharan Africa or the Amazonian rainforests.

Civilization (:capital) -- climate

Mehrgarh -- arid

Indus Valley -- arid, semi-arid

Mahajanapadas -- arid, semi-arid, humid sub-trop

Magadha: Rajgir -- humid sub-trop

Maurya: Patna -- humid sub-trop

Satavahana: Pune, Paithan, Amaravati -- humid sub-trop

Kushan: Charikar -- highland, semi-arid; Taxila -- semi-arid; Mathura -- semi-arid

Gupta: Ujjain -- semi-arid; Patna -- humid sub-trop

Pala: Varendra / Rajshahi area -- humid sub-trop; also trop wet & dry

Chola: Tiruchirappalli -- semi-arid, trop wet & dry; Poomphuhar -- trop wet & dry; Gangaikonda Cholapuram -- trop wet & dry

Delhi Sultanate -- semi-arid

Deccan Sultanates -- semi-arid, trop wet & dry

Hoysala: Belur, Halebidu -- trop wet & dry

Kakatiya: Warangal -- trop wet & dry

Vijayanagara -- semi-arid

Mughal: Agra, Delhi -- semi-arid

Sikh Confederacy -- semi-arid, humid sub-trop

Maratha: Pune -- trop wet & dry

Post-Independence: New Delhi -- semi-arid; Islamabad -- semi-arid; Dhaka -- humid sub-trop, trop wet & dry

NB: I left out the period of colonial India for a few reasons that you might object to. First, Europeans certainly cope differently with non-European climates than do the locals, and I want to see whether climate affects degree of civilization even for those who are most adapted to life there. And second, it's my understanding that Europeans were more concerned with establishing superior trading posts and practicing mercantilism than they were with encourgaging civilization per se in South Asia.

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In what season are you most productive?   posted by agnostic @ 8/05/2007 11:34:00 AM

The inescapable lassitude of summers in the DC metro area has gotten me thinking more about climate and civilization. Pursuing a hunch, I looked over the dates for all of my posts here at Gene Expression. While admitting this is a data-set of convenience, and that I'm no Einstein, I think it still suggests something real. The data-set is worth trusting because I don't post a lot, only when a neat idea strikes me and I've given it some thought. Also, as a tutor, my summer-fall schedule is always more free than winter-spring, so I should have lower productivity during winter-spring. And I live in a four-season region, so that the weather varies enough to be a potential source of variance in some outcome. [1]

The results: in total (excluding this accounting post), I've written 58 posts, 50 of which I consider "serious" and 8 of which I consider "diversions." By "serious," I mean anything from mentioning and offering a viewpoint on a new study, even if the post is only a paragraph or two, to long reviews or "think pieces." Then "diversions" are things like poking fun at Finnish video game nerds or linking to videos of Brazilian babes dancing samba. In the Mid-Atlantic, Summer-Fall (SF) runs from June to November, while Winter-Spring (WS) runs from December to May.

It so happens that 7 of the 8 diversions are from SF and 1 of 8 are from WS, but the numbers are too small to be confident about, and anyway I'm more interested in when I get more serious work done. Of the 50 serious posts, 14 are from SF and 36 are from WS. Because I started posting in February of 2006 and have continued through the end of July 2007, that makes 8 SF months and 10 WS months that I've been a poster. Multiplying 50 by 8/18 and 10/18 respectively gives the expected number of serious posts for SF and WS. The observed frequencies deviate from expectation significantly: chi-squared = 5.45, df = 1, p less than 0.03. It may also be worth noting that the Just Science project among science-related blogs to forget the silliness and churn out quality research-related posts took place in February.

Long-time readers will guess that I would attribute some of this to the greater chance in winter-spring of contracting an infection that might make my thinking a little nuttier and "outside the box." That could be, but I think that applies more strongly at the earliest stages of brain development. Now that I'm in my mid-20s, I think this seasonal variation is just due to feeling like my brain is melting under the heat and humidity, my body losing more essential vitamins and minerals due to sweating more, or something else (although I doubt it's a simple nutritional matter).

Like I said, how far this applies outside of my blogging experience is uncertain. Still, even if there is no general pattern, it's worth doing this sort of personal reckoning so that you can plan better for the future -- I will make sure to apportion my tedious and mechanical work to the summer and autumn months as much as possible, and take on more cognitively and creatively demanding projects in the winter and spring.

Notice that that's the opposite of the assumption that schools operate on: i.e., that you will go through the academic motions from autumn to spring, and devote your entire summer to independent, creative projects or internships, now that you're unencumbered by an academic routine. It goes to show that the schedules our institutions run on may match the schedules of the comfort-seeking parts of our brain (getting downtime while there's beach-going weather), but perhaps not matching the schedules of the creative parts of our brain. It's certainly worth looking into, and wouldn't be that hard to study.

[1] I prefer this method to looking at publication dates of peer-reviewed articles since we can't tell when the initial idea and most of the work happened. If individuals kept a diary, that would be more reliable, though, and that's pretty much what my posts are. I don't think over a post for months -- usually not more than a week after the idea hits -- so there's not the lag you'd see between starting an article and having it published.

Flip that switch!   posted by Razib @ 8/05/2007 11:32:00 AM

A functional circuit underlying male sexual behaviour in the female mouse brain:
We report here that Trpc2-/- female mice show a reduction in female-specific behaviour, including maternal aggression and lactating behaviour. Strikingly, mutant females display unique characteristics of male sexual and courtship behaviours such as mounting, pelvic thrust, solicitation, anogenital olfactory investigation, and emission of complex ultrasonic vocalizations towards male and female conspecific mice...These findings suggest that VNO-mediated pheromone inputs act in wild-type females to repress male behaviour and activate female behaviours. Moreover, they imply that functional neuronal circuits underlying male-specific behaviours exist in the normal female mouse brain.

Yes, yes, I know people aren't mice. But check out this piece on female autistics in The New York Times Magazine. Here's an interesting part:
No doubt part of the problem for autistic girls is the rising level of social interaction that comes in middle school. Girls' networks become intricate and demanding, and friendships often hinge on attention to feelings and lots of rapid and nuanced communication - in person, by cellphone or Instant Messenger. No matter how much they want to connect, autistic girls are not good at empathy and conversation, and they find themselves locked out, seemingly even more than boys do. At the University of Texas Medical School, Katherine Loveland, a psychiatry professor, recently compared 700 autistic boys and 300 autistic girls and found that while the boys' "abnormal communications" decreased as I.Q. scores rose, the girls' did not. "Girls will have more trouble with social networks if they're having greater difficulty with communication and language," she says.

I have offered the conjecture before that a lot of the social phenomena we see around us has to be filtered through the reality that men and women socialize very differently. Roughly, I believe that male socialization norms are more coarse, inflexible and girded by clear heuristics. In contrast, I think female social networks are more natural and leverage innate abilities of women to read faces, manner and engage in extreme intentionality. I believe this is one reason that patriarchy emerges in mass societies: though more coarse and less informative, I believe that simpler male interaction dynamics scale much more easily than the way women operate in groups. It naturally makes sense that high IQ autistic males could "fake it" or "get by" much more easily than high IQ autistic females, the male social system is much more clumsy and probably requires less innate cognitive skill.

Addendum: An example by analogy. A typical human has lighting fast numeracy perception. For example, compare someone who "recognizes" a set of objects from the 1 to 4 in quantity vs. someone counting 1, 2, 3, 4. Obviously the latter method is relatively slow and depends on a lot more cognitive scaffolding (various aspects of human intelligence). Gestalt recognition on the other hand is fast and almost unconscious. But now imagine the number of objects increasing. Soon you really don't have a good sense of numbers via innate numeracy, you can recognize proportions, but you can't recognize 73 objects. On the other hand, though counting is slow, and continues to take more time as the number of objects increases, but it scales so that you can feasible continue to count an increasing number so long as you're willing to put more time in it.


Saturday, August 04, 2007

Talking about religion without a shared religon   posted by Razib @ 8/04/2007 03:46:00 PM

Via Daniel Larison I came upon this YouTube of Mitt Romney freaking out about a radio talk show host's characterizations of his religion. A few years ago I wrote about Mormonism with the Romney candidacy in mind. My main aim was to get some facts out there, and offer a tentative prediction that the candidate's Mormonism would be a serious problem. The main line of evidence I offered was that Romeny's core target audience, Christian social conservatives, would also be the same group most allergic on abstract theological grounds toward supporting a Mormon (I believe that only a few very liberal Episcopalian churches accept Mormon baptism as valid when taking converts, for example). I don't believe it will prevent the majority of social conservatives from backing Romney, rather, I simply believe that the erosion of support could be great enough to be a deal breaker (the fact that Romney has evolved from being a moderate to a conservative recently and rather quickly doesn't help). I doubt Romney will get the nomination, but I do think that his candidacy will pave the way for the viability of future Mormons because the exoticism factor will be somewhat defused. After all, two generations ago many conservative Protestants were skeptical of John F. Kennedy because of his nominal Catholicism, but 3 years ago there was skepticism of John Kerry because he wasn't Catholic enough from the same sector. Though the underlying differences between Protestantism and Catholicism remain (though one could argue that post-Vatican II Catholicism is more congenial toward accommodation with Protestantism), the familiarity with Catholics & Catholicism on the part of many evangelical Protestants has taken the bite off in terms of comfort (though in many parts of the American South Protestants are likely to make a distinction between "Christian" and "Catholic," which I've noted even percolates into the pages of periodicals such as The Houston Chronicle).

My post from a few weeks ago, In the name of a word, highlighted what I believe to be the power of nominal terms and theories in coalescing groups around the banner of unified community set against others. The Mormon Church has some exotic beliefs, but the reality is that the typical Mormon really isn't that different from the typical American Jew, Protestant or Catholic. Nevertheless, the theological differences between Mormonism and other American religions is not something that is going to disappear in the near future. Rather, the reason that I believe that Mormon candidates for president will be less dogged by after Mitt Romney is that his campaign will humanize Mormonism. Once people can think of Mormons in a concrete manner they can focus less on the abstract differences, which most people have only the vaguest grasp of anyhow. That being said, I do think it is important to note that America is becoming a more religiously diverse nation in absolute terms, in other words, the variance in the characters which define the major religions is increasing.

I think it can be argued that the period between 1950-1980 was the high water mark in homogenization of American religion since the first wave of Irish famine immigrants, as Jews and Catholics were brought under the umbrella of mainline Protestantism. Today the majority of Catholics are sociologically difficult to distinguish from Protestants, and they tend to even speak of their religion in a very "Protestant" way. But after 1980 the rise of the Christian Right, and the great increase in those with "no religion" and New & Eastern religions fragmented the theological marketplace. A few years ago I reviewed The impossibility of religious freedom, a book where the author argues that separation of church and state was only viable because of a very narrow understanding of religion as such in a Protestant America. Because our government, and to some extent or laws, gives special dispensations toward religion those in positions of authority come into play in terms of defining exactly what the bounds of a particular religion might be. If someone says "my Muslim religion prevents me from engaging in x," that is very different operationally from "my personal philosophy prevents me from engaging in x." In America someone who espoused a philosophy which violated laws would simply be prosecuted, this is not a nation where philosophies are given special consideration, but, it is a nation where religions are given special considerations. Therefore, the authorities have to determine if the religion of Islam does entail what the individual who claims to be Muslim believes it entails. The fact that religions are diverse, riven with faction and difference of opinion, naturally leads toward the subjective opinions of outsiders carrying great weight in terms of who and what is a legitimate expression of a given faith.

This means that people of different religions need to communicate to each other, often about rather obscure terms which the typical religionist has an imprecise grasp of. Though higher religions are generally supplemented by a large philosophical body of work, in a day to day context in nations such as Japan, India, Spain or Iran, where one religious tradition is overwhelmingly dominant, such details are irrelevant and religion as such is simply a lived experience that emerges out of the conventional social experience. That is not necessarily true in the United States, where there is no common religion, and one can not take for granted the religious truths held by others or a common grounding of premises. Because one can not expect a Christian to bone up on the nitty-gritty details of Islam, Muslims are likely to engage in usage of analogy. For example, a mosque is like a church, an imam is like a minister, and so on. These analogies are imprecise and always lose subtly and nuance. Communicating the details of religion across different religions isn't like working through a mathematical proof together, there's a lot of fuzziness and disagreement, and the native in one religious tradition might not necessarily be clear or reflecting unified consensus within their religion in the first place (the quest for the "Muslim Martin Luther" always seems to end up at the tail of the distribution of belief).

This results in a lot of confusion. If you watched the Romney video you'll see that he gets into a religious argument with the host of the radio show, who reads him some church authorized text. Romney is rather incensed, and tries to get across the reality that he is the expert on his own religion and that the host is not understanding some nuanced details. I won't get into whether Romney is trying to pull a fast one, rather, I will agree that those outside of a religious tradition will often attempt to assemble some Truths and work with them as if they are axioms from which one can derive clear and distinct propositions. In this way one can communicate with a religionist on their own ground, just as someone enters a technical field of study from the outside and masters the formalism so as to be fluent in the discussion. Unfortunately, this is not really something that works. I simply do not believe that most religious propositions derive from clear & distinct axioms, and the elasticity of interpretation is something that is very difficult to comprehend or conceive of from the outside of a religious tradition. Atheists (like myself at one point) often tend to engage in this sort of behavior, stating religious axioms and then showing they are absurd and contradictory, ergo, the religious system is shown to be false or incoherent. But it does not happen with atheists alone, I have entered into discussions with non-Christians who brandish the Nicene Creed to show exactly what Christianity really says and is. The fact is that the history of Christianity can not be reduced to a set of creeds or short axioms, it is a cultural brand which is highly contingent upon historical events and its particular social matrix. Now, I don't believe that Christianity is predicated on divine revelation, nor do I think that the way Christians live today is the most straightforward application of their foundational texts, but the reality of how Christians practiced and have practiced shows that looking closely at texts for determination as to why human action is the way it is is pretty futile (it doesn't help that a person of a particular religion will tell you they do what they do because their religious text tells them, even if other members of the same religion come to wildly different interpretations and justifications). Personally, I am generally skeptical of the inferences made by Christians, whatever their stripe, from their holy texts. But then, I am not Christian, and critically, I am not embedded in their social environment, and so my plausibility matrix is very, very, different.

As Americans we live in, and will continue to live in, a religiously pluralistic environment. Additionally, particular religions will have material consequences on us all because the tribunes of our state are themselves religious and will exhibit natural influences from that direction. The fact that a minority of American Christians have specific theological beliefs intertwined with the geopolitics of the Middle East is a background condition of our world, the fact that I might think those theological beliefs are absurd is irrelevant in the proximate framework. As an American it is probably important to have a minimal level of familiarity with the primary religious dispensations which dominate the marketplace of ideas. That being said, it is important not to pretend that the reading of the Bible, the Koran, the Vedas, the Book of Mormon, and so on, result in a perfect understanding of the religious phenomenon. Less than a month ago I got into a pretty long internet discussion about the factual claims of Mormonism with a group of Mormons. I went to a high school that was about half Mormon, and most of my closer friends by graduation were of that religion. I have read the Book of Mormon and some supplemental literature about the Church before, so I thought I went into the discussion "knowing my shit," so to speak. Well, it didn't turn out that way. To make a long story short some sophisticated Mormons don't read the Book of Mormon in a very obvious way, to my understanding. Instead of believing in magnificent civilizations seeded by mass migrations from the Old World, they offered a much more parsimonious and frankly nearly unfalsifiable narrative of minimal colonization by a small family in a very small geographic area that was absorbed by the indigenous substrate. Most Mormons don't believe this from what I can tell (personal communication with my friends), but enough do that I had to pause and reassess what I believed about what Mormons believed. Similarly, a few years ago I asserted blithely that Sunni Muslims do not believe in free will in response to a commentary by an American Sunni Muslim who blandly seemed to assert exactly such a thing. Now, the reality is that there were always counter-trends within Sufi groups to the normative consensus in Sunni Islam, but I suspect that another thing that is happening today with American Sunni Islam is that in the process of assimilating American religious terminology it is becoming operationally "Protestantized." There are thousand "real Islams," and it just seems to turn out that the real Islam maps on pretty well to local cultural conditions.

Where does that leave us? I think there are several dynamics we have to keep in mind. First, American religions seem to be converging upon common characteristics which are descended from the Radical Reformation (e.g., individualism, operational Arminianism, etc.). Second, the theological variance is increasing, at least in the short term, as the marketplace is being saturated with new denominations and religious groups. Third, the increased diversity means that it is extremely difficult to talk about religion in a straightforward manner without getting into a lot of overhead to clarify definitions. After all, there are many different interpretations of Islam, Catholicism, Protestantism, Judaism, etc., which are numerous on the American landscape. Before even one can map concepts from one religion to another, one must clarify exactly which flavor of religion one is encountering when one talks to Muslims, Christians, Hindus, and so on. I don't know where this is going, but if I had to bet I suspect that a vague civil religion will become identified with the elites that marginalizes the numerous sects in the public space. The sects will continue to be vibrant with a large number of Americans, but they won't be important players in public policy because there will just be too many different loci of power to deal with. The protection and respect a religion receives will be directly proportional to its numbers & power. Very small religions won't be religions at all, but cults. So I suppose in the end nothing really changes, there is simply a quantitative shift in emphasis.


Friday, August 03, 2007

Convergent evolution of lactase persistence - part n   posted by Razib @ 8/03/2007 02:40:00 PM

Note: I got this article via AJHG's RSS. It doesn't seem to have gone live on the site so there might be temporary problems accessing the link.

Evidence of Still-Ongoing Convergence Evolution of the Lactase Persistence T-13910 Alleles in Humans:
A single-nucleotide variant, C/T-13910, located 14 kb upstream of the lactase gene (LCT), has been shown to be completely correlated with lactase persistence (LP) in northern Europeans. Here, we analyzed the background of the alleles carrying the critical variant in 1,611 DNA samples from 37 populations. Our data show that the T-13910 variant is found on two different, highly divergent haplotype backgrounds in the global populations. The first is the most common LP haplotype (LP H98) present in all populations analyzed, whereas the others (LP H8-H12), which originate from the same ancestral allelic haplotype, are found in geographically restricted populations living west of the Urals and north of the Caucasus. The global distribution pattern of LP T-13910 H98 supports the Caucasian origin of this allele. Age estimates based on different mathematical models show that the common LP T-13910 H98 allele (~5,000-12,000 years old) is relatively older than the other geographically restricted LP alleles (~1,400-3,000 years old). Our data about global allelic haplotypes of the lactose-tolerance variant imply that the T-13910 allele has been independently introduced more than once and that there is a still-ongoing process of convergent evolution of the LP alleles in humans.

Two things to note

1) A recent common origin for much of the Eurasian lactase persistence phenotype is interesting. The period between 5 and 12 thousand years ago was obviously very significant and an inflection point in many ways in terms of the history of our species. Surveys of neutral markers which are supposedly reasonable proxies for ancestry imply that we should be cautious about mass population replacements across Eurasia. For example, it seems likely that the majority of Europeans and South Asians are descended from lineages already extant within their current geographic bounds at the end of the last Ice Age (though more or less significant impacted by population waves of advance triggered by the Neolithic revolution in the Middle East). Nevertheless, some biologists have argued that the sweeping action across demes of mutations of large effect are powerful enough to maintain species continuity and drive broad phenotypic convergences. One can conceptualize the genetic dynamics at work as a broad substrate of ancestrally informative alleles clustered across Eurasia, but tightly laced together by synchronous sweeps and pulses of functionally salient genes.

2) The newer, localized, LP variants are intriguing. The time window is very narrow here. Evolutionary theory tells us that in reaction to a strong selective force phenotypic change may immediately be affected by mutations of large effect. These mutants may be good at what they are meant to do, but also have negative side effects. Over time various selection pressures will reshape the genetic architecture with a host of modifiers and smaller effect mutants which result in a population subject to less stress via correlated responses due to the initial mutant of large effect. I wonder if the newer variants are signals that the genetic background is still working to optimize adaptation to a high lactose diet.

Related: See here and here.

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Thursday, August 02, 2007

The Way of the master   posted by Razib @ 8/02/2007 07:42:00 PM

Confucius Making a Comeback In Money-Driven Modern China. The article notes that there is some debate about what exactly "Confucianism" is. The original ideas of Confucius were a distillation of the traditional customs & rites of ancient China which he attempted to preserve and promote through his tumultuous times. The original canon was modified and interpreted by by his successors, Mencius & Xunzi, transformed by the rise of the Chinese Empire, and finally influenced by Buddhist metaphysics (Neo-Confucianism). Like many elite religio-philosophical systems Confucianism is extremely flexible & rich, providing precedent & justification both for service to the a autocrat as well as moralistic objection to his tyranny. After the first Chinese Empire collapsed because of its totalitarian tendencies, encapsulated by the amoral utilitarian Legalist philosophy, the ruling dynasty which succeeded that of the First Emperor buttressed their legitimacy with Confucian thought. Though the outer facade spoke with a gentle Confucian voice the state apparatus in some ways was more indebted to the blind efficiency of Legalism. The point is not the words one speaks, it is that adherence to the Way allows one speak with more authority, the voice of Heaven. I wonder if in the near future Chinese will view the genuine Communist period (i.e., between 1950-1980) as similar to the Qin dynasty, which was at its peak for only 16 years.


Computational neuroscience & evolution   posted by Razib @ 8/02/2007 03:01:00 PM

Distributed Representations Accelerate Evolution of Adaptive Behaviours:
Some behaviours are purely innate (e.g., blinking), whereas other, "apparently innate," behaviours require a degree of learning to refine them into a useful skill (e.g., nest building). In terms of biological fitness, it matters how quickly such learning occurs, because time spent learning is time spent not eating, or time spent being eaten, both of which reduce fitness. Using artificial neural networks as model organisms, it is proven that it is possible for an organism to be born with a set of "primed" connections which guarantee that learning part of a skill induces automatic learning of other skill components, an effect known as free-lunch learning (FLL). Critically, this effect depends on the assumption that associations are stored as distributed representations. Using a genetic algorithm, it is shown that primed organisms can evolve within 30 generations. This has three important consequences. First, primed organisms learn quickly, which increases their fitness. Second, the presence of FLL effectively accelerates the rate of evolution, for both learned and innate skill components. Third, FLL can accelerate the rate at which learned behaviours become innate. These findings suggest that species may depend on the presence of distributed representations to ensure rapid evolution of adaptive behaviours.


Wednesday, August 01, 2007

Really recent human evolution   posted by Razib @ 8/01/2007 02:26:00 PM

Recent Genetic Selection in the Ancestral Admixture of Puerto Ricans:
Recent studies have used dense markers to examine the human genome in ancestrally homogeneous populations for hallmarks of selection. No genomewide studies have focused on recently admixed groups-populations that have experienced admixing among continentally divided ancestral populations within the past 200-500 years. New World admixed populations are unique in that they represent the sudden confluence of geographically diverged genomes with novel environmental challenges. Here, we present a novel approach for studying selection by examining the genomewide distribution of ancestry in the genetically admixed Puerto Ricans. We find strong statistical evidence of recent selection in three chromosomal regions, including the human leukocyte antigen region on chromosome 6p, chromosome 8q, and chromosome 11q. Two of these regions harbor genes for olfactory receptors. Interestingly, all three regions exhibit deficiencies in the European-ancestry proportion.

The settlement of the New World in the Iberian colonies is characterized by two broad dynamics. First, the mass die offs of many populations due to the introduction of Eurasian pathogens. Second, the hybridization of indigenous female lineages with European male ones (and later African ones). Until recently it was assumed that the Puerto Rican population was dihybrid, that is, Africans and Europeans. But new data suggests a substantial indigenous maternal contribution.