Monday, August 31, 2009

Recession = less death?   posted by Razib @ 8/31/2009 09:33:00 PM

The effect of economic recession on population health:
Economic recessions have paradoxical effects on the mortality trends of populations in rich countries. Contrary to what might have been expected, economic downturns during the 20th century were associated with declines in mortality rates. In terms of business cycles, mortality is procyclical, meaning it goes up with economic expansions and down with contractions, and not countercyclical (the opposite), as expected. So while most nations enjoyed sustained declines in mortality during the last century, the pace of the decline has been slower during economic booms and greater during so-called busts. The first rigorous studies demonstrating this trend have appeared only in the past 9 years, although the concept is not new. In contrast, for poor countries, shared economic growth appears to improve health by providing the means to meet essential needs such as food, clean water and shelter, as well access to basic health care services. But after a country reaches $5000 to $10 000 gross national product (GNP) per capita (or gross domestic product or gross national income per capita, all of which are similar for our purposes here), few health benefits arise from further economic growth...Health trends in Sweden illustrate this effect.

Greg Cochran told me about this phenomenon in regards to the Great Depression last year.

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The evolution of pigmentation in deer mice   posted by p-ter @ 8/31/2009 09:20:00 PM

Much of evolutionary biology focuses on ultimate causation--identifying the evolutionary forces that have led the world to be as it is today, without much regard for the nuts and bolts of how organisms work. Much of molecular biology, on the other hand, focuses on proximate causation--understanding how the world works without much regard to how it came to be that way.

It's nice, then, to see the two joined in an elegant fashion; a recent paper on the evolution of pigmentation in deer mice does just that. About 8-10 thousand years ago, a novel habitat arose in the middle of Nebraska in the form of a large field of sand dunes. Since then, the a population of deer mice adapted to the habitat by evolving a lighter coat color (though I'm having issue with images on blogger, an example is in part A of this figure).

The authors show that this decrease in pigmentation is due to changes in the temporal expression of the agouti protein (this protein is part of the "canonical" pigment type-switching pathway)--light mice express agouti for longer than dark mice during hair development. They're able to show that this change in expression pattern correlates perfectly with a deletion of a single amino acid in agouti, though they hesitate to claim that this is the true causal mutation (this polymorphism is perfectly correlated with others in the region).

The allele shows classical signatures of having experienced a selective sweep, and the authors estimate that the allele arose sometime after 10kya, after the formation of the dunes that produced the selective advantage. It's difficult, of course, to prove that this polymorphism wasn't segregating prior to the formation of the dunes, but if it was, it was certainly at very low frequency. In all, this is a very nice story, and a great example of the power of molecular approaches to the study of evolution, even in non-model organisms.

Citation: On the Origin and Spread of an Adaptive Allele in Deer Mice. Catherine R. Linnen, Evan P. Kingsley, Jeffrey D. Jensen, and Hopi E. Hoekstra (28 August 2009). Science 325 (5944), 1095. [DOI: 10.1126/science.1175826]

Curly haired dogs   posted by Razib @ 8/31/2009 12:40:00 AM

Since I see p-ter hasn't posted on this, in Science, Coat Variation in the Domestic Dog Is Governed by Variants in Three Genes:
Coat color and type are essential characteristics of domestic dog breeds. While the genetic basis of coat color has been well characterized, relatively little is known about the genes influencing coat growth pattern, length, and curl. We performed genome-wide association studies of more than 1000 dogs from 80 domestic breeds to identify genes associated with canine fur phenotypes. Taking advantage of both inter- and intrabreed variability, we identified distinct mutations in three genes, RSPO2, FGF5, and KRT71 (encoding R-spondin-2, fibroblast growth factor-5 and keratin-71, respectively), which together account for the majority of coat phenotypes in purebred dogs in the United States. This work illustrates that an array of varied and seemingly complex phenotypes can be reduced to the combinatorial effects of only a few genes.

See ScienceDaily for summary. This will help us cure cancer! OK, probably not, but hopefully perhaps we might get toward understanding hair form beyond EDAR.

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Sunday, August 30, 2009

Empires of the Silk Road   posted by Razib @ 8/30/2009 11:44:00 PM

I'm now reading Empires of the Silk Road. I'm about 2/3 of the way through the main text, and being slowed down by the fact that I keep reading the footnotes on almost every page. Additionally, there are 40 pages or so of endnotes which I haven't gotten to yet, but each one reads like a very interesting blog post (I do not refer to it as such to cast aspersions but praise!). I'll probably have my full thoughts up in a few days. It has a little less ecology and archaeology than I'd like so far, but the density of fact is pretty awesome (The Ruin of the Roman Empire is a book where the opposite is the case, it could have been about half as long due to its repeated exposition of the same series of facts with a slight twist). There are some issues where genetics might offer a slightly different perspective than the author, and I'll definitely mention that....


Saturday, August 29, 2009

Non-Black voting Democrat in 2008 presidential election   posted by Razib @ 8/29/2009 10:56:00 PM

Map from Andrew Gelman's post, Race, region, and vote choice in the 2008 election: implications for the future of the Voting Rights Act (which has many more charts):

Compare with the last map in my post What's not the matter with Appalachia.


We are all Protestants now....   posted by Razib @ 8/29/2009 01:34:00 AM

There are different models of how religion and society interact with each other. The American model is not universal, and Americans sometimes are confused about the relationship between religion and society in other cultures. Nevertheless, the American model is robust and seems to be capable of powerful assimilative feats.* In the early 19th century the Roman Catholic church was rapidly Americanizing in a manner we would recognize today, but the enormous influx of Irish and German Catholic immigrants at mid-century reversed this process. The Irish dominated hierarchy attempted to force the American political order to accept a form of official pillarization, but by and large this failed. Catholics did form a separate stream of civil society, but the persistence of a religious subculture seems to have been a function of the constant stream of new immigrants. Over a century later American Catholics, excepting a small "traditionalist" minority, have transformed themselves into another denomination.

A very similar process occurred with American Jews, though due to their small numbers they never faced-off against the Anglo-Protestant elite in the manner which the Catholics did. Orthodox Judaism, which most Jews around the world, secular or religious, would recognize as Judaism, is a minority faction in the United States. Rather, the more acculturated Reform and Conservative movements dominate. The Reform in particular has a long history of attempting rather consciously to transform itself into another Protestant denomination in form if not belief (though with the liberalization of mainline Protestantism there has been some convergence with Reform Jewish religious ideas).

The Japanese Americans who remain Buddhists (most of the community converted to Christian or are secular) adhere to the Buddhists Churches of America. And so on. Now the same with Hinduism, Old Faith Innovates in a New Land:
Ganesha is revered as the remover of obstacles, and his festival is considered an auspicious time to begin new endeavors, not least an experiment in adapting an old religion for a new land. And of the singers, most of whom grew up in India, none had ever heard of a Hindu choir before.
Choirs are virtually unheard of in temples in India because worshipers tend not to cohere into anything resembling an attentive congregation, said Vasudha Narayanan, a professor of religion and the director of the Center for the Study of Hindu Traditions at the University of Florida.

Some religious people get offended when I contend that it is the fate of all American religions to turn Protestant (non-Protestants that is). But unless you seal yourself off such as the Amish and Hasidic Jews have done to various extents, or replenish yourself with unassimilated immigrants, this is what simply happens. As someone not invested in any particular religious belief I generally think it best that the religions of the United States operate in a common cultural currency, the currency of confessional denominationalism. Even religions devoid of a creed such as Unitarian-Universalism wear their New England Congregationalist (ergo, Protestant Christian) origins on their sleeve.

Addendum: Though to be fair, even within the United States it seems that Greater New England and the South have developed in two very different trajectories when it comes to their interpretation of the appropriate exterior forms of Protestant worship and organization. It would be interesting to see if non-Protestants in these regions reflect these differences between Baptists and Congregationalists, for example.

* I would contend that the American model has been successfully planted in South Korea, much of Africa and parts of Latin America.



Body mass changes & personality   posted by Razib @ 8/29/2009 01:11:00 AM

Anyone know of scientific literature on the biologically rooted psychological changes which might occur due to changes in body mass? I always assumed that weight loss or gain induced personality changes because of differences in the social acceptability of an individual's weight, but am wondering about the possible shifts in the body's biochemical pathways due to change in the amount of body fact. I began to wonder about this because of the average increases in body mass over the past generation, and what social and cultural ramifications it might have besides those of health.


Friday, August 28, 2009

Bad headlines?   posted by Razib @ 8/28/2009 10:59:00 AM

Nature News headline: Human-chimp interbreeding challenged. Makes it seem like there's a breeding program somewhere, and others are challenging it on ethical grounds....


Thursday, August 27, 2009

Computing the spread of lactase persistence   posted by Razib @ 8/27/2009 08:08:00 PM

As most readers of this weblog know most humans as adults cannot digest lactose. The ability to digest lactose via the persistence of the enzyme lactase is differentially distributed. Both inferential methods and a small number of ancient genetic extractions suggest that this ability arose within the last 10,000 years. A new paper, The Origins of Lactase Persistence in Europe:
Most adults worldwide do not produce the enzyme lactase and so are unable to digest the milk sugar lactose. However, most people in Europe and many from other populations continue to produce lactase throughout their life (lactase persistence). In Europe, a single genetic variant, −13,910*T, is strongly associated with lactase persistence and appears to have been favoured by natural selection in the last 10,000 years. Since adult consumption of fresh milk was only possible after the domestication of animals, it is likely that lactase persistence coevolved with the cultural practice of dairying, although it is not known when lactase persistence first arose in Europe or what factors drove its rapid spread. To address these questions, we have developed a simulation model of the spread of lactase persistence, dairying, and farmers in Europe, and have integrated genetic and archaeological data using newly developed statistical approaches. We infer that lactase persistence/dairying coevolution began around 7,500 years ago between the central Balkans and central Europe, probably among people of the Linearbandkeramik culture. We also find that lactase persistence was not more favoured in northern latitudes through an increased requirement for dietary vitamin D. Our results illustrate the possibility of integrating genetic and archaeological data to address important questions on human evolution.

Here's a graphical illustration of their conclusion:

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Web 2.0 party is over -- you're going to pay for the news again, and hopefully more   posted by agnostic @ 8/27/2009 12:52:00 AM

Recently at my personal blog I've been focusing on the idiocy of Web 2.0's central strategy for growth, namely creating online networks or communities where costly participation is given away for free. (The profitable online papers charge, YouTube and Facebook still not profitable, and a more general round-up of the second dot-com bust.) The hope was that hosting a free party with an open bar would attract a large crowd, and that this in turn would lead to ever-increasing ad revenues. That business model was doomed to failure during the first dot-com boom, and it is just as doomed during the second one (Web 2.0). In the meantime, following this strategy leads to cultural output typical of attention whores rather than the output of inventors and creators with secure patronage.

I was delighted today to discover that all of this is about to change. It's still pretty hush-hush -- no "buzz in the blogosphere" -- as I've read a fair number of articles on the topic, yet none has mentioned the coming change, even if they've mentioned the change earlier in the year. Starting sometime this fall, online newspapers will finally start to charge for access to their sites, although who they charge, how much, and in what manner (yearly, per article, etc.), is entirely up to the individual papers, and we don't know what shape that will take just yet. The business model of Journalism Online, the group that's spearheading the change, says they're aiming to get revenues from the top 10% of readers by visit frequency. In any case, the point is that the era of unlimited free access to online journalism is dead.

Journalism Online seems to be a central hub that readers will go through to get to the various member organizations' publications, perhaps the way college students go through their university library's website to get access to various journals. According to co-founder Leo Hindery (as I heard on Bloomberg TV today), there are over 600 papers on board, and you can bet that includes most or all of the big ones, as they provide the best quality and yet receive no money from users (other than the FT and WSJ). All of the customer's payments will be kept track of through this one site. I don't have much more detail to give, since the Journalism Online website lays it out succinctly. Go read through the business model section and the press section (the 31-page PDF listed under "Industry Reports" is the most detailed).

This is the first nail in the coffin of Web 2.0, and once the other give-it-away internet companies see how profitable it is to actually -- gasp! -- charge for your product, they will wake up from their pipe dream of growing by attracting a big crowd and pushing ads. YouTube, Facebook, MySpace, perhaps other components of Google, Wikipedia -- they can either charge and profit or get shoved out of the market by those who are growing by charging. The winners will have more to invest in improving their products and maybe even funding their industry's equivalent of basic R&D, we'll see a cultural output that won't pander quite so much to the lowest common denominator to chase ad revenue, and best of all -- the quality newspapers, social networking sites, and so on, will continue to exist and grow rather than be claimed as further casualties of the moronic dot-com boom mentality. At last the internet is sobering up from its 15-year Bender of Free.

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Wednesday, August 26, 2009

Monogamy by ethnicity   posted by Razib @ 8/26/2009 12:38:00 PM

The Audacious Epigone has a post up where he queries the GSS to see what proportion of which European ethnic groups has had one lifetime sexual partner.


Tuesday, August 25, 2009

Microsoft myths that won't die   posted by agnostic @ 8/25/2009 10:42:00 PM

At the end of an otherwise good reflection in the WSJ on where Google can go from here, we read the following:

It would be foolish to predict that Google won't have another business success, of course. Microsoft managed to leverage its strength in PC operating systems into a stranglehold over the word-processing and spreadsheet applications.

Stan Liebowitz and Stephen Margolis debunked this at least 10 years ago in their book Winners, Losers, and Microsoft, and probably earlier, though I can't recall which journal article it originally appeared in. Scroll down to Figure 8.18 at Liebowitz's website, which shows the market share of Excel and Word in the Macintosh vs. Windows markets. They conclude:

Examination of Figure 8.18 reveals that Microsoft achieved very high market shares in the Macintosh market even while it was still struggling in the PC market. On average, Microsoft's market share was about forty to sixty percentage points higher in the Macintosh market than in the PC market in the 1988-1990 period. It wasn't until 1996 that Microsoft was able to equal in the PC market its success in the Macintosh market. These facts can be used to discredit a claim sometime heard that Microsoft only achieved success in applications because it owned the operating system, since Apple, not Microsoft, owned the Macintosh operating system and Microsoft actually competed with Apple products in these markets.

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Lives of the ancients   posted by Razib @ 8/25/2009 10:45:00 AM

John Hawks has a long post on ancient lifespans. It seems likely that the range has not shifted much, though the shape of the distribution naturally has. Child mortality has obviously declined, but it seems likely that death at any given age in adulthood has probably decreased as well. But for what it's worth, several of the Roman Emperors from aristocratic backgrounds whose ages are probably reliable and died natural deaths expired at an advanced age. Augustus at 76, Tiberius at 77, Claudius 63 (there is debate whether he died a natural death), Vespasian 69, Nerva 67, Trajan 63, Hadrian 62, Antinuous Pius 74 and Marcus Aurelius 58. As most of you probably know, hell broke loose after Aurelius at many Emperors did not die of natural causes until the late 3rd century after his reign. Note that some of these Emperors, such as Nerva or Vespasian, were already at very advanced ages when they came to power, so there is probably some selection effect at work in terms of age at death. Vespasian's son Titus died of fever at the age of 41.

H/T Dienekes.


Monday, August 24, 2009

Trends in depression and medication   posted by Razib @ 8/24/2009 10:12:00 PM

U.S. Antidepressant Use Doubled in A Decade. I'm not against the usage of medicine, but I'm skeptical that this increase is really attributable to chronically depressed people with serious neurochemical imbalances getting treated. Rather, a substantial number of people whose lives "suck" at a given moment convince doctors to prescribe these medications. I'm willing to be corrected by data on the usage patterns, but that's just my limited personal experience with a range of people who get on these drugs in response to general suckiness, and the smaller number of people with modestly bizarre personality shifts makes me wonder as to more "modest" side effects which are not gossip-worthy.


Risk, personality and testosterone   posted by Razib @ 8/24/2009 09:37:00 PM

Gender differences in financial risk aversion and career choices are affected by testosterone:
Women are generally more risk averse than men. We investigated whether between- and within-gender variation in financial risk aversion was accounted for by variation in salivary concentrations of testosterone and in markers of prenatal testosterone exposure in a sample of >500 MBA students. Higher levels of circulating testosterone were associated with lower risk aversion among women, but not among men. At comparably low concentrations of salivary testosterone, however, the gender difference in risk aversion disappeared, suggesting that testosterone has nonlinear effects on risk aversion regardless of gender. A similar relationship between risk aversion and testosterone was also found using markers of prenatal testosterone exposure. Finally, both testosterone levels and risk aversion predicted career choices after graduation: Individuals high in testosterone and low in risk aversion were more likely to choose risky careers in finance. These results suggest that testosterone has both organizational and activational effects on risk-sensitive financial decisions and long-term career choices.


Sunday, August 23, 2009

The origins of China   posted by Razib @ 8/23/2009 08:01:00 PM

Until the overthrow of the Manchus in the early 20th century the Chinese political-cultural system had exhibited an incredible amount of continuity for over 2,000 years, from the Qin and Han dynasties on. It seems a defensible position that just as the Mycenaean Greeks of 3,200 years ago were cultural aliens to Western elites in a way that the Classical Greeks of 2,500 years ago were not, so the Chinese bureaucrats could see themselves in the lettered gentry of 500 B.C.E, but not among the warlords of 1200 B.C.E, thanks to the crystallization of the canon during this critical axial age.

But the Greeks of the Classical period did not emerge out of a historical vacuum, and neither did the Chinese of the Spring and Autumn period. In hindsight the Duke of Zhou has been characterized in some ways as both the Lycurgus and Solon of ancient China, but one assumes that later commentators shaved off his harder edges and refashioned him in their own image, just as the Iliad which purports to tell a Bronze Age tale clearly reflects much of a Dark Age society.

Because of the thinness of the ancient textual evidence (if it exists at all), archaeology is often the only game in town. The new issue of Science has a series of articles putting a spotlight on the ancient physical history of what became China.


Friday, August 21, 2009

What Darwin Said: Part 4 - Speciation   posted by DavidB @ 8/21/2009 03:03:00 AM

This is the fourth in a series of posts about Charles Darwin's view of evolution. Previous posts were:

1: The Pattern of Evolution.
2: Mechanisms of Evolution.
3: Heredity.

The present part deals with the subject of speciation, that is, the formation of new species. Modern commentators often regard this as one of the weaker parts of Darwin's theory. They complain either that Darwin didn't understand the problem of speciation, or that he did, but gave the wrong solution. On the other hand, some biologists reject the current orthodoxy, and suggest that Darwin's approach was closer to the truth.


Speciation. By speciation I mean the formation of a new species. This may either occur by change of an existing species to the point where it is classified as a new species, or by the splitting of an existing species into two or more different species. Some authors prefer to confine the term speciation to the latter process (splitting, or 'cladogenesis'), but I will use it in the broader sense.

The term 'speciation' was not coined until early in the 20th century, and therefore was not used by Darwin himself. In letters he occasionally used the term 'specification' with much the same sense: Life and Letters, vol.3, p.160, letter of 26 November 1878 to Karl Semper, and More Letters, vol.1, p.380, letter of 25 November 1869 to George Bentham.

Species. The most widely used modern definition of 'species' is Ernst Mayr's Biological Species Definition (BSD), according to which species are 'groups of actually or potentially interbreeding natural populations which are reproductively isolated from other such groups' [Mayr, 19]. If two sets of organisms are living in the same place at the same time, and are successfully interbreeding, then they belong to the same species. If they are living in the same place at the same time, but are not successfully interbreeding to any significant extent, then they belong to different species. If two populations live at different places and/or times, they cannot be 'actually' interbreeding, and the question is then whether they are 'potentially' interbreeding. As Mayr recognises, this cannot usually be directly tested [Mayr, 22]. The crucial question is whether there are 'isolating mechanisms' that would be sufficient to prevent successful interbreeding if the two populations were combined under natural conditions [Mayr, chapter 5]. Geographical barriers or distance by themselves do not count as isolating mechanisms, since two separated populations may be reunited and then interbreed. Some intrinsic difference of genetics or behaviour, sufficient to prevent successful interbreeding, is necessary for reproductive isolation [91].

The BSD is not universally accepted. Some taxonomists find little use for it, as the status of 'potential interbreeding' is often uncertain. Mayr himself admitted that the BSD is not always applicable (for example, to wholly asexual species). The BSD does however have one great merit for theoretical purposes. If the pattern of evolution is 'tree-like', as generally accepted by modern biologists, then a crucial part in any system of classification is played by the points at which branching takes place. A species, under the BSD, marks the lowest level of classification at which two populations have passed such a point. It is desirable to have a term to mark this distinction, and the BSD meets this requirement. The problem remains that in many cases there is no way of verifying whether two populations have passed the point of separation.

Modes of speciation A large number of different terms have been used to describe processes, observed or hypothetical, by which speciation (in accordance with the BSD) may occur. Usage by different authors is not always consistent. I will use the following terms.

Allopatric speciation occurs when two or more populations of the same species, living in different places (the literal meaning of 'allopatric') are separated by a geographical barrier or unoccupied space, and become reproductively isolated from each other. (This is equivalent to what Mayr calls 'geographic' speciation.) Reproductive isolation may be acquired by evolutionary changes in the populations following their geographic separation, or by the extinction of intermediate forms in part of a continuous range, leaving the remaining forms reproductively as well as geographically isolated from each other.

Sympatric speciation occurs when two or more species are formed out of a single species living in the same place (the literal meaning of 'sympatric'). On this interpretation of 'sympatric', the terms 'allopatric' and 'sympatric' do not exhaust the possibilities, because there could be a third case where new species arise in adjacent parts of a continuous range. Mayr, on the other hand, uses 'sympatric' to cover every case other than 'allopatric'.

Parapatric speciation is the third case just mentioned, where new species arise in adjacent areas without geographical separation between them. Mayr calls this hypothetical proceess 'semigeographic' speciation [Mayr 525] .

Peripatric speciation is a form of allopatric speciation where new species arise from relatively small geographically isolated populations on the periphery of a species range.

Stasipatric speciation occurs when a new species is formed in a relatively small locality within an existing species range, displacing or coexisting with the parent species, but not interbreeding with it. It is generally assumed that in this case reproductive isolation occurs as a result of polyploidy or some other major change in the chromosomes, and some authors make this part of the definition of 'stasipatric'. I prefer to avoid assuming a particular mechanism of reproductive isolation, and will use 'stasipatric' to refer to any form of speciation in a small area within a species range.

Theories of speciation

In the second half of the 20th century the dominant theory of speciation was that of Ernst Mayr. Mayr maintained that, except for speciation by polyploidy and other major chromosomal changes, the only major form of speciation was allopatric (or geographic in Mayr's terminology). He particularly stressed the importance of peripatric speciation in small isolated areas. He argued vigorously against sympatric and parapatric speciation. His main theoretical argument was that major divergence between populations, to the point of reproductive isolation, is not possible without geographical obstacles to gene flow. He did however define 'geographical obstacles' very widely, so that, for example, different host species of parasites could be regarded as spatially separated [Mayr 349]. There might be geographical obstacles even within a single fresh water lake [Mayr 465]. Mayr accepted that polyploidy was an important mode of speciation among plants and some invertebrates, but disputed the importance of chromosomal changes in speciation among vertebrates.

Mayr's views dominated post-war thinking on speciation, but were increasingly challenged from about 1970 onwards. Mayr's rejection of sympatric and parapatric speciation was based mainly on verbal arguments, whereas quantitative models showed that sympatric and parapatric speciation were theoretically possible. There also seemed to be cases, like species swarms of fishes in lakes, which were difficult to explain by allopatric speciation. However, recent reviews of the evidence suggest that there are few clear examples of sympatric speciation [C&O 178], while it is very difficult to distinguish between the effects of allopatric and parapatric speciation [C&O 118] in those situations where the question arises.

Darwin on Speciation

There is no single section in the Origin devoted to what we now call speciation, so the first step is to identify which parts of Darwin's work are relevant. Many parts of the Origin could have some bearing on the subject, but the following are the main ones:

'Variation under Nature' - important for its discussion on the distinction between species and varieties

'Natural Selection' - important for the discussion of circumstances favourable and unfavourable to natural selection, including isolation and interbreeding, and for the 'principle of divergence'

'Difficulties of the theory' - probably the most important chapter for the problem of speciation, because it deals with the question how varieties and species can be formed despite interbreeding

'Hybridism' - discusses the evidence on interspecific breeding and the viability and fertility of hybrids

'Geographical Distribution' (two chapters) - important for discussion of isolation and means of dispersal.

'Recapitulation and Conclusion' - contains brief statements of most of Darwin's key propositions.

Relevant comments may also be found in other works, and in Darwin's correspondence.

Darwin's definition of species

Darwin does not propose a formal definition of 'species', and he implies that any such definition would be arbitrary. He argues, especially in the section 'doubtful species' [Origin, 126-38], that there is no sharp distinction between varieties and species: 'Certainly no clear line of demarcation has as yet been drawn between species and sub-species - that is, the forms which in the opinion of some naturalists come very near to, but do not quite arrive at the rank of species; or again between sub-species and well-marked varieties, or again between lesser varieties and individual differences'. Summing up his position, he says: 'From these remarks it will be seen that I look at the term species as one arbitrarily given for the sake of convenience to a set of individuals closely resembling each other, and that it does not essentially differ from the term variety, which is given to less distinct and more fluctuating forms'. In the chapter on Hybridism Darwin discusses the varying degrees of intersterility and viability of offspring between recognised species, and concludes that 'neither sterility nor fertility affords any clear distinction between species and varieties' [427]. Darwin was of course concerned to refute the traditional view that species were created with unbridgeable differences between them, and that intersterility was a special endowment designed by the Creator to keep them separate. This may have led him to play down the importance of reproductive isolation as a criterion of species status. It is unlikely that he would have accepted the BSD, if it had been put to him.

Darwin on Speciation

Regardless of whether or not Darwin would have accepted the BSD, we may still ask whether his theory can account for the division of existing species into new species as defined under the BSD. In other words, does he adequately explain reproductive isolation?

Some critics would claim that Darwin did not even recognise the problem, and that he therefore did not offer a theory of speciation at all. But this is an inaccurate criticism, as a section of the chapter on 'Difficulties of the theory' is devoted to the problem. Whether or not one agrees with Darwin's 'solution', he did offer one.

First, it may be noted that Darwin deliberately rejected one tempting option: the proposal that the barriers to interbreeding between species were due to the natural selection of sterility between them. In a lengthy correspondence Alfred Russel Wallace tried to persuade Darwin to accept this solution, but after much agonising Darwin rejected it. He concluded that the observed pattern of sterility and fertility was difficult to reconcile with an explanation by natural selection, for example because species from widely separated areas, where there could be no selective pressure against interbreeding, were nevertheless often intersterile, or produced sterile hybrids, in captivity. He also saw a fundamental theoretical objection to Wallace's theory. Wallace argued that intersterility would be selected because it was beneficial to the species, or to the variety, but Darwin pointed out that there would be no advantage to individuals, (or indirectly to their 'nearest relatives' or other individuals of the same variety) in a reduction of fertility. [444] He therefore did not see how the sterility could be initiated and gradually increased by natural selection. This is one of Darwin's most important discussions of 'levels of selection', and I will return to it in another post. Since intersterility could not be explained by natural selection, or by a 'special endowment', Darwin concluded that it was a by-product, 'an incidental result of differences in the reproductive systems of the parent species' [425]. This would be generally accepted by modern biologists.

So how did Darwin explain the divergence of varieties to the extent of what we now call speciation?

An important part of the answer was always geographical isolation. Long before the Origin, in a letter of 1844 to Joseph Hooker, Darwin wrote that 'the most general conclusion, which the geographical distribution of all organic beings, appears to me to indicate, is that isolation is the chief concomitant or cause of the appearance of new forms' [L&L, ii, 28]. In the Origin the emphasis on isolation is somewhat reduced, but it is still one of the most important factors, for example in the chapters on geographical distribution.

For highly mobile animals, Darwin comes close to regarding isolation as essential for speciation: 'intercrossing will affect those animals most which unite for each birth, which wander much, and which do not breed at a very fast rate. Hence in animals of this nature, for instance in birds, varieties will generally be confined to separate countries, and this I believe to be the case' [194].

In contrast, for 'hermaphrodite organisms which cross only occasionally, and likewise in animals which unite for each birth, but which wander little and which can increase at a very rapid rate, a new and improved variety might be quickly formed on any one spot, and might there maintain itself in a body, so that whatever intercrossing took place would be chiefly between the individuals of the same new variety. A local variety when thus formed might subsequently slowly spread to other districts' [194]. This might be regarded as a form of stasipatric speciation.

For the generality of organisms, which are neither highly mobile nor static, the problem remains of explaining how distinct species are formed, rather than a smooth continuous distribution, now called a cline [323]. Darwin considers the possibility that intermittent periods of isolation have always been involved in speciation. But Darwin rejects this option, saying ' I will pass over this way of escaping from the difficulty; for I believe that many perfectly defined species have been formed on strictly continuous areas; though I do not doubt that the formerly broken condition of many areas now continuous has played an important part in the formation of new species, more especially with freely crossing and wandering animals' [324] To account for the formation of distinct species within a continuous area, Darwin describes what would now be called a form of parapatric speciation. He stresses that the organic and inorganic environment seldom change smoothly. Within the range of a species, there are likely to be zones where conditions are relatively unfavourable, and the population will be sparse and liable to periodic 'extermination' (325), for example when a predator or prey species fluctuates in numbers. For these reasons the population of a species will be much larger and more continuous (in time) in some areas than others. The areas where the population flourishes will be more favourable to evolution, since there will be more chance for new variations to arise, whereas in sparsely populated intermediate areas there will be less variation, the population will be liable to 'accidental extermination', and intermediate forms will be constantly at risk of being overrun by the more successful surrounding varieties, which are more sharply distinct. [326]

This account of the processes leading to parapatric speciation has much in common with more modern approaches. There is however still one element missing from Darwin's theory. Modern theories generally incorporate the idea that behavioural mechanisms will evolve to discourage mating between different varieties in 'border' zones, where the offspring of such matings would be disadvantaged. There is perhaps a hint of such mechanisms in one remark of Darwin, where he says that 'I can bring a considerable category of facts, showing that within the same area, varieties of the same animal can long remain distinct, from haunting different stations [ecological niches], from breeding at slightly different seasons, or from different varieties of the same kind preferring to pair together' [194]. But this passage is a long way from Darwin's discussion of his 'parapatric' model, and it would be straining interpretation to suppose that he intended them to be connected.

We may conclude that Darwin believed in the occurrence of allopatric, parapatric, and possibly stasipatric modes of speciation, even if he did not by modern standards have fully worked-out models of the process.

There remains the question whether Darwin also believed in the occurrence of sympatric speciation. Of course, if 'sympatric' is defined so as to include 'parapatric', then the answer is trivially 'yes'. But if we define 'sympatric' more narrowly, to require divergence of two populations living together in the same or widely overlapping areas, then the answer is not so clear. Some modern commentators are confident that Darwin did accept sympatric speciation in this sense [C&O 125] . Against this, we may set a quite explicit denial by Darwin himself: 'I do not believe that one species will give birth to two or more new species, as long as they are mingled together within the same district. Nevertheless I cannot doubt that many new species have been simultaneously developed within the same large continental area; and in my 'Origin of Species' I endeavoured to explain how two new species might be developed, although they met and intermingled on the borders of their range. [Darwin's emphasis] It would be a strange fact if I had overlooked the importance of isolation, seeing that it was such cases as the Galapagos Archipelago, which chiefly led me to study the origin of species' [letter of 13 October 1876 to Moritz Wagner, Life and Letters, iii, 159]. One could hardly expect a clearer statement of the distinction between parapatric and sympatric speciation, or a clearer rejection of the latter. How then can it be maintained that Darwin believed in sympatric speciation?

It is, unfortunately, common for an author to be confused or inconsistent in his or her views, so a clear denial by Darwin of sympatric speciation in one passage does not rule out his acceptance of the process elsewhere. The interpretation of Darwin as an advocate of sympatric speciation rests on the section on 'divergence of character' in the chapter on Natural Selection. Here Darwin attempts to explain why the descendants of a single species diverge into many different types. The general explanation is that there are advantages in an ecological 'division of labour': 'the more diversified the descendants from any one species become in structure, constitution and habits, by so much will they be better enabled to seize on many and widely diversified places in the polity of nature, and so be enabled to increase in numbers'. [207] They may, for example, feed on different kinds of prey, or live in different habitats such as trees or water. Even in the same patch of ground, a diverse mixture of species and genera of plants will produce more vegetation than a single species or variety. [207]

The principle of divergence of character is important and in general plausible, but its application to varieties within a single species and in a single geographical area is problematic. If Darwin had confined the principle to varieties which had already reached the stage of distinct species, there would be no problem, but some of his wording does seem to apply to sub-specific varieties. Darwin opens his discussion by asking, 'how then does the lesser difference between varieties become augmented into the greater difference between species?' [205], and the principle of divergence is his ostensible answer [208]. There would still be no problem if he confined the divergence of varieties to cases where they live in different areas, but he does not explicitly limit the principle in this way, and some of his illustrations of the principle seem to involve such cases; notably, he refers to different varieties of grass in the same patch of ground [207]. Yet the evolution of different varieties within the same small area would conflict not only with Darwin's clear contrary statement to Wagner, but with those passages of the Origin itself which deal with the 'blending' of varieties through interbreeding. Moreover, even in the section dealing with divergence of character, Darwin goes on to say that the animals and plants living on a small patch of ground, and which therefore compete most severely with each other, in general belong to different genera or orders: 'where they come into the closest competition with each other, the advantages of diversification of structure, with the accompanying differences of habit and constitution, determine that the inhabitants which thus jostle each other most closely, shall, as a general rule, belong to what we call different genera and orders' . [208] In this case they cannot be recently descended from different varieties of the same species. It is all rather confusing. The charitable interpretation is that Darwin wished to deal only with one issue at a time, and intended his discussion of divergence to be qualified by the discussion of 'blending' in the chapter on 'Difficulties of the Theory'. I think however it is more likely that Darwin simply overlooked the tension between his comments on divergence and his comments on blending.

Overall, Darwin's position on the modes of speciation is pluralistic. He recognised what we call allopatric and parapatric speciation, and possibly also stasipatric speciation. His position on sympatric speciation is more doubtful.

This pluralism contrasts with the dominant modern doctrine of Ernst Mayr, which recognises only allopatric speciation (with polyploidy and other major chromosomal changes admitted as a special exception). Mayr and his adherents therefore found Darwin's position unsatisfactory. Orthodox 'Mayrism' has however come under increasing criticism in the last few decades. Not surprisingly, some of those who criticise Mayrism have found support in Darwin's writings, and applaud his supposed acceptance of sympatric speciation [H&B 90]. The importance and prevalence of different modes of speciation remain open questions in evolutionary biology.


Origin: Charles Darwin: The Origin of Species: a Variorum Text, edited by Morse Peckham, 1959, reprinted 2006.
Mayr: Ernst Mayr, Animal Species and Evolution, 1963
C&O: Jerry Coyne and H. Allen Orr, Speciation, 2004
H&B: Endless Forms: Species and Speciation, ed. D. J. Howard and S. H. Berlocher, 1998.
Life and Letters of Charles Darwin 3 vols, ed. Francis Darwin.
More Letters of Charles Darwin, 2 vols, ed. A. C. Seward and Francis Darwin.

Friends & fat   posted by Razib @ 8/21/2009 12:05:00 AM

In the McArdle vs. Frum diavlog I alluded to earlier there was a dispute centered around two seemingly contradictory results. First, the fact that heritability of obesity is rather high, in twins-separated-at-birth studies the correlation between monozygotic twins raised apart is on the order of ~0.75. And yet people tend to track the weight of their peer group. The causality here has to be teased apart of course, but consider this study, The presence of friends increases food intake in youth:
Design: Twenty-three overweight and 42 nonoverweight youths had the opportunity to play and eat with a friend (n = 26) or with an unfamiliar peer (n = 39). The dependent variables of interest were the amount of nutrient-dense and energy-dense foods children consumed and their total energy intake.

Results: Participants eating with a friend ate substantially more than did participants eating with an unfamiliar peer. Furthermore, overweight youth, but not nonoverweight youth, who ate with an overweight partner (friend or unfamiliar peer) consumed more food than did overweight participants who ate with a nonoverweight eating partner. Matching of intake was greater between friends than between unfamiliar peers.

Naturally twins raised apart were not placed into a "design" whereby they were forced to eat with strangers. Rather, they selected their peer groups. Heritability of many traits increases with age because individuals seek out particular environments which eventually dampen the "noise" which reduces the correlation between those with similar genetic propensities. Assortative friendship by weight then might result in amplifiers of mean deviation from phenotypic norms; that is, thin peer groups might model specific behaviors and apply certain pressures which differ greatly from overweight peer groups. Gene-environment correlation. So naturally in the interests of public health we need integration across weight classes....

Also see ScienceDaily.

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Thursday, August 20, 2009

MECP2 and brain structure   posted by Razib @ 8/20/2009 11:37:00 PM

ScienceDaily, Genetic Variations Linked To Brain Size. The write-up seems a bit garbled to me, so probably best to read the paper, A common MECP2 haplotype associates with reduced cortical surface area in humans in two independent populations, when it is live on the PNAS site.

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Differences in human universals on the margins   posted by Razib @ 8/20/2009 10:55:00 PM

Neuroskeptic reviews new research which reports that East Asians and Europeans perceive facial expressions differently. Yes, differences do seem to exist, at least within the small sample studied, but there is a great deal of overlap. Of course much of the phenomena of interest are on the margins anyhow. Speaking of which, Genetic and Molecular Basis of Individual Differences in Human Umami Taste Perception:
Population diversities of SNPs in TAS1R1 and TAS1R3 have been reported by Kim et al...Minor allele frequencies of the SNP at 372 in TAS1R1 vary among eight populations; 10% in Cameroonian, 0% in Amerindian (native Americans), 25% in North European, 35% in Japanese, 5% in Russian, 35% in Hungarian, 40% in Chinese and 6% in Pakistani, whereas those at 757 in TAS1R3 showed no obvious difference among populations. These results suggest that there may be differences in umami sensitivity related with TAS1R1-A372T among populations in the world.

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Nudge the fat; satiety & the implicit mind   posted by Razib @ 8/20/2009 09:58:00 PM

Megan McArdle has has been talking about the high heritability of BMI again. I have expressed concern about her putting the high heritability numbers out there when it comes to its relevance for public policy, though I do tend to agree with her general stance that glib assertions about the importance of will-power are probably non-starters. And, rather than point to arguments such as "I have a slow metabolism," it is probably more critical emphasize the complexity of the chain of events and framing of how we make decisions, much of which occurs "under the hood" and outside the purview of conscious explicit control. Interestingly, the reality that choice is highly conditioned by details of our environment combined with innate predispositions, and proximately is driven by many implicit factors, has pushed me in a less libertarian direction.

In any case, the whole discussion got me interested in the topic of obesity & heritability, and I found this review, Human Obesity: A Heritable Neurobehavioral Disorder That Is Highly Sensitive to Environmental Conditions. You can read the full text, it's Open Access now, but this part caught my attention:
...He hypothesizes that random natural variation in "hypothalamic energy balance set points" has occurred over millions of years of primate evolution. Whereas variants that would tend to produce a state of low energy stores would have been systematically selected against, at least in part because of their adverse impact of reproductive success, upward drifts in such set points would have been allowed to persist (rather than being positively selected for, as the “thrifty gene” hypothesis would have it). This upward drift would be particularly prominent because the formation of organized social groups and the discovery of fire, both of which occurred around 2,000,000 years ago, made our ancestors less susceptible to predation. Not particularly emphasized by Speakman, but likely to be important, is the probability that such natural tendencies toward an upward drift in adipose stores may rarely have actually manifested themselves as obesity because of the high energy cost of obtaining food during most of human evolution. It is only in the past 50 years or so, when for the first time in human history the majority of people in the developed and developing world can readily access sufficient daily calories to exceed the calories expended in acquiring them, that those with intrinsically higher set points have manifested their "obesity potential" on a grand scale. Unlike the “thrifty gene” hypothesis, this scenario provides a credible explanation for the fact that even in places where obesity is very common, a substantial proportion of the population remains lean.

This is an old hobby horse of mine: if you see a quantitative trait which can be conceived of as normally distributed with a high degree of heritability, such as body mass index, then its fitness implication can't have been too stark. In other words, if a very heritable trait still has a great deal of extant genetic variation, then it is either in transient, or, more likely the fitness implication of any particular trait value was low or there is balancing dynamics preserving the variance. Like IQ, body weight has been increasing over the past century. Many people think that they know the reason why this is occurring. If the reasons are ever established to a high degree of certitude, is it possible to reverse the slouch toward obesity without coercion?

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Wednesday, August 19, 2009

The greater fool theory 1: A mostly verbal mathematical model   posted by agnostic @ 8/19/2009 09:22:00 PM

Here is a brief description of the idea that price bubbles are caused by people buying something, not necessarily because they think it's worth anything, but because they think they can find an even greater fool to buy it at a higher price. This continues until no more such fools can be found, and this bust drives prices back down to what they were before the boom began.

I didn't see any references to mathematical models of the theory at Wikipedia or through Googling around a bit, so I made one up today at Starbucks since I didn't have anything to read to pass the time. Because I'm not an economist, I don't know how original it is, or how it compares with alternative models of the greater fool theory (if they exist). So, this is intended just as an exercise in modeling, explaining the model, and hopefully shedding some light on how the world works. I've kept most of the exposition straightforward and largely verbal, so that you don't need to know much math at all to understand what the model says and what its implications are.

In part 1, I lay out the logic of the model and explain enough of it to show that it is capable of producing a single round of boom-and-bust for price hype. Part 2 will provide more mathematical detail about how the dynamics unfold, a phase plane analysis, and graphs of how the variables of interest would change over time, to better wrap your brain around what the model predicts.

This is a dynamic model, or one that tracks how things change over time -- after all, we want to see how price, the number of fools, etc., evolves. It is made of several differential equations, and all these equations say is what causes something of interest to go up or go down over time. (You may recall that the sign of a derivative tells you whether a function is increasing or decreasing, and the magnitude says by how much.) I'll only explain what is absolutely necessary for the reader to see what's going on, with the less necessary math being confined to footnotes.

First, we set up the basic picture before we write down equations. My version of the greater fool theory goes like this. There is a population of people, and during a price bubble they can fall into three mutually exclusive groups: suckers (S), who are susceptible to joining in on the bubble; investors (I), who currently own the speculative stuff (such as a home bought for speculation); and those who are retired from the bubble (R), who used to be investors but have gotten rid of their investment. And of course there is the price of the thing -- I model only the extra price that it enjoys due to hype (P), above its fundamental value, since this is the only component of price that changes radically during the bubble.

I set the population to be fixed in size during the bubble, since growth or decline is negligible over the handful of years that the bubble lasts. I also set the amount of speculative stuff to be fixed, which is less general -- supply should shoot up to meet the rising demand during a bubble. So, this model is restricted to cases where you can't produce lots more of the stuff, relative to how much already exists, on the time-scale of the bubble's boom stage (say, 5 years or less). Or perhaps no more of it will be produced at all, such as video game consoles from decades ago that the original manufacturers will never bring back into production, but which nostalgic fans have taken to buying and selling speculatively (like NEC's TurboDuo). Last, the amount of stuff that each investor has is the same across all investors and stays constant -- say, if each investor always owned just one speculative home.

At the start of the bubble, there is a certain number of early investors. In order to sell their stuff, they need to meet a sucker to sell it to. When they meet -- and I assume the two groups are moving around independently of each other -- there is a probability that the sale will be made. If they make a deal, the sucker is now an investor, and the former investor is now retired. In this model, retireds do not again become suckers -- they consider themselves lucky to have found a greater fool and stay out of the bubble for good afterward. That's the extent of how people change between groups.

As for price hype, again I'm not an economist, so the exact formula may differ from what's standard. I take it to respond positively to demand -- namely, the number of suckers -- and that there is a multiplier that serves as a reality check. This reality check should be weak at the start when most non-investors are suckers, and should be strong near the end when most non-investors are retired. In other words, the price hype at the beginning is a near total distortion -- nearly 0% accurate -- whereas the price hype near the end is nearly 100% accurate. This will make more sense once we write down formulas.

Now we get to the differential equations for how these things change. We write down one equation for each variable whose values we're tracking over time. I use apostrophes to denote the derivative with respect to time (i.e., rate of change):

S' = -aSI

Since suckers can only lose members (by turning into investors), there is only one term, and it shows how suckers decline (negative sign). Remember, retireds do not go back into the pool of potential buyers. And investors either make a sale and go into the retired group, or they sit on their stuff in hope of selling, so they never contribute to the growth of suckers. Thus, there is no growth term. The parameter a shows the probability that, when a sucker and an investor meet, the investor will transfer his stuff to the sucker. ("Parameter" is another word for "constant," in contrast to a variable that changes.) The reason we use the product of S and I is that this is essentially the rate at which the two groups encounter each other when they move around independently of each other. [1]

I' = aSI - aSI = 0

Investors both grow and decline, so one term is positive and the other negative. They grow by having a sucker join their ranks, which as we saw above happens at rate aSI. However, each time that happens, the investor loses his stuff and becomes retired. That happens at the same rate, and the negative sign just shows that this causes I to decline. When we simplify, we get I' = 0 -- that is, the number of investors does not change over time. That makes sense because each bundle of stuff always has an owner, regardless of how it may change hands, somewhat like the game of hot potato. When something doesn't change, it is constant, so whenever we see I from now on, we'll know that this is just another parameter, not a variable that changes. In particular, it refers to the initial number of early investors who get the bubble going.

R' = aSI

Retireds never join the suckers again. And recall the mindset of a retired person -- they knew the stuff was junk and are glad to have gotten through the selling process, so they cannot be sold the stuff again to become investors once more. Thus, there is no way for them to lose numbers. They grow by former investors making a sale and becoming retired, which once again happens at rate aSI.

Here's the neat thing: notice that S' + R' = -aSI + aSI = 0. The sum of the two derivatives equals zero, and since taking a derivative shows the distributive property, this also means that (S + R)' = 0. That is, the sum of suckers and retireds does not change over time. This makes sense since, if the number of investors stays constant, the leftovers -- suckers and retireds -- is constant, regardless of how each separate group grows or shrinks. We can take this further to note that S' + I' + R' = 0, which means (S + I + R)' = 0. That is, the combined size of all three groups does not change over time -- which is just what we claimed by keeping total population size constant. (Otherwise, each group would have birth and death terms, aside from the terms that show how their members switch between groups.)

We'll call this constant total population size N. So, S + I + R = N. Now, I is just a constant, so we'll move it to the other side: S + R = N - I. We have two variables, S and R, but we just wrote an equation connecting them, so we can re-write one in terms of the other. I'll choose R, but it doesn't matter. So, R = N - I - S, and anywhere we see R, we can replace it with N - I - S. In other words, we've removed R from our focus -- we can always get it from knowing what the variable S is, as well as the two parameters N and I. That means the equation for R' only gives us redundant information, and we can ignore it. We can also ignore the I' equation, since it just tells us that I is constant, and we're only interested in things that change. So we're left with just the S' equation.

Now we move on to the price hype formula and how it changes over time. First, the formula for price as a function of demand and the reality check, since hype is never totally irrational and at least tries to take stock of reality:

P = bS(R / Rmax) = bS(R / (N - I))

Demand is driven by the number of suckers -- the ones who eventually want to get in on the bubble -- and the parameter b says how strongly demand responds to the number of suckers. The multiplier (R / Rmax) provides a reality check. If you landed from Mars and only knew the number of suckers, you would also want to know how many retireds there were -- if there were few retireds, that would tell you the bubble had only just begun, so that hype is likely to be high and to go even higher short-term. Thus, this filter should not let much of the demand information through. Indeed, when R is very low compared to Rmax, the multiplier is near 0.

However, if you saw that there were many retireds, that would say the bubble was near its bust moment, and that the information from demand is very accurate by this point. Indeed, when R is near Rmax, the multiplier is near 1 and the filter lets just about all of the demand information through. What is Rmax? It is the value when no one is a sucker and everyone is retired, aside from the constant number of investors. Looking above at the equation S + R = N - I, we see that when there are no suckers, R = N - I.

Now we need to find the differential equation for how P changes over time. Using the product rule for derivatives [2], we get:

P' = (abI / (N - I)) * S(2S + I - N)

Since a, b, I, and N - I are always positive, and since S is positive except for the very end of the bubble when it is 0, in the meantime, whether price hype shoots up or crashes down depends on whether the term 2S + I - N is positive or negative. It is positive and price hype grows when S exceeds (N - I) / 2, which is half the size of non-investors. It is negative and price hype declines when S is below (N - I) / 2. It is 0 and price hype momentarily stalls out when S is exactly (N - I) / 2.

Because the bubble starts with all non-investors being suckers, S is initially N - I, which is greater than (N - I) / 2. So at first the price hype shoots up. However, remember that S only declines -- as more and more of the suckers are drawn into the bubble (some of whom may also make sales and become retireds), S will inevitably fall below (N - I) / 2 and price hype will start to contract.

When S inevitably reaches 0 -- when all non-investors are out of the bubble for good -- then P = 0 (recall that P = bS(R / Rmax)). Moreover, at that time P' = 0 too. Thus, at the end, price hype has completely evaporated and it will stay that way. This is a single round of boom-and-bust for price hype.

In this post, I've shown how some pretty simple "greater fool" dynamics can lead to a boom-and-bust pattern for price hype. You can quibble with all of the assumptions I've made, but the model shows that the greater fools theory is a viable explanation for price bubbles. I've relaxed some of the assumptions to see if it makes a difference, like making the decline of S be a saturating rather than linear function of S, and so far they don't seem to affect things qualitatively. A more realistic model would have P appear in the equation for S' -- that is, to have price hype affect the probability of making a sale. Or rather, the trend of prices (P' ) should affect sale probability -- if suckers see that price hype is increasing, they should want to get in on the bubble, and to stay put if price hype is dropping. Also, allowing retireds to re-enter the pool of suckers would be more general and would almost certainly lead to sustained cycles of boom-and-bust, rather than a single round. But that's for another slow afternoon.

In part 2, I'll go into more mathematical detail about how we see what states this system is at rest in, and whether they are stable to disruptions or not. I'll look more at the formula for the maximum level of price hype, and interpret that in real-world terms in order to see what things will give us larger-amplitude bubbles. I'll provide a picture of the phase plane, which shows what the equilibrium points are, and how the variables will change in value on their way from their starting values to the final ones. I'll also have a couple of graphs showing how the number of suckers and retireds, and the amount of price hype, change over time.

[1] Draw one person at random, and the chance that they're a sucker reflects S. Draw another one at random, and the chance that they're an investor reflects I, since the draws are independent. The chance of doing both is just the product of the two separate probabilities.

[2] P' = (bS(R / Rmax))' = (b / (Rmax)) (S' * R + S * R')
A little algebra, which you can confirm by hand or using Maple, gives the equation in the main body for P'.

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Tuesday, August 18, 2009

In defense of big genetics   posted by p-ter @ 8/18/2009 08:19:00 PM

Greg Mayer, filling in for Jerry Coyne, has a post up on a somewhat odd objection to the appointment of Francis Collins as director of NIH: that he's a geneticist. The argument seems to be that diseases are complicated and not entirely genetic, and that Collins isn't hip to non-genetic subtleties. To be frank, this is silly--while it's sometimes a revelation to non-biologists that the "gene for X" way of framing things is inaccurate, Collins is not incompetent. If I had to guess what direction he's planning on taking the NIH, I'd look to what he's actually written.

In the comments to the post, there's the additional worry that Collins represents "big science", which I suppose is considered to be a bad thing (apparently Collins thinks it would be nice to catalogue all the transcripts in a cell, which for whatever reason really pissed off this dude). It's not a bad thing at all; in many cases, big, relatively hypothesis-free science is actually really nice for rationally choosing which "little science" projects to pursue.

Let's take a couple recent examples from genome-wide association studies (these studies over the past few years have exponentially increased our understanding of complex disease; whether that exponential increase is enough for you depends on your prior expectations). First, a little over two years ago, an association was found between a genetic variant in the FTO gene and obsesity in humans. At the time, the gene had unknown function. Now, there's a mouse model and focused biochemical analysis being done on this gene, and we're light years closer to understanding what it does and how nearby variation influence obesity. Would all of this been done without the "hypothesis-free" GWAS? Not anytime soon.

Second, consider the genome-wide association studies in several cancers that all pointed to the same, gene-free region on chromosome 8. In the last few weeks, three separate groups have published their "small-scale" molecular biology work establishing that the associated region appears to be an enhancer important for either proper temporal or spatial gene expression. How does it work? It's not clear, but that's the point--this is an interesting question. Much of "small-scale" molecular biology is done in a few model systems, or on a few "popular" genes. There's a very good reason for this--these systems or genes are already known to be interesting either scientifically or medically. One efficient way to identify novel, potentially interesting systems is through large-scale work.

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Monday, August 17, 2009

Breeding a better athlete   posted by Razib @ 8/17/2009 02:43:00 PM

Taller, heavier: the speedy evolution of the fastest people on the planet:
While the average person has gained about five centimetres since 1900, the height of champion runners has increased 16.2 centimetres, say Duke University researchers, Jordan Charles and Adrian Bejan, who studied the heights and weights of 100-metre world record holders.

''The trends revealed by our analysis suggest that speed records will continue to be dominated by heavier and taller athletes,'' said Mr Charles, whose study was published last month in The Journal of Experimental Biology .


While Dr Norton dismissed those predictions, he believed that the laws of genetics, thanks to the habit of athletes marrying athletes - and possibly even the creation of athlete sperm banks - meant runners would continue growing taller, more powerful and faster.

Remember the "Little Hercules" with the myostatin mutation? His mother was very muscular, and reportedly there was a family history of mesomorphicity. One way population level quantitative trait mean value can shift through selection beyond the most extreme values of the original population without new mutation being necessary is simply to change the underlying allele frequencies enough so that originally unlikely combinations become common. Assortative mating is another variant of this dynamic, if people several sigmas from the mean mate, then new combinations are likely to emerge.

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Sunday, August 16, 2009

Including genetic information in clinical trials: hepatitis C and IL28B   posted by p-ter @ 8/16/2009 06:41:00 PM

Online this week, Nature has published a genome-wide association study for response to treatment for chronic hepatitis C infection-the authors identify a polymorphism in an interleukin gene that is a strong predictor of how well an individual is able to clear the virus. Interestingly, the frequency of the polymorphism in different populations tracks the previously noted population difference in drug response, and the authors claim to explain half the difference in response rate between African- and European-Americans with this single polymorphism.

This paper is also interesting in that it represents one of the first (if not the first?) studies to coordinate a drug trial (in this cases, three different treatments for hepatitis C) with a genome-wide association study. This promises to lead to both important advances--as researchers are able to identify genetic subgroups of individuals who respond (or not) to a drug, even if it is ineffective in the population as a whole--as well as (my cynical side speaks) additional opportunities for misleading post hoc analyses by drug companies to try to salvage and market drugs that don't work. Hopefully, mostly the former--this could be an important step towards legitimizing genetic information in the eyes of MDs, and an ever-so-slight step towards personalized medicine.


Wars we know   posted by Razib @ 8/16/2009 11:28:00 AM

I've decided to read up on the World Wars recently. I don't know much about World War I & II aside from what I've seen on The History Channel and some books I read in elementary school. I've read The Pity Of War: Explaining World War I and The First World War, and am almost finished with A World at Arms: A Global History of World War II. I'm struck by the fact though I've learned many details of interest about World War I, almost everything I've read about World War II so far in A World at Arms (which is ~1,000 pages) is totally unsurprising. To me that emphasizes how much World War II still looms in our popular culture, while the Great War is an ignored prologue. Some of this is surely time, there are fewer than 10 World War I veterans alive today. But another factor is that you couldn't invent evil on the scale of the German regime plausibly. The banal barbarity of the Second Reich pales in comparison. If one could find someone totally unfamiliar with World War II and lay out the course of events and the nature of the insane dictators (Hitler and Stalin), I suspect their initial response would be that it was implausible science fiction or alternative history, and you need to go to a writer's workshop to brush up on the craft. In contrast the First World War I exhibited a human-scaled level of folly and hubris.


What's not the matter with Appalachia   posted by Razib @ 8/16/2009 12:17:00 AM

In the post from a few days ago showing areas where Non-Hispanic white proportions over & under predicted the % for Obama there were some interesting comments. One of the issues is that lumping different regions together obscures some information. Some readers wondered about regional differences, and I did too. So I thought it might be interesting to look at the South as distinct from the non-South. For the purposes of this post the "South" means: Virginia, West Virginia, North & South Carolina, Georgia, Tennessee, Alabama, Mississippi, Louisiana, Texas, Oklahoma, Kentucky and Arkansas. I excluded Maryland, Delaware and Missouri because I don't think these can be considered culturally Southern, especially the first two. In any case, first, scatterplots and loess best fit lines for the South & the non-South. The South is red/black, the non-South is blue/green.

For me the interesting point is that the "upturn" where the % for Obama increases is notable in the South, but not the non-South. That surprised me. What counties are these? Click for the larger image.


Some of the counties are not surprising in terms of being above the trendline, such as the "Research Triangle" region of North Carolina. But Elliott County, Kentucky? Who knew that this was the second-whitest county in the country to vote for Barack Obama. A map illustrating the trendline might be interesting. Blue is above the trendline, red below the trendline. I limited the data to the South here. Click for the larger image.

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Friday, August 14, 2009

Sleep genetics   posted by p-ter @ 8/14/2009 06:21:00 PM

A remarkable study published in Science this week identifies a rare mutation in the gene DEC2 which influences the duration of sleep in humans. The authors started with a family where patterns of short sleep (about 6 hours of sleep a night on non-workdays, versus ~8 hours for other people in the family) seemed to follow a Mendelian inheritance pattern. In a candidate gene resequencing study, they identified a mutation in all of two people--a mother and daughter--with the short sleep pattern.

In what can only be described as a ballsy move, the authors then invested what must have been a considerable amount of time and money on following up this mutation. Which, I emphasize again, was found in only two individuals in a single family. In particular, they generated mice carrying both of the human versions of the gene, and were thus able to explicitly compare the two human alleles in an animal model. (This is in contrast to most mouse studies, which completely remove a gene or dramatically up-regulate it). Not wishing to show any mammalian bias, they did the same thing in flies. In all cases, the results were consistent with the human data--the low-sleep allele led to increased activity in both species.

Out of curiosity, is 6 hours of sleep (without an alarm clock) really all that odd for people? It certainly would be for me, but I feel like I know plenty of people who claim to naturally need only about that much.


Wednesday, August 12, 2009

Before the apple   posted by Razib @ 8/12/2009 05:08:00 PM

To those with more accrued years of wisdom, or a greater knowledge of intellectual history, what was social science like in the pre-computer era? E. O. Wilson once commented on Charlie Rose's show that social science hasn't discovered anything of note (I know Robin Hanson disagrees). Has the introduction of computation changed much?


Where the Whiter Folk Are   posted by Razib @ 8/12/2009 02:00:00 AM

Today I combined some Census data with 2008 election results (thanks Cosma). Though Barack Obama won the vote last fall, he lost the Non-Hispanic white vote. It stands to reason then that the whiter and less Hispanic a county is, the more likely it would be to tilt McCain. I was curious as to geographic variation within this general rule-of-thumb. So I plotted the % who voted for Obama in a county vs. the % who were Non-Hispanic whites (according to the 2000 Census*). I then generated a line of best fit via loess, and used the deviations from the trend to generate a map shaded proportionately. In other words, the bluer a county is the more it voted for Obama above expectation based on the overall relationship of the % white Non-Hispanic within a county and vote for Obama (the converse for red naturally). Again, click the map for the larger image.



I also decided to constrain the data set to those counties which were at minimum 80% Non-Hispanic white. Mostly because the "Black Belt" counties are showing up on the above map.


Finally, a shaded map of the results.


1) Don't mess with Texas Obama. Despite Obama winning the Hispanic counties in the South, those counties are always underperforming relative to other majority-minority districts. Since some of those counties are 90% Hispanic it probably isn't just Non-Hispanic white swing in the other direction.

2) Though Obama lost much of the rural North and East, he overperformed when you use the whole nation as a reference point, in particular rural areas in the West and South.

3) Pennsylvania kind of does look like Pittsburgh + Philadelphia, with Alabama in the middle.

4) Obama did well in Greater New England. Less well in the Butternut Region of the southern Midwest settled from the South.

Here are a list of the 200 counties furthest from the trendlines. The first 100 are the most pro-Obama above expectation when the predictor is Non-Hispanic white %. The last 100 the most pro-McCain.

Deviation From Trend Line % For Obama County & State
0.4 0.78 Marin, California
0.39 0.77 Multnomah, Imbler
0.38 0.78 Santa Cruz, California
0.38 0.77 San Miguel, Colorado
0.36 0.74 Sonoma, California
0.36 0.75 Dukes, Massachusetts
0.35 0.75 Berkshire, Massachusetts
0.35 0.74 Pitkin, Colorado
0.34 0.73 Dane, Wisconsin
0.34 0.72 Orange, North Carolina
0.34 0.72 Boulder, Colorado
0.33 0.73 Windham, Vermont
0.33 0.73 Franklin, Massachusetts
0.33 0.72 Hampshire, Massachusetts
0.32 0.7 Washtenaw, Michigan
0.32 0.7 Mendocino, California
0.32 0.7 King, Washington
0.31 0.71 Lamoille, Vermont
0.31 0.84 San Francisco, California
0.31 0.7 New Castle, Delaware
0.31 0.7 Johnson, Iowa
0.31 0.69 Tompkins, New York
0.3 0.7 Washington, Vermont
0.3 0.7 San Juan, Washington
0.3 0.69 Imbler, Wisconsin
0.3 0.77 Suffolk, Massachusetts
0.3 0.83 Philadelphia, Pennsylvania
0.3 0.72 Arlington, Virginia
0.3 0.69 Windsor, Vermont
0.29 0.69 Addison, Vermont
0.29 0.69 Silver Bow, Montana
0.29 0.68 Nantucket, Massachusetts
0.29 0.72 Montgomery, Maryland
0.29 0.69 Cuyahoga, Ohio
0.28 0.68 Chittenden, Vermont
0.28 0.66 Ingham, Michigan
0.28 0.66 Ramsey, Minnesota
0.28 0.75 Denver, Colorado
0.28 0.67 Iowa, Wisconsin
0.28 0.67 Camden, New Jersey
0.27 0.67 Deer Lodge, Montana
0.27 0.66 Summit, Colorado
0.27 0.66 Blaine, Idaho
0.27 0.65 Lucas, Ohio
0.27 0.65 Genesee, Michigan
0.27 0.65 Hartford, Connecticut
0.27 0.66 Monroe, Indiana
0.27 0.66 Jefferson, Washington
0.27 0.66 Bennington, Vermont
0.26 0.66 Athens, Ohio
0.26 0.76 Durham, North Carolina
0.26 0.66 Douglas, Wisconsin
0.26 0.68 Milwaukee, Wisconsin
0.26 0.67 Mercer, New Jersey
0.26 0.65 Benton, Oregon
0.26 0.76 Cook, Illinois
0.26 0.64 Hennepin, Minnesota
0.26 0.64 Muskegon, Michigan
0.26 0.65 Napa, California
0.26 0.64 Middlesex, Massachusetts
0.26 0.64 Douglas, Kansas
0.26 0.77 Santa Fe, New Mexico
0.26 0.74 Wayne, Michigan
0.26 0.65 Orange, Vermont
0.26 0.74 San Mateo, California
0.25 0.65 St. Louis, Minnesota
0.25 0.64 Hood River, Oregon
0.25 0.63 Humboldt, California
0.25 0.63 Albany, New York
0.25 0.64 Bayfield, Wisconsin
0.25 0.64 Marion, Indiana
0.25 0.64 Rock, Wisconsin
0.25 0.67 Lake, Indiana
0.25 0.79 Alameda, California
0.24 0.64 Cumberland, Maine
0.24 0.68 Contra Costa, California
0.24 0.83 Clayton, Georgia
0.24 0.62 Mahoning, Ohio
0.24 0.62 Rock Island, Illinois
0.24 0.62 Hampden, Massachusetts
0.24 0.63 Lane, Oregon
0.24 0.63 Trempealeau, Wisconsin
0.24 0.63 Carlton, Minnesota
0.24 0.63 Cheshire, New Hampshire
0.24 0.63 Grand Isle, Vermont
0.23 0.63 Crawford, Wisconsin
0.23 0.63 Orleans, Vermont
0.23 0.63 Gunnison, Colorado
0.23 0.63 Lackawanna, Pennsylvania
0.23 0.63 Grafton, New Hampshire
0.23 0.63 Portage, Wisconsin
0.23 0.63 Routt, Colorado
0.23 0.67 Broward, Florida
0.23 0.65 Clarke, Georgia
0.23 0.62 Palm Beach, Florida
0.23 0.61 New Haven, Connecticut
0.23 0.61 Eagle, Colorado
0.23 0.62 Howard, Iowa
0.23 0.62 Jackson, Iowa
0.23 0.62 Green, Wisconsin

-0.22 0.26 Ector, Texas
-0.22 0.18 Kiowa, Kansas
-0.22 0.18 Sioux, Iowa
-0.22 0.18 Piute, Utah
-0.22 0.18 Cleburne, Alabama
-0.22 0.18 Brantley, Georgia
-0.22 0.18 Campbell, Wyoming
-0.22 0.24 Upton, Texas
-0.22 0.27 Seward, Kansas
-0.22 0.16 Wichita, Kansas
-0.22 0.25 Ward, Texas
-0.22 0.17 Donley, Texas
-0.22 0.16 Morton, Kansas
-0.22 0.17 Alfalfa, Oklahoma
-0.22 0.17 Holmes, Florida
-0.22 0.17 Rock, Nebraska
-0.22 0.17 Leslie, Kentucky
-0.22 0.24 Winkler, Texas
-0.22 0.17 Box Elder, Utah
-0.22 0.17 Hooker, Nebraska
-0.22 0.16 Jack, Texas
-0.22 0.17 Crook, Wyoming
-0.22 0.17 Morgan, Utah
-0.23 0.17 Bear Lake, Idaho
-0.23 0.17 Cullman, Alabama
-0.23 0.17 Archer, Texas
-0.23 0.17 Caribou, Idaho
-0.23 0.17 Sevier, Utah
-0.23 0.16 Kingfisher, Oklahoma
-0.23 0.15 Hutchinson, Texas
-0.23 0.37 Pecos, Texas
-0.23 0.16 Jefferson, Idaho
-0.23 0.16 George, Mississippi
-0.23 0.16 Duchesne, Utah
-0.23 0.16 Sterling, Texas
-0.23 0.16 Millard, Utah
-0.23 0.16 Carter, Montana
-0.23 0.16 Roger Mills, Oklahoma
-0.23 0.16 Dewey, Oklahoma
-0.23 0.21 Garza, Texas
-0.24 0.16 Banks, Georgia
-0.24 0.16 Sioux, Nebraska
-0.24 0.16 Dawson, Georgia
-0.24 0.16 Logan, Kansas
-0.24 0.16 Cameron, Louisiana
-0.24 0.16 Haakon, South Dakota
-0.24 0.17 Clark, Idaho
-0.24 0.14 Gray, Texas
-0.24 0.14 Hemphill, Texas
-0.24 0.14 Wheeler, Texas
-0.24 0.15 Garfield, Montana
-0.24 0.15 Loving, Texas
-0.24 0.15 Glascock, Georgia
-0.24 0.15 Rich, Utah
-0.24 0.15 McPherson, Nebraska
-0.25 0.27 Hale, Texas
-0.25 0.15 Blount, Alabama
-0.25 0.15 Hayes, Nebraska
-0.25 0.14 Uintah, Utah
-0.25 0.15 Scott, Kansas
-0.25 0.15 Arthur, Nebraska
-0.25 0.15 Ellis, Oklahoma
-0.25 0.15 Major, Oklahoma
-0.25 0.14 Sherman, Texas
-0.25 0.15 Banner, Nebraska
-0.25 0.15 Texas, Oklahoma
-0.25 0.13 Hartley, Texas
-0.25 0.13 Stevens, Kansas
-0.25 0.22 Crane, Texas
-0.25 0.14 Blaine, Nebraska
-0.25 0.14 Jackson, Kentucky
-0.25 0.14 Carson, Texas
-0.25 0.28 Dawson, Texas
-0.25 0.14 Shackelford, Texas
-0.26 0.14 Harper, Oklahoma
-0.26 0.12 Lipscomb, Texas
-0.26 0.12 Cimarron, Oklahoma
-0.26 0.24 Sutton, Texas
-0.26 0.16 Gaines, Texas
-0.26 0.13 Thomas, Nebraska
-0.26 0.18 Martin, Texas
-0.27 0.13 Armstrong, Texas
-0.27 0.13 Livingston, Louisiana
-0.27 0.11 Motley, Texas
-0.27 0.11 Oldham, Texas
-0.27 0.21 Moore, Texas
-0.27 0.11 Borden, Texas
-0.28 0.12 Wallace, Kansas
-0.28 0.17 Andrews, Texas
-0.28 0.12 Franklin, Idaho
-0.28 0.12 Madison, Idaho
-0.28 0.11 Beaver, Oklahoma
-0.28 0.11 Grant, Nebraska
-0.29 0.11 Hansford, Texas
-0.29 0.26 Deaf Smith, Texas
-0.3 0.19 Parmer, Texas
-0.3 0.09 Glasscock, Texas
-0.31 0.2 Reagan, Texas
-0.32 0.08 Roberts, Texas
-0.32 0.08 Ochiltree, Texas
-0.34 0.05 King, Texas

* This is 8 years out of date, but by far the most complete and precise data set until the 2010 Census.


Tuesday, August 11, 2009

Autistic like We   posted by Razib @ 8/11/2009 09:53:00 AM

Tyler Cowen and Will Wilkinson in discussed Tyler's most recent book, Create Your Own Economy, in a recent Tyler mentions how he believes there are a diversity of "cognitive profiles" out there, and that the autism spectrum oversimplifies and pathologizes one aspect of this reality. One feature of the modal human cognitive profile which Tyler seems to suggest might be somewhat suboptimal for information processing and gathering is the tendency to construct stories or narratives (because of the distortions that a general story arc might introduce into one's perception of the facts). What struck me was a personal datum which I've never thought too deeply about until now: I never read fiction outside of assigned schoolwork until I was 13. The only exception to this was Greek mythology (e.g., The Iliad). Of course I did read a lot, but it was all non-fiction. In later years I came to understand that this was atypical. When I did start reading fiction almost all of it was science fiction, fantasy or historical fiction. To this day I have a very attenuated interest in conventional mainstream fiction. I suspect a large number of readers of this weblog can recount similar experiences.

One point of Will & Tyler's diavlog which I might want to take issue with is the idea that specialization is a net benefit for most of humanity because they can find the particular occupational niche which leverages their strengths and satisfies their preferences. To some extent this is surely true, but to not put a too fine point on it I think the cost vs. benefit toward specialization is much greater for those on the "tails" of the cognitive spectrums; whether nerdy or arty. For a modal human who is more focused on concrete interpersonal dynamics I suspect "clocking in & out" at their job might not be unsatisfying since work is simply the time between socialization.


Census confirms Mormons have many children   posted by Razib @ 8/11/2009 12:35:00 AM

I've been poking around the Census data sets for a few days now. I want to merge them with the longevity stuff soon, but while was at it I decided to check to see how variation in geography related to variation in fertility. You can go to the GSS and see all sorts of national trends, but I thought a county-by-county view would be of interest. Click the images for bigger versions. The fertility is defined as "women with births in the past 12 months; rate per 1,000 women." Coming out of the American Community Survey. All the data are for Non-Hispanic white women.

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Monday, August 10, 2009

Heather Mac Donald on The Evolution of God   posted by Razib @ 8/10/2009 12:35:00 PM

Heather Mac Donald reviews Robert Wright's The Evolution of God.

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Sunday, August 09, 2009

Less house for your money....   posted by Razib @ 8/09/2009 12:24:00 AM

One of the problems with the maps I've been generating is that when one looks at income one has to take into account cost of living. Unfortunately I'm only finding state-level maps, not county-level ones. I'm sure there're out there, but the US Census has a lot of data files handy if you are persistent and know where to look, so I'm going to poke around and do my own calculations. The Census has home values for 2005-2007, the peak bubble years, as well as median household income for the early 2000s. Naturally one expects the housing value and income to track each other. That is, areas with higher median incomes should probably have higher median home values. But, some areas will have lower incomes vis-a-vis the value of the housing stock, and others higher. Below is a scatterplot which shows median home value vs. median household income (log-transformed). The outlier is New York county, Manhattan.

Since Manhattan is such an outlier I dropped it out of the data set, and did what I did previously, I calculated the deviation from the trendline of each point, above and below. Those counties above the trendline exhibited greater housing values in relation to median income, while those below were the inverse. The map below is shaded blue for those above the trendline, and red for those below. Shading is proportional to deviation from the trendline.

Things that jump out at me:

1) 2-4 years ago the Washington D.C. area seemed to have relatively affordable housing stock in relation to median income.

2) The West coast did not. Urban areas such as New York or Boston exhibited a decoupling between income and home values, but much of their hinterland remained relatively affordable. The same does not apply to the West.

3) The "resort counties" in the Intermontane West are not a surprise.

4) Interestingly, unlike the Northeast the South seems to be characterized by large metropolitan areas such as Atlana, Houston and Dallas remaining affordable, while the hinterlands are not nearly as underpriced as one might expect. I think the issue here is simply very low income in the rural South, so that any upward pressure on home values is not matched by increased wages.

Bottom 10 below trendline
Loudoun, Virginia -$136661.4
Fort Bend, Texas -$116864.8
Goochland, Virginia -$116020.9
Prince William, Virginia -$115841.1
Stafford, Virginia -$109999.9
Calvert, Maryland -$109217.2
Campbell, Wyoming -$109136.2
Powhatan, Virginia -$106159.3
Howard, Maryland -$105386.7
King George, Virginia -$100267.0

Top 10 above trendline
Summit, Colorado $128227.5
Blaine, Idaho $129168.4
Santa Barbara, California $134643.1
Eagle, Colorado $171239.4
Teton, Wyoming $181064.5
Santa Clara, California $190223.8
Santa Cruz, California $195552.2
San Francisco, California $206232.6
San Mateo, California $218667.7
Marin, California $255949.7

If I put New York county back into the data, it is $822057.7 above the trendline.

Saturday, August 08, 2009

Genome sequencing shop talk   posted by p-ter @ 8/08/2009 10:43:00 AM

There's a nice post over at Genetic Future getting into the details of a recent paper using ABI SOLiD to resequence a human genome. The comments are quite instructive as well. For those not dealing with these sorts of technologies regularly, it can all seem a bit incomprehensible, but the outcome of these sorts of debates will determine who dominates the sequencing business for the next few years...


Friday, August 07, 2009

The genome, more than coding   posted by Razib @ 8/07/2009 06:12:00 PM

Evolutionary Processes Acting on Candidate cis-Regulatory Regions in Humans Inferred from Patterns of Polymorphism and Divergence. Let me just jump to the final paragraph since that's probably what most readers are curious about:
Our analysis of human polymorphism and divergence in conserved non-coding sites suggests that the evolution of candidate cis-regulatory regions is often driven by both positive and negative selection. Our findings reinforce the idea that the non-coding portion of our genome has an important functional and evolutionary role, and suggest that patterns of natural selection in non-coding DNA are often distinct from that of protein-coding regions. Many of the adaptive changes in candidate cis-regulatory regions might have occurred near genes expressed in the fetal brain, supporting the hypothesis that the evolution of the developing brain may be largely attributable to changes in gene regulation. Our results add to the increasing evidence that non-coding DNA is not all selectively neutral, and that selection on candidate cis-regulatory regions has played an important role throughout hominid evolution.

Gene regulation has of course been one possible solution to how humans can be so phenotypically different from chimpanzees despite close sequence level identity.

Related: Dissecting the regulatory differences between human and chimp.

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Religion & sex   posted by Razib @ 8/07/2009 12:38:00 PM

It seems looking at the GSS that:

1) The more secularized a population segment is, the bigger the sex difference in beliefs. This is in keeping with Bryan Caplan's thesis that males become more secular once social and institutional pressures are relaxed to a greater extent than females.

2) Among the segment of the population which is rather religious to begin with (which includes more women than men) males & females are in accord in terms of beliefs.


Thursday, August 06, 2009

Bill James' silence   posted by Razib @ 8/06/2009 07:09:00 PM

Steve has the details. I haven't followed baseball in a long time, and I never did follow it closely, but I remember not be able to align the Sammy Sosa of the White Sox years with that of 1998. If it weren't for drugs would Ken Griffey Jr. have been a much bigger deal in the 1990s and 2000s?


Tuesday, August 04, 2009

The neuroscience of psychopathy   posted by Razib @ 8/04/2009 09:15:00 PM

Altered connections on the road to psychopathy:
... Earlier studies suggested that dysfunction of the amygdala and/or orbitofrontal cortex (OFC) may underpin psychopathy. Nobody, however, has ever studied the white matter connections (such as the uncinate fasciculus (UF)) linking these structures in psychopaths. Therefore, we used in vivo diffusion tensor magnetic resonance imaging (DT-MRI) tractography to analyse the microstructural integrity of the UF in psychopaths (defined by a Psychopathy Checklist Revised (PCL-R) score of 25) with convictions that included attempted murder, manslaughter, multiple rape with strangulation and false imprisonment. We report significantly reduced fractional anisotropy (FA) (P<0.003), an indirect measure of microstructural integrity, in the UF of psychopaths compared with age- and IQ-matched controls. We also found, within psychopaths, a correlation between measures of antisocial behaviour and anatomical differences in the UF. To confirm that these findings were specific to the limbic amygdala–OFC network, we also studied two 'non-limbic' control tracts connecting the posterior visual and auditory areas to the amygdala and the OFC, and found no significant between-group differences. Lastly, to determine that our findings in UF could not be totally explained by non-specific confounds, we carried out a post hoc comparison with a psychiatric control group with a past history of drug abuse and institutionalization. Our findings remained significant. Taken together, these results suggest that abnormalities in a specific amygdala–OFC limbic network underpin the neurobiological basis of psychopathy.

I'm a little skeptical about psychiatry's ability to diagnose distinctive phenotypes in general, but from what I have read genuinely amoral psychopaths are a real phenomenon, and not a politicized constructed pathology. Readers with more neuroscience chops are invited to weight in if this another sexy neuro paper with little substance. Also see ScienceDaily.

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What does the decline in homicide rates look like?   posted by agnostic @ 8/04/2009 08:40:00 PM

Steve points us to a brief review by Steven Pinker on the decline in war and violence. Focusing just on homicide rates, what exactly does that mean -- a decline in violence during modern times? It is impossible to have a solid feel for the observation Pinker wants to explain without seeing time series data on homicide rates (one of which he includes in his TED talk on the same subject). The pictures come from Manuel Eisner's review article in the British Journal of Criminology.

This is required reading (only 20 pages) for anyone who wants to understand crime, and especially changes in crime -- changes in the overall rate, differences across regions in the decline, differences in the decline across social classes, etc. If you don't have access to it, it's one of those rare articles that is worth the one-time price of $28 -- or just request it from one of your friends or colleagues who does have university access.

Below the fold, I've included the pictures for all countries that Eisner found data for, along with a brief remark on the trend for each country. The vertical axis is homicides per 100,000 population and is on a logarithmic scale (so that the visible changes are by orders of magnitude). Also note that the recent decline in crime since the early-mid 1990s may not be easily visible in these pictures, given that Eisner's article came out in 2001 -- not very long for the reversal to jump out of the graphs.

First, England:

Increases during the High Middle Ages, decreases sometime starting in the Late Middle Ages or Early Modern period.

Netherlands and Belgium:

Decreases starting in Early Modern period.


Decreases starts as late as the 17th C -- Scandinavia being one of the last parts of Western Europe to become civilized.


Apparent increase during High Middle Ages, decreases starting in Late Middle Ages or Early Modern period.


Barely visible change during 18th C, while steady decline only starts in 19th C -- Italy having lacked a strong central state until then. Article says that Northern Italy shows a much earlier decline than Southern Italy (no surprise).

Also notice the presence of cycles about the overall trend. Just because there were recurring crime waves and abatements of crime waves during the 19th and 20th centuries -- see here for the US, or see the Scandinavian graph above -- should not distract us from the clear downward trend going only a few centuries farther back. Any account of rises or declines must deal with all of these patterns, making it impossible to generalize the narrow hypotheses for the 1990s decline in crime -- there were no cell phones before then, the trend since 1500 has been toward less corporal punishment and harsh sentencing rather than more, and so on.

What we would do is write down a system of differential equations that claimed how two or more groups of people interacted with each other -- say, "criminals," "law-abiders," and "police" -- and fool around with them until they produced a solution that would show cycles or oscillations around an overall downward trend. The interactions between these groups of people are what real historical causes are made of -- not the sudden introduction of some technology or law (or sudden disappearance of some technology or repealing of a law).

I'm up for a math modeling jam session if anyone else is. I remember seeing ODE models from ecology where one species replaces another, although the values oscillate around the upward trend of the winner, as well as around the downward trend of the loser.

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Monday, August 03, 2009

Whence Canis familiaris?   posted by p-ter @ 8/03/2009 09:20:00 PM

The NY Times reports on a new paper calling into question the theory that the dog was first domesticated in East Asia.

The evidence for an East Asian origin of dogs came from a study of mitochondrial DNA, which showed that dog populations in East Asia harbored more diversity than their counterparts in other parts of the world (the reasoning is that more diverse populations are likely to be the origin of a species; populations which split off and move about will be less diverse). The authors of the new paper, however, point out that this study included more semi-wild "village dogs" from East Asia than from other parts of the world, and that these village dogs tend to be more diverse than purebreds from the same part of the world.

When African village dogs are included in the analysis, the East Asian dogs no longer stand out as extremely diverse (see right; the fitted line is what would be expected is diversity were equal in all places). Though this places the East Asian origin hypothesis in serious doubt, for now the authors--having only sampled African dogs (Africa does not have the wolf from which dogs are thought to have been domesticated)--do not present an alternative. As more data is collected from dogs around the world, this state of affairs in unlikely to last.


New blog: Black IQ and climate, rethinking the decline in formality, and changes in arts appreciation   posted by agnostic @ 8/03/2009 02:13:00 AM

Those are the first three articles that I've posted to a new blog of mine, Patterns in science and culture, where all of my data-rich posts will go from now on. I'll still review existing work or throw out "what if?" posts here, but if it requires looking up and analyzing data, you'll only be able to read about it there. These are the longer, original, buzz-starting ones I usually put up here or at my personal blog. The only change is that now the data-driven ones will be for-purchase. (If it takes a lot to put together, I can't do it for free.) For $10, you'll get access to 20 "feature-length" articles -- ones that require a decent amount of investigation, labor, or ingenuity -- plus all of the shorter ones that strike my fancy or that you request. They will be put up roughly once or twice a week. After the first 20 are done, I'll start another site will 20 more, and so on. Purchase info is at the bottom of the full entry.

The first three are already up:

1) Climate and civilization among Blacks, where I look at how climate affects IQ, imprisonment rates, and college degree-earning rates among Blacks, using state-level data. This is a follow-up to a similar post I wrote about Whites.

2) Was there a decline in formality during the 20th C? Here, I look at data on changes in naming preferences that question the widespread view that we've "become less formal."

3) Are the arts in decline? I've dug up annual data on theater attendance and the number of playing weeks for both Broadway and road shows from 1955 to 2006. I discuss the overall trend, the notable departures from the trend, and how in-synch or out-of-synch the Broadway and road show data have been over time.

Upcoming articles will include a look at turnover rates in Billboard #1 songs as far back as the various charts go -- when has there been rapid turnover, and when has there been stagnation, and do these accord with what we think is good or bad music? I've also put together a series of graphs that show quite striking generational changes in the popularity of getting a driver's license among teenagers of different ages. I also plan to round out a series where I looked at the elite vs. popular valuation of painters and of composers, using Charles Murray's Human Accomplishment and sales data. Next I'll look at literary figures. As usual, I will put the data into a larger picture (or story).

Just as a reminder for older readers, or as further examples of what I've done for newer readers, here's a brief selection of original work I've done:

The death of silly academic theories such as Marxism, psychoanalysis, and even postmodernism, using JSTOR archives. This story was picked up by the Toronto Globe and Mail, Arts and Letters Daily, and a few others I'm forgetting. (Here's a follow-up.)

How different social classes react to adolescent sex
, using the GSS, and proposing a life history account of these differences.

Debunking a study on the supposed hindering effect that feminine names have on women's progress in the sciences. To this day, the study has not been published, and I can only hope that we were part of that (cyber peer review).

How much different generations enjoy various music genres, using the GSS. This provides pretty clear data that you imprint on the popular music from when you were about 15 and stay that way for the rest of your life.

How the American diet has changed over the 20th C., using pretty fine-grained data such as red meat, fish, poultry, etc., rather than just "meat." There's also data showing that heart disease and obesity has only gotten worse as we've switched to a more carboholic diet since the 1970s.

How the blondness of Playboy Playmates has changed over time, as well as some speculation about why it changes the way it does.

The stagnating pace of revolutionary technological innovation, linking it to the decline in monopolistic bodies like AT&T's Bell Labs or the Defense Department.

Purchase info

Although blogging doesn't eat up a lot of time, the more data-intensive posts do. This is not something that most bloggers do -- most are linkers or gasbags, some very entertaining and others very boring. But I actually do a bit of investigation, find clever ways to attack a question, provide data, and put it into an easy-to-read visual. Not everyone will agree with my interpretation, but at least I've done lots of homework that others will benefit from, and that's something you find at very few places on the internet, especially if it's a new finding. But these more exciting posts take time away from earning money, so I'm asking fifty cents per long article, with all the briefer data-containing posts thrown in free.

The new blog is by invitation only, so you're simply paying to be put on the list of allowed readers. There is a PayPal button at the end of this entry. You will need a PayPal account, and a Google account -- they're free, and you just provide them with an email address. When you pay, leave me a message via PayPal with the email address associated with your Google account. I need this to invite you to the blog. If you don't say so, I'll assume it's the one attached to your PayPal account. If you forget to mention it, you can always send me a correction through your PayPal account.

Once I invite you, you'll get an email that has a "join this blog" link that you click on. And with that, you're all set. You will need to be signed into your Google account, but you can stay signed in forever.

I expect that most purchasers will not be trolls or flamers -- they want to harass people for free -- but if you exhibit classical spammer behavior, you'll be kicked out with no refund. It just takes a couple people like that to ruin a site, so I'll be strict about that.

If you have any questions, feel free to leave a comment here or email me at icanfeelmyheartbeat at the hotmail-ish site.

Sunday, August 02, 2009

Sperm Function   posted by DavidB @ 8/02/2009 03:14:00 PM

This research report suggests that some genes in human sperms can be 'read' by the cytoplasm of the egg immediately after fertilisation. Some interesting implications for hybridism, infertility, and other issues.

Male life expectancy, the story of region & income   posted by Razib @ 8/02/2009 12:54:00 PM

My post below alluded to the fact that there seems to be a non-trivial between region difference in male life expectancy, even controlling for race, in the United States. From what I can tell Americans seem to have a somewhat schizophrenic attitude toward the reality of regionalism. On the one hand we are a relatively mobile people, and the original social-political aspect of states has been superseded by states as simply arbitrary sub-national units. And yet regional identities are still alive, most notably in the case of Southerners (with Texas as perhaps a special particular case even in the South, along with other areas such as Cajun Country). The differences are obvious in the case of accent and dialect, but one might think of these as simply indicators of a host of implicit underlying variables which are often imperceptible until one takes oneself "out of region." In Albion's Seed David Hackett Fisher explored the possible cultural roots of American regionalism as a work of history, while in The Nine Nations of North America Joel Garreau treated the subject in the manner of contemporary human geography.

These works paint with a broad brush, and explore the variation on a relatively coarse scale. Most Americans are aware of local religionalisms to a far greater level of detail, something which they are often not explicitly cognizant of. As a personal example I spent my adolescence in an area of the Intermontane West where both Mormons and "cowboys" were well represented. Though both groups were politically conservative, culturally there were stark differences which everyone was implicitly aware of. It was only later on that I learned that this region had experienced an influx of people from the Upper South in the 19th century, and later "Okies", which was evident in the speech patterns of some individuals. On the other hand many of the Mormons had roots in Utah and eastern Idaho, and were cultural descendants of New England Yankees or later Northwest European converts who emigrated to Utah (the Mormon fixation on genealogy meant that if you had Mormon friends you would usually find out where their family was from through casual conversation since they knew). Last fall Steve Sailer pointed out that the counties where Barack Obama underperformed John Kerry, against the national trend, were those settled by and dominated by the Scots-Irish in the 18th century. Greg Cochran has told me that he was aware as a child the differences between Midwesterners whose origins were in the Upper South, and those who were Yankees.

Why does this matter? Because American public policy is often predicated on ceteris paribus assumptions once race and income are accounted for. Public policy prescriptions generated on the federal level will make the nod to race and class as interaction effects, but rarely allude to the possibility that white Americans even controlling for class may behave differently because of distinct cultural traditions. American regionalism is often conceived of as how you speak and what you eat, but I believe that these are simply the most obvious aspects of whole folkways, which are often assumptions and behaviors we take for granted.

But I come here not to talk, but to explore. The paper Eight Americas: Investigating Mortality Disparities across Races, Counties, and Race-Counties in the United States has the data for the white male longevity for each county in the United States. The Census has data on median household income, as well as the proportion of non-Hispanic whites in each county, or at least a subset. Unfortunately the tables I found had many counties missing for income and the proportion non-Hispanic white, so when I merged them with the one from the supplemental data from the paper above I was left with far fewer counties. I invite readers to point to better data sets in the comments than what I found poking through the Census website. There are certainly many likely variables which might explain longevity differences between regions, from climate to military service to participation in risky behaviors (the Mormon ban on alcohol probably means fewer men die of stupid acts at younger ages). But income is the primary predictor people think of, so it is what I focused on. Below are a set of charts and maps where I try and tease out regional variation. The x-axis is always median household income, while the y-axis is male life expectancy. Keep in mind that I filtered and constrained the data set in various ways when viewing the results, as my choices naturally have an effect. My point in presenting these results is to leverage reader knowledge about local variation. I am not interested in offering general explanations of why variation exists within the United States, rather, I am interested in outliers, and sharp local gradients. As the data was limited to counties which are at least 80% or more non-Hispanic white, there is a strong skew toward some regions, rural areas and less populous counties. This is not optimal, but I think it does the trick for this cursory examination.

All counties where non-Hispanic whites are 80% or more, male life expectancy vs. median household

All counties where non-Hispanic whites are 80% or more, male life expectancy vs. median household, labeled only with states

What I'm really interested in is the middle of the distribution, not the really rich or really poor counties. So I limited to incomes between $35,000 and $65,000 dollars. So the same as above, but now constrained as noted.

Focus on the outliers. What is going on in Baker County, Florida? Raw data is below, but I want to map these results above. Again these are the counties from the chart above (income between $35 and $65 K) shaded in proportion to the value of of the residual. In other words, a "dark" blue county is far deviated from the trendline by being above it, while a "dark" red county is deviated by being below it. Being above the trendline means that the county has a high life expectancy for its income, while below means it has one below what one would expect for income.

As I said above, there are constraints with these data. Some counties are missing from the source tables which I used, and only those counties present in all of the source datasets remain. Additionally, the map excludes very wealthy areas (parts of New England) and very poor ones (much of Appalachia), as well as those areas where less than 80% of the population is non-Hispanic white. The income data here surely exaggerations differences in real consumption; it isn't taking into account cost of living. But, I think the general insight from the earlier map remains: being close to Canada is good for a county's average life expectancy.

Here are the counties 2 or more years above the trendline:
FL - Charlotte 2.008085
ND - Ward 2.015647
SD - Lawrence 2.050383
MT - Gallatin 2.058849
ND - Cass 2.079347
WI - Marathon 2.112865
WA - Kittitas 2.146117
WI - Dunn 2.153582
MN - Steele 2.156426
IA - Bremer 2.200543
TX - Bandera 2.202348
MN - Stearns 2.262364
WA - Whatcom 2.280879
MN - Winona 2.289539
MN - Crow Wing 2.296179
ID - Kootenai 2.319326
WI - Wood 2.365409
NE - Madison 2.386554
MN - Martin 2.407487
MI - Emmet 2.418643
NY - Tompkins 2.437007
NY - Seneca 2.546057
PA - Union 2.568985
CO - Larimer 2.582040
NE - Buffalo 2.583082
IA - Henry 2.662992
MN - Freeborn 2.683949
MN - Mower 2.770022
KS - Douglas 2.811094
CO - La Plata 2.815263
WI - Eau Claire 2.821042
WI - Clark 2.920767
MN - Brown 2.980544
MN - Kandiyohi 3.064475
WA - Island 3.071250
IA - Mahaska 3.080397
UT - Iron 3.114267
WA - Jefferson 3.229158
PA - Centre 3.274080
IA - Winneshiek 3.305467
MI - Leelanau 3.378293
ID - Latah 3.605875
IA - Johnson 3.618503
OR - Polk 3.661479
MO - Nodaway 3.750706
IA - Story 3.761283
KS - Riley 3.812826
UT - Washington 3.857329
MN - Douglas 3.871383
SD - Brookings 3.893517
ID - Madison 4.116757
UT - Cache 4.261088
IA - Sioux 4.312095
OR - Benton 4.544464

And 2 or more years below:
FL - Baker -7.775926
AL - Walker -4.976348
AR - Greene -4.273662
MD - Cecil -3.862680
TX - Hardin -3.856310
TN - Carroll -3.577800
GA - Bartow -3.459386
IN - Starke -3.429478
WV - Berkeley -3.344611
GA - Jackson -3.282126
MS - George -3.254395
TN - Wilson -3.244293
AL - Chilton -3.208314
TX - Orange -3.199165
AL - Marshall -3.176659
OK - Garvin -3.107875
TN - Henry -3.006837
NC - Currituck -2.953442
WV - Jefferson -2.951280
GA - Walker -2.876994
VA - Warren -2.823080
AL - St. Clair -2.801636
TX - Fannin -2.779233
AR - Lonoke -2.673197
MS - Hancock -2.639797
FL - Nassau -2.636036
KY - Scott -2.605132
TN - Robertson -2.579745
GA - Murray -2.565466
TN - Lawrence -2.544601
TN - Maury -2.534866
MO - Jefferson -2.503979
TN - Dickson -2.490682
GA - Walton -2.475931
GA - Gordon -2.433042
MI - Osceola -2.378020
FL - Clay -2.370529
GA - Paulding -2.369467
TX - Wise -2.366306
IA - Marshall -2.331662
MS - Pearl River -2.283195
OK - Grady -2.256928
340 MO - St. Francois -2.224602
WY - Sweetwater -2.212283
IL - Lee -2.204632
AZ - Mohave -2.203554
TX - Van Zandt -2.147798
MI - Calhoun -2.143441
TN - Obion -2.138999
KY - Kenton -2.124380
WV - Kanawha -2.121422
OH - Madison -2.115574
IN - Dearborn -2.089985
GA - Oconee -2.077321
KY - Nelson -2.059997
TN - Rhea -2.056843
TN - Cheatham -2.053162
WV - Raleigh -2.006031

(all these are the counties between $35 and $65 K in median household income. The trendline was generated from this constrained sample as well)

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