Friday, October 31, 2008

An Updated Database of Genome-Wide Association Studies   posted by ben g @ 10/31/2008 10:48:00 PM

While reading through a Nature Genetics Review article, I came cross a link to this catalog of published genome-wide association studies. Pretty cool stuff.


Statistics and religious trends   posted by Razib @ 10/31/2008 09:59:00 AM

I have a piece up for The Guardian's new Comment is Free Belief site, The use and abuse of statistics - Prophecies of the extinction of religion, or its triumph, fall prey to the weaknesses of linear prediction. Implicit in my argument are these sorts of dynamics:
Bearman and Bruckner have also identified a peculiar dilemma: in some schools, if too many teens pledge, the effort basically collapses. Pledgers apparently gather strength from the sense that they are an embattled minority; once their numbers exceed thirty per cent, and proclaimed chastity becomes the norm, that special identity is lost....

fvl6wy.jpgThis is in regards to virginity, but the insight is generalizable. You don't have to know anything about dynamics though, just read a cultural history of France since the Revolution and you'll see what I mean.

Thursday, October 30, 2008

Portfolio rollback   posted by Razib @ 10/30/2008 11:45:00 PM

Condé Nast Cuts Focus on 2 Magazines:
Through the first nine months of the year, ad pages in all United States magazines were down 9.5 percent from the same period in 2007. Most magazines produced by Condé Nast - including Vogue, GQ, Architectural Digest and Wired - have had much smaller declines, but they are also among the most expensive magazines to produce.

Portfolio, started last year amid much fanfare, is Condé Nast's first business magazine and its most expensive new project in years. Executives said the company was willing to lose more than $100 million on it.

I immediately thought of this, Can Si Newhouse Keep Condé Nast's Gloss Going?:

Some extravagances have been curtailed, but no one in the business disputes that Condé still spends far more money than its competitors. Magazine publishers and editors in chief haul in $400,000 to $2 million in salary and bonuses, current and former executives say, and many executives have clothing allowances in the high five figures.


Last July, Vanity Fair printed 20 different versions of its cover, a daisy chain of celebrity pairs shot over many months and on multiple continents by Ms. Leibovitz, a project that cost millions. It paid for itself, says the magazine’s editor, Mr. Carter, in increased newsstand sales and buzz.

Mr. Phillips, the investment banker, observed, "I would say if you look across their whole portfolio, Condé Nast does a better job of producing high-quality magazines than anybody else in the industry." But, he adds, "you really could spend a lot less money on those magazines without affecting quality."

I remember thinking at the time that when the bubble bursts they'll regret not running a more efficient operation. To some extent it seems like Advance treats its glossies like performance art as opposed to a business operation. Of course, S. I. Newhouse is nearly a 10 billionaire so I guess he can afford to be less orthodox than the typical billion-pinching mogul. At least The Big Money isn't going anywhere.

H/T Tyler.

Wednesday, October 29, 2008

Evolution and trustworthiness   posted by Razib @ 10/29/2008 11:20:00 PM

Evolution of trust and trustworthiness: social awareness favours personality differences (Open Access):
Interest in the evolution and maintenance of personality is burgeoning. Individuals of diverse animal species differ in their aggressiveness, fearfulness, sociability and activity. Strong trade-offs, mutation-selection balance, spatio-temporal fluctuations in selection, frequency dependence and good-genes mate choice are invoked to explain heritable personality variation, yet for continuous behavioural traits, it remains unclear which selective force is likely to maintain distinct polymorphisms. Using a model of trust and cooperation, we show how allowing individuals to monitor each other's cooperative tendencies, at a cost, can select for heritable polymorphisms in trustworthiness. This variation, in turn, favours costly 'social awareness' in some individuals. Feedback of this sort can explain the individual differences in trust and trustworthiness so often documented by economists in experimental public goods games across a range of cultures. Our work adds to growing evidence that evolutionary game theorists can no longer afford to ignore the importance of real world inter-individual variation in their models.

The fact that evolutionary psychology traditionally focuses on universal traits which are genetically fixed while behavior genetics is preconditioned on heritable variation of similar traitshas been a distinction which has been brought to light by skeptics of any biological component to human behavior. In The Undiscovered Mind John Horgan attempted to throw cold water on the rise of neuro and cognitive sciences precisely using this sort of tactic. Though I think many critics of evolutionary psychology argue in bad faith, at the end of the day some of their criticisms land on target because of the huge sample space of laugh-out-loud "theorizing" by scholars fixated on an outmoded paradigm.

Humans are not the same. We vary. And we vary in part because of heritable biological factors. Some evolutionary psychologists, Satoshi Kanazawa comes to mind, work under an old model where deviations from their expectation of human modal behavior is treated simply as trivial holdovers along the transient from the ancestral to the derived phenotype, or noise introduced by environmental factors. Because of he elegant simplicity of their model evolutionary psychologists of this school are expert verbal showmen.

Certainly there are plenty of human universals. But there are plenty of non-universals. We are familiar with the Red Queen hypothesis in relation to our immune systems. This model arose in large part because of the necessity for constant evolution in the forever war with parasites. If humans are a cultural animal par excellence for whom the flexibility of their behavioral toolkit is essential, should it surprise us if frequency dependent evolutionary dynamics result in a large number of morphs constantly cycling? Perhaps H. sapiens is the environment of evolutionary adaptedness of H. sapiens?

Related: Heritability of the Ultimatum Game, Altruism and Risk-Taking: Kinda Heritable and Variation as the ultimate.

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Who-whom?   posted by Razib @ 10/29/2008 10:45:00 PM

I'll yank this up from the comments:
...Would it really be worse to have a future civilization full of ultra-intelligent robotic minds pushing science forward tirelessly than the Jerry Springer-esque Idiocracy that we are careening towards?

So did anyone root for the AIs in The Galactic Center Saga? In the Dune universe there was an explicit emphasis on keeping tech relatively low because of the fear of Thinking Machines (though the post-Frank Herbert sequels did have a "happy ending" in the man vs. machine conflict). In the Foundation universe (specifically the sequels not written by Asimov) one element of the back story which emerged was that benevolent robots actually created diseases which made the average human less intelligent than they would have otherwise been because that was the only way that social equilibrium could be maintained (Hari Seldon was brilliant in part because he was never infected).

This is the sort of post which brings out a lot of opinions because it is explicitly designed to smoke out norms and values. Frankly, I think most of the human race would prefer the Idiocracy. The minority who would be more ambivalent, or even prefer the idea of intelligence which is not tied to our particular human substrate, are likely to be non-modal in their psychology. Additionally, the non-modals are more likely be in research positions where they could forward the project of post-human sentience. To be explicit, I wonder if post-human sentience would simply be the apotheosis of the Nerd. Movies like Twelve Monkeys play on the idea of a Doomsday Cult which releases a deadly pathogen which kills most humans, but what about the possibility of a group of social outcasts intent on giving rise to a species which better encapsulates the set of values which reflect the priorities of nerds?


Disease driven human evolution?   posted by Razib @ 10/29/2008 09:04:00 PM

Gene Expression Profiles during In Vivo Human Rhinovirus Infection (also, ScienceDaily summary):
Rhinovirus infection significantly alters the expression of many genes associated with the immune response, including chemokines and antivirals. The data obtained provide insights into the host response to rhinovirus infection and identify potential novel targets for further evaluation.

About those viruses:
Epidemiologists have established minimal population size and density thresholds for particular diseases (such as measels, mumps, rubella, smallpox, influenza, rhinovirus) to survive and spread. In small hunter-gatherer groups or even small farming villages, such diseases would have been incapable of spreading very far and woul have disappeared (Black 1975). This implies that many diseases must be recent.

There's a reason that some of the cites for the adaptive acceleration theory use microbial models; here are lot's of them and they breed fast. Microbiologists are fond of reminding people that on the order of 90% of the cells in your body are bacteria resident in your gut; but I wonder if the last 10,000 years might not have been a boon for a whole host of virulent less friendly microbes which "tag along" with H. sapiens.

Related: Toxoplasma gondii & human culture, Obesity germs, thrifty genes, Another Nobel for the New Germ Theory of disease and Toxoplasma gondii's South American origins and its influence on culture.

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Sunday, October 26, 2008

Which countries does the NYT cover most and least?   posted by agnostic @ 10/26/2008 09:16:00 PM

Greg Cochran left the following comment in a Matt Yglesias blog entry:

What you need is a map of the world in which the sizes of the countries are adjusted to the number of column-inches they get in the New York Times and the Washington Post. I think it would be illuminating.

Well, I've done something close enough. I only looked at the NYT, and I made a bubble chart instead of one of those distorted cartograms. Also, I used number of articles rather than column inches -- but these must correlate highly. It's not as if Tonga gets a few 10,000-word articles, while Iraq gets many 50-word articles. At any rate, let's see what the results look like.

Here are the results for the 192 members of the United Nations. Move the mouse over an unlabeled blob to see who it is, or search for a specific country. The results cover 2000 to the present, and are standardized by dividing by the number of articles for the entire period. To ensure that the graphing algorithm would pick up order-of-magnitude differences, I multiplied the fractions -- which ranged in order from 10^(-5) to 0.1 -- by 10^5, so that they range in order from 1 to 10,000. Some countries I had to estimate rather than get the exact number, since their names are shared with other things, like Turkey (see Note).

The first thing you notice is a few big blobs and lots of tiny blobs, in accord with a Power Law. Rather than futz around with getting my pictures to post here, I'll simply list the frequency distribution, where the first column is the fraction of all NYT articles devoted to some country, binned by order of magnitude:


The one country in the 0.1 bin is the US. Everyone else is lucky to get something on the order of a percent in coverage. Still, the modal country gets mentioned on the order of once every thousand articles -- not too shabby if you're Qatar. Here is the full dataset, in case you want to download and play around with it yourself.

How do we infer the level of insanity in our foreign policy implied by these data? Looking at the countries from greatest to least emphasis, the low-ranking ones make sense -- they belong to the parts of the world you've never heard of, and will not have reason to hear about within your lifetime, such as Tuvalu and Bhutan.

But there are some funny ones at the top. For example, it takes the top 9 to discover all 5 permanent members of the UN Security Council. The remainder of the top 9 are Germany and Japan -- which at least are G8 countries -- but also Iraq and Israel. Speaking of the G8, it takes the top 12 to discover them, which adds another lesser country to this elite list -- Mexico (China is not G8 but is still important). Afghanistan, Iran, and Pakistan also rank pretty high.

This is a perfectly rational outcome -- our foreign policy may obsess over these places, but by placing criteria on them like "permanent member of UN Security Council" or "member of G8," we can see which ones don't deserve the attention. They represent the parts of the world, like Iraq, where we're wasting a bunch of money to squat over an over-glorified sandbox, hoping that our colonial piss will transform it into a lush oasis. Or they're the places, like Mexico, where we're importing a large illiterate peasant underclass from. This seems like a useful way to change our foreign policy: see who we're obsessed with, but who don't really matter, and cut them loose (relatively speaking).

By the way, the Many Eyes website has a global map feature, but it only allows an additive scale for bubble size, with the three smallest orders-of-magnitude collapsed into one bubble-size. So it didn't look very good. Maybe at some point I'll screen-capture the bubble chart, and cut and paste each bubble onto a picture of a world map, but that probably won't happen.

Note: I used the common English names for countries -- e.g., Syria rather than Syrian Arab Republic -- and made the following modifications to make sure I picked up the country rather than something else by that name:

Chad: added "Africa" to search
Georgia: added "Tbilisi" -- probably an undercount, but not my much
Guinea: subtracted "Equatorial Guinea," "Guinea-Bissau," and things like "guinea pig"
Jordan: added "Israel" -- again, an undercount, but not by much
Palau: subtracted "Barcelona" and "Catalonia" (it means "palace" in Catalan)
Turkey: subtracted "Thanksgiving" -- probably an overcount, but not by much
United States: searched "America," and subtracted "Latin America," "South America," and "Central America"

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Some people better language learners?   posted by Razib @ 10/26/2008 05:23:00 PM

Well, I assume most people probably accept that some people are better than average at learning languages, while others are not as good. But the reasons for this aren't quite clear. PNAS has a paper out on this topic, Brain potentials to native phoneme discrimination reveal the origin of individual differences in learning the sounds of a second language. I find the ScienceDaily summary comprehensible, and one of the researchers says:
"Therefore, these results show that there is a positive correlation between specific speech discrimination abilities and the ability to learn a second language, which means that the individual ability to distinguish the specific phonemes of the language, both in the case of the mother tongue and in the case of other languages, is, without a doubt, a decisive factor in the learning process, and the ability to speak and master other languages," concludes Begona Diaz.


The post-human robot future   posted by Razib @ 10/26/2008 04:25:00 PM

I recently attended a talk by Marshall Brain. He made the argument that the shift toward intelligent robots in the labor force will result in a much higher degree of structural unemployment in our economy. Brain presented some economic data which showed that gains in productivity over the past 10 years have not yield median wage gains or maintained a demand for labor. There were some details where I thought Brain undercut his plausibility (e.g., he didn't seem to be using the most wildly accepted definition of a recession, instead simply focusing on the metric of full employment as the only worthwhile economic indicator). An irritated audience member asked him if he had heard about a discipline called history which suggests that these sorts of predictions never pan out.

Brain's response was that the difference between labor saving technology in the past and the emergence of intelligent robots is that the latter are a new species. In other words, the demand for labor may increase with an expanding economy, but intelligent robots will have incredible comparative advantages compared to humans for the new occupational opportunities. Additionally, while technology expands and leverages human abilities, opening up opportunities, intelligent robots with agency would not need the complement of particular human cognitive skills.

The empirical argument is based on the peculiarities of the recent past, so the historical argument looking back to the "industrial revolution" and its effect on economic growth and long term demand for labor and the impact on wages is compelling. In Farewell to Alms Greg Clark points out that in fact since the Great Divergence the rise of the mass consumer society has been enabled by enormous comparative and absolute gains of wealth accrued toward unskilled labor. Only since 1970 has this dynamic been somewhat reversed. But I think that one point to remember is that the pattern of 1800-1970 itself is a relatively short time window. Obviously a future where intelligent robots substitute for human labor and management is not analogous to a pre-modern agrarian economy caught in the Malthusian trap, but I think it is important to remember that refuting Brain's argument by an appeal to history itself relies on fixing a particular set of background conditions which themselves are relatively new.

All that being said, I can imagine intelligent robots replacing humans in a wide range of service, manufacturing and even professional jobs. Imagine for example a robot doctor who has immediate access to the total body of the latest research, but can intelligently weight these results appropriately so the swell of most recent likely false positives don't hold so much sway. There would be no worries that a robot doctor would not be able to engage in Bayesian logic. But does that mean there won't be roles for humans? Perhaps there are niches for human art and cultural production where robots might crave organic authenticity? After all, why couldn't there be Bobo robots who are willing to shell out extra for human-made products which exhibit the imprecise, irrational and wild creativity characteristic of the organic substrate mind? Humans would have an enormous advantage over robots in Outsider Art. One could spin many scenarios of this sort, as Brain's model seems to be predicated on the standard opposition between man and machine which goes back to the Luddites.

Finally, I wonder if a nation like Japan might not be well positioned if the rise of the machines does result in reduced demand for human labor. Japan's native labor force is shrinking. This sort of thing is generally considered to be bad, but if robots entered the labor force and increased total productivity greatly then the problem of an imbalance between a large retired class and a smaller labor force goes away. The remaining younger humans in the labor force could focus on jobs where humans have a shot; e.g., instead of the Salaryman the Freeter might be the modal human Japanese.


Friday, October 24, 2008

Increasing partisanship since the 1990s: more evidence   posted by agnostic @ 10/24/2008 02:56:00 AM

In the book Red State, Blue State, Rich State, Poor State (see Razib's review here and the book's blog here), the authors note that the two major political parties have become more polarized in various ways since the 1990s, even though the average voter hasn't changed much. Also, the key message of the book is that the red state - blue state culture war is mostly restricted to high-income, and to a lesser extent middle-income voters.

They searched some mainstream media outlets for the words "polarizing / polarization," as well as buzzwords for the cultural split like "NASCAR dad" and "soccer mom," and found that they either show up for the first time or increase during the early/mid-1990s and remain as high today. I've searched the NYT for "partisan," as well as a variety of newspapers for the pejorative "partisan hack," and they show the same pattern.

Here are the graphs:

For the first graph, I took the number of articles with "partisan" and standardized this by dividing by the number of articles with "the" -- basically, all articles. (The 2008 point is an estimate based on the year so far.) Aside from 1984, when there was a huge divide between the two presidential candidates, there is nearly no change from 1981 to 1991. However, in 1992, when the culture war begins to take center stage, the frequency increases to about twice as high as during the 1980s.

For the second graph, I did a Lexis-Nexis search for "partisan hack," a common culture war swear-word for what the other guy is. I included the 12 newspapers with the highest counts, and that covered most of the major papers as well as some lesser known ones (see full list below). Not being able to search the database for "the," I couldn't standardize these data, but they show the same pattern as above, so I doubt the year-to-year variation in total output explains it. Here is the total output per year for the NYT, for comparison. Again, the 2008 point is for the year so far.

Aside from a few jabs from The Imblerian in the early 1990s, the first time this phrase shows up is in 1994, and it spreads to an order of magnitude larger by the 2000s. Outside of newspapers, Lexis-Nexis returns a result from 1984 where a politician is quoted as calling another a partisan hack. So the term must have been invented before the 1990s, but surged during the culture war.

These data agree with the larger picture in the book: the topic of partisanship has become much more talked about since the 1990s, and the specific slander "partisan hack" has increased noticeably during the same time.

List of newspapers included in the Lexis-Nexis results: New York Times, Washington Post, Washington Times, Boston Globe, Arkansas Democrat-Gazette, The Star-Ledger, Richmond Times, Palm Beach Post, St. Petersburg Times, Pittsburgh Post-Gazette, Atlanta Journal-Constitution, and The Oregonian.

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Thursday, October 23, 2008

Notes on Sewall Wright: The Shifting Balance Theory - Part 1   posted by DavidB @ 10/23/2008 03:52:00 AM

Finally, Sewall Wright's Shifting Balance theory of evolution. This will positively, definitely, categorically be my last note on Sewall Wright. Unless I think of something else.

For convenience I will split the note into two parts, one dealing with the theory in its original form, and the second dealing with subsequent developments.

Two catch-phrases indissolubly linked with Sewall Wright are the adaptive landscape, and the shifting balance. In preparing my note on Wright's concept of the adaptive landscape I was surprised to discover that Wright himself seldom if ever used this expression. I could not find a single example. I was therefore half-expecting that I would not find any reference to the shifting balance either - and I would have been half-right. Wright did use that term, but not, as far as I can find, until surprisingly late in his long career....

All page references are to Evolution: Selected Papers unless otherwise stated. See the References for details.

The first mention of 'the shifting balance'

Wright refers extensively to the 'shifting balance theory' in Volume 3 of his treatise Evolution and the Genetics of Populations, published in 1977, but I have not found this term in the first two volumes (1968 and 1969), or in anything else published by Wright before 1970. Nor was it used by authors such as Dobzhansky, Mayr, and Simpson, when describing Wright's ideas. The earliest use of the term I have found is in Wright's article of 1970 on 'Random drift and the shifting balance theory of evolution'. Admittedly, I have not read all of his 200-odd papers published before that year, but unless anyone can unearth an earlier use I suggest that the term was in fact coined in this article of 1970, some 50 years into Wright's career. The terminology of a theory is less important than its substance, but the absence of the term 'shifting balance' before 1970 (if I am right about this) does have two implications: first, we should not expect other authors (such as Fisher and Haldane) to have commented on the 'shifting balance theory' as such, and second, in the absence of a single label, it may not have been perceived as a single unified theory at all.

Earlier terminology

The apparent absence of the phrase 'shifting balance' before 1970 does not mean that Wright had never previously used the terms 'balance' or 'shifting', sometimes in close proximity. Wright was fond of the term 'balance', and related terms such as 'equilibrium' or 'poise', and used them for a variety of purposes, sometimes with a precise mathematical meaning, and sometimes more loosely. Here are some examples, chronologically arranged:

1931: 'The conditions favorable to progressive evolution as a process of cumulative change are neither extreme mutation, extreme selection, extreme hybridization nor any other extreme, but rather a certain balance between conditions which make for genetic homogeneity and genetic heterogeneity' (96)

1931: 'Evolution as a process of cumulative change depends on a proper balance of the conditions which... make for genetic homogeneity and genetic heterogeneity of the species' (158)

1941: 'The most general conclusion that can be drawn from the attempt to develop a mathematical theory of the simultaneous effects of all statistical processes that affect the genetic composition of populations is that in general the most favorable conditions for evolutionary advance are found when these are balanced against each other in certain ways, rather than when any one completely dominates the situation' (488)

1951: 'The general qualitative conclusion would still seem to hold that this [the evolution of culture] or any other evolutionary process depends on a continuously shifting but never obliterated state of balance between factors of persistence and change, and that the most favourable condition for this occurs when there is a finely subdivided structure in which isolation and cross-communication are kept in proper balance' (596)

1959: 'It is concluded that the most favorable conditions are those of balance: a balance among the directed processes that insures the maintenance of a high degree of heterozygosis in minor factors and a balance between the directed processes as a group and various sorts of random ones that insures extensive random drift around the equilibrium positions of the gene frequencies. All these conditions are met in the highest degree where there is a certain balance between isolation and crossbreeding within each of a large number of local populations of the species' (Tax, 470-1)

1960: 'In developing the balance theory of evolution, I was trying to arrive at a judgement of the most favorable conditions for evolution under the Mendelian mechanism' (619)

It will be noted that in the last of these passages Wright refers to the 'balance theory of evolution', and in another the 'balance between factors of persistence and change' is said to be 'continuously shifting'. Wright therefore comes very close to using the phrase 'shifting balance theory', but the fact that even in these passages he does not actually use it strengthens the suspicion that he had not yet coined the term as such.

What balance? And what shifts?

Many other uses of the terms 'balance' and 'shift' by Wright could be cited. I have quoted only those which come closest to his explicit term 'the shifting balance'. But even these examples, on a careful reading, leave it unclear what is the 'balance' that is seen by Wright as essential to effective evolution. Many different things are said to be 'balanced'. What exactly is a 'balance between factors of persistence and change', and is it the same as 'balance between conditions which make for genetic homogeneity and genetic heterogeneity'? Migration, for example, is a factor usually making for genetic homogeneity, but it is also often a factor making for 'change'. So which side of the balance does it fall on?

It might be hoped that in Wright's 1970 article, or in Volume 3 of Evolution and the Genetics of Populations, where the 'shifting balance theory' is discussed at length, we would find a clear statement of the meaning of the term itself. What is the relevant balance, how does it shift, and how does Wright's theory of evolution depend on the shifting of the balance? It may be that the answers are there, but if so, I have not found them. While Wright discusses various component parts of his theory, the overarching term 'the shifting balance' is not itself defined or explained. Moreover, whatever interpretation we give to the term 'balance', it does not seem that the 'shifting' of the balance itself plays any essential part in Wright's conception of the evolutionary process. The balance between the various factors of evolution, including selection, mutation, migration, environment, genetic drift, and population structure - to list the obvious ones - might stay constant, yet the process of evolution as described by Wright could still work, if the balance of factors is right. It is not the shifting of the balance, but the existence of the right kind of balance, which according to Wright is favourable to evolutionary progress. I conclude that the 'shifting balance theory' is a convenient and memorable label, but one without a precise literal meaning in isolation.

When was the theory first published?

Even if the label 'shifting balance theory' was not adopted until 1970, the doctrines covered by that label may have been propounded earlier. Wright himself, in 1970, claimed to have first published the theory as long ago as 1929. It can be confirmed that some of the key elements of the theory were contained in Wright's great 1931 paper 'Evolution in Mendelian populations', and summarised in shorter related papers beginning in 1929. Notably, these contain several key propositions which Wright maintained consistently to the end of his life:

a) The most favourable circumstances for evolution are in large populations subdivided into many small partially isolated populations;

b) Large freely interbreeding populations are not favourable to continuing evolution;

c) Genetic drift is an important part of the evolutionary process; and

d) The differential success of subpopulations, which Wright describes as 'intergroup selection', is an important contributor to cumulative evolutionary change.

If we regard these four propositions as constituting the shifting balance theory, then it was indeed first published in 1929.

Changes to the theory

This does not mean that there were no important changes to the theory after 1929. I believe there were changes both of substance and of emphasis, which I would summarise as follows:

1. In 1932 Wright adopted the metaphor of a multidimensional field of gene combinations and fitness values, which was later described (though not by Wright) as the 'adaptive landscape'. In my view this was more than just an illustrative device. The concept of selective peaks as alternative states of stable equilibrium was a valuable addition of substance to the theory, not corresponding to anything clearly stated in the original version.

2. Whereas in 1929-31 Wright had denied that temporary changes in environmental conditions would have major evolutionary effects, in 1932 he changed his position and accepted that environmental fluctuations could 'shuffle' populations from one evolutionary position of equilibrium to another, usually higher, one.

3. As a consequence of change (2), Wright reduced his emphasis on the importance of genetic drift, which he had originally claimed as essential to long-term evolutionary progress. After 1932 genetic drift was in principle only one of several mechanisms for change. But Wright did not make it sufficiently clear that his position had changed, and did not follow through the implications of the change for his views on the importance of population structure.

4. Throughout his career Wright maintained that the evolutionary process was partly adaptive and partly non-adaptive or 'random', but the emphasis he put on these elements shifted from the non-adaptive aspect to a greater emphasis on adaptation.

5. In his later writings on the subject Wright identified three 'phases' in the shifting balance process, but these are much less clear in the earlier versions of the theory.

Some but not all of these changes have already been identified in William Provine's admirable biography of Wright. The remainder of this note will mainly be concerned with documenting the various changes.

The original version of the theory (1929-31)

The key propositions of the original version of the theory were conveniently summarised by Wright himself in a short paper of 1929, which I will quote in full:

The frequency of a given gene in the population is affected by mutation, selection, migration and chance variation. The pressure exerted by these factors (excluding chance) and the position of equilibrium between opposing pressures are easily found. Gene frequency fluctuates about this equilibrium in a distribution curve, determined by size of population and the various pressures. The mean and variability of characters, correlation between relatives and the evolution of the population, depend on these distributions. In too small a population, there is nearly complete random fixation, little variation, little effect of selection and thus a static condition, modified occasionally by chance fixation of a new mutation, leading to degeneration and extinction. In too large a freely interbreeding population, there is great variability, but such a close approach of all gene frequencies to equilibrium that there is no evolution under static conditions. Changed conditions cause a usually slight and reversible shift of the gene frequencies to new equilibrium points. With intermediate size of population, there is continual random shifting of gene frequencies and consequent alteration of all selection coefficients, leading to relatively rapid, indefinitely continuing, irreversible and large fortuitous but not degenerative changes even under static conditions. The absolute rate, however, is slow, being limited by mutation pressure. Finally, in a large but subdivided population, there is continually shifting differentiation among the local races, even under uniform static conditions, which through intergroup selection brings about indefinitely continuing, irreversible, adaptive and much more rapid evolution of the species as a whole. (78)

These propositions are all stated more fully and supported by arguments in the 1931 papers 'Statistical theory of evolution' and 'Evolution in Mendelian populations'. (Although 'Statistical theory of evolution' was published first, it seems that 'Evolution in Mendelian populations' was completed first and 'Statistical theory of evolution' written as a summary of it.) Some of them are also covered in Wright's 1930 review of Fisher's Genetical Theory of Natural Selection. Most of them are restated and defended throughout Wright's career. The arguments given by Wright to support the key propositions (quoted in italics from the 1929 article) can be summarised as follows:

In too small a population, there is nearly complete random fixation, little variation, little effect of selection and thus a static condition, modified occasionally by chance fixation of a new mutation, leading to degeneration and extinction.

For this purpose 'too small' a population is one in which 1/4N (where N is the effective population size) is much larger than selection and mutation rates. (148) In this case genetic drift will be the main factor in evolution. Most genes will soon be fixed, there will be little variation within each population, and random unadaptive changes will lead to extinction. (93, 142, 148)

In too large a freely interbreeding population, there is great variability, but such a close approach of all gene frequencies to equilibrium that there is no evolution under static conditions.

For this purpose 'too large' a population is one in which both selection and mutation rates are much larger than 1/4N. (148) In this case, genetic drift will have little effect, and gene frequencies will be determined by the balance of selection and mutation. If selection on a gene is much stronger than mutation pressure, there will be almost complete fixation at each locus and therefore no evolution under fixed conditions. (148-50) If selection is not much stronger than mutation pressure, there will be more genetic diversity, but all gene frequencies will be close to equilibrium and evolution will be very slow unless conditions change. (150) Note that these arguments tacitly assume that there are no new favourable mutations, or existing ones still under selection.

Changed conditions cause a usually slight and reversible shift of the gene frequencies to new equilibrium points.

In 'Statistical theory of evolution' Wright says that 'Changes in conditions should be followed by systematic changes in gene frequencies until all have reached the new positions of equilibrium. Return to the old conditions should be followed by return to the old equilibria' (92). No specific reason is given for this conclusion. In 'Evolution in Mendelian populations' the explanation is slightly fuller. Following a strengthening of selection, gene frequencies will change, but 'The rapid advance has been at the expense of the store of variability of the species and ultimately puts the latter in a condition in which any further change must be exceedingly slow. Moreover, the advance is of an essentially reversible type. There has been a parallel movement of all the equilibria affected and on cessation of the drastic selection, mutation pressure should (with extreme slowness) carry all equilibria back to their original positions. Practically, complete reversibility is not to be expected, and especially under changes in selection which are more complicated than can be described as alternately severe and relaxed. Nevertheless, the situation is distinctly unfavorable for a continuing evolutionary process' (150). Note that Wright does not claim the changes are always reversible, only that this is 'essentially' or 'usually' the case. Bur he gives no clear reasons for this position, and only a year later (1932) he abandons it. As this is one of the major developments in the theory I consider it more fully in Part 2 of this note.

With intermediate size of population, there is continual random shifting of gene frequencies and consequent alteration of all selection coefficients, leading to relatively rapid, indefinitely continuing, irreversible and large fortuitous but not degenerative changes even under static conditions. The absolute rate, however, is slow, being limited by mutation pressure.

For this purpose an intermediate size of population is one where, for many genes, the selection pressure is not much stronger than the mutation rate, and neither selection pressure not mutation rate are much higher than 1/4N (150-1). (Since mutation rates were known by Wright not to be much higher than 1 in 100,000, this implies an effective population size of the order of 25,000.) In these circumstances genetic drift will be strong enough to cause considerable fluctuation in gene frequencies, but not to lead to rapid fixation of genes and loss of genetic diversity. Wright describes the result as 'a kaleidoscopic shifting of the average characters of the population through predominant types which practically are never repeated' (95, see also 151). But Wright emphasises that it would be a very slow process, as 'hundreds of thousands of generations are required for important evolutionary changes' (95). He mentions the effect of mutation rates as limiting the speed of change (78, 95, 151), presumably because with mutation rates not very different from the rate of genetic drift, mutation pressure tends to maintain genetic uniformity. But surely the main reason for slowness is that genetic drift itself is very slow in a population of many thousands.

Finally, in a large but subdivided population, there is continually shifting differentiation among the local races, even under uniform static conditions, which through intergroup selection brings about indefinitely continuing, irreversible, adaptive and much more rapid evolution of the species as a whole.

This is the most important proposition of the shifting balance theory in its original form. Wright never abandoned his view that a large subdivided population is most favourable to evolution. The subdivisions must be small enough, and isolated enough from each other, that the subpopulations can diverge in gene frequencies (151-2). Curiously, there is an important difference between Wright's accounts in his two 1931 presentations of the theory. In 'Statistical theory of evolution' Wright mentions only 'random drift' as causing the divergence between subpopulations, with the result that there is a 'geologically rapid drifting apart of the various sub-groups, even under uniform conditions. This is a non-adaptive radiation, but, on the average, not such as to lead to appreciable deterioration' (95). In 'Evolution in Mendelian populations', on the other hand, Wright mentions both genetic drift and local variation in selection pressures, so that the result is 'a partly nonadaptive, partly adaptive radiation among the subgroups' (151). There is of course no reason why both processes should not occur at once, perhaps in different subgroups or at different loci in the same subgroups at the same time. But the difference does have implications for the final phase of the process, which is 'intergroup selection'. On this, Wright says that 'Those [subgroups] in which the most successful types are reached presumably flourish and tend to overflow their boundaries while others decline, leading to changes in the mean gene frequencies of the population as a whole' (152). But if adaptive variation among subgroups is due only to local circumstances of selection (as seems to be suggested in 'Evolution in Mendelian populations'), those types which have highest fitness in their own locality cannot be expected to succeed elsewhere. If on the other hand the variation among subgroups is purely due to random drift (as seems to be suggested in 'Statistical theory of evolution'), it is not obvious that they will differ significantly in fitness for genetic reasons. 'Statistical theory of evolution' does however contain a very important development or clarification of the theory: 'Exceptionally favorable combinations of genes may come to predominate in some of the subgroups. These may be expected to expand their range while others dwindle. This process of intergroup selection may be very rapid as compared with mass selection of individuals, among whom favorable combinations are broken up by the reduction-fertilization mechanism in the next generation after formation' (95). The reference to 'favorable combinations' here is the first sign of the emphasis on epistatic fitness interactions which becomes increasingly important in the later development of the theory. But in the original statement, in 1931, it comes out of the blue and unsupported by any detailed analysis.

Likewise, the concept of 'intergroup selection' is not explored in any depth, and the claim that it would be more rapid than 'mass selection of individuals' is little more than a bare assertion. The suggested advantage that 'favorable combinations' are not immediately broken up by sexual reproduction seems to require not only a high degree of genetic unity within the subgroups, but the maintenance of that unity during the process of 'intergroup selection', despite the probable intermingling of different groups. The credibility of this process has been one of the main areas for recent controversy and research on the shifting balance theory. It should incidentally be stressed (see also Provine, p.288) that 'intergroup selection' as envisaged by Wright has little to do with 'group selection' as envisaged by most of its recent advocates. Wright does not suggest that successful groups have evolved adaptations for group living, or that their members behave 'altruistically' towards each other (though his theory does not exclude this either, and he later made some comments in this direction). His claim is rather that the subdivided population structure allows some groups, by chance, to form combinations of genes that are advantageous to individual fitness. The higher mean fitness of the groups is the resultant of these individual fitness advantages.

Wright also gives mixed messages about the adaptiveness of the process. While repeatedly claiming that in the long run the process is adaptive, Wright accepted the common view of many biologists at the time that the differences between subspecies and even between species of the same genera are usually non-adaptive (154, see also Provine p.288-99), a view which would seem to require the adaptive process of 'intergroup selection' to occur mainly between different genera or even higher taxa! But in this case 'intergroup selection' between small subgroups of the same species would be irrelevant to the process. Yet in 'Evolution in Mendelian populations' Wright also suggests that intergroup selection within the species may be responsible for 'peculiar adaptations' and 'extreme perfection' (154-5), a claim which is not, I think, repeated anywhere else. Overall, the emphasis in these early writings is more on the nonadaptive than the adaptive aspects of the process.

Taking stock

Before exploring the subsequent development of the theory (in Part 2), I will try to take stock of the position reached by 1931.

Already in his summary note of 1929 Wright had stated some of the key propositions of the shifting balance theory. In the two articles of 1931 he began the task of justifying these propositions. The arguments he put forward were ingenious, stimulating, and not implausible, but far from conclusive. There were moreover a number of tensions, if not actual inconsistencies, within Wright's accounts. One of these concerned the extent to which the process was adaptive, as has been explored fully by Provine. Another is the respective roles of genetic drift and local selection, on which I have pointed out an apparent difference between the two articles of 1931. Another is the problem of migration between groups. As suggested in my earlier note on migration, Wright did not attempt to quantify the effects of migration until after he had committed himself to the importance of random drift within semi-isolated subgroups. Only then, in 1929, did he discover 'that isolation in districts must be much more nearly complete than I realized at first' for the process to work. 'Evolution in Mendelian populations' makes an attempt to remedy the deficiency (128), but further work was clearly needed.

Several important aspects of the theory in its mature form are also lacking from the original version. Notably, there is nothing clearly corresponding to Wright's later emphasis on alternative local optima - 'selective peaks' - available to populations or subpopulations. These local optima depend heavily on epistatic fitness interactions, which are hardly mentioned in the original version. In the mature theory, subpopulations 'explore' the field of possibilities under the influence of random factors (genetic drift, but also environmental fluctuations) until they wander into the zone of attraction of a new selective peak. The stage of 'exploration' is Phase 1 of the process, while the climbing of the population up a peak is Phase 2, and intergroup selection is Phase 3. In the original version of the theory there is no clear distinction between Phase 1 and Phase 2, because there is nothing to suggest that the process of 'exploration' ever stops, short of the exhaustion of genetic variation by random fixation of genes. The phrase 'continually shifting differentiation' seems inconsistent with any sharp distinction between two phases. The first signs of a new approach are to be found in 'Statistical theory of evolution', with its reference to some groups finding 'exceptionally favorable combinations of genes', implying epistatic peaks of fitness. Quite possibly this had been in Wright's mind all along, but I do not think it can be identified in anything written before 'Statistical theory', including the much more widely read 'Evolution in Mendelian populations'.

Another important omission is any serious discussion of the probability of favourable new mutations. Wright's negative assessment of the prospects for evolution in large freely interbreeding populations depends on the tacit assumption that new mutations can be neglected. Wright later developed arguments to support this position.

Overall, a careful reader of Wright's publications up to 1931, without knowledge of subsequent developments, might reasonably conclude that Wright had put forward a remarkably original, ingenious, and comprehensive theory of evolution, consistent with most of what was then believed about the observed pattern of evolution, and free of any obvious fatal defects. This is itself was a very major achievement. But the same reader might also think that the theory was sketchy and speculative, and in need of further elaboration, not to mention empirical tests. Wright himself was no doubt aware of this, and continued to develop the theory for another 50 years, as I will discuss in Part 2.

William B. Provine, Sewall Wright and Evolutionary Biology, 1986.
Sewall Wright: 'Physiological genetics, ecology of populations, and natural selection', in Evolution After Darwin, vol. 1, ed. Sol Tax, 1960 (Tax). (Article first published in 1959.)
Sewall Wright: Evolution: Selected Papers (ESP), ed. William B.Provine, 1986.
Sewall Wright: 'Random drift and the shifting balance theory of evolution', in Mathematical Topics in Population Genetics, ed. Kojima, 1970.

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Wednesday, October 22, 2008

Islam in China   posted by Razib @ 10/22/2008 03:32:00 PM

It's a big blogosphere. Aziz points me Islam in China. They have an interesting post up which reiterates much of what I said about the diversity of Chinese Muslims, along with obscure facts such as that the second ranking Vice Premier of China is Hui. Not that there's anything wrong it....


Father Absence theory in hip-hop   posted by agnostic @ 10/22/2008 11:12:00 AM

I've been somewhat out of the loop of hip hop music, though I'm catching up. A club that I go to regularly has been playing a song whose lyrics argue for the Father Absence theory of why some people grow up to be wilder than others. (See the video here.)

It used to be that art referred to theories that weren't even plausible on their face -- Freud's idea of the Oedipus Complex being one. Whether Teairra Mari's song "No Daddy" reflects a shift over time to more plausible ideas, or simply the contrast between moronic intellectuals and those who believe their lying eyes, I couldn't say. Also unknown is whether she's read Harpending & Draper (1982) or just figured it out on her own. If the latter, she must have been pretty perceptive, as the song was released when she was 17.

Polls Are Smarter Than You   posted by ben g @ 10/22/2008 10:30:00 AM

Andrew Sullivan points to a post by DJ Drummond which makes the claim that the polls are significantly biased towards the Democrats. This is a perfect example of partisanship taking precedence over facts, and it thus deserves a thorough fisking. Drummond begins:

it needs noting that all of the major polling organizations are based in locations where liberals are strongest and conservatives weakest, where 'democrat' and 'republican' take on meanings wildly different from the rest of the country. The people making the executive decisions at these polls, most likely including the wording and order of polling questions, whether to focus on urban or suburban areas, the weighting of political affiliation, and the definition of 'likely voter', are most likely in regular contact and association with the most liberal factions of politics. It does not mean that they have deliberately skewed their decisions to support Obama, but it is obvious that there is an apparent conflict of interest in their process modality.

To begin with, most major *conservative* media outlets (e.g Fox News, the National Review) are located in these regions. Drummond suggests that through some kind of opinion osmosis, pollsters in urban areas tilt their polls towards liberals. The evidence suggests this contention is wrong:
  1. Fox News and Rasmussen (both Republican-owned) are going in the same direction as the average of all the other polls (including those funded by liberal/democrat organizations). The latest Fox Poll shows Obama leading by 9. Contrast this with the current pollster average difference of 8.
  2. Pollsters polled the Bush-Kerry election correctly, accurately predicting a close victory by Bush. Also, they under-polled Gore by 3 points.
  3. John McCain is campaigning most heavily in the swing states identified by the supposedly liberal-biased polls. His campaign, like all presidential campaigns, has its own internal polling. Apparently it matches up with Gallup et. al to a great degree.

Drummond goes on to make some specific arguments for his point of view:

most people do not have the interest to stop and take an 8-to-10 minute interview, especially from someone they do not know calling them up when they are likely to be busy doing something else. It's been established as well, that democrats in recent years are more willing to take part in polls than republicans, possibly due to perceived bias on the part of the media. But it is quite important to know if the pollsters were getting one person in ten to take the poll, or only one person in fifty, because the people not interviewed matter just as much as those who do participate. Yet I have never yet seen a poll this year that publishes response rates.

Although this has nothing to do with the claimed liberal bias of polling organizations, it is a generic methodological issue worth discussing. Response rates are typically in the 10 to 25% range (PDF link). In general, the candidate who excites their base more (regardless of party) will have a higher response rate from telephone polls. The argument is that this inflates estimates of their support. However, the evidence suggests the opposite; the candidate with more enthusiasm behind him/her inspires people not only to pickup the phone but also go to the voting booth.

It's also worth noting that Drummond ignores any methodological biases which would inflate McCain's estimated share of the vote. For example, people who either have no home phone or use cell phones are typically not being sampled. These people are disproportionately young and/or poor (both demographics favor Obama).

This is a big one that a lot of folks miss. I have noticed in the details, that all of the polls are asking about the public's opinion of the economy, and of their opinion of President Bush, even though he is not running this time.

These questions have been asked for decades, under both Republican and Democratic presidents. That Drummond is unaware of this shows that he doesn't know enough about polling to criticize it.

many polls ask a question about John McCain just after asking about the voter's opinion of President Bush, subtly linking the two men.

Polls that ask about the election first match the current polling trend. See, for example, that recent Fox News Poll where Obama leads by 9 (PDF link). This poll is in following with the majority of them in asking about Bush *after* they ask about the election.

no questions have been asked about approval of the specific performance of either Majority Leader Reid or Speaker Pelosi, and no other politician is linked to Barack Obama in the same way that polls link President Bush to John McCain.

First off, it's a rarity to poll about the performance of the Speaker or Majority Leader, regardless of whether they're Republican or Democrat. Second, it's not true that there haven't been polls dealing with Obama's connections. There have been several polls asking about voters' opinions on Obama's connections to Ayers and Wright.

Polls taken since Labor day have not mentioned foreign policy at all. There are no questions regarding Russia's invasion of Georgia, nor of Iran's nuclear weapons programs, nor about China's intentions viz a viz Taiwan, even though these are current events which have great significance in a presidential race, yet all of the polls are ignoring them. Again, the economy-only focus betrays a bias which violates the principles of the NCPP.

There have been polls on foreign policy since labor day, and it takes only a simple Google search to know this. See for example this one by the New York Times. The focus on the economy (both by the polls and by the candidates themselves) has not come about because of liberal bias, but because voters indicate that this is what matters to them.

The thing most folks forget about polls which get published in the media, is that the polls' first need is not to accurately reflect the election progress and report on actual support levels; it's about business.

This is a false dichotomy. These needs overlap to a great deal. SurveyUSA went from a no-name to the most respected pollster among bloggers (and, eventually the press) during the dem primaries simply because it more accurately predicted outcomes in the Democratic primary than anyone else. (They were frequently the outlier from the pack, by the way, and we'll get to that in a second). As a result they got more web traffic and citations. So there's definitely an economic and social incentive to give accurate polls. For a "conservative", this guy sure has a great disrespect for market efficiency.

you really think republicans or independents got more excited about Obama because of his convention, or that democrats and independents were more likely to vote for McCain because of the GOP convention? When you think about it, it should be obvious that these bumps are artificial unless there is a clear cause to show a change in support.

A simpler hypothesis is that the polling companies are accurately registering a slight increase in support for a given candidate in response to their increased positive media attention.

There has been unprecedented manipulation of demographics, corrupting even the raw data to the point where effective resolution of public opinion is doubtful. This might be described as an honest mistake, if one is willing to accept greed as an honest motive. Gallup, for example, who has more experience than any other polling group and who therefore should have known better more than anyone else to fiddle with the weights.

Where is the data? Where is the evidence that Gallup is not weighting demographics accurately? Drummond says he has written on it previously, but a search of his site for "gallup census" shows no posts which actually show the gallup weighting to be at odds with the US census. Demographics weighting varies as a function of the pollster. It's worth noting that despite their different weightings, the major pollsters agree that Obama is leading by at least 5 points right now.

So OK, Gallup is having a bad year, but what about the rest? Well, there the phrase to consider is follow the leader.

I've been following the polls since the primaries, and I can safely say: that hasn't been very true for this election or the dem primaries. There have been spreads as great as 15 points (see for example New Hampshire in the Democratic Primary) between various pollsters at several points in this year and last. The models, and occasionally the outcomes, have been significantly different from one pollster to the next. This guy needs to compare SurveyUSA to Gallup to Public Policy Polling before he writes another post accusing them of following one another.

So, could I be wrong? I have to be honest and admit that I could.

That's good to hear, because he actually is wrong. Here's why:

That McCain is more experienced with the key issues than Obama was ignored, that the historical significance of the debates shows that the effects appear several weeks later was also ignored. That the economy could be as reasonably blamed on the democrat-controlled Congress as on the republican President was never considered. That character would be a salient factor in the decisions of voters was rejected out of hand.

Wishful partisan thinking. Drummond wishes that people supported his president and candidate and issues, but because they don't he criticizes the data which proves otherwise.


Tuesday, October 21, 2008

John Hawks on Peter Turchin   posted by Razib @ 10/21/2008 06:48:00 PM

A post commenting on Peter Turchin's philosophy in regard to the utility of formal models, The utility of theoretical models. As I've been wont to say recently, error in the cause of clarity is no vice.

Culture & cognition   posted by Razib @ 10/21/2008 01:09:00 AM

There is a new blog some readers might find of interest, Culture and Cognition. Dan Sperber, who did a 10 questions nearly 3 years ago, is a contributor. Imagine, what if cultural anthropology was dominated by people who didn't behave like literary critics or aspire to be political revolutionaries?

Do you like the sound of your own voice?   posted by Razib @ 10/21/2008 01:04:00 AM

Daniel Larison is surprised by the sound of his own voice (he did a Does anyone like the way their own voice sounds when recorded? Please leave comments if you do.

Friday, October 17, 2008

Dark Age giants?   posted by Razib @ 10/17/2008 10:58:00 PM

From Barbarians to Angels: The Dark Ages Reconsidered:
Measurements taken on skeletal remains in cemeteries in southwestern Germany indicate that the average height for men was about five feet eight inches, for women about five feet four inches, statures well above those of late medieval and early modern times. Measurements taken on skeletons in other regions are comparable. In Denmark, for example, the average height for men was about five feet nine inches-just above those for southwestern Germany-and for women about five feet four inches. These average heights were not achieved again until the twentieth century. Compared with earlier and later populations in the same regions, these average measurements show that most people had adequate nutrition during most of their lives and their living conditions were generally good
This is in line with the charts I posted below. With the introduction of the three-field system, mouldboard plow and horse collar northwest Europe, in particular the regions of northern France, the Low Countries and the Rhineland, surpassed the Mediterranean as the population center of the continent (at least its western half). During the expansionary phase, i.e., 500-800, the span covered by Barbarians to Angels, the Malthusian pressures would have been relatively modest. The screws would have been tightened up to the medieval demographic peak before 1300.

In any case, remember my focus on morbidity vs. mortality? It might be apropos in this case. The uncertainty and political instabilities due to the collapse of the Pax Romana could plausibly have increased mortality as peasants were exposed to the erratic depredations of barbarian warrior bands. But as depopulation occurred, in part because of withdrawal from the frontiers in places like Gaul (France) an western Germany of most farmers, those who opted to remain and take on the risks would be relieved of some Malthusian pressures. I think the chart of European heights does point to this as well, you can discern a slight upward trend after the Black Death due to a radical population reduction. I've reedited one of the charts for clarity:

As for Barbarians to Angels, the author doesn't really make me reconsider. I've talked about my skepticism of the idea of revisionism in regards to the decline of Rome. The author argues that technological advances occurred during the Dark Ages, and that many cities remained active nodes in trade networks. But the author's treatment is highly qualitative where he had concrete examples of how complex society persisted after the collapse of the Pax Romana, and he repeatedly scolds the readers to not judge Dark Age societies by modern standards which would tend to align more with the priorities of Roman civilization (e.g., reading, writing, arithmetic, public architecture, basically what we might term civilization). If the author wants to strip the term "civilization" of any normative biases brought to bear due to the prejudice of moderns, the argument is won, amassing a large collection of ornate weapons with which one might be buried is just as Cultured as writing letters to your friends laced with literary references. A good cup of mead is at the same level as a Falernian.

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Red State, Blue State, Rich State, Poor State: Why Americans Vote the Way They Do   posted by Razib @ 10/17/2008 09:47:00 PM

I have a review of Red State, Blue State, Rich State, Poor State: Why Americans Vote the Way They Do up at my other weblog. A quick, enjoyable, and valuable read.


Human evolution & height?   posted by Razib @ 10/17/2008 12:52:00 PM

In the posts below I wanted to make clear my assumption that morbidity was likely more prevalent during the Neolithic than the Paleolithic. This does not mean of course that the Neolithic people were necessarily poorer than the Paleolithic peoples; Greg Cochran recently told me that people got healthier for obvious reasons during the Great Depression. I would not be surprised if the rate of mortality was somewhat higher than during the Paleolithic simply because the hunter-gatherer lifestyle had less buffering against disasters because trade and social networks were poorly developed so that environmental variation took a greater toll.

For me the biggest point to favor the idea of increased morbidity is that heights seem to have decreased after the Neolithic revolution. It seems plausible that nutritional shifts are the main reason that humans would shrink in size. Below the fold I have reproduced some charts from various papers for your reference.

The cite is Long Bone Dimensions as an Index of Socioeconomic Change in Ancient Asian Populations. Of course, height is not the only thing that changed. From Stature in Early Europeans:
...The sexual dimorphism creased in the more recent populations. Upper Palaeolithic humans not only were taller and had more robust bones in comaprison with the LInear Band Pottery Culture Neolithic people; they also had longer lims, a shorter trunk, and similar to modern African people, very long forearms and crural segments. The low brachial index is a very recently acquired characteristic of white Europeans.
... is interesting to note that, though moern humans have returned to the body structure of their Early Palaolithic ancestors, they retain the modern proportions with short forearms and short crural segments

Agricultural populations as a whole have shifted toward a less robust physique. The increase in height due to better nutrition doesn't seem to have resulted in a more robusticity or a Palaeolithic dentition. So there may be some biological evolutionary parameters at work here as well. The first paper notes that between region differences in height seem to persist over long periods of time (East Asians are smaller). Phenomena such as Bergmann's rule point to changes in body form and size correlating with climatic shifts, and certainly the rise of agriculture is coincident with our current Interglacial.

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Thursday, October 16, 2008

Hunter-gatherers and farmers, the continuing saga   posted by Razib @ 10/16/2008 04:18:00 PM

Sandy made another response to my assertions about HG's vs. farmers and quality of life, Agriculture Reduced The Periodicity & Amplitude Of Nutritional Stress. He's done a lot of research to support his specific contentions, and certainly everything he reports is generally true. But, I don't think it's necessarily relevant or representative of the issues at hand.

First, he says:
I've done some reviewing of the literature and I still think that the probability that a child of an agriculturalist will reach reproductive maturity is higher than that of a hunter gatherer. Hell, that's why there's been a population boom ever since the Neolithic revolution.

No, not necessarily. In a previous post he alludes to r vs. K strategies. Agriculture could simply be a r strategy. Children never born are not children ever had. So agriculturalists could have a higher growth rate by simply increasing the total number of infants produced over a reproductive lifetime. To make it explicit:

Woman 1 = 6 live births and 3 survive to reproduce
Women 2 = 12 live births and 4 survive to reproduce

Obviously the second woman's offspring have a higher mortality rate before reproductive age, but that doesn't matter, there are more copies of her genes floating around. Population growth or decline is a dynamic which can be the outcome of many combinations of the parameters (e.g., fertility, mortality and generation time). If you know that in population A the mean number of children per woman is 3, and in B it is 4, you can not conclude that B has a higher population growth than A without knowing the death rates.

Over the long term agriculturalists have had on average somewhat higher growth rates, otherwise hunter-gathering wouldn't have been totally marginalized as a way of life. But, that doesn't mean that populations grew very fast; the logic of compounding growth means that very small differences in average growth rates can result in great divergences over long periods of time.

But, as I said in my previous post the issue isn't really about looking over the long term. When the Europeans arrived in North America and Australia they perceived the land to be "empty." Now, obviously there were peoples settled in these territories, but they're average density was simply far lower than was typical in Europe. Why? Because these peoples did not have the cultural toolkit to extract as many calories per unit out of land. Europeans, with their more productive agricultural toolkit could naturally support far larger populations than the natives from the same land because of culturally contingent factors.

I think the same sort of dynamic can be projected back into the past. Imagine a group of agriculturalists who landed on the Breton coast 8,000 years ago, coming via sea from Portugal. The locals are hunter-gatherers who need enormous areas of range territory to support a small population. A group of farmers might be able to win or negotiate a "small" tract of land from the natives to farm. The natives might see this concession as minor; after all, they might not comprehend that a "small" territory from the perspective of farmers is actually going to be a "large" plot when conditioned on the agricultural techniques farmers had. During the early years farmers would experience plentitude as there is a surplus of land. Soon though they would need to expand, and here their ability to organize and project force because of their numbers would come to the fore. Not only would they be able to push back the hunter-gatherers, but likely powerful infectious diseases would sweep in front of their demographic wave. Soon, the only hope that hunter-gatherer tribes would have of defending against this would be take up farming themselves and become sedentarists. As this occurred the remaining hunter-gatherers would be pushed into marginal and less desirable land, further making the lifestyle relatively less attractive (any quality of life advantaged would be swamped out). There are plenty of data points which support these points from the last 500 years, from the European settlement of North America down to the relationship between hunter-gatherers and farmers in Botswana.

Most of the rest of Sandy's post is an analysis of correct, but irrelevant or unrepresentative data. Or at least I think it is irrelevant, and suspect it is unrepresentative. To a great extent much of the human race today lives outside of the Malthusian trap, and the conditions of the past do not necessarily apply to today. Additionally, though over the long term populations grew rather slowly in the pre-modern era, there were local fluctuations up and & down. We know this for a fact from cultures where we have demographic data (e.g., England and China), so a "snapshot" of a given period does not allow us to generalize well across time. Comparing contemporary hunter-gatherers today with contemporary agriculturists is probably not representative of past conditions. For me the biggest problem is that hunter-gatherers today are selection biased toward regions where agriculture is not at much of a comparative advantage. This is why I tend to be more interested in comparisons of remains within a particular region which went through the lifestyle transition in the past. My general impression is gross physiological health declined. In other words, farmers are, on average, subject to greater morbidity, even if hunter-gatherers have more mortality.

In any case, one of the problem here is bigger meta-issue in the debate between Sandman and myself:
Anyways, in my previous post I outlined some of the ethnographic reasons why I think so. In this post, I'll share some of the demographic data that supports my hypothesis.

I know less cultural anthropology than he does, and I'm not interested getting to know the whole literature. I could go to google scholar and look up some research articles which support my view because there are a lot of articles out there, and I'm sure I could find some trash which would support any contention I make. That's why I'm leaning back on the theory about Malthusian assumptions that I can be rather certain of, even if I'm wrong as an empirical matter I can argue the logic with some concreteness and consistency. I'm not convinced by Sandman for all the reasons above, but, at the end of the day I wouldn't be convinced by a few surveys of the literature because I'm sure I could selectively troll through the literature and find authorities to support me too. If I actually knew the literature with any fluency I could ascertain the value of any given citation I dig up, but since I don't know the literature I'm really concerned about just selection biasing what I get based on the way I formulate a google scholar query. This is also why I'm pretty down on the citation wars which occasionally crop up in the comments, I strongly have the suspicion that the interlocutors aren't really digging into each other's citations, but rather just going to search for more papers to support their own argument. What's really the point of all that? So I have decided to ask some people who really are in the "know" (that is, anthropologists who aren't CAFRs) what they think.

Oh, and also:
Razib equates hunter-gatherers to lions, and farmers to antelopes. Lion cub mortality rates are higher than antelopes, upwards of 80% of cubs do not make it to adulthood. Whereas antelope calves, if they survive predation, have much more greater chances at seeing sexual maturity. It is much more precarious to count on mom to provide milk and hunt at the same time, than it is to graze. So, this issue is less about absolute availability and more about reducing the periodicity and amplitude of nutritional stress. And this is one of the reasons why the agricultural diet has 'won' over many humans, even despite the many shortcomings it has.

To the first approximation I somewhat accept this, but I'm not totally sure, and the characterization might elide some of the details. Imagine a scenario like the chart below, where Y = nutritional quality and X = generation. The average for a hunter-gatherers might be higher, but the far higher "floor" of farmers might make all the demographic difference over the long term.

Addendum: I don't know cultural anthropology well, aside from the fact that CAFRism is endemic, but I do know something like the society of the Roman late antique period relatively well for a lay person, so I have seen people make arguments based on obviously retarded citations. Now, since these people are frankly retarded, dishonest or ignorant (or any combination thereof) any well informed response is really totally futile; people who can't evaluate the plausibility of their own argument based on the quality of the authorities which they cite aren't going to be able to evaluate the plausibility of someone else's authority. This explains why I'm responding to Sandman in broad theoretical generalities and methodological objections; if I "dug in" by spending time looking for literature support my case I'd turn this into a lawerly dialogue, and what's the point of that? Granted, I know Sandman better than if he was just a "random" from the internet, but still, life is short.


Lions and antelope   posted by Razib @ 10/16/2008 12:45:00 AM

Sandy has a post up, Why Do Women Have More Cavities?, where he reviews the John Lukacs paper I pointed to yesterday. He says:
So ultimately female physiology combined with the the changes in diet and increased feritlity are the reasons why women have more cavities than men. Razib mentions that with increased fertility comes a reciprocal increase infant mortality, especially because the agricultural revolution increased communicable diseases. He concludes that hunter-gatherer infants are far more likely to reach reproductive age than infants of an agriculturalist.

But I disagree. Despite the recent popularity of the paleo-diet, the real hunter gatherer lifestyle is not easy. Many hunter gatherer societies have erratic sources of nutrition, very few have regular caloric intakes. John Hawks explained that among hunter gatherers, like the Hiwi, only 43% of the adults were expected to see the age of 30. Furthermore, many hunter gatherer cultures also have food taboos which dictate the diets of females. For example, Australian aboriginal societies restrict protein and fat foods for pregnant and lactating women. Similar traditions exist in Africa too. In Athapaskan societies, females at menarche cannot eat fresh meat.

Mothers who do not consume many calories, reach menarche at an older age and become amenorrheic - irregularly menstruate. If and when they do have a child, they are often of low birth weights, and have a higher risk of dying because they have little to no fat reserves. They consume inadequate amounts of nutrition since the mothers cannot make insufficient amounts of milk. All of which influences birth spacing significantly.

Despite the increased probability of cavities, the Neolithic revolution has generally been a good thing for women and children.

I mentioned in the comments that I'm pretty sure that he misunderstood me. So I'll clarify my conception in this post. Unfortunately, though I'm obviously interested in this particular topic (you know this if you read the blog) I'm not that familiar with the cultural anthropological literature, so all my assertions are very provisional because I don't feel confident I know the literature well. Nevertheless, in regards to my basic logic I'm confident that if Lukacs and others are right in regards to birthrate, what I said has to be true.

Here is what I said:

... In contrast, hunter-gatherer women typically have a reduced number of pregnancies because of behaviors such as extended breastfeeding. Of course, most agricultural societies quickly reached the Malthusian limit (ecological carrying capacity), so the higher fertility was likely balanced out by higher infant mortality. If agricultural women gave birth to more infants a greater proportion of these offspring ended up dying of diseases, etc., than for hunter-gatherers. So at birth any given hunter-gatherer infant is far more likely to reach reproductive age than any given offspring of peasants....

I was careful with the words I used here. I was working with a Malthusian assumption in regards to pre-modern populations. In short, most of the time populations did not exhibit the sort of long term sustained growth rates of the last few centuries. In medieval England, where we have some documentary demographic sources, we know that the population crashed during the Black Death and didn't reach its pre-crash peak for over two centuries. I recount this to make clear I do understand that the flat population growth curves you see for pre-modern demographics are generally "smoothed" and there were wild local fluctuations. But, these fluctuations oscillated around an "ecological carrying capacity."

There is of course another dynamic which occurs some of the time. If, for example, a human population discovers new territory where there is a surplus of land and Malthusian pressures are minimal, you will see a transient logistic growth curve. That is, population will increase up the Malthusian limit, what biologists would term the "carrying capacity." The United States during the period between 1650-1850 is a really good case for this. The number of white Americans rose because of immigration, yes, but there was a very high endogenous rate of growth driven by natural increase. In Albion's Seed David Hacket Fisher reports that in New England there were many towns where the average number of live births in a woman's reproductive span was north of 10! This is of course feasible when you have such a asymmetry between land, resources from which humans can derive sustenance, an the number of humans. Not only were New England families fertile, but European observers such as John Crevecoeur commented upon the relative physiological health of Americans during this period compared to those of the British Isles or the Continent (large, plump, vigorous). When you are below the Malthusian limit there is far less constraint on resources and so individuals are at their nutritional optimum.

Carrying capacity does vary as a function of ecology and culture. There is a reason that Yangtze delta was more densely populated than European Russia in 1700; not only is rice more efficient at producing calories from any unit of land in comparison barely, wheat or oats, but the climate in that region of China allows multiple croppings over the year. These sorts of ecological parameters are common sense. But though the population density might differ by around an order of magnitude, Russian and Chinese peasants had a similar quality of life (though there is differences on the margins, they are not predicted by the difference in density). This is because both populations were pushing up against the Malthusian limit, or carrying capacity, of their locality.

When you compare agriculturalists to hunter-gatherers, you will likely know that the former live at higher densities than the latter. You will also know the former to be far more sedentary than the latter. This is not strictly a function of ecology; almost all regions where agriculture came to dominate were once inhabited by hunter-gatherers. In fact, there is plenty of evidence that many of the latter switched lifestyles to become farmers. Sometimes the process could take some time, for example there is a fair amount of archaeological evidence in southern Sweden that non-agricultural societies had a flourishing trade with agriculturalists for thousands of years. Why so long for the switch? The crops of the Middle East emerged in the Middle East, and so the cultural toolkit took some time to evolve so that it was attractive and preferable to northerners.

Why did hunter-gatherers become farmers? One can posit many reasons. But remember what I said about the logistic growth along the transient? This can take some time. We in the United States don't really know how long it would have taken America to "fill up" so that the European misery index was recapitulated among Yankee yeoman (the frontier did not close until almost 1900). The demographic transition in the late 19th century changed the whole game. If you are a hunter-gatherer, and you see that your neighbor can extract many more calories out of a smaller amount of land and so have a larger family, it might seem like a rather rational choice. If thinly scattered hunter-gatherers switched to agriculture they would slide along the transient of the logistic growth curve for many generations. In fact, the early adopters would never know of the misery which later generations would take for granted! The cultural invention of agriculture changes the whole game, at least temporarily. But eventually the law of diminishing returns kicks in, an the balance between land and population returns. The stationary state has been achieved.

And it is because of the stationary state that I said what I said about fewer offspring reaching reproductive age. If a population is stable then parents only replace themselves. This is true whether one is a hunter-gatherer or a farmer. But, what about Lukacs' assertion that females in agricultural societies had a higher birth rate? Well, naturally then there must have been a higher mortality rate. That is why I referred to pregnancies; if hunter-gatherer women space their births through weaning an abstinence then they might have had many fewer pregnancies than the wives of farmers. But if both populations were at the Malthusian limit the surplus must be "pruned" by mortality, and more surplus implies greater mortality.

Why did hunter-gatherer women wish to space their births? The general hypothesis is that mobile groups need to maintain a reasonable ratio of productive adults to very young children. A hunter-gatherer woman would have had a more difficult time of managing multiple toddlers because of the need to move them on occasion. In contrast, a woman living in a village might be able to manage with multiple toddlers. Additionally, once the children reached the age of 5 or 6 they might have been economically valuable producers. If many of them died of disease before they reached the age of reproduction then the society could gain their production without having to worry about them contributing to higher population growth or taking care of them in their dotage.

As for all the stuff about how miserable hunter-gatherers were, that's pretty much irrelevant without a reference point to the misery of farmers. As I said, I don't know the literature very well. A Malthusian model should predict basically the same wealth for hunter-gatherers an farmers over the long term. That's close to what Greg Clark in Farewell to Alms assumes, though there are qualitative differences in the way farmers consume and hunter-gatherers consume. Life is not a continuous trait, you're alive, or your'e not. Farmers tend to have much less diverse diets than hunter-gatherers for rather obvious reasons. Because of the density of villages an the emergence of higher order social structures which foster more trade and commerce farmers are subject to more powerful epidemics. It seems though that hunter-gatherers often live violent lives, and without economies of scale and recourse to mass social collective action they might be more vulnerable to various types of environmental perturbations over the short term. In other words, these two pre-modern groups both lived like crap compared to today, but somewhat differently.

From all I have read if called on to give the quality of life award to either lifestyle anthropologists would today seem to tap the hunter-gatherers as being on top. It isn't just about dental carries. Farmers are physically smaller and exhibit more evidence of chronic nutritional stress than hunter-gatherers (that is, comparing remains from a locality which made the transition across a span). As noted in some of the papers below the higher fertility of farmers was almost certainly balanced by a higher mortality; a conscious human at the age of 5 seems to have had a greater likelihood of dying early among farmers because there were just more of them floating around.

Here are some papers to support the above claims (more or less):
The origins of agriculture: Population growth during a period of declining health
Biological Changes in Human Populations with Agriculture
Testing the Hypothesis of a Worldwide Neolithic Demographic Transition
Agents Adopting Agriculture:Modeling the Agricultural Transition

If you're a cultural anthropologist who knows more about this please add citations and results in the comments, I'm curious but I don't have the time to really familiarize myself with the literature to make strong judgments. Don't be a CAFR and ramble on about something you don't know about or spend 12 paragraphs on problematizing the word "farmer."

Note: The title: I sometimes think of hunter-gatherers as lion and farmers as antelope. There are many more of the latter because there's a lot more grass than antelope. Additionally, if a lion gets injured there's no way they're going to catch an antelope, it's a high risk profession. But who would you rather be? Note that the European aristocracy generally hunted as opposed to gardened. See Tim Blanning's The Pursuit of Glory: The Five Revolutions that Made Modern Europe: 1648-1815.

Addendum: Unfortunately, this isn't for pre-modern populations necessarily, but I thought readers would find this chart of interest....


Wednesday, October 15, 2008

Are doctors this clueless?   posted by Razib @ 10/15/2008 11:54:00 PM

I was browsing info on for cholesterol meds after reading Matt's comment about them.. This sentence was somewhat amusing: "People of Asian descent may absorb Crestor at a higher rate than other people. Make sure your doctor knows if you are Asian. You may need a lower than normal starting dose."

(before a humorless M.D. takes me to task, the title was just a joke)

Geordies are dirty?   posted by Razib @ 10/15/2008 05:51:00 PM

English Northerners' Hands Up To 3 Times Dirtier Than Those Living In England's South:
The results indicated that commuters in Newcastle were up to three times more likely than those in London to have faecal bacteria on their hands (44% compared to 13%) while those in Birmingham and Cardiff were roughly equal in the hand hygiene stakes (23% and 24% respectively). Commuters in Liverpool also registered a high score for faecal bacteria, with a contamination rate of 34%.

In Newcastle and Liverpool, men were more likely than women to show contamination (53% of men compared to 30% of women in Newcastle, and 36% of men compared to 31% of women in Liverpool), although in the other three centres, the women's hands were dirtier. Almost twice as many women than men in Cardiff were found to have contamination (29% compared to 15 %) while in Euston, they were more than three times likelier than the men to have faecal bacteria on their hands (the men here registered an impressive 6%, compared to a rate of 21% in the women). In Birmingham, the rate for women was slightly higher than the men (26% compared to 21%).

GNXP readers will know that these sorts of data might imply more than just public health issues.


Why women breakdown; maybe it's agriculture?   posted by Razib @ 10/15/2008 02:41:00 AM

Why Do Women Get More Cavities Than Men?:
"The role of female-specific factors has been denied by anthropologists, yet they attain considerable importance in the model proposed here, because the adoption of agriculture is associated with increased sedentism and fertility," Lukacs said. "I argue that the rise of agriculture increased demands on women's reproductive systems, contributing to an increase in fertility that intensified the negative impact of dietary change on women's oral health. The combined impacts of increased fertility, dietary changes and division of labor during the move into agricultural societies contributed to the widespread gender differential observed in dental caries rates today."

The original paper is Fertility and Agriculture Accentuate Sex Differences in Dental Caries Rates:
The transition from foraging to farming is associated with a widespread and well-documented decline in oral health, wherein women experience a more rapid and dramatic decline than men. Historically, anthropologists have attributed this difference to behavioral factors such as sexual division of labor and gender-based dietary preferences. However, the clinical and epidemiological literature on caries prevalence reveals a ubiquitous pattern of worse oral heath among women than men. Research on cariogenesis shows that women's higher caries rates are influenced by changes in female sex hormones, the biochemical composition and flow rate of saliva, and food cravings and aversions during pregnancy. Significantly, the adoption of agriculture is associated with increased sedentism and fertility. I argue that the impact of dietary change on women's oral health was intensified by the increased demands on women's reproductive systems, including the increase in fertility, that accompanied the rise of agriculture and that these factors contribute to the observed gender differential in dental caries.

Honestly, my first thought was "maybe women just like sugar more?" In any case, one thing I assume is that the higher "fertility" of agricultural women is going to be due to the fact that they do not space their births. In contrast, hunter-gatherer women typically have a reduced number of pregnancies because ofbehaviors such as extended breastfeeding. Of course, most agricultural societies quickly reached the Malthusian limit (ecological carrying capacity), so the higher fertility was likely balanced out by higher infant mortality. If agricultural women gave birth to more infants a greater proportion of these offspring ended up dying of diseases, etc., than for hunter-gatherers. So at birth any given hunter-gatherer infant is far more likely to reach reproductive age than any given offspring of peasants....

Related: Group lifespan differences? Maybe it's agriculture, Maybe it's agriculture?, Demon rum, Maybe it's agriculture - soft sweep TRPV6, Maybe it's agriculture?, Maybe it's agriculture - skin color edition.... and Tall, to short, to tall (again).


Tuesday, October 14, 2008

Reproductive variance of white American males and females   posted by Razib @ 10/14/2008 05:24:00 AM

This chart shows the proportion of white men and women age 50 and over who have 0, 1, 2, etc. children, up to 7. I got this from the GSS via CHILDS. I dropped 8 or more since that's unbounded, but very few had that many (on the order of 1%). Red is female, and navy male.

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Monday, October 13, 2008

Uyghurs, Chinese Muslims, etc.   posted by Razib @ 10/13/2008 04:55:00 PM

Chinese Muslims, Uyghurs, have been in the news a bit. When I'm listening to them the radio I notice there's some confusion among some presenters as to the difference, if any, between Uyghurs and Chinese Muslims. Last spring I recall Chinese government mouthpieces basically make stuff up out of whole cloth about Tibet without any fluent rebuttal or challenge in the media, so it might be worthwhile to just clarify some issues here.

1) Uyghurs are Muslim

2) Most Muslims in China are not Uyghurs

3) A greater number of Muslims in China are Hui, Chinese dialect speaking Muslims (called Dungan in Central Asia)

4) Uyghurs as we know them today are to a great extent an artificial identity which served specific imperial and bureaucratic interests of the Russian, Chinese and Soviet states

The last is probably a bit confusing to you. In short who occurred in Central Asia in the 19th and the 20th centuries was that nation-empires sliced and diced various tribal and local level identities into discrete ethnicities. The broad substratum of sedentary peoples who spoke Turkic dialects from the Caspian to what is today Western China were traditionally bracketed under the appellation Sart. These peoples were often ruled by descendants of nomadic groups (they were to some extent sedentarized nomads themselves, though admixed with indigenous Indo-European elements), or, dominated by contemporary nomadic populations. The term "Uzbek" originally applied specifically to a ruling elite who conquered the sedentary populations after the decline of Timurlane's lineage in Central Asia. Russian ethnologists simply labeled all Turkic speaking peoples under Uzbek hegemony as Uzbeks; that is how all Turkish speaking peoples within the boundaries of the political borders of Uzbekistan became Uzbek. The Kazakh and Kirghiz populations were given national identities though these were in fact more realistically confederations of different tribes ("hordes") with minimal cross-linkages. The term Uyghur comes from an early medieval ethnic-political group which was hegemonic in the Tarim basin, but Uyghur identity had disappeared in this region with its more thorough Turkicization and Islamicization (the originally Uyghurs were Manichaean, though later they turned Buddhist, and their empre encompassed a far greater expanse than the Tarim Basin). There is a minor ethnic group in Central China which actually derives from the original Uyghurs, and is called by that name as well. By analogy, some Maronite Christians in Lebanon deny that they are Arabs and claim that they are descendants of the Phoenicians. Though this may be true, obviously there is little real cultural continuity between Phoenicians and Maronite Christians who speak Arabic and whose ancestors have likely spoken Arabic for ~1,000 years.

The above is just to make clear that if you scratch under the artificial construction of Uyghur national identity, you basically have Turkish speaking Muslims. In Sons of the Conquerors the author observes that Uyghur dissidents tend to congregate in Istanbul. This emphasizes the Pan-Turkic aspect of Uyghur nationalism, and in fact the Turkish dialect of the Uyghurs is intelligible with the Turkish spoke in Turkey. Just as the French authorities may tell the children of African immigrants about their "ancestors" the Gauls, so Uyghur elites have accepted the glorious past of the Uyghur nation (the early medieval Uyghur Empire was very influential in Chinese politics as foederati). On the other hand, ethnographic surveys suggest that non-elite Uyghurs have little Uyghur nationalist self-conception, and just identify as Muslims. To some extent this parallels what exists in Turkey between a Turkic and European identified secular elite, and non-elite segment which is Islamically oriented.

What gets more complicated when you talk about Chinese Muslims is that the most numerous group are Chinese speaking and physically and culturally resemble the Han majority. These are termed "Hui people," to denote the fact that they are conceived of as a national minority, and not necessarily a religion. That is, many Hui may be secular or atheistic, just as many Han are, but they will nevertheless retain a Hui self-conception. Unlike the Uyghurs the Hui have long been embedded in a Han Chinese cultural milieu. Their religious orientation obviously separates them from the Han, for it is understood that though a Han may be Christian, Buddhist or Daoist, a Han who accepts Islam becomes a Hui. Nevertheless, the Hui have traditionally been part of the Chinese national experience for nearly 1,000 years; the famous Ming admiral Zheng He was from a Hui Muslim background (though the extant evidence suggests he was not particularly orthodox in the way most Muslims would recongize and leaned toward the syncretistic orientation of the Han majority; a tendency which was probably common enough to explain rather widespread evidence of Hui in much of South China assimilating to Han society). This is in stark contrast to the Uyghur, who were generally outside the purview of Chinese cultural influence. Within the last 1,000 years when polities based out of China had power over what is now Xinjiang, those polities were not Chinese (e.g., the Mongol Yuan and the Manchus). Though the Manchu dynasty ruled as Confucian emperors within China proper, in Mongolia, Manchuria, Tibet and Turkic Central Asia they ruled as tribal warlords. By analogy, consider that the British Hanoverian dynasty ruled for nearly a century as kings of Great Britain but were the electors of Hanover, and so subjects for most of that period to the Hapsburg dynasty. In other words, for much of the Manchu period the rule over non-Chinese territories was one of personal fealty, not one of integration into the Chinese bureaucratic state.

This changed during the 19th century, and especially the 20th. A more direct attempt at rule of Xinjiang naturally led to resistance and rebellion. One of the more interesting ways that the Chinese central government attempted to integrate Xinjiang into the state was to use Hui, Chinese speaking Muslims, as proxies against Turkic Muslims. Though Hui groups in China proper revolted during the 19th century, in Central Asia they have often been seen to be tools of Chinese political and cultural hegemony. A disproportionate number of the Chinese settlers in Xinjiang, and merchants who trade in the former Soviet republicans of Central Asia, are Hui. While in China proper the Hui are a separate and distinct ethnic group with peculiar folkways (in many areas of China they are the only minority of appreciable numbers), in Turkic Central Asia their Chinese cultural characteristics become much more salient to both themselves and to other Muslims. Though with the rise of mass communication the religious Hui have become generally conventional Muslims, it is notable that during Islamic reformist revolts the Hui used Daoist motifs to motivate mass risings because that was the most efficient way to communicate to a Chinese speaking population with a Chinese sense of cultural history despite their religious distinctiveness.

All this is to clarify the point that anti-Chinese feeling in Xinjiang intersects with both religious and ethnic differences, and the existence of the Hui as a group whose relation to the Han majority is highly conditional on circumstances complicates the picture. Though the Hui are often at tension with the Han majorities among whom they live there is an established modus vivendi, facilitated in large part by the fact that linguistically and physically the Hui are no different than the Han (some Hui show evidence of their non-Chinese origins in their features, but these exemplars are actually outliers). The Han Chinese push into Xinjiang on the other hand brings to mind a different dynamic, while the Hui are Jews among gentiles, the Uyghurs are like the Sioux being encircled by homesteaders. Though Xinjiang has been under political rule of a China based government since the 18th century, for most of that period it was operationally indirect enough so that it had little effect on the average Uyghur peasant in the oases. Local Turkic elites served as intermediaries and proxies for the Manchu political elite, just as in China proper the Confucian bureaucracy administered the country under the direction of a non-Chinese military elite.

At this point numbers are hard to come by, but it is assumed that Han Chinese are probably a majority of the population of Xinjiang. But, an important point must be made that Xinjiang as a cultural-administrative unit is a creation of the Chinese government. During the 18th century the northern half of the province, Dzungharia, was populated predominantly by Buddhist Mongolian peoples. During a series of wars these regions were ethnically cleaned and Muslim Kazakhs and Uyghurs entered into this vacuum. It is in this region that the city of Urumqi is situated, and where most Han in Xinjiang reside. Until recently the heartland of the Uyghurs, the string of oases and cities around the Tarim Basin were spared large scale immigration by the Han (in part for reasons of lack of transportation). But with the completion of railroads all the way to Kashgar that isolation is ended and there are reports that the number of Han Chinese is now increasing. Naturally this will result in more ethnic conflict. Unlike in Tibet proper the elevation in Xinjiang is not so extreme as to make it physiologically uncomfortable for outsiders. On the other hand, like Alaska Xinjiang is strongly geared toward a resource extraction economy at this point, and it seems plausible that if the Chinese rate of growth decreases to a point which chokes demand somewhat then the net flow of settlement might reverse. But I suspect that that will only occur a generation from now when the development of China starts to approach a more stationary state.

Until then, it seems likely that the cities of the Tarim Basin where Uyghurs remain a majority, albeit a progressively marginalized majority, will be loci for conflict. Religion is often a very good way to mobilize, motivate and coalesce group identity, so it seems likely that the banner of Islamic resistance will come to the fore in future decades. But, it is important to remember that the Uyghurs are not the most numerous Muslim group in China, the Hui are, and the ultimate root of the conflict is probably less to do with religious differences as it does with the fact that the ethnic groups of China proper, the Han and the Hui, seem likely to dispossess the Turkic Muslim groups of Xinjiang in their own lands in the coming years.

Note: Numerical note. The Chinese census suggests that about 50% of the population of the traditionally Muslim nationalities in China are Hui, that is, Chinese speaking Muslims. 40% are Uyghur, with the balance being taken up mostly by other Central Asian groups. I say traditionally Muslim nationalities because it seems likely that a large percentage of the Hui are not religious believers, just as a large percentage of Han are not religious believers. Since they are tabulated as an ethnic group this is irrelevant to their identity as Hui. Now, consider if a subset of Hui become involved in radical transnational Islam which attempts to subborn the Chinese state; the fact that Hui identity is both ethnic and religious will come to the fore. Whatever issues that an atheist Hui might have as a perceived ethnic minority in Han China, it seems implausible that they would align themselves with the Islamic world over their identification with China, in particular since many of these Hui have abandoned Islamic ritual prescriptions in the compromises necessary to live in an urban milieu (think the orthodox Jews from Poland who arrived to America's shores to work in the textile factories and what not). In contrast, the non-Hui Muslims are far less well integrated into Chinese culture and are ill equipped to piggy-back upon the rise of the Chinese economy. Additionally, anecdotally I've read reports which suggest that the Uyghurs are generally practicing Muslims, to a far greater extent than the Turks of the former Soviet republics. So a "buy in" to some abstract pie-in-the-sky Caliphate seems much more plausible from that sector.

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Sunday, October 12, 2008

It's about institutions within nations?   posted by Razib @ 10/12/2008 09:23:00 PM

Check out Calculated Exuberance, a weblog focused on macroeconomics and geography from an institutionalist perspective (from what I can gather). Though it would be nice if the charts to words ratio was a little more balanced! :-)

Genes which predict baldness?   posted by Razib @ 10/12/2008 05:58:00 PM

Male-pattern baldness susceptibility locus at 20p11:
We conducted a genome-wide association study for androgenic alopecia in 1,125 men and identified a newly associated locus at chromosome 20p11.22, confirmed in three independent cohorts (n = 1,650; OR = 1.60, P = 1.1 10-14 for rs1160312). The one man in seven who harbors risk alleles at both 20p11.22 and AR (encoding the androgen receptor) has a sevenfold-increased odds of androgenic alopecia (OR = 7.12, P = 3.7 10-15).

ScienceDaily has a somewhat amusing headline, Baldness Gene Discovered: 1 In 7 Men At Risk:
"I would presume male pattern baldness is caused by the same genetic variation in non-caucasians," said Richards, an assistant professor in genetic epidemiology, "but we haven't studied those populations, so we can't say for certain."

Well, the SNP at 20p11 exhibits different frequencies of the alleles across the HapMap populations (Europeans are the outgroup to Africans and Asians, just as they are to a great extent on the phenotype). I was amused at the use of the term "risk," I understand the technical reason, but it seems to make male pattern baldness seems like a much more problematic condition than it really is.


Adaptive Landscapes: Miscellaneous Points   posted by DavidB @ 10/12/2008 03:23:00 AM

My post here discussed Sewall Wright's concept of the adaptive landscape, and a post here discussed R. A. Fisher's views on the subject. Before I come to my planned note on Sewall Wright's Shifting Balance theory, there are some points about adaptive landscapes which didn't fit easily into the earlier posts...


As mentioned in the post on Wright's 'landscapes', he used two different versions of a multi-dimensional model of fitness. In one interpretation the dimensions, except for that of fitness, represent the number of alleles of different types in an individual genotype. I will call this a genotype landscape. In the other interpretation, the dimensions except for that of fitness represents the proportion of alleles of different types in a population. I will call this a frequency landscape. Both interpretations can be called genetic landscapes.

While Wright's interpretations always have genetic dimensions, other authors have used concepts in which the dimensions of the landscape represent phenotypic or ecological variables. I will call these phenotype landscapes. Peaks in such a landscape represent optimal phenotypes or ecological niches.

In both genetic and phenotype landscapes one of the dimensions usually represents reproductive fitness, but some alternative measure of adaptation may be used. For example if the phenotype is the shape of a fish, the measure of adaptation might be some aspect of swimming efficiency.

Some authors draw a distinction between a fitness landscape and an adaptive landscape, but the distinction is not consistently used. For example, according to Gavrilets (p.30) these terms are used to designate what I have called genotype and frequency landscapes respectively, but McGhee (p.1) uses them to designate genetic and phenotype landscapes. Most authors seem to use the terms 'adaptive landscape', 'fitness landscape', 'genetic landscape', and 'selective landscape' interchangeably, though each of them may also have other meanings. (For example, 'genetic landscape' may be used to describe the geographical distribution of genes.) Anyone searching for relevant studies should try all of these variants. I will use adaptive landscape as a general term embracing all of them.


There are at least two recent books devoted to adaptive landscapes, by Gavrilets and McGhee (see refs.). Gavrilets deals mainly with genetic landscapes, McGhee with phenotype landscapes. The book by Gavrilets has an extensive bibliography, which provides a good way into the literature on genetic landscapes. The studies I have looked at deal mainly with genotype landscapes. There seems to be comparatively little work on frequency landscapes, perhaps because the subject is less amenable to study by computer simulation.

The number of peaks in genotype landscapes

There is an extensive literature on the number of peaks in genotype landscapes, mainly based on the work of Stuart Kauffman.

To begin with, consider a model devised by Kauffman and Levin (1987). Suppose a genome has N loci. For simplicity, assume the loci are haploid and that there 2 possible alleles at each locus. There are therefore 2^N possible different genotypes. Now, suppose that each distinct genotype has a fitness which is independent of the fitness of any other genotype. We may then represent the fitnesses by numbers chosen at random (Kauffman and Levin use the range of rational numbers between 0.0 and 1.0). For simplicity we stipulate that no two genotypes have exactly the same fitness. If we choose one of the 2^N possible genotypes at random, there are N other genotypes which can be derived from that chosen genotype by varying an allele at a single locus. We call these the neighbours of the chosen genotype. The chosen genotype is a local optimum if it has higher fitness than all of its neighbours. But by the stated assumptions the fitnesses of the N + 1 genotypes concerned are random numbers, each of which must have a probability of 1/(1 + N) of being the largest in the set. There is therefore a probability of 1/(N + 1) that the chosen genotype is a local optimum. But the chosen genotype is randomly chosen from the 2^N possible genotypes, and any other genotype (by the given assumptions) would have an equal chance of being a local optimum within its own 'neighbourhood'. Since there are 2^N possible genotypes in total, the total expected number of local optima in the system is therefore (2^N)/(N + 1) [Note 1].

It is obvious that this number increases rapidly with increasing N. It is equally obvious that the assumption of independent fitnesses for each possible genotype is biologically unrealistic. It implies that no single locus, or combination of fewer than N loci, has any predictable effect of its own on fitness. As an extreme alternative to this, suppose that each locus makes a contribution to fitness which is independent of all other loci. In this case one of the alleles at each locus must be unambiguously fitter than the other allele, regardless of the alleles at other loci. Suppose we designate the fitter of the two alleles by an even number, and the less fit allele by an odd number. It is clear that no genotype containing an 'odd' allele can be a local optimum, because the fitness of the genotype could always be increased by substituting an even allele for the odd one. The only local optimum in the system is therefore the single genotype containing exclusively 'even' alleles, no matter how many genotypes there are in the system. This result can be extended to systems with diploid loci and/or multiple alleles at each locus, provided that one of the alleles at each locus is unambiguously fitter than all other alleles. We could also allow the fitness contribution of a locus to be affected by the alleles at other loci, provided the effect is not so great as to reverse the rank order of fitness of the alleles at each locus. This would be the case, for example, if each allele has a primary effect on one trait which makes a large difference to fitness, and a secondary effect on other traits, provided the secondary effects do not exceed the fitness difference due to the primary effect.

Between the two extreme models, there could be a variety of systems in which the rank order of the contributions of loci to fitness is partly but not entirely independent of other loci. Kauffman has devised a framework known as the NK model. [Note 2] In the NK model there are N haploid loci, with 2 possible alleles at each locus, while the fitness contribution of each locus is affected by the alleles at K other loci as well as itself. The fitness contribution of each possible combination of alleles at each such group of K + 1 loci is a random number chosen from the interval 0.0 to 1.0. For any particular assignment of alleles to the K+ 1 loci, this number determines the fitness contribution of the locus in question. The fitness of the genome as a whole, for any particular assignment of alleles to all N loci, is the average of the contributions for each locus.

The precise way in which the loci are connected to each other may vary. According to Kauffman (p.55) this usually makes little difference to the outcome. It may be useful to consider a simple special case which is not treated by Kauffman. Suppose we divide the N loci into N/(K + 1) discrete sets (assuming for simplicity that N/(K + 1) is a whole number). Let each of the K + 1 loci in each such set be 'connected' to the remaining K loci in the set. There are 2^(K + 1) possible combinations of alleles for each such set, and let each combination be assigned a fitness value randomly chosen from the interval 0.0 to 1.0. For any particular assignment of alleles to the loci, this number constitutes the fitness contribution of every locus in the set to the fitness of the genome. But each such set of K + 1 loci can be treated as a case of the Kauffman/Levin model, and has an expected number of [2^(K+ 1)]/[K + 2] local optima. Since each such set of loci, by assumption, has no effect on the fitness contribution of any loci outside the set, it follows that any combination of local optima for all of the N/(K + 1) discrete sets will also be a local optimum for the entire genome, since any change at a single locus would reduce the overall fitness of the genome. Since there are ([2^(K+ 1)]/[K + 2])^[N/(K + 1)] such combinations, this is the expected number of local optima for the entire genome. It may be easily checked that for the value K = N - 1, where each locus is connected to every other locus in the genome, this reduces to (2^N)/(N + 1), as in the first of the extreme models, while for K = 0, where no locus is connected to any other locus, it reduces to 1, as in the other extreme model. For values of K between 1 and N - 2, the number of local optima increases with increasing K and/or N.

In my simple example the genome is divided into non-overlapping sets of loci. But more generally in the NK model there will be overlap. For example, the sets of connected loci may be arranged cyclically, like abcde, bcdef, cdefg ......zabcd. Or the connections could be chosen at random, in which case there is a non-zero probability that the same locus will enter into more than one set of connected loci. This makes the problem of determining the number of local optima much more complicated. A given set of alleles may be a local optimum with respect to one set of connected loci, but one or more of those alleles may be sub-optimal for another set to which it belongs. In this case, changing one of those alleles will reduce fitness at some loci but increase it at others. The effect on the overall number of local optima for the genome as a whole is not intuitively obvious, and does not seem amenable to calculation by a general formula. Kauffman and others have relied on computer simulations. The most important result is that the number of local optima increases rapidly with increasing N and/or K (Kauffman p.60). This is not surprising, but it may be taken as vindicating Sewall Wright's intuition that in genotype landscapes with a lot of epistatic relations, the number of selective peaks will be very large. In general one may say that for a realistic size of genome (i.e. with thousands of loci) the number of peaks will be very large unless the value of K (averaged over the genome) is close to zero.

Kauffman's NK model is in many ways simplistic, but it does seem quite robust as a basis for exploring the theory of genotype landscapes. Other researchers have developed it in various ways. I don't know (or understand) this work well enough to summarise it, but I recommend the book by Gavrilets, which applies the theory to the problem of speciation. He notably claims that if a sufficient proportion of alleles are allowed to be selectively neutral, then in genotype landscapes of high dimensionality there will usually be a 'network' of ridges connecting the peaks, and along which populations can evolve without crossing fitness 'valleys'.

The number of peaks in frequency landscapes

As noted earlier, there seems to be much less work on frequency landscapes. In my post on Fisher I mentioned that in private letters Fisher argued that as the number of dimensions rises, the proportion of 'level points' which are all-round maxima will fall, and will be about 1/2^N of the total, where N is the number of dimensions. Fisher may have assumed that (a) in each dimension of gene frequencies, only about half of the level points will be maxima, and (b) the location of the maxima in each dimension is usually independent of the other dimensions. [Note 3] With these assumptions, the probability that a level point will be simultaneously maximal in all dimensions will only be about (1/2)^N, or 1 in 2^N, as suggested by Fisher. It does not follow that the number of maxima would not rise. If the number of level points in a single dimension is n, the expected number of level points in N independent dimensions would be n^N, so the expected number of all-round maxima would be (n^N)/2^N. For any n much greater than 2, this will increase rapidly with increasing N; for example, if n = 4, the number of maxima for N = 2, 3, 4.... will be 4, 8, 16... which rapidly becomes enormous.

The validity of the two key assumptions - that about half of the level points in each dimension will be maxima, and that these will be independent of each other - is debatable. First, if we consider loci without epistasis, there are three cases. If one homozygote is superior to the other, while the heterozgyote is either intermediate in fitness or equal to one of the homozygotes, then there will be one maximum and one minimum in the relevant dimension. If the heterozygote is superior to both homozygotes, there will be one maximum and two minima. If both homozygotes are superior to the heterozygote, there will be two maxima and one minimum. There are no cases in which there would be more than two minima or maxima. (If there are more than two alleles at the locus the possibilities are more complicated, but it is difficult to think of realistic scenarios in which there are more than two maxima or minima in each dimension.) For loci without epistasis the assumption that about half of the level points in each dimension will be maxima is therefore plausible as a rough average. But for loci with epistasis the key assumptions are doubtful. The assumption of independence for each dimension is no longer generally valid, as the fitness for all the interacting loci has to be considered simultaneously. For the important case of two interacting loci under selection for an intermediate phenotype (see the post on Wright) there will be two maxima, two minima, and only one saddle point. The key assumptions therefore do not hold even approximately in this case, and if it is at all common, the number of all-round maxima for the genome as a whole may be very large.

It has indeed been claimed (Gavrilets p.37) that the number of maxima is bound to rise with the number of dimensions. But as already discussed in connection with Kauffman's systems, there is no necessity about this: it is quite easy to conceive of a system with only one all-round maximum.

The accessibility and stability of peaks

From an evolutionary point of view, what is important is not just the number of adaptive peaks, but whether they are accessible to the population - i.e. whether the population will evolve towards them - and whether, if the population reaches them, they will be stable under disturbances such as temporary changes in the environment or influxes of migrants. For both purposes, in a frequency landscape we need to consider the 'zone of attraction' of the peaks, i.e. the range of gene frequencies within which the population will move towards the peak under the influence of natural selection. I have not found much discussion of this issue in the literature (which, as I have said, deals mainly with genotype rather than frequency landscapes), but a few general points seem clear.

First, we expect that, other things being equal, higher peaks will have wider zones of attraction. In geometrical terms, if two solid figures have the same shape, the taller figure will have the larger base. In genetic terms, the higher the fitness of a genotype relative to the average fitness of the population, the wider will be the range of gene frequencies within which the genes making up that genotype will be positively selected.

Second, peaks will have a wider zone of attraction if their component genes have an advantage in the heterozygote as well as the homozygote state. If the optimum genotypes contain recessive homozygotes, the genotypes will be rare, and therefore will not contribute much to the fitness of their component alleles, until the relevant alleles are already frequent in the population.

Third, even if a peak has very high fitness, it will not have a wide zone of attraction if the high fitness depends on the epistatic combination of a large number of alleles which do not otherwise have a fitness advantage. In such a case, the advantageous combinations will not appear with significant frequency in the population until all of the component genes already have a high frequency. The peak will be like a spike with a narrow base. Such a peak will be neither easily accessible nor stable, since even if the peak is reached, any fluctuation in the landscape is liable to push the population out of the zone of attraction.

Finally, whether or not a peak is easily accessible to a population depends on the population's current gene frequencies. Here it should be noted that in most of the plausible scenarios for multiple fitness peaks, such as Wright's favourite example of traits under stabilising selection, some of the alleles in the optimum genotypes will (at the peak) be fixed in the population, with alternative peaks at opposite sides or corners of the landscape. (This fact tends to be obscured by illustrative diagrams, including Wright's, which usually show peaks somewhere in the middle of landscape.) If alleles are fixed, the population can only move to another peak if new alleles are introduced by mutation or migration. These new alleles will be opposed by selection unless the environment changes so that the peak itself shifts. In order to move to another peak without migration or a change in environment, a long period of genetic drift, opposed by selection, will be required unless the population is very small. This is one of the key issues of credibility with Wright's shifting balance theory in its original form.

Note 1: Kauffman and Levin, pp.20-21. There might be a suspicion of fallacy somewhere in this argument, as the probability that a genotype is a local optimum is not independent of the probability for other genotypes. It would certainly be fallacious to conclude that there is a probability [1/(N + 1)]^[2^N] that all of the genotypes are local optima, since this is impossible. However, Kauffman and Levin's formula for the number of local optima appears to be valid.

Note 2: Kauffman p.42. Kauffman's description of the model is very concise and not ideally clear, partly because of ambiguity in his use of the terms 'gene', 'allele' and 'locus'. But I think my interpretation is consistent with what Kauffman and others say about the NK model.

Note 3: since Fisher gave no reasons for his claim, this is just speculation. He may quite possibly have had other reasons, but didn't spell them out. In his statistical work Fisher was very familiar with applications of N-dimensional geometry, so he would have had a better understanding than most people of the properties of high-dimensional landscapes .


Sergey Gavrilets, Fitness Landscapes and the Origin of Species, 2004.
Stuart Kauffman, The Origins of Order, 1993
Stuart Kauffman and Simon Levin, 'Towards a general theory of adaptive walks on rugged landscapes', J. Theoretical Biology, 1987, 128, 11-45.
George R. McGhee, The Geometry of Evolution: Adaptive Landscapes and Theoretical Morphospaces, 2007

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Moderation is on   posted by Razib @ 10/12/2008 12:57:00 AM

I've received a few emails which suggest that not everyone is aware that I've turned "moderation" on. That means I have to approve your comment. It was going to be a temporary measure, but so far I rather like how it's working out, so I'll leave it on. If I'm going to be away from the computer for more than 24 hours I'll probably turn it off temporarily, but otherwise expect latency on when your comments show up after posting.


'Here be dragons' in the mind   posted by Razib @ 10/12/2008 12:19:00 AM

A few days ago I ran across Worldly Goods: A New History of the Renaissance at a used book store. As suggested by the title the author focuses a great deal on mercantile happenings during this period. I read this book 10 years ago on a train ride. As I picked it up again I remembered that much of the narrative centered on the Fuggers, a prominent banking family which prefigured the role that the Rothchilds would play more recently in international affairs. Flipping through the chapters I refamiliarized myself with the contents, much of it was vaguely familiar to me. On the one hand if you had asked me to repeat anything from Worldly Goods I would have offered a general point about the importance of the Fugger financial network in the geopolitics of Central Europe during the 16th century. And yet I think there are many other facts and structures of facts which I retain implicitly in my mind. A great deal of cognition emerges out of these thickets of implicit data; networks which are essential in giving one a mental map of the world. Though I might not be able to explicitly recall in detail facts and arguments from a specific book when asked to do such a thing, in the course of a conversation or thought which might relate to the topicality of a given work I often experience data bubbling up from what might be termed the "subconscious."

I recount this because a few years ago a friend expressed an interest in the Middle Ages. I told him that Christopher Tyerman's God's War: A New History of the Crusdades might be worth his time. Later I asked if my friend had looked into Tyerman's book, and he told me had, but it was just too long (~1000 pages) and there was extraneous material he didn't find interesting. All fair enough, but then he proceeded to explain that felt he had little recall of anything he read and that he didn't know if there was any point. At that time something struck me as very strange about this claim. Now I feel I can elucidate more fully what I think my friend was missing: very few people have explicit on the spot recall of very much of a given work. So the contention that one does not retain much is plausible when viewed purely reflectively. But, the sum totality of data ingested does leave a mark on the implicit mind, sketching out structures and analytic sieves which can constrain and guide how one processes information and generates inferences.* You may not remember what happened to you on Janary 20th of 1999, but you have a sense of the general arc of that year in your life.

* More pointedly, many people assert rather dumb things because they are too ignorant to know any better. In fact, all people do. Some ignorant people are smart enough to assert very little, and some are not so smart.


Friday, October 10, 2008

Why some material is unmentionable   posted by Razib @ 10/10/2008 07:18:00 PM

Slate has some very interesting excerpts from The Big Necessity: The Unmentionable World of Human Waste and Why It Matters posted today. The reality that a great deal of the illness in today's world is caused by fecal contamination is well known. The proximate cause of many minor illnesses is mild food poisoning, but food poisoning itself is ultimately generally caused by poor hygiene.  It seems straightforward to imagine that poor sanitation can be a significant drain on economic productivity. But on this weblog we've also addressed the possibility of pathogens playing a role in changing personalities and temperaments. In Farewell to Alms Greg Clark made the case that the greater mortality due to poor hygiene shifted the death schedule and so relieved Malthusian pressure. In contrast, East Asia was notable for having a rather efficient system of human waste disposal and reuse, and the concomitant lower death rate resulted in more Malthusian pressures and lower per capita wealth. One of the positive developments in the historical disciplines has been the a shift away from narrative annals describing political and social happenings on the elite level, to a more thorough quantitative analysis of the state of mass culture and material condition. Both perspectives are important; in War and Peace and War Peter Turchin reports military historical research which suggests that the presence of Napoleon at a battle was the equivalent of the French having 30% more troops! This suggests that to some extent Great Men do matter, but one must remember that the emergence of parvenu such as Napoleon was conditioned upon the Malthusian economic and social stresses of late 18th century France.

But the Slate piece also puts the spotlight on the particular nature of human psychology and its relation to feces:

Reuse works better when it involves camouflage. This technique is used, appropriately for a militarized country, in Israel. During a presentation at a London wastewater conference, a beautiful woman from Israel's Mekorot wastewater treatment utility, who stood out in a room full of gray suits, explained that they fed the effluent into an aquifer, withdrew it, then used it as potable water. "It is psychologically very important," she told the rapt audience, "for people to know that the water is coming from the aquifer." This is a clever way of getting around fecal aversion. Not having wastewater-and not wasting water-would be better still.

I'm sure this is not surprising to most readers, especially if you have read something like Paul Bloom's Descartes' Baby. One can posit pretty straightforward adaptive reasons for why humans tend to have an aversion to feces and rot; but whatever the ultimate root of these instincts they're pretty universal. Of course, like eating spicy peppers humans seem able to get around these hardwired instincts, or leverage them in some way so as to invert their effect. For example, the application of feces upon wounds had a long history in pre-modern medicine, all the way back to the Egyptians. The detailed inferences can sometimes be surprising, but the point is that though most humans reflectively accept the atomic and molecular understanding of the world, reflexively they are Aristotelians. Intuitions can be overcome or unlearned to a great extent, but if one wishes to reform the human outlook one needs to take into account its a priori biases. The human mind is not amorphous clay which one can mold into any shape in an infinite manner of ways, rather, it is a collection of blocks and units which likely have innumerable combinatorial possibilities, but certainly a finite number subject to various constraints and conditions.

The cultural variation in attitudes which is overlain on human universals illustrates the reality that despite innate tendencies human minds are elastic. Consider:
Sanitation professionals sometimes divide the world into fecal-phobic and fecal-philiac cultures. India is the former (though only when the dung is not from cows); China is definitely and blithely the latter. Nor is the place of excrement confined to the fields. It has featured prominently in Chinese public life and literature for at least a thousand years.

The recycling of "night soil" mentioned in the Slate piece was also highly developed in Tokugawa Japan. Not only did the practice increase crop yields so that a large population was feasible with pre-modern agricultural techniques, but it had a byproduct effect of fostering public hygiene and reducing the disease burden (noted above). As far as the Chinese go, the attitude toward utilization of human waste, as well as other cultural traits such as minimal food taboos, illustrate the deep strain of pragmatic rationalism which many early or proto-Enlightenment philosophers so admired. As for the South Asia tendency to extend and elaborate on human intuitions and tendencies as opposed to channeling toward material ends, if you have nothing good to say, say nothing at all....

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Thursday, October 09, 2008

Lactase persistence variation in Britain   posted by Razib @ 10/09/2008 11:29:00 AM

Yann reviews a recent paper, Lactase persistence-related genetic variant: population substructure and health outcomes.

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Wednesday, October 08, 2008

The Metropolitan online   posted by Razib @ 10/08/2008 12:05:00 PM

The Whit Stillman film The Metropolitan is viewable online for free (at Hulu).

Tuesday, October 07, 2008

Another Nobel for the New Germ Theory of disease   posted by agnostic @ 10/07/2008 09:41:00 PM

In 2005, Barry Marshall and J. Robin Warren won the Nobel Prize in Physiology or Medicine for showing that a pathogen was behind the common diseases gastritis and peptic ulcers. Now the 2008 Prize goes to Harald zur Hausen, who showed that pathogens cause the common disease cervical cancer. As far as theory is concerned, these findings are not surprising (PDF). The most recent New Germ Theory winner before these two was Peyton Rous in 1966, whose work on cancer-causing pathogens began in 1911. You might also count Johannes Fibiger's 1926 Prize for what was thought to be a cancer-causing nematode.

And two of the early winners -- Koch in 1905 and Laveran in 1907 -- contributed to the Original Germ Theory of disease. So after 100 years, perhaps people are finally starting to take the idea seriously? Common disease-common variant researchers in human genetics may get more media coverage, including the science media, but the Germ Theory people are cleaning up where it counts.


McCain v. Obama: turning cognitive elites to blithering fools   posted by birch barlow @ 10/07/2008 06:19:00 PM

I think a lot of the reason for the unfounded hyperbole that has been spewed by many people at GNXP and elsewhere (especially by myself) is that this election is just plain ugly...there are no good choices. While no candidate may be Big Brother, O'Brien, HitlerStalinTojo, or the devil incarnate, they are almost certainly amongst the worst candidates Americans have had to choose from in U.S. history (is worst 10 percent reasonable?)

While there has been a lot of hyperbole against all candidates, there has been also a lot of unfounded praise and optimism, I think in hopes that there is a bright spot somewhere amongst these four candidates. I think this is where some commentators and posters such as myself have been driven to hyperbole.

In any case I apologize to anyone who had to dredge through my inappropriate, polemical, and unfocused posts. Time to go back to science or at least non-tabloid grade history.

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cis vs. trans & evolution   posted by Razib @ 10/07/2008 01:14:00 PM

Over at evolgen, more on the cis vs. trans debate:
...First, there is an excess of trans variation within populations. And, second, cis changes tend to be additive, while trans changes are dominant/recessive. That means recessive trans mutations can segregate in populations without phenotypic effects, while cis changes are exposed to selection from the get go (either purged by purifying selection or fixed by positive selection).


Deep Sea Video   posted by DavidB @ 10/07/2008 11:09:00 AM

The video of deep ocean fish in this news report is fantastic (for broadband browsers).

Monday, October 06, 2008

Following up association studies   posted by p-ter @ 10/06/2008 07:55:00 PM

Many recent posts on this site have been dedicated to genome-wide association studies, in which variants across the genome are tested for their association with a phenotype. These studies, if successful, identify a relatively small candidate region that presumably contains some sort of polymorphism that plays a role in the phenotype. Identifying that causal polymorphism is far from trivial.

A recent study on cleft lip provides a glimpse into how these sorts of follow-up might proceed. The authors had earlier shown (through a candidate gene study) that SNPs in IRF6 (a transcription factor) were associated with cleft lip. In particular, a non-synonymous SNP in the gene was repeatedly and reliably associated with the phenotype. In this follow-up study, however, the authors find another, non-coding SNP that shows the strongest association with the phenotype.

The authors are then able to show that this SNP falls in a binding site for another transcription factor, and that the region is an enhancer element that drives expression of IRF6 in the developing face. They don't show that the SNP changes expression patterns, but it's still a pretty impressive piece of work, and exemplifies the extensive experimental work that will be needed to ultimately refine the glut of genome-wide association signals being published.


Can someone put the psychic unity of makind out of its misery?   posted by Razib @ 10/06/2008 07:14:00 PM

Evolutionary emergence of responsive and unresponsive personalities:
In many animal species, individuals differ consistently in suites of correlated behaviors, comparable with human personalities. Increasing evidence suggests that one of the fundamental factors structuring personality differences is the responsiveness of individuals to environmental stimuli. Whereas some individuals tend to be highly responsive to such stimuli, others are unresponsive and show routine-like behaviors. Much research has focused on the proximate causes of these differences but little is known about their evolutionary origin. Here, we provide an evolutionary explanation. We develop a simple but general evolutionary model that is based on two key ingredients. First, the benefits of responsiveness are frequency-dependent; that is, being responsive is advantageous when rare but disadvantageous when common. This explains why responsive and unresponsive individuals can coexist within a population. Second, positive-feedback mechanisms reduce the costs of responsiveness; that is, responsiveness is less costly for individuals that have been responsive before. This explains why individuals differ consistently in their responsiveness, across contexts and over time. As a result, natural selection gives rise to stable individual differences in responsiveness. Whereas some individuals respond to environmental stimuli in all kinds of contexts, others consistently neglect such stimuli. Interestingly, such differences induce correlations among all kinds of other traits (e.g., boldness and aggressiveness), thus providing an explanation for environment-specific behavioral syndromes.

Related: Heritability of the Ultimatum Game, Chimps, the ultimatum game & time preference and Altruism and Risk-Taking: Kinda Heritable.

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Steven Jones is being silly   posted by Razib @ 10/06/2008 03:53:00 PM

Leading geneticist Steve Jones says human evolution is over. Steve Jones has an appointment in the Galton laboratory, and has written several books on human genetics (e.g., Y: The Descent of Man and Darwin's Ghost: The Origin of Species Updated). But he says things like this:
"Small populations which are isolated can evolve at random as genes are accidentally lost. World-wide, all populations are becoming connected and the opportunity for random change is dwindling. History is made in bed, but nowadays the beds are getting closer together. We are mixing into a glo-bal mass, and the future is brown."

First, we're nowhere close to panmixia.* Second, there is going to be a large variance around the expectation. Even if you remove new mutations, there are a lot of variants out there for selection to pick up from the extant genetic background I would think. The future will not be brown for the same reason that people in an English village do not all have the same hair color despite there being a lot of intermarriage.

Lots of other things to point to that leave you confused in that piece, but I'll leave it as an exercise for the readers....

* And what about the lack of importance of population size as a parameter effecting substitutions in Neutral Theory? I know there are ways you can object to this, but Jones' quote seems to garble many issues here.

Update: I emailed an academic who I suspected would know if Jones was being quoted out of context or misrepresented. But they say that this is probably an accurate representation of his views (and they also seem to think that his coherency leaves a bit to be desired).

Update II: Here is Chris Stringer's rebuttal to Jones:
But Professor Chris Stringer, research leader in human origins at the Natural History Museum, London, said the idea that evolutionary pressures were no longer taking their toll on humanity was true of only western civilisation.

He said: "The argument that modern life has stemmed the effects of evolution is true in some areas, such as the way in which medicine has improved health and wellbeing, and the fact I am not out in the cold and wet, but sitting in a nice, warm office with heat and clothing. But that is very much something that applies only in developed, western countries. You only need look to Africa to see how HIV/Aids is still having an enormous impact on selection, and I believe that genetics will continue to play a part in our evolution."

*roll eyes* Someone should tell these guys that you don't need to die to not reproduce.

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Sunday, October 05, 2008

South Park   posted by Razib @ 10/05/2008 09:59:00 PM

New episode of South Park this Wednesday. As always you can watch it online.   posted by Razib @ 10/05/2008 07:08:00 AM

Think Gene has a new digg-like site up, Worth checking out.

Friday, October 03, 2008

Beyond Belief III   posted by Razib @ 10/03/2008 07:01:00 AM

Beyond Belief III is going down right now, the 3rd to the 6th. Free registration is soldout, but it looks like there are still some pay slots. If you're in the San Diego area you might be able to attend....

Wednesday, October 01, 2008

Russian dudes are imperialists   posted by Razib @ 10/01/2008 05:23:00 AM

Dynamics of Alliance Formation and the Egalitarian Revolution:

Arguably the most influential force in human history is the formation of social coalitions and alliances (i.e., long-lasting coalitions) and their impact on individual power. Understanding the dynamics of alliance formation and its consequences for biological, social, and cultural evolution is a formidable theoretical challenge. In most great ape species, coalitions occur at individual and group levels and among both kin and non-kin. Nonetheless, ape societies remain essentially hierarchical, and coalitions rarely weaken social inequality. In contrast, human hunter-gatherers show a remarkable tendency to egalitarianism, and human coalitions and alliances occur not only among individuals and groups, but also among groups of groups. These observations suggest that the evolutionary dynamics of human coalitions can only be understood in the context of social networks and cognitive evolution.

Their conclusion:

We propose a simple and flexible theoretical approach for studying the dynamics of alliance emergence applicable where game-theoretic methods are not practical. Our approach is both scalable and expandable. It is scalable in that it can be generalized to larger groups, or groups of groups. It is expandable in that it allows for inclusion of additional factors such as behavioral, genetic, social, and cultural features. Our results suggest that a rapid transition from a hierarchical society of great apes to an egalitarian society of hunter-gatherers (often referred to as “egalitarian revolution”) could indeed follow an increase in human cognitive abilities. The establishment of stable group-wide egalitarian alliances creates conditions promoting the origin of cultural norms favoring the group interests over those of individuals.

The title is a joke because the lead author is Sergey Gavrilets, who is a product of Moscow State University in the 1970s, just like Peter Turchin. And like Turchin Gavrilets is all over the place trying to produce formal models to elucidate a range of diverse questions. Gavrilets' research interests are social and cultural evolution, speciation and adaptive radiation, sexual conflict, holey fitness landscapes (this is how I knew him originally) and microevolutionary processes and macroevolutionary patterns. Good luck with all that, as they say....


Punctuation Error?   posted by DavidB @ 10/01/2008 04:59:00 AM

Readers who lived through the Punctuated Equilibrium controversy of the 70s and 80s will recall that it petered out rather inconclusively, largely for lack of decisive empirical evidence one way or the other. The fossil record is seldom good enough to distinguish unambiguously between punctuational and gradual modes of evolution, one problem (noted already by Darwin) being that the sudden appearance of a new form in a given locality may result from migration rather than rapid evolution in the same place.

Given these difficulties, a disproportionate amount of attention was focused on a handful of examples that seemed to show good evidence either of punctuational or gradual evolution. One of the best examples on the punctuationist side of the debate was a study of molluscs in the Turkana Basin of Africa by P. G. Williamson [Note 1] Williamson's study was criticised at the time on various grounds - for example that the changes observed might be due to environmental stress rather than genetic evolution - but the critics did not produce new evidence from the field.

That is changed by an article [Note 2] by a Dutch team in a recent issue of the journal Evolution....

The Abstract of the article is as follows:

A running controversy in evolutionary thought was Eldredge and Gould's punctuated equilibrium model, which proposes long periods of morphological stasis interspersed with rapid bursts of dramatic evolutionary change. One of the earliest and most iconic pieces of research in support of punctuated equilibrium is the work of Williamson on the Plio-Pleistocene molluscs of the Turkana Basin. Williamson claimed to have found firm evidence for three episodes of rapid evolutionary change separated by long periods of stasis in a high-resolution sequence. Most of the discussions following this report centered on the topics of (eco)phenotypy versus genotypy and the possible presence of preservational and temporal artifacts. The debate proved inconclusive, leaving Williamson's reports as one of the empirical foundations of the paradigm of punctuated equilibrium. Here we conclusively show Williamson's original interpretations to be highly flawed. The supposed rapid bursts of punctuated evolutionary change represent artifacts resulting from the invasion of extrabasinal faunal elements in the Turkana palaeolakes during wet phases well known from elsewhere in Africa.

I have read the full article (available here), which looks convincing on this particular case (but what do I know about old African molluscs?) [Added: a more easily readable pdf version is also available. Google 'bocxlaer turkana' and you should find it.] The strongest point is that it is not just armchair criticism but based on extensive new fossil collecting. But since I specialise in armchair criticism I can hardly throw any stones.

Obviously one such case doesn't disprove punctuated equilibrium, but Williamson's study was in some ways the 'poster child' for the theory (more so than even Eldredge and Gould's own studies), so its demolition (if accepted) would be a serious blow.

Note 1: P. G. Williamson, 'Palaeontological documentation of speciation in Cenozoic molluscs from Turkana Basin', Nature, 1981, 293, pp.437-43. Also reprinted in Evolution Now, ed. John Maynard Smith, 1982. I can't find any publications by Williamson after 1990, and I believe I have read somewhere that he died at a sadly early age. My apologies if I am mistaken.

Note 2: Bert van Bocxlaer, Dirk van Damme, and Craig S. Feibel, 'Gradual versus punctuated equilibrium evolution in the Turkana Basin molluscs: evolutionary events or biological invasions?', Evolution, 2008, 62, pp.511-20.

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The Mongol Art of War   posted by Razib @ 10/01/2008 01:23:00 AM

If Genghis Khan and the Making of the Modern World grated on you because of the transparent lack of scholarly objectivity, I recommend Timothy May's The Mongol Art of War. May usually attempts to present "both sides" in any given scholarly debate, but he also tells you which side is the majority and which the minority. And there's good quantitative data, like the fact that Mongol light cavalry had a range of up to 300 meters in terms of their bows. The Mongol Art of War makes it pretty obvious that courage is sometimes overrated as an ingredient of conquest, the Mongols rarely engaged in pitched battles because they weren't exceptional hand-to-hand fighters. Rather, when battling an enemy on open field they simply barraged their opponents with missile fire until attrition wore them down. Their reputedly high accuracy from long distances meant that they could stay out of danger while simultaneously inflicting casualties on the opposition. Not to be trite but it sounds like a precursor to "shock & awe" via air power medieval style.

It seems understandable that chivalry might emerge in societies where martial elites have incentives to formalize & codify and so minimize the risks inherent in the art of war, which is after all their primary profession. In contrast, the Mongol war machine which emerged in the early 13th century was notable for its relatively exceptional social egalitarianism. The Mongol army did not consist of an elite professional war-band, but rather was drawn from vast swaths of the adult male tribal population of Mongolia (on the order of perhaps 1/2 of the adult males served in the mobile armies during the initial years). Like the Roman legions before 100 BCE this was a nation of soldiers on the march, not the soldiers of a nation. Genghis Khan's light cavalry simply leveraged the typical skills of a nomad on a horse with bow in hand. The rapid expansion from the Yellow to the Black seas was due less to the calculated glory seeking of status seeking aristocrats than the random-walk rapaciousness of nomads whose lives had been characterized by existence on the margins of subsistence supplemented by raiding of surplus producing sedentary farmers. To some extent the emergence of the Mongol Empire was a series of raids writ-large.

Addendum: One thing I found interesting was the suggestion that one of the major reasons that Mongol expansion into the Middle East ran out of steam was lack of pasture for their horses. Each Mongol warrior might have had 5-15 horses. In South China the Mongols under Kublai Khan had to reinvent themselves because light cavalry did not offer any comparative advantage in the local ecology. And later Mongol attempts to expand into Southeast and Maritime Asia generally failed more often than not. In many parts of Eurasia the Mongols were defeated, but like the Romans before them they kept coming and eventually overcame resistance. This makes me wonder about true historical significance of the Mamluk defeat of the Mongols at the Battle of Ain Jalut, as in many accounts this is a great historical turning point. The implication is that if the Mongols had not been defeated in this battle they would have gone on to conquer all of North Africa. But as I alluded to above in Russia there were defeats but the Mongols bounced back. In contrast they were defeated several times by the Mamluks after Ain Jalut. This to me points to ecological constraints on the comparative advantage of the Mongol-way-of-war. Of course it is also quite plausible that empires have natural limits to their size contingent upon the scalability of communication lines as well as the diminishing returns on additional increments of territory.