Gene Expression

Gene Expression Survey

2010-02-09T01:04:00.000-08:00

That time of the year. Please take the Gene Expression Survey. I'll put up the analysis and the csv file next week. I have the usual questions, but also added a few more that might seem a bit weird. There are 30 questions total, and you don't need to answer all of them, but as I said the more you answer the more data there'll be. I did a trial run and it took less than 5 minutes; most people can answer a question about their sex or religious identity pretty quickly.

Delayed childbearing & autism

2010-02-08T11:22:00.000-08:00

Independent and dependent contributions of advanced maternal and paternal ages to autism risk:

Reports on autism and parental age have yielded conflicting results on whether mothers, fathers, or both, contribute to increased risk. We analyzed restricted strata of parental age in a 10-year California birth cohort to determine the independent or dependent effect from each parent. Autism cases from California Department of Developmental Services records were linked to State birth files (1990-1999). Only singleton births with complete data on parental age and education were included (n=4,947,935, cases=12,159). In multivariate logistic regression models, advancing maternal age increased risk for autism monotonically regardless of the paternal age. Compared with mothers 25-29 years of age, the adjusted odds ratio (aOR) for mothers 40+ years was 1.51 (95% CI: 1.35-1.70), or compared with mothers <25 years of age, aOR=1.77 (95% CI, 1.56-2.00). In contrast, autism risk was associated with advancing paternal age primarily among mothers <30: aOR=1.59 (95% CI, 1.37-1.85) comparing fathers 40+ vs. 25-29 years of age. However, among mothers >30, the aOR was 1.13 (95% CI, 1.01-1.27) for fathers 40+ vs. 25-29 years of age, almost identical to the aOR for fathers <25 years. Based on the first examination of heterogeneity in parental age effects, it appears that women's risk for delivering a child who develops autism increases throughout their reproductive years whereas father's age confers increased risk for autism when mothers are <30, but has little effect when mothers are past age 30. We also calculated that the recent trend towards delayed childbearing contributed approximately a 4.6% increase in autism diagnoses in California over the decade.

See ScienceDaily for more detail.

Beautiful butterflies & localized adaptation

2010-02-06T21:17:00.000-08:00

Two new papers are out in PLoS Genetics which make inferences about adaptation using butterfly species which exhibit Mullerian mimicry. I'll give the author summaries instead of the abstracts.

Genomic Hotspots for Adaptation: The Population Genetics of Mullerian Mimicry in the Heliconius melpomene Clade:

The diversity of wing patterns in Heliconius butterflies is a longstanding example of both Mullerian mimicry and adaptive radiation. The genetic regions controlling such patterns are "hotspots" for adaptive evolution, with small regions of the genome controlling major changes in wing pattern. Across multiple hybrid zones in Heliconius melpomene and related species, we no find no strong population signal of recent selection. Nonetheless, we find significant associations between genetic variation and wing pattern at multiple sites. This suggests patterning alleles are relatively old, and might be a better model for most natural adaptation, in contrast to the simple genetic basis of recent human-induced selection such as pesticide resistance. Strikingly, across the region controlling the red forewing band, a very strong association with phenotype implicates three genes as potentially being involved in control of wing pattern. One of these, a kinesin gene, shows parallel differences in expression levels between divergent forms in the two mimetic species, making it a strong candidate for control of wing pattern. These results show that mimicry involves parallel changes in gene expression and strongly suggest a role for this gene in control of wing pattern.

Genomic Hotspots for Adaptation: The Population Genetics of Mullerian Mimicry in Heliconius erato:

Identifying the genetic changes responsible for beneficial variation is essential for understanding how organisms adapt. Here, we use a combination of mapping, population genetic analysis, and gene expression studies to identify the genomic regions responsible for phenotypic evolution in the Neotropical butterfly Heliconius erato. H. erato, together with its co-mimic H. melpomene, have undergone parallel and concordant radiations in their warningly colored wing patterns across Central and South America. The "genes" underlying the H. erato color pattern radiation are classic examples of Mendelian loci of large effect and are under strong natural selection. Nonetheless, we do not see a clear molecular signal of recent natural selection, suggesting that the H. erato color pattern radiation, or the alleles that underlie it, may be quite old. Moreover, rather than being single locus, the genetic patterns suggest that multiple, widely dispersed loci may underlie pattern variation in H. erato. One of these loci, a kinesin gene, shows parallel expression differences between races during wing pattern formation in both H. erato and H. melpomene, suggesting that it plays an important role in pattern variation. High rates of recombination within naturally occurring H. erato hybrid zones mean that finer genetic dissection will allow us to localize causative sites and better understand the history and molecular basis of this extraordinary adaptive radiation.

Here's a section from the first paper which I found intriguing:

The results therefore appear to support the 'shifting balance' model for the evolution of Heliconius colour pattern races...whereby novel wing patterns arise and spread through otherwise continuous populations behind moving hybrid zones...The 'Pleistocene refuge' model seems less likely, as recent contact after extended periods of geographic isolation would presumably have left a stronger signal of genetic differentiation between divergent races, perhaps across the genome but especially more strongly in regions linked to patterning loci...

I have no idea why they necessarily think this validates the shifting balance. You can see David's critique of the model, but reading Will Provine's intellectual biography of Sewall Wright it seems that the shifting balance sometimes becomes the evolutionary genetic version of "it's complicated."* What they seem to have done here though is refute a simple model of powerful selective sweeps giving rise to these morphs recently. Rather, these seem to be ancient local adaptations, whose frequencies and genetic architectures are perhaps perturbed by long term exogenous (e.g., environment) and endogenous (e.g., complex frequency dependencies) dynamics.

Despite my lack of clarity on a few theoretical issues, I found the papers very interesting, and haven't really processed them fully.

Citation:

Baxter SW, Nadeau NJ, Maroja LS, Wilkinson P, Counterman BA, et al. 2010 Genomic Hotspots for Adaptation: The Population Genetics of Mullerian Mimicry in the Heliconius melpomene Clade. PLoS Genet 6(2): e1000794. doi:10.1371/journal.pgen.1000794

Counterman BA, Araujo-Perez F, Hines HM, Baxter SW, Morrison CM, et al. 2010 Genomic Hotspots for Adaptation: The Population Genetics of Mullerian Mimicry in Heliconius erato. PLoS Genet 6(2): e1000796. doi:10.1371/journal.pgen.1000796

* I see one reference to epistasis in both papers, and that concept is very important in the shifting balance. Though I assume the LD and supergenes might point to that.

Eliezer Yudkowsky & Razib Khan on bloggingheads.tv

2010-02-06T00:52:00.000-08:00

Hayek vs. Keynes

2010-02-05T17:59:00.000-08:00

You've probably watched the Hayek vs. Keynes rap by now:

Am the only one who was a little weirded out by the incongruity of John Maynard Keynes kickin' it with the honeys in the back of the limo? It isn't as if he was exactly on the down-low. He was a freak, swinging both ways, though not symmetrically....

Language goes extinct, human race to follow....

2010-02-05T09:23:00.000-08:00

Last speaker of ancient language of Bo dies in India:

Professor Anvita Abbi said that the death of Boa Sr was highly significant because one of the world's oldest languages - Bo - had come to an end.

...

"It is generally believed that all Andamanese languages might be the last representatives of those languages which go back to pre-Neolithic times," Professor Abbi said.

"The Andamanese are believed to be among our earliest ancestors."

I have a tendency to eye roll when people come out with these weepy stories about dying languages. When a language dies a people dies, more or less. No doubt there are particular stories, memories passed down which maintain continuity of identity, which disappear. But humans do not necessarily die. If members of obscure tribe X all learn English, or Chinese, tribe X as tribe X disappears, more or less. This is not trivial, I believe most humans would prefer that the cultural forms which pervade their own lives would pass down to future generations. Memory is to a great extent the only form of immortality we've had access to. But for members of obscure tribe X learning a widely spoken language is often a boon, and brings great benefit as they can engage in more fruitful exchanges with the broader human race. The implicit contract that peoples make with their own ancestors extracts too high a cost at some point, and when the present ceases to uphold its pact with the past, the past becomes obscured in the mists.

On a specific note about this article, the Andaman Islanders are actually a real concrete human population, they're not "among our earliest ancestors." Additionally, I thought that languages which were purely oral tended evolve faster than languages which were written down. Is it then plausible to make great claims for Bo's antiquity?

Related: The tragedy of dying languages. Larded with specious banalities or outright falsities, but good for a laugh.

Ibn Khaldun In Our Time

2010-02-05T01:09:00.000-08:00

Ibn Khaldun on In Our Time. Excellent program. Khaldun's assessment that the Mamluks of Egypt had developed a system of rule which was robust against the decay of asabiyyah was born out by 450 years of subsequent history (that is, until the liquidation of the Mamluk ruling caste of Egypt in the 19th century). Unfortunately, the pervasive Islamic system of channeling slaves into the military and bureaucracy from the time of Al-Mu'tasim in the early 9th century seems to have been a local optimum. Like a Confucian bureaucratic state it was relatively stable and robust, maintaining a modicum of peace and order, but over the long term it produced stasis. These are social systems geared toward squeezing more "efficiencies" (operationally, rents for the elite) out of the system, not reinventing it so as to generate growth in wealth which compounds.

"Synthetic associations" and sickle cell anemia

2010-02-01T19:40:00.000-08:00

Last week, I made a silly error in describing a problem in the sickle cell anemia example given by Dickson et al. (2010) as an empirical example of the phenomenon they call "synthetic association". So allow me to take a mulligan, and re-try this:

The authors performed an association study in African-Americans, using ~200 individuals with sickle cell anemia as cases, and >7,000 controls. From their description, they simply performed a logistic regression of disease status on common polymorphisms genome-wide. This turned up a large (~2.5Mb) region surrounding HBB (known to harbour the rare disease-causing mutation) as highly associated with the phenotype. This large region of association stands in contrast, they argue, to the known patterns of linkage disequilibrium in the region, which extends over a few kilobases at most.

This observation, they argue, is an empirical example of how associations due to rare variants can lead to large blocks of associations at common variants. This effect is due to the fact that haplotypes surrounding rare variants are longer and have had little time to be broken up by recombination. Under certain genetic models, this effect of "synthetic associations" is plausible, however, this example is a poor one for making their case.

The reason is that individuals with sickle cell anemia have two chromosomes of African ancestry in the region of HBB, while individuals without sickle cell anemia have approximately the background distribution of European and African chromosomes at the locus--~20% European and ~80% African. To put it another way, let X_d be number of chromosomes of African ancestry of an individual some distance d from HBB (X can be 0, 1, or 2), and Y be the number of chromosomes of African ancestry of an individual at HBB. In the cases, they've conditioned on the fact that Y=2, while in the controls they have not. P(X_d) != P(X_d | Y =2), so much of their association is likely due simply to differences in ancestry between the cases and controls in the HBB region (recall that admixture linkage disequilibrium in African-Americans extends for megabases).

More concretely, any SNP near the HBB locus that happened to be fixed for opposite alleles in Europe and Africa would have a whopping 20% allele frequency difference between cases and controls in their analysis, attributable simply to differences in local ancestry. That's the extreme (and unlikely) situation, but alleles with more modest allele frequency differences between populations will show the same effect.

To some extent, this is their point--the haplotype carrying the causal mutation is long. But the effect in this case is massively exaggerated by admixture, and the presentation of this exaggerated effect is misleading.

Half Sigma's flawed post on DTNBP1

2010-02-01T10:33:00.000-08:00

A while back, Mark and I were working on a comprehensive post which would try to tally the results of the various IQ-gene studies to see what they said about racial differences. We began this quest bright-eyed and hopeful that we would help contribute to ending a calamitous debate that has gone on for way too long. However, as we learned more about genetics, and these studies in particular, we came to realize that it's too early to take IQ-genes seriously.

We began with an approach similar to what Half Sigma did 2 years ago with the DTNBP1 gene. However, we soon learned that this approach was incredibly flawed and misleading. I wasn't going to write this post, but recently Half Sigma's DTBP1 post was linked from Reddit and tens of thousands of people are viewing it. When I saw that, I frustratedly criticized HS. He responded that I should give a more diplomatic and reasoned response, so here it is:

You cannot simply add up SNPs from the same gene or chromosome. Half Sigma simply adds the observed effects of the SNPs to one another, ignoring that the alleles are highly correlated with one another, and not independently inherited, which is referred to as linkage disequilibrium (LD). The study that Half Sigma used provides the following table of LD for its SNPs:

	rs2619539	rs3213207	rs1011313	rs2619528	rs760761	rs2619522	rs2619538
rs2619539	-	0.156	0.111	0.0	0.0	0.001	0.055
rs3213207	1.0	-	0.014	0.334	0.403	0.34	0.076
rs1011313	0.916	1.0	-	0.037	0.033	0.036	0.081
rs2619528	0.024	0.955	1.0	-	0.838	0.737	0.128
rs760761	0.015	1	1.0	0.96	-	0.854	0.166
rs2619522	0.04	0.955	1.0	0.867	0.96	-	0.182
rs2619538	0.242	0.823	0.825	0.648	0.772	0.778	-

As can be seen in this table, pairwise LD goes as high as 1.0, meaning that two of the alleles are always inherited together. Adding these SNP's together is therefore like counting them twice.

Group comparisons require replication in both groups. Because different populations have systematic genetic and environmental differences, an effect in one group may not occur in another. The study that Half Sigma uses relies primarily on a (small) sample of Dutch people. It is unclear whether these effects would exist in a population of African ancestry, let alone another European one.

Candidate-gene association studies are not reliable. This is the most important point. Candidate gene association studies have largely failed to replicate. In fact, there have been no common IQ polymorphisms which have been replicated. Genome-wide association studies, which don't suffer as severely the various biases of candidate-gene association studies like publication bias or the winner's curse have not shown common SNP-associations with IQ.

IQ is highly heritable, so the problem is the current methods, not the search for genes. With the development of sequencing technology and huge cohorts, we will be able to see the genes that are really behind normal IQ variation. With replication in multiple ethnicities and races, we will also see to what extent various genes and environments are responsible for group differences. There's no need to make proclamations of victory for hereditarianism or environmentalism in the mean time.

Jersey Shore coming back

2010-01-31T00:56:00.000-08:00

They've been signed for $10,000 per episode the next go around. Years ago Joel floated the idea of using Reality TV to test theories in social science. Paying the cast of Jersey Shore this much is going to mean that they'll be under serious pressure to produce high quality "product." I assume that means they're crank up the magnitude of their "character." For example, Ronnie Magro will be under pressure to beat up more d-bags next season. "The Situation" is going to have to do the nasty with even nastier.

Proud to be red

2010-01-29T14:15:00.000-08:00

A friend pointed me to this YouTube clip of a young red-haired man objecting to the term "ginger," and the opprobrium he's been subjected to since the South Park episode "Ginger Kids" popularized ideas such as the possibility that redheads have no soul. I assume the kid is joking. On the other hand, I have read that red-haired males are at some disadvantage on online dating sites, just like non-white males. Have any readers of the red persuasion ever felt put upon due to their rare pigment status?

Darwin wuz wrong, part n

2010-01-29T00:44:00.000-08:00

A review of a new book, What Darwin Got Wrong. Co-authored by Jerry Fodor, who has been continuing his war against natural selection. I've already read Darwinian Fairytales: Selfish Genes, Errors of Heredity, and Other Fables of Evolution (at the suggestion of a reader who found the arguments within incredibly persuasive, convincing me to simply ignore anything that reader ever asserted after finishing the book), so I think I have my quota of philosopher-declaring-evolution-the-naked-emperor under my belt. Meanwhile, there are real scholars grappling with the issues which emerged in the wake of the Neo-Darwinian Synthesis and its discontents, and pushing science forward.

Yes, Darwin was wrong about many things. But how many scientists will still have such an impact 150 into the future? He's a big enough figure that people can sell books just by putting his name into the title! Only a few others fall into that class.

Note: Here you can read a draft of the third chapter of What Darwin Got Wrong.

Peer groups & bourgeois virtues

2010-01-28T17:36:00.000-08:00

Self-Control and Peer Groups:

However, according to a new study by Michelle vanDellen, a psychologist at the University of Georgia, self-control contains a large social component; the ability to resist temptation is contagious. The paper consists of five clever studies, each of which demonstrates the influence of our peer group on our self-control decisions. For instance, in one study 71 undergraduates watched a stranger exert self-control by choosing a carrot instead of a cookie, while others watched people eat the cookie instead of the carrot. That's all that happened: the volunteers had no other interaction with the eaters. Nevertheless, the performance of the subjects was significantly altered on a subsequent test of self-control. People who watched the carrot-eaters had more discipline than those who watched the cookie-eaters.

I assume time preference is heritable (at least via its correlation with other traits such as IQ), but, that assumes you control background social and cultural variables.

Race: A Social Destruction of a Biological Concept

2010-01-28T14:19:00.000-08:00

What is the single best reference for refuting the notion that "race is only a social construct" for a non-scientist? I don't know. (Suggestions welcome in the comments.) But Neven Sesardic (previously praised here) does a marvelous job in "Race: A Social Destruction of a Biological Concept," (pdf) Biology and Philosophy (2010, forthcoming).

It is nowadays a dominant opinion in a number of disciplines (anthropology, genetics, psychology, philosophy of science) that the taxonomy of human races does not make much biological sense. My aim is to challenge the arguments that are usually thought to invalidate the biological concept of race. I will try to show that the way ‘‘race’’ was defined by biologists several decades ago (by Dobzhansky and others) is in no way discredited by conceptual criticisms that are now fashionable and widely regarded as cogent. These criticisms often arbitrarily burden the biological category of race with some implausible connotations, which then opens the path for a quick eliminative move. However, when properly understood, the biological notion of race proves remarkably resistant to these deconstructive attempts. Moreover, by analyzing statements of some leading contemporary scholars who support social constructivism about race, I hope to demonstrate that their eliminativist views are actually in conflict with what the best contemporary science tells us about human genetic variation.

Nothing new for the GNXP faithful, but the presentation is clear and compelling throughout. He opens with "Those who subscribe to the opinion that there are no human races are obviously ignorant of modern biology." --- Ernst Mayr, 2002. Great quote!

Maps of white teen birthrate and abortion rates by state

2010-01-27T20:55:00.000-08:00

A supplement to the previous two posts. Below are maps which are shaded proportionally. Note how New York seems to be the abortion capital of the USA. Total surprise to me. Remember that these data are for white females from the ages of 15-19.

Red State, Blue State, Teen Birthrate, Teen Abortion rate

2010-01-27T19:58:00.000-08:00

A reader pointed to this post in Free Exchange:

Here are the 15 states with the biggest percentage drop from 1988-2005 in the ratio of teen abortions—the percentage of teen pregnancies that ended in abortion, not counting miscarriages. Crudely put, these are the states where pregnant white teens stopped having abortions between 1988-2005.

1. Kentucky
2. Nebraska
3. Arkansas
4. Oklahoma
5. South Dakota
6. Tennessee
7. Kansas
8. Iowa
9. Texas
10. North Dakota
11. Alabama
12. Indiana
13. Missouri
14. North Carolina
15. Utah

I have 2008 exit poll data handy by state, as well as the 2005 birth and abortion data. Abortion ratio = (Abortion rate)/(Abortion rate + Birthrate); basically pregnancy rate minus miscarriages. "Teen" here defines females in the age range 15-19. As you'd expect:

1) Whites voting Democrat is correlated with lower white birthrates
2) Whites voting Democrat is correlated with higher white abortion rates
3) Whites voting Democrat is correlated with higher white abortion ratios

#3 is stronger than #2, and I believe that's because teen pregnancy rates are lower in areas where whites are strongly Democrat, so the abortion rates are also going to be lower. The abortion ratio is somewhat normalized to pregnancy rate.

Teen birthrates and abortion rates

2010-01-27T14:46:00.000-08:00

The New York Times has a new article, After Long Decline, Teenage Pregnancy Rate Rises. The graphic is OK, but it focuses on aggregate teen pregnancy rates (age group 15-19) instead of splitting it out so as to show births and abortions. The original report is chock full of tables, but not the charts I was looking for. So I decided to go ahead and create them. All the "teen" data is for the 15-19 age range. The trends are a bit difference from that in the chart because I split up births and abortions, and also added in "abortion ratio," which simply illustrates the proportion of pregnancies which result in abortions excluding miscarriage and stillbirths. The other rates are per 1,000 of females of the given age range. First, the overall trends by time, broken out by race & ethnicity. White = Non-Hispanic white in all that follows.

Since Latinos have high birthrates, so surprise that their abortion rate is higher than whites. On the other hand, the relatively low abortion ratio vis-a-vis white teens points to some cultural expectations among this group which we'd expect from Roman Catholics (though more generally Catholics don't differ much from Protestants in the United States in regards to abortion, so I think that this is less causal than correlated).

There is also state level data, though it is spotty in regards to abortions. I decided to see if the different groups tracked each other in regards to rates. Here's what I found:

	Correlation	R-squared
White Birthrate – Black Birthrate	0.41	0.17
White Birthrate – Hispanic Birthrate	0.44	0.19
Black Birthrate – Hispanic Birthrate	0.42	0.18

White Abortion rate – Black Abortion rate	0.6	0.36
White Abortion rate – Hispanic Abortion rate	0.79	0.62
Black Abortion rate – Hispanic Abortion rate	0.8	0.64

White Abortion rate – White Birthrate	-0.44	0.19
Black Abortion rate – Black Birthrate	0.01	0
Hispanic Abortion rate – Hispanic Birthrate	-0.07	0

And the scatterplots, as well as some dot plots which show the ratio of the rates of two minority groups, as a function of geography.

Looking closely at the data it seems that that local state law/and/or/culture matters a lot for teen abortion ratios. Vermont for example has a very high abortion ratio. Might look at it later....

Note: I excluded DC from the state level analysis because it's a bizarre outlier. White teen birthrates of 1 per 1,000, black & Hispanic above 100.

A bold prediction: "synthetic associations" are not a panacea

2010-01-26T20:48:00.001-08:00

There's a bit of press surrounding the interesting result from David Goldstein's group that, in certain situations, a number of "rare" (defined as an allele frequency less than 5% [1]) variants influencing a trait can lead to an association signal at "common" SNPs. This phenomenon they authors call a "synthetic association".

The authors claim this is potentially the cause of many of the associations found in genome-wide association studies (with common SNPs), as well as a potential solution to the "missing heritability problem" (this isn't mentioned in the paper itself, but rather in a Times article describing it). In other words, this could be a panacea for all the ills of the human genetics community. Unfortunately, this seems rather unlikely.

1. There are a range of parameter values for which "synthetic associations" are plausible--where the effect of the rare variants is small enough to have avoided detection by linkage studies but big enough to show up via correlation with common variants. This range of parameters is kind of small--from Figure 2, it looks like maybe a set of mutations at a gene with a genotypic relative risk greater than 2 but less than 6. Will this be the case for some loci? Sure, that sounds plausible. Is it going to explain everything? No, of course not.

2. It has been pointed out (rightly) that diseases that are selected against should have their genetic component enriched for rare variants. Goldstein himself has made this argument about diseases like schizophrenia. So if schizophrenia has all these rare variants, and rare variants cause rampant "synthetic associations" at common SNPs, why hasn't anyone picked up whopping associations using common SNPs in schizophrenia?

3. The sickle cell anemia example, as presented in the paper, is extremely misleading. It seems the authors did a simple case control test for sickle cell in an African-American population. Recall that African-Americans are an admixed population, with each individual carrying large chunks of "European" and "African" chromosomes. Anyone will sickle cell will have at least one block of African chromosome surrounding the beta-globin locus, while those without will have two chromosomes sampled from the overall distribution of chromosomes in the population--15-20% of which, approximately, will be of European descent [2]. So any SNP with an allele frequency difference between African and European populations in this region will show up as a highly significant association with the disease due to the way they've done the test, and these associations will extend out to the length of admixture linkage disequilibrium--well, well beyond the LD found in African populations alone. The presentation of this example in the paper--the large block of association contrasting with the small blocks of LD in the Yoruban population--is a bit silly.

If I had to guess, and put a concrete bet on how this will play out, let's take the associations listed in their Table 1, which they call candidates for being due to synthetic associations. My bet: none of them are. Ok, maybe one.

[1] These sorts of thresholds are important to watch--in a year people will be calling things at 1% frequency "common" if it suits them for rhetorical purposes.

[2] Corrected from: "... will have two large blocks of "African" chromosomes surrounding the beta-globin locus, and everyone without will have at least one European chromosome in the same area"; see comments.

Confucius biopic

2010-01-26T12:14:00.000-08:00

I noticed that a new biopic of Confucius just opened in China. It's pretty obvious that they "sexed up" his life, as you can see in the trailer. In terms of a big-budget biopic it seems to me that the life of Confucius is a very thin source of blockbuster material in relation to other social-religious figures of eminence. Jesus, Moses and Buddha have supernatural aspects to their lives. Muhammad's life offers the opportunity for set-piece battles. Confucius was in many ways a failed bureaucrat, a genius unrecognized in his own day. His life can't be easily appreciated unless you have the proper context of his impact on Chinese history in mind. Stepping into it without a grand frame can lead one to conclude that he was quite a pedestrian man. Confucius was a man of ideas (though even those ideas can seem somewhat obscure, e.g. rectification of names). You see this in Annping Chin's The Authentic Confucius: A Life of Thought and Politics; I can't imagine Karen Armstrong writing such a dense and slow book.

How much is "The Situation" worth?

2010-01-25T13:59:00.001-08:00

'Jersey Shore' -- MTV Tries to Divide and Conquer:

Sources tell TMZ the network has told the cast if they don't accept MTV's deal by the end of business Monday, they will be replaced. And, MTV has told them it does not have to be a package deal -- the cast members who accept the offer will stay ... those who do not can have a nice life.

As we first reported, MTV offered each cast member a $10,000 signing bonus and $5,000 per episode. We're told the cast rejected the offer and made it clear they would all stand together and hold out for their price, though they didn't say what it was.

MTV made a new offer of $10,000 an episode -- there are 12 episodes in the new season -- but so far the cast hasn't responded.

We're told MTV already has replacements if Snooki, Pauly D, The Situation and the others don't accept the offer on Monday. But, we're told, MTV is happy to mix and match if some of the cast accepts the offer and others don't.

As for who's being the most hard-headed in the negotiations -- The Situation and Pauly D.

Lactase persistance in India

2010-01-24T13:55:00.000-08:00

Frequency of lactose malabsorption among healthy southern and northern Indian populations by genetic analysis and lactose hydrogen breath and tolerance tests:

Volunteers from southern and northern India were comparable in age and sex. The LTT result was abnormal in 88.2% of southern Indians and in 66.2% of northern Indians...The lactose HBT result was abnormal in 78.9% of southern Indians and in 57.1% of northern Indians...The CC genotype was present in 86.8% and 67.5%...the CT genotype was present in 13.2% and 26.0%...and the TT genotype was present in 0% and 6.5%..of southern and northern Indians, respectively. The frequency of symptoms after the lactose load...and peak concentrations of breath hydrogen...both of which might indicate the degree of lactase deficiency, were higher in southern than in northern Indians.

The north Indian samples were from Lucknow on the mid-Gangetic plain, and the south Indian samples from Bangalore. The genetic variant conferring lactase persistence is the Central Asian one, T_-1390. You can see the distribution of the genotypes by phenotype in the table to the left. These authors assume that the T allele was brought by the Indo-Aryans; this seems plausible seeing its clinal variation, as well the fact that this variant seems to be common in European and Central Asian populations. The frequency of the T allele in the Lucknow sample was 39%, and 13% in the Bangalore sample. Here are a selection of frequencies for the T allele in other populations:

17% - Saami
13% - Greeks (Athens)
82% - Scandinavians (Stockholm)
6% - Tuscans (Florence)
24% - Russians (Moscow)
73% - English (London)
66% - Basques
10% - Roma (Prague)
56% - Germans (Hamburg)
95% - North Irish (Enniskillen)
1% - Armenian (Yerevan)
5% - Uygur (Beijing)
10% - Mongolian (Beijing)
13% - Indians (Madras)
19% - Indians (New Dehli)
36% - Balochi (Islamabad)
51% - Pathan

You can see more here. This looks like a case of local adaptation.

What era are our intuitions about elites and business adapted to?

2010-01-21T01:36:00.000-08:00

Well, just the way I asked it, our gut feelings about the economically powerful are obviously not a product of hunter-gatherer life, given that such societies have minimal hierarchy, and so minimal disparities in power, material wealth, privileges of all kinds, etc. Hunter-gatherers don't even tolerate would-be elite-strivers, so beyond a blanket condemnation of trying to be a big-shot, they don't have the subtler attitudes that agricultural and industrial people do -- these latter groups tolerate and somewhat respect elites but resent and envy them at the same time.

So that leaves two major eras -- agricultural and industrial societies. I'm going to refer to these instead by terms that North, Wallis, & Weingast use in their excellent book Violence and Social Orders. Their framework for categorizing societies is based on how violence is controlled. In the primitive social order -- hunter-gatherer life -- there are no organizations that prevent violence, so homicide rates are the highest of all societies. At the next step up, limited-access social orders -- or "natural states" that sprung up with agriculture -- substantially reduce the level of violence by giving the violence specialists (strongmen, mafia dons, etc.) an incentive to not go to war all the time. Each strongman and his circle of cronies has a tacit agreement with the other strongmen -- who all make up a dominant coalition -- that I'll leave you to exploit the peasants living on your land if you leave me to exploit the peasants on my land.

This way, the strongman doesn't have to work very much to live a comfortable life -- just steal what he wants from the peasants on his land, and protect them should violence break out. Why won't one strongman just raid another to get his land, peasants, food, and women? Because if this type of civil war breaks out, everyone's land gets ravaged, everyone's peasants can't produce much food, and so every strongman will lose their easy source of free goodies (rents).

The members of the dominant coalition also agree to limit access to their circle, to limit people's ability to form organizations, etc. If they let anybody join their group, or form a rival coalition, their slice of the pie would shrink. And this is a Malthusian economy, so the pie isn't going to get much bigger within their lifetimes. So by restricting (though not closing off) access to the dominant coalition, each member maintains a pretty enjoyable size of the rents that they extract from the peasants. Why wouldn't those outside the dominant coalition not try to form their own rival group anyway? Because the strongmen of the area are already part of the dominant coalition -- only the relative wimps could try to stage a rebellion, and the strongmen would immediately and violently crush such an uprising.

It's not that one faction of the coalition will never raid another, just that this will be rare and only when the target faction has lost some of its share in the balance of power -- maybe they had 5 strongmen but now only 1. Obviously the other factions aren't going to let that 1 strongman enjoy the rents that 5 were before, while they enjoy average rents -- they're going to raid him and take enough so that he's left with what seems his fair share. Aside from these rare instances, there will be a pretty stable peace. There may be opportunistic violence among peasants, like one drunk killing another in a tavern, but nothing like getting caught in a civil war. And they certainly won't be subject to the constant threat of being killed and their land burned in a pre-dawn raid by the neighboring tribe, as they would face in a stateless hunter-gatherer society. As a result, homicide rates are much lower in these natural states than in stateless societies.

Above natural states are open-access orders, which characterize societies that have market economies and competitive politics. Here access to the elite is open to anyone who can prove themselves worthy -- it is not artificially restricted in order to preserve large rents for the incumbents. The pie can be made bigger with more people at the top, since you only get to the top in such societies by making and selling things that people want. Elite members compete against each other based on the quality and price of the goods and services they sell -- it's a mercantile elite -- rather than based on who is better at violence than the others. If the elites are flabby, upstarts can readily form their own organizations -- as opposed to not having the freedom to do so -- that, if better, will dethrone the incumbents. Since violence is no longer part of elite competition, homicide rates are the lowest of all types of societies.

OK, now let's take a look at just two innate views that most people have about how the business world works or what economic elites are like, and see how these are adaptations to natural states rather than to the very new open-access orders (which have only existed in Western Europe since about 1850 or so). One is the conviction, common even among many businessmen, that market share matters more than making profits -- that being more popular trumps being more profitable. The other is most people's mistrust of companies that dominate their entire industry, like Microsoft in computers.

First, the view that capturing more of the audience -- whether measured by the portion of all sales dollars that head your way or the portion of all consumers who come to you -- matters more than increasing revenues and decreasing costs -- boosting profits -- remains incredibly common. Thus we always hear about how a start-up must offer their stuff for free or nearly free in order to attract the largest crowd, and once they've got them locked in, make money off of them somehow -- by charging them later on, by selling the audience to advertisers, etc. This thinking was widespread during the dot-com bubble, and there was a neat management-oriented book written about it called The Myth of Market Share.

Of course, that hasn't gone away since then, as everyone says that "providers of online content" can never charge their consumers. The business model must be to give away something cool for free, attract a huge group of followers, and sell this audience to advertisers. (I don't think most people believe that charging a subset for "premium content" is going to make them rich.) For example, here is Felix Salmon's reaction to the NYT's official statement that they're going to start charging for website access starting in 2011:

Successful media companies go after audience first, and then watch revenues follow; failing ones alienate their audience in an attempt to maximize short-term revenues.

Wrong. YouTube is the most popular provider of free media, but they haven't made jackshit four years after their founding. Ditto Wikipedia. The Wall Street Journal and Financial Times websites charge, and they're incredibly profitable -- and popular too (the WSJ has the highest newspaper circulation in the US, ousting USA Today). There is no such thing as "go after audiences" -- they must do that in a way that's profitable, not just in a way that makes them popular. If you could "watch revenues follow" by merely going after an audience, everyone would be billionaires.

The NYT here seems to be voluntarily giving up on all its readers outside the US, who can’t be reasonably expected to have the ability or inclination to pay for web access. It had the opportunity to be a global newspaper, leveraging both the NYT and the IHT brands, and has now thrown that away for the sake of short-term revenues.
[...]
As such, a project which was meant to bring nytimes.com into the same space as Wikipedia will now become largely irrelevant.

This sums up the pre-industrial mindset perfectly: who cares about getting paid more and spending less, when what truly matters is owning a brand that is popular, influential, and celebrated and sucked up to? In a natural state, that is the non-violent path to success because you can only become a member of the dominant coalition by knowing the right in-members. They will require you to have a certain amount of influence, prestige, power, etc., in order to let you move up in rank. It doesn't matter if you nearly bankrupt yourself in the process of navigating these personalized patron-client networks because once you become popular and influential enough, you stand a good chance of being allowed into the dominant coalition and then coasting on rents for the rest of your life.

Clearly that doesn't work in an open-access, competitive market economy where interactions are impersonal rather than crony-like. If you are popular and influential while paying no attention to costs and revenues, guess what -- there are more profit-focused competitors who can form rival companies and bulldoze over you right away. Again look at how spectacularly the WSJ has kicked the NYT's ass, not just in crude terms of circulation and dollars but also in terms of the quality of their website. They broadcast twice-daily video news summaries and a host of other briefer videos, offer thriving online forums, and on and on.

Again, in the open-access societies, those who achieve elite status do so by competing on the margins of quality and price of their products. You deliver high-quality stuff at a low price while keeping your costs down, and you scoop up a large share of the market and obtain prestige and influence -- not the other way around. In fairness, not many practicing businessmen fall into this pre-industrial mindset because they won't be practicing for very long, just as businessmen who cried for a complete end to free trade would go under. It's mostly cultural commentators who preach the myth of market share, going with what their natural-state-adapted brain reflexively believes.

Next, take the case of how much we fear companies that comes to dominate their industry. People freak out because they think the giant, having wiped out the competitors, will enjoy a carte blanche to exploit them in all sorts of ways -- higher prices, lower output, shoddier quality, etc. We demand the protector of the people to step in and do something about it -- bust them up, tie them down, resurrect their dead competitors, just something!

That attitude is thoroughly irrational in an open-access society. Typically, the way you get that big is that you provided customers with stuff that they wanted at a low price and high quality. If you tried to sell people junk that they didn't want at a high price and terrible quality, guess how much of the market you will end up commanding. That's correct: zero. And even if such a company grew complacent and inertia set in, there's nothing to worry about in an open-access society because anyone is free to form their own rival organization to drive the sluggish incumbent out.

The video game industry provides a clear example. Atari dominated the home system market in the late '70s and early '80s but couldn't adapt to changing tastes -- and were completely destroyed by newcomer Nintendo. But even Nintendo couldn't adapt to the changing tastes of the mid-'90s and early 2000s -- and were summarily dethroned by newcomer Sony. Of course, inertia set in at Sony and they have recently been displaced by -- Nintendo! It doesn't even have to be a newcomer, just someone who knows what people want and how to get it to them at a low price. There was no government intervention necessary to bust up Atari in the mid-'80s or Nintendo in the mid-90s or Sony in the mid-2000s. The open and competitive market process took care of everything.

But think back to life in a natural state. If one faction obtained complete control over the dominant coalition, the ever so important balance of power would be lost. You the peasant would still be just as exploited as before -- same amount of food taken -- but now you're getting nothing in return. At least before, you got protection just in case the strongmen from other factions dared to invade your own master's land. Now that master serves no protective purpose. Before, you could construe the relationship as at least somewhat fair -- he benefited you and you benefited him. Now you're entirely his slave; or equivalently, he is no longer a partial but a 100% parasite.

You can understand why minds that are adapted to natural states would find market domination by a single or even small handful of firms ominous. It is not possible to vote with your dollars and instantly boot out the market-dominator, so some other Really Strong Group must act on your behalf to do so. Why, the government is just such a group! Normal people will demand that vanquished competitors be restored, not out of compassion for those who they feel were unfairly driven out -- the public shed no tears for Netscape during the Microsoft antitrust trial -- but in order to restore a balance of power. That notion -- the healthy effect for us normal people of there being a balance of power -- is only appropriate to natural states, where one faction checks another, not to open-access societies where one firm can typically only drive another out of business by serving us better.

By the way, this shows that the public choice view of antitrust law is wrong. The facts are that antitrust law in practice goes after harmless and beneficial giants, hamstringing their ability to serve consumers. There is little to no evidence that such beatdowns have boosted output that had been falling, lowered prices that had been rising, or improved quality that had been eroding. Typically the lawsuits are brought by the loser businesses who lost fair and square, and obviously the antitrust bureaucrats enjoy full employment by regularly going after businesses.

But we live in a society with competitive politics and free elections. If voters truly did not approve of antitrust practices that beat up on corporate giants, we wouldn't see it -- the offenders would be driven out of office. And why is it that only one group of special interests gets the full support of bureaucrats -- that is, the loser businesses have influence with the government, while the winner business gets no respect. How can a marginal special interest group overpower an industry giant? It must be that all this is allowed to go on because voters approve of and even demand that these things happen -- we don't want Microsoft to grow too big or they will enslave us!

This is a special case of what Bryan Caplan writes about in The Myth of the Rational Voter: where special interests succeed in buying off the government, it is only in areas where the public truly supports the special interests. For example, the public is largely in favor of steel tariffs if the American steel industry is suffering -- hey, we gotta help our brothers out! They are also in favor of subsidies to agribusiness -- if we didn't subsidize them, they couldn't provide us with any food! And those subsidies are popular even in states where farming is minimal. So, such policies are not the result of special interests hijacking the government and ramrodding through policies that citizens don't really want. In reality, it is just the ignorant public getting what it asked for.

It seems useful when we look at the systematic biases that people have regarding economics and politics to bear in mind what political and economic life was like in the natural state stage of our history. Modern economics does not tell us about that environment but instead about the open-access environment. (Actually, there's a decent trace of it in Adam Smith's Theory of Moral Sentiments, which mentions cabals and factions almost as much as Machiavelli -- and he meant real factions, ones that would war against each other, not the domesticated parties we have today.)

We obviously are not adapted to hunter-gatherer existence in these domains -- we would cut down the status-seekers or cast them out right away, rather than tolerate them and even work for them. At the same time, we evidently haven't had enough generations to adapt to markets and governments that are both open and competitive. That is certain to pull our intuitions in certain directions, particularly toward a distrust of market-dominating firms and toward advising businesses to pursue popularity and influence more than profitability, although I'm sure I could list others if I thought about it longer.

How much faster

2010-01-21T01:29:00.000-08:00

Athlete Atypicity on the Edge of Human Achievement: Performances Stagnate after the Last Peak, in 1988:

The growth law for the development of top athletes performances remains unknown in quantifiable sport events. Here we present a growth model for 41351 best performers from 70 track and field (T&F) and swimming events and detail their characteristics over the modern Olympic era. We show that 64% of T&F events no longer improved since 1993, while 47% of swimming events stagnated after 1990, prior to a second progression step starting in 2000. Since then, 100% of swimming events continued to progress.

We also provide a measurement of the atypicity for the 3919 best performances (BP) of each year in every event. The secular evolution of this parameter for T&F reveals four peaks; the most recent (1988) followed by a major stagnation. This last peak may correspond to the most recent successful attempt to push forward human physiological limits. No atypicity trend is detected in swimming. The upcoming rarefaction of new records in sport may be delayed by technological innovations, themselves depending upon economical constraints.

Not as the crow flies

2010-01-21T00:29:00.000-08:00

A comment below:

This thought has probably occurred to others as well, but isn't it interesting that if this theory of Baltics being the "true" Europeans is correct, that history repeated itself several thousand years later when the Baltic peoples became the last Europeans...to adopt Christianity, a Middle Eastern Religion? There must be something repelling about the region.

This is a good point. The Baltic sea is a bit closer on a straight line than Ireland and Scotland, but pre-modern transport and communication was much more dependent on water. The comment references the fact that Lithuania became a Christian nation only in the late 1300s. Some of this was a matter of geopolitics, the Baltic peoples were being subjected to what we'd probably term genocidal assaults from various German military orders whose notional rationale was to spread the Christian faith in a series of crusades. Christianity was therefore broadly construed as the religion of the enemy, with the Christian God being termed the "German god" in some cases. But another issue was that in the 14th century Lithuania expanded into the lands of the West and East Slavs, Roman Catholics and Eastern Orthodox Christians, respectively, and the religious neutrality of the Lithuanian elite allowed them to play off the two subject populations usefully. Once the Lithuanian elite chose Roman Catholicism, it began the centuries long process of total assimilation of that elite into the Polish nobility and their alienation from their East Slavic Orthodox subjects and allies (the final completion of which occurred after the Union of Lublin).

But even accounting for the historical and geopolitical contingencies, the relatively late conversion of the Baltic peoples to Roman Catholic Christianity is notable. The Sami of northern Fenno-Scandinavia actually were only nominally Christianized during the medieval period, and maintained their shamanistic indigenous religion until the 18th century (along with a few beliefs and practices adopted from their Norse neighbors, there are woodblocks which seem to depict Sami venerating an idol of Thor). One Finnic group in Russia actually claims an unbroken line of non-Christian religious belief & practice down to the modern day. The lesson here is that it is in northeastern Europe that the homogenizing processes which swept across much of the rest of the continent were felt last, and to the least effect.

Why? I assume it's ecology. Or as some would say, maybe its agriculture (or the lack thereof). The climate of northeastern Europe is very unsuitable for crops which originate in the Middle East, so it would take some time for them to adapt them appropriately. The historical and genetic data imply a relatively recent push of Slavic-speaking farmers into northeastern European Russia. A model which posits that northeastern Europeans are particularly deep reservoirs of ancient European lineages would rely on the ecological parameters as the primary reason.

The parallelism between the spread of cultures and genes here is notable, because the two often interact. Just as northeastern Europe may be the last redoubt of the hunter-gatherer relict populations within the continent, so it was also the region which was the last to join the medieval "Christian Commonwealth." In Guns, Germs and Steel Jared Diamond introduced the importance of geography in understanding historical patterns. This is quite clear when it comes to something like the history of the native populations of the New World; the critical role of environment in the lives of aboriginal peoples is something we're preconditioned to assume as an important background parameter. But the same factors are at work in Europe, in both prehistory and history.

Controlling the means of reproduction

2010-01-19T14:22:00.000-08:00

The title says it all, Should Obese, Smoking and Alcohol Consuming Women Receive Assisted Reproduction Treatment? The press release is based on a position statement from the European Society of Human Reproduction and Embryology. The link is here (not live yet).