Friday, February 19, 2010

Armenian genetics   posted by Razib @ 2/19/2010 04:40:00 PM

Armenian genes: Scientist in Yerevan launches a project to reveal genetic history of the nation. The description of the science in the piece is very garbled. But, it would be nice to elucidate the genetics of Armenians in more detail. Their language, like Greek and Albanian, is a singleton in the Indo-European family tree. Additionally, the Armenian nation has an extremely long history. Their identity crystallized in the wake of the Persian and Hellenistic Empires just like that of the Jews.

Demographically we know that historically much of eastern Anatolia was dominated by Armenians. Many of the prominent Byzantine dynasties were of Hellenized Armenian lineages. I would predict that one will likely find that most of the Turks of eastern Anatolia would cluster with Armenians, just as those Turks from the west and coastal Anatolia might cluster more with Greeks, because it seems likely that the ethnogenesis of most Turks in Anatolia was a process whereby Greeks and Armenians assimilated to the identity of a small minority of eastern Turkish invaders.


Tuesday, February 16, 2010

10 questions for Peter Turchin   posted by Razib @ 2/16/2010 12:19:00 PM

Peter Turchin has appointments in ecology & evolution and mathematics at the University of Connecticut. He is the author of five books, three of which, Historical Dynamics, Secular Cycles and War and Peace and War, outline tests of models derived from the new field of cliodynamics. I have reviewed Historical Dynamics and War Peace and War. Below are 10 questions.

1) Your initial research program was in quantitative ecology. What prompted your switch into modeling historical dynamics?

At some point I simply realized that most of the big questions in population dynamics were solved, or about to be solved. So I wrote my book on Complex Population Dynamics, where I synthesized what I thought these answers were, and started looking for some more challenging field. It turned out that the last scientific discipline that has not yet been mathematized was history. At first, I thought that I would simply write some mathematical models for historical dynamics, as a hobby. But once I did that, I wanted to see whether their predictions could be tested with data. To my great surprise, it turned out that there is a lot of quantitative data for historical processes, so testing models and theories is eminently possible. As a result, at this point my main thrust is empirical, rather than mathematical; or, more precisely, I am primarily interested in testing theories with data.

2) You have been at the forefront of creating the new field of "cliodynamics." Is this necessary? It seems that economists have been at the forefront of cliometrics and they have their own theoretical framework. What's the value-add of your specific framework?

I believe that it is necessary. Historical processes are very complex, they involve not only economic, but also demographic, social, political, ideological, climatological, and many other kinds of factors. Probably because one has to approach history with such a massively interdisciplinary approach, it is the last of social sciences to become amenable to the scientific method. I have a lot of respect for economists, but in many ways it is difficult for them to make progress with history. For example, until recently, they have been hobbled with a bankrupt model of homo economicus. The other problem is that traditional economic theory focuses too much on equilibria, so that also does not predispose economists to deal well with historical dynamics. Both of these barriers are being dismantled right now, but still economists are not in the forefront of the cliodynamic community. We have much greater representation from historical sociologists, anthropologists, and political scientists.

3) In terms of discipline, where have the reactions been most positive and most negative to your project?

Positive response came from the disciplines named above - historical sociology, social and cultural anthropology, political science, economic and social history, demogrpahy. There has not been really much of a negative reaction. The main defensive mechanism is to ignore us, which is what 95% of historians do. That's fine with me. In fact, I was pleasantly surprised by the positive reception of these ideas among historical social scientists and the (estimated) 5% of historians. It suggests to me that the time of cliodynamics has come. Incidentally, we are launching a peer-reviewed journal this year.

4) I have speculated that the fact that you were born in the former Soviet Union might have made you more open to the concept of a scientific study of history, seeing as how Marxist thought originated as an attempt to scientifically describe the human past and predict its future. Do you think that your current interests might have some relationship to your cultural background, or not?

Yes, I think that my Russian background was a strong contributing factor, but no, not because of Marxism. You have to realize that before I started my historical project I had completely rejected Marxism, because of my upbrining (my father was a human rights activist in the Soviet Union and was exiled abroad in late 1970s). Only recently, as a result of becoming a social scientist, I learned to appreciate certain insights of Marx and incorporate them into my theories, although I am not a Marxist by any stretch of imagination. The Russian factor, I believe, comes into play because Russians tend to be very broad thinkers. As I think Dostoyevsky once said, the Russian is very broad, I would narrow him down, or something like that. So Russians have a tendency to produce cosmic theories (there is even a philosophical current called Russian Cosmism). In my work I attempt to integrate this Russian tendency with the Anglo-Saxon practicality and empiricism.

5) You make recourse to group selection models in your scholarship. But the work I am familiar with seems to focus on cultural group selection. What do you think of biological level group selection posited by Samuel Bowles for hunter-gatherers, and its possible relevance to agricultural populations?

I think that group selection mechanisms work at both genetic and cultural levels, and also on gene-culture interactions. The mix of factors have been changing from primarily genetic in the early human evolution to much more cultural today. However, genetic evolution continues, so even today it's not 100% cultural. There is a preprint on my cliodynamics site, in which I focus on evolution of ultrasociality, our ability to form cooperative groups of millions of individuals, and there my main emphasis is on cultural group selection.

One thing that we should not expect is a neat separation between genes and culture. Coevolution of these two information carriers is where the action is.

6) In your models of the rise and fall of agricultural-based polities you seem to emphasize the importance of institutional religions in generating "meta-ethnic" identities. One of the historical quirks which scholars have noted is the rise of world religions between 600 BC and 600 AD, and the relative stability in number of religions after that period. Do you have any explanation for this pattern, or is there nothing to be explained?

In fact, this is one of the most striking patterns in history, and it fits very neatly with my theories. Rather than repeat myself, let me direct your readers to my recent artcile, a reprint of which is posted here:

See p. 201 for my explanation of the Axial Age. And then check out the section on the Middle East during the Axial Age (p. 209).

7) I believe in China: A Macro History, by Ray Huang, he notes that the interregnums between Chinese dynasties became shorter and shorter. Is this explicable through your models of historical processes?

Yes, and the same observation was made for other world regions by Victor Lieberman in his book, Strange Parallels, the second volume of which was recently published. I think that the case for cultural evolution of state capacity is quite convincing - each new state starts not from a blank page, but already equipped with techniques of political integration that were developed during previous attempts. As a result, both the scale of polities and their cohesion tend to increase with time, and interregnum periods become shorter.

8) You observe the importance of meta-ethnic frontiers across history.
In the modern world with ease of travel and communication it seems that spatial boundaries are less relevant, as civilizations seem somewhat intercalated with each other (e.g., Western enclaves in the Third World, Muslim diasporas in the West, Chinese in Africa, etc.). Is the concept of a meta-ethnic frontier transferable to the modern context?

I think it is, although at this point this is purely speculation. The above-mentioned Victor Lieberman has another striking idea, that modern Europeans are really 'White Inner Asians'. So after 1500 the primary locus of cultural evolution shifted from steppe frontiers to European colonial frontiers. We are probably still in the same era, so the most intense evolution occurs where Western societies impinge on other societies.

Also don't forget that ethnic and religious diasporas were not an invention of modernity. What is more important is that information flows today are much less local. So a person in Saudi Arabia, a thousand kilometers from Iraq, can see the news about Abu Ghraib in real time, and perhaps with visual material, and decide to become a mujahedeen. So my guess is that the basic dynamic is still playing out, but it's not as localized in space as it was prior to modern communications.

9) Is there insight about the modern post-Malthusian world we can obtain from the secular cycles of the past?

My working hypothesis is that the two out of three mechanisms of the demographic-structural theory, elite overproduction and state fiscal fragility, continue to operate in the modern world. See the answer to the next question.

10) What's your next big project?

My main project on which I am currently working is a demographic-structural analysis of American history, from 1780 to the present. So we will see whether the hypothesis, to which I alluded under #9 above, will be borne out by the empirical analysis.

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Sunday, February 14, 2010

Small genetic effects do not preclude drug development   posted by p-ter @ 2/14/2010 08:37:00 AM

Daniel MacArthur points me to a Newsweek article on the bankruptcy of Decode Genetics. The author describes (one of) Decode's problems like this:
The genetics of illness turned out to be more complex than researchers expected. At deCODE and elsewhere, the new genes linked to common diseases turned out to be rare or to have only small effects on individual risk. That killed any prospect of using deCODE's discoveries to make blockbuster drugs.
The leap--that small genetic effect sizes means no prospects of drug discovery--sounds reasonable, but is actually wrong. Here's an example of why:

Consider a trait like, say, cholesterol levels. Massive genome-wide association studies have been performed on this trait, identifying a large number of loci of small effect. One of these loci is HMGCR, coding for HMG-CoA reductase, an important molecule in cholesterol synthesis. The allele identified increases cholesterol levels by 0.1 standard deviations, meaning a genetic test would have essentially no ability to predict cholesterol levels. By the logic of the Newsweek piece, any drug targeted at HMGCR would have no chance of becoming a blockbuster.

Any doctor knows where I'm going with this: one of the best-selling groups of drugs in the world currently are statins, which inhibit the activity of (the gene product of) HMGCR. Of course, statins have already been invented, so this is something of a cherry-picked example, but my guess is that there are tens of additional examples like this waiting to be discovered in the wealth of genome-wide association study data. Figuring out which GWAS hits are promising drug targets will take time, effort, and a good deal of luck; in my opinion, this is the major lesson from Decode (which is not all that surprising a lesson)--drug development is really hard.


Friday, February 12, 2010

Homo erectus and EDAR?   posted by p-ter @ 2/12/2010 07:17:00 AM

In Why Evolution is True, Jerry Coyne has the following parenthetical aside about population variation in morphology in H. erectus:
(H. erectus from China...had shovel-shaped incisor teeth not found in other populations)
This stopped me dead in my tracks: modern East Asian populations have similar tooth morphology, caused in part by a positively-selected nonsynonymous change in the gene EDAR. Could this be an example of convergent evolution of tooth morphology in hominins?

However, a cursory google suggests that shovel-shaped incisors might be thought to be a trait general to H. erectus, not specific to Asian populations. Can anyone clarify this?


Wednesday, February 10, 2010

Low IQ correlated with cardiovascular disease?   posted by Razib @ 2/10/2010 01:03:00 AM

Second Only to Cigarette Smoking in Large Population Study:
While lower intelligence scores -- as reflected by low results on written or oral tests of IQ -- have been associated with a raised risk of cardiovascular disease, no study has so far compared the relative strength of this association with other established risk factors such as obesity, smoking and high blood pressure. Now, a large study funded by Britain's Medical Research Council, which set out to gauge the relative importance of IQ alongside other risk factors, has found that lower intelligence scores were associated with higher rates of cardiovascular disease and total mortality at a greater level of magnitude than found with any other risk factor except smoking.


The relative strengths of the association were measured by an "index of inequality," which summarised the relative risk of a health outcome (cardiovascular death) in the most disadvantaged (high risk) people relative to the most advantaged (low risk). This relative index of inequality for the top five risk factors was found to be 5.58 for cigarette smoking, 3.76 for IQ, 3.20 for low income, 2.61 for high systolic blood pressure, and 2.06 for low physical activity.

The investigators note "a number of plausible mechanisms" whereby lower IQ scores could elevate cardiovascular disease risk, notably the application of intelligence to healthy behaviour (such as smoking or exercise) and its correlates (obesity, blood pressure). A further possibility, they add, "is that IQ denotes 'a record' of environmental insults" (eg, illness, sub-optimal nutrition) accumulated throughout life.

Related, Calorie Posting in Chain Restaurants:
...In Table 5 we present estimates of how the effect of calorie posting on calories per transaction differs across sub-groups. The estimates in column (1) are based on the transaction data. Although the anonymous transaction data contain no information about the demographics of the consumers who made each transaction, we do know the store location of each transaction, and census data provide us with zip-level demographics. Using this information, we find that the decrease in calories per transaction was larger in zips with higher income and in zips with more education (i.e., more people with college degrees).


Jersey Shore nickname   posted by Razib @ 2/10/2010 12:56:00 AM

What's your Jersey Shore nickname? I like "The Prediction" for myself.

Tuesday, February 09, 2010

Books & guidance   posted by Razib @ 2/09/2010 11:52:00 PM

Read More Books!:
If you really want to understand any issue more complex than Brad and Angelina's marital status, there's really no substitute for a book. Not instead of blogs and newspapers and Twitter, but in addition to them. So: read more books! They're good for you.

I've heard and read about how awesome Charles Darwin was as a thinker, but I had to (re)read The Origin of Species to really grok what was being communicated here. So yes, books are important. The point that the content of what is being examined is critica can't be overemphasized.

It seems that disciplines which exhibit a great deal of tight contingency, such as the natural sciences, are easier to digest in purely non-book form, than those more humanistic domains which are messier and less causally clear in the network of the relationship of facts to frameworks. As an example, very little of Charles Darwin's argument in The Origin of Species was illuminating as such, it was by and large integrated seamlessly into the body of science if it was worthy, and discarded if it was not. This applies much more forcefully to the physical sciences which have been more strictly formalized. There is also the problem that if you picked up a scholarly book which discussed evolutionary fitness landscapes or the physics of quasars it would probably be unintelligible to you unless you had absorbed the prerequisite scholarship. The structure of learning in extremely contingent disciplines is relatively straightforward. If you want to learn quantum physics, there are necessarily specific math and physics prerequisites. If you want to learn about Russian history from the time of Ivan the Terrible to the rise of the Romanov dynasty, some prior knowledge of late Byzantine history might be useful to understand the cultural-political roots of Russian Orthodoxy, but it is not necessary.

When it comes to "softer" disciplines I think books are critical, because it is so easy to mislead yourself on the shape of scholarship. When I occasionally hear Creationists observe that there is a scientific controversy about evolutionary theory, or even more blatantly that evolutionary theory has fallen into disrepute within biology, they are either being lied to, or, they are lying. It is simply impossible to avoid the fact that there is no alternative universe of Creationist scholarship which has a credible scientific framework which explains the pattern and nature of biological diversity. But what about a discipline such as economics, one of the "harder" domains outside of natural science? You'll get a very different perspective if you read Greg Mankiw (PhD, MIT) vs. Paul Krugman (PhD, MIT). More outlandishly, many individuals with a political ideology of libertarianism are strongly attracted to the Austrian school of economics, despite the fact that this is a totally marginalized heterodox tradition today. In this case, normative preferences generate a positive feedback loop in terms of how one explores the sample space of scholarship. One can debate whether the marginalization of Austrian economics is justified or not (see The Eclipse of Darwinism), but it is also an empirical fact that it is marginalized.

Reading a wide range of books is a good way to diminish the power of preferences when exploring scholarly landscapes with which one is unfamiliar. When searching for journal articles it becomes easy to get caught in circular networks of citation, or fixating on particular journals which one finds congenial. Additionally, in less contingent disciplines the synoptic vision of a scholar who has dedicated their life to absorbing and reprocessing a mountain of data and generating insight and inference can often be helpful. If they are honest they will sample from the distribution of data in a manner which is not selection biased, something that you as an outsider will likely not be able to do because you do not know the shape of the distribution.


Gene Expression Survey   posted by Razib @ 2/09/2010 01:04:00 AM

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.

Update: You can view the results of the survey here.


Monday, February 08, 2010

Delayed childbearing & autism   posted by Razib @ 2/08/2010 11:22:00 AM

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.