Archive for September, 2010

The city that kills you makes you strong!

By Razib Khan | September 24, 2010 12:09 am

ResearchBlogging.orgOver the past day I’ve seen reports in the media of a new paper which claims that long-term urbanization in a region is strongly correlated with genetic variants for disease resistance. I managed to find the paper on Evolution‘s website as an accepted manuscript, ANCIENT URBANISATION PREDICTS GENETIC RESISTANCE TO TUBERCULOSIS:

A link between urban living and disease is seen in recent and historical records, but the presence of this association in prehistory has been difficult to assess. If the transition to urbanisation does result in an increase in disease-based mortality, we might expect to see evidence of increased disease resistance in longer-term urbanised populations, as the result of natural selection. To test this, we determined the frequency of an allele (SLC11A1 1729 + 55del4) associated with natural resistance to intra-cellular pathogens such as tuberculosis and leprosy. We found a highly significantly correlation with duration of urban settlement – populations with a long history of living in towns are better adapted to resisting these infections. This correlation remains strong when we correct for auto-correlation in allele frequencies due to shared population history. Our results therefore support the interpretation that infectious disease loads became an increasingly important cause of human mortality after the advent of urbanisation, highlighting the importance of population density in determining human health and the genetic structure of human populations.

298px-Pericles_Pio-Clementino_Inv269In some ways this seems plausible. There are a priori reasons why we’d expect to see a great deal of evolutionary change in regions of the genome correlated with variations in immune response. Diseases are one of the most likely reasons for why sex exists in complex multicellular species; sex allows a slow-reproducing population to bend with the rapid-fire punches of their pathogens by shuffling their defenses constantly. The results from recent work mapping patterns of variation in relation to natural selection generally indicate that immune related regions show plenty of signs of adaptation. No surprise, a “Red Queen” model whereby pathogens and their hosts constantly co-evolve would imply that immunologically relevant genes would never be at equilibrium frequencies for long, so we’d have a good shot at catching “selective sweeps” on some of the immune loci.

So how do cities play into this picture? I suspect that the picture is more complicated than the presentation in the paper, though I believe that the authors were constrained by considerations of space from evaluating all possibilities in full depth. There are two facts which I think are critical to understanding the pattern of variation here:

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CATEGORIZED UNDER: Anthroplogy, Culture, Human Evolution

Simple rules for inclusive fitness

By Razib Khan | September 23, 2010 5:05 pm

ResearchBlogging.orgWith the recent huge furor over the utility of kin selection I’ve been keeping a closer eye on the literature on inclusive fitness. The reason W. D. Hamilton’s original papers in The Journal of Theoretical Biology are highly cited is not some conspiracy, rather, they’re a powerful framework in which one can understand the evolution of social behavior. They are a logic whose basis is firmly rooted in the world of how inheritance and behavior play out concretely. But because of their formality and spareness inclusiveness fitness has also given rise to a large literature derived from simulations “in silico,” that is, evolutionary experiments in the digital domain.

375px-Green_Beard_GeneOne can elucidate inclusive fitness through Hamilton’s Rule, but it is also rather easy to exposit verbally via a “gene’s eye view.” Imagine for example a dominant mutation in a diploid organism which produces the behavior of altruism toward near kin. Initially the altruist will have offspring whose probability of carrying the dominant mutation is 50%, because there is also the probability that they will carry the ancestral non-altruistic variant. Imagine an altruistic behavior which incurs a small, but not trivial, cost to the individual performing the behavior, and a large gain to the individual who is on the receiving end of the altruism. The logic of favoring near kin is such that in the initial generation the parent which behaves altruistically toward near kin is increasing their own “inclusive fitness” because their offspring share 50% of their genes identical-by-descent (in the case of a diploid sexually reproducing organism). But from a gene’s eye perspective what is really occurring is that there is a 50% chance that the gene which fosters altruism is promoting the fitness of a copy of itself. So inclusive fitness operates by modulating the parameters of costs and gains to focal individuals as a function of their relatedness, but it is the genes, the “replicators,” which persist immortally across the generations. We “vehicles” are just the ocean through which genes sail.

But like Darwin’s theory of evolution through natural selection the fruit of these logics are in the details. A new paper in The Proceedings of the Royal Society puts the focus on different means by which inclusive fitness may be maximized. In particular, the paper offers up a reason for why what Richard Dawkins termed the “green-beard effect” is not more common. Selective pressures for accurate altruism targeting: evidence from digital evolution for difficult-to-test aspects of inclusive fitness theory:

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CATEGORIZED UNDER: Evolution, Genetics, Genomics

Daily Data Dump – Thursday

By Razib Khan | September 23, 2010 11:40 am

Nobel-winning brain researcher retracts two papers. Looks like there’s the typical blame-it-on-the-Asian going on here, so perhaps this won’t blow up.

In Our Time is back. This week: Imaginary Numbers.

“200 genes potentially associated with academic performance in schoolchildren”. Most genes of small effect. We’ll see. Don’t get too excited yet, you might be disappointed.

Through the Language Glass (Part 2). Second part of a review of Through the Language Glass: Why the World Looks Different in Other Languages.

Blogging out of Balance. Dave Munger did some serious legwork on analyzing the data sets available. For what it’s worth 75% of the readers of this weblog are male. 75% of at least some European descent. 60% are irreligious. 80% atheists and agnostics. 1/3 have graduate school degrees. 85% have completed calculus. I’ve done surveys regularly of the readership since 2004 or so, and they’re always 75-85% male, with the other figures about the same. The main difference is that the median reader is becoming more politically liberal.

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What's the matter with Finland?

By Razib Khan | September 23, 2010 1:27 am

450px-Tarja_Halonen_2003I was browsing The European Journal of Human Genetics and I saw this short article from last summer which I missed, NordicDB: a Nordic pool and portal for genome-wide control data. The portal is at The data itself is for Very Special People, instead of having a simple web form you actually have to download a document and sign a bunch of stuff. The WVS has a web form which takes about 1 minute to fill to get all their data so you can load it in R, as a point of comparison (the GSS makes you register a little more, but I don’t recall that it took too long). Of course this is human genetic data, so way more sensitive, but I thought one of the benefits of socialized medicine was that a lot of the downside risks of having your info in the public record were ameliorated? (I’m kind of being flip here)

There wasn’t anything too new in the paper, but the same old questions cropped up in my head. They basically merged a lot of different medical genetics studies where patients were typed with SNP-chips in Denmark, Sweden and Finland, and put all the info in a common central clearinghouse so you could pool them for analysis. Below is a plot of the genetic variation using MDS, as well as an Fst table.

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CATEGORIZED UNDER: Genetics, Genomics

The Social Darwinist and the Priests

By Razib Khan | September 22, 2010 6:58 pm

I was going through my stack of podcasts today and I decided to listen to a discussion between the linguist John McWhorter and the linguist Ben Zimmer, and at one point McWhorter addresses the issue of linguistic diversity, and wonders aloud if perhaps we wouldn’t be better off with one world language, though more as an intellectual thought experiment than in any seriousness. His arguments are laid out in this article The Cosmopolitan Tongue: The Universality of English. McWhorter recounts how the piece resulted in his cameo appearance as one of history’s greatest monsters in a book by a linguist who is fighting language extinction.

You can listen to Zimmer and McWhorter’s exchange on the topic yourself:

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Daily Data Dump – Wednesday

By Razib Khan | September 22, 2010 11:35 am

Freshman Weight Gain: Women With Heavy Roommates Gain Less, Study Finds. I guess the model makes sense, but it really makes one wonder about the power of prior expectations about these sorts of things. There just so many plausible stories for any given set of data.

Why Does Spicy Food Taste Hot? The feeling of “heat” from the active ingredient in spicy food is an illusion due an accident of physiology. I obviously really love spicy food, even though the heat isn’t “real.” It makes me wonder about the idea that we shouldn’t just plug ourselves into sensation generation machines if we ever had the technology.

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Toward human phylogenetic intuitions

By Razib Khan | September 22, 2010 2:37 am


100 years ago a science based physical anthropology offered up very little as to a systematics of mankind beyond what you could intuit from visual assessments of phenotypic similarity alone. Instead, there were fantastical taxonomies which had little basis in the true pattern of variation and more in the nationalistic debates of that period. The Nordic, Mediterranean, and Alpine trichotomy of the European peoples had only marginally more concrete reality than the division between the Vanyar, Noldor, and Teleri.

We don’t live in such a fantastic age. Much of the mystery, and so potential for mischief, is gone. The “post-genomic” era means that old questions only vaguely perceived in the past are now well resolved. Quite often readers will ask a question as to the phylogenetic relationship between population A & B. If I don’t know off the top of my head, which is the norm, I’ll go to the search engine and look up what I’ve written on the topic. This has started to become tedious, in part because WordPress’ search engine leaves something to desired. So I have some papers bookmarked for immediate reference. They’re of wide scope (i.e., they don’t focus on just one population such as the Jews) and draw from a large number of markers to get a good picture of total genome relatedness. The focus within these papers tends to be genetic distances and relationships, not other topics of great interest such as natural selection. Also, I’ve tried to find links accessible to people without institutional access (for the Science link free registration will do it). If you can think of other papers, please leave the link in the comments.

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CATEGORIZED UNDER: Genetics, Genomics

The illusions of intuition

By Razib Khan | September 21, 2010 12:39 pm

414NJ526e2L._SS500_Sometimes books advertise themselves very well with their title. The Invisible Gorilla: And Other Ways Our Intuitions Deceive Us is one of those books. Alternatively it could have been titled: “Giving thinking a second chance.” Or, with an eye toward pushing copies: “Why everything Malcolm Gladwell tells you is crap.” And finally, a more highbrow possibility: “Reflection: man’s greatest invention.”

The “hook” for The Invisible Gorilla is the experiment which goes colloquially by the same name. The authors of the book, Christopher Chabris and Daniel Simons, actually wrote the paper Gorillas in our midst: sustained inattentional blindness for dynamic events (though they note that the basic insight goes back to the 1970s). Here’s a YouTube clip illustrating Chabris & Simons’ set up. Despite the eye-catching way the authors grab your attention the core message of The Invisible Gorilla is often very Plain Jane: thinking is hard, it yields real results, and, beware of short-cuts. Many sections of the book read as counterpoints to the counterintuitive defenses of intuition which Malcolm Gladwell presents in Blink: The Power of Thinking Without Thinking (Gladwell as it happens played a key role in popularizing knowledge of “the invisible gorilla” phenomenon). Despite being “sexed” up in the past few decades the defense of intuition, of “gut,” has a long intellectual history. For every Kant there is a Wang Yangming. And yet the borderlands between intuition and deduction, reflex and reflection, can often be gray. I would argue that much of human culture actually emerges from rational extensions of intuition. David Hume famously asserted reason’s slavery to passion, but I think a less grand way of characterizing the nature of different aspects of cognition is that they complement and supplement each other (see How We Decide).

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Daily Data Dump – Tuesday

By Razib Khan | September 21, 2010 10:17 am

Price’s Second Equation. David B continues his technical review of the Price Equation.

Selective pressures for accurate altruism targeting: evidence from digital evolution for difficult-to-test aspects of inclusive fitness theory. “Our investigations also revealed that evolution did not increase the altruism level when all green beard altruists used the same phenotypic marker.” Read a university press release here.

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Swedes are not sexist or nativist

By Razib Khan | September 21, 2010 1:32 am

A party, the Sweden Democrats, is about to enter the Swedish parliamanent which is described in this way in Wikipedia:

The party has its origins in the nationalist movement Bevara Sverige Svenskt (“Keep Sweden Swedish”)…During the mid 1990s, the party leader Mikael Jansson strove to make the party more respectable, modelling it after other “euronationalist” parties, most prominently the French National Front. This policy continues to be followed by the present leader Jimmie Åkesson. This effort included ousting openly extremist members.

Yes. More respectable by modeling itself on the National Front. Here’s a bit about the organization which eventually grew into the Sweden Democrats:

Bevara Sverige Svenskt (“Keep Sweden Swedish”) was a Swedish nationalist movement based in Stockholm and is a slogan used by various Swedish nationalist parties. The stated objective of the BSS movement, and the aim of the slogan, was to initiate a debate in order to reduce immigration from non-European countries and repatriate non-ethnic Swedes.

The Swedes, and the world, are shocked. Should they be? From what I can tell the Social Democratic Party of Sweden no longer has a hegemonic grip on Sweden’s politics. But the core working class base of such coalitions is shrinking because of economic restructuring throughout the developed world, with the remnants often defecting to Right-populism. Today Gunnar Mydral would have to look to writing a book about his own nation, which has about the same foreign born proportion as the USA (though that is a touch deceptive as many of these are other Scandinavians or Finns).

This prompted me to look in the World Values Survey. Specifically, the last wave which started around 2005. One thing you notice in the survey is that Swedes are very politically correct, even compared to their Nordic neighbors. I have read that the ecological awareness imputed to Native Americans in part because of the Noble Savage idea has actually resulted in a real shift and striving by many Native Americans to actually implement those ideals. Sometimes I wonder if the Swedes are so “progressive” and “forward thinking” in surveys because everyone always pats them on the back for being progressive and forward thinking. Sweden sure is the least sexist and nativist nation in the WVS.

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CATEGORIZED UNDER: Anthroplogy, Data Analysis, Politics

Pakistanis are just like Indians (not that there's anything wrong with it)

By Razib Khan | September 20, 2010 9:45 pm

In the comments below a strange conversation grew out of the politicized nature of Pakistani identity, and its relationship to India the nation-state, and India the civilization. I assume that a typical reader, or more accurately commenter, on this weblog would be sanguine if they found out they were 10% chimpanzee. After all, it’s what’s between your ears that really matters, not who your ancestors were. I do understand that some readers have strong genealogical-nationalist interests in human population genetics, and that’s fine so long as you don’t presume that the rest of us share such priorities (this is a problem for some commenters, so please be aware that I get annoyed when you project this way, though it’s obviously not a banning offense).

But readers who come via search engines are a different case, and that’s why I’ve started to get worried about over-reading of PCA and such. Nevertheless, I do think PCA can answer the question of whether there is any real genetic discontinuity between Pakistanis and Indians. The answer is no. Page 19 of Reich et al. supplement 1 includes in the HGDP Pakistani populations in their plot of genetic variation of Indian groups. I’ve added some labels, but the top-line is rather clear. AP = Andhara Pradesh, UP = Uttar Pradesh, GUJ = Gujarat and RAJ = Rajasthan. I assume Ind. and Pak. abbreviations are self-evident.

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MORE ABOUT: India, Pakistan

Raging against the population genetics machine

By Razib Khan | September 20, 2010 5:32 pm

An interesting readable review in PLoS Genetics taking on population genetics, Frail Hypotheses in Evolutionary Biology:

In conclusion, I return to Michael Lynch’s challenging questions about blind spots and bad wheels in evolutionary biology which motivated this review…Concerning blind spots I have pointed out some limitations of current population genetics. There is too much emphasis on elegant mathematics, and not enough concern for the real values of the critical parameters -in particular, in models of mutation spread and fixation, or in models of optimal mutation rates. Recombination, a crucial genetic mechanism, is misrepresented in the models. Features that looked anecdotal, such as recombination between sister chromatids and germ-line mutations are perhaps central to the mechanisms of evolution in higher organisms. My proposals on mutation strategies…—see also Amos…—lead to rather precise insights on compensatory mutations or polymorphism propagation, yet they are largely ignored by population geneticists.

The beauty of population genetics is that it leads to relatively simple algebras which one can use to guide one’s intuitions. Phenomena such as selection or drift are more than words, they’re specific values. That being said, plenty of readers of this weblog have expressed caution, and skepticism, at the over-utilization of monogenic diallelic models as “quick & dirty” prototypes for evolution more generally. More concretely small changes in parameter values can lead to radically different inferences within the real context of natural history. Excessive reliance on elegant population genetic theory can lead one astray just as excessive reliance on economic theory can. The real world introduces so many complications that discarding too many of them to make a model tractable may render the framework of trivial importance, or even lead one down false paths. I don’t find author’s specific objections of distinction, but the paper is useful as an entry-point into the debate within the literature. The fact that R. A. Fisher, J. B. S. Haldane, and Sewall Wright, did not predict the full path of empirical discovery over the 20th century indicates very concretely the limitations of theoretical frameworks within biology.

CATEGORIZED UNDER: Genetics, Genomics

Daily Data Dump – Monday

By Razib Khan | September 20, 2010 2:58 pm

Summer is almost over.

What was malt liquor? The history of malt liquor, and also Pabst Blue Ribbon. No idea that malt liquor used to have an upscale association.

The Genetics & Linguistics Of Central Asia. Excellent overview from a somewhat different angle from my own. Excellent map.

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Gypsies on a genetic island

By Razib Khan | September 19, 2010 3:14 pm

Romanis-historical-distributionIf you live in the States one of the things you hear a lot about Europe in regards to its relationship to its ethno-religious minorities are the problems with Muslims. This is probably an Americo-centric perspective shaped by 9/11, when many of the hijackers had turned out to have spent time in Germany. Additionally, terrorist actions in both London and Madrid highlight the persistence of these problems over the years. These sorts of shocking events put a sharp focus on the geopolitical cross-hairs which Europe finds itself in in the second age of mass migration. Though this time it is a destination, and not a source.

But having been to Europe recently it was notable that in several regions the day-to-day tension when it came to ethnicity often focused on Gypsies (I use the older term because the ethnonym “Roma” which has become politically correct in the USA includes only a subset of Europe’s Gypsy population, even if the greater number). Many regions of Europe now have two distinct populations of Gypsies, a long resident local group, as well as Roma from the eastern nations of the EU. Though the relationships between these traditionally nomadic peoples and indigenous populations has never been without tension, it is clear that something close to a modus vivendi has been achieved in many European nations between the majority and their small native Gypsy populations. The influx of the Balkan Roma add a new variable.

ResearchBlogging.orgBut the political fuss for me simply rekindled a curiosity as to the genetic origins of the Gypsies. Culturally their South Asian provenance couldn’t be clearer; they speak an Indo-Aryan language. Their term for themselves in many parts of Europe comes from the  Indo-Aryan word for “black,” as they are are darker than the natives of the lands in which they have settled , and in fact often look visibly South Asian. This seemed especially true of Balkan Roma. On the other hand the Kale of Finland looked to be brunette Europeans.

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CATEGORIZED UNDER: Genetics, History, Select

The empty heartland

By Razib Khan | September 18, 2010 11:34 am

800px-Two-point-equidistant-asiaIn a comment below I alluded to my idea that the heart of Eurasia was relatively unpopulated before the Holocene, explaining why many Central Asian groups seem to be recent hybrids from very distinct populations. Normally the sort of model which posits K ancestral groups is an idealization to some extent. To assign every K to a real known ancient population is probably not tenable in most cases. Not so for many Central Asian groups, for the K’s often seem rather clear and distinct, and we have a fair amount of historical pointers. Thanks to Herodotus, the early Han dynasty chroniclers, and the Avesta, we have some sense of what the ethnography of Central Asia was like several thousand years ago. Additionally, it seems possible that highly advanced societies such as that of Bactria-Margiana were transferred from elsewhere. The heart of Eurasia may have been to a great extent a thinly populated frontier before the dawn of civilization, and so presaged our own “New World.” But whereas the caravel opened up the trans-oceanic lanes, I assume that in Inner Asia it was the horse which allowed populations to cross the great waterless wastes efficiently enough that trade and people could flow robustly between the oases.

The analogy between Inner Asia and the New World came to me when rereading Haplotype-Sharing Analysis Showing Uyghurs Are Unlikely Genetic Donors. Figure 2 shows “haplotype sharing” between various populations. The left panels compare Uyghurs to their putative parental populations, and the right panels African Americans. Observe how few “private haplotypes” the two populations which came out of a recent admixture have proportionally. The first shaded region in each panel are the private haplotype proportions, while the last shows haplotypes which span all three populations. The two intermediate regions are pairwise comparisons with the ancestral groups.

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MORE ABOUT: Heartland, History

Open Thread – September 18th, 2010

By Razib Khan | September 18, 2010 12:41 am

Last weekend of summer. I plan to have my reviews of The Invisible Gorilla and The Lost History of Christianity up very soon. I recommend both heartily! Next in the stack: Stanislas Dehaene’s Reading in the Brain. A question was asked about the focus on extremes when it came to perceptions of the genetic influence on an outcome. The table below has mean values, 1-21, 1 = 100% genes, 21 = 0%, so 11 = 50%.

Obese white woman Drunk Asian man Saintly Hispanic woman Athletic black man
Liberal 11.24 11.8 11.94 11.83
Moderate 12.12 12.2 12.41 12.02
Conservative 12.95 12.44 12.91 12.49
No College 12.42 11.76 12.03 11.78
College 13.26 12.9 13.23 12.79
Not intelligent 12.27 10.85 11.2 10.99
Average 13.08 11.91 12.3 11.95
Intelligent 13.52 13.01 13.04 12.93
MORE ABOUT: Open Thread

Melody Dye & Jason Goldman on BHTV

By Razib Khan | September 17, 2010 11:35 pm

Just wanted to give a shout-out to my friend Jason Goldman who has a discussion up at with his co-blogger at Child’s Play Melody Dye. Recommended.


Friday Fluff – September 17th, 2010

By Razib Khan | September 17, 2010 4:05 pm


1. First, a post from the past: Why patriarchy?

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Of Iran, Turan, and Turks

By Razib Khan | September 17, 2010 12:27 pm

uzbekmanThere’s a new paper out in The European Journal of Human Genetics which is of great interest because it surveys the genetic and linguistic affinities of two dozen ethno-linguistic groups from the three Central Asian nations of Uzbekistan, Kyrgyzstan, and Tajikistan. This is what the Greeks referred to as Transoxiana, and the Persians as Turan. Originally inhabited by peoples with close cultural affinities with those of Persia, indeed, likely the root of the peoples of Persia, by the historical period Turan developed a distinctive identity as a frontier or march. It was in Turan where the Turk met the Iranian (a class which included non-Persian groups, such as the Sogdians), from the pre-Islamic Sassanians down to the present day. It is a region of the world which has a very ancient urban culture, cities such as Merv, as well as peoples that were only recently nomads, forcibly made sedentary by the Soviet regime.

To add another twist to the picture many of the ethno-linguistic groups which we are familiar with today and which serve as the cores of the new Central Asian nations only came into being within the last few centuries, with a particular “push” from Russian Imperial and Soviet ethnologists who were tasked with fleshing out national identities with which the center could negotiate. A “Tajik” is after all simply part of the Persian-speaking residual population of Central Asia, spreading down into Afghanistan. The carving out of an independent Tajikistan out of the Central Asian landscape is as much a creation of the modern age as the state of Israel. The “Uzbek” identity was once simply that of the ruling caste of Transoxiana who came to power after the decline of the Timurids. Today it is an appellation which brackets the settled Turkic speaking peoples of Uzbekistan and beyond.

ResearchBlogging.orgInto this near Gordian knot of history and ideology walk the naive and well-meaning geneticists. There is no great objection one can make to the genetics within the paper, but the historical framework and some of the assertions are peculiar and tendentious indeed. It’s a problem which starts within the abstract. In the heartland of Eurasia: the multilocus genetic landscape of Central Asian populations:

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CATEGORIZED UNDER: Anthroplogy, Genetics, Genomics, History

Liberals more hereditarian than conservatives?

By Razib Khan | September 17, 2010 12:13 am

Sometimes I run into things in the GSS which just don’t fit expectations. On occasion the results are so weird or unexpected I check my coding over and over. Or, I have a suspicion that something was input incorrectly. This is one of those cases. As often happens a comment was made as to the acceptance of biological explanations for behavior, and their political correlates. I decided to poke around and confirm what I knew: that liberals are more environmentalist than conservatives, who are more hereditarian. This is not what I found!

The gene related questions have the following form:

… what percent of the person’s behavior you think is influenced by the genes they inherit, and what percent is influenced by their learning and experience. After each question, type the number of the box that comes closest to your answer. Remember, the higher the number, the more you think the behavior is influenced by learning and experience; the lower the number, the more you think it is influenced by genes

Each respondent could select from 21 values, from 1 to 21, with 1 = 100% genetic, 21 = 0% genetic, at 5% increments. So 3 = 90% genetic. This isn’t technically correct as an understanding of heritability, but I think it gets across the intuitions of heritability. All the questions were asked in 2004. They were:

– GENENVO1: Carol is a substantially overweight White woman. She has lost weight in the past but always gains it back again.

– GENENVO2: David is an Asian man who drinks enough alcohol to become drunk several times a week. Often he can’t remember what happened during these drinking episodes.

– GENENVO3: Felicia is a very kind Hispanic woman. She never has anything bad to say about anybody, and can be counted on to help others.

– GENENVO4: George is a Black man who’s a good all-around athlete. He was on the high school varsity swim team and still works out five times a week.

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MORE ABOUT: GSS, Hereditarianism

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