Archive for June, 2010

Daily Data Dump – Wednesday

By Razib Khan | June 23, 2010 5:06 pm

GDP PPP inhabitant by European region. Combining Italy or the UK into one GDP number is deceptive. Lombardy has twice the GDP PPP of much of southern Italy. The regional differences are not nearly as stark in Spain, where poor regions like Andalusia and Galicia exhibit less of a gap from prosperous regions. By the way, does anyone know if there’s the ability in R to map these differences easily? I’ve only done USA mapping.

Separation Between Neanderthal and Homo Sapiens Might Have Occurred 500,000 Years Earlier, DNA from Teeth Suggests. Not sure if this makes any difference evolutionary genetic wise, though these sorts of issues are relevant for paleoanthropologists trying to reconstruct paleoecologies of hominins.

Mystery of the pregnant pope: New film reopens one of the Vatican’s most enduring wounds. I saw this film on a Lufthansa flight a few months back. I liked it. Though the article doesn’t make it clear enough that it’s 99.9% likely to be based on a legend concocted for purposes of propaganda.

New Nicaraguan sign language shows how language affects thought. As Joe Biden would say, this is a big f**king deal.

Anthrogenetics. A reader pointed me to this interesting weblog/review page. Feel free to point to other interesting science weblogs in the comments.


Daily Data Dump – Tuesday

By Razib Khan | June 22, 2010 12:56 pm

Sexual urges overcome cultural taboo. So it turns out that the female children of immigrants from conservative societies (South Asian and Islamic) are paying for hymen restoration surgeries. The more interesting question would be if these children become sexually conservative themselves, perpetuating the life history trajectory so that their own children have to go through these sorts of reconstructions.

Vitamin D Deficiency Due To Genetic Variants. Vitamin D supplementation is all the rage right now. What if its efficacy and necessity is conditional on genetic background?

Is the “missing heritability” right under our noses? The issue may have to do with the exigencies of research programs, not a deep scientific mystery.

A Singular Kind of Eugenics. It seems “privilege” is the new hot-button for Lefties who are skeptical of assisted reproductive technologies and genetic modifications. I suspect it’s a Left-wing buzzword which is equivalent to Righties who bring up “dignity” or the “wisdom of repugnance.” Much easier than having to generate clear prose and understand the complex motives which underpin an issue. Buying really expensive smartphones and pure entertainment machines like iPads also are manifestations of privilege. So what distinguishes X from Y? Not the commonality, privilege, but perhaps the same gut intuitions which Right bioconservatives are willing to man up to, repugnance. Some privileges are repugnant (biological interventions) and some frivolous (iPad). Also, when did discourse replace discussion and privilege replace class?

Saltie Makes a Sandwich Almost Entirely Out of Lettuce. There is nothing magical about meat; it’s all about the flavor.

MORE ABOUT: Daily Data Dump, Links

The future of fertility; more kids please

By Razib Khan | June 22, 2010 10:52 am

After my post yesterday on Bryan Caplan’s argument for having more children, I was curious as to what the public perceptions of the ideal number of children was in the General Social Survey. There’s a variable with large N’s which is already in there: CHLDIDEL. It asks:

What do you think is the ideal number of children for a
family to have?

Curiously I noticed a bounce back in terms of ideal numbers in the 2000s plotting CHLDIDEL by year, YEAR. This could be just due to demographic changes (a larger proportion of pro-natalist immigrants after 1965), so I sliced the sample in a few different ways. More specifically, I focused on women aged 18-40, since these are presumably the ones who are the ultimate agents in terms of family size, and combined years by decade to increase sample size for the demographic slices.

It does seem that there was a broad societal shift among women of child-bearing age to prefer larger families in the 2000s in relation to the previous decade. Below the fold I have some charts with the means (the small dots) by decade as well as the 95% confidence interval for various demographics.

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CATEGORIZED UNDER: Culture, Data Analysis, GSS

ResearchBlogCast #9: Genetics, Fertility, And Disease

By Razib Khan | June 21, 2010 2:46 pm

The 9th ResearchBlogCast is up. We talk about the recent paper on cystic fibrosis genetics which I blogged.

MORE ABOUT: ResearchBlogCast

Daily Data Dump – Monday

By Razib Khan | June 21, 2010 12:51 pm

I won the 3 Quarks Daily Science Prize. ‘Top quark’. Heh. “I” = Ed Yong. ‘nuf said.

Brown-eyed men perceived to be more dominant. Dienekes offers up a more banal explanation, that the disjunction between blue vs. brown-eyed males in dominance perception has to do with a correlation that’s a holdover from past population differences which are being eliminated through admixture. Plausible enough to me, excepting that I do wonder at models which presume that continental populations were ever so isolated.

Chimpanzees murder for land. In biology Malthus was right. Intrapspecific competition is the norm quite often because of reproduction up to the carrying capacity. This is why I think Brian Ferguson’s idea that war is a product of agriculture is highly naive; hunter-gatherers were up at their carrying capacity as well.

Bernie Madoff, Free at Last. Celebrity sociopath.

If it’s OK to reject blood from gay men, what about blacks? Will Saletan takes things to their logical conclusion to undermine the premise.


To be fruitful and multiply

By Razib Khan | June 21, 2010 9:14 am

Over at The Wall Street Journal Bryan Caplan has an op-ed, The Breeders’ Cup: Social science may suggest that kids drain their parents’ happiness, but there’s evidence that good parenting is less work and more fun than people think. Bryan Caplan makes the case for having more children. Much of the op-ed focuses on behavior genetic insight as to the relative lack of long term importance of shared environment (read: parental environmental input). But the section on happiness and diminishing returns on the misery cost of children piqued my interest:

…closer look at the General Social Survey also reveals that child No. 1 does almost all the damage. Otherwise identical people with one child instead of none are 5.6 percentage points less likely to be very happy. Beyond that, additional children are almost a happiness free lunch. Each child after the first reduces your probability of being very happy by a mere .6 percentage points.

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MORE ABOUT: natalism

Animal Apartheid

By Razib Khan | June 21, 2010 7:46 am

Here’s an article from Canada on the debate about whether hybridization should be discouraged. I understand the impulse toward preserving nature as it is, but the drive for presumed purity seems almost fetishistic. Consider this sentence: ” Or could hybrids actually weaken genetically pure populations of disappearing wildlife?” What does “genetically pure” mean in a deep sense here? We know what it means instrumentally for the purposes of conservation genetics, but the way people talk about pristine lineages makes it seem an almost ethical concern.

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"Here be dragons"

By Razib Khan | June 20, 2010 9:21 am

I just stumbled onto two amusing articles, Ancient legends once walked among early humans?, and The discovery of material evidence of a distinct hominin lineage in Central Asia as recently as 30,000 years ago is no surprise. The second is a letter from a folklorist:

Sir, The discovery of material evidence of a distinct hominin lineage in Central Asia as recently as 30,000 years ago (report, Mar 25) does not come as a surprise to those who have looked at the historical and anecdotal evidence of “wild people” inhabiting the region. The evidence stretches from Herodotus to the present day. The Russian historian Boris Porshnev suggested that they are relict Neanderthals, although the lack of evidence of material culture suggests a type closer to Home erectus.

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Cuckoldry more common in past generations

By Razib Khan | June 20, 2010 8:21 am

We have some data that in fact older generations were more sexually promiscuous, contrary to the moral panic perpetually ascendant. As a follow up to my previous post, there is some scholarship which suggests that misattributed paternity rates have been declining. Recent decline in nonpaternity rates: a cross-temporal meta-analysis:

Nonpaternity (i.e., discrepant biological versus social fatherhood) affects many issues of interests to psychologists, including familial dynamics, interpersonal relationships, sexuality, and fertility, and therefore represents an important topic for psychological research. The advent of modern contraceptive methods, particularly the market launch of the birth-control pill in the early 1960s and its increased use ever since, should have affected rates of nonpaternity (i.e., discrepant genetic and social fatherhood). This cross-temporal meta-analysis investigated whether there has been a recent decline in nonpaternity rates in the western industrialized nations. The eligible database comprised 32 published samples unbiased towards nonpaternity for which nonoverlapping data from more than 24,000 subjects from nine (mostly Anglo-Saxon heritage) countries with primarily Caucasian populations are reported. Publication years ranged from 1932 to 1999, and estimated years of the reported nonpaternity events (i.e., the temporal occurrence of nonpaternity) ranged from 1895 to 1993. In support of the hypothesis, weighted meta-regression models showed a significant decrease (r = -.41) of log-transformed nonpaternity rates with publication years and also a decrease, albeit not significant (r = -.17), with estimated years of nonpaternity events. These results transform into an estimated absolute decline in untransformed nonpaternity rates of 0.83% and 0.91% per decade, respectively. Across studies, the mean (and median) nonpaternity rate was 3.1% (2.1%). This estimate is consistent with estimates of 2 to 3% from recent reviews on the topic that were based on fewer primary studies. This estimate also rebuts the beliefs and hearsay data widespread among both the public and researchers which contend nonpaternity rates in modern populations might be as high as about 10%.

I don’t have academic access, so I can’t say much more than that (if someone wants to email me the paper, contactgnxp -at – gmail -dot- com will work). Obviously I don’t think this is implausible on the face it; the “good old days” were often a lot less “good” than we remember (or what our elders remember and tell us).

Addendum: If you are from the cuckold enthusiast community, yes, I am aware that your perspective on whether the good old days were good may differ….

CATEGORIZED UNDER: Culture, Genetics
MORE ABOUT: Cuckoldry, paternity

The paternity myth: the rarity of cuckoldry

By Razib Khan | June 20, 2010 7:02 am

An urban myth, often asserted with a wink & a nod in some circles, is that a very high proportion of children in Western countries are not raised by their biological father, and in fact are not aware that their putative biological father is not their real biological father. The numbers I see and hear vary, but 10% is a low bound. People are generally not convinced when I point out that this would mean that nearly 30% of paternal grandfathers are not paternal grandfathers. Most of my scientist acquaintances fancy up the myth by suggesting that they received this datum from research on family groups (where you have to take into account the error introduced by paternity misattribution) or organ matching for purposes of donation.

Evolutionary biologist Marlene Zuk has some informal survey data which she presents in an article in The Los Angeles Times:

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CATEGORIZED UNDER: Biology, Genetics

How "Predator" should have ended

By Razib Khan | June 19, 2010 10:50 pm



America in 2050 may still be majority white

By Razib Khan | June 19, 2010 1:50 pm

I have expressed some skepticism at the idea that in the year 2050 the United States of America will perceive itself as a majority-minority nation; that is, non-Hispanic whites will be be a minority. This projection is repeated and asserted so often that it’s a plausible background assumption when you’re making a model of the American future. But there are other factors which make this a shakier inference from current trends. A new article in The New York Times which has nothing to do with racial identity as such is a good tell as to the other factor at work, Plea to Obama Led to an Immigrant’s Arrest:

he letter appealing to President Obama was written in frustration in January, by a woman who saw her family reflected in his. She was a white United States citizen married to an African man, and the couple — college-educated professionals in Manhattan — were stymied in their long legal battle to keep him in the country.

One of the principals is introduced as white, but later on, you learn:

“I’ve been feeling very confused and ashamed as an American citizen,” she said, evoking her family’s eclectic immigrant origins.

Her father, an emeritus professor of East Asian languages and cultures at the University of California, Berkeley, is the son of Scottish immigrants; her mother’s family were refugees from North Korea; her stepmother is Chinese; and her sister’s husband is Egyptian.

Vanessa HugdensIf her mother is one of the tiny minority of white European-descended Koreans, she happens to be one of those who also has a Korean first name (it isn’t too hard to find these data on the internet). In other words, The New York Times felt that it was permissible for the purposes of this article to frame one of the individuals profiled as white despite the fact that more precisely she’s Eurasian as is clear within the text of the article itself (she may also have identified herself as white to the reporter). I am not sure that she would have been defined as white if her husband was not an African immigrant, as for narrative purposes that is probably a better contrast effect. But imagine if her mother’s family were black immigrants from Jamaica: The New York Times would not define her as white I would hazard in that case.

Image Source: Wikimedia Commons

MORE ABOUT: Ethnicity, Race

Another perspective on Facebook

By Razib Khan | June 19, 2010 1:25 pm

From Ruchira Paul, who analyzes her own friend network. One issue which I think is relevant is that many people have several Facebook accounts for several different purposes. It’s an interesting window into the psychology of different individuals, as some seem happy to go along with Facebook’s preference of a unitary identity, while others resist it and suborn the intent with Facebook itself.

MORE ABOUT: Facebook

Daily Data Dump – Friday

By Razib Khan | June 18, 2010 12:52 pm

Subprime for Students – Why does so much federal money go to for-profit schools—and what happens when the system crashes? Steve Eisman, a Cassandra of the subprime meltdown in real estate, is now focused on the student loan & grant racket in the for-profit education industry. I have nothing against competition forcing the relatively static higher education complex to evolve. In fact I favor it. But with massive government subsidies with minimal oversight being directed toward higher education the market is producing entities which emerge not to provide a genuine service to potential students, but to capture as much of the cash flow from the feds as possible. Barring elimination of government subsidies more aggressive oversight seems the only avenue of correcting the problems in this sector.

Is Google Docs Destined To Be a Revolutionary or Footnote?. First, Google Docs lacks some of the power for presentations which desktop office packages have. Second, the flakiness of internet connections means that many people won’t use it for ‘mission critical’ tasks yet. But I assume that over the next ten years you will start to see a shift from desktop applications to web applications even in office productivity software.

Do Not Log-Transform Count Data, Bitches! R gives you no excuse.

The Essence of Pleasure. Human flourishing is more than “doing the sums.”

Anthropology, Primatology, and the Definition of Culture: Reply to Sperber. Eric Michael Johnson presents a powerful case. Though do note that in general Dan Sperber, the target of Johnson’s critique, views the overall research program he’s criticizing positively.

MORE ABOUT: Daily Data Dump, Links


By Razib Khan | June 18, 2010 9:23 am


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The "how" of cystic fibrosis through the "why"

By Razib Khan | June 18, 2010 6:39 am

It’s just a fact that contemporary human evolutionary genetics has relied upon its potential insights into disease to generate funding, support and interest. I don’t think that this is much of a silver lining when set next to the suffering caused by disease, but it’s a silver lining nevertheless.  Therefore findings which would be of interest in and of themselves are able to push to the front of the line because of possible medical relevance. A new paper in PLoS Genetics illustrates the relationship between what seem like esoteric evolutionary insights and diseases of importance to the medical community. It takes a look at the gene whose disruption results in the horrible illness cystic fibrosis, CFTR, and uncovers some interesting genetic patterns of possible evolutionary relevance. The paper is The CFTR Met 470 Allele Is Associated with Lower Birth Rates in Fertile Men from a Population Isolate. From the author summary:

Cystic fibrosis (CF) is the most common lethal recessive disorder in European-derived populations and is characterized by clinical heterogeneity that involves multiple organ systems. Over 1,600 disease-causing mutations have been identified in the cystic fibrosis transmembrane regulator (CFTR) gene, but our understanding of genotype–phenotype correlations is incomplete. Male infertility is a common feature in CF patients; but, curiously, CF–causing mutations are also found in infertile men who do not exhibit any other CF–related complications. In addition, three common polymorphisms in CFTR have been associated with infertility in otherwise healthy men. We studied these three polymorphisms in fertile men and show that one, called Met470Val, is associated with variation in male fertility and shows a signature of positive selection. We suggest that the Val470 allele has risen to high frequencies in European populations due a fertility advantage but that other genetic and, possibly, environmental factors have tempered the magnitude of these effects during human evolution.

The high frequency of alleles which result in cystic fibrosis is something of a mystery. Basic population genetic theory tells us that lethal (at least in the pre-modern era) recessive traits should be extant only at very low frequencies so that most of the deleterious alleles are “masked” by normal copies. The ΔF508 mutation is found in 1 in 30 people of Northern European descent (you see somewhat different ratios, but all in the same ballpark). That means that assuming a random mating Hardy-Weinberg Equilibrium a touch more than 0.1% of offspring would exhibit the disease due to the coming together of the ΔF508 allele in a homozygote state, not a trivial proportion when you consider that the fitness of these individuals converges upon zero.

In this paper they don’t get at ΔF508 and the other disease causing alleles directly. Rather, they find that one particular SNP has a strong effect on fertility, as well as having a relationship in some contexts to disease implicated alleles. Not too surprising considering that cystic fibrosis is associated with infertility. I presume that the overarching logic is that  understanding the genetics of CFTR in its details will give us a better picture of its internal architecture and the various networks and pathways which result in its proper, or improper, function.

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CATEGORIZED UNDER: Genetics, Genomics

Daily Data Dump – Thursday

By Razib Khan | June 17, 2010 3:44 pm

Eye Color Predicts and Doesn’t Predict Perceived Dominance. First, the study replicates the common finding of some differences in perceived dominance between blue vs. brown-eyed males. But, they observed that when the eye colors were digitally manipulated the dominance ranking did not change. In other words the eye colors seem to have correlated with other traits of masculinity, rather than been a causal signal. The authors offer up a model whereby socialization of blue eyed individuals for longer periods as children (because the trait is neotenous) produces less facial masculinization. But I don’t buy the idea that this couldn’t be genetically mediated by variation on the HERC2/OCA2 locus (where most blue vs. non-blue eye color variation is controlled). In particular, I believe there’s a body of literature that melanin and testosterone production pathways affect each other so that there is a positive correlation, though the exact causal connections are still to be worked out. Note that all this only applies within populations; between population complexion differences don’t necessarily predict dominance differences because the genetic variates are not controlled as they are within populations.

Were The Americas Settled Twice? In the USA this scientific question has social-political implications, as Native American/Amerindian political rights have become excessively (to my mind) connected to self-identity as primal autochthons. Doing a reductio ad absurdum on this is too easy.

Population size predicts technological complexity in Oceania. This sort of result has obvious general implications (see McNeill and McNeill’s The Human Web). I assume Garett Jones would not be surprised.

Google Scholar Blog.

How to always have interesting conversations. Interesting is obviously a relative term. Additionally, probably best to apply a two-tier strategy. Tier-1 involves avoiding expending time/energy talking to boring people outside of cognitive autopilot, and tier-2 involves seeking out those with common interests among the non-boring set.

MORE ABOUT: Daily Data Dump

Time & mind & tipping

By Razib Khan | June 17, 2010 2:10 pm

I just got back from a European trip, and I have to say I did not miss tipping. I especially appreciated not having to do the song & dance typical of larger groups in sit-down restaurants in the USA where you figure out how much you’re going to tip on a communal basis, when everyone has different tipping set points and perceptions of service and such. The money is less of an issue than the extra wasted time at the end of a meal & drinks which are spent on the terms of calculation rather than more conventional conviviality. In fact now that I think about it way too much time in my life has been spent discussing the etiquette of tipping, often outside of a situation where people are going to have to tip imminently. I thought about this after seeing this post in The Atlantic on tipping. One correspondent observes:

I lived in Japan for a while. There is no tipping there, and it works great. If we could be like Japan, I’d be all for it. However, I don’t think we’d be like Japan. Anytime I have ever eaten somewhere that does not practice tipping, service has been abysmal. Customers herded through like cattle, dishes brought out late, then diners rushed through them, eyes rolled, etc. We just do not have the service culture that would allow us to disconnect pay from performance and continue to expect the same kind of service.

The point about national culture is well taken. I experienced some bad service in Italy and Finland, but the quality of badness was very different, in keeping what with you’d expect from the respective national cultures (though in general I experienced service as good as in the states in both places).* But the empirical observation about American restaurants without tipping having lesser service suffers from sampling bias. Establishments which don’t have tipping are generally lower-end, verging on cafeterias. So it’s not an apples to apples comparison. A better one would be looking at higher end restaurants which have mandatory gratuities for large groups vs. those which do not. Even here you have the peculiar distortion of the larger group, which can often be more difficult for a server to manage.

Of course one’s perspective on this probably varies by the amount of disposable income one has. If you don’t have much disposable income the small but repeated investments of time & energy which go into tipping might be worthwhile if you can manage to pay less than you would otherwise. If you have a fair amount of disposable income the marginal potential savings introduced by greater price variation which you can control at the cost of time & energy needed may not be worth it.

* I had to bargain very hard with a Finnish server on whether I could handle Indian levels of spiciness. This was obviously a well rehearsed conversation on her part, but I thought she should have updated her priors in my case. The lighting was dim, but not that dim. Usually American servers at Indian restaurants aren’t too resistant when I assert I can handle high levels of spice.


Death of email = death of Facebook

By Razib Khan | June 17, 2010 10:09 am

Reihan Salam points me to a presentation by a Facebook executive who claims that “E-mail…is probably going away….” Well, remember Google Wave? I assume that email-as-we-know-it will evolve. But one thing I pointed out to a friend the other day: remember when you were excited to get “new mail?” (perhaps the reference will be lost on younger readers, but there was a time when it was cool and special to have an email account, and be able to receive messages from people who lived in Ecuador at digital speed) Now it’s more like, “now what!?!?!” Email is a utility through which your boss may contact you. The excitement factor has now shifted to Facebook, where old friends you’ve lost touch with may request to be your friend. But if Facebook becomes as ubiquitous as email, as taken-for-granted, you might start getting wall messages from your boss. And at that point Facebook will become a utility you’ll want to not log into, not because you want to avoid wasting time procrastinating, but because the “real world” has infected it.

Technology has been one reason we humans have by and large broken out of the Malthusian trap. But a key difference between innovation on the physical dimension (e.g., the combustion engine) and technologies which have social utility is that human psychological faculties can shift only on the margins by much smaller degrees. In theory you can have as many Facebook friends as Facebook will allow you to have; it’s a scalable phenomenon. But in reality a small circle of friends become Facebook “friends” who you barely know, because your mind isn’t geared to really keep track of so many social relations.

Of course the people who run tech companies are smart and many know this. But their jobs hinge on you becoming invested in the idea that their firm is going to Change Everything. So they’re not going to emphasize too much the fact that human utilization of technology is substrate constrained, so to speak.

CATEGORIZED UNDER: Culture, Technology
MORE ABOUT: Email, Facebook, Technology

Hobbits on NOVA

By Razib Khan | June 15, 2010 3:25 am

This looks interesting, Aliens from Earth:

An ancient legend on the Indonesian island of Flores tells of an elflike creature similar to the fictional hobbit of novels and film. But a controversial 2003 archeological find not only suggests that there could be some truth behind the legend but promises to rewrite a key chapter in the human evolutionary story. This program investigates the discovery, analysis, and startling implications of the hobbit of Flores.

Airs tonight in the USA.

MORE ABOUT: Flores, Hobbits

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This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!

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