Razib Khan One-stop-shopping for all of my content

June 28, 2012

The end of blog & comments

Filed under: Admin,Administration — Razib Khan @ 10:39 pm

Chad Orzel may be giving up blogging. And no, it’s not an April Fool’s Day joke. He’s been at it for 10 years, so no big surprise. I may be where he is at some point in the near future. For me, I always have something to say (or at least I think it’s worth saying!). But writing takes a little time out of my day, and many days I’m not gifted with a surplus of time. So we’ll see. I’ve been telling people I might give up blogging since 2004, and it just never seems to happen. But I never had a small person with whom I enjoyed wrestling with before.


Second, Sean Carroll has a funny post up on comment policy. Over the 10 years of running my own blog(s) I’ve shifted in my own perspective and outlook. In the beginning I was rather laissez faire. But it became rather obvious that most people were either stupid or ignorant, or, they took advantage of the anonymity of the internet to waste other peoples’ time. The biggest issue which I think some readers don’t seem to internalize well is that not only am I engaging comments, I’m ...

Tomatoes!

Filed under: Anthroplogy,Genetic Engineering,Genetics — Razib Khan @ 10:19 pm

This story in The New York Times, Flavor Is Price of Scarlet Hue of Tomatoes, Study Finds, is pretty cool:

Yes, they are often picked green and shipped long distances. Often they are refrigerated, which destroys their flavor and texture. But now researchers have discovered a genetic reason that diminishes a tomato’s flavor even if the fruit is picked ripe and coddled.

The unexpected culprit is a gene mutation that occurred by chance and that was discovered by tomato breeders. It was deliberately bred into almost all tomatoes because it conferred an advantage: It made them a uniform luscious scarlet when ripe.

Now, in a paper published in the journal Science, researchers report that the very gene that was inactivated by that mutation plays an important role in producing the sugar and aromas that are the essence of a fragrant, flavorful tomato. And these findings provide a road map for plant breeders to make better-tasting, evenly red tomatoes.

The paper, Uniform ripening Encodes a Golden 2-like Transcription Factor Regulating Tomato Fruit Chloroplast Development:

Modern tomato (Solanum lycopersicum) varieties are bred for uniform ripening (u) light green fruit phenotypes to facilitate harvests of evenly ...

Population replacement in Neolithic Spain?

Filed under: Agriculture,Anthroplogy,Neolithic,Paleolithic Europeans — Razib Khan @ 12:16 pm

There’s a new ancient DNA paper out which examines the maternal lineage and the autosomal background of two individuals extracted from a Spanish site dated to 7,000 years before the present. That is, during the European Mesolithic. In other words, these are the last wave of Iberian hunter-gatherers before agriculture. I have placed the PCA, with some informative labels, to illustrate the peculiarity of these samples. Here’s the abstract:

The genetic background of the European Mesolithic and the extent of population replacement during the Neolithic…is poorly understood, both due to the scarcity of human remains from that period…The mitochondria of both individuals are assigned to U5b2c1, a haplotype common among the small number of other previously studied Mesolithic individuals from Northern and Central Europe. This suggests a remarkable genetic uniformity and little phylogeographic structure over a large geographic area of the pre-Neolithic populations. Using Approximate Bayesian Computation, a model of genetic continuity from Mesolithic to Neolithic populations is poorly supported. Furthermore, analyses of 1.34% and 0.53% of their nuclear genomes, containing about 50,000 and 20,000 ancestry informative SNPs, respectively, show that these two Mesolithic individuals are ...

June 27, 2012

Heritability of behavioral traits

Filed under: Behavior Genetics — Razib Khan @ 11:48 pm

As a father the content of my conversations with friends and acquaintances has changed somewhat. Whereas in my offline life discussions of behavior genetics rarely came up, now they loom large implicitly and explicitly. Though the vast majority of people I interact with have graduate degrees or are pursuing graduate degrees in the life sciences almost none of them are aware of the magnitude of the heritability of most bio-behavioral traits.

For those of you who forgot, heritability is a population wide statistic which assesses the proportion of variation in the population you can attribute to heritable genetic variation. So if heritability is 1.0 all of the variation is due genetic variation; offspring are just a linear combination of their parents. If heritability is ~0.0, then there’s basically no correlation between parents and offspring. Though, as I said, heritability is a population-wide statistic, it can be informative on an individual level. For example, the heritabiilty of height is ~0.90 in the Western world. To give you a sense of the expected height of the offspring of two individuals, just take the average (in sex-controlled standard deviation units) and shift it back toward the mean by 10%. There is going to be ...

Heritability of behavioral traits

Filed under: Behavior Genetics — Razib Khan @ 11:48 pm

As a father the content of my conversations with friends and acquaintances has changed somewhat. Whereas in my offline life discussions of behavior genetics rarely came up, now they loom large implicitly and explicitly. Though the vast majority of people I interact with have graduate degrees or are pursuing graduate degrees in the life sciences almost none of them are aware of the magnitude of the heritability of most bio-behavioral traits.

For those of you who forgot, heritability is a population wide statistic which assesses the proportion of variation in the population you can attribute to heritable genetic variation. So if heritability is 1.0 all of the variation is due genetic variation; offspring are just a linear combination of their parents. If heritability is ~0.0, then there’s basically no correlation between parents and offspring. Though, as I said, heritability is a population-wide statistic, it can be informative on an individual level. For example, the heritabiilty of height is ~0.90 in the Western world. To give you a sense of the expected height of the offspring of two individuals, just take the average (in sex-controlled standard deviation units) and shift it back toward the mean by 10%. There is going to be ...

Do consumatory scholars need tenure?

Filed under: academia,Education — Razib Khan @ 11:27 pm

John Hawks pointed me to this really strange article, Just Because We’re Not Publishing Doesn’t Mean We’re Not Working:

We have no concise term to describe what we spend much of our time doing. Our colleges are focused on scholarly products that can be peer-reviewed and published, but the reality is that many of us spend much of our time on being scholarly, not on producing scholarship. We are, and should be, consuming the scholarship of others. Consuming scholarship includes preparatory time for teaching but is much broader. We need a name for this ubiquitous activity. I offer “consumatory scholarship.”

I suppose the arguments is that by consuming the production of others you become a better teacher and communicator. But is this good bang-for-the-buck? One could argue that argue that I’m a “consumatory scholar,” but at least I have 10 years of a huge amount of text production of commentary which is widely circulated (e.g., I’ve been cited in a few books, just query “Razib Khan”).

Obviously there is some truth to the charge that publish-or-perish leads to a surfeit of crap. Quantity over quality. But this seems to take it to the extreme level. Publications do end up being ...

June 26, 2012

The end of corruption?

Filed under: Anthroplogy,Culture — Razib Khan @ 11:05 pm

Steve Sailer has been on the cousin marriage “beat” for a while now, every since his 2003 piece on the practice in Iraq. Why is cousin marriage bad? Because large interrelated clans can create sets of societies within societies. Here’s a Bedouin proverb: “I against my brother, my brothers and I against my cousins, then my cousins and I against strangers”  Like polygyny hyper-endogamy as a normative practice is corrosive to the institutional and civic skeleton which a liberal democracies rest upon. Remember, these are societies where you don’t need to look outside the family for friends or marriage partners. The incentive for nepotism and corruption becomes very strong, and every extended family unit is operationally a “firm,” analogous to the mafia.

But there’s one issue about this narrative which has always made me hopeful: what happens to nepotism when you don’t have nephews? This is what I’m talking about:


As much of the world experiences demographic transition the “circle of cousins” begins to shrink. You can’t have extended families in great quantity when you don’t have many siblings. If Dunbar’s number is true then in societies ...

Genes can be criminogenic

Filed under: Behavior Genetics — Razib Khan @ 10:40 pm

As a follow-up to my post below, I just wanted to check some recent literature on crime and heritability. I found this, Heritability, Assortative Mating and Gender Differences in Violent Crime: Results from a Total Population Sample Using Twin, Adoption, and Sibling Models:

Research addressing genetic and environmental determinants to antisocial behaviour suggests substantial variability across studies. Likewise, evidence for etiologic gender differences is mixed, and estimates might be biased due to assortative mating. We used longitudinal Swedish total population registers to estimate the heritability of objectively measured violent offending (convictions) in classic twin (N = 36,877 pairs), adoptee-parent (N = 5,068 pairs), adoptee-sibling (N = 10,610 pairs), and sibling designs (N = 1,521,066 pairs). Type and degree of assortative mating were calculated from comparisons between spouses of siblings and half-siblings, and across consecutive spouses. Heritability estimates for the liability of violent offending agreed with previously reported heritability for self-reported antisocial behaviour. While the sibling model yielded estimates similar to the twin model (A ≈ 55%, C ≈ 13%), adoptee-models appeared to underestimate familial effects (A ≈ 20–30%, C ≈ 0%). Assortative mating was moderate to strong (r spouse = 0.4), appeared to result from both phenotypic assortment and ...

Technology that brought down civilization

Filed under: Technology — Razib Khan @ 9:58 pm

The IVF Panic: ‘All Hell Will Break Loose, Politically and Morally, All Over the World’:

For many, IVF smacked of a moral overstep — or at least of a potential one. In a 1974 article headlined “The Embryo Sweepstakes,” The New York Times considered the ethical implications of what it called “the brave new baby”: the child “conceived in a test tube and then planted in a womb.” (The scare phrase in that being not “test tube” so much as “a womb” and its menacingly indefinite article.) And no less a luminary than James Watson — yes, that James Watson – publicly decried the procedure, telling a Congressional committee in 1974 that a successful embryo transplant would lead to “all sorts of bad scenarios.”

Specifically, he predicted: “All hell will break loose, politically and morally, all over the world.”

The past is not always prologue, but it’s very instructive to look at newspapers from a given time period and see what the public mood was. Fear is a natural human reaction to new technology. My general bias is that technology itself usually isn’t as disruptive as social innovation. That being said, when technology is genuinely revolutionary it can have a much bigger impact than ...

Remembering failed engineering

Filed under: Culture,History — Razib Khan @ 8:46 pm

When I was growing up in the 80s and 90s “hippies” were figures of amusement and the 1960s was all The Wonder Years. As a child you’re not told of the “dark side,” the true history, which may seem disturbing. When I was in college I met someone who did clue me in to some of the more “adult” aspects of the 1960s they had experienced through their recollections. For example, this man had been to the original Woodstock. While there he had taken a fancy to a young girl (underage), something her brother did not approve of. So he chased my friend down, smacked him upside the head, dragged him into the bushes, and raped him (also, I don’t recall seeing the interracial group sex protesting anti-miscegenation laws he told me about in Eyes on the Prize).

My own interest in history is of the more esoteric and antique kind. More Byzantium than the Beats. But as I grow older I am more and more aware of the lacunae in my knowledge, and the childlike vision of the 1960s which I unconsciously continue to hold. This is why more fully fleshed out pictures of the “Summer of Love,” ...

June 25, 2012

The sea as it was

Filed under: History,The Great Sea — Razib Khan @ 11:48 pm

I haven’t mentioned that a few months ago I read an incredible book, The Great Sea: A Human History of the Mediterranean. It weighs in at ~650 pages of dense narrative text, and you’ll want to jump to the footnotes as well! There isn’t much I can say in this space that would do justice to the book, the author has produced a tour de force of macrohistory. As someone with more scholarly tastes in history and culture I have noticed a definite bias toward monographs on my part. Too often generalist tomes are superficial surveys; no author can command all of the literature, and Wikipedia has truly replaced many of the entry-level works. The Great Sea has some of the typical problems with broad sweeping histories, but they’re usually evident only in closer inspection of footnotes (there seems a particular weakness in prehistory and far antiquity).

But ultimately this is definitely a book that’s worth it because it shows you exactly how one can generate an intellectual scaffold. Too often people know densely but narrowly, and more often thinly but superficially. Both of these modes lack heft ...

The sea as it was

Filed under: History — Razib Khan @ 11:48 pm

I haven’t mentioned that a few months ago I read an incredible book, The Great Sea: A Human History of the Mediterranean. It weighs in at ~650 pages of dense narrative text, and you’ll want to jump to the footnotes as well! There isn’t much I can say in this space that would do justice to the book, the author has produced a tour de force of macrohistory. As someone with more scholarly tastes in history and culture I have noticed a definite bias toward monographs on my part. Too often generalist tomes are superficial surveys; no author can command all of the literature, and Wikipedia has truly replaced many of the entry-level works. The Great Sea has some of the typical problems with broad sweeping histories, but they’re usually evident only in closer inspection of footnotes (there seems a particular weakness in prehistory and far antiquity).

But ultimately this is definitely a book that’s worth it because it shows you exactly how one can generate an intellectual scaffold. Too often people know densely but narrowly, and more often thinly but superficially. Both of these modes lack heft ...

Why marriage & fatherhood might not matter as much as you think

Filed under: Behavior Genetics,blank slate,Conservatism — Razib Khan @ 11:11 pm

While I was on blogging hiatus single motherhood and the whole Dan Quayle flap came back into the news. Here’s Mitt Romney:

The American culture promotes personal responsibility, the dignity of work, the value of education, the merit of service, devotion to a purpose greater than self, and, at the foundation, the pre-eminence of the family.

The power of these values is evidenced by a Brookings Institution study that Senator Rick Santorum brought to my attention. For those who graduate from high school, get a full-time job, and marry before they have their first child, the probability that they will be poor is 2%. But, if those things are absent, 76% will be poor. Culture matters.

I’ve been ragging on the cultural Left on this weblog recently because of the delusions that those of this bent simply won’t let go of in the quest for utopian egalitarianism. But one aspect of the American cultural and political scene is that Left and Right often operate with similar presuppositions, only weighting the emphasis differently. While the cultural Left puts the focus on nearly infinite possibilities of individual self-actualization, the cultural Right has backed itself into a corner of individual moral perfectionism which borders ...

Brown books

Filed under: Books — Razib Khan @ 10:32 pm

Since I have some time to read again, I thought I’d ask for brown related books which might be of interest. Here are some I’ve enjoyed in the past….

India: A History

In Spite of the Gods: The Rise of Modern India

The Argumentative Indian: Writings on Indian History, Culture and Identity

The Hindus: An Alternative History

The Mughal Throne: The Saga of India’s Great Emperors

The Rig Veda

Self-Knowledge: Sankara’s “Atmabodha”

Early India: From the Origins to AD 1300

The Rise of Islam and the Bengal Frontier, 1204-1760

Castes of Mind: Colonialism and the Making of Modern India

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Ummah, take care of your own shit!

Filed under: Geopolitics,Islam,Ummah — Razib Khan @ 10:16 pm

There’s a lot of nasty stuff going down in Syria. Toddlers are being killed in front of their parents. This is prompting liberal internationalists like Shadi Hamid to demand that the USA intervene in Syria. This is the same Shadi Hamid, liberal internationalist, who admits that democracy in the Muslim world is going to manifest an illiberal Islamist cast. Tough Copts, that’s how democracy rolls he explains us (no doubt he understands that American Muslims should be happy that we let them practice their religion, and shouldn’t make a big political fuss about their rights and dignity for the purposes of social comity).

Thank god most of the American public is totally exhausted from foreign wars. But here’s what’s been getting on my nerves: Muslims constantly complain that the USA is too involved in the Muslim world. They’re right about this in my opinion. But Muslims talk about it as if there is a “Muslim world.” Many Western Muslims follow the interpretation of their religion where they can’t take arms up against co-religionists. Muslim nations have their own international organization. And, this organization has been pushing its own distinctive form of Islamic human rights.

Here’s a suggestion for Muslims and Muslim nations who are used to thinking about a Muslim world and Muslim civilization: why don’t you take care of your own near abroad problems yourself for once, instead of appealing to the greatest kuffar power of them all? The reality is American intervention brings no great joys to the world, nor does it redound to our reputation. Combined with the Muslim world’s ostentatious assertion of cultural distinctiveness, it makes me wonder who really has the “responsibility to protect.” This is really a philosophy where America minds its own business when Muslims want it to mind its own business, but America better be the beacon of universal rights when Muslims wish to avail themselves of universal human rights, no?

Memo to the world: America is exhausted. We have to take our own trash out before we can clean up your disaster of a front-lawn. If Islam is the solution fucking prove it for once.

Addendum: Iraq’s Shia dominated government, underwritten by the American tax-payer, has tacitly been supporting the Assad regime.

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Sleeping like a Neandertal

Forgot to highlight one of the coolest abstracts from SMBE 2012, A genomewide map of Neandertal ancestry in modern humans:

2. The map allows us to identify Neandertal alleles that have been the target of selection since introgression. We identified over 100 regions in which the frequency of Neandertal ancestry is extremely unlikely under a model of neutral evolution. The highest frequency region on chromosome 4 has a frequency of Neandertal ancestry of about 85% in Europe and overlaps CLOCK, a key gene in Circadian function in mammals. The high frequency, Neandertal-derived variant is specific to Europeans; it is not very common in East Asians. This gene has been found in other selection scans in Eurasian populations, but has never before been linked to Neandertal gene flow


One of the predictions of assimilation of a large intrusive population with a small but long endemic population is that there will be biased representation of adaptive alleles from the latter into the former. In other words, if genome-wide admixture is on the order of 5% from the latter into the former, alleles which confer local fitness benefits will be present in the descendants of the asymmetric admixture in proportions of out ...

Sleeping like a Neandertal

Forgot to highlight one of the coolest abstracts from SMBE 2012, A genomewide map of Neandertal ancestry in modern humans:

2. The map allows us to identify Neandertal alleles that have been the target of selection since introgression. We identified over 100 regions in which the frequency of Neandertal ancestry is extremely unlikely under a model of neutral evolution. The highest frequency region on chromosome 4 has a frequency of Neandertal ancestry of about 85% in Europe and overlaps CLOCK, a key gene in Circadian function in mammals. The high frequency, Neandertal-derived variant is specific to Europeans; it is not very common in East Asians. This gene has been found in other selection scans in Eurasian populations, but has never before been linked to Neandertal gene flow


One of the predictions of assimilation of a large intrusive population with a small but long endemic population is that there will be biased representation of adaptive alleles from the latter into the former. In other words, if genome-wide admixture is on the order of 5% from the latter into the former, alleles which confer local fitness benefits will be present in the descendants of the asymmetric admixture in proportions of out ...

June 24, 2012

Higher vocabulary ~ higher income

Filed under: data,Data Analysis,GSS,Income,IQ — Razib Khan @ 7:54 pm

Prompted by a comment below I was curious as to the correlation between intelligence and income. To indicate intelligence I used the GSS’s WORDSUM variable, which has a ~0.70 correlation with IQ. For income, I used REALINC, which is indexed to 1986 values (so it is inflation adjusted) and aggregates the household income. Finally, I limited my sample to non-Hispanic whites over the age of 30 (for what it’s worth, this choice also limited the data set to respondents from the year 2000 and later).

The results don’t get at the commenter’s assertions, because 10 out of 10 on WORDSUM does not imply that you’re that smart really. But the trendline is suggestive. Note that aggregated 0-4 because the sample size at the lower values is small indeed.

SMBE 2012

Dienekes has summaries up of human-related abstracts of Society for Molecular Biology & Evolution 2012.

1) Remember these are not papers, and some of the abstracts may never become papers, at least in recognizable form

2) Speaking of which, Estimating a date of mixture of ancestral South Asian populations:


Linguistic and genetic studies have demonstrated that almost all groups in South Asia today descend from a mixture of two highly divergent populations: Ancestral North Indians (ANI) related to Central Asians, Middle Easterners and Europeans, and Ancestral South Indians (ASI) not related to any populations outside the Indian subcontinent. ANI and ASI have been estimated to have diverged from a common ancestor as much as 60,000 years ago, but the date of the ANI-ASI mixture is unknown. Here we analyze data from about 60 South Asian groups to estimate that major ANI-ASI mixture occurred 1,200-4,000 years ago. Some mixture may also be older—beyond the time we can query using admixture linkage disequilibrium—since it is universal throughout the subcontinent: present in every group speaking Indo-European or Dravidian languages, in all caste levels, and in primitive tribes. After the ANI-ASI mixture that occurred ...

The Neandertal Olympics?

Filed under: Bioethics — Razib Khan @ 12:39 pm

In the comments:

And yes, species concepts are much more fuzzy in many cases. Were mice to hold their own Olympics, they might well have learned (if slightly furry) discussions about whether musculus/domesticus/castaneus should compete in the same events, and if so, which events molossinus or other hybrid individuals should compete in. As humans, we dodge that bullet by having no closely enough related species to confuse the issue. The difference between us and a chimp is well defined. If Neanderthals were still around, that would be a different matter.

What happens is a nation (e.g., China?) reconstructs a Neandertal individual from the sequence in the public domain as well as segments from living human beings. Do they get to compete as power-lifters? This might seem like a crazy question, but I’m not totally unconvinced that it will be just academic within our lifetime. Genetic modification is likely to become ubiquitous within a generation.

Image credit: Wikipedia

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