Archive for June, 2012

The end of blog & comments

By Razib Khan | June 28, 2012 11:39 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.

Read More

CATEGORIZED UNDER: Administration
MORE ABOUT: Admin

Tomatoes!

By Razib Khan | June 28, 2012 11:19 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:

Read More

CATEGORIZED UNDER: Anthroplogy, Genetics

Population replacement in Neolithic Spain?

By Razib Khan | June 28, 2012 1:16 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 not related to current populations from either the Iberian Peninsula or Southern Europe.

Here’s another PCA showing one individual on a more fine-grained representation of European populations:

Read More

CATEGORIZED UNDER: Agriculture, Anthroplogy

Heritability of behavioral traits

By Razib Khan | June 28, 2012 12:48 am

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 a lot of variation around this average. The rule of thumb seems to be that the standard deviation across siblings is roughly similar to the standard deviation within the population (though it seems to be a bit lower, with sibling I.Q. deviations being 2/3 of the magnitude of population-wide deviations).

Below the fold is a table reproduced from the paper Genetic Influence on Human Psychological Traits A Survey. Please do not read the table as a gauge of the “geneticness” of the trait. (whatever that means) Rather, it should give you a rough sense of the “pull” that biological inheritance will have on an individual. Biology may not be destiny, but it is definitely probability.

Read More

CATEGORIZED UNDER: Behavior Genetics
MORE ABOUT: Behavior Genetics

Do consumatory scholars need tenure?

By Razib Khan | June 28, 2012 12:27 am

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 a way to maintain careers, but the reason publishing is important is that you become part of the record of scholarship. Consumatory scholarship has much more individualized and evanescent outcomes.

CATEGORIZED UNDER: Education
MORE ABOUT: Academia

The end of corruption?

By Razib Khan | June 27, 2012 12:05 am

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:

Read More

CATEGORIZED UNDER: Anthroplogy, Culture

Genes can be criminogenic

By Razib Khan | June 26, 2012 11:40 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 social homogamy, but had only minor effect on variance components. Finally, we found significant gender differences in the etiology of violent crime

A = additive genetic variance component
C = shared family environment

This table from the paper shows the influence of study design….

Read More

CATEGORIZED UNDER: Behavior Genetics
MORE ABOUT: Behavior Genetics

Technology that brought down civilization

By Razib Khan | June 26, 2012 10:58 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 social or institutional shifts.

CATEGORIZED UNDER: Technology
MORE ABOUT: Technology

Remembering failed engineering

By Razib Khan | June 26, 2012 9:46 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,” such as can be found in this July’s Vanity Fair is of particular interest. In this way the past can become real, without the antiseptic tint of our media or the nostalgia of the baby boomers.

Read More

CATEGORIZED UNDER: Culture, History
MORE ABOUT: History

The sea as it was

By Razib Khan | June 26, 2012 12:48 am

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 and the ability to cut thickly through reality. It takes a genuinely dense and interlaced work such as The Great Sea to give you a good model for the true shape of reality.

CATEGORIZED UNDER: History
MORE ABOUT: The Great Sea

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

By Razib Khan | June 26, 2012 12:11 am

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 on the farcical.

Read More

CATEGORIZED UNDER: Behavior Genetics

Sleeping like a Neandertal

By Razib Khan | June 25, 2012 9:36 am

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

Read More

MORE ABOUT: Human Evolution

Higher vocabulary ~ higher income

By Razib Khan | June 24, 2012 8:54 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.

Read More

CATEGORIZED UNDER: Data Analysis
MORE ABOUT: Data, GSS, Income, IQ

SMBE 2012

By Razib Khan | June 24, 2012 7:34 pm

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:

Read More

The Neandertal Olympics?

By Razib Khan | June 24, 2012 1:39 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

CATEGORIZED UNDER: Bioethics
MORE ABOUT: Bioethics

It's science, not math

By Razib Khan | June 24, 2012 1:30 pm

My post below elicited this response:

Here are a couple of cases which seem to defy easy classification.
A “chimera”. This is a person who has cells derived from two zygotes. It can happen if two fertilized eggs merge very early in development. The individual may appear entirely normal (there may be chimeras reading this who are unaware of their condition); but the cells in their body will come from two quite distinct origins. If the original zygotes were male and female, then the adult individual will have some cells in their body with the XY (male) chromosomes, and others with the XX (female) chromosomes. There may be no external sexual ambiguity as long as the sex organs all come from the one lineage; in general all kinds of sexual ambiguity might arise.

Second case; more common (though still unusual) is where an individual is genetically of one gender, and phenotypically of the other. This can be either an XX individual who develops with external male genitalia; or XY who develops with female genitalia. This is usually caused (I think) by excess or deficit of the appropriate hormones during fetal development.

For most people, gender is unambiguous. But there is no sharp dividing line or easy way of classifying that covers all individuals.

The examples I’m considering are entirely independent of psychology or choice. They are real physical conditions in which the conventional physical basis for determining gender becomes ambiguous.

Read More

CATEGORIZED UNDER: Science
MORE ABOUT: Gender, Sex

Calcification of the merit castes

By Razib Khan | June 23, 2012 11:38 pm

After ragging on Chris Hayes for a week I decided to check out the conversation above between Hayes and Mike Konzal about his new book, Twilight of the Elites: America After Meritocracy. As Mike suggested the book does seem more nuanced in its take than the piece in The Nation which highlighted the role of high-stakes testing at Hunter College High School. In the conversation above Hayes supports his suppositions that test-prep was excluding blacks and Latinos by asserting that that is what the teachers themselves believe. I wouldn’t dismiss this out of hand, but it certainly isn’t enough to make me accept that portion of Hayes’ argument. People have all sorts of weird misconceptions.

Read More

CATEGORIZED UNDER: Culture
MORE ABOUT: Culture

Sex & sport

By Razib Khan | June 23, 2012 10:26 pm

The New York Times has an article up on a new I.O.C. ruling on who can compete as a woman. Basically they look at testosterone levels. This seems a different tack than cases where women were banned from competing as women because they had a male karytoptype (AIS). This article came on my radar because I had already read this op-ed from about a week ago, You Say You’re a Woman? That Should Be Enough. This sentence jumped out at me:

Second, when it comes to sex, sports authorities should acknowledge that while science can offer evidence, it cannot dictate what evidence we should use. Scientifically, there is no clear or objective way to draw a bright line between male and female.

What do people think of this assertion? I’m aware of intersex individuals. But if we start to assert that dioecy is just a “social construct” then let’s revisit species concepts. I’m sure there are some farmers and loggers who might assert that one can’t draw objective bright lines between populations. Distinctions between male and female in most species is much more clear and distinct than various taxonomic categories.

CATEGORIZED UNDER: Bioethics
MORE ABOUT: Sex

Attitudes toward genetically modified crops & science

By Razib Khan | June 23, 2012 12:20 pm

In the further interests of putting quantitative data out their instead of vague impressions, I noticed two GSS variables which might be of interest. One queries the impression of effect on the environment of genetically modified crops. The second asks about whether science does more harm than good. The latter question exhibited almost no year to year variation of note, so I just threw them in a pot together. But for the environment and genetically modified crop question I show responses for the year 2000 and 2010. As you can see there is a modest difference in regards to the first where liberals are more skeptical.

Read More

CATEGORIZED UNDER: Data Analysis
MORE ABOUT: Data

One test to rule them all

By Razib Khan | June 22, 2012 11:16 pm

Educational Realist elaborates on some of the concerns I have had with Chris Hayes’ ballyhooed piece on the failure of elites:

Hayes is correct about one thing, though: the elites are locking out the hoi polloi from highest-level institutions. But it takes a real ignorance to pretend that the rich are doing this because of over-reliance on test scores or test prep, as opposed to buying their way in, using their powerful networks to only hire from the “right” schools, and the fuzzy math of the “holistic” evaluation process. Give me test scores any day.

ER also observes that in fact minorities, and in particular Asians, make use of test prep:

Use of Test-Prep Courses and Gains, by Race and Ethnicity

Group % Taking Test-Prep Course Post-Course Gain in Points on SAT
East Asian American 30% 68.8
Other Asian 15% 23.8
White 10% 12.3
Black 16% 14.9
Hispanic 11% 24.6

Read More

CATEGORIZED UNDER: Culture
MORE ABOUT: Education
NEW ON DISCOVER
OPEN
CITIZEN SCIENCE
ADVERTISEMENT

Discover's Newsletter

Sign up to get the latest science news delivered weekly right to your inbox!

Gene Expression

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!
ADVERTISEMENT

See More

ADVERTISEMENT

RSS Razib’s Pinboard

Edifying books

Collapse bottom bar
+

Login to your Account

X
E-mail address:
Password:
Remember me
Forgot your password?
No problem. Click here to have it e-mailed to you.

Not Registered Yet?

Register now for FREE. Registration only takes a few minutes to complete. Register now »