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.
Month: June 2012
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:
Population replacement in Neolithic Spain?
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:
Heritability of behavioral traits
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.
Do consumatory scholars need tenure?
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.
The end of corruption?
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:
Genes can be criminogenic
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….
Technology that brought down civilization
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.
Remembering failed engineering
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.
The sea as it was
I haven’t mentioned that a few months ago I read an incredible book, . 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. 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 to give you a good model for the true shape of reality.