Archive for August, 2012

The cheating of the chosen

By Razib Khan | August 31, 2012 11:44 am

Update: Harvard Students in Cheating Scandal Say Collaboration Was Accepted.

Harvard Says 125 Students May Have Cheated on a Final Exam:

Officials said that nearly half of the more than 250 students in the class were under investigation by the Harvard College Administrative Board and that if they were found to have cheated, they could be suspended for a year. The students have been notified that they are suspected and will be called to give their accounts in investigative hearings.

“This is unprecedented in its scope and magnitude,” said Jay Harris, the dean of undergraduate education.

Administrators would not reveal the name of the class or even the department, saying that they wanted to protect the identities of the accused students. The Harvard Crimson, the university’s student newspaper, reported that it was a government class, Introduction to Congress, which had 279 students, and that it was taught by Matthew B. Platt, an assistant professor.

Anyone have opinions on this? I know plenty of readers are in the local area in various capacities. My working assumption is that these kids will get off with a slap on the wrist. The meritocracy does not eat its own young. With such widespread cheating in this course this not a matter of intellectual incompetents, but very smart kids who simply wanted to push their advantages on the margin. This is the university that was sending half its graduates to investment banks a few years ago, so what’s new?

Seeing the workings of the hyper-elite probably turn the average person in two directions. If they lean Right, it’s guns & gold. If they lean Left, some sort of Red revolutionary urge. There’s a reason history goes in cycles….

CATEGORIZED UNDER: Culture
MORE ABOUT: Harvard

Deep dive into the Denisovans

By Razib Khan | August 31, 2012 1:25 am

By now you have probably seen the new Denisovan paper in the media. John Hawks has an excellent overview, as you’d expect. The only thing I will add is to reiterate that I think population movements in near and far prehistory significantly obscure our comprehension of the patterns of past genetic variation. One reason that the Denisova hominin presents conundrums (e.g., how did Australians and Melanesians admix with a population whose only remains are found in Siberia) is that we’re viewing it through the lens of the present. What other lens can we view it through? We’re not time travelers. But we should be perhaps more conscious of the filter which that imposes upon our perception and model of the world. This is probably a time when it is best to have only a modest confidence in any given proposition about the prehistoric past.

Also, I don’t know why, but I much like this tree:

MORE ABOUT: denisovan

Being fat is like being gay (?)

By Razib Khan | August 31, 2012 12:21 am

Anti-obesity: The new homophobia?:

Consider the many parallels between the treatments advocated by those who claim being gay is a disease, and those being pushed by our public health establishment to “cure” fat children and adults of their supposedly pathological state.

The advocates of so-called conversion or reparative therapy believe that “homosexuality” is a curable condition, and that a key to successful treatment is that patients must want to be cured, which is to say they consider same-sex sexual orientation volitional. These beliefs mirror precisely those of the obesity establishment, which claims to offer the means by which fat people who want to choose to stop being fat can successfully make that choice.

Those who seek to cure homosexuality and obesity have tended to react to the failure of their attempts by demanding ever more radical interventions. For example, in the 1950s Edmund Bergler, the most influential psychoanalytical theorist of homosexuality of his era, bullied and berated his clients, violated patient confidentiality and renounced his earlier, more tolerant attitude toward gay people as a form of enabling. Meanwhile, earlier this year a Harvard biology professor declared in a public lecture that Mrs. Obama’s call for voluntary lifestyle changes on the part of the obese constituted an insufficient response to the supposed public health calamity overwhelming the nation, and that the government should legally require fat people to exercise.

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CATEGORIZED UNDER: Health
MORE ABOUT: Health

Quantifying the great flip

By Razib Khan | August 30, 2012 1:13 am

The two maps above show the Democratic and Republican counties in blue and red respectively. Carter in the 1976 presidential election, and Obama in 2008. A few days ago it was brought to my attention that Matt Yglesias was curious about how Maine become a Democratic leaning state in the past generation. How is a deep question I’ll leave to political scientists, but how about the patterns of voting Democratic over elections by state for the past 100 years? That’s not too hard to find, there’s state-level election data online. So I just calculated the correlations between past elections and Democratic results, and Obama’s performance in 2008. If you’re a junkie of political science I assume you’ve seen something like this….

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CATEGORIZED UNDER: Politics
MORE ABOUT: Politics

Evolution: its ideological self-refutation

By Razib Khan | August 29, 2012 11:24 pm

 

Recently I stumbled upon the fact that Honey Boo Boo‘s sister had a child at age 18. The grandmother, Honey Boo Boo’s mother, is 33 years old. Younger than I am! Then I see headlines in trashy British tabloids of the form: The three men who have fathered 78 children with 46 different women… and they’re not paying child support to any of them. Here I am, in the fullness of man-childhood, a new father, groping to understand evolutionary process in all its glory, and here are they who live evolution! There are those around us who don’t blink at maximizing their fitness in the modern world. Here’s some data from the GSS:

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CATEGORIZED UNDER: Evolution
MORE ABOUT: Idiocracy

The future of the three "Pakistans"

By Razib Khan | August 29, 2012 10:55 pm

Over at Econlog Bryan Caplan bets that India’s fertility will be sup-replacement within 20 years. My first inclination was to think that this was a totally easy call for Caplan to make. After all, much of southern India, and the northwest, is already sup-replacement. And then I realized that heterogeneity is a major issue. This is a big problem I see with political and social analysis. Large nations are social aggregations that are not always comparable to smaller nations (e.g., “Sweden has such incredible social metrics compared to the United States”; the appropriate analogy is the European Union as a whole).

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CATEGORIZED UNDER: Data Analysis, Demographics
MORE ABOUT: India, Pakistan, Population

The eternal question of calorie restriction

By Razib Khan | August 29, 2012 9:22 pm

There’s a lot of buzz about a new paper in Nature (yes, I know there’s always buzz about some Nature paper or other), Impact of caloric restriction on health and survival in rhesus monkeys from the NIA study. You’ve probably heard about calorie restriction before. For me the issue I have with it is that people who are very knowledgeable (i.e., researchers who know a great deal abut human physiology, etc.) have given me contradictory assessments of this strategy of life extension. But it’s not totally crazy, there are serious scientists at top-tier universities who practice calorie restriction themselves. This isn’t the final word, but I wouldn’t be surprised if it is going to take decades for it to resolve itself for humans specifically (because some people will always be, and perhaps rightly, extrapolating from short-lived organisms to humans when it comes to modulations of lifespan in the laboratory).  The New York Times piece had a really strange coda:

Dr. de Cabo, who says he is overweight, advised people that if they want to try a reduced-calorie diet, they should consult a doctor first. If they can handle such a diet, he said, he believes they would be healthier, but, he said, he does not know if they would live longer.

Some scientists still have faith in the low-calorie diets. Richard Weindruch, a director of the Wisconsin study, said he was “a hopeless caloric-restriction romantic,” but added that he was not very good at restricting his own calories. He said he might start trying harder, though: “I’m only 62. It isn’t too late.”

Then there is Mark Mattson, chief of the laboratory of neurosciences at the National Institute on Aging, who was not part of the monkey study. He believes there is merit to caloric restriction. It can help the brain, he said, as well as make people healthier and probably make them live longer.

Dr. Mattson, who is 5-foot-9 and weighs 130 pounds, skips breakfast and lunch on weekdays and skips breakfast on weekends.

CATEGORIZED UNDER: Health

What I do is what I do

By Razib Khan | August 29, 2012 12:31 am

This morning on Twitter the estimable Carl Zimmer stated that I had “reported” on the recent paper on European skin pigmentation evolution. I wondered, wait, am I a reporter? I don’t really know, and this really is rooted in the “am I a journalist” thread. I’m starting to get worn down by those who claim I am a journalist. My main issue is that once you’re pegged as a journalist, you’re held to journalistic standards. So, for example, people might demand that I selectively misquote and misrepresent the opinions of others, because I might alienate readership by telling them what I think, instead of using mouthpieces who I don’t even bother depicting with any accuracy. I’m only half-kidding here. I’ve had great experiences with journalists, and not so great experiences. I really, really, hate it when people go fishing for quotes to fit their story arc.

In regards to papers, I don’t exactly take the tack of someone like Ed Yong or Dave Munger. I’m just a guy offering my own unvarnished opinions, and the reality is what I do “on the blog” intersects strongly with the way I talk and behave in “real life.” If this blog is journalism than a huge portion of my time chilling with my boys is journalism And, a substantial proportion of the posts here emerge directly from reader questions. Oh, and sometimes I tell readers what I really think of them, which is often not much. All of this just doesn’t seem right to me as journalism. So I don’t feel it is. Randall Parker suggests a new word, “rifting.” Though that got me to thinking: a lot of what I do is “sifting.” The content of others, but also my own thoughts.

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CATEGORIZED UNDER: Blog
MORE ABOUT: Navel gazing

Not all genes are created the same

By Razib Khan | August 28, 2012 11:52 pm

The map to the right shows the frequencies of HGDP populations on SLC45A2, which is a locus that has been implicated in skin color variation in humans. It’s for the SNP rs16891982, and I yanked the figure from IrisPlex: A sensitive DNA tool for accurate prediction of blue and brown eye colour in the absence of ancestry information. Brown represents the genotype CC, green CG, and blue, GG. Europeans who have olive skin often carry the minor allele, C. While SLC24A5 is really bad at distinguishing West Eurasians from each other, SLC45A2 is better. Though both are fixed in Northern Europe, the former stays operationally fixed in frequency outside of Europe, in the Near East. As I stated earlier the proportions of the ancestral SNP in the Middle Eastern populations in the HGDP seem to be easily explained by the Sub-Saharan admixture you can find in these groups.

In contrast major SNPs in SLC45A2 are closer to disjoint between Europeans and South Asians. For example I’m a homozygote for the C allele. And yet even here we need to be careful. I want in particular to draw your attention to the frequencies in the Middle Eastern populations, the Sardinians, and the Kalash of Pakistan.

The Kalash, and their Nuristani cousins, have often been observed to have “European” physical features. These populations even trade in legends of descent from the Macedonians of Alexander. And the genetics here shows why. Though the Kalash far are more closely related to other Northwest South Asians than to Europeans, on the subset of genes which are implicated in pigmentation many of them could actually “pass” for Europeans. In fact, it is interesting to me that by these measures the Sardinians are no more European than groups like the Kalash and the Druze (in contrast to the total genome, where Sardinians may be the best reference for Western Europeans). They have a lower frequency of the SNP strongly associated with blue eyes than either of these groups, for example.

In the above paper they also produced a chart which illustrated the relationships of HGDP populations as a measure only of the six SNPs they used in their prediction method. These are markers which distinguish blue and brown eye color in Europeans efficiently.

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A political animal in the genes

By Razib Khan | August 28, 2012 9:49 pm

Trends in Genetics has a review article, The genetics of politics: discovery, challenges, and progress. The main reason I point to these sorts of papers isn’t that I think they’re revolutionary. Usually they aren’t. Rather, the public domain has totally forgotten about this domain of study. Most of the informed and high-toned discussion presumes that almost everything of worthy note is socially constructed. If not, then the counterpoint is a crude caricature of genetic determinism which is refutable in a blink of the eye. It’s as if someone was commissioned to paint R. Daneel Olivaw, and ended up using crayon to sketch out the Frankenstein monster.

For example, in sex differences the public debate veers between evolutionary psychological Leave It To Beaver, pre-scientific cultural traditionalism, and de facto Blank Slatism. On the one hand you have to deal with people who use “scare quotes” around the “highly speculative” “hypothesis” that males have a greater tendency toward inter-personal physical aggression than females (including in the comments of this blog, so spare with lectures about how this is a marginal perspective; I’m pretty sure I talk to people about behavior genetics a lot more than you do, though if not I’d like to hear from you!). Set against this you have an elevation of a particular specific and historically contingent nuclear family structure in the post-World War II West as normative by the laws of biology. Never mind that you need to leave the hearth to gather, and that someone must have been minding the farm when citizen soldiers were away at war. Some aspects of the ideal of American social conservatives may actually be socially constructed and economically contingent, rather than being a consequence of the natural laws of society. And just because something is socially constructed does not mean that it is not good or worth defending. And just because you believe that something is natural does not mean that you think that one should never rein in one’s natural impulses. Is and ought are not the same, and they do have relationships, but they’re complex and need to be teased apart precisely. As it is most discussions deal in rhetorical preening and misrepresentation of one’s interlocutors.

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CATEGORIZED UNDER: Behavior Genetics
MORE ABOUT: Behavior Genetics

Evolutionary & population genetics preprints – Haldane's Sieve

By Razib Khan | August 28, 2012 11:47 am

OK, perhaps I can help with that. Dr. Coop speaks of the collaboration between himself & Dr. Joseph Pickrell, Haldane’s Sieve, which I added to my RSS days ago (and you can see me pushing it to my Pinboard). From the “About”:

As described above, most posts to Haldane’s Sieve will be basic descriptions of relevant preprints, with little to no commentary. All posts will have comment sections where discussion of the papers will be welcome. A second type of post will be detailed comments on a preprint of particular interest to a contributor. These posts could take the style of a journal review, or may simply be some brief comments. We hope they will provide useful feedback to the authors of the preprint. Finally, there will be posts by authors of preprints in which they describe their work and place it in broader context.

We ask the commenters to remember that by submitting articles to preprint servers the authors (often biologists) are taking a somewhat unusual step. Therefore, comments should be phrased in a constructive manner to aid the authors.

It might be helpful if other evolution/genetics bloggers reblog this so we can push it up the Google search results. If you google “Haldane’s Sieve” some of the results are interesting…and not necessarily in a good way. I do feel guilt blogging on stuff my readers can’t get, so the more preprints become acceptable the more we (as in, the general public) can understand about evolution.

Back to the 70s?

By Razib Khan | August 28, 2012 12:35 am

Peter Turchin has basically implied that it’s 1970 again, and we’re in for a new age of disturbance. I’m rather skeptical…but, today a co-worker pointed out that I have “70s hair.” My sideburns, yes, but that’s just Gen-X irony or whatever. But she argued that there was a notable pre-1980 shagginess to my hair. Off to the barbershop! And yet…look at the mops that One Direction is sporting. When I last spoke about this group I wasn’t even aware that the group is already big in the United States! Am I old enough now that the styles of my pre-conscious age are now creeping back into fashion? Though I would still bet against polyester and plaid, perhaps David Frum’s unread book about the 1970s will start selling a few copies soon.

CATEGORIZED UNDER: Culture, Uncategorized
MORE ABOUT: 1970s

A note on open genomics

By Razib Khan | August 28, 2012 12:25 am

A few months ago I purchased a decent desktop just to crunch ADMIXTURE and other packages to analyze genomic data. More recently I set up a ~100 GB Dropbox account, and have started to “push” all of my output files from ADMIXTURE, PLINK, etc., as well as various scripts (Perl, shell, R, etc.) into the public folder (more precisely, a script is running ADMIXTURE and moving the files into the appropriate Dropbox folders as I type this, and Dropbox syncs with the online folders). I’m doing this for two reasons.

First, I want to make the pipeline of data generation easier for me. Instead of running ADMIXTURE, and then processing the files laboriously with R to generate plots, I’ve now created a system where a few automated scripts begin ADMIXTURE runs, and then another script creates files for distruct, and runs distruct, and then trims the images output and converts them into PNGs. This should allow me to resurrect my side projects, even while I’m rather busy with the “main events” of my life.

Second, I am beginning to feel that the promise of the “genome blogging revolution” kind of faded out. Granted, there’s only so much you can do with the same data sets, so I’m going to try and put together large pedigree files in my Dropbox account. But it seems like people need more of a push. Toward that end I hope that distribution of scripts which make the process more “turnkey” will stimulate people going forward.

Addendum: I know that some of the first paragraph is going to be gibberish to some readers. But I hope you’ll appreciate the outcomes of that gibberish!

CATEGORIZED UNDER: Genomics
MORE ABOUT: Open genomics

Europeans got less shaded in stages

By Razib Khan | August 27, 2012 11:55 pm

The Pith: the evolution of lighter skin is complex, and seems to have occurred in stages. The current European phenotype may date to the end of the last Ice Age.

A new paper in Molecular Biology and Evolution, The timing of pigmentation lightening in Europeans, is rather interesting. It’s important because skin pigmentation has been one of the major successes of the first age of human genomics. In 2002 we really didn’t know the nature of normal human variation in skin color in terms of specific genes (basically, we knew about MC1R). This is what Armand Leroi observed in Mutants in 2005, wondering about our ignorance of such a salient trait. Within a few years though Leroi’s contention was out of date (in fact, while Mutants was going to press it became out of date) . Today we do know the genetic architecture of pigmentation. This is why GEDmatch can predict that my daughter’s eyes will be light brown from just her SNPs (they are currently hazel). This genomic yield was facilitated by the fact that pigmentation seems to be a trait where most human variation is controlled by half a dozen genes. In contrast, height or I.Q. are controlled by innumerable genes.

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Non-whites consistent on "life" issues

By Razib Khan | August 27, 2012 12:07 am

Over at Darwin Catholic a commenter asked whether a pro-choice commenter on this weblog also supported the death penalty. I presume that they were here pointing to the consistent life ethic issue. Many liberals who oppose capital punishment support abortion rights, and many conservatives who support capital punishment oppose abortion rights. These camps both have their viewpoints, which I’m not interested in re-litigating in the comments. But I was curious as to the overall societal support for the combinations of positions.

So I looked at the GSS, using the CAPPUN and ABANY variables (capital punishment, and abortion for any reason). In this post I will show you screenshots of the GSS output. It’s ugly, but it shows you deviation away from the expected proportions. Basically, if two variables are independent you can predict what you’d expect to be the crossed percentages over the four cells. If the results deviate from that you can ascertain particular associations. In the GSS output red means that the cell has a higher value than it should, and blue a lower value. Additionally, the intensity signals the magnitude of the deviation. I limited all results to the year 2000 and later.

First, the general aggregate result:

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CATEGORIZED UNDER: Data Analysis, Ethics
MORE ABOUT: Death Penalty

A circumcision compromise?

By Razib Khan | August 26, 2012 10:17 pm

The New York Times has a piece on an update to the American Academy of Pediatrics position statement on circumcision (shifting toward a more pro-circumcision position of neutrality). In the United States the rates of circumcision for infant boys has gone from 80-90% to ~50% (there are regional variations, so only a minority of boys in the Pacific Northwest are circumcised). A few years ago Jesse Bering put up a post, Is male circumcision a humanitarian act?, where he actually wrote “Nobody knows where your child will live as an adult (perhaps Africa), or how rampant HIV will be there….” I like taking probabilities into account, but this is ridiculous.

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CATEGORIZED UNDER: Health

The heritability of impulse control

By Razib Khan | August 26, 2012 9:35 pm

The above figure is from a paper I stumbled upon, Genetic and environmental influences on impulsivity: a meta-analysis of twin, family and adoption studies:

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CATEGORIZED UNDER: Behavior Genetics
MORE ABOUT: Behavior Genetics

America, these are (some) your graduate students

By Razib Khan | August 26, 2012 8:19 pm

If you haven’t, you should check out The Shadow Scholar, The man who writes your students’ papers tells his story. This is the conclusion:

“Thanx u so much for the chapter is going very good the porfesser likes it but wants the folloing suggestions please what do you thing?:

“‘The hypothesis is interesting but I’d like to see it a bit more focused. Choose a specific connection and try to prove it.’

“What shoudwe say?”

This happens a lot. I get paid per assignment. But with longer papers, the student starts to think of me as a personal educational counselor. She paid me to write a one-page response to her professor, and then she paid me to revise her paper. I completed each of these assignments, sustaining the voice that the student had established and maintaining the front of competence from some invisible location far beneath the ivory tower.

The 75-page paper on business ethics ultimately expanded into a 160-page graduate thesis, every word of which was written by me. I can’t remember the name of my client, but it’s her name on my work. We collaborated for months. As with so many other topics I tackle, the connection between unethical business practices and trade liberalization became a subtext to my everyday life.

So, of course, you can imagine my excitement when I received the good news:

“thanx so much for uhelp ican going to graduate to now”.

The author claims that his three primary customer demographics are “English-as-second-language student; the hopelessly deficient student; and the lazy rich kid.” In the above case it looks like the first category. But what are the proportions? I assume that the lazy rich kids are mostly undergraduates or MBA students.

CATEGORIZED UNDER: History
MORE ABOUT: Academia

Eat smarter, don't work out harder?

By Razib Khan | August 26, 2012 5:53 pm

There have been several recent studies reemphasizing diet over exercise (timely because Americans are kind of fat, on average). A new piece in The New York Times looking at the Hadza of Tanzania, who are hunter-gatherers, seems to reiterate this point, Debunking the Hunter-Gatherer Workout:

We found that despite all this physical activity, the number of calories that the Hadza burned per day was indistinguishable from that of typical adults in Europe and the United States. We ran a number of statistical tests, accounting for body mass, lean body mass, age, sex and fat mass, and still found no difference in daily energy expenditure between the Hadza and their Western counterparts.

How can the Hadza be more active than we are without burning more calories? It’s not that their bodies are more efficient, allowing them to do more with less: separate measurements showed that the Hadza burn just as many calories while walking or resting as Westerners do.

We think that the Hadzas’ bodies have adjusted to the higher activity levels required for hunting and gathering by spending less energy elsewhere. Even for very active people, physical activity accounts for only a small portion of daily energy expenditure; most energy is spent behind the scenes on the myriad unseen tasks that keep our cells humming and our support systems working. If the Hadza’s bodies somehow manage to spend less energy in those areas, they could easily accommodate the elevated energy demands of hunting and gathering. And indeed, studies reporting differences in metabolic-hormone profiles between traditional and Western populations support this idea (though more work is needed).

As noted in the paper the researchers used urine samples to ascertain caloric expenditure. I’ve seen this in surveys of overweight people. One result was that many overweight people inadvertently under report their consumption (e.g., not writing down snacks that they ate) by as much as 1/3, so this is an essential check on self-reports. A reader brings up this relevant point:

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CATEGORIZED UNDER: Anthroplogy, Human Evolution
MORE ABOUT: Human Evolution

Consent and genomics

By Razib Khan | August 26, 2012 5:15 pm

Interesting story in The New York Times, Genes Now Tell Doctors Secrets They Can’t Utter:

One of the first cases came a decade ago, just as the new age of genetics was beginning. A young woman with a strong family history of breast and ovarian cancer enrolled in a study trying to find cancer genes that, when mutated, greatly increase the risk of breast cancer. But the woman, terrified by her family history, also intended to have her breasts removed prophylactically.

Her consent form said she would not be contacted by the researchers. Consent forms are typically written this way because the purpose of such studies is not to provide medical care but to gain new insights. The researchers are not the patients’ doctors.

But in this case, the researchers happened to know about the woman’s plan, and they also knew that their study indicated that she did not have her family’s breast cancer gene. They were horrified.

“We couldn’t sit back and let this woman have her healthy breasts cut off,” said Barbara B. Biesecker, the director of the genetic counseling program at the National Human Genome Research Institute, part of the National Institutes of Health. After consulting the university’s lawyer and ethics committee, the researchers decided they had to breach the consent stipulations and offer the results to the young woman and anyone else in her family who wanted to know if they were likely to have the gene mutation discovered in the study. The entire family — about a dozen people — wanted to know. One by one, they went into a room to be told their result.

“It was a heavy and intense experience,” Dr. Biesecker recalled.

Around the same time, Dr. Gail Jarvik, now a professor of medicine and genome science at the University of Washington, had a similar experience. But her story had a very different ending.

She was an investigator in a study of genes unrelated to breast cancer when the study researchers noticed that members of one family had a breast cancer gene. But because the consent form, which was not from the University of Washington, said no results would be returned, the investigators never told them, arguing that their hands were tied. The researchers said an ethics board — not they — made the rules.

Dr. Jarvik argued that they should have tried to persuade the ethics board. But, she said, “I did not hold sway.”

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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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