Gene Expression

Vitamin D & influenza - randomized trial  permlink

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Randomized trial of vitamin D supplementation to prevent seasonal influenza A in schoolchildren:

Design: From December 2008 through March 2009, we conducted a randomized, double-blind, placebo-controlled trial comparing vitamin D3 supplements (1200 IU/d) with placebo in schoolchildren. The primary outcome was the incidence of influenza A, diagnosed with influenza antigen testing with a nasopharyngeal swab specimen.

Results: Influenza A occurred in 18 of 167 (10.8%) children in the vitamin D3 group compared with 31 of 167 (18.6%) children in the placebo group [relative risk (RR), 0.58; 95% CI: 0.34, 0.99; P = 0.04]. The reduction in influenza A was more prominent in children who had not been taking other vitamin D supplements (RR: 0.36; 95% CI: 0.17, 0.79; P = 0.006) and who started nursery school after age 3 y (RR: 0.36; 95% CI: 0.17, 0.78; P = 0.005). In children with a previous diagnosis of asthma, asthma attacks as a secondary outcome occurred in 2 children receiving vitamin D3 compared with 12 children receiving placebo (RR: 0.17; 95% CI: 0.04, 0.73; P = 0.006).

I will attest to improvement in my own respiratory health since I began taking vitamin D supplements in 2007, but more studies need to be done to confirm that this is a robust finding.

Citation: Am J Clin Nutr (March 10, 2010). doi:10.3945/ajcn.2009.29094

Posted by Razib Khan at 5:56 AM • 3 Comments

God is too cute to be a literalist  permlink

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And God Said: How Translations Conceal the Bible's Original Meaning is a litany of how the mapping from Hebrew to other languages has resulted in a distortion of the precise idiom of the original. I actually thought the best example of this given was a non-Biblical one, the fact that English-speakers are totally clueless as to the implication of the title of the Mexican film Like Water for Chocolate, which sends a rather clear message only intelligible in a Spanish speaking context. English speakers have tended to generate novel meanings from the cryptic title at total variance with the original intent and clarity in Spanish (I actually recall spending some time trying to figure out the deeper meaning of the title when I first watched this film).

This all got me to thinking: what exactly was God thinking in delivering his revelation in verbal form? It seems clear that formal logic would have been much more precise, or even some form of ancient mathematics. The fact that God delivered his revelation in the flexible form of language seems to weigh in on the side of those Christians who are not Biblical literalists, since literalism is pretty much a joke. This sort of assertion by me is a rejection of a position I held several years back whereby non-literalist Christians were slippery types who always attempted to fit the scripture to the context of their times. That may be true, but it is likely true for self-described Fundamentalists as well, except they don't admit it. Some atheists, myself in the past, are wont to declare that the Fundamentalist despite the falsity of his beliefs at least adheres to an honest "plain" reading of the text of the Bible. The reality is that there is no "plain" reading, for believer and non-believer alike.

Posted by Razib Khan at 5:38 AM • 9 Comments

Small dogs guide  permlink

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Via a comment, a site which you will love, or which will drive you insane, Complete Small Dogs Guide. I found this story about a chihuahua carried away by a large bird, only to return to its owner.

Posted by Razib Khan at 5:16 AM • 2 Comments

The great productivity transient  permlink

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This comment from Chris is interesting:

I would speculate that the the massive productivity gains were due to a massive resorting of American society along cognitive lines; from 1940 to 1970 a large number of high ability people who were previously locked into agriculture and industry were able to sort themselves into more innovative positions. This would lead to a massive burst of innovation, which led to increases in productivity, as previously unlocked talent was put to use.

From 1970 to 1990 this resorting was mostly winding down and productivity in the economy was heavily constrained by the population due to people still being necessary for most tasks and most of the potential innovation overhang being used up from 1940 to 1970.

Although computers were increasingly able to challenge people on some tasks during the 1970's, their effect was small (although increasingly noticeable in how long it took employment to rebound after recessions from 1980 on). From 1995 on productivity gains began to accelerate due to computers hitting a tipping point and their increasing ability to replace or augment people in areas across the economy.

Wages remain stagnant post-2000, because a growing number of people are being displaced at the lower levels of economic activity and competing for jobs that are ultimately constrained by the population, services (this would have happened earlier, but was masked by the initial burst of innovation following the cost of information falling to zero). Most of those displaced do not have the cognitive ability to perform economically useful innovation due to the sorting during the 1940-70 period and are unable to take advantage of the jobs on the high end of the income scale. An income gap forms and begins to accelerate.

There's a huge literature on this topic, so don't take the speculation here as the last word, but food for thought.

In Farewell to Alms Greg Clark asserts that the main beneficiaries of the regime of perpetual economic growth since 1800 have been the unskilled workers, who closed the wage gap with skilled workers up until 1970. At that point, the wage gap between the skilled and unskilled started to open up again. Also remember that though it is conventional wisdom to bemoan the increase in inequality in the modern capitalist economies, every civilized society before 1800 was far less egalitarian in the distribution of wealth and power than modern economies (in contrast to "savages," who had egalitarianism because of the lack of a very wealthy class; everyone was poor more or less).

Posted by Razib Khan at 6:34 PM • 5 Comments

Private interest + Government Cheese = for-profit education racket  permlink

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In Hard Times, Lured Into Trade School and Debt:

At institutions that train students for careers in areas like health care, computers and food service, enrollments are soaring as people anxious about weak job prospects borrow aggressively to pay tuition exceeding $30,000 a year.

...

The Apollo Group -- which owns the for-profit University of Phoenix -- derived 86 percent of its revenue from federal student aid last fiscal year, according to BMO. Two years earlier, it was 69 percent.

For-profit schools have proved adept at capturing Pell grants, which are a centerpiece of the Obama administration's efforts to make higher education more affordable. The administration increased financing for Pell grants by $17 billion for 2009 and 2010 as part of its $787 billion stimulus package.

Two years ago, students at for-profit trade schools received $3.2 billion in Pell grants, according to the Department of Education, less than went to students at two-year public institutions. By the 2011-12 school year, the administration now estimates, students at for-profit schools should receive more than $10 billion in Pell grants, more than their public counterparts. (Those anticipated increases may shrink, depending on the outcome of wrangling in Congress over health care and student lending.)

The market works; the for-profit schools are good at what they do, increase their student enrollments. Arguably they're better than many conventional institutions of higher education because they utilize modern mass marketing techniques which hook into cognitive biases. If you're a halfway intelligent student and you see an advertisement for an institution of higher education on a subway, you know to take that as a signal that that institution is definitely one to avoid (this could be turned into a Chris Rock joke). Those who lack the requisite class savvy and are less intelligent don't take the same lesson, and in fact are the ones who may make an impulsive decision to matriculate based on an advertisement.

But problem here is the fact that these institutions receive massive public subsidies. Grants are a direct subsidy, but subsidized student loans also come with a cost, students can't discharge them in bankruptcy (the lower interest rates naturally have to have trade offs or the loans would not be forthcoming to 18 year olds). The ultimate aim of providing public funds toward higher education are the presumed investments that this makes in human capital, which earns returns in greater tax receipts through economic growth driven by innovation and increased labor productivity. The theoretical spillover effects are presumably large. But in this case the main beneficiaries are likely the intermediaries, the for-profit institutions which provide trivial marginal utility to many students while charging for nearly worthless credentials. The downside risk of failure to repay the loans are taken up by the students (there is no way that the largest Pell Grants can cover the tuitions which are the norm at these institutions).

The bigger issue which is masked by the fixation on subsidizing higher education are the failings in primary and secondary education. A disproportionate segment of the students who matriculate at for-profit institutions seem to academically weak, and a bit low on the totem pole in the ability to plan far into the future (high real time preference*). The profit motive ideally drives firms toward excellence and efficiency, but in this case it seems quite likely that the excellence and efficiency is not educating students but coupling gullible individuals with massive debt obligations which they have no liability obligations toward. In other words, maximizing individual firm utility at the expense of the aggregate. The costs are distributed broadly, the gains more locally.

Note: A concurrent issue is that of graduate educational debt (or, earnings f orgone in the case of those who are in programs where debt is not necessary). This highlights that the problem in decision making isn't just low individual intelligence, but he values and ideals which our society holds up. In particular, excessive optimism as to where any given person will lay on a distribution of outcomes. Most law school graduates will not work in "Big Law," and most people who enter Ph.D. programs will not gain a tenured position in academia.

* Someone willing to take up debt and forgo labor force participation obviously is willing to have a general notion of planning for the future. But it seems that many of those who are enticed by advertisements on television for "technical institutes" and the like are more attracted by the notion of large later paychecks in the future, and have only a poor grasp of what the probability distribution of real outcomes is going to be.

Posted by Razib Khan at 5:35 PM • 6 Comments

Katz  permlink

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Posted by Razib Khan at 8:11 AM • 1 Comments

Only technology will save us  permlink

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The New York Times has a scary but numerically rich piece on the impending pension crisis in Europe. As in the days of yore Greece looks to be a pioneer. Here's an interesting pair of numbers:

According to research by Jagadeesh Gokhale, an economist at the Cato Institute in Washington, bringing Greece's pension obligations onto its balance sheet would show that the government's debt is in reality equal to 875 percent of its gross domestic product, which is the broadest measure of a nation's economic output. That would be the highest debt level among the 16 nations that use the euro, and far above Greece's official debt level of 113 percent.

The article goes on to survey the problems in much of Europe, and even hints at the impending issues with the retirement of the Baby Boomers in the United States (yes, I know Medicare is the short-term problem, not Social Security, but for people my age Social Security is something we're not too confident of gaining return on to the same extent as past generations). But the issue is bigger, declining fertility rates are occurring across much of the world. Here are a few nations with sub-replacement fertility:

Read on »

Posted by Razib Khan at 1:07 AM • 24 Comments

Whatever happened to "synthetic life"?  permlink

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I remember Craig Venter talking about synthetic life in the fall of 2007 with Carl Zimmer. Last summer he said that we'd have the first "synthetic species" by the end of the year. I haven't heard about it in 2010, have you? Anyone have info on what's going on here? No surprise that project deadlines get pushed back, it happens. But it seems like I've been hearing "wait 6 months" since the beginning of 2008. Does it actually work out so that only God can pull this off? Or is this vaporscience (OK, he got the genome part nailed down, but that was a while ago)?

Posted by Razib Khan at 11:55 PM • 9 Comments

Two papers on Ancient DNA  permlink

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Reviewed by other ScienceBloggers:

Prehistoric DNA reveals the story of a Pleistocene survivor, the muskox

Ancient DNA Isolated from Fossil Eggshells May Provide Clues to Eggstinction of Giant Birds

Posted by Razib Khan at 11:08 PM • 0 Comments

Walking & racing to modernity  permlink

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Two quantitative facts of note from When China Rules the World: The End of the Western World and the Birth of a New Global Order:

From page 33:

Although the passage to modernity universally involves the transition from an agrarian to service-based society via an industrial one, here we find another instance of European exceptionalism. European countries (sixteen in all)...are the only ones in the world that have been through a phase in which the relative size of industrial employment was larger than either agrarian or service employment. In Britain, industrial employment reached its peak in 1911, when it accounted for 52.2 percent of the total labor force...the peak figure for the United States was 35.8 percent in 1967 and for Japan 37.1 percent in 1973...From a global perspective, a different and far more common path has been to move directly, in terms of employment, from a largely agrarian to a mainly service society, without a predominantly industrial phase....

From page 103-104:

...In 1950 79% of South Korea's population worked in agriculture...by 1960 the figure was 61%, and today it is it around 10%. In the late 1960s the farming population still comprised half of Taiwan's total population, whereas today it accounts for a mere 8%...In 1950 76% of Taiwanese lived in the countryside, whereas by 1989...that figure had been almost exactly reversed...The urban population in South Korea was 18% in 1950 and 80% in 1994...In China the urban population represented 17% of the total population in 1975 and is projected to be 46% by 2015....

Compared with Europe, the speed of the shift from the countryside to the cities is exceptional. Germany's urban population grew from 15% in 1850 to 49% in 1910...and 53% in 1950...The equivalent figures for France were 19% in 1850 and 38% in 1910 (and 68% in 1970). England's urban population was 23% in 1800, 45% in 1850, and 75% in 1910. In the United States, the urban population was 14% in 1850, 42% in 1910, and 57% in 1950. If we take South Korea as our point of comparison...the proportion of its population living in cities increased by 62% in 44 years, compared with 52% for England over a period of 110 years, 34% over 60 years for Germany (and 38% over 100 years), 19% over 60 years for France (and 49% over 120 years), and 28% over 60 years (and 43% over 100 years) for the United States....

The author emphasizes the extreme rapidity of the economic transition from an agricultural economy to a post-industrial one in much of East Asia, with the long slow simmer of the British Industrial Revolution as a contrast. He points out that the relative gradual nature of industrialization in Europe likely explains the historic and antique aspects of its cities; evolutionary change allows for preservation and appreciation of the past, while very rapid economic growth as has been the norm in East Asia since 1950 tends to overturn the old order in its haste. I would suggest though that the ephemeral nature of East Asian architecture, with its dependence on wood, is something which has a deeper historical basis. But in any case, I think it is plausible that the extremely rapid shift from agrarian to post-industrial societies makes East Asians particularly open to novel technologies and fads.

When China Rules the World is interesting, it occupies a space between The Clash of Civilizations and the Remaking of World Order and The End of History and the Last Man. The title is a bit hyperbolic, and doesn't really reflect what's within. In fact the subtitle is far more an accurate reflection of the content.

Note: The author points out in the book that the Jin Dynasty was Mongol. It was not, it was Jurchen, the same group which gave rise to the Manchus.

Posted by Razib Khan at 5:39 AM • 7 Comments

Disqus and Echo  permlink

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I'm starting to see Disqus and Echo all over the web. Anyone else notice this? I wasn't happy when I had to move Gene Expression Classic off Haloscan, so the whole "death of comments" fad isn't something I'm a fan of. But it seems like Facebook's creation of a successful private web is now driving the Facebookification of the public web. The main issue I have with all this revolution of the "discussion" is that in my experience as a blogger most "discussion" is retarded and most discussants are barely sentient.

Posted by Razib Khan at 1:05 AM • 7 Comments

Vitamin D & T cells  permlink

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I have mentioned before the current fad in vitamin D related papers in the medical literature. It's also broken into the pop culture Zeitgeist as well, I regularly get forwards on the topic. Here is a Google Trends chart for the United States:

The history of medicine is, unfortunately, rather similar to the history of astrology. In fact for much of history doctors are likely to have increased, rather than decreased, mortality, thanks to an ignorance of germ theory and false paradigms such as Humorism. The demand-side pressures for cures & prevention seems to still exert a powerful push toward the rise & fall of fads (see google trends for "low carb" for example). A difference between pre-modern and contemporary fads though is that they're not all capricious today. Unfortunately though medicine is still complex, and the demand-side pressures often require an Answer. You have rafts of correlational studies, with each correlation adding to a positive feedback loop until the fad crests, and a new "it-cure" emerges on the scene (and no surprise that the beer industry is supposedly behind some of the studies which show that drinking in moderation is correlated with greater life expectancy).

All this is why papers like this are important, Vitamin D controls T cell antigen receptor signaling and activation of human T cells:

Phospholipase C (PLC) isozymes are key signaling proteins downstream of many extracellular stimuli. Here we show that naive human T cells had very low expression of PLC-γ1 and that this correlated with low T cell antigen receptor (TCR) responsiveness in naive T cells. However, TCR triggering led to an upregulation of ~75-fold in PLC-γ1 expression, which correlated with greater TCR responsiveness. Induction of PLC-γ1 was dependent on vitamin D and expression of the vitamin D receptor (VDR).Naive T cells did not express VDR, but VDR expression was induced by TCR signaling via the alternative mitogen-activated protein kinase p38 pathway. Thus, initial TCR signaling via p38 leads to successive induction of VDR and PLC-γ1, which are required for subsequent classical TCR signaling and T cell activation.

ScienceDaily has a good summary. This schematic represents the biochemical steps:

Read on »

Posted by Razib Khan at 12:01 AM • 12 Comments

On content redundancy  permlink

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Felix Salmon, Link-phobic bloggers at the NYT and WSJ:

The problem, here, is that the bloggers at places like the NYT and the WSJ are print reporters, and aren't really bloggers at heart. I discovered this a couple of weeks ago, after I posted a long and detailed blog entry on the court case between JP Morgan and Mexico's Cablevisión. The WSJ's Deal Journal blog didn't link to it, but a couple of days later, the blog's lead writer, Michael Corkery, had a piece in the print version of the newspaper which added nothing to the story, quoted the same Cablevisión executive that I had spoken to, and didn't mention my post at all.

The decision not to cite or link to my blog was made by Dennis Berman, the editor of the WSJ story and a former Deal Journal blogger himself. Corkery and Berman read my piece and spent a couple of days re-reporting it, yet despite the fact that both of them have worked as bloggers, neither felt any need to link to me -- or even to link to the court ruling in question. It's a print-newspaper mindset, and it reveals something important: if even the WSJ's bloggers eschew obvious links, there's really no hope that the newspaper will genuinely embrace the power of the web at any point in the foreseeable future.

Both the NYT and the WSJ have built blogs as something of a link ghetto: if you want to find an external hyperlink anywhere on their sites, the only place you'll have a decent chance of finding one is on the blogs. (There are a few noble and notable exceptions, Frank Rich being one of them: the web version of his column is always full of interesting external links.)

That's depressing enough -- but what's more depressing still is that even the bloggers at the NYT and WSJ are link-phobic, often preferring to re-report stories found elsewhere, giving no credit to the people who found and reported them first. It's almost as though they think that linking to a story elsewhere is an admission of defeat, rather than a prime reason why people visit blogs in the first place. It's a print reporter's mindset, and it should have no place at Dealbook, Deal Journal, or any other blog.

Conventional media organs are great with all their resources and ability to dig deep into a story. But the replication of nearly the exactly same "breaking news" all over the place is a bit much. If there's something that comes out that I want to talk about, one of my first instincts is to see if Ed Yong or Dr. Daniel MacArthur have already covered that ground, there's no point in doing work which has been done, when a link would suffice. But obviously you'll never see CNN or The New York Times just link the AP wire story, let alone each other, when it's something which has just broken and everyone knows the exactly same few facts. In contrast, if Ed or Dr. MacArthur cover the bases, I might extend upon their own angle and see if I have a value-add. Though sometimes even when we don't intend to complement, we may. See How inbreeding killed off a line of kings and Inbreeding & the downfall of the Spanish Hapsburgs; both were published at the exact same moment because were under embargo and had our posts written ahead of time.

Posted by Razib Khan at 9:37 PM • 3 Comments

Finding "cousins" through personal genomics  permlink

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The odds of knowing your cousins: 23andme Part 1:

Bizarrely, Jonathan Zittrain turns out to be my cousin -- which is odd because I have known him for some time and he is also very active in the online civil rights world. How we came to learn this will be the first of my postings on the future of DNA sequencing and the company 23andMe.

Just read the whole thing. This is really a matter of the humanities, not science. Specifically, the almost mystical significance people seem to put into the finding that they share genetic ancestry with people, even people who they knew and were friendly with before they knew this datum.

Also, I think this sort of thing makes hang-wringing about the ethical conundrums that genetic counselors might have in regards to paternity issues which a wife might know of, but the husband might not, seem totally ridiculous. With the plethora of personal genomic data which will likely be part of everyone's information portfolio circa 2020 you'd have to be retarded, or very exceptional, not to notice a "extra-pair paternity event" within a family.*

H/T Dr. Daniel MacArthur.

* Exceptional as in the putative father is dead, and all his relatives are dead, or he has no relatives (e.g., only child whose parents were only children, etc.).

Posted by Razib Khan at 4:51 PM • 22 Comments

Iceland tells them to shove it  permlink

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Icelanders reject deal to repay British and Dutch:

The outcome of the referendum had not been in doubt since Iceland had recently been offered better repayment terms than those contained in the deal on which residents were voting.

Partial referendum results from around a third of the cast votes showed 93 percent opposed the deal and less than 2 percent supported it. The rest cast invalid votes.

But the rejection will still have major repercussions, keeping financial aid on hold and threatening to undermine the center-left government of Prime Minister Johanna Sigurdardottir.

"This has no impact on the life of the government. We need to keep going and finish the (Icesave) debate. We have to get an agreement," Sigurdardottir told public television.

Global capital is really lucky that direct democracy isn't that widespread and that regulatory capture is ubiquitous. On a microeconomic scale we know humans can operate spitefully. I won't go into the evolutionary ideas for why this might be (though W. D. Hamilton wrote a whole paper on the evolution of spite using the inclusive fitness framework), but the inclination is strong enough obviously that you have a whole nation willing to engage on it. How's that for systematic bias in our cognitive faculties?

The big picture problem is that for most of human history. No, for 99% of it, we've operated under zero sum dynamics. That crops up in human behavior, but a variety of historical events and institutions (and I consider science & technology fundamentally institutional products) have converged so that non-zero sum dynamics have produced rapid growth in productivity and post-Malthusian consumerism over the past two centuries. But there is no inevitable reason for why individual rational action should lead to positive sum outcomes; for most of human history it didn't, for there to be some with more others had to have less. I would have to put recent financial innovation by & large into the category of dynamics which recapitulate the dynamics of the Malthusian era, moving wealth from some to others, as opposed to growing the pie (England actually banned the joint-stock corporation during the century leading up to the industrial revolution, so there is debate whether even such primitive capitalist institutions are necessary for the technological breakout).

Note: The consequences of the vote may be somewhat more symbolic than not. See the story linked above.

Posted by Razib Khan at 8:07 PM • 12 Comments