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

December 31, 2009

Decade in race, all brown people are the same

Filed under: Culture — Gene Expression @ 8:46 pm

Noticed a piece at The Root, The Decade in Race: WTF Was That?:

After the tragedy of 9/11, Arab American stereotypes morph from harmless convenient store owner to new American nigger. The Simpsons' Apuh is suddenly nowhere near as funny

There really needed to be more said here. The convenience store owners were not usually Arab (though some were), generally, they were South Asian, most often Indian American. "Apuh" (it's spelled Apu, no "h") is an Indian American, and is depicted as Hindu on The Simpsons. Also, on the order of 50%* of Arab Americans aren't Muslim, they're Christian. Like the governor of Indiana, or Ralph Nader. In other words, a disproportionate amount of prejudice directed against "Arabs" is actually directed against Muslims who dress visibly in a way that marks them as Muslim, no matter their ethnicity, and South Asians who are more visibly non-white than most Arabs, especially Sikhs who "dress like Arabs."

It is possible that the author of the above piece in The Root knows all this, and he was simply pointing to the fact that Indian Americans and South Asians generally are perceived as Arab, despite reality that they aren't. But this detail should probably have been stated explicitly, since broad swaths of the public are totally unaware of this.

* The usual assertion is that the majority of Arab Americans are Christian, but the data I've seen suggests to me that there is a strong likelihood that sometime in the teens of the 21st century a majority of self-identified Arab Americans (as opposed to those with some Arab ancestry) are likely to be Muslim.

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Contagious Tasmanian Devil cancer

Filed under: Genetics — Gene Expression @ 4:24 pm

Carl Zimmer has a nice write up of the a new paper in Science which characterizes the nature of the cells which are manifest during devil facial tumor disease. The Tasmanian Devil Transcriptome Reveals Schwann Cell Origins of a Clonally Transmissible Cancer:

The Tasmanian devil, a marsupial carnivore, is endangered because of the emergence of a transmissible cancer known as devil facial tumor disease (DFTD). This fatal cancer is clonally derived and is an allograft transmitted between devils by biting. We performed a large-scale genetic analysis of DFTD with microsatellite genotyping, a mitochondrial genome analysis, and deep sequencing of the DFTD transcriptome and microRNAs. These studies confirm that DFTD is a monophyletic clonally transmissible tumor and suggest that the disease is of Schwann cell origin. On the basis of these results, we have generated a diagnostic marker for DFTD and identify a suite of genes relevant to DFTD pathology and transmission. We provide a genomic data set for the Tasmanian devil that is applicable to cancer diagnosis, disease evolution, and conservation biology.

In Carl's article, he reports:

The cancer, devil's facial tumor disease, is transmitted when the animals bite one another's faces during fights. It grows rapidly, choking off the animal's mouth and spreading to other organs. The disease has wiped out 60 percent of all Tasmanian devils since it was first observed in 1996, and some ecologists predict that it could obliterate the entire wild population within 35 years.

I think that the ecologists need to be careful here, as the public might think that the cancer itself is going to be the immediate proximate cause of extinction. Rather, it seems more likely that the disease will reduce the numbers of the devils, of which there are on the order of 10 to 100 thousand on the island. And small populations, say less than a 1,000, are subject to random fluctuations in population size which could drive them to extinction (imagine a short-term climatic regime which reduces the food supply). It seems that some individuals are already immune to the disease, so over time if nature took its course the population would probably bounce back. Projecting extinction because of disease necessarily and sufficiently is just part of the linear fallacy, which isn't really good at predicting over the long term in biological contexts. Australia still has rabbits. It's called evolution.

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The Google Years

Filed under: Technology — Gene Expression @ 4:19 pm

The Google Decade Ends: If the search king hasn't ripped up your business yet, just wait. 10 years is a long time in the tech industry. I wonder which company will be the center of retrospectives in 2010? It seems that the time cycle of the rise & fall of "It" firm is speeding up; from IBM to Microsoft to Google. So perhaps it isn't even around right now.

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Happy New Year!

Filed under: Politics — David Hume @ 3:38 pm

And let’s have a great teens.


Africa’s urban poor becoming obese

Filed under: Health — Gene Expression @ 3:36 pm

Yeah, you read that right. Overweight and obesity in urban Africa: A problem of the rich or the poor?:

Descriptive results showed that the prevalence of urban overweight/obesity increased by nearly 35% during the period covered. The increase was higher among the poorest (+50%) than among the richest (+7%). Importantly, there was an increase of 45-50% among the non-educated and primary-educated women, compared to a drop of 10% among women with secondary education or higher. In the multivariate analysis, the odds ratio of the variable time lapse was 1.05 (p<0.01), indicating that the prevalence of overweight/obesity increased by about 5% per year on average in the countries in the study. While the rate of change in urban overweight/obesity did not significantly differ between the poor and the rich, it was substantially higher among the non-educated women than among their educated counterparts.

Here's a chart showing the urban/rural difference by nation:

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Fungus adapts fast…at first

Filed under: Genetics — Gene Expression @ 10:57 am

The Properties of Adaptive Walks in Evolving Populations of Fungus:

The rarity of beneficial mutations has frustrated efforts to develop a quantitative theory of adaptation. Recent models of adaptive walks, the sequential substitution of beneficial mutations by selection, make two compelling predictions: adaptive walks should be short, and fitness increases should become exponentially smaller as successive mutations fix. We estimated the number and fitness effects of beneficial mutations in each of 118 replicate lineages of Aspergillus nidulans evolving for approximately 800 generations at two population sizes using a novel maximum likelihood framework, the results of which were confirmed experimentally using sexual crosses. We find that adaptive walks do indeed tend to be short, and fitness increases become smaller as successive mutations fix. Moreover, we show that these patterns are associated with a decreasing supply of beneficial mutations as the population adapts. We also provide empirical distributions of fitness effects among mutations fixed at each step. Our results provide a first glimpse into the properties of multiple steps in an adaptive walk in asexual populations and lend empirical support to models of adaptation involving selection towards a single optimum phenotype. In practical terms, our results suggest that the bulk of adaptation is likely to be accomplished within the first few steps.

I've discussed this issue before. The general logic here is that when a population is subject to new selection pressures it uses whatever tricks and tools are handy in the short term even if they're suboptimal in the long term. Over time adaptation should "refine" the phenotype so that there are fewer trade-offs so that fitness gradually converges upon an idealized peak. Consider the various malaria adaptations, which arose in the past 5,000 years, some of which still have major side effects such as sickle cell anemia in homozygotes. But in a malarial environment the side effects, the risk of morbidity and mortality, is worth the overall the reduction in mortality. One imagines that over time new mutations would emerge to mask the deleterious consequences of new adaptations, which are basically evolutionary kludges.

They illustrate this process experimentally:

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Last second charitable donations

Filed under: Culture — Gene Expression @ 10:23 am

If you're getting in at the last second, please see GiveWell's top charities.

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The bear market rally of 2009?

Filed under: Culture — Gene Expression @ 5:01 am

The Massive Stock Market Rally of 2009 Ends Today:

In what the Wall Street Journal calls "a comeback of historic proportions," the U.S. stock market's banner year closes later on today. The paper says, "With one trading day remaining in 2009, the Dow is on track for its biggest annual gain since 2003, when it rose 25%. It finished Wednesday up 3.1 points, at 10548.51, a fresh peak for the year and the highest since October 2008." Leading its business section, New York Times also takes note of this year's rallying stock markets, which "will ring out one of their most volatile periods in history" in a few hours....

Earlier this year a friend of mine argued that we were going through a bear market rally. It seemed a very defensible position to me. But earlier this month I sent him a link to this chart:


The current trend is the dark blue. If this is a bear market rally, this is an unprecedented one. It would be the longest and most robust bear market rally on record. On the other hand, recent macroeconomic events have been somewhat unprecedented. I don't really see where this rally is based on the soundness of the economic fundamentals of the American economy. Before some might have argued that the efficient wisdom of the market was giving us a signal to which we should pay heed, but the American (and to some extent world) economy has been through two exuberant bubbles in the past 10 years. There's a flaw in the short term logic, so to speak. The market may point in the right direction in the long run, but in the short run we might still be screwed.

My friend is putting his money where his mouth is, so I tend to listen closely to his judgement as I know he is more than simply talk. I'm sure that readers also have opinions and are making decisions appropriately, so I'm curious the word out on the street is.

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What Darwin Never Knew (online)

Filed under: Evolution — Gene Expression @ 2:31 am

If you missed it, you can still watch it online.

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December 30, 2009

Tools to analyze gene expression

Filed under: Genetics — Gene Expression @ 11:55 pm

Disease Gene Characterization through Large-Scale Co-Expression Analysis:

Celsius, the largest co-normalized microarray dataset of Affymetrix based gene expression, was used to calculate the correlation between all possible gene pairs on all platforms, and generate stored indexes in a web searchable format. The size of Celsius makes UGET a powerful gene characterization tool. Using a small seed list of known cartilage-selective genes, UGET extended the list of known genes by identifying 32 new highly cartilage-selective genes. Of these, 7 of 10 tested were validated by qPCR including the novel cartilage-specific genes SDK2 and FLJ41170. In addition, we retrospectively tested UGET and other gene expression based prioritization tools to identify disease-causing genes within known linkage intervals. We first demonstrated this utility with UGET using genetically heterogeneous disorders such as Joubert syndrome, microcephaly, neuropsychiatric disorders and type 2 limb girdle muscular dystrophy (LGMD2) and then compared UGET to other gene expression based prioritization programs which use small but discrete and well annotated datasets. Finally, we observed a significantly higher gene correlation shared between genes in disease networks associated with similar complex or Mendelian disorders.

Citation: Day A, Dong J, Funari VA, Harry B, Strom SP, et al. 2009 Disease Gene Characterization through Large-Scale Co-Expression Analysis. PLoS ONE 4(12): e8491. doi:10.1371/journal.pone.0008491

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The engineer terrorist

Filed under: Terrorism — Razib @ 10:25 am

Slate reviews the scholarly literature. Explaining the mechanics of the over-representation of engineers at the higher echelons of transnational terrorism is a guessing game, but the empirical reality seems relatively robust. Though I suspect that sociological and economic factors are necessary (see the linked paper in the article), I think the ultimate precondition has to be the psychology and training of engineers, who are geared toward analysis of a problem and devising a solution. The most ingenious/ridiculous models of Young Earth Creationism seem to spring from the minds of fundamentalist engineers, who must resolve their Biblical literalist premises with the world as it is. One can foresee how the same sort of mentality would be much more explosive in the Islamic world, where the fundamentalist premises lead to a set of inferences (e.g., Islam’s manifest superiority over the West) which seems at variance with the state of the world. The engineer resolves this contradction by devising “solutions.”

Four Stone Hearth & Avatar

Filed under: Anthroplogy — Gene Expression @ 10:17 am


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Science in Berkeley, it’s a white thing

Filed under: science — Gene Expression @ 7:24 am

Several readers have pointed me to this development at Berkeley High School:

Berkeley High School is considering a controversial proposal to eliminate science labs and the five science teachers who teach them to free up more resources to help struggling students.

The proposal to put the science-lab cuts on the table was approved recently by Berkeley High's School Governance Council, a body of teachers, parents, and students who oversee a plan to change the structure of the high school to address Berkeley's dismal racial achievement gap, where white students are doing far better than the state average while black and Latino students are doing worse.

Paul Gibson, an alternate parent representative on the School Governance Council, said that information presented at council meetings suggests that the science labs were largely classes for white students. He said the decision to consider cutting the labs in order to redirect resources to underperforming students was virtually unanimous.

There's a small issue here, and that's the allocation of resources efficient to solve proximate problems. In other words, California is currently under fiscal strain, as are localities. Secondary education is always under strain in this country. Berkeley High School has always had issues with disparities between whites & Asians and blacks & Latinos (though this is no exceptional dynamic). Here's the demographic data for Berkeley High School:


The 2006-2008 American Community Survey says that Berkeley's overall population is:

Non-Hispanic white - 57.4%
Black - 9.3%
Hispanic - 10.7%
Asian - 18.1%

One issue is UC Berkeley students who are being counted in the ACS are probably inflating the proportion of Asians. The modal age bracket in Berkeley is 20-24. The modal bracket is in the 35-50 range in both Oakland to the south, and Albany to the north. But it is striking that Non-Hispanic whites are so underrepresented and blacks so overrepresented. There is only one public high school in Berkeley. It is likely correct that blacks in Berkeley are more fertile than the whites, but I don't think the disparity is striking enough to account for the demographics of Berkeley High School. Rather, many whites must be sending their children to private schools.

This action will reinforce this tendency; the type of engaged parents which a public school benefits from won't consider sending their child to one which has to slash science laboratories to focus on remedial education. So Berkeley High School is simply accelerating its long death spiral.

More generally, the bizarre racialist logic used to justify the slashing of the science curriculum, that science implicitly benefits whites, is objectionable (at least to me, and likely to readers of this weblog). Our civilization is grounded fundamentally in science. Additionally, Berkeley High School is just a few blocks from UC Berkeley, where there are plenty of non-whites who do science. 42% of the undergraduates at UC Berkeley are Asian, as opposed to 31% who are white. The word "Asian" of course is not found in the story above, because it doesn't fit the whites-against-the-rest narrative. From what I can tell a substantial proportion of the citizenry of Berkeley and similar communities remain stuck in a 1960s time-warp when it comes to ethnic relations. Back then this was an America in black & white.

Here's the most recent ACS on California:

42.3% White (not including White Hispanic)
36.6% Hispanic or Latino (of any race)
12.5% Asian
6.7% Black or African American
2.6% Multiracial
1.2% American Indian

Berkeley is much whiter and blacker than California as a whole. As I noted above, the transient presence of Cal students probably inflates the Asian American proportion, but these students are not going to be long term members of the community. The city's peculiar and anachronistic demographics may explain the unselfconsciousness of Berkeley's racialist politics.

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December 29, 2009

Why do we delay gratification even when there is no downside?

Filed under: Behavioral Economics,Psychology — agnostic @ 9:10 pm

Earlier this year, John Tierney reviewed several studies on how delaying gratification makes us feel better in the short term by preventing guilt but makes us feel more miserable in the long term by causing regret over missed opportunities. I added my two cents here, just to note that this sounds like part of the Greg Clark story about recent genetic change in the commercial races that adapted them to the emerging mercantile societies they found themselves in. What I had in mind was the delaying of vice — investing a dollar today rather than splurging, moderating the amount of drink or sweets you enjoy, and so on.

But now Tierney has another review of related studies which show that we delay gratification even for what should be guilt-free pleasures like redeeming a gift card, using frequent flier miles, and visiting the landmarks in your local area. And don’t we all have enjoyable books and DVDs we’ve been putting off? After indulging in these cases, there is no potential bankruptcy, no hangover, and no tooth decay — so why do we indiscriminately lump them in with genuine vices and put off indulging in them? Obviously this tendency too is a feature of agrarian or industrial groups — hunter-gatherers would never leave gift cards lying around in their drawers.

It must be because of how recent the change toward delaying gratification has been. Given enough time, we might evolve a specialized module for delaying gratification in vices and another module for doing so in guilt-free pleasures, which would be better than where we are now. But when our genetic response to a change is abrupt, typically we have broad-brush solutions that take care of the intended target but also leave plenty of collateral damage. Over time our solutions get smarter, but it takes awhile. Just look at how crude the responses to malaria are.

We see this domain-general taste for (or aversion of) risk in other areas. People who lead more risky lifestyles buy much less insurance than people who lead cautious lifestyles. Those who ride motorcycles without helmets would be richer and more likely to pass on their genes if they bought a lot of insurance, while those who play it safe would be richer by not buying all that superfluous insurance. Instead, daredevils are daredevils all the way — including a contempt for insurance.

This casts doubt on how easy it is to change our behavior so that we no longer postpone our indulgence in guilt-free pleasures. Because we have a domain-general delay of gratification, it will still just feel wrong. You can also argue the logic of buying lots of insurance to the motorcyclist who rides without a helmet, but that won’t change his mind because his tastes for risk is across-the-board.

Cheers for the coming tech-war!

Filed under: Blog — Gene Expression @ 9:43 am

Google, Past and Future:

Ah, but what about 2010? That, claim the editors at Smartgrid, will be the year that Google and Microsoft really roll up their sleeves and go to war. In everything from search to office apps and Internet browsers, the two behemoths will roll out fancy new services designed to erode their rivals' revenue streams. "Both companies are largely betting their collective futures on this battle, so the stakes are huge," said industry analyst Rob Enderle. "Microsoft is going to partner and try to starve Google out of content and partners. Google is going to work against Microsoft's pricing model and starve them out of money. Both are, for once, largely going after each other's relative weaknesses and leveraging their respective strengths, so this will likely be a battle for the history books."

This sort of competition is good for consumers. I think only a company with Google's prestige can convince many purchasers of Office that its price point is a relict of the 1990s and the era of shrink-wrapped software. Free is probably not viable (or at least not exclusively), but there's no natural reason that Microsoft has to reap the margins it currently does.

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The less intelligent you are, the more bored you are

Filed under: Culture — Gene Expression @ 6:57 am

The Audacious Epigone has an interesting post up, Burden of boredom borne by blockheads:

This isn't just me speaking from personal experience--the data confirm it. The GSS asked respondents in 1982 and again in 2004 how often they have time on their hands that they don't know what to do with. Using the familiar categorization method employed here before*, the following table shows the percentage of each group's members who reported to "almost never" be without something worthwhile to do in their free time:

He presented his data in tabular format. I decided to use the variables he kindly provided and produce some charts. Below are the frequency bored from lowest WORDSUM score, 0, to highest, 10. 0 meaning 0 out of 10 words correct on a vocabulary test, and 10 meaning 10 out of 10 correct. I also checked degree attainment. For those who have a hard time making out the legend, the darker the shading, the more bored the class.

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One year after the financial collapse, Gotham in a downward spiral

Filed under: data — Razib @ 12:59 am

Actually, not really. New York on Track for Fewest Homicides on Record. I assume that those who project long term fiscal problems due to a contraction in the financial sector in New York City are probably correct (assuming that the financial sector actually doesn’t expand back to its pre-2009 size). But the assumption that the economic fallout would lead to 1970s levels of anomie doesn’t seem to be panning out. As I indicated earlier I found suggestions of such a reversion plausible at the time because I had a rather economistic mental model of the “root causes” of crime. But that seems less plausible when you look over the arc of the past century. Another model of course is that in fact it was financial sector workers who were driving much of the crime directly by subsidizing illicit activity through their enormous incomes generated by the efficiencies of capital allocation which they drove (I’m not being serious here).

December 28, 2009

How to Teach Physics to Your Dog

Filed under: science — Gene Expression @ 5:38 am

Chard Orzel's book, How to Teach Physics to Your Dog, is out. Much props to Chad for being able to write a book while being a professor and father. A man for all seasons indeed!

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December 27, 2009

New comment format

Filed under: Admin — Razib @ 3:34 pm

A lot of people (including paying readers! kidding!) are complaining about the new commenting format. I’ll be euphemistic and observe that it’s suboptimal. But I don’t have time to work on tweaking and beautifying it now, so please be patient. Over time it’ll move up the stack of my priorities, and hopefully your awesome contributions to the discussion will be facilitated by a more elegant and user-friendly commenting interface by the end of January.

Additionally, I am thinking that posting “admin” messages in this space is also suboptimal. It uses space which should be allocated to real posts about science and such. If you’re in the minority of readers who actually cares enough about your blog-reading experience to gripe in the comments, I invite you to subscribe to/follow my twitter feed, I’m gonna put “admin” related stuff there from now on. You can also send messages via twitter. Email is fine as always, but if you’re someone who I don’t recognize, there’s a non-trivial chance that you’ll stay at the bottom of the task stack and I’ll never get back to you. I have my twitter feed on my Google homepage, so I am more likely to see random direct messages (as I noted earlier, I get a non-trivial number of messages from PR people, so it isn’t unlikely that I’m forgetting emails in the “none of the above” folder).

Mutation and selection in stickleback evolution

Filed under: Genetics — p-ter @ 8:46 am

Understanding the precise molecular mechanisms underlying changes in animal morphology is a tricky problem–usually two species which have diverged morphologically (say, mice and humans) are now so unrelated as to make genetic study exceedingly difficult, if not impossible. For years, a group led by David Kingsley has been addressing this problem in a cleverly-chosen model–three-spined sticklebacks. Importantly for the question of morphological evolution, freshwater populations of this fish have lost many of the spines and pelvic girdle carried by the saltwater populations (there are a number of hypotheses, probably not all mutually exclusive, for why this has been under selection).

In a new paper, this group demonstrates the precise genetic alteration underlying this change in a number of freshwater populations. Perhaps surprisingly, it appears to be due to the recurrent deletion (in different freshwater populations) of an enhancer of an important developmental gene. Strikingly, creating a transgenic freshwater fish with a copy of this enhancer (which normally is missing) leads to freshwater fish with a pelvis like the saltwater fish.

In fact, this enchancer seem to fall in a “fragile” (read: repeat-laden) region of the genome, which presumably increases the rate of deletion at this site. If one imagines there are a number of genetic paths to get to the reduced pelvis size favored in freshwater environments, the probability of each path depends on the mutation rate of each genetic change. In this case, many (though not all) freshwater populations have independently taken the same path, likely due to the increased mutation rate at this fragile site.


Citation: Chan et al. (2009) Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 Enhancer. Science. Published Online December 10, 2009 [DOI: 10.1126/science.1182213]

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