Archive for December, 2009

Decade in race, all brown people are the same

By Razib Khan | December 31, 2009 11:46 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.

CATEGORIZED UNDER: Culture

Contagious Tasmanian Devil cancer

By Razib Khan | December 31, 2009 7:24 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.

CATEGORIZED UNDER: Ecology, Genetics

The Google Years

By Razib Khan | December 31, 2009 7:19 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.

CATEGORIZED UNDER: Technology

Africa's urban poor becoming obese

By Razib Khan | December 31, 2009 6:36 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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CATEGORIZED UNDER: Health

Fungus adapts fast…at first

By Razib Khan | December 31, 2009 1:57 pm

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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CATEGORIZED UNDER: Evolution, Genetics

Last second charitable donations

By Razib Khan | December 31, 2009 1:23 pm

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

CATEGORIZED UNDER: Culture

The bear market rally of 2009?

By Razib Khan | December 31, 2009 8:01 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:
four-bears-large.png
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.

CATEGORIZED UNDER: Culture, Economics

What Darwin Never Knew (online)

By Razib Khan | December 31, 2009 5:31 am

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

CATEGORIZED UNDER: Evolution

Tools to analyze gene expression

By Razib Khan | December 31, 2009 2:55 am

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

CATEGORIZED UNDER: Genetics

Four Stone Hearth & Avatar

By Razib Khan | December 30, 2009 1:17 pm

Here.

CATEGORIZED UNDER: Anthroplogy

Science in Berkeley, it's a white thing

By Razib Khan | December 30, 2009 10:24 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:
berkdata.png
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.

CATEGORIZED UNDER: Science

Cheers for the coming tech-war!

By Razib Khan | December 29, 2009 12:43 pm

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.

CATEGORIZED UNDER: Blog, Technology

The less intelligent you are, the more bored you are

By Razib Khan | December 29, 2009 9:57 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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CATEGORIZED UNDER: Culture

How to Teach Physics to Your Dog

By Razib Khan | December 28, 2009 8:38 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!

CATEGORIZED UNDER: Science

Katz

By Razib Khan | December 25, 2009 4:28 pm

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CATEGORIZED UNDER: Blog

Merry Xmas

By Razib Khan | December 24, 2009 5:20 pm

& a happy New Year.

CATEGORIZED UNDER: Blog, Culture

Africans Americans mostly West African, but some mostly European

By Razib Khan | December 23, 2009 6:33 am

I referenced a paper in PNAS yesterday, and I thought it might be good to actually point to it today. There’s nothing that new in the paper. It confirms the finding that ~20% of the ancestry of African Americans is European, and, that African ancestry seems to be much more dominant when it comes to components of the genome presumably disproportionately contributed by females (2/3 of X chromosomes). In any case, the paper, Genome-wide patterns of population structure and admixture in West Africans and African Americans:

Quantifying patterns of population structure in Africans and African Americans illuminates the history of human populations and is critical for undertaking medical genomic studies on a global scale. To obtain a fine-scale genome-wide perspective of ancestry, we analyze Affymetrix GeneChip 500K genotype data from African Americans (n = 365) and individuals with ancestry from West Africa (n = 203 from 12 populations) and Europe (n = 400 from 42 countries). We find that population structure within the West African sample reflects primarily language and secondarily geographical distance, echoing the Bantu expansion. Among African Americans, analysis of genomic admixture by a principal component-based approach indicates that the median proportion of European ancestry is 18.5% (25th-75th percentiles: 11.6-27.7%), with very large variation among individuals. In the African-American sample as a whole, few autosomal regions showed exceptionally high or low mean African ancestry, but the X chromosome showed elevated levels of African ancestry, consistent with a sex-biased pattern of gene flow with an excess of European male and African female ancestry. We also find that genomic profiles of individual African Americans afford personalized ancestry reconstructions differentiating ancient vs. recent European and African ancestry. Finally, patterns of genetic similarity among inferred African segments of African-American genomes and genomes of contemporary African populations included in this study suggest African ancestry is most similar to non-Bantu Niger-Kordofanian-speaking populations, consistent with historical documents of the African Diaspora and trans-Atlantic slave trade.

One of the value-adds from this paper is that the authors explored how African Americans related to disparate African populations. The historical records indicate that American slaves arrived disproportionately from the regions to the west of the Bight of Bonny. In other words, black Americans derive predominantly from the non-Bantu populations of West Africa, from Senegal down to Nigeria. This is in contrast to Brazil, where the black population was reputedly of more diverse origin, including many Bantu speakers from Angola as well as West Africans.
I reedited part of figure 1 to show which African groups are in the study and how they relate to each other genetically:

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CATEGORIZED UNDER: Anthroplogy, Genetics

Error in the age of personal genomics

By Razib Khan | December 22, 2009 7:20 pm

danielx.pngOver at Genetic Future Dr. Daniel MacArthur points out some errors in deCODE’s interpretation services. Dr. MacArthur presumably knows his maternity, though if the X chromosome results were correct one would guess that Dr. MacArthur is actually adopted and that his mother might be a Lumbee Indian.
But it makes me wonder how confused people are going to be due to problems with false results. In particular, as these technologies become very cheap many families with make recourse to them. Sometimes this will highlight “extrapair paternity events,” but sometimes there will be errors and siblings may face a period of uncertainty in relation to possibly discordant results. The likelihood of a false result creating an unexpected situation is conditional on various probabilities, the error rate of the results, and the likelihood of an extrapair paternity event (which varies from demographic to demographic and family to family). I guess we’ll have more data in the near future….

CATEGORIZED UNDER: Genetics

When mammoths roamed (rarely)

By Razib Khan | December 22, 2009 6:02 pm

Brian Switek, The extended twilight of the mammoths:

So, if the team’s analysis is correct, both mammoths and horses lived in the interior of Alaska between about 11,000 and 7,000 years ago. This is significantly more recent than the youngest fossil remains of horses and mammoths, dated between 15,000 and 13,000 years ago. There are at least two factors that might contribute to this disparity. The first is that fossils from this more recent time were preserved but have not yet been found. More likely, though, is that the populations of both mammoths and horses had dwindled to the point where fossil preservation was becoming increasingly unlikely. There were so few of them that the death of an individual in circumstances amenable to preservation was becoming rarer and rarer.
Either way, this discovery has important implications for the extinction of horses and mammoths in North America. Based upon the fossil data alone it had been hypothesized that both disappeared around the time that humans became established in North America.* Some have taken this association to suggest that humans engaged in a blitzkrieg in which naive New World megamammals were quickly dispatched by the human hunters. If the new evidence is correct, though, humans did not wipe out horses and mammoths overnight. Instead humans lived alongside dwindling populations in Alaska for thousands of years. Likewise, these new findings also contradict the favored hypothesis of one of the study’s authors, Ross MacPhee, who previously proposed that some kind of “hyperdisease” carried by humans (or animals that traveled with humans) quickly wiped out these animals. The pattern of extinction was obviously more protracted.

This seems about right. Excuse the analogy, but it sometimes seems that models of human-caused extinction of mega-fauna portray ancient hunter-gatherers as Einsatzgruppen, and the mega-fauna as Jews and Communists. Though genocides of human populations in the concerted manner of the Germans against the Jews, Gypsies and other groups during World War II have occurred periodically, more often what we see is a slow wearing down and attrition of marginal groups at the expense of dominant ones.
It seems a plausible model that when mega-fauna were plentiful hunters would focus on them, but once the mega-fauna became rare naturally the return on investment would decrease and it would become rational to shift to other prey organisms. This implies that many mega-fauna likely persisted in isolated pockets as relict populations, and may have been killed off only far later, or perhaps even succumbed to a natural environmental calamity. In another era the last herds of wild horses would probably have gone extinct due to drought, or perhaps been hunted down by a random group of humans who had no idea that they were decreasing the biological diversity of the planet.

CATEGORIZED UNDER: Ecology

On scales of norms

By Razib Khan | December 22, 2009 5:32 pm

There has been more blogospheric discussion on the topic of my post Doing the right thing, doing the legal thing. Megan McArdle, who started the discussion, has a long post elaborating on her objections to strategic defaults. Steve Waldman has two good posts up. Finally, at The Big Money Daniel Gross concludes:

Of course, corporate managers and financiers don’t suffer from these neuroses. Do you think billionaire investor Sam Zell feels any guilt or shame because his buyout of the Tribune Co., which had $12.9 billion in debt, ended in a Chapter 11 filing last December? Rather than worry about whether Americans will take cues from modest homeowners who make a tough decision not to stay current on debt, perhaps we should worry about middle-class Americans taking cues from billionaires and Fortune 500 companies who make the rational decision not to stay current on debt.

As I admitted earlier, as a matter of description a society where people are relatively trustworthy, and do the right thing as opposed to the legal thing, is a happier place than one where trust is in short supply. The problem is that these societies don’t emerge out of thin air, but are created though vigilant policing of norms, and frankly a level of interpersonal nosiness or homogeneity which is probably considered uncouth or retrograde today.
Perhaps what we saw in the last generation was the slow but steady exhaustion of values which arose in the context of small towns and urban neighborhoods. With the decline of the small town and the decay of close-knit urban neighborhoods perhaps the modern state is one where atomistic rational actors are intent on doing what they can get away with because of the anonymity which is the normal course of existence. The power of modern media means that Americans, no matter where they live, see how the high and might live and how they comport themselves in their peer groups. The “community” has now expanded into cyberspace and the norms are not just created by interaction with those whom you meet face to face.
Instead of demanding that Americans stay true to the values of old, and basic decency, I think it is perhaps time to engage with the future which we are facing. The horse of old-time values has left the barn. Perhaps more transparency in personal records and immediate access by anyone in relation to anyone will bring back some accountability to the choices one makes.

CATEGORIZED UNDER: Culture, Economics
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