Archive for July, 2010

Linguistic diversity, other views

By Razib Khan | July 24, 2010 9:08 pm

Readers might find these responses of interest. Mostly I just laughed, though some of you may be a bit more serious than I, so if anthro-gibberish drives you crazy, don’t follow the links. As I told “ana” below a lot of the discussion we had was basically just talking past each other. I kept telling her she was vacuous because she was assuming presuppositions which I simply did not share as empirical background descriptions of the world (e.g., a strong form of linguistic relativism where the specific nature of a language shapes cognition). Though at least she was concise. On the other hand, see this small section of Creighton’s response:

I think this is what bothered me the most about Khan’s piece. No discussion of what poverty means, what it is, how it’s defined. I could be completely wrong, but that led me to feel that there was a high degree of Eurocentric neo-colonialism behind Khan’s proposition. Who is saying to who what “median human utility” means? Are we assuming that homeownership, vehicle ownership, and other tangible measures of economic prosperity are involved? Is access to fresh food and water part of this measurement? Khan didn’t discuss poverty at all and he didn’t acknowledge that the neo-colonial policies of certain nations are at least partially responsible for the long-term economic suffering of many of the people he is referring to. I just got the feeling that he was telling the people who belong to small language communities to accept defeat and learn English. It incited me even more that his justification for making this decision was in purely economic terms. Abandoning your heritage will pay out in the end. But will it?

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CATEGORIZED UNDER: Anthroplogy, Culture
MORE ABOUT: Anthropology

10,000 years ago there were no "Southeast Asians"

By Razib Khan | July 24, 2010 3:34 pm

Mexico Ancient WomanMexico: Ancient woman suggests diverse migration:

A scientific reconstruction of one of the oldest sets of human remains found in the Americas appears to support theories that the first people who came to the hemisphere migrated from a broader area than once thought, researchers say.
Mexico’s National Institute of Anthropology and History on Thursday released photos of the reconstructed image of a woman who probably lived on Mexico’s Caribbean coast 10,000 to 12,000 years ago. She peeks out of the picture as a short, spry-looking woman with slightly graying hair.

Anthropologists had long believed humans migrated to the Americas in a relatively short period from a limited area in northeast Asia across a temporary land corridor that opened across the Bering Strait during an ice age.

But government archaeologist Alejandro Terrazas says the picture has now become more complicated, because the reconstruction more resembles people from southeastern Asian areas like Indonesia.

I think this gets at the fallacy:

But Gillespie cautioned against comparing a reconstructed face from 10,000 years ago to modern populations in places like Indonesia, which have also probably changed over 10 millennia.

“You have to find skeletons of the same time period in Asia, or use genetic reconstructions, to make a strong connection, and cannot rely on modern populations,” she wrote. “Do we have any empirical data on what Southeast Asian women looked like … 10,000 years ago?”

A few years ago some scholars asserted that Kennewick Man resembled “South Asians.” I’m open to the possibility of a more complex peopling of the Americas, but until we get ancient DNA (something that is very difficult in the USA), it seems rather strange to make assessments of phylogenetic descent based on phenotypic similarities between one ancient specimen and modern populations.

Image Credit: AP Photo/ Mexico’s National Institute of Anthropology and History

CATEGORIZED UNDER: Evolution
MORE ABOUT: Anthropology

Open Thread – July 23rd, 2010

By Razib Khan | July 23, 2010 2:44 pm

I was travelling on Monday so couldn’t post the open thread and then forgot. But now that I think about I think Friday would be better in any case, because I don’t post much on the weekends. So again, questions, links, what you’re reading. You know my motto, “Don’t be stupid” (fwiw, posting links to flickr photos of your cats is not stupid).

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Daily Data Dump – Friday

By Razib Khan | July 23, 2010 2:17 pm

Have a good weekend.

Ancestry-Shift Refinement Mapping of the C6orf97-ESR1 Breast Cancer Susceptibility Locus. Many single nucelotide polymorphisms associated with a risk factor may actually not be the causal agent in a mechanistic sense. It’s just very close to and tightly associated with the real genetic cause. If the tightness of that association varies by population, then the utility of that marker varies between populations as a predictor. This is why us colored folk should be wary of risk alleles discovered in studies of European populations insofar as we apply those results to ourselves.

Will Your Children Grow Up To Be Servants And Nannies? In the period between 1800 and 1970 the wage gap between unskilled and skilled workers closed, the wage premium on education and specialized skills decreased. Since 1970 in the developed world the gap has started to grow again (see Farewell to Alms). I won’t explore in depth the long term implications of assortative mating, heritability of psychological and behavioral traits, and a genuine meritocracy which rewards skill, diligence and intelligence fairly. Think on it though if you have the brains and the knowledge base, and feel compassion unless you’re a psychopath.

Adaptive Evolution of Genes Duplicated from the Drosophila pseudoobscura neo-X Chromosome. The target of selection is more than just SNPs. The unit of selection may be more than just the individual.

Anguish of Romantic Rejection May Be Linked to Stimulation of Areas of Brain Related to Motivation, Reward and Addiction. I’ve never been addicted to a drug, have no fixation on shopping, and such. But now I guess I can imagine what that feels like, and I feel really sorry for people who are addicted in any way.

Ford Makes Money Again. But What About That Debt? I really hope Ford does well. They’re in a bind because they didn’t fail and get bailed out by the government. The world turned upside down.

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Katz

By Razib Khan | July 23, 2010 11:29 am

bravesteed

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Personal genomics & the state

By Razib Khan | July 23, 2010 11:13 am

Dr. Daniel MacAthur & Dan Vorhaus offer their takes on the recent hearings in Congress on the direct-to-consumer genomics industry, A sad day for personal genomics & “From Gulf Oil to Snake Oil”: Congress Takes Aim at DTC Genetic Testing. I guess I lean toward light regulation. I don’t think that DTC personal genomics will result in systemic decrease in human happiness, and tight regulation will increase the costs of innovation and constrain access and reduce affordability. Though I guess that for some that’s a feature, not a bug.

My main point, which I think I got across on the Genomes Unzipped comments is that fraud, error and misrepresentation are rife across many health-related sectors in American society. The nutrition and diet industry are prime examples. Bad journalism on the health beat causes way more suffering than DTC genomics kits ever will, as people who are not intelligent make precipitous decisions based on the latest result which managed to slip through the p-value gauntlet and are sexy enough to be written up in USA Today. And, there are widespread distortions within our health care sector which really need to be addressed (I’m thinking in particular of frank talk about end of life palliative care). With that as the basis for judgement I don’t think that the fraud and misrepresentation one can find in DTC personal genomics is exceptionally worrisome or notable to warrant such attention or focus. This is an inefficient allocation of concern and regulatory resources, driven more by the industry’s puffed up claims and the apocalyptic projections of the skeptics.

CATEGORIZED UNDER: Genomics, Health

One principal component to rule them all?

By Razib Khan | July 23, 2010 1:50 am

ResearchBlogging.orgDespite the reality that I’ve cautioned against taking PCA plots too literally as Truth, unvarnished and without any interpretive juice needed, papers which rely on them are almost magnetically attractive to me. They transform complex patterns of variation which you are not privy to via your gestalt psychology into a two or at most three dimensional representation which can you can grok immediately. That is why History and Geography of Genes was so engrossing. You recognize patterns which were otherwise unrecognizable. But how you interpret those patterns, that’s a wholly different matter. And how those patterns arise is also not something one can ignore.

price_fig1First, let’s start with an easy case. To the left is a PCA plot with four populations. Nigerians, East Asians (Chinese + Japanese), Europeans (whites from Utah), and finally, African Americans. The x-axis is the first principal component of variation, and the y-axis the second. That means that the x-axis is the independent dimension of variation within the patterns of genetic data which explains the largest fraction of the total amount of genetic variation. The sum totality of the variation can be decomposed into an large set of independent dimensions which can be rank ordered from the largest explanatory components to the smaller ones, successively by number. In a human genetic context the first principal component invariably separates Africans from non-Africans, and the second principal component often maps onto a west-east axis from Europe to the New World. Subsequent principal components can often be useful in smoking out fine scale distinctions, or relationships which are confused by the existence of similar but different signals in admixed populations.

The interpretation of this plot is rather easy. You see that African Americans lay along a continuum between Nigerians and Europeans, skewed toward Nigerians, with some outliers toward East Asians. We know from other genetic findings that ~20% of the African American ancestral quanta is European, but, that quanta is not equally distributed across the population. ~10% of the African American population is more than 50% European in ancestry, while 90% is less than 50% European. And so you have a distribution which reflects this variation. As for the outliers, I will speculate and suggest that these are indications of Native American ancestry among some African Americans.

The story I presented above is probably plausible as an explanation of the visual because we have a wealth of historical data to corroborate the plausibility of that narrative. The fit between the results from the technique of analysis of genetic variation and what scholars have long inferred from textual sources is relatively easy. It is far more difficult to look at a PCA plot, and generate a plausible narrative that you yourself accept with a high degree of confidence with little external support. It is with that caveat in mind that I present Toward a more uniform sampling of human genetic diversity: A survey of worldwide populations by high-density genotyping:

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CATEGORIZED UNDER: Biology, Genetics, Genomics

Daily Data Dump – Thursday

By Razib Khan | July 22, 2010 4:46 pm

Kele’s Science Blog. Undergrad who is a double major in biology and history. Attempting to produce content, as opposed to simply opining.

Yes, We Should Clone Neanderthals. Even if modern humanity decides to not do something like this (though at some point in the medium-term future I assume the technological feasibility will be a low enough hurdle that a private lab could do it without much notice), there is fruit in having the discussion.

Brain Scans May Help Guide Career Choice. I wonder at what point “brain scan” will no longer be so sexy. I doubt brain scans as such add that much value to something like career choice over standard psychometrics.

‘Counterintuition’, the Human Microbiome, and Why Fluency in Math Matters. If you are person who likes to think a fluency in mathematics is essential.

Why Do Some Like It Hot? Because we like the sensation of danger! Three years ago I did 7 days of hot sauce.

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Readership survey soon (again)

By Razib Khan | July 22, 2010 10:24 am

Since I’ve moved to Discover Blogs I suspect my readership has changed a bit. I have the results of a previous survey from early in 2010, back when I was at ScienceBlogs, but haven’t posted on it in detail. I’ll try and do that in the next few days, but I also will put up a survey for this incarnation of the weblog to see if there are changes. I’ll ask the standard demographic questions (age, sex, race, income, education, etc.), but the comments are open if you are curious about something about the readership of this weblog and would like me to include a question regarding that issue. I can’t guarantee I’ll add it, but I might.

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CATEGORIZED UNDER: Uncategorized

Dave Appell: remember the messenger

By Razib Khan | July 22, 2010 9:58 am

David Dobbs has a long measured response up to David Appell’s strange argument that Pepsi’s “free speech” rights were violated during the recent ScienceBlogs kerfuffle, by way of which he casts some aspersions on the character and agenda of specific bloggers. Here’s the thing about Appell, he has a long history of confused and surly criticisms and interrogations of others and himself. I know that history because I first became familiar with Dave Appell in May of 2002. In between pointers and commentary on physical science, his primary beat as a science journalist, he would offer some personal reflections, frustrations, and worries. I’m not big into bloggers who “overshare,” especially science bloggers, so I tried to ignore that as I focused on the substance of Appell’s posts.

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CATEGORIZED UNDER: Blog
MORE ABOUT: Blog, Culture

Disease as a byproduct of adaptation

By Razib Khan | July 22, 2010 12:34 am

How we perceive nature and describe its shape are a matter of values and preferences. Nature does not take notice of our distinctions; they exist only as instruments which aid in our comprehension. I’ve brought this up in relation to issues such as categorization of recessive vs. dominant traits. The offspring of people of Sub-Saharan African and non-African ancestry where the non-African parent has straight or wavy hair tend to have very curly hair. Therefore, one may say that the tightly curled hair form is dominant to straight or wavy hair. But, it is also the case that there is some modification in relation to the African parent in the offspring, so the dominance is not complete. When examining the morphology of the follicle, which determines the extent of the hair’s curl, the offspring may in fact exhibit some differences from both parents. In other words our perception of the outcomes of inheritance are contingent to some extent on our categorization of the traits as well as our specific focus along the developmental pathway.

Or consider the division between “traits” and “diseases.” The quotations are necessary. Lactose intolerance is probably one of the best cases to illustrate the gnarly normative obstructions which warp our perceptions. As a point of fact lactose intolerance is the ancestral human state, and numerically predominant. It is the “wild type.” Lactose tolerance is a relatively recent adaptation, found among a variety of West Eurasian and African populations. A more politically correct term, lactase persistence, probably better encapsulates the evolutionary history of the trait, which has shifted from the class of disease to that of genetic trait when we evaluate the bigger picture (obviously diseases are simply “bad” traits”).

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Daily Data Dump – Wednesday

By Razib Khan | July 21, 2010 5:51 pm

Association of Trypanolytic ApoL1 Variants with Kidney Disease in African-Americans. Same subject as a paper I linked to a few days ago. The fact that they came out around the same date and overlap so much in topicality is a window into the competitive aspect of science.

Polyandry increases offspring viability and mother productivity but does not decrease mother survival in Drosophila pseudoobscura. My rule of thumb is to extrapolate from model organisms the closer the phenomenon is to the biomolecular scale. Nevertheless, variation in behavior and its consequences can give us insight into generalities on a higher order of organization as well.

History of asthma or eczema and cancer risk among men: a population-based case-control study in Montreal, Quebec, Canada. This needs a lot more follow up to be something that you want to bank on. Still, of interest to many of us.

Healthy Families, Religious Involvement Buffer Youth Against Risk Factors Related to Drug Abuse. This is for American Indian youth. When it comes to these correlations one has to specify clearly the population that the correlation shows up in. Other studies have shown reverse directions of correlation when it comes to religion and outcome of social pathology for different ethnic groups, probably because of divergent patterns in the confounds. Another similar case are recommendations for circumcision as protective practice against HIV. This may have positive cost vs. benefit utility in South Africa, where HIV seropositive proportions are north of 20%, but basically none in Japan where they’re below 1% (lower than almost all Sub-Saharan African nations where circumcision is widely practiced, and about the same as South Korea, where circumcision is also widely practiced).

Britain’s Leader Carves Identity as Budget Cutter. David Cameron will be remembered.

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Daily Data Dump – Tuesday

By Razib Khan | July 20, 2010 7:03 pm

Patrimony and the Evolution of Risk-Taking. Possible reason that organisms “mix it up” in behavioral morphs.

John Zogby’s Cri de Coeur. Creative destruction in the polling business. What is bad for producers is often good for consumers.

‘More poor’ in India than Africa. Concentrated in the “Deep North”. The social underdevelopment of the subcontinent as a whole gets little press because people would rather focus on the liftoff of the upper segments, and their integration into the global economy. “People” here includes the Indian press, which I presume comes from the upper segments themselves and so prioritize the success of the open and global market because it has benefited those they know.

Rich Countries in the Grip of Zero-Sum Thinking About Chinese Economic Growth. I tend to lean against neo-mercantilism myself. The rise of China’s economy will cause problems because of cultural-ideological differences with the West, but massive numbers of poor people is also a major problem and source of discord.

What Do I, As A Blogger, Want From A Network? No matter where Jason Goldman lands, I’m sure we can find him at ResearchBlogging.

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Knowledge is not value-free

By Razib Khan | July 20, 2010 3:52 pm

This isn’t The New Yorker, and I’m not writing twenty page essays which flesh out all the nooks and crannies of my thought. When I posted “Linguistic diversity = poverty” I did mean to provoke, make people challenge their presuppositions, and think about what they’re saying when they say something.

I think knowledge of many languages is awesome. I am weak at language acquisition myself, but, as someone with an interest in Bronze Age Near Eastern history I’m obviously invested in people having some comprehension of Sumerian and Akkadian (not to mention Hittite or ancient Egyptian). And I’m not someone who has no interest in the details of ethnographic diversity. On the contrary I’m fascinated by ethnic diversity. Like many people I enjoy reading monographs and articles on obscure groups such as Yazidis (well before our national interest in Iraq) and the Saivite Chams of Vietnam. Oh, wait, I misspoke. I actually don’t know many people who have my level of interest in obscure peoples and tribes and the breadth of human diversity. If you’re the type of person who reads monographs on Yazidis not because it pertains to your scholarly specialty, but because you’re interested in a wide range of facts and topics, and would like to have discussions with someone of similar disposition (me), contact me with your location and if I swing through town we can have coffee or something. I’m interested in meeting like minds who I can explore topics with (and here I’m not talking about someone who is a Hakka and so knows a lot about the history of the Hakka; I’m not Hakka and I know something about the Hakka and I’m not an Oirat I know something about the Oirat, and so forth). All things equal the preservation of linguistic diversity is all for the good, and not only does it enrich the lives of humanity as a whole, it enriches my life in particular because of my intellectual proclivities. But all things are not equal.

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CATEGORIZED UNDER: Anthroplogy, Culture

ScienceBlogs has good blogs

By Razib Khan | July 20, 2010 2:35 pm

I don’t have real value to add on the ScienceBlogs controversy. The only thing I want to mention is that there are some nascent superstar weblogs on that network which aren’t big names, yet, but perhaps will be. You can miss them coming in via the front page because they don’t crank out 10-15 posts per day, but they make them count when they do post. Two new weblogs which have caught my attention are Thoughtful Animals and Observations of a Nerd. There are others too if you poke around (your disciplinary focus may differ).

At this point I think for some people ScienceBlogs is not a the optimal venue. Obviously I was one of those people, as I left in late March. But for other people the reach of a prominent network still has utility. No need to throw the baby out with the bathwater. So by all means, let’s keep track of the SB Diaspora, but there are also diamonds in the rough who aren’t budging.

CATEGORIZED UNDER: Blog
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Daily Data Dump – Monday

By Razib Khan | July 19, 2010 4:05 pm

A Farewell to Scienceblogs: the Changing Science Blogging Ecosystem. Bora Zivkovic is leaving ScienceBlogs, and has a very long retrospective. The only portion I would take some issue with is the ambivalence toward the introduction of bloggers who focused mostly on science and less on politics. Bora says: “In this effort to dilute politico-religious content with science content, Sb grew, in my opinion, too big. I think 80-something blogs with 90+ bloggers is too big.” Probably it did grow too big…but I think the addition of science-focused blogs served as a critical dampener to the deteriorating reputation of the network, and more seriously the cohesion of the bloggers. But, for the reasons Bora alludes to above, politics still remained a major focus of the website because 5 bloggers focused on controversial non-science topics can easily outproduce 80 bloggers focused on science. (for the record, by the time I left I felt that the network was going in the right direction when it came to science/non-science balance)

Adventures in Very Recent Evolution. Nicholas Wade reviews the last few years of human evolutionary genomics. I assume we’ll see some stuff coming out with the addition of new populations to the HapMap in the near future.

Missense mutations in the APOL1 gene are highly associated with end stage kidney disease risk previously attributed to the MYH9 gene. This variant may be responsible for the elevated kidney failure rates of African Americans vis-a-vis other populations.

More Than Half the World’s Population Gets Insufficient Vitamin D, Says Biochemist. Remember that even if you live in a sunny clime, that doesn’t mean that you’re exposed to much sun. Consider Arab women who live in the Gulf. Therefore deficiency may be common even in regions where it once was not due to human activity outdoors.

Washington Post – Can we take the higher road? If this blogger is to be believed The Washington Post basically had a thesis, and went looking for confirmatory quotes, or, consciously distorted and misrepresented communication to transform them into confirmatory quotes. This is not totally surprising, and most of us now assume that this happens with the media all the time, making the pretense they make of objectivity something of a farce, but nice to see it unmasked so explicitly.

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Genome-wide association for newbies

By Razib Khan | July 19, 2010 3:20 pm

It looks like Genomes Unzipped has their own Mortimer Adler, with an excellent posting, How to read a genome-wide association study. For those outside the biz I suspect that #4, replication, is going to be the easiest. In the early 2000s a biologist who’d been in the business for a while cautioned about reading too much into early association results which were sexy, as the same had occurred when linkage studies were all the vogue, but replication was not to be. Goes to show that history of science can be useful on a very pragmatic level. It can give you a sense of perspective on the evanescent impact of some techniques over the long run.

CATEGORIZED UNDER: Genomics

Katz

By Razib Khan | July 16, 2010 12:09 pm

adored

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More Jews, fewer markers

By Razib Khan | July 16, 2010 11:43 am

At around the same time that the two big Jewish genetics papers came out, there was another one in BMC Genetics which I had overlooked. It’s open access so you can read the whole thing, but seems like they used 32 STR‘s as markers. Their primary finding about Jewish populations was that there was a north vs. south distinction, illustrated in this map:

1471-2156-11-48-2

Update: The main author sent me this email:

Hi, I’m the main author of the paper. Although the map (figure 2 from the paper) does depict differences in the northern vs southern assignment values for a subset of the samples in our study, it does not tell the whole story which might be helped by figure 1. The map figure is based only on subjects who had all 4 grandparents from a single country while the STRUCTURE figures (figure 1) are based on all subjects. There were two main points to the paper. 1. There is a difference, on average, between Ashkenazi and non-Ashkenazi Jewish gene pools and 2. It was only possible to detect this with a small marker panel when hypothetical ancestral or “host” populations were included in the analysis.
In the absence of representative major continental populations, the Ashkenazi and non-Ashkenazi Jewish populations were not distinguishable with the small set of markers. I believe that the dependence of ancestry assignment on which markers and which reference populations are included in an analysis has been mentioned a few times by Razib. This is relevant to the way in which certain gene mapping studies are carried out. For medical genetics studies it is important to know if subjects are from the same population or not; if they are not it can lead to false positive results. Jewish populations are heavily studied in medical research and so we wanted to demonstrate that Jewish populations from different parts of the world should not be lumped together for analysis in medical genetic studies.

Based on published mtDNA and y-chromosome studies as well as historical records we assume that the “”Southern” component of ancestry is Middle Eastern in origin and that differences between Ashkenazi and non-Ashkenazi populations are due to both genetic drift and differences between the populations that contributed to the Jewish gene pools in a given location.

CATEGORIZED UNDER: Genetics, Genomics

Linguistic diversity = poverty

By Razib Khan | July 15, 2010 4:05 pm

In yesterday’s link dump I expressed some dismissive attitudes toward the idea that loss of linguistic diversity, or more precisely the extinction of rare languages, was a major tragedy. Concretely, many languages are going extinct today as the older generation of last native speakers is dying. This is an issue that is embedded in a set of norms, values which you hold to be ends, so I thought I could be a little clearer as to what I’m getting at. I think there are real reasons outside of short-term hedonic utility why people would want to preserve their own linguistic tradition, and that is because I am no longer a total individualist when it comes to human identity. I have much more sympathy for the French who wish to preserve French against the loss of their linguistic identity against the expansion of English than I had a few years ago.

Language is history and memory. When the last speaker of English dies, or, when English is transmuted to such an extent that it is no longer English as we today understand it, our perception of the past and historical memory, our understanding of ourselves, will change. There is a qualitative difference when Shakespeare becomes as unintelligible as Beowulf. Though I tend to lean toward the proposition that all languages are a means toward the same ends, communication, I agree that there are subtleties of nuance and meaning which are lost in translation when it comes to works of literature and other aspects of collective memory. Those shadings are the sort of diversity which gives intangible aesthetic coloring to the world. A world where everyone spoke the same language would lose a great deal of color, and I acknowledge that.

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CATEGORIZED UNDER: Culture, Economics
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