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    Most of you have probably seen this stylized graphic somewhere along the away (I think it was on PBS at some point). But it's still cool....
  • three.Feasibility: analysis around how reasonable the specifications are in phrases of energy, time, charges.

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  • The video was new to me. Thanks.

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  • @ Chris

    There’s a really good reason the lagging strand has to be done in such a weird backward fashion, rather than allowing DNA to be polymerized ‘in both directions’; its proofreading. As the polymerase moves along, it sometimes incorporates an incorrect base, and usually catches itself and removes the improperly paired base. It can then try again, and almost always adds the correct letter. (this in itself if insanely awesome.)

    But a polymerase that evolved to elongate “backwards” wouldn’t have this proofreading option, because of the chemistry of the DNA backbone. Chew backwards from the growing end of a DNA strand, and you are always left with a reactive oxygen exposed to add the next base to. But from the other direction, if you chew away, you leave an unreactive phosphate group, to which no further bases can be added. So DNA can only grow in one direction!

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  • Simply amazing on two fronts. That this is happening all the time in our bodies and the fact that we can actually show how this is working. Although I always wondered why that second strand has to be put together in such an odd fashion. You’d think it’d be pretty easy to evolve helicase to do one forward and backward rather than twisting the DNA around.

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  • DNA replication leads to genetic mutation.An imperfect process means there is no perfect designer. freethoughthiphop.com

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  • I’m as godless as they come but whenever I see this clip its difficult to not ask yourself certain questions. What an amazing process.

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  • I really love the fact that I live in the early 21st century for a host of reasons. That being said, one aspect that's certainly true is that when it comes to charismatic natural variety and geography there are very few "blank spots" on the map. You can get a sense of what I'm talking...
  • Growing up I found a cache of old school world maps, 1800s versions. Large portions were simply marked ‘Unknown’. Very exciting. Especially as I went through my Tarzan reading phase. My mom later threw them out. ;–(

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  • While there are no more Darkest Africas or Shangri-Las, there are a lot of ecosystems that have not been explored yet. Some of them are very small, e.g. one recently discovered in Indonesia where unique species involved in the large inaccessible crater of a volcano. I get the National Geographic facebook page, and there’s always something new and interesting.

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  • Oddly enough I never read National Geographic but yesterday I caught the same article. Also it was interesting considering we’re discussing about the Kalash at BP that in Nuristan it has the highest ecological diversity in Afghanistan because it benefits from the South Asian monsoon moisture.

    Anyway its a great article and good to see something’s thriving in Afghanistan at least.

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  • BEHOLD, REIFICATION! In the comments below Antonio pointed me to this working paper, What Do DNA Ancestry Tests Reveal About Americans’ Identity? Examining Public Opinion on Race and Genomics. I am perhaps being a bit dull but I can't figure where its latest version is found online (I stumbled upon what looks like another working...
  • As for my experience with genetic genealogy, it has been interesting for me. As a Mexican American, all I knew about my background was some sparse family oral history that mostly concentrated on a few “exotic” European ancestors (English and German . . . maybe not exotic to white Americans, but felt special to my family when everyone else has a Spanish surname). I knew what I learned in Chicano studies classes about “la raza cosmica,” the triracial composition of colonical Mexico, but knew next to nothing about my Amerindian ancestors, and didn’t even suspect African ancestors. Growing up in southern California where many people have multiethnic ancestry, I was used to the question “what are you?” and hearing peers answer in terms of fractions. But when we have been mixing for 500 years, how could we untangle our history in such a straightforward way like US Amerindians and their blood quantum cards? I wished my background was so cut and dried. I didn’t know “what” I was, and having a white-looking appearance when others in my family looked like what American society thought Mexicans ought to look like just puzzled me. Having my DNA tested answered some questions I’ve always had about myself, and also gave me some surprises, like African and Jewish ancestry that no one in my family knew about.

    But now I have new questions that may not be answerable. I don’t know anything about the ~1/3 of my ancestors who were Amerindian, not even their tribe names. Many paper records were lost or never that complete in the first place. I hope some genome blogger somewhere will start a project specifically for Amerindian ancestry someday. Likewise I wish I knew more about the history of the African slave ancestors or Jewish ancestors that every Mexican seems to share, but are hardly talked about in official histories. This experience makes me realize that there is so much academic research that has yet to be done despite the history being less than 500 years old. But I now have a whole new understanding of my ancestral home and I feel more of a personal connection to it.

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  • My parents and I (of Mexican descent) are used to referring to ourselves as Hispanic. In Spanish we use the term “Hispano,” and take “Hispanic” as the cognate of that word (although they may have developed via different paths and not really be cognates). I grew up in Southern California hearing “Hispano” as the usual term among the community and on local TV news. Actually my parents don’t really like using the term Latino . . . they seemed to think it sounded artificial. “Hispano” to my family just means Spanish-speaking people, and so includes people of different ethnic appearances. I was told by some white and Asian Americans not to say Hispanic because some people are offended by it, but I never met someone who was actually offended. To avoid the controversy, lately I say “Latin American” because the word “Latino” by itself to me still implies people who lived in Italy 2500 years ago.

    Unfortunately, as Anthony says, many people on the street still think Hispanic/Latino is a race and don’t understand it could refer to anyone with any sort of appearance. This misconception has caused problems for me socially. Although both my parents are of Mexican descent and genetic testing says I have 1/3 Amerindian ancestry, I have light skin and everyone (whether Mexican, white, other Latin American, etc) assumes I’m white. So when people (usually white people) find out my ethnicity sometimes their reaction is negative. They may actually back away from me in shock, or suddenly get very quiet and start avoiding me, give me a hard stare, etc. I wish I looked more like a stereotypical Mexican so I could avoid these awkward situations. Even Jessica Alba, who is only half Mexican, looks more stereotypically Amerindian than me.

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  • “Hispanic/Latino” has two different definitions in the U.S.: The bureaucratic definition, and the “street” definition.

    To a college admissions officer, or a “human rights commission” DBE clerk, “hispanic” means a person with ancestry in the Americas south of the United States. It might also mean people whose ancestry is directly from Spain or Portugal, though that’s controversial, and depends on the specific agency.

    On the “street”, it means you’re likely to respond reasonably correctly if addressed in Spanish, which usually means having some visible American Indian ancestry, or at least a good tan and black hair. Until I got my 23andme results, I thought my mother’s ancestry was purely European, but when I was working outdoors a lot, the Mexican construction laborers would usually address me in Spanish first. It turns out I’m about 6% American Indian, which shocked my mother.

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  • For me the major revelation in my 23 and Me result was that I had to throw my ‘found in a crashed ufo’ theory right out the window.

    But ‘lost time traveler’ still has some utility.

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  • #23, hispanic/latino in the USA is a function of american social policy and cultural trends. it doesn’t map onto the self-definitions of people from latin america themselves. hispanic was a term promoted in 1970 by the US gov. for purposes of census classification. latino tends to be more popular on the west coast i think.

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  • Yes, my father’s concept of “pure Spanish” is a bit different than the reality, given the historical occupation of the Iberian peninsula by the Moors for centuries. Even with the inclusion of native American Ancestry to help describe and define the term “Hispanic,” I have always wondered how a definition of “Hispanic” could be very ethnically or racially descriptive. If anything, it’s more of a catch-all term for any descendent of a Spanish-speaking person who once lived in any part of the Americas except for The US, Canada, or Brazil. Though Brazil is still an enigma to me. Are they “Hispanic” too? The terms “Hispanic,” and “Latino” make little sense to me. The variation is incredibly great, (and normally includes the big three ‘races’ European, African and Asian) which is part of the reason I ran my DNA. Even if the analyses are still in their infancy, I’ve found a lot of useful data. Far more than from oral history, to be sure!

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  • Incidently – my father just got his first Nigerian born relative today

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  • a-ha, the paper’s been broadened and re-worked (for the better!). here it is:

    https://www.appam.org/conferences/fall/boston2010/sessions/downloads/4407.1.pdf.

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  • mpc says:

    this paper seems to be basing responses on skip gates’ pbs genealogy programs, which have a very definite “roots”-like agenda, and on the media that followed or imitated them. many people asked about “blurring” in that context are probably thinking negatively about slavery and jim crow, and the genealogical brick wall of slavery, not forward about mixed relationships of choice in a better world. so it reads black reactions in that very limited context but doesn’t mention that context. i and my family, who always thought we were just black, have been open to any new info and insights concerning ancestry paintings and other results. i’m exploring those connections and questions for us as the family genealogist. and there plenty of others like me doing the same. and every other afram thread on 23andMe focuses on mexed ancestry in one way or another, usually as a matter of fact or positively.

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  • ID010 – Paul Conroy

    Yes, I’m Irish, but what I’m interested in is not that swath of blue (European), but all those other bits – the how and why of it all. Like my small percentage Papuan, what is this, is this Denisovan (aka Home Erectus) or Neanderthal?

    On a more general note, I’m still trying to figure out how my number of matches (about 650 now) is in the Colonial US range and how most of them are concentrated in 5 adjoining states in the US South – and the fact that this is the same for both of my parents, even though one is Native Irish and one is Anglo-Irish. How I have about 25 or so relatives where I have 2 or more shared segments, and they came from different parents. So somehow my parents share a common ancestor back in time.

    Also, how my father happens to have relatives all over Scandinavia, Eastern Europe, South Eastern Europe (Bulgaria, Romania, Albania, Greece) and around the Carribbean (Barbados, Bahamas, Jamaica, Mexico) – even though he’s Native Irish, with only one known emigrant – to Iowa in the 1840′s?

    Also how both my parents have 100% Ashkenazi Jewish relatives, and of my top 12 closest relatives, 3 of them are mtDNA K1a1b1a – when I have no known Jewish ancestry, and indeed Jews in Ireland were historically about 1,500 people total.

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  • “pure spanish” might entail north african. so i don’t see that that’s an issue. a spanish identity with castilian at its center only crystallized during the and after the reconquest.

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  • My father swore we were pure Spanish…until the Native American and North African DNA matches couldn’t be explained…still can’t figure out how the Ashkenazi got in there either.

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  • re: mongol, etc., the fractions are low, but it doesn’t look THAT northern to me. there is a pathan with likely turkic admixture, and look at the very good balance between light blue and violet:

    the yakut turks are all violet. to further explore i could run a different “eastern biased” admixture.

    you have some violet, but that’s probably not that abnormal among tibetans (look at the japanese).

    but you’re right, your dad is the one to go too.

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  • Ian says:

    To get back to Razib’s question about what the experience has been like, as I mentioned yesterday, I think the most interesting finding had to do with my mt DNA lineage. Anything unexpected is interesting, but this also suggests that my suspicion of Slavic substratum in my maternal line seems reasonable, and also adds the possibility of some ‘steppe nomad’ ancestry. Until Razib posted that article about the Sorbs, I just didn’t expect to learn anything from my mother’s ancestry that I didn’t already suspect – they’re German, going back several hundred years. It’s fun to find hints of things that were entirely forgotten.

    My Indian ancestry is consistent with the idea that my great-grandfathers were Pathans. Not proof, but it’s one additional data point. The “east Asian” element is also not terribly surprising. I suppose the next question, which may or may not be answerable, is whether this is Turkic or Mongol, or whether it’s Tibeto-Burman. I’m hoping that Zack’s HAP project will tell me something about the female lines, but the reality of it is that I’m much more likely to find something interesting but I strongly suspect that my best bet would be to get my father to submit a sample…

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  • haven’t you never seen any (american, of course) movie where the cop asks whether the suspect is white or black or hispanic? It is pretty much racialized. Imagine if I attack someone in US and run: wouldn’t the victim tell the cops the suspect is white? even if they get my accent? (then I would be probably a russian :) )

    what is really fascinating for me is that it seems to me you americans don’t really realize how these stereotypes actually dominated your world view.

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  • doh, i meant right. i do remember getting an ID, but I couldn’t find it. haha, white! but not as much as 009.

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  • no. your right. i gave you an ID remember? i’ll out you, you’re ID03.

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  • Am I on the chart to the left?

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  • Somehow I am reminded of the first time I had an X-ray, for a bunged-up knee. I had the irrational suspicion that they would see something really unusual – that my insides were not the same as those of other people. This was inspired by a certain Twilight Zone episode that had scared the hell out of me as a kid.

    I feel the same way about a gene scan: complicated, of course, by worries about intellectual property.

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  • I know, I was just joking. It wouldn’t be him anyway, hez Bengali!

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  • @Michelle, I don’t think he’s putting himself down – sounds more like he’s clarifying that he’s not that specific “wildly attractive…Indian male”. Of course, if Razib were #29, someone would have to break the news to him that he’s adopted :)

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  • You shouldn’t put yourself down like that, Razib!

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  • one of the authors included in her cv her ethinic/racial information: hispanic…
    however, different from you i’m not no longer surprised about of this type of assertion …. it is pretty much US ideology nowadays …

    fascinating. ironic that those who (rightly) reject race as a platonic biological concept have their own platonic social ideals which they impose on the realized distribution!

    just to clarify#5, the indian male is not me :-)

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  • I’m going to venture a guess that 12 and 29 are a wildly attractive and completely anonymous white female and Indian male.

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  • id 39: Half German, half Indo-Trinidadian. Two great-grandfathers who claimed to be Pathan. One great-grandmother who was Indian Muslim of unknown origin. One great-grandmother who was of Hindu stock – one light-skinned parent (allegedly Kashmiri Brahmin), one “dark” parent.

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  • id 21: Old stock Brazilian (descend of the founders) with some more recent European mix; Western Europe. Iberian/ Mediterranean maternal lineage ( mtdna u6a3) Northern-European from the paternal side (R1b1b2a1a). Very distant Chinese component from Macau (admixture with Swiss-German branch of the family). Unknown African or Amerindian ancestry.

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  • just to make my point clear: of course you’re technically right on the hyspanic suff but the way they are perceived is as a basicallly mixed people; and this is so also thanks to their own efford since many hispanics sell themselves as such.

    Actually sometimes is even more confusing than that since many hispanics try to sell themselves as even non-us citzens though they were born and raised here in us! they refer to places that they barelly know but since they sound so sure and they also taking about such exotic lands that the american americans, either white or black, really believe them!

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  • one of the authors included in her cv her ethinic/racial information: hispanic…
    however, different from you i’m not no longer surprised about of this type of assertion …. it is pretty much US ideology nowadays …

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  • I've been taking about 'meat things' for nearly 10 years, so I was really excited by the new Michael Specter piece in The New Yorker about artificially grown meat, Test-tube Burgers. You can't read most of it online, so I want to copy this small section: I say real factories because we are all aware...
  • Vogie says: • Website

    I can see more of this line of thinking as our world gets smaller. I remember a “Bluff the Listener” from NPR’s Wait Wait about a cancelled casino thinking about turning itself into an inland Oyster/scallop/fish farm after BP decided to wax the Gulf of Mexico. Sure, it was fiction, but we’re getting to that type of thinking now. Things like Aquaculture, vertical farms and the like should be on their way not so far into the future.

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  • I’ve been wondering, if you’re growing meat in a test tube, where does the nutrient for that come from? It takes a lot of land area to feed a cow, so what is the origin of this artificial nutrient?

    On the other hand this process would allow you to make all kinds of tweaks to it you never could in nature. You could perfectly balance the vitamins and proteins and add in other beneficial elements.

    You could make combinations that would otherwise be impossible, like crossing pork with an ostrich or whale shark.

    And you could make tissue of rare or endangered animals without ethical qualms.

    And you could expand tiny little tissues, like grasshopper chops, or a t-bone mouse steak, or a mosquito shoulder roast, to a size where you actually enjoy it.

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  • I think meat factories will come first to places with high population densities and limited agricultural land, such as the East Asian countries. Also, specialty items such a crab meat and other kinds of seafood will be produced by meat factories before land animal meat. Meat factories will probably not be common here in the U.S. because land in the U.S. is still comparatively cheap and we have large ranches.

    Can fruits and vegetables be produced by this technology? If so, that’s another growth market since fruit and vegetable cultivation is labor intensive. E.g. illegal immigrant labor that will go away as Latin America develops and passes through the demographic transition (Mexico already has below replacement fertility).

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  • It’s a wonderful idea. All ethical concerns about eating meat go away right with this kind of production. Unfortunately there will be a lot of resistance. Let’s hope that in this case Resistance is futile.

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  • I recently read that subjecting these test-tube meats to electrical stimulation works in much the same way as exercise. Experiments are now being undertaken to test this. And as for the “yuk” factor, it wouldn’t’t bother me at all. At least we wouldn’t’t be killing (in the usual meaning of the word) this “meat”!

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  • I wonder if you could get around the need for absolute sterility by growing skin as well, completely enclosing the muscle. You’d still need to compensate for the lack of an immune system but you’d probably have less trouble than with naked muscle. As an added bonus it could be a source for leather and gelatin (most of which is produced from skin, rather than hooves). We might finally see armchair “moral” vegetarians being less hypocritical, i.e. condemning someone eating a steak while wearing leather shoes.

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  • So what does it taste like? It seems like the essential components for good meat are muscle and fat. I can see them culturing the muscle but can they do that for fat? And what a cow eats has a big effect on the flavor of the meat. I wonder how they do that here.

    My prediction is that unless it tastes good it’ll do not much better than the soy bean pseudo-meats.

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  • Ken says:

    1) The yuck factor can be overcome. After all, when you think about where meat, eggs, milk, cheese, etc. come from, they’re all pretty yucky.

    2) Energy use would presumably be lower because you are growing less or no bone, hooves, skin, tripe, brain, and other less-desirable organs (though of course all can be eaten, see point 1). Also the culture is not wasting energy moving, chewing, digesting, breeding, and so on.

    3) Keeping the tissue cultures sterile is a problem, but perhaps it can be solved with massive doses of antibiotics. The advantage of this is it will not change the meat from what we get from factory-raised animals….

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  • #6, i think the lack of investment is a “signal” from the market, and would support your contention. but when it comes to innovation i’m not sure that the market is that great (i think the market is great to squeeze efficiencies and improvements out of innovations though).

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  • DK says:

    My first instinctive reaction: don’t believe it. It would take a lot of solid data to convince me in the reality of “the production of cultured meat could consume roughly half the energy” thing. Not to mention cost. Why is cost not mentioned? Sure you can make meat today – but at what expense? Tissue culture is expensive. Very expensive. And there are many good reasons why it is so. Yeah, I know – improvements, progress, economy of scale, etc. Still hard to believe. E.g., there are no ways around requirement of absolute sterility. May sound minor but it is actually a major expense that does not scale very well.

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  • #4, peta gave some funding to this research. though some people high up in peta were really opposed.

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  • Soylent Green my friends!!!!!

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  • Josh Roseneau, when he's taking time off from the evolution-creation wars, is poking around his own genome. Some sage advice: On DNA Day, 23 and Me had a sale on their personal genomics service. They'd do their standard scan of your genome for free, as long as you paid for a year's worth of their...
  • Regarding the concept that: “Just as everyone in the mid- to late 20th century needed some grasp of physics to be able to think sensibly about nuclear energy, nuclear war, and a host of related issues.” — it is important to point out that this didn’t happen if by “everyone” the author meant the US population beyond those already interested in science. We are still seeing the effects today, from how we’re dealing with the Japanese nuclear crisis to how we are addressing alternative energy (an area in which hope seems to play a much bigger role than math). Perhaps it will be different with biology and DNA, but its hard to picture this technology being anything less than magic to most of the folks wandering around the big box stores.

    James Aach
    Author – “Rad Decision”

    The novel “Rad Decision” culminates in an event very similar to the Japanese tragedy. (Same reactor type, same initial problem.) The author has worked in the US nuclear industry for 25 years. The novel is free online at the moment at http://RadDecision.blogspot.com . (No adverts, nobody makes money off this site.)

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  • I've been taking about 'meat things' for nearly 10 years, so I was really excited by the new Michael Specter piece in The New Yorker about artificially grown meat, Test-tube Burgers. You can't read most of it online, so I want to copy this small section: I say real factories because we are all aware...
  • Last I heard the Netherlands still produced a substantial amount of meat and dairy, and as a result was overwhelmed in shit it had no idea what to do with. Shit is valuable for those growing crops, but the Netherlands doesn’t have enough cropland to the amount of shit its livestock produce.

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  • This is actually a very good idea, even if it would take some getting used to. It would allow land currently used to feed animals to be diverted to other uses, such as growing food for people.

    50 years hence, we shall escape the absurdity of growing a whole chicken in order to eat the breast or wing, by growing these parts separately under a suitable medium. -Winston Churchill

    He was a bit off, but the argument is still good.

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  • Josh Roseneau, when he's taking time off from the evolution-creation wars, is poking around his own genome. Some sage advice: On DNA Day, 23 and Me had a sale on their personal genomics service. They'd do their standard scan of your genome for free, as long as you paid for a year's worth of their...
  • People learn things that have practical relevance in their lives.

    For example, many reasonably sophisticated high school and college kids have a surprisingly broad working knowledge of the purpose, name variants and characteristic side effects of most of the couple dozen most commonly prescribed drugs and have a fairly good system in place for quickly figuring out what is relevant about any new one that they encounter.

    Indeed, their knowledge is in some ways more useful than the official propoganda that appears when drugs are dispensed by a pharmacy, because it incorporates more realistic probabilities and severities of side effects rather than a throw in the kitchen sink approach driven by FDA regulation and product liability laws. Yet, some of that information is only really relevant when a decision to start taking a prescription in the first place is made, not in day to day usage after the risks and benefits of the drug have been weighed and a decision made. And, other risks are either described in a way that is hard for someone who isn’t quite functionally literate to understand.

    The folk wisdom focuses on the parts of that information that are most pertinent. In contrast, someone without that folk knowledge who isn’t quite functionally literate can easily get bogged down in the verbosity and difficult vocabulary of a prescription drug label and have trouble intelligently winnowing it down to what they really need to know.

    I suspect that we are going to see similar kinds of folk wisdom develop with personal genomics.

    A few gene variants will become notorious and will probably develop their own slang descriptions because they are fairly common and have practical or short to medium term consequences that matter. Some of the likely early candidates are gene variants associated with language learning disabilities, with resiliance in the face of traumic events, with novelty seeking, and with high propensities to have unstable marriages. Don’t be surprised if the word “Fox” (for the FOXP gene) develops a secondary meaning that corresponds to dylexic rather than to pretty or wiley. These will be the roofies and ambiens of genomics. Revealing these facts or keeping them secret may be have some of the character in the twenty-teens and twenty-twenties that coming out or not coming out as gay has in the last couple of decades.

    I suspect that folk wisdom will develop some other folk term for the elements of a genome that are individually uncommon and less immediately relevant, but have some kind of empirically established relationship to something that people care about but that doesn’t have high salience socially. The APOE4 gene in the original post, the genes associated with breast cancer risk, high blood pressure or LDL accumulation risk genes, and who knows what else may fit in the category. I imagine them developing a name like “zits” that conceptualizes them as little blemishes that different people have in differering amounts, which one wishes one didn’t have but doesn’t lose sleep over.

    Then, there will be large parts of genomics that will not enter folk wisdom at all as content specific knowledge. But, some folk wisdom may develop regarding how to approach these parts of genome data when you receive it. Googling a gene variant that you or someone you know has will probably become as instinctive a reaction as googling a propective blind date, new business contact or new hire. Mostly, these results will end up being “ho-hums.”

    But a few of these results “oh shit” tragedies on a par with a diagnosis of an early stage of something like A.L.S. or lupus or M.S. or asymptomatic cancer that has already spread that is the stuff of diadactic after school TV specials, self help books, and sleep inducing oscar wannabe movies. There are going to be some small number of people who discover, for example, that they have an extremely high chance of developing some incurable disease with a 50% chance of killing you from sudden heart failure by the time you turn fifty, or are at a very high risk on very early onset Alzheimers, or have strongly predisposed to not yet symptomatic schitzophrenia or bipolar disorder. It will have all the psychological horror of diagnosis with a dreaded chronic degenerative dreaded disease without the immediate physical discomfort. FWIW, Western culture has had Greek tragedies that have explored the consequences of having fate dump a load on you like this for a few thousand years already, so it won’t take our society much innovation to develop philosophical approaches to dealing with them.

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  • The Pith: Biological complexity may be a particular evolutionary path taken due to to random acts of nature, not because there is a selective advantage to complexity. The title above basically describes the message of evolutionary biologist Mike Lynch from what I can gather. His basic argument is outlined in long form in The Origins...
  • Anonymous • Disclaimer says: • Website

    If you guys think there’s nothing new in the paper, then you clearly misunderstood it. For one thing, many biochemists are seldom even trained in population genetics, let alone applying it to their work, so the blend of biochemistry and population genetics is already a quite novel thing, even if it does seem obvious.

    The key point of the paper is that relaxed selection associated with reduction in effective population size (eg in cumbersome stupid things like animals…) is consistently associated with an increase in complexity of protein interactions (even at finer levels than just unicellular vs. multicellular), and one mechanism that could explain that is that reduction in selective efficiency allows for more biochemically unstable and less efficient proteins to be tolerated. A major contributor to protein instability is exposure of the polar backbone, so more exposed proteins tend to be subject to more errors just because the optimal stage for the organism doesn’t have as much of thermodynamic edge over suboptimal foldings (given the same sequence). Thus, and their data show that, species with lower effective population sizes have more poorly wrapped proteins, on average.

    This ties in with interaction networks in that exposed backbone sites have an affinity for recruiting secondary proteins for greater stability. After time, these proteins become dependent on each other as more deleterious mutations are now compensated for and therefore allowed (see “presuppression”, eg Stoltzfus 1999 J Mol Evol) , and more components are required for a system of roughly the same functionality/adaptive value. Eventually, some of these interactions may be exapted to something useful, but that’s not *why* they stuck together initially.

    That’s a pretty new model. Haven’t come across anything similar anyway, and I’m quite obsessed with non-adaptive evolution so I’d probably have heard of it by now if it’s so “common knowledge”. Clearly the paper wasn’t particularly well-read by some critics…

    Oh, and I blogged about it here, FYI: http://skepticwonder.fieldofscience.com/2011/05/sticky-proteins-complexity-drama-and.html

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  • [...] Gene Expression blog at Discover magazine looks at the protein errors and biological complexity study featured here yesterday. Some [...]

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  • But figuring out how proteins work one by one is messy and boring and would require “systems biologists” to spend time in actual labs instead of sitting at computers drinking Coke, writing PERL scripts and inventing new words for old concepts

    lol. i did get that sense. if u want to write a theoretical paper write it :-) doesn’t seem like that a letter to nature gave them enough to really get anything out the synthesis.

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  • DK says:

    I would like to just second everything miko wrote. The paper is a weak illustration of what everyone already knew long ago anyway. “The complex protein architectures and interactions
    essential to the genesis of phenotypic diversity may initially emerge by non-adaptive mechanisms”. really? Jeez, what news.

    And to call yeast two hybrid and co-IPs (as far as high throughput is concerned) a freaking disaster is a huge understatement.

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  • miko says:

    Yes,we are exactly in the Windows kernel situation. But I don’t think it’s news that the robust properties of networks (and chaperones, the UPR, and pretty much all cellular quality-monitoring systems) buffer variation, or that most variation is deleterious when unmasked. This was Susan Lindquist’s point with hsp90, and Waddington’s long before. These guys seem to have just put it in the new(ish) network jargon of systems biology.

    I haven’t looked at the data sources in their paper, but most protein-protein interaction databases are a freaking disaster. The false positive rates for the common methods are astounding, particularly when you are measuring interactions for multicellular eukaryotes (where the interaction network of every tissue, cell type, organelle, and subcellular compartment can be distinct) in some heterologous system like yeast two-hybrid. Co-IPs are even worse. Lots of proteins stick to each other under a given set of conditions, it does not mean they have biologically meaningful “interactions” in normal, living cells. But figuring out how proteins work one by one is messy and boring and would require “systems biologists” to spend time in actual labs instead of sitting at computers drinking Coke, writing PERL scripts and inventing new words for old concepts.

    OMG. I just skimmed the paper…I think even their interaction data is “theoretical,” based on PDB structures to predict the relative likelihood of homologous proteins participating in protein-protein interactions. It seems like a very complicated, fraught, and weak way to make a point that has been already demonstrated using, like, living organisms.

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  • Biological complexity may be a particular evolutionary path taken due to to random acts of nature, not because there is a selective advantage to complexity.

    Sounds like MS Windows.

    And also Gould’s spandrels and exaption.

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  • John Hawks and Jerry Coyne are mooting the 'species concepts' debate, with particular focus on recent human origins (specifically, the relationship of modern humans to Neandertals and Denisovans). Coyne, who coauthored the book Speciation and remains preoccupied with the issue in his academic work, knows of what he speaks. And of course he wouldn't think...
  • #3 Bob: the legal definition of species under the ESA for vertebrates doesn’t match a biological definition. That doesn’t make the legal definition wrong: preserving the existence and genetic diversity of subspecies or even less-isolated subcategories has biological value, even if biologists might not like how “their” word is being used by lawyers.

    In any event, it’s only for vertebrates, not for invertebrates or plants.

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  • As biologist Joan Roughgarden puts it, Nature abhors a category. In a universe of multitudinous patterns and structures, working from fundamental particles upwards, our abstractions cannot be definitive “all the way down” but they can usefully pick up aspects of reality, provided we do not expect too much of them. (Which natural law theory generally does, for example. And racism really does.)

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  • Even animals can get weird. What do we make of two animals that could potentially interbreed, but if left alone in the wild, would not?

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  • I agree with others that you’ve balanced this well. I think a lot of people who think about this subject intelligently come down to having to balance pretty much the same fixed points you mention: a species is not normally just arbitrary; but then again there are reasons to say that species are not perfectly well defined. Thanks.

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  • Just a note that Zeno’s Paradox is not a paradox at all. Zeno was trying to prove (by contradiction) that nothing moved. His paradox assumes that with a converging series in length you cannot have a converging series in time. This is clearly false: Both series must agree so for Zeno then the series in length was also not converging (i.e., infinite), and movement is an illusion. The reality of course is that both series converge, hence no paradox.

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  • Look at Oak trees of various kinds in North America for a failure of the species idea to match up the genetics and morphology of “species”. It is a total smash. Gene frequencies do not match up well with what plants look like, and gene “transfer happens all over the “species” map and looks quite different to a morphological map.

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  • Thanks for the reference to Hawkes and Coyne.

    As a retired environmental engineer/scientist, I have long followed the debate about species. It is very confusing indeed. The classic Dobzhansky/Mayer definition (breeding population) works very well for animals. It is largely irrelevant for Bacteria/Archaea, which are mostly clones with occasional DNA transfer.

    But what is most interesting is that conservationists, especially those engaged in species preservation, will have none of the Dobzhansky/Mayer definition. Instead, they rely entirely on morphology, and often trivial bits of morphology at that. E.g., the Florida panthers bent tail. This makes all sorts of decisions required by the Endangered Species Act to be unavoidably arbitrary and capricious. So much for science-based policy.

    Most working biologists also depend on morphology over breeding, in large part because applying the Dobzhansky/Mayer theory to long-lived animals is all but impossible. Of course, if your studies cover a restricted geographic region, morphology is a very good species criterion.

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  • Nicely done. I, too, liked the analogy to physicality.

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  • I like the “physical objects” analogy. “Species” remains a mirage of a term for many. For that matter even “evolution” is a far more ambiguous, amorphous term than some would imply. Their lack of precision doesn’t take away from their scientific applicability, but it does lead to very prolonged, nuanced (and maybe unresolvable) debates/discussion.

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  • This morning I received an email from the communication director of the American Anthropology Association. The contents are on the web: AAA Responds to Public Controversy Over Science in Anthropology Some recent media coverage, including an article in the New York Times, has portrayed anthropology as divided between those who practice it as a science...
  • Anonymous • Disclaimer says:

    It is well known that when foreign Arabs with obvious black admixture visited the American South there was often a debate as to whether they were subject to segregation, illustrating the tensions between social norms (which would have coded them as black), bureaucratic function (which coded them as non-black usually), and biological reality (where they were an amalgam of a minor black African component with a dominant white Arab component).

    Do you have any citations for this?

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  • ‘I often use “human” or “humankind” where earlier norms would be to use “man” or “mankind.” My main rationale is I don’t want annoying comments objecting to the term. The concept which I’m pointing to is the same no matter the pointer, and so I don’t mind changing it to facilitate my intent to communicate clearly and without undue extraneous baggage.’

    I can’t believe that you have *caved* to the forces of *leftist political correctness* by using this so-called “inclusive language”!

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  • there is no real coherent argument that “race” as a biological constuct actually exists or – indeed – even makes any sense. At least as it relates to humans.

    Biologically, there is nothing particularly special or even unique to H.sapiens in comparison to other species.

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  • When they say anthropology is holistic, are they saying they reject reductionism, or do they just mean they look at the big picture?

    @ french reader, you’re doing a hell of a lot better at English than a lot of the people here for whom it is their first language. Thanks.

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  • “i don’t usually use the word for that reason. but the way that the anthropologists refute “race,” they basically refute population too.”

    Understood. Some of them talk this way and they are wrong, (or right for the wrong reason), and I think I agree with you on that. I think in some ways vineviz and I are more interested in the details of this than the original subject matter of the article, (those anti-scientific anthropologists) concerning which I think we both agree with you. I’d point to this paragraph in your blog as the point I was interested to talk more about:-

    “All that said, the word “race” is fraught with a lot of historical baggage. Therefore to study population wide variation you need to focus on “fine-scale population structure” and what not. This trend would be something of interest for cultural anthropologists of science to study. Race is just a word. Even a term as widely accept as species exhibits a fair amount of flexibility on the margins. But the underlying biological patterns, and the instrumental utility of those patterns, can not be denied.”

    I guess my point is yes, race is just a word, but like you say it is a word with baggage. You clearly see the point: Words, though just words, can have heavy baggage and we can not just tell the world to use them a new way. I do not see an enormous gap between my “ex cathedra” statements and yours.

    Re. “i don’t react well to ex cathedra argumentation styles from readers.”

    No problem. Who does? But anyway, stating some apparent facts is a quick way to write on the internet. Sorry if it grated, but I don’t think you’d like me to write through a whole chain of reasoning which contained lots of over-obvious stuff either? Maybe I’ve mis-estimated what you meant though, because my main assertions apparently agree with what is already between the lines of your paragraph I quote above?

    Cheers

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  • [...] my post below I quoted my interview L. L. Cavalli-Sforza because I think it gets to the heart of some confusions [...]

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  • The statement lauds a fusion of “humanistic and scientific perspectives.” But is the line dividing “scientific” and “humanistic” perspectives the same line dividing the social, biological and physical sciences from the humanities? What would an example be of a “humanistic perspective” not informed by social science? And where it says “the Executive Board recognizes and endorses the crucial place of the scientific method in much anthropological research,” that seems to imply that there are some areas of anthropological research where “the” scientific method is not crucial. What would they be?

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  • mmm, i’m not a scientist but my father is jewish from algeria and my mom is from the east of france, i have indeed inherited my dad’s middle eastern last name and when meeting people i have to deal with surprise and disbelief, noone french or arab considers me anything other than white, same for my sister; my brother has less to explain but perharps it’s because he has curly black hair (from my dad) and high cheekbones (from my mom), so maybe he looks more exotic.

    ex:
    * at a job interview being asked if i changed my last name because i converted to islam.

    everytime i meet people i always have the same conversation where people ask more or less tactfully what my origins are, and yeah even after learning my name people still consider me a white person, in fact it’s happened to me several times that arabs thought i was making fun of them… -_-

    sorry if i made any mistakes, english is not my first language.

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  • @Razib you don’t know what you’re talking about.
    I think you probably just didn’t understand what I wrote.

    Which is fine: not everyone can understand everything. Or maybe I wasn’t clear (though others seemed to catch my meaning just fine).

    But, please: why bother to reply to my comment at all if you are not even going to address it? A disturbingly high proportion of your comments are ad hominem attacks. I’m embarrased for you. If you can’t think of anything to say, then just don’t say anything.

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  • vineviz, i just looked you up. you have to know your comment doesn’t make sense, you’re into genetic genealogy (and you should know PCA too)….

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  • Race has a clear meaning in English which goes beyond population specifically because it can not easily be recovered without keeping something of the Platonistic “luggage” you refer to.

    i don’t usually use the word for that reason. but the way that the anthropologists refute “race,” they basically refute population too.

    i’m not respond to most of your arguments because you make a lot of assertions in each comment which i disagree with, fwiw. i don’t react well to ex cathedra argumentation styles from readers.

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  • “people may need to come up with a word.”

    Why not use the normal words of non-human biology like population?

    Race has a clear meaning in English which goes beyond population specifically because it can not easily be recovered without keeping something of the Platonistic “luggage” you refer to.

    To strain and try to translate from normal English into biologically meaningful terms, “race” is a word which implies the existence of an inherently special level of sub-speciation that is more distinct and meaningful than all other levels. Post Darwin however, biology does not assume anything about how many levels of valid categorization of populations can and should be made: parts of Reykyavik are just as valid “populations” (if the DNA or other evidence says so) as “Alpine” and “Mediterranean”.

    I think you also mentioned that there is a parallel problem even with the word species. In real biology the word can be fuzzy because we know since Darwin that what the word refers to really is a “fuzzy” category. But the old idea that a species is something fixed in nature is hard to let go of. A lot of energy gets wasted on arguments about what the real and proper definition should be when in fact it hardly matters any more.

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  • “When was the last time you were flipping through channels and saw a kickass documentary about Derrida instead of about Lucy or Neandertals or human genetics?… Get to work! ”

    One more thought. There’s a growing bunch of anthropologists, of cultural, not scientific extraction, who work in the government or the industry and are salient in the media, without using Lucy, Neanderthals, Bushmen or chimps as proxies. These are applied anthropologists such as Genevieve Bell, head of user experience at Intel, Montgomery MacFate, head of the Human Terrain program in U.S. Army, Gillian Tett, assistant editor of the Financial Times and others. These scholars/practitioners (especially MacFate) are controversial with the AAA because they violate another taboo, namely on “selling” humanistic knowledge, not the taboo on doing science, which they don’t, but they also defy the tendency to treat anthropologists as only useful for society as advocates for and students of human evolution.

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  • In other words, it may be possible for any particular phenotypic trait or genetic locus to be resolved into a strictly cladistic system but humans, being an amalgam of such traits and locii, defy such resoution.

    you don’t know what you’re talking about.

    re: miko #1, because it is more than about bio anthropology for me. the study of human cultural variation is important.

    We don’t have another word handy to refer to biological “race”, but we should realize when we use that word a lot of people will misunderstand us, willfully or not.

    people may need to come up with a word. people willfully have a dumb platonic model in mind, but most people also still don’t understand the concept that acceleration due to gravity is constant for two objects of different mass when take away fraction. but race-is-a-myth proponents always promote confusion and obscurantism at the reality that there are non-trivial elements of variation. so, in the sickle cell example above they refute the platonic idea, but do not replace with an explicit probabilistic framework. that’s the problem.

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  • “Scientific anthropology is better funded, more high profile, and certainly has more political and popular cache outside the academy than humanistic navel gazing, which as we know induces nothing but incomprehension and/or eye-rolling outside its natural habitat.”

    I agree with your general point. But at Stanford, when I was there, the situation was quite the opposite from the one you describe. Cultural anthropologists/post-processual archaeologists were stars in their fields – vocal, prolific and controversial -, while anthroscientists were survivals from the 1970s-1980s trying to sell primitive trees, graphs, charts and site plans to funding agencies and complaining about “intellectual honesty.” HumBio and genetics folks were a bit more sophisticated and glamorous, but scientific anthropologists were often dowdy. At the end of the day, Joanna Mountain, who I liked, worked with and learned from, didn’t get tenure, while Akhil Gupta, who wasn’t even an anthropologist but a politically active engineer earlier did. If cultural anthropologists are engaged in power politics, as you claim, then they will find ways to put out “Derrida”, instead of “Lucy”, on prime time. If we still have Lucy there, then it’s likely that cultural anthropologists are not as good at politics as they are painted. So, the picture is, as always, messy and complicated. It needs an ethnography.

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  • 1. Anthropologists: Why does anyone care about the power politics within the AAA (including members of the AAA)? Perhaps a certain type of cultural anthropology is tacitly favored, so what? Scientific anthropology is better funded, more high profile, and certainly has more political and popular cache outside the academy than humanistic navel gazing, which as we know induces nothing but incomprehension and/or eye-rolling outside its natural habitat. When was the last time you were flipping through channels and saw a kickass documentary about Derrida instead of about Lucy or Neandertals or human genetics? Are any biological anthropologists having trouble getting work published because you are realist empiricists? Ever gotten a grant proposal returned because you failed to consider the implications of Foucault on your method for extracting DNA from bones? What a bunch of babies. Get to work! Or, if you really like dithering about who likes who’s seminar, start your own professional society that fails to sufficiently stroke non-scientific approaches to the social sciences in its mission statement.

    2. Race: Obviously people can be sorted into groups based on any set of criteria one chooses, whether “socially constructed” or based in biological traits. Which are “real” depends on what you’re talking about. Clearly, skin color is a “real” operational category in many societies, and whether or not it correlates with “real” genetic relationships is irrelevant. The problem arises because the term “race” is used fuzzily and to refer to different things, or worse to imply equivalence between different types of categories. We don’t have another word handy to refer to biological “race”, but we should realize when we use that word a lot of people will misunderstand us, willfully or not.

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  • “It’s a bit of a strawman, in that people who argue that race is entirely a social construct don’t actually deny that human genetic variation exists. What they deny is that there are non-arbitrary and mutually exclusive categories into which humans can be resolved…So while the study of human genetic variation does, indeed, have “instrumental utility” the concept of biological races is, itself, an archaic relic.”

    Yes and no. I doubt that “strawmen” of any nature exist. Cultural anthropologists not only deny that there are non-arbitrary exclusive biological categories into which humans can be sorted, they also deny (or refuse to explore) that long-term cultural practices such as “polygyny” or “monogamy” went into the evolution of some human racial characteristics such as skin color (the darkest in polygyny-rich agricultural Africa, lightest in highly monogamous northern Europe). If some fraction of human skin color variation is attributable to social (and sexual) selection (in addition to nutrition and environment), then whatever “races” are out there cannot be deemed as simple icing on an essentially uniform human cake. They become somewhat non-arbitrary (because stemming from a long history of purposeful maintenance of a concrete cultural practice) and rather mutually exclusive, albeit not immutable and cultural in origin.

    I guess you could tell the story in this way: Neutral population-genetic reality of human intergroup differences was first clouded by popular Western ignorance thereof and now revealed and accepted by cultural and biological anthropologists alike. But what’s interesting is that we continue to observe transcultural/transracial behaviors across both academic and popular circles. Razib referred to Islamic converts. I studied Europeans imitating American Indians (and African Maasai and Australian aborigines, to a lesser degree). Turnbull went native among the Pygmies. Reichel Dolmatoff did the same thing in South America. Boas was caught imitating Kwakiutl dancers. The list of examples is endless. People constantly adopt other people’s “nature” into some kind of new cultural package that is historically durable and has modified biological consequences (as in the case of offspring of German-Amerindian unions originally driven by the passion of one parent for the culture/race of the other or, again, extremes of skin color). I think modern discussions of “race” on both biological and cultural sides have unique behavioral correlates: they are like litmus test for some deeply-seated cultural practices. They are not just rational conversations determining whether “race” is real or not.

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  • Isn’t it ironic that the humanists now argue that we should read the statement completely uncritically? I mean, ignore the selective deletion of several instances of the word “science” — that is completely uninformative about the power relations in the association!

    Pay no attention to the cdesign proponentists!

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  • As far as I can see, there is no real coherent argument that “race” as a biological constuct actually exists or – indeed – even makes any sense. At least as it relates to humans.

    Razib’s final concession (that genetic variation exists) is revealing because I think that’s as far as the argument can really be taken. It’s a bit of a strawman, in that people who argue that race is entirely a social construct don’t actually deny that human genetic variation exists. What they deny is that there are non-arbitrary and mutually exclusive categories into which humans can be resolved. This is, I think, the point being made by the “Race by Fingerprints” etc. rhetorical device cited earlier.

    In other words, it may be possible for any particular phenotypic trait or genetic locus to be resolved into a strictly cladistic system but humans, being an amalgam of such traits and locii, defy such resoution. So while the study of human genetic variation does, indeed, have “instrumental utility” the concept of biological races is, itself, an arcahic relic.

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  • Why don’t we just say “breeds”, as in Kipling’s “lesser breeds without the law”? People say that he was alluding to Germans, a thought that can cheer us all up.

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  • “interesting, god has come to define and tell us everything. he goes by the name andrew lancaster, and his opinion is the writ itself!”

    Hmm. I did not just proclaim an opinion but also explained why. Have you ever anyone use the word “race” in a way which would fit sub-populations of Reykyavik?

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  • In fact, they reject the naive realism at the heart of science as it is practiced.

    I am not sure that science can be defined by adherence to naive realism, it is more the realm of physicalism and it usually stems from “physics envy”.
    More than only one epistemological posture can be deemed scientific and they surely need more than 1 or 2 dimensions to be described.
    My point is that objects and concepts are mental constructions (not necessarily social) and are only maps and models of reality.
    The fact that physical models are pretty stable and persistent does not mean that they are the only valid tools to grasp reality (re another comment of mine about latent variables), consistency and predictability about yet unrealized experiments are better criteria for the scientific method, the only parts which need to be “physical” are the data collection procedures.

    As for the politically driven rejection of naive realism it could be called an instance of “naive emotionalism”, LOL…

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  • english and saxons. everyone else a wog. you read me right. it was stupid. and franklin was a brilliant man. though i don’t know his personal correspondence to know how seriously he took this dumb idea.

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  • Just a minor point: “Benjamin Franklin stupidly contended that only the English and Saxons were true whites, with all other Europeans, including Nordics, being swarthy.” Obviously this is ignorance, no question. Yet, it seems to me at the time Nordics we still a kind of second class Europeans (most maps from that time describe them as nordic tribes). But what about the French and Italians, especially the latter? To me understanding, Italy and its Rinascimento, were pivotal in the development of the Modern European identity while Germanic and English people were very behind in the process.

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  • The word “race” quite obviously does not mean just any type inter-breeding sub-population.

    interesting, god has come to define and tell us everything. he goes by the name andrew lancaster, and his opinion is the writ itself!

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  • The word “race” quite obviously does not mean just any type inter-breeding sub-population. Of course there are species whose sub-populations break up into neat races or sub-species, but I do not see anything in human genetics tellings us humanity is one of them. Over on the Dienekes blog I’ve remarked a few times, in response to Dienekes’ desire to resuscitate the word race, that his self-proclaimed favorite example of how science proves that races are real was actually a study of populations WITHIN Reykyavik. But surely no English speaker has ever used the word “race” in a way which is even consistent with referring to such small populations. To re-define this word like this seems a useless exercise with no scientific motive.

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  • [...] To study humankind, AAA responds | Gene Expression (blogs.discovermagazine.com) [...]

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  • “also, many muslims who are anti-western align with this tendency. but they play a double game often, as white muslims (arabs, turks, iranians) are often rather racist as non-white muslims. compare how south asians are treated in the UK to the persian gulf.”

    It does seem, at least to my perception, in the US/Canada at least, the idea of Muslims as non-whites is an identity given to them by the public and not self-imposed (ie. black, S.Asian or S.European Muslims see themselves as the same religion but would probably not identify think of themselves as the same race, other than they’re seen as non-white), rather than Hispanic, which is more self-identified.

    I wonder how much of seeing all Muslims as non-white by default (even including white converts) first emerged? Did it happen as soon as Muslims starting having a presence in the West, or was it partly triggered (or at least influenced) after 9-11 when the opposition of the “Muslim world” to the “Western” became more salient?

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  • btw, some of this might be a particular oppositional aspect of islamic culture and religion in relation to non-muslims. as i have observed before, chinese who convert to islam become hui in china, and are no longer han. in contrast, chinese who adhere to other world religions remain han. in southeast asia chinese muslims who are from non-hui backgrounds retain some separate identity, but quickly in ensuing generations assimilate to a native identity (e.g., many malays have chinese ancestry). though in thailand the same happens when chinese intermarry with thais and become theravada buddhist…but my impression is that the boundaries and categories are more fluid and less crisp.

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  • also, many muslims who are anti-western align with this tendency. but they play a double game often, as white muslims (arabs, turks, iranians) are often rather racist as non-white muslims. compare how south asians are treated in the UK to the persian gulf.

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