Open Thread, 9/23/2018

Curious how many readers recognize the reference on the shirt to the left? You probably know if you’ve read The Double Helix. On the DNAGeeks website now.

Salon is stiffing freelancers of $150. I think this is more a commentary on the market for freelancers than Salon‘s always tenuous finances. The market-clearing price for a lot of web journalism/commentary is pretty low. Salon does this because it knows freelancers will tolerate and accept this behavior more often than not.

This long article from Huffington Post (and boosted on the editor in chief’s Twitter), Everything You Know About Obesity Is Wrong, is being widely shared on Facebook (I haven’t seen it much on my Twitter, but that’s because I follow mostly scientists).

Of course it’s really really light on the science of nutrition. Or should I say “science”? Because the truth is that nutrition science has a lot of problems, so there is space to criticize it. But that being said, this piece is being shared by people who seem to think that there is a conspiracy make it seem like being obese is unhealthy. But most of the article is about how cruel people are to the obese, especially medical professionals. There’s really little evidence presented that being obese doesn’t cause issues with morbidity and mortality. Quotes like this are representative: “But individuals are not averages: Studies have found that anywhere from one-third to three-quarters of people classified as obese are metabolically healthy.” That’s a huge interval. Why?

Ultimately the article should have been titled Everyone Is Cruel to Obese People and That is Wrong and Ineffective.

If you want some real nutrition science, What I learned about weight loss from spending a day inside a metabolic chamber.

I bought Early China: A Social and Cultural History. A lot of archaeology. But that’s what you get! I figure I should know more about Zhou China though. I think next I’ll try to read up on Neo-Confucianism, a topic I’ve been lax in because of my leaning toward “Han learning.”

Highly recommend Viet Nam: A History from Earliest Times to the Present. Most of the book does not deal with the Vietnam War. One curious thing I learned: the Vietnamese identity in the period around 0 AD was strong influenced by the influx of Yue people from southern China, as they imparted their culture and statecraft on the proto-Vietic populace. Of course on top of that came later Chinese migration, which resulted in the emergence of Vietnamese as a tonal language.

Though you’ll probably really want Phở as you read the book….

Also, I knew this, but Viet Nam makes it clear in all the gory details that the Austronesian Cham people of central and southern coastal Vietnam were undergoing the same shift to Islam from Hinduism that was occurring further south in the period after 1500. It seems rather clear that the emergence of a Cham sultanate on the model of Mataram or Johor never occurred because the Vietnamese conquered the Cham kingdom, and then assimilated or exterminated most of the natives. Many Cham fled to Cambodia, where they form the Muslim minority of that nation.

But, a small minority of Cham remain in Vietnam, and amongst these are a substantial Saivite Hindu community. It seems entirely possible that if the Cham had retained their independence as a nationality one would have seen total Islamicization, as occurred among the Malays. As is this, this process was retarded by Vietnamese conquest, and so some Chams still remain Hindu (the same process applies to the Philippines, where the native population was influenced by Hinduism first, and was in the first stages of Islamicization, when the Spaniards conquered the archipelago).

Indonesia: Peoples and Histories is worth a quick read. Not as dense and informative as Viet Nam: A History from Earliest Times to the Present.

Change in sexual signaling traits outruns morphological divergence in a recent avian radiation across an ecological gradient. Not a surprising result I guess.

This AJ+ video about “white feminism” is getting a lot of attention. Mostly because AJ+ is backed and owned by a conservative Salafist regime which runs an oligarchic state on the backs of dark-skinned South Asian indentured labor. I’ve spent a week in Qatar at a really nice hotel. I’ve never encountered service staff as solicitous and courteous in the United States. At some point I may write about how certain organizations and institutions use political movements as instruments…but I always feel this is so obvious.

Digging Into the Genetics of Drug Targets. Derek Lowe, the science blogger who has been blogging for the longest time. This is why it’s worth reading him.

Next week on The Insight we’ll be talking about Indian genetics, again. Partly in anticipation of the ancient DNA paper, which should drop any day now (I have no inside information). Question suggestions welcome.

Quantifying Heterogeneity in the Genetic Architecture of Complex Traits Between Ethnically Diverse Groups using Random Effect Interaction Models

Evolution and Selection of Quantitative Traits has finally been published in book form. It’s a good value on a pound-for-pound basis….

Individual selection leads to collective efficiency through coordination. The last sentence of the abstract is key: “This finding reveals a general principle that could play a role in nature to smoothen the transition to efficient collective behaviors in all games with multiple equilibriums.” You need to figure out ways to get to cooperation.

Late Pleistocene human genome suggests a local origin for the first farmers of central Anatolia. It seems within the Near East farming spread mostly through cultural diffusion. My suspicion is that that is due to the fact that it didn’t provide that huge of a demographic boost in its primitive form. Once the various farmer groups perfect their toolkit, they expanded into areas dominated by hunter-gatherers, not other farmers.

The Austronesian expansion actually makes me consider the possibility that we may never understand why the modern humans in the Near East ~55,000 years ago “broke out” and absorbed all the other hominin groups.

Cornell Just Found Brian Wansink Guilty Of Scientific Misconduct And He Has Resigned. If Wansink hadn’t become famous through his self-promotion, he could have continued on with his career. What he’s guilty of lots of people are guilty of, and the media and the public are complicit by demanding sexy and practical results.

Detecting archaic introgression using an unadmixed outgroup.

How Connected Is Your Community to Everywhere Else in America? This is incredible data journalism.

Rediscovery of red wolf ghost alleles in a canid population along the American Gulf Coast.

Large-scale investigation of the reasons why potentially important genes are ignored.

Polygenicity of complex traits is explained by negative selection.

The effects of demography and genetics on the neutral distribution of quantitative traits.

When I’m working sometimes I listen to the Men of the West YouTube channel. It’s run by a Tolkienist who does some serious work in this area.

28 thoughts on “Open Thread, 9/23/2018

  1. This is kind of outside my area of competence, but I’ve tried to follow the results on ancient human genetics, and there is something I’ve come across that I wanted to ask about. And since its an open thread, I thought I’d try here:

    Hajdinjak, Fu et al published “Reconstructing the genetic history of the Neanderthals” in march 2018, and in it they remarked that the gene flow, or at least most of it, into early modern humans appear to have originated from one Neanderthal population. Which we have not so far identified from DNA. Apparently they diverged from the neanderthals we have DNA from between 90 – 150 kyears ago. They hedge it with expressions like “one or more populations” and “most of the gene flow” but as far as I can understand the paper the results seem to indicate one population.

    How is that possible? We seem to have overlapped with Neanderthal populations in the middle east for 10 000 years, Europe 5 000 years and Asia at least 10 000 years, maybe more. And yet there is no indication we exchanged genes with these populations?

    Surely this would indicate that the barriers to gene flow were at least in part biological. I mean, I lived in Wales for 10 years, and my observation is that without biological barriers, we’d be at least 50 % sheep by now. We’re not a fussy species on this subject.

    Also, the current idea seems to be that we interbred with Neanderthals in the middle east in the out-of-Africa pulse, and then spread out carrying the genes with us, but then we stopped outcrossing when we already had done so?

    I can see at least two scenarios in my head where something like this could happen but there are problems with both of them.

    If I can ask, what is the current thinking on this?

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  2. “Curious how many readers recognize the reference on the shirt to the left?”

    In May we visited friends in Cambridge UK. One of them is a geneticist at the Sanger institute. We walked around Cambridge with them. We stopped at the Eagle pub and had a pint.

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  3. Freelancers need some type of insurance/collection service specializing in their needs. Maybe they’d pay a monthly fee, and in exchange it would work like selling your debt to a collection agency – you’d get paid a fraction of what you contracted for immediately so you could get money immediately, and then the service would put the screws on the publication to get the full face value of the debt (with far greater resources and lawyers).

    I didn’t care much for the obesity piece either, although it did make two good, pretty disturbing points. The first is one that I’d heard about after watching a Healthcare Triage video, about the extremely high failure rate of all diets after about 12-14 months. The second was that apparently no country has had success in getting obesity rates noticeably down after they’ve gone up. That’s not encouraging in public policy terms.

    I was talking with my father about that, and he noted that back when he was a young man (in the 1960s), there weren’t nearly as many fat people. He wasn’t sure why, either, other than maybe more people had an active life-style. The fast food was scarcer, but he didn’t remember people’s diets being that much healthier (less access to fresh food and fruits and vegetables, lots more meat and potatoes stuff).

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  4. brett, agree that it makes good points re: obesity. that being said, ppl need to be honest that morbid obesity (and the woman whose photo was pictures is that class) is not optimal for health. a 1% chance of getting slimmer is a chance u got to take….

    that being said, the part of how social debilities of being obese and cruelty were really a separate piece. it’s like making a sausage. all that shiz shouldn’t be together.

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  5. ” AJ+ is backed and owned by a conservative Salafist regime which runs an oligarchic state on the backs of dark-skinned South Asian indentured labor. ”

    For naive listeners (e.g. moi) to your upcoming India DNA podcast, will you address caste pigmentation? Is that a thing? Should I go back and listen to the earlier India podcast?

    Preference for Insight podcasts would be if also available transcribed. Is there such? Takes 4x+ longer to listen to, vs. read, most podcasts, especially since much of the content is beneficent didactic back-fill that can be selectively scanned-through depending upon prior levels of knowledge. Not a complaint. I just don’t have much laundry to fold, or whatever it is that people do while they are also listening to podcasts.

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  6. we’re thinking of doing transcripts. the problem is we’re not reading from a script but going off an outline, so the transcription is going to read somewhat strangely.

    will you address caste pigmentation?

    no. we’re not talking traits. we got enuf stuff to cover. what do you want to do? obviously, castes differ in color and that’s due to genes. but there is overlap. i’ve linked to papers on topic before. https://www.ias.ac.in/article/fulltext/jgen/092/01/0135-0139

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  7. Thanks for going back, finding, and re-tossing the link. Will think on request for other Q’s.

    Transcripts: edit lightly for continuity (can excise much intro fluff) and who cares about precisely verbatim? Nobody, unless it’s an SJW powder-keg issue. Just so’s the concepts are relatively cleanly laid out, following flow of conversation, with some of the good personality quirks, like Spencer suddenly spouting, “People not Pineapples.” from the Polynesia podcast, then your deadpan rejoinder “That’s way too funny for me.” are the type of character gems that could be left in. Slate’s interview editing style is generally pretty good–personality plus tight content comes through.

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  8. You guys did a whole damn podcast on the Polynesian expansion without once mentioning Disney’s massive success Moana? No excuse–you have kids.

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  9. Obesity: You are right, that article is pretty dreadful.

    My theory of obesity.

    We used to smoke cigarettes which controlled our appetites, but we died young.

    They got us to quit smoking, so our weight went up, and we got be older. Old people are fatter than young people and have a harder time losing weight.

    We tried to lose weight but diets don’t work so we got depressed. So they gave us anti depressants. Anti depressants notoriously cause weight gains. Which made us even more depressed.

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  10. More thoughts on obesity.

    Razib: has any work been done to determine if there are specific genes that cause obesity?

    Second: Within the past month, I read a study that showed lifetime medical expenditures on obese people are substantially lower than expenditures on people who are not fat. Smokers are really cheap. I can’t remember where the study was.

    Third. I have lost weight in the past when I have had a gastrointestinal infection that killed my appetite. Why can’t they bottle and sell whatever the stuff is that causes the loss of appetite?

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  11. “has any work been done to determine if there are specific genes that cause obesity?”

    Yes, I read up on this recently – there are some, but the effects are small (5%?) in comparison to simply kilojoules in/kilojoules out.

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  12. As for losing weight, cancer is much more effective than gastro.

    I had chemo + radiotherapy in early 2015 and dropped 30kg. It has been a long hard road back, with a lot of perseverence in the gym, but I have managed to get back 10kg so far, and further gains in muscle mass seem to be coming faster now, so weight gain is accelerating.

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  13. I went to Cambridge alumni talk on genes and obesity by Dr Giles Yeo at the weekend. Another version of the talk (this one at the RI) is posted at: https://www.youtube.com/watch?v=pOJYTMe_bp4 (Worth watching, I think). Anyway, he said that a hundred or so risk alleles had been identified and a graph showing the effect of having different numbers of the “bad” versions of these was shown at 47:20 (sum of 0, 1 or 2 copies for each one). The average BMI goes from just over 27 for those with as score of 104. Not a huge effect, but not trivial.

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  14. Stephan Guyenet’s The Hungry Brain is a good book on why so many are obese. At the end, he tries to be optimistic about losing weight and keeping it off (he makes 6 suggestions) but I was underwhelmed.

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  15. Derek Lowe has been a must-read for me for decades. A great and very realistic look at the drug industry from an insider on the discovery front (plus lots of organic chemistry).

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  16. “I was underwhelmed”

    What was it I read? Once people become overweight, only 1% of them succeed in losing weight and keeping it off beyond a year or so. That’s a fairly underwhelming prognosis.

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  17. To be accurate, Guyenet’s suggestions are directed not only at people who want to lose weight but at people who don’t want to get fat in the first place. They are:

    1) Get enough sleep (people who don’t eat more).

    2) Deal with stress (those who don’t eat more).

    3) Move. Every bit helps.

    4) To the extent possible, don’t have highly palatable foods where you live or work. In any case, never never never leave them out where you can see them and easily get to them. Just the sight will trigger you.

    5) “Eat foods that tell your brain you aren’t starving”: “foods that have a lower calorie density, higher protein and or/fiber content, and a moderate level of palatability.”

    6) “Beware of food reward”: “ice cream, brownies, french fries, chocolate, and bacon …are a lot more rewarding than anything our distant ancestors ate, and they can powerfully drive cravings, overeating, and eventually, deeply ingrained unhealthy eating habits.”

    More detail in the book.

    Guyenet’s answer to Brett’s question why there are so many more obese people now than the 1960s is the advent of cheap “hyperpalatable” foods. Then you might go out once or twice a month for a big meal that tasted better than anything you could make at home. Today you can have a Big Mac, soda, and fries every day, along with a bag of Nacho Cheese Doritos as you watch TV.

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  18. Guyenet is a serious person, and I think he’s right – the obesity epidemic has resulted from a perfect storm: many fewer people smoking, most people moving less, more stress and less sleep, and the much greater easy availability of energy-dense but nutrition-poor, highly palatable foods everywhere you look.

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  19. Regarding weight, among my patients (cardiac nurse) obese, and particularly diabetic patients have what I consider a disordered appetite. They eat the way smokers smoke. They wake up at 3AM and demand food, and complain of starvation if breakfast is at 0900 instead of 0700. People get really angry and demanding if snacks are not continuously available. I truly doubt many of these people have ever actually dieted in a way that cut their caloric consumption.

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  20. bacon

    Hey now, my wife’s great grandparents lived till their late 90’s on a diet of eggs, bacon, and steak… and bread and pie. Great grandpa was a small town banker, but lived on a farm. He did farm work in the early morning hours, went to work by 9 am, had lunch with his close friends, came home by 5:30 and ate supper with his wife. Did more farm work, then smoked a pipe while reading the Bible (and later listening to radio). Went to bed by 9 pm. Weekends were for more farm work, occasional hunting, visiting their families, and church and social activities. And they raised several children among whom two were decorated war heroes.

    Into his late 90’s he was mentally sharp and played with my wife, his great grand daughter who remembers him fondly – he gave her her first piggy bank.

    If you have clean (and fruitful) living, you can indulge in some bacon and pie and live to be old. Ok, I’m sure good genes helped too.

    My boys and I go to all-you-can-eat Korean BBQ and consume enormous amount of fatty brisket and pork belly, usually 2-3 plates of meat per person. Even my 10-year old clears two plates of meat on top of all the side dishes. Friends who eat with us are almost shocked at how much we eat. “How can you stay in such good shape while eating like that?”

    The answer is Judo and Jujutsu everyday – I probably burn 1000-1500 calories in 1.5-2 hours of training pretty much every day (I’m in my late 40’s – I used to train 3-4 hours a day at my peak). And very clean living. No smoking, very moderate drinking, one woman for 25+ years… and that woman likes to cook “healthy.”

    People tend to fixate on intake in the U.S., but I think output matters more.

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  21. I’m midway through the Hungry Brain. It has many interesting elements of now neuroscience illuminates why we overeat, but practically speaking, his weight loss advice seems to come down to “eat only bland food and you won’t overeat.”

    Maybe it’s answered later in the book, but I wonder how “bland” is defined here. He explicitly says that foods which are sweet and fattening (and especially both in combination) are very bad because they drive us to overeat. But if you personally enjoy things with spicy, sour, or bitter flavors, do those drive you to overeat as well?

    On a completely different note, does anyone have any opinion on the whole Nicotinamide adenine dinucleotide (NAD+) craze? It’s been shown to “rejuvenate” mice and I saw a Harvard Medical School researcher is starting human trials. But it’s available on the market as fairly affordable supplements right now. I’m not sure if this is all just quackery, because the researcher also founded a company to develop his own formulation of said supplement.

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  22. Always have some trouble with the idea of specific modern “hyper palatable” and hyper rewarding foods, because my low n of obese people is that the one person I know who is seriously obese basically tends to clear away loaves of white bread, packs of biscuits, eggs, butter, pints of milk and blocks of cheddar cheese every day – pretty familiar products to any early 20th century person, just way more than they could typically afford.

    They’re certainly foods which are cheap compared to 50-60 years ago, so cheaper to eat more of, but not really what I would think of as highly evolved products of flavorists and focus groups, all products long available, and are what I’d think of as “bland”.

    I would tend to the impression that you could clear away virtually the entire convenience food products industry, and if you leave the price of fats, starch and sugar the same, obesity rates would be untouched. If you eat a Big Mac and fries every day, and that’s it, you’re Bill Gates; if you eat the same diet that someone in 1940 ate, but twice as much of it (or more) because it’s twice as cheap and you can, you’re gonna be obese.

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