Monday, October 8, 2018

October 8th Links

  • For a start, wheat's genome is monstrously big. While the genome of Arabidopsis—the first plant to be sequenced—contains 135 million DNA letters, and the human genome contains 3 billion, bread wheat has 16 billion. Just one of wheat's chromosomes—3B—is bigger than the entire soybean genome. To make things worse, the bread-wheat genome is really three genomes in one. About 500,000 years ago, before humans even existed, two species of wild grass hybridized with each other to create what we now know as emmer wheat. After humans domesticated this plant and planted it in their fields, a third grass species inadvertently joined the mix. This convoluted history has left modern bread wheat with three pairs of every chromosome, one pair from each of the three ancestral grasses. In technical lingo, that’s a hexaploid genome. [Atlantic]
  • The history and physical exam are are a dying artform. Some conditions, such as Guillain-Barré, you see nothing on imaging. Surgical residents, if they even have a stethoscope, put the diaphragm on the "Surgeon's triangle" — where they can hear the abdomen, heart and lungs in one place. I ask what they got out of it and they respond, 'Umm, they are alive.' The answer is in the patient. You should know what is wrong with 95 percent of patients after taking the history. If you leave the room without knowing, DO NOT order tests. Go back in and take a good history, then do a good physical, and then order those unnecessary $5,000 imaging studies. [Greenspun]
  • You would be surprised how many terminologies in genetics have had to be changed over the years because they are no longer politically correct. We've changed simian crease to single palmar crease. We no longer use the term Mongoloid to describe upward-sloping eyes. (Most people have two palmar creases.) [Greenspun]
  • As per usual for Massachusetts, however, they are forecasting imminent doom for both the country and the planet due to Donald Trump’s existence. When I asked "What have you personally suffered as a result of Donald Trump being in the White House?" the answer is that it is not legitimate to think of one's own welfare. They are especially virtuous because they are thinking on a planetary scale and are virtuously concerned with all of humanity, not merely their thriving personal finances and situation. [Greenspun]
  • Shepard (the rich guy) was previously married. That wife sued for divorce and, during the litigation, filed for a restraining order alleging domestic violence (police report and Petition for Order of Protection). Having married a man who was accused of assaulting a woman, McCaskill could offer to join for the trip and talk with Dr. Ford about the circumstances under which it should be #BelieveTheSurvivor. [Greenspun]
  • Take an afternoon or evening flight from LAX to Hawaii. Spend the night there and catch the 7am flight to the Marshall Islands from Gate 14. It made several stops along this once-a-day route, and one of them was the Kwaj. [link]
  • As may be concluded from the air pressure, the atmosphere's material is equivalent to about 10 m of water. Since ice has about the same density as water, an ice cube from space travelling at 15 km/s or so must have a length of 10 m to reach the surface of the earth at high speed. A smaller ice cube will be stopped in mid-air and explode. An ice cube with a diameter of 50 m or more, however, may also be stopped in mid-air, as long as it comes in at a very low angle and thus has to pierce through a lot of atmosphere. The Tunguska event is sometimes explained this way. An iron meteorite with a length of 1.3 m would punch through the atmosphere; a smaller one would be slowed by the air and fall at terminal velocity to the ground. [Wiki]
  • Many HIV-infected people, now in their 50s and 60s, who have lived for years with HIV under control, are developing aging-related conditions — heart, liver and kidney disease, certain cancers and frailty, for example — at a rate significantly higher than uninfected people of the same age. "These are things that people develop all the time as they get old, but they are occurring at an earlier age in HIV-positive people," Hardy says. "The first goal was to save someone from dying of HIV infection," agrees Anthony S. Fauci, director of the National Institute of Allergy and Infectious Diseases (NIAID) and a leading researcher involved in developing the AIDS drug combinations. "After we started successful therapy that suppressed the virus and extended lives, we began to notice that people were getting diseases associated with aging sooner than their chronological age would indicate they should be getting them." [WaPo]
  • Every 2500 years or so there is an epochal, civilization-changing invasion of the West involving a technical innovation. Let's see 7500 – 5000 – 2500... so the next one is due... ooooh right about now. This very moment, the entire third world invades the West using the internet and aircraft and ships. [Sailer]
  • Combining Yelp and Census data, we find that gentrification, as measured by changes in the educational, age, and racial composition within a ZIP code, is strongly associated with increases in the numbers of grocery stores, cafes, restaurants, and bars, with little evidence of crowd-out of other categories of businesses. We also find that changes in the local business landscape is a leading indicator of housing price changes, and that the entry of Starbucks (and coffee shops more generally) into a neighborhood predicts gentrification. Each additional Starbucks that enters a zip code is associated with a 0.5% increase in housing prices. [SSRN]
  • This reminds me of the centenarian research on immune system, and also the cytomegalovirus line of research - much of the problem with aging is that immune cells get 'used up' on CMVs and lineages die off constantly, so by the time you're old, your remaining immune cells are all hunting harmless stuff and can't handle real threats. Also reminds me of the link between childhood vaccinations and adult life expectancy increases: apparently the early infections, regardless of mortality, permanently damage health in a subtle fashion which manifests decades down the line. [Gwern]
  • I noticed that almost none of the newly constructed homes have garages. The typical suburban obsession with cars, parking, and lawns appears to take a back seat to the desire to house more humans instead. A typical two car garage is 24' x 20' which is just big enough to fit two more bedrooms and another bath. Why waste that space and money on a little house for a couple of cars? [Granola Shotgun]
  • The most famous collaboration is Jennens' libretto for Messiah, drawn entirely from the Bible, about 60% from the Old Testament (with occasional small alterations). Musicologist Watkins Shaw describes it as "a meditation of our Lord as Messiah in Christian thought and belief", and which "amounts to little short of a work of genius". Some attribute Messiah's emphasis on the Old Testament – and choice of the Old Testament title "Messiah" – to Jennens' theological beliefs. Jennens was less than wholly approving of the musical setting, writing to Edward Holdsworth: "I shall show you a collection I gave Handel, called Messiah, which I value highly. He has made a fine entertainment of it, though not near so good as he might and ought to have done. I have with great difficulty made him correct some of the grossest faults in the composition; but he retained his overture obstinately, in which there are some passages far unworthy of Handel, but much more unworthy of the Messiah." [Wiki]
  • One of the more memorable things about Bouchard's course was that, occasionally, after presenting a compelling empirical demonstration to the class, on the power that psychological variables can hold for predicting important socially-valued outcomes (educational achievements, occupational accomplishments, or life in general), Bouchard would turn to the class and say: "See, see, see what happens when psychologists choose to study real variables." This point of view was not unrelated to that of Bouchard's colleague Paul E. Meehl; Meehl would occasionally wonder out loud whether it would be scientifically prophylactic to require graduate students in psychology to take a minor in a natural science like biology or genetics. By going so, Meehl speculated, they might be able to recognize a meaningful scientific contribution, if they should ever happen to encounter one in psychology! [link]
  • This is a major issue for those thinking about splitting up California. The rich liberal parts of the state subsidize a big chunk of government expenditures in the poor parts of the state. On the other hand, they also impose high cost policies on less desirable parts of the state that, leaving aside the tax subsidy question, would do better under a Texas-style low cost system. (A similar argument has been made about the state of New York: the vast tax revenues generated by Wall Street pays for a lot of stuff in Upstate New York, but policies that make sense for NYC keep Upstate too expensive relative to the limited returns that can be generated there.) [Sailer]
  • Between 2000 and 2017, roughly 2.5 million people were murdered in Latin America and the Caribbean, as if Chicago were wiped out. That compares with about 900,000 killed in the armed conflicts of Syria, Iraq and Afghanistan combined, according to U.N. figures and estimates by groups like Iraq Body Count. During that same period, all the world’s terrorist attacks killed 243,000 people, according to the University of Maryland’s Global Terrorism Database. "Large swaths of Brazil, Colombia, El Salvador, Honduras, Mexico and Venezuela are experiencing a war in all but name," says Robert Muggah, head of the Igarapé Institute. [WSJ]

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