linkstream2 microblog

Did natural #selection make the Dutch the tallest people on the
planet? http://news.sciencemag.org/biology/2015/04/did-natural-selection-make-dutch-tallest-people-planet Height spurt in last century not all nurture

QT:{{”
“This study drives home the message that the human population is still subject to natural selection,” says Stephen Stearns, an evolutionary biologist at Yale University who wasn’t involved in the study. “It strikes at the core of our understanding of human nature, and how malleable it is.” It also confirms what Stearns knows from personal experience about the population in the northern Netherlands, where the study took place: “Boy, they are tall.”
…
“For many years, the U.S. population was the tallest in the world. In the 18th century, American men were 5 to 8 centimeters taller than those in the Netherlands. Today, Americans are the fattest, but they lost the race for height to northern Europeans—including Danes, Norwegians, Swedes, and Estonians—sometime in the 20th century.

Just how these peoples became so tall isn’t clear, however. Genetics has an important effect on body height: Scientists have found at least 180 genes that influence how tall you become. Each one has only a small effect, but together, they may explain up to 80% of the variation in height within a population. Yet environmental factors play a huge role as well. The children of Japanese immigrants to Hawaii, for instance, grew much taller than their parents. Scientists assume that a diet rich in milk and meat played a major role.

The Dutch have become so much taller in such a short period that scientists chalk most of it up to their changing environment. As the Netherlands developed, it became one of the world’s largest producers and consumers of cheese and milk. An increasingly egalitarian distribution of wealth and universal access to health care may also have helped.”
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America’s Epidemic of Unnecessary Care
http://www.newyorker.com/magazine/2015/05/11/overkill-atul-gawande QT: Facing a doctor, what are you going to fear: doing too little or too much?

Annals of Health Care MAY 11, 2015 ISSUE
Overkill
An avalanche of unnecessary medical care is harming patients physically and financially. What can we do about it?
BY ATUL GAWANDE

QT:{{”
Still, when it’s your turn to sit across from a doctor, in the white glare of a clinic, with your back aching, or your head throbbing, or a scan showing some small possible abnormality, what are you going to fear more—the prospect of doing too little or of doing too much?” …
“Right now, we’re so wildly over the boundary line in the other direction that it’s hard to see how we could accept leaving health care the way it is. Waste is not just consuming a third of health-care spending; it’s costing people’s lives. As long as a more thoughtful, more measured style of medicine keeps improving outcomes, change should be easy to cheer for. Still, when it’s your turn to sit across from a doctor, in the white glare of a clinic, with your back aching, or your head throbbing, or a scan showing some small possible abnormality, what are you going to fear more—the prospect of doing too little or of doing too much?”
“}}

How [to] Build a Safer Car?
http://www.newyorker.com/magazine/2015/05/04/the-engineers-lament QT: Pessimist sees glass as 1/2 empty; optimist, 1/2 full; engineer, 2X what it should be

Dept. of Transportation MAY 4, 2015 ISSUE
The Engineer’s Lament
Two ways of thinking about automotive safety.
BY MALCOLM GLADWELL

QT:{{”
There is an old joke about an engineer, a priest, and a doctor enjoying a round of golf. Ahead of them is a group playing so slowly and inexpertly that in frustration the three ask the greenkeeper for an explanation. “That’s a group of blind firefighters,” they are told. “They lost their sight saving our clubhouse last year, so we let them play for free.”

The priest says, “I will say a prayer for them tonight.”

The doctor says, “Let me ask my ophthalmologist colleagues if anything can be done for them.”

And the engineer says, “Why can’t they play at night?”

The greenkeeper explains the behavior of the firefighters. The priest empathizes; the doctor offers care. All three address the social context of the situation: the fact that the firefighters’ disability has inadvertently created conflict on the golf course. Only the engineer tries to solve the problem.
…
Almost all engineering jokes—and there are many—are versions of this belief: that the habits of mind formed by the profession enable engineers to see things differently from the rest of us. “A pessimist sees the glass as half empty. An optimist sees the glass as half full. The engineer sees the glass as twice the size it needs to be.” “}}

Analysis of the Sputum Transcriptome Discriminates Clinical Phenotypes of Asthma http://www.atsjournals.org/doi/abs/10.1164/rccm.201408-1440OC Consistent blood expression patterns

Noninvasive Analysis of the Sputum Transcriptome Discriminates
Clinical Phenotypes of Asthma (ATS Journals)

Yan, X., Chu, J.-H., Gomez, J., Koenigs, M., Holm, C., He, X., Perez,
M. F., Zhao, H., Mane, S., Martinez, F. D., Ober, C., Nicolae, D. L.,
Barnes, K. C., London, S. J., Gilliland, F., Weiss, S. T., Raby, B.
A., Cohn, L., and Chupp, G. L. “Non-Invasive Analysis of the Sputum
Transcriptome Discriminates Clinical Phenotypes of Asthma” American
Journal of Respiratory and Critical Care Medicine (2015):
doi:10.1164/rccm.201408-1440OC,

QT:{{"
Conclusions: There are common patterns of gene expression in the
sputum and blood of children and adults that are associated with near
fatal, severe and milder asthma.
"}}

QT:{{”
Andreessen laughed and continued, “They were doomed from the start, because Apple in Cupertino”—in Silicon Valley—“had spent three years building that. I’ve been totally determined to be on the other side of that dynamic by being here, because success in software follows a power-law distribution. It’s not Coke and Pepsi and a bunch of others; it’s winner take all. Second prize is a set of steak knives, and third prize is you’re fired.”
“}}

http://www.newyorker.com/magazine/2015/05/18/tomorrows-advance-man

TOMORROW’S ADVANCE MAN

by Joe Pugliese

QT:{{”

“Against this Barnum-like theatricality, spontaneous gestures stand out. There’s a poignant scene in which Durst is found not guilty of his neighbor’s murder: he turns to his lawyer and says, uncertain, “Did they say ‘not’?” The most unsettling example comes in the fourth episode, when Jarecki suggests that he and Durst take a break from discussing his testimony in Texas. Durst has confirmed that his lawyers hinted that he could answer specific questions about the dismemberment with “I don’t know”; that way, he’d sound less coldhearted. As soon as the filmmaker leaves the room, Durst, who is still wired for audio, lowers his head and mutters a sentence to himself. “I did not knowingly, purposely lie,” he says, and then pauses, considering, to add a word: “I did not knowingly, purposely, intentionally lie. I did make mistakes.”

Durst was rehearsing the interview, the way one might rehearse one’s testimony—but does that make him seem more guilty or just more realistic about documentaries? His lawyer tells him that his microphone is hot. Durst is fascinatingly unconcerned. He says again, “I never intentionally, purposefully lied. I made mistakes.” Then, with the shrug of an honest man, he adds what might be the tagline for the series: “I did not tell the whole truth. Nobody tells the whole truth.”

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Robert Durst’s New Trial
http://www.newyorker.com/magazine/2015/03/23/what-about-bob

Related to the Jinx

QT:{{”
“I am a noisy introvert. My sister Randi made up that phrase and it describes lots of people I know. Lots of writers seem to be introverts who love to now and then be on stage. Lots of radio people too. I covet large amounts of time alone, and I’m most comfortable and very happy when I’m alone, but obviously there’s another side to me because true introverts don’t end up with their own national radio shows.” “}}

http://lifehacker.com/im-ira-glass-host-of-this-american-life-and-this-is-h-1609562031

http://www.the-scientist.com/?articles.view/articleNo/42950/title/Microbiome-Fingerprints/

QT:{{”

As microbiome signatures mature, law enforcement or intelligence agents could theoretically track people by looking for traces of them left in the microbes they shed. Mark Gerstein, who studies biomedical informatics at Yale University and was not involved in the new study, suggested, for instance, that one could imagine tracking a terrorist’s movements through caves using their microbiome signature.

Huttenhower and his colleagues were identifying individuals out of pools of just hundreds of project participants, however. It is currently unclear how well the algorithm will perform when applied to the general population, though the researchers estimate that their code could likely pick someone out from a group of 500 to 1,000. “I would expect that number to get bigger in the future as we get more data and better data and better coding strategies,” Huttenhower said.

But the work raises privacy concerns similar to those faced by scientists gather human genomic data. Microbiome researchers are already wary of the human genomic DNA that gets caught up in microbiome sequences, but it increasingly appears that the microbiome sequences themselves are quite personal.

In the genomics field, researchers have increasingly limited access to databases containing human genomic sequencing data. Researchers must apply to use these data. “People might increasingly want to put the microbiome data under the same type of protection that they put normal genomic variants under,” said Gerstein. “Your microbiome is associated with various disease risks and proclivities for X and Y. I don’t think it’s a completely neutral identification. It potentially says things about you.”

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Characterization of #SVs w. single molecule & hybrid sequencing http://bioinformatics.oxfordjournals.org/content/30/24/3458.abstract Probabilistic read mapping, re-evaluating adjacencies

QT:{{"
We present MultiBreak-SV, an algorithm to detect structural variants
(SVs) from single molecule sequencing data, paired read sequencing
data, or a combination of sequencing data from different platforms.
"}}

QT:{{"The research system does not recognize bioinformaticians for doing what the scientific community needs most. “People realize the importance, but currently there are no real solutions,” says Xiaole Liu, a bioinformatician at the Dana-Farber Cancer Institute in Boston, Massachusetts, and at Tongji University in Shanghai, China. This is why it can take more than six months to fill positions at a core, why many of biology’s brightest are leaving science for technology companies, and why conventional biologists wait nine months to get help to dissect their data.
"}}

Reward bioinformaticians [for collaboration] http://www.nature.com/news/core-services-reward-bioinformaticians-1.17251 Despite #bigdata boom, biomedical analysis could be made more appealing