Cool Links

Large population-scale studies powered by high-throughput sequencing technologies have generated massive amounts of genomic data, with the potential to revolutionize genetics and medicine.

But the translation of these data to actionable medicine is complicated by the challenges of extracting meaningful information from high-throughput sequencing  data. The challenge is beyond computational, as bioinformatics is bound by the experimental methods employed to produce genomic data. A successful experiment minimizes false positives and depends on the optimization of an entire pipeline, from sample preparation to computational analysis.
What was Earth like 5 million years ago?  

We had camels in North America and got an Arctic ice cap due to the fact that Earth got cooler and drier.  And the atmosphere had 400 parts per million, about what the northern hemisphere could have next month, according to according to the National Oceanic and Atmospheric Administration's Earth System Research Lab.

Old air preserved as bubbles in the Antarctic ice sheet tell us CO2 levels never exceeded 300 parts per million during the last 800,000 years but they started to rise with the advent of industry. Tuesday of this week the reading was 398.44 ppm as measured at Mauna Loa, Hawaii. It was 316 ppm when Charles Keeling, who the Keeling Curve is named after, began taking measurements there.
I don't follow "I F*cking Love Science" on Facebook for the most transparent, stodgy old guy reason; I don't like the name.  Sure, it's edgy and in-your-face and therefore cool to a lot of people who think that sort of thing is cool, it is just a turn-off for me.

But being edgy and cool doesn't mean you get to rip people off.  The Ellen Degeneres Show is also cool and edgy and hip and the host comes dancing out to music every day; it's actually quite entertaining. The problem is that part of the program involved music they didn't have rights to use. In 1,000 different cases. 

Maybe they thought they were exempt because they were having fun. Or maybe they thought they were doing the artists a favor and giving them free publicity.
The Emotional Freedom Technique is a kind of psychotherapy, developed in the 90s, that draws on a variety of pseudoscientific bollocks, including accupressure, our old friend NLP (neurolinguistic programming), various kinds of laying-on-of-hands-type ‘energy’ therapies and a good dose of very confused neurobollocks.

Essentially, what happens in an EFT counselling session is that you discuss your problem, while stimulating the ‘end points of the body’s energy meridians’. This stimulation takes the form of tapping yourself; on the head, the face, wherever.
2012 was the year that global warming came roaring back - in science media, anyway. Despite the IPCC asking the media to help a little less when it came to attributing every weather event to climate change, science media insisted global warming created a 'superstorm' named Sandy and that global warming had finally hit the American Mid-West, after peskily not rising in temperatures since the 1930s.
A study by the University of Winnipeg -   2,300 first-year psychology students were surveyed online for three consecutive years - found that psychology students who do a lot of texting tend to be more shallow and ethnically prejudiced (that's racist, south of the border) and place less importance on moral, aesthetic and spiritual goals and greater importance on wealth and image. The one hour online psychology research survey included self-reported measures of texting frequency, personality traits and life goals.
Are your eggs free range?  Do you care?

Well, chicken farmers care, because marketing success for 'free range' labels has made it a big business. 

There actually is a somewhat fuzzy limit, 1,500 birds a hectare, but a group in Australia says some larger producers are using the "free range" label for their chickens, even if they have 20,000 per hectare. Basically, the farmers claim, the eggs are being laid by caged hens even if they are not in cages. And the public does not know the difference and is paying $1-2 more per dozen.
Mark Bittman of the New York Times has never seen a paper about a miracle vegetable he didn't coo over - as long as it's about his friends in the $29 billion organic food industry. And he has never seen a study showing no benefit to organic food where he didn't suddenly put on his skepticism monocle and find all kinds of methodological flaws.  

But he hates biology in that special way only a true left-wing, anti-science crank can hate biology. So much he'd easily fit in at Grist or Mother Jones if he could afford the pay cut. If there is a logical fallacy or a set of blinders he needs to wear to appeal to his base, he will don it. He's Ann Coulter, without the intelligence, humor or nice hair.
British archaeologists have unearthed a sprawling complex - the size of a football field - near the ancient city of Ur in southern Iraq, home of the biblical Abraham.

The structure, thought to be about 4,000 years old, probably served as an administrative center for Ur, around the time Abraham would have lived there before leaving for Canaan, according to the Bible. 
The compound is near the site of the partially reconstructed Ziggurat, or Sumerian temple, said Stuart Campbell of Manchester University's Archaeology Department, who led the dig.
Want a job with terrible pay, long hours and in which you’ll never have time to read books, and when you talk about them, you’ll mostly be using made-up words like “deterritorialization” and “Othering”—because, as Ron Rosenbaum pointed out recently, the “dusty seminar rooms” of academia have the chief aim of theorizing every great book to death?

Then become a professor in a literature department.

Don’t get that PhD in literature, just don’t, warns one in Slate.  And she isn't trying to discourage potential competitors, but rather because "my doctorate ruined books and made me obnoxious."

Her thesis was on Kafka so it sounds plausible. I thought Proust was all the rage these days but maybe not.
The 2011 5.6-magnitude quake in Oklahoma was probably caused when oil drilling waste was pushed deep underground, says a team of federally-funded scientists.

That assessment was in contrast to Oklahoma's state seismologists, who said it was natural. The federal group says a slightly smaller quake in an old oil well used to get rid of wastewater triggered the bigger one, and then a third smaller aftershock.

One thing both groups agree on; the waste was from traditional drilling, not hydraulic fracturing, commonly called fracking. 
Since it's Easter season, all of Christendom will be awash in articles and television shows about the Shroud of Turin. 

The Shroud, if you are new to the western world, is a cloth imprinted with the face and body of a bearded man; that would be Jesus Christ, according to the theological believers, because the Bible says he was wrapped in cloth and place in the sepulcher.  That this imprinting happened at all is one of those random mysteries that make the natural world so appealing.

It's now kept in a sealed case in Turin, but various analyses have been done over time and they showed the cloth was not old enough to have been used to cover Jesus. 
Because most politics is instead political theater, the government has made a show of canceling White House tours and Easter egg hunts and told airline travelers to expect longer lines. The White House calligraphy staff has managed to write along just fine, though.

And science is continuing to move also. Despite claims that sequestration would harm projects, in reality it has little to do with project funding (outside the political theater of writing grant applicants and telling them sequestration hurts their chances - vote Democrat), as this NSF study on duck penises getting approved shows
England’s Prince Charles famously said, “(GMOs) are not in God’s plan.” If you don't have a direct line to God like he does, that's okay, you can still easily see that most resistance to GMOs is based on quasi-religious belief in a perfect natural Eden rather than reason. 

"A ban on any GMO products would limit consumer choice. As a farmers market manager, I am reluctant to do so," writes  Mike Broadhurst, who manages the Cambria Farmers Market with his wife, Carol, but also worked for 30 years as a chemist for a company that commercialized GMO seeds.

If you care about food and understand biology, it's much easier to separate fact from doomsday fantasy. That is why anti-science progressives instead rely on fomenting fear and doubt.
There's no question Europe is more anti-science than North America; it's the home of the 'vaccines cause autism' craze, anti-biology fanaticism, anti-energy fanaticism and the belief that cell phones cause cancer and scientists should go to jail if they can't predict an earthquake.

Like America, as government has taken more control of science research, science research has become more politicized. 
It used to be that women lived a comfortable length longer than men. That gap has closed and men's life spans have increased more than women recently; 4.6 years for men since 1989 and 2.7 years for women, according to the Institute for Health Metrics and Evaluation.

Amanda Fiegl at National Geographic says that this is alarming - a "troubling trend" that men live almost as long as women and blames inadequate health care for why women have not continued to unfairly live much longer than men. It's almost like that old saw about the Washington Post - 'World Destroyed: Women, Minorities Impacted Most'.

It's not news if it is positive for men.
“I am not going to tell some twirp with an accountancy diploma who my professional colleagues are so that he can call around and embarrass me,” said McGill University psychology professor Avi Chaudhuri to the dean of his department in 2008, when accountants wanted to find out where a large chunk of money disappeared.
Media and politicians have focused on one common denominator in the shooting sprees that have occurred during the last few years; guns. What they leave out is that every instance also had shooters on psychiatric medication.

Diagnoses of serious psychological and psychiatric disorders have skyrocketed alongside the Diagnostic and Statistical Manual of Mental Disorders' expanding list of what constitutes mental illness. Example: The frequency of bipolar disorder in children, which has jumped 40-fold in the last two decades - though you could also get similar results for ADD and even being 'on the spectrum' of autism as those caught media attention.
The Biggest Loser is a hit reality show which follows a group of obese people as they attempt to lose weight and regain their health. The contestants maintain a grueling workout routine and eat a birdseed diet, all while being yelled at by attractive personal trainers. It's brilliant TV. The problem, however, is that the show is based on bad science and sends the wrong message to people who want to lose weight.
If you are anything like me, you were surprised that the LHC announced a 5-sigma result for the Higgs boson last July.  Not because it wasn't there - it clearly was - but because usually physicists are really, really conservative in their claims. While astronomers start every press release with 'may mean life on other planets' and biologists love to invoke missing links ten times a year, experimental physicists play things pretty close to the vest.