Thursday, August 20, 2015

Bad Science, Fraud, and Peer Review - Updated

Updated below.

Article: A Scientific Look at Bad Science


  • "By one estimate, from 2001 to 2010, the annual rate of retractions by academic journals increased by a factor of 11..."
  • "A study in the Proceedings of the National Academy of Sciences reviewed 2,047 retractions of biomedical and life-sciences articles and found that just 21.3 percent stemmed from straightforward error while 67.4 percent resulted from misconduct, including fraud or suspected fraud (43.4 percent) and plagiarism (9.8 percent)." 
  • In 2012, a researcher then at the biotechnology company Amgen wrote in Nature that when his team tried to reproduce 53 landmark cancer studies, they could replicate just six." [Ed: that is, about 11%]
  • "And according to a news report in Nature, a project aiming to reproduce the findings of 100 psychology papers has managed to replicate results for only 39 of them (the project’s findings are still under peer review)." 
A retracted paper means that it is has been published, after being peer reviewed. And 43% of the papers above were peer reviewed and later found to involve fraud.

What is peer review?
Peer review means that a board of scholarly reviewers in the subject area of the journal review materials they publish for quality of research and adherence to editorial standards of the journal before articles are accepted for publication. If you use materials from peer-reviewed publications they have been vetted by scholars in [the] field for quality and importance.  
Peer review is often waved as a magic wand conferring legitimacy on a controversial paper. While peer review may find some misconduct, it is mostly used for quality control.

The article points out that the need for a paper to be "important" is actually driving the misconduct. The research reported must have "positive" results, even though a lot research give "negative" results. However, negative results are important, but they are not "sexy" enough for the popular press, the scientific press and for the peer reviewers.

At its worst, peer review has been used to weed out results that are controversial and go against the "consensus" position in a field.

One reviewer of papers in neurobiology was notorious for demanding that the paper reference something about prions, and that the paper had to agree with the reviewer's position regarding prions.

Press Release: Retraction of articles from Springer journals
Springer confirms that 64 articles are being retracted from 10 Springer subscription journals, after editorial checks spotted fake email addresses, and subsequent internal investigations uncovered fabricated peer review reports.
And how many have not been found?

The EPA Contaminates Colorado River: Updated and Bumped, again

It is now 3 million gallons. See below.

Updated again.

Article: Animas River fouled by 1 million gallons of contaminated mine water
A spill that sent 1 million gallons of wastewater from an abandoned mine into the Animas River, turning the river orange, set off warnings Thursday that contaminants threaten water quality for those downstream. 
The Environmental Protection Agency confirmed it triggered the spill while using heavy machinery to investigate pollutants at the Gold King Mine, north of Silverton. 
Downstream in Durango, hundreds of people gathered along the Animas River to watch as the blue waters turned a thick, radiant orange and yellow just after 8 p.m., nearly 34 hours after the spill started.
The orange color is apparently due to iron oxide.

Article: EPA confirms Colorado mine spill contains heavy metals
The mustard-colored muck that spilled from a Colorado mine and surged into a river contains heavy metals including lead and arsenic, federal environmental officials confirmed Friday, but they didn't immediately discuss amounts in the water or health risks. 
The spill also contained cadmium, aluminum, copper and calcium, the Environmental Protection Agency said. During a public meeting in Durango, EPA Regional Director Shaun McGrath did not mention whether the elements posed a health hazard but said local authorities were right to close the Animas River to human activities.
The Animas River is part of the Colorado River system and the spill "pulse" will contaminate drinking and irrigation water all the way to the Gulf of Mexico.

Fortunately for the EPA, the refusual to hold bureaucrats responsible for their failures, even catastrophic ones, usually means no one will be punished.
EPA and contractor crews accidentally unleashed 1 million gallons of wastewater from the shuttered Gold King Mine on Wednesday, and it flowed into the river through a tributary.
Well, maybe the contractor will be fired.

Update: EPA Says It Released 3 Million Gallons Of Contaminated Water Into River

NPR does a straight news article, blaming the EPA, and talking about the toxic waste.

Hoot: Abandoned Mine Leaks Millions Of Gallons Of Bright Orange, Toxic Water Into A Colorado River

On the other hand, left wing site,, produces an amazing piece of propaganda full of blame-shifting in the linked article. 

The waste "leaks," the EPA is trying to contain the waste (the opposite of what it did), "unexpectedly," the article blames the locals for not being to clean up the mess, the mine operators "just walked away," and so on.

Arrogant: EPA: No health risks to wildlife after Colorado mine spill, but impact to humans still unknown

And the tobacco companies claimed for years that cigarettes did not cause harm.

And still more: 'They're not going to get away with this': Anger mounts at EPA over mining spill

"They are not going to get away with this," said Russell Begaye, president of the Navajo Nation, which intends to sue the EPA. 
Begaye said Saturday at a community meeting in Shiprock, N.M., that he intends to take legal action against the U.S. Environmental Protection Agency for the massive release of mine waste into the Animas River near Silverton, Colorado. 
"The EPA was right in the middle of the disaster and we intend to make sure the Navajo Nation recovers every dollar it spends cleaning up this mess and every dollar it loses as a result of injuries to our precious Navajo natural resources," Begaye said. "I have instructed Navajo Nation Department of Justice to take immediate action against the EPA to the fullest extent of the law to protect Navajo families and resources."

The EPA waited 24 hours before warning towns downstreams that it had dumped the waste.

The EPA had not filed any sort of environmental impact statement, had not notified the state or local governments what they were up to, and never did any work to study the site and determine the best way to proceed. A private industry that did this would be under federal criminal investigation and there would be jail terms and fines.
The craven acquiescence of environmental organizations, which are completely in bed with the EPA, is disgusting. 

Article: Transgender Regret Is Real Even If The Media Tell You Otherwise

The article is written by a person, Walt Heyer, who underwent sex-reassignment surgery, male-to-female, and now regrets it.
Fair-minded individuals would see the cumulative effect of the findings—20 percent have regret, 41 percent attempt suicide, 90 percent have a “significant form of psychopathology”, 61 percent also have other psychiatric disorders and illnesses, 50 percent had depressive symptoms, 40 percent showed symptoms of anxiety—and be troubled by the push to surgery and transition as the first course of treatment for transgenders. 
Apparently transgender lives do not matter: not to the LGBT and not to the media. 
I have given this a "bad science" tag because 1) the one reporter cherry-picked one study to prove her point and 2) the science shows that "transgender regret is real."

Article: Johns Hopkins Psychiatrist: Transgender is ‘Mental Disorder;' Sex Change ‘Biologically Impossible’

This is a republishing of the original report, plus some new reporting.
Dr. Paul R. McHugh, the former psychiatrist-in-chief for Johns Hopkins Hospital and its current Distinguished Service Professor of Psychiatry, said that transgenderism is a “mental disorder” that merits treatment, that sex change is “biologically impossible,” and that people who promote sexual reassignment surgery are collaborating with and promoting a mental disorder.

Thursday, August 13, 2015

Article: Genetically engineered yeast produces opioids
It typically takes a year to produce hydrocodone from plants, but scientistst have now genetically modified yeast to make it in just a few days. The technique could improve access to medicines in impoverished nations, and later be used to develop treatments for other diseases. 
After a decade's work a team led by Stanford bioengineer Christina Smolke succeeded in finding more than 20 genes from five different organisms and engineering them into the genome of baker's yeast. In so doing they created two different microbial assembly lines, each of which took less than five days to convert sugar into one of two medicinal compounds: either thebaine, which can be refined into painkillers, or hydrocodone which is a prescription painkiller.
My first thought is, "Great! No more dependence on poppy growers in war-torn parts of the world. Poppy plants can be eradicated without a problem."

My second thought is, "Oh, no! Anyone who can make beer can now make opioids."

Article: Humans responsible for demise of gigantic ancient mammals
Scientists claim their research settles a prolonged debate over whether mankind or climate change was the dominant cause of the demise of massive creatures in the time of the sabretooth tiger, the woolly mammoth, the woolly rhino and the giant armadillo. 
Humans arrive, and megafauna went extinct. The authors had no way of determining if the extinctions due to hunting, competition, or habitat change.
Examining different regions of the world across these scenarios, they found coincidences of human spread and species extinction which illustrate that man was the main agent causing the demise, with climate change exacerbating the number of extinctions. However, in certain regions of the world -- mainly in Asia -- they found patterns which patterns were broadly unaccounted for by either of these two drivers, and called for renewed focus on these neglected areas for further study.

Article: Grammar: Eventually the brain opts for the easy route
Languages are constantly evolving -- and grammar is no exception. The way in which the brain processes language triggers adjustments. If the brain has to exert itself too much to cope with difficult case constructions, it usually simplifies them over time, as linguists demonstrate in a study on languages all over the world. 
The grammar of languages keeps reorganizing itself. A prime example of this is the omission of case endings in the transition from Latin to Italian. 
Then how did language get complicated in the first place?

Climate change and corruption

Article: Is Climate Change Now Its Own Industry?
The $1.5 trillion global “climate change industry” grew at between 17 and 24 percent annually from 2005-2008, slowing to between 4 and 6 percent following the recession with the exception of 2011’s inexplicable 15 percent growth, according to Climate Change Business Journal.
Global warming activists make hysterical accusations about one "skeptic" who earned $2500/day for consulting, 20 years ago, and is still a skeptic today. How many scientists, pundits, politicians and bureaucrats can $1.5 trillion buy?