Bad Science, Fraud, and Peer Review - Updated

Updated below.

Article: A Scientific Look at Bad Science

Statistics: 

• "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. 

[snip] 

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, thinkprogress.org, 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."

Article: THE GOLD KING MINE FIASCO: WHAT IT TELLS US ABOUT THE EPA

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.

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?

Article: Peak Oilers Shut Up Forever Please

"Peak oil" was a Malthusian fad, just like the Club of Rome predictions about the stuff we would run out of by 2000, and Paul Ehrlich's "Population Bomb." [Other failed projections.]

Some people just off on doom, especially doom due to their (or their parents') evil ways.

Princeton University geologist Ken Deffeyes predicted that global oil production would peak on Thanksgiving Day, 2005. In 2005, daily global oil production averaged 85 million barrels per day. Daily petroleum liquids production in July was 96 million barrels per day.

Linked article: OPEC just kicked oil into the $30s

Diet and Observational Studies

Woody Allen, Sleeper:

Dr. Melik: This morning for breakfast he requested something called "wheat germ, organic honey and tiger's milk."
Dr. Aragon: [chuckling] Oh, yes. Those are the charmed substances that some years ago were thought to contain life-preserving properties.
Dr. Melik: You mean there was no deep fat? No steak or cream pies or... hot fudge?
Dr. Aragon: Those were thought to be unhealthy... precisely the opposite of what we now know to be true.
Dr. Melik: Incredible.

Two more pieces of traditional dietary advice take a beating.

Article #1: Trans fats, but not saturated fats like butter, linked to greater risk of early death and heart disease

Contrary to prevailing dietary advice, a recent evidence review found no excess cardiovascular risk associated with intake of saturated fat. In contrast, research suggests that industrial trans fats may increase the risk of coronary heart disease. 

Saturated fats come mainly from animal products, such as butter, cows' milk, meat, salmon and egg yolks, and some plant products such as chocolate and palm oils. Trans unsaturated fats (trans fats) are mainly produced industrially from plant oils (a process known as hydrogenation) for use in margarine, snack foods and packaged baked goods. 

To help clarify these controversies, de Souza and colleagues analysed the results of 50 observational studies [ed., emphasis added; see below] assessing the association between saturated and/or trans fats and health outcomes in adults.

Or: Butter Good, Margarine Bad

Article #2: The science of skipping breakfast: How government nutritionists may have gotten it wrong

Researchers at a New York City hospital several years ago conducted a test of the widely accepted notion that skipping breakfast can make you fat. 

For some nutritionists, this idea is an article of faith. Indeed, it is enshrined in the Dietary Guidelines for Americans, the federal government’s advice book, which recommends having breakfast every day because “not eating breakfast has been associated with excess body weight.” 

As with many nutrition tips, though, including some offered by the Dietary Guidelines, the tidbit about skipping breakfast is based on scientific speculation, not certainty, and indeed, it may be completely unfounded, as the experiment in New York indicated.

The scientific speculation was based on some concept of how metabolism might work.

This is not some moldy, old-wive's tale piece of advice that has been hanging around for decades (like needing to drink 8 glasses of water a day). This was only added to the guidelines in 2010.

The advice was based on "observational studies." That is, researchers simply observe people behaving naturally. The self-selected "fasters" where more likely to obese than those who ate breakfast.

However, if "observational studies" are replaced by actual experiments, with randomized controlled trials and all the rest of the modern scientific method, the experiments disprove the conclusions of the observational studies 90% of the time.

[Note: the study in the first article was an "observational study".]

This may be due to "confounders."

One of the primary troubles in observational studies is what scientists refer to as “confounders” — basically, unaccounted factors that can lead researchers to make mistaken assumptions about causes. For example, suppose breakfast skippers have a personality trait that makes them more likely to gain weight than breakfast eaters. If that’s the case, it may look as if skipping breakfast causes weight gain even though the cause is the personality trait.

And moralizing the dietary guidelines creates problems.

Allison attributes the widespread adoption of the breakfast hypothesis at least in part on researchers who read too much into observational studies, and wrongly ignore the stronger evidence from the randomized controlled trials. In addition, he speculates that there “maybe some sense that eating breakfast is ‘moral’ and ‘upstanding,’” and that makes people more willing to believe it’s good for you.

For the record, most of the hypothesis of catastrophic anthropogenic global warming is based on observational studies that have been moralized.

Two articles on global warming computer models. The first is a lucid explaination of how the climate models work, and why it is impossible to verify the models.

The second one is on how the modelers themselves have it impossible for the models to be validated (a usually necessary step in determining how well models actually work).

Article #1: The Trouble with Global Climate Models

Article #2: Validation Of A Climate Model Is Mandatory: The Invaluable work of Dr. Vincent Gray

Fudging and Nudging
The climate models cannot be validated because they should be set up so that they accurately predict the past ("hindcasting"). However, the models cannot do so until the modelers have added a number of fudge factors that nudge the curves into the right shape BEFORE they run it. So, of course, it looks like the models are doing what they are supposed to.

To put this into computer programmer terms.

Imagine a computer programmer programming a computer that runs a robot that makes light bulbs or wraps candies (I know people who do that).

Evaluation of the model is like the programmer giving the program to a systems analyst to check the program. The analyst may run parts of it in a simulation, but does not actually use it run the robots.

Validation of the models is like the programmer running the program and seeing if the robots do what they are supposed to do. If the robots correctly wrap candies, the program is valid.

The programmers of the climate models have made it impossible to actually validate their models by throwing in enough "fudge factors" to make the model work on the past ("hindcasting") that the models cannot predict future ("forecasting"). The fudge factors push the models to predict things that are not happening.

Headlines of Deadlines to Doom

Article: Six climate headlines from 2009 that tell us something important about the run-up to the 2015 Paris climate conference

In the run-up to the 2009 Copenhagen Climate Conference, the usual suspects made the usual hysterical headlines of doom. Several of those deadlines have now expired, with nothing catastrophic happening.

Revisit the hysteria of yesteryear in order to guard against the hysteria sure to be generated in the run-up to this year's global climate conference.

Article: Corrected sunspot history suggests climate change not due to natural solar trends

The Sunspot Number is a crucial tool used to study the solar dynamo, space weather and climate change. It has now been recalibrated and shows a consistent history of solar activity over the past few centuries. The new record has no significant long-term upward trend in solar activity since 1700, as was previously indicated. This suggests that rising global temperatures since the industrial revolution cannot be attributed to increased solar activity. 

The Maunder Minimum, between 1645 and 1715, when sunspots were scarce and the winters harsh, strongly suggests a link between solar activity and climate change. Until now there was a general consensus that solar activity has been trending upwards over the past 300 years (since the end of the Maunder Minimum), peaking in the late 20th century -- called the Modern Grand Maximum by some. 

I am skeptical about this. First, this is first time I have heard about the "prevously indicated" increase in solar activity. However, I will take that as a given, even though I have been reading everything I can about sunspot activity for over 20 years.

Second, this is hard on the heels of researchers suddenly, and miraculously, finding all the heat that has been missing for last 20 years in the oceans, despite the fact no one measuring the oceans had noticed it before. The Hiatus has been magically wiped out.

Now, long-standing sunspot activity data has been suddenly, and miraculously, been recalibrated to show steady levels of sunpot activity since the end of the Maunder Minimum.

I would like to see confirmation of this by independent researchers.

Since the industrial revolution followed both the uptick in sunspots following the Maunder Minimum and the end of the Little Ice Age, it still is not clear if the warming earth has experienced since then is anthropogenic or due to increased solar activity.

Now, I believe that there has been a modest uptick in global temperature over the last 150 years, but whether that was totally anthropogenic or only partly is unknown.

Third, a long held belief among researchers that the Great Modern Maximum exists has just been overturned. Global warming consensus, anyone? 

This is how science advances. By asking questions, being skeptical about received knowledge, and performing one's own research. 

Article: The timebomb under Yellowstone: Experts warn of 90,000 immediate deaths and a 'nuclear winter' across the US if supervolcano erupts

A nice long article with lots of graphics, bullet points, and information boxes.

Low chance of blowing any given year, but likely to happen sooner or later.

Article: Massive toxic algae bloom reaches from California to Alaska

SAN FRANCISCO (Reuters) - Oceanographers are studying whether climate change is contributing to an unprecedented bloom of toxic algae that spans the Pacific Coast of the United States and Canada, raising health concerns and leading to multimillion-dollar income losses from closed fisheries. 

The runaway bloom of pseudo-nitzschia algae is believed to have been spawned in part by unusually warm ocean water along the West Coast that scientists have dubbed "the blob."

"The blob" is a natural and recurrent phenomenon, possibly linked to El Nino. And large blooms are common where water is warmer than normal or high in plant nutrients (usually from human sources).

However, half of the article tries to tie it into catastrophic anthropogenic global warming, i.e., climate change.

The article is full of tentative words/phrases: whether climate change is contributing; have yet to determine; global climate change; may be a harbinger; things to come; climate change; a window to the future; could see happen; climate change scenarios.

Two reporters and two editors are responsible for this mash-up.

Article: Airplane Poop Could Help Track Global Disease Outbreaks

IN THE SUMMER of 2013, researchers at the Technical University of Denmark headed to the Copenhagen airport for a special delivery: poop. The crew who clean out airplane toilets had siphoned it from flights arriving from around the world just for them. 

Back in the lab, the researchers turned the samples into DNA soup and fed them through a sequencing machine. Out the other end came antimicrobial resistance genes and potential pathogens—all traceable to the individual plane’s country of origin.

[snip]

From the airplane waste, the Danish researchers could identify regional patterns. Genes for antimicrobial resistance, for example, were more abundant in samples from South Asia than North America. They found differences in specific bacteria, too: Salmonella enterica, which can cause diarrhea, was more common in South Asian samples while Clostridium difficile, the bacteria behind a difficult-to-treat hospital-acquired infection that often follows a course of antibiotics, was most common in North American samples. 

Article: Pocket-calculator climate model outperforms billion-dollar brains

Money quote:

Unlike the complex climate models, each of which uses as much power as a small town when it is running, the new, “green” model – which its inventor runs on a solar-powered scientific calculator – had not been repeatedly regressed (i.e., tweaked after the event) till it fitted past data. 

Lord Monckton, the inventor of the new model and lead author of the paper, said: “Every time a model is tweaked to force it to fit past data, one departs from true physics. The complex models are fudged till they fit the past – but then they cannot predict the future. They exaggerate.

The new model uses straightforward physics to model the changing climate. It both accurately predicts the past, and the future, unlike the billion dollar models.

There is a list of "refutations" from the "profiteers of doom” that the authors of the original article point out are wrong.

Additional links:
The Pause draws blood – A new record Pause length: no warming for 18 years 7 months

Satellite data shows continued hiatus.

Indian Environment Minister dismisses Himalaya Global Warming concerns

Title says it all.

Article: MSNBC. Obama’s climate policy is ‘practically worthless,’ says expert 

Hat tip: Obama’s climate policy is ‘practically worthless,’ says Dr. James Hansen

“The actions are practically worthless,” said James Hansen, a climate researcher who headed NASA’s Goddard’s Institute for Space Studies for over 30 years and first warned congress of global warming in 1988. “They do nothing to attack the fundamental problem.”

Considering that Mr. Obama's policy proposal is to end reliance on coal to fuel electrical power generation in the US by government fiat, one wonders exactly what a "worthy" policy actually involves.

Hansen suggested a gradually rising fee for fossil fuel extraction, collected at the port of entry or, in domestic cases, the place where the material actually comes out of the ground. “As long as fossil fuels are allowed to (appear to be) the cheapest energy, someone will burn them,” he wrote in an email to msnbc. “It is not so much a matter of how far you go. 

"Gradually rising" to how much? Until all fossil fuels are too expensive to use? What will substitute for them? ("Renewables" are too unreliable.)

Article: Saudi Arabia may go broke before the US oil industry buckles

This is a reminder that the US may not be as nimble as a dictatorship, but a free market economy always beats a centrally planned one in the long run.

An extended look at the US shale oil (and natural gas) revolution, its continued and rapid technological advances, and the economic and political ramifications to the Saudi Arabians.

While it may be too optimistic about the US oil industry and too pessimistic about the Saudis, a lot of it confirms what I am reading elsewhere, in one neat package.

And, at least partly, the bad news for the Saudis is good news for the US; they will have less money to spend on fundamentalist Islam.

Video Clip: Moon’s Farside Crosses Earth’s Face | DSCOVR Satellite Time-Lapse Video

Repeated loop of moon crossing earth's face.

Warning: autostart.

Article: Senate Passes Commercial Space Bill

Good news.

NASA does a lot of things well. However, it has become a sclerotic mess: over-regulated, pork-barrelled, and with a bad case of mission creep. Its core "space" mission is doing well with awesome work like the missions to the various planets and the various space telescopes.

Further, its reputation has been damaged by association with some of the more hysterical global warming activists who have hijacked the climate data.

It has also lost the sense of adventure and derring do it had during the 1960's