Junk Science: Poor science, pseudoscience, errors, and fraud

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Junk Science: Poor science, pseudoscience, errors, and fraud

Postby Typhoon » Thu Jan 12, 2012 7:52 pm

Error cascade

. . .

And yes, preference falsification distorts individuals’ models of what others around them actually believe even in hard science. I once tripped over this in an amusing way, when I volunteered to be on a panel on cosmology and dark matter at some SF convention (might have been Arisia 2004). I did this in the belief that I’d probably be the lone dark-matter skeptic on the panel — the stuff smells altogether too damned much like phlogiston to me. But all four of the other panelists (all of them working physicists or astronomers) also turned out to be dark-matter skeptics, surprising not only me but each other as well!

For anybody who wonders, I favor the alternative explanation of why galaxies don’t fly apart that gravity departs from inverse square at sufficiently long distances (admittedly, this is a purely aesthetic difference, because that theory is not yet testable). But I digress. I didn’t tell that story to argue for this theory, but to illustrate how social pressure to falsify preferences scientists can lead scientists to get stuck in erroneous models of what their peers believe, as well as ignoring experimental evidence.

In extreme cases, entire fields of inquiry can go down a rathole for years because almost everyone has preference-falsified almost everyone else into submission to a “scientific consensus” theory that is (a) widely but privately disbelieved, and (b) doesn’t predict or retrodict observed facts at all well. In the worst case, the field will become pathologized — scientific fraud will spread like dry rot among workers overinvested in the “consensus” view and scrambling to prop it up. Yes, anthropogenic global warming, I’m looking at you!

But climatology is far from the only field to get stuck in a rathole. I have reason to suspect, for example, that Noam Chomsky’s theory of universal grammar may have done something similar to comparative linguistics. I have spoken with linguists who will mutter, if no colleague can hear them, that Chomskian “universal grammar” has Indo-European biases and has to be chopped, diced, and bent out of shape to fit languages outside that group, to the point where it becomes vacuous (and effectively unfalsifiable). The gods alone know what distorting effects this rathole has had on analysis of language morphology (which would be like electron-mass measurements or chromosome counts in this case), but we’re not likely to be shut of them until Chomsky is dead.

There an important difference between the AGW rathole and the others, though. Errors in the mass of the electron, or the human chromosome count, or structural analyses of obscure languages, don’t have political consequences (I chose Chomsky, who is definitely politically active, in part to sharpen this point). AGW theory most certainly does have political consequences; in fact, it becomes clearer by the day that the IPCC assessment reports were fraudulently designed to fit the desired political consequences rather than being based on anything so mundane and unhelpful as observed facts.

. . .
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Re: Junk Science: Unintentional errors and outright fraud

Postby Typhoon » Thu Jan 12, 2012 7:53 pm

Typhoon wrote:Interesting and controversial article.

Wired | Trials and Errors: Why [Medical] Science Is Failing Us

Added [Medical] as the examples cited by the author apply specifically to that field.

But here’s the bad news: The reliance on correlations has entered an age of diminishing returns. At least two major factors contribute to this trend. First, all of the easy causes have been found, which means that scientists are now forced to search for ever-subtler correlations, mining that mountain of facts for the tiniest of associations. Is that a new cause? Or just a statistical mistake? The line is getting finer; science is getting harder. Second—and this is the biggy—searching for correlations is a terrible way of dealing with the primary subject of much modern research: those complex networks at the center of life. While correlations help us track the relationship between independent measurements, such as the link between smoking and cancer, they are much less effective at making sense of systems in which the variables cannot be isolated. Such situations require that we understand every interaction before we can reliably understand any of them. Given the byzantine nature of biology, this can often be a daunting hurdle, requiring that researchers map not only the complete cholesterol pathway but also the ways in which it is plugged into other pathways. (The neglect of these secondary and even tertiary interactions begins to explain the failure of torcetrapib, which had unintended effects on blood pressure. It also helps explain the success of Lipitor, which seems to have a secondary effect of reducing inflammation.) Unfortunately, we often shrug off this dizzying intricacy, searching instead for the simplest of correlations. It’s the cognitive equivalent of bringing a knife to a gunfight.


The comments section is certainly worth reading.


W. Briggs | Statistics Compared To Ladies Of Ill Repute?

And then there’s the National Institute of Statistical Sciences Stanley Young and Alan Karr’s “Deming, data and observational studies“. Here’s their abstract:

“Any claim coming from an observational study is most likely to be wrong.” Startling, but true. Coffee causes pancreatic cancer. Type A personality causes heart attacks. Trans-fat is a killer. Women who eat breakfast cereal give birth to more boys. All these claims come from observational studies; yet when the studies are carefully examined, the claimed links appear to be incorrect. What is going wrong? Some have suggested that the scientific method is failing, that nature itself is playing tricks on us. But it is our way of studying nature that is broken and that urgently needs mending.

Part of what’s broken is statistics.
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Re: Junk Science: Unintentional errors and outright fraud

Postby Typhoon » Tue Mar 27, 2012 1:44 pm

Briggs | How To Present Anything As Significant

We show that despite empirical psychologists’ nominal endorsement of a low rate of false-positive findings (≤ .05), flexibility in data collection, analysis, and reporting dramatically increases actual false-positive rates. In many cases, a researcher is more likely to falsely find evidence that an effect exists than to correctly find evidence that it does not. We…demonstrate how unacceptably easy it is to accumulate (and report) statistically significant evidence for a false hypothesis.
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Re: Junk Science: Unintentional errors and outright fraud

Postby noddy » Tue Mar 27, 2012 3:24 pm

ill be following this.. ive needed to improve my language massively when it comes to explaining my dislike of the common abuses of statistics.
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Replication in cancer research

Postby Typhoon » Thu Apr 05, 2012 7:57 pm

Reuters | In cancer research, many 'discoveries' don't hold up [to relication]

(Reuters) - A former researcher at Amgen Inc has found that many basic studies on cancer -- a high proportion of them from university labs -- are unreliable, with grim consequences for producing new medicines in the future.

During a decade as head of global cancer research at Amgen, C. Glenn Begley identified 53 "landmark" publications -- papers in top journals, from reputable labs -- for his team to reproduce. Begley sought to double-check the findings before trying to build on them for drug development.

Result: 47 of the 53 could not be replicated. He described his findings in a commentary piece published on Wednesday in the journal Nature.

"It was shocking," said Begley, now senior vice president of privately held biotechnology company TetraLogic, which develops cancer drugs. "These are the studies the pharmaceutical industry relies on to identify new targets for drug development. But if you're going to place a $1 million or $2 million or $5 million bet on an observation, you need to be sure it's true. As we tried to reproduce these papers we became convinced you can't take anything at face value."
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Re: Junk Science: Unintentional errors and outright fraud

Postby Typhoon » Sat May 12, 2012 5:33 pm

Nature | Beware the creeping cracks of bias

Evidence is mounting that research is riddled with systematic errors. Left unchecked, this could erode public trust, warns Daniel Sarewitz.


It would therefore be naive to believe that systematic error is a problem for biomedicine alone. It is likely to be prevalent in any field that seeks to predict the behaviour of complex systems — economics, ecology, environmental science, epidemiology and so on. The cracks will be there, they are just harder to spot because it is harder to test research results through direct technological applications (such as drugs) and straightforward indicators of desired outcomes (such as reduced morbidity and mortality).

Nothing will corrode public trust more than a creeping awareness that scientists are unable to live up to the standards that they have set for themselves. Useful steps to deal with this threat may range from reducing the hype from universities and journals about specific projects, to strengthening collaborations between those involved in fundamental research and those who will put the results to use in the real world. There are no easy solutions. The first step is to face up to the problem — before the cracks undermine the very foundations of science.


Nature 485, 149 (10 May 2012) doi:10.1038/485149a
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Re: Junk Science: Unintentional errors and outright fraud

Postby Simple Minded » Sat May 12, 2012 11:27 pm

Excellent series of posts Typhoon. Those of us who are not fart smellers and refuse to blindly worship the fart smellers as omniscient gods salute you!

This sentence alone is worth its weight in gold or methane....

"social pressure to falsify preferences scientists can lead scientists to get stuck in erroneous models of what their peers believe, as well as ignoring experimental evidence."

Robert Prechter would be proud. Scientists are human, and apparently even the smart cows herd sometimes.......
Last edited by Simple Minded on Sat May 12, 2012 11:39 pm, edited 1 time in total.
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Re: Junk Science: Unintentional errors and outright fraud

Postby Simple Minded » Sat May 12, 2012 11:37 pm

Another sentence worth its weight in gold:

"Nothing will corrode public trust more than a creeping awareness that scientists are unable to live up to the standards that they have set for themselves."

Both on the way up..... and on the way down!!! Those who claimed to be gods will often be burnt as witches.

I have often noticed the following at work. Six reviews accompanied by six signatures designating six technical reviews of a document were performed, often means no one actually took the time to understand the content, determine if it made sense, and if the task could be performed as described! All just assume someone else will handle it.

"No snowflake in an avalanche ever feels responsible."

AGW is a perfect example, the same person who thinks billions of $ of OPM should be spent based a projection of future temp rises accurate to 1/10 C over decades won't bet you $100 of their own money that they can predict the temperature at the Seattle Airport two weeks from tomorrow at 10 am to within +/-3C.

Personal cost determines perspective.
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Re: Junk Science: Unintentional errors and outright fraud

Postby Marcus » Sun May 13, 2012 1:26 am

Simple Minded wrote:. . Those who claimed to be gods will often be burnt as witches. . .


". . from the one who has been entrusted with much, much more will be asked."

—Jesus


You guys know the difference between God and a doctor, don't you?



God doesn't think He's a doctor.

Alternative medicine, anyone?
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Re: Junk Science: Unintentional errors and outright fraud

Postby Typhoon » Sun May 13, 2012 5:41 pm

Marcus wrote: . . .

Alternative medicine, anyone?


No, thank you.
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Re: Junk Science: Unintentional errors and outright fraud

Postby Typhoon » Mon May 14, 2012 12:16 am

NYT | Diagnosing the D.S.M. [Diagnostic and Statistical Manual of Mental Disorders]

The fourth edition of the manual, released in 1994, tried to contain the diagnostic inflation that followed earlier editions. It succeeded on the adult side, but failed to anticipate or control the faddish over-diagnosis of autism, attention deficit disorders and bipolar disorder in children that has since occurred.

Indeed, the D.S.M. is the victim of its own success and is accorded the authority of a bible in areas well beyond its competence. It has become the arbiter of who is ill and who is not — and often the primary determinant of treatment decisions, insurance eligibility, disability payments and who gets special school services. D.S.M. drives the direction of research and the approval of new drugs. It is widely used (and misused) in the courts.

Until now, the American Psychiatric Association seemed the entity best equipped to monitor the diagnostic system. Unfortunately, this is no longer true. D.S.M.-5 promises to be a disaster — even after the changes approved this week, it will introduce many new and unproven diagnoses that will medicalize normality and result in a glut of unnecessary and harmful drug prescription. The association has been largely deaf to the widespread criticism of D.S.M.-5, stubbornly refusing to subject the proposals to independent scientific review.
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Re: Junk Science: Unintentional errors and outright fraud

Postby Typhoon » Wed May 23, 2012 9:14 pm

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Re: Junk Science: Unintentional errors and outright fraud

Postby Azrael » Wed May 23, 2012 9:51 pm

Interesting article in Discover Magazine about arson investigations; It turns out that a lot of what arson investigators do is pseudoscience, which has been refuted by scientific studies, sometimes even decades in the past. This pseudoscience has lead to at least one innocent person getting executed.
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Re: Junk Science: Unintentional errors and outright fraud

Postby Azrael » Wed May 23, 2012 10:00 pm

James Randi on pseudoscience

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Re: Junk Science: Unintentional errors and outright fraud

Postby Typhoon » Tue Jul 03, 2012 10:51 pm

Science | Fraud-Detection Tool Could Shake Up Psychology

The most startling thing about the latest scandal to hit social psychology isn’t the alleged violation of scientific ethics itself, scientists say, or the fact that it happened in the Netherlands, the home of fallen research star and serial fraudster Diederik Stapel, whose case shook the field to its core less than a year ago. Instead, what fascinates them most is how the new case, which led to the resignation of psychologist Dirk Smeesters of Erasmus University Rotterdam and the requested retraction of two of his papers by his school, came to light: through an unpublished statistical method to detect data fraud.

The technique was developed by Uri Simonsohn, a social psychologist at the Wharton School of the University of Pennsylvania, who tells Science that he has also notified a U.S. university of a psychology paper his method flagged.
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Re: Junk Science: Unintentional errors and outright fraud

Postby Typhoon » Wed Jul 04, 2012 4:11 am

Science | A New Record for Retractions?

An investigating committee in Japan has concluded that a Japanese anesthesiologist, Yoshitaka Fujii, fabricated a whopping 172 papers over the past 19 years.
Among other problems, the panel, set up by the Japanese Society of Anesthesiologists, could find no records of patients and no evidence medication was ever administered.

"It is as if someone sat at a desk and wrote a novel about a research idea," the committee wrote in a 29 June summary report posted in Japanese on the society's Web site.
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Re: Junk Science: Unintentional errors and outright fraud

Postby Miss_Faucie_Fishtits » Wed Jul 04, 2012 9:10 pm

hweh....... like roaches, for every one you find there are ten more in hiding. I speculate that a casual google search can scare up another one or two right off, and I'm not even talking about the obvious pest-ridden rubbish piles........
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Re: Junk Science: Unintentional errors and outright fraud

Postby Nonc Hilaire » Thu Jul 05, 2012 1:56 am

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Re: Junk Science: Unintentional errors and outright fraud

Postby Typhoon » Fri Jul 20, 2012 3:02 am

AP | US CDC: Whooping cough cases may be most in 5 decades

ATLANTA (AP) — Health officials say the nation is on track to have the worst year for whooping cough in more than five decades.

Nearly 18,000 cases have been reported so far — more than twice the number seen at this point last year. At this pace, the number of whooping cough cases will surpass every year since 1959.

"There is a lot of this out there, and there may be more coming to a place near you," Dr. Anne Schuchat of the Centers for Disease Control and Prevention said Thursday.
Wisconsin and Washington state each have reported more than 3,000 cases, and high numbers have been seen in a number of other states, including New York, Minnesota, Kansas and Arizona.

Whooping cough, or pertussis, is a highly contagious bacterial disease. It leads to severe coughing that causes children to make a distinctive whooping sound as they gasp for breath. In rare cases it can be fatal, and nine children have died so far this year.

Children get vaccinated against whooping cough in five doses, with the first shot at age 2 months and the final one between 4 and 6 years. Then a booster is recommended around age 11. The vaccine's protection does wane and health officials have debated moving up the booster shot.

The CDC is urging adults and especially pregnant women to get vaccinated so they don't spread it to infants who are too young to get the vaccine.

Whooping cough used to cause hundreds of thousands of illnesses a year but cases fell after a vaccine was introduced in the 1940s. Starting in the late 1960s, fewer than 5,000 cases were reported annually in the United States, for a stretch of about 25 years. But the numbers started to rise in the 1990s.


A result of the anti-vaccination hysteria.
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Re: Junk Science: Unintentional errors and outright fraud

Postby Antipatros » Mon Jul 23, 2012 2:22 pm

Typhoon wrote:AP | US CDC: Whooping cough cases may be most in 5 decades

ATLANTA (AP) — Health officials say the nation is on track to have the worst year for whooping cough in more than five decades.

Nearly 18,000 cases have been reported so far — more than twice the number seen at this point last year. At this pace, the number of whooping cough cases will surpass every year since 1959.

"There is a lot of this out there, and there may be more coming to a place near you," Dr. Anne Schuchat of the Centers for Disease Control and Prevention said Thursday.
Wisconsin and Washington state each have reported more than 3,000 cases, and high numbers have been seen in a number of other states, including New York, Minnesota, Kansas and Arizona.

Whooping cough, or pertussis, is a highly contagious bacterial disease. It leads to severe coughing that causes children to make a distinctive whooping sound as they gasp for breath. In rare cases it can be fatal, and nine children have died so far this year.

Children get vaccinated against whooping cough in five doses, with the first shot at age 2 months and the final one between 4 and 6 years. Then a booster is recommended around age 11. The vaccine's protection does wane and health officials have debated moving up the booster shot.

The CDC is urging adults and especially pregnant women to get vaccinated so they don't spread it to infants who are too young to get the vaccine.

Whooping cough used to cause hundreds of thousands of illnesses a year but cases fell after a vaccine was introduced in the 1940s. Starting in the late 1960s, fewer than 5,000 cases were reported annually in the United States, for a stretch of about 25 years. But the numbers started to rise in the 1990s.


A result of the anti-vaccination hysteria.

Indeed. A two-week-old infant here died of whooping cough recently. She was too young to be vaccinated, but if the disease were not present in the population around her.... Not getting your children vaccinated -- presumably due to misguided religious views or hysteria about vaccines or their preservatives causing autism -- endangers not just your own children but others as well.
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Re: Junk Science: Unintentional errors and outright fraud

Postby Typhoon » Fri Sep 28, 2012 1:35 am

Luboš Motl - The Reference Frame | Fifty years after Silent Spring

Nevertheless, I said that it is right for humans to look critically at themselves, to have feedback mechanisms. But what Rachel Carson did was something else and almost entirely negative. She introduced all the basic pernicious features of environmentalism as an ideology that we're still witnessing and struggling against today. I would summarize these features by the following list. She has introduced the following bad habits and beliefs:

1. A small effect, usually a hypothetical one, may be taken out of the context and inflated.

2. The industrial activity (and human activity in general) may always be assumed to be bad for Nature.

3. Claims that are compatible with the previous point may be claimed to be scientific even though there is no actual scientific evidence supporting such claims or if there is even evidence showing that these claims are wrong.

4. When a particular threat is no longer fashionable or powerful enough, when it "loses steam", the main problem with the human activity must be "continuously redefined" even though nothing has actually changed about the human activity or the scientific evidence.


Instead, I want to say that she was a pioneer of an ideologically driven pseudoscience pretending to be science. When she talked about the life of birds and their interactions with the environment, it sounded like a science – ecology. When she talked about pesticides, it sounded like a science, too – some kind of biochemistry. So by the choice of words, she could have pretended she was speaking as a scientist. A problem is that the claims she was making were actually never scientifically justified, at least not with good enough standards. They were ideological slogans. And she was one of the first people in the West who intensely insisted that the compatibility of a proposition with her ideology may replace the scientific rigor that was normally needed to establish scientific claims.

To prove her predetermined conclusion that the industrial activity was wrong, she picked a random technicality – some possible yet mostly hypothetical bad side effects of pesticides – and she inflated them out of proportion and added lots of accusations that weren't really true. At some moment, it became obvious that her scaremongering was indefensible (well, the population of birds was actually growing even when her very book was published) so the particular pesticide hysteria ended. However, what didn't end was her copyrighted dishonesty. It's been recycled many times.
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Re: Junk Science: Unintentional errors and outright fraud

Postby Typhoon » Thu Oct 04, 2012 8:43 pm

PNAS | Misconduct accounts for the majority of retracted scientific publications

Abstract

A detailed review of all 2,047 biomedical and life-science research articles indexed by PubMed as retracted on May 3, 2012 revealed that only 21.3% of retractions were attributable to error. In contrast, 67.4% of retractions were attributable to misconduct, including fraud or suspected fraud (43.4%), duplicate publication (14.2%), and plagiarism (9.8%). Incomplete, uninformative or misleading retraction announcements have led to a previous underestimation of the role of fraud in the ongoing retraction epidemic. The percentage of scientific articles retracted because of fraud has increased ∼10-fold since 1975. Retractions exhibit distinctive temporal and geographic patterns that may reveal underlying causes.


Fraud in scientific research, while still rare, is growing at a troubling pace, a new study finds.
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Re: Junk Science: Unintentional errors and outright fraud

Postby Nonc Hilaire » Fri Oct 05, 2012 12:22 am



When I was at Tulane, a friend was an volunteer subject for Rogaine and quickly discovered it made him impotent. Needless to say, he dropped out and his data was never included.

Didn't stop me from teasing him, though.
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Re: Junk Science: Unintentional errors and outright fraud

Postby Typhoon » Wed Oct 10, 2012 6:03 am

HAL9000 wrote:
What I am going to say is a digression, it is not the same topic, but still relevant: Consider the Food and Drug Administration. It turns out that any new drug must undergo very rigorous testing until it is marketed, to prove that its toxicity is within acceptable limits. These specific toxicity limits are determined by the government.

Similarly, as science becomes more advanced, much more exotic materials will be invented, and already many of the electronic components are very toxic if they are broken down and mixed with drinking water. Some of the solar panels contain arsenic, but the company says that these toxic materials are properly sealed and won't leak even if there is rain on the roof...

So far there is only very little brain cancer caused by cell phones, but in the future much more exotic electromagnetic devices will be invented, and more scrutiny will be needed. For instance, there are already plans to develop new technologies for transmitting electricity to electric cars on highways, without using wires, but nobody knows how this will affect people.


There is no evidence that cell phones cause brain tumours. People have been living near high voltage power lines for nearly century with no increase in the incidence of cancer.
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