Critiques of Science as Currently Praticed

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I basically agree with you, except that you still seem to think that most of the problems in science are statistical.

I'm pretty sure I said that I didn't think that the only problems were statistical.

As I acknowledged above, they are in the case of statins, but if we take that example and explore it a bit further.

If researchers ignore evidence that high cholesterol levels are associated with longer life, it isn't about the statistics as such, it is just very blinkered reasoning.

I agree with that. However, you seem to be jumping to the conclusion that researchers are ignoring this aspect.

The focus, from what I can tell, in most studies has been on cardiovascular risk, and the research seems to consistently show a link between high LDL and higher risk of coronary disease. But what seems to be coming out of the research as well in recent years, is a finding that there is also an association between High LDL and lower risk of all-cause mortality.

This is an issue that should be investigated, and indeed it seems to be something that is being investigated. A study just came out this month looking at that question exactly: Lack of an association or an inverse association between lowdensitylipoprotein cholesterol and mortality in the elderly: a systematic review.

What is makes me wonder is if high LDL increases one risk factor, but also lowers some other risk factors. I imagine they are going to have to break down that all-cause mortality stat to find out which factors vary based on LDL levels.

The link is still, as far as I can tell, well established to the higher risk of heart disease. What this probably points to is that people with other heart disease risk factors are still well advised to seek to lower LDL levels, but that it may be less of a concern for others. Note that the Ibaraki Health Study that you've brought up several times was done on a population that already had low LDL to begin with.

But what you paint as a scandal "why didn't they know this before?????" I see as the steady growth in understanding about these really complicated issues! Your suggestion seems to be that if researchers are doing their jobs well they should be able to figure out all this stuff right off the bat! I don't think its that simple. It takes time to sort all of this out. As the paper I linked above says:

"It is well known that total cholesterol becomes less of a risk factor or not at all for allcause
and cardiovascular (CV) mortality with increasing age, but as little is known as to whether lowdensity
lipoprotein cholesterol (LDLC), one component of total cholesterol, is associated with mortality in the elderly, we decided to investigate this issue."
In terms of advising the public we're in the unenviable position of having to make decisions on this kind of thing with imperfect information. Inevitably this is going to result at times in pushing bad advice. But I'm not sure what the alternative is? Stop public policy health promotion?

Then there is the question of just how effective a drug has to be in order to be prescribed. An effect may be statistically valid, but too small to be of any real use - see my comments above. That isn't a question of statistics, so much as common sense.

Medical studies address this kind of question all the time, from what I've seen. The precise cut off between worth it and not will always be a bit arbitrary, but this is something that is discussed in the literature.

I think the Cochrane 2013 review found that statin use would prevent something like 18 out of 1000 people from dying of heart disease. Whether not that is worth it is a value judgment to be sure. Some people may not consider it worth it, side effects or not, while others will. I guess the question is who should decide? And it may turn out that the research that has been coming out on LDL and all-cause mortality may impact on the advice for statin use as well. That has been brought up in the studies I've looked at too.

I suspect what we're going to see as this research continues is less broad-based advice being given, with specific advice being given to those with certain risk factors.

Many of the problems are quite awful, such as cancer research done on contaminated cell lines. The point about such contamination is that the contaminant cells may grow faster than the intended cells, and overtake the culture completely - so a whole set of research papers are based on totally wrong research.

David

I'm not familiar with the specific case that you're talking about, but I'm sure that its not isolated. Did you think that I would disagree that effort should be made to reduce contamination? Isn't that a methodological issue? It is unfortunate that a single contaminated cell line can impact on a set of research papers coming out of that lab (or labs where they send the cell line), but this highlights the importance on replication. That first line should be the start of the investigation, not the end. Other labs should create their own versions, hopefully uncontaminated, and see if the results replicate. This is exactly the kind of thing I've been talking about!
 
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I'm pretty sure I said that I didn't think that the only problems were statistical.



I agree with that. However, you seem to be jumping to the conclusion that researchers are ignoring this aspect.

The focus, from what I can tell, in most studies has been on cardiovascular risk, and the research seems to consistently show a link between high LDL and higher risk of coronary disease.

You would think that, but look at this:

http://www.zoeharcombe.com/2010/11/...is-a-relationship-but-its-not-what-you-think/

As far as I can gather, the official line (when really pushed by someone who knows the facts) is to claim that the epidemiological evidence is skewed because people with naturally low cholesterol are ill in some unspecified way.

A must read if you haven't already
http://vernerwheelock.com/179-cholesterol-and-all-cause-mortality/

Notice also that some of the studies in the above did test LDL and still got a positive correlation between levels of LDL and longevity!

Using overall mortality is a more definitive measure than recording rates of specific diseases, and of course, it really represents what we all want to know.

I came across this while researching statins on the internet while recovering from statin poisoning, and I didn't believe it to begin with, but it is all laid out in Dr Malcolm Kendrick's book, and remember he is still a practising GP in England:

(This book is fully referenced using actual medical/epidemiological studies of various sorts - it just spills the awful truth!)

http://www.doctoringdata.co.uk/

The medical establishment seems to be embarrassed and just wish he would go away! However, there are doctors and researchers popping up all over the place, and all basically telling the same story.

The situation is totally absurd!

David
 
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You would think that, but look at this:

http://www.zoeharcombe.com/2010/11/...is-a-relationship-but-its-not-what-you-think/

As far as I can gather, the official line (when really pushed by someone who knows the facts) is to claim that the epidemiological evidence is skewed because people with naturally low cholesterol are ill in some unspecified way.

A must read if you haven't already
http://vernerwheelock.com/179-cholesterol-and-all-cause-mortality/

Notice also that some of the studies in the above did test LDL and still got a positive correlation between levels of LDL and longevity!

I think you need to take another look at my last post. I don't think you caught much of what I wrote. You may have missed the bit above where I discussed that the papers show two findings: 1) that high LDL is positively associated with higher heart disease, and 2) that higher LDL was also positively associated with longevity. I referred to the first study in the link you provided (you can find it here if you are interested), and gave you the link to another study, published just this month, showing the same correlation (actually, I think I forgot to attach the link to the title, but I've added it now).

Reading blogs is fine, but its always better to also read the original studies. The Ibraki study that the blog links to shows both higher heart disease (in men, actually, not women), and longevity. The second paper I linked to explores the longevity link further, by meta-analysis.

I understand you have the impression that these issues are ignored by researchers, but I think you should be open to the possibility that more research is going into this stuff than you may know about. Don't just accept someone else's word for it that this or that subject is being ignored - check it out - especially if they have their own agenda.

Using overall mortality is a more definitive measure than recording rates of specific diseases, and of course, it really represents what we all want to know.

I suggested above that I thought it could be more subtle than that. You haven't considered the possibility, I don't think, that high LDL could both increase the risk of heart disease, but decrease some other risk of death. Also the fact that the risk changes depending on other risk factors, such as obesity. Like I said above, I suspect the advice that is going to come out of this is going to be more targetted than the blanket advice previously given.

I came across this while researching statins on the internet while recovering from statin poisoning, and I didn't believe it to begin with, but it is all laid out in Dr Malcolm Kendrick's book, and remember he is still a practising GP in England:

(This book is fully referenced using actual medical/epidemiological studies of various sorts - it just spills the awful truth!)

http://www.doctoringdata.co.uk/

But have you read the actual papers? How about this statin Cochrane study? http://www.ncbi.nlm.nih.gov/pubmed/23440795

The medical establishment seems to be embarrassed and just wish he would go away! However, there are doctors and researchers popping up all over the place, and all basically telling the same story.

The situation is totally absurd!

David
If they just wish it would go away, why do I not seem to have trouble finding studies that are - well - studying these issues?

Are you sure your perception about how medical researchers handle these topics is accurate? How much time to you spend on google scholar or pub med? How often do you go and read the original study that a blogger is writing about? What efforts do you go through to verify if the information is correct?

I'm not suggesting abuses don't happen, they do. But I think you are oversimplifying the work that goes on in these areas, and not giving enough credit where it is due.
 
An Era of Doubt: Scientific Misconduct Is Jeopardizing the Quality and Integrity of Journals

Enter a new era of doubt for scientists, one where the uncertainty lies within. Questions around scientific misconduct and publishing ethics are creating distrust on fields that not only rely on corroboration, but also have the ability to impact our health and wellbeing.

Scientific publication is running at a breakneck pace. In PubMed alone there are more than 26 million citations from more than 5,600 journals. Few would be surprised that a certain portion, about .04% of the annual biomedical literature says the Office of Research Integrity, will be sanctioned for flaws in a process known as retraction. But what raised eyebrows was the fact that the retraction rate has increased ten-fold and could continue to rise. What’s worse was news from the Proceedings of the National Academy of Science (PNAS) that the vast majority of papers retracted—67%—was due to fraud or suspected fraud, duplication, or plagiarism.

Scientific misconduct is not the only source of doubt and distrust. A study published by Science, “Estimating the reproducibility of psychological science,” found that less than half, and by some measures only about 36%, of studies in psychology had reproducible results. Reproducibility, a cornerstone of the scientific method, is also coming under fire.

The industry is still grappling with questions about rigor in science. A cottage industry of ethics groups and watchdog organizations such as the Center for Scientific Integrity has risen up to support and scrutinize publication ethics. COPE, the Committee on Publication Ethics for example, has seen their ranks grow from a small group of medical journal editors in 1997 to more than 10,000 members worldwide.

Critics point to new influences like technology and the rise of unscrupulous “predator” publications and call into question the validity of the peer review process and the tremendous pressures on a system based on incentives. Some, like former British Medical Journal Editor Richard Smith, take it a step further and declare that the age of journals is over.
 
But have you read the actual papers? How about this statin Cochrane study? http://www.ncbi.nlm.nih.gov/pubmed/23440795


If they just wish it would go away, why do I not seem to have trouble finding studies that are - well - studying these issues?

Are you sure your perception about how medical researchers handle these topics is accurate? How much time to you spend on google scholar or pub med? How often do you go and read the original study that a blogger is writing about? What efforts do you go through to verify if the information is correct?

Interesting that when I asked Arouet questions like these he claimed I was attacking him and said he would no longer talk to me....
 
Was it due to actual side effects, or a fear of side effects? The medical literature is pretty clear that a certain proportion of patients will experience side effects, even bad ones, and it seems perfectly reasonable to stop taking them in those cases.
I took statins for 3 years, and felt very positive about them. I wasn't afraid of the side effects, and when they started I assumed it must be something else, and so did my doctor! Send me a PM if you want the whole story.
But if it is fear of side effects that is the primary reason one decides not to take them, then perhaps they should try them out first to see if they are among the unlucky (note: this reasoning only applies if fear of side effects is the main reason for not wanting to take them, there can be other reasons someone may have for not taking them).

(My doctor hasn't brought up statins for me yet, so I haven't ever tried them myself).
The thing that shocked me, was the number of people that I knew for real (i.e. not on the internet) that reported statin problems, though most encountered them much sooner.

Trying them first to see if they give muscle problems may not be such a good idea because they also raise blood sugar - pushing some people into the diabetic category! They can also produce memory problems - remember that the brain uses a lot of cholesterol - I actually know someone who had both muscle problems and memory problems - sufficient that he nearly messed up his business.

I now eat butter (i.e. saturated fat) rather than margarine, don't both too much about salt, and don't take a statin!

Do read the links I gave you, because otherwise you will never believe what a mess this field is in!

David
 
Science’s Sacred Cows (Part 1)

"The violations of science’s domain by religion are numerous, well known and egregious. Particularly odious was the church’s burning of Giordano Bruno at the stake in 1600 for multiple “heresies” that included the promotion of Copernicanism (the idea that the Earth orbits the Sun rather than vice versa), a suspicion that the stars are suns like our own and a belief in the plurality of worlds. Close on the heels of Bruno’s demise came the trial of Galileo of 1632-3 in which the Inquisition convicted the world’s most eminent scientist of heresies “more scandalous, more detestable, and more pernicious to Christianity than any contained in the books of Calvin, of Luther, and of all other heretics put together.” Galileo’s life was spared when he signed a confession recanting the “heresy” of Copernicanism; however, he remained under house arrest for the duration of his life.

Skirmishes between science and religion persist. Today’s religious fundamentalists periodically attempt to force the teaching of creationism (or one of its many guises) in public schools, in violation both of science’s domain and the constitutional separation of church and state. For a short summary of the most recent major skirmish, the 2005 U.S. Supreme Court case Kitzmiller v. Dover Area School District, see pages 89-90 of Jason Rosenhouse’s Among the Creationists (Oxford, 2012).

Science’s infractions are subtler but equally damaging to the human spirit. During an enlightening lecture in 2000 by religion scholar Huston Smith, I began to appreciate how science infringes on religion’s domain. Smith thoughtfully distinguished science from scientism. The former is an investigative protocol; the latter is a religion, complete with dogma. Science is a formalized procedure for making sense of the world by studying its material properties, perceived through the awareness of the senses, albeit senses heightened by modern marvels such as the electron microscope, the Hubble Space Telescope or the Chandra X-Ray Observatory. Scientism (or scientific materialism), on the other hand, adds to science a statement of faith: The universe is only material. Moreover, given the spectacular successes of science over the past three centuries, it is more than fair to acknowledge that science represents a powerful way to learn about the world. But scientism ups the ante: Science is the best (or only) way to make sense of the world. In short, scientism is to science what fundamentalism is to religion: cocksure and inflexible.

Science remains most true to itself and of greatest value to humanity when it assiduously avoids unnecessary assumptions. Over the long arc of history, science has initially embraced — then discarded — most of the following tacit assumptions: dualism, determinism, reductionism, absolute time, absolute space, the principle of locality, materialism and, most recently, realism. In subsequent posts, we’ll examine each of these in some detail. For now, let’s summarize..."
 
http://www.huffingtonpost.com/dave-pruett/newtons-laws_b_2431074.html
Pruett then goes into a historical overview...

Science’s Sacred Cows (Part 2): Absolute Space and Time


Science’s Sacred Cows (Part 3): Determinism

Science’s Sacred Cows (Part 4): Dualism

Science’s Sacred Cows (Part 5): Locality

Science’s Sacred Cows (Part 6): Realism

Science’s Sacred Cows (Part 7): Reductionism

To arrive at the concluding piece:

Science’s Sacred Cows (Part 8): Materialism


Materialism, I believe, harbors a multitude of sins. Today I’ll argue that the materialistic paradigm is detrimental both to science and to the human condition. And in the final post of the series, we’ll examine some evidence that the paradigm, at long last, is collapsing.

In fairness, materialism is a tacit rather than a formal assumption of modern science. Nevertheless, it remains the prevailing paradigm, especially among many prominent scientists, as the following example illustrates.

On page 14 of Ever Since Darwin (1977), a collection of beautifully written essays by the late evolutionary biologist Stephen Jay Gould, the writer drops a bombshell: “Evolution is purposeless, nonprogressive, and materialistic.” When a scientist of Gould’s gravitas makes such claims, it is tantamount to engraving them in stone.

One wonders why Gould felt the need to interject the sentence. Such assertions, which ultimately lie beyond the ken of science, are more akin to religious dogma than scientific fact. Scientists are often quick to challenge incursions of religion into the domain of science, and rightly so. But those same scientists may be blind to their own infractions. Why should science be wary of overreaching?

Polls show that 46 percent of Americans self-identify as “young-earth creationists” by responding affirmatively to the following statement: “God created human beings pretty much in their present form at one time within the last 10,000 years.” (Seehttp://ncse.com.) Surprisingly, the percentage of affirmative responses has hardly varied in the 30 years since Gallup began conducting the survey. Why do nearly half of Americans reject evolution despite 150 years of substantiating evidence? And why is America, which has produced 270 Nobel laureates — far more than any other country — so anti-science?

I suspect it is because of the cognitive dissonance between science’s intimations of our “purposeless” origins in a “materialistic” cosmos and our own instincts to the contrary. Faced with the choice between “an antiscientific philosophy and an alienating science,” many Americans opt for the former. “Do we really have to make this tragic choice?” pleaded the late Nobel laureate in chemistry, Ilya Prigogine.

In the current era, the choice is indeed “tragic.” There is strong correlation between those who deny evolution and those who deny climate science. Climatologists pull out their hair in frustration at the difficulty of awakening Americans to the seriousness of the crisis. The wake-up call goes unheeded because nearly half the American public is tone-deaf to science. Could science’s “alienating” overreach be partly at fault?
 
I think you need to take another look at my last post. I don't think you caught much of what I wrote. You may have missed the bit above where I discussed that the papers show two findings: 1) that high LDL is positively associated with higher heart disease, and 2) that higher LDL was also positively associated with longevity. I referred to the first study in the link you provided (you can find it here if you are interested), and gave you the link to another study, published just this month, showing the same correlation (actually, I think I forgot to attach the link to the title, but I've added it now).

Reading blogs is fine, but its always better to also read the original studies. The Ibraki study that the blog links to shows both higher heart disease (in men, actually, not women), and longevity. The second paper I linked to explores the longevity link further, by meta-analysis.

I understand you have the impression that these issues are ignored by researchers, but I think you should be open to the possibility that more research is going into this stuff than you may know about. Don't just accept someone else's word for it that this or that subject is being ignored - check it out - especially if they have their own agenda.



I suggested above that I thought it could be more subtle than that. You haven't considered the possibility, I don't think, that high LDL could both increase the risk of heart disease, but decrease some other risk of death. Also the fact that the risk changes depending on other risk factors, such as obesity. Like I said above, I suspect the advice that is going to come out of this is going to be more targetted than the blanket advice previously given.



But have you read the actual papers? How about this statin Cochrane study? http://www.ncbi.nlm.nih.gov/pubmed/23440795


If they just wish it would go away, why do I not seem to have trouble finding studies that are - well - studying these issues?

Are you sure your perception about how medical researchers handle these topics is accurate? How much time to you spend on google scholar or pub med? How often do you go and read the original study that a blogger is writing about? What efforts do you go through to verify if the information is correct?

I'm not suggesting abuses don't happen, they do. But I think you are oversimplifying the work that goes on in these areas, and not giving enough credit where it is due.

Well look, we are both obviously looking at this from a high level. Clearly one of the problems here is that these studies don't all come to the same conclusion, and I suspect the differences are greater than would be due to pure chance. For example:
In the Isehara Study, data was collected from those who had an annual check-up. The final database contained information on 8,340 men (aged 64±10 years) and 13,591 women (61±12 years). Again it was found that the level of LDL cholesterol was inversely related to the all-cause mortality rate. Interestingly it was reported that, the mortality rates due to cancer in men and to respiratory disease without cancer (mostly pneumonia) in men and women were lowest in those groups with the highest values.

However, part of the issue here may be that total mortality is a better defined number than deaths due to a specific disease.

Fortunately, all cause mortality is what we care about! I don't think the health services should be advising people to get their cholesterol levels down, when the data seems to show that they live on average a little longer with high cholesterol!

Surely that is a scandal!

When I was prescribed Simvastatin, I thought of it as a "live longer" pill, not as a "live not quite so long but with less CVD" pill - an effect that seems to come and go from study to study!

David
 

William Reville:Fraud is now the biggest enemy of science

"Scientists are not required to subscribe to any universal code of ethics. This needs to change"

Governments routinely cover up scientific misdeeds. Let’s end that


If you read that researchers were faking X-rays, retinal scans, and lab tests in their work, you might think — or hope — that it was something out of science fiction. But as Charles Seife reported in a JAMA Internal Medicine paper earlier this year, that has all happened in real life, and the Food and Drug Administration is covering it up. “The FDA has repeatedly hidden evidence of scientific fraud not just from the public,” Seife wrote in a Slate piece about the findings, “but also from its most trusted scientific advisers, even as they were deciding whether or not a new drug should be allowed on the market.”

The problem isn’t limited to the United States.
Reports of research misconduct by Canadian researchers are heavily redacted, with names of people, institutions, and even relevant journal articles blacked out.

But why is publicity for science fraudsters important? Well, consider the obverse: Why do they deserve protection from the public eye? Research cheats are no different from other bad actors who misuse taxpayer dollars. Ignominy can be a powerful deterrent against the temptation to cut corners. And across the globe, we could use more of it.
 

Why is it so damn hard to get a paper retracted?

In 2014, David Allison noticed something wonky with a paper in the journal Childhood Obesity. The article purported to find that children who regularly ate kids’ meals with toys inside — we won’t name them, but an example might rhyme with “shmappy shmeal” — were liable to consume excess calories. But Allison spotted that the researchers had incorrectly analyzed their data, causing them to exaggerate the effects by more than tenfold.

That realization prompted a letter from Allison, a biostatistician at the University of Alabama at Birmingham — which, in full disclosure, receives funding from the National Restaurant Association — and his colleagues. Several months later, the journal retracted the paper.

Hurray for science and its much-vaunted self-correcting mechanism, right?

If only.

In an article in Nature this week, Allison and colleagues report that such corrective action by a journal is far from the norm. Over a period of 18 months the group submitted corrections and retraction requests to 25 papers in a variety of publications and had one other successful retraction. A few other journals published their letters but did not retract the studies.

Mostly, though, Allison’s group found the effort a waste of time. “Too often, the process spiralled through layers of ineffective e-mails among authors, editors and unidentified journal representatives, often without any public statement added to the original article,” Allison and colleagues write.

The problem gets worse: “Some journals that acknowledged mistakes required a substantial fee to publish our letters: we were asked to spend our research dollars on correcting other people’s mistakes.” One unnamed publisher even had the gall to declare that it would exact a fee of $10,000 from authors of withdrawn papers — a draconian amount that clearly poses a disincentive to doing the right thing.

So this is the state of scientific self-correction in the 21st century. Despite the opportunities for instant access to studies, international and public scrutiny, and rapid communication, getting a paper retracted or corrected turns out to be well-nigh impossible.
 
Wow - this thread is now so chock full of evidence against science, it makes me reel!

David

I think we can lean toward supporting the relational information conveyed by experiments that have been applied to reliable technology/medicine/etc?
 
I think we can lean toward supporting the relational information conveyed by experiments that have been applied to reliable technology/medicine/etc?
Yes, but that is saying valid science is science that produces tangible results. So much of science doesn't and can't - environmental science, cosmology, high energy physics, archaeology, big chunks of medical research, the history of the earth and of humanity, forensic science(?), ......................

David
 
Yes, but that is saying valid science is science that produces tangible results. So much of science doesn't and can't - environmental science, cosmology, high energy physics, archaeology, big chunks of medical research, the history of the earth and of humanity, forensic science(?), ......................

David

Well some of what you list probably can produce something if the science is cleaned up.

I think speculative/forecasting research can be useful but part of the challenge is consensus in these arenas can be more influenced by academic culture. There's at least one (admittedly previously mentioned) study on this, though as per the rest of this thread obviously more examination needs to be done to really know:

Study: Elite scientists can hold back science
 
Well some of what you list probably can produce something if the science is cleaned up.

I think speculative/forecasting research can be useful but part of the challenge is consensus in these arenas can be more influenced by academic culture. There's at least one (admittedly previously mentioned) study on this, though as per the rest of this thread obviously more examination needs to be done to really know:

Study: Elite scientists can hold back science

I mean, all the information in this thread leads me to a pretty radical conclusion.

How is modern science validated? We seem to be approaching the conclusion that apart from practical gadgets or techniques, it can't be validated - peer review doesn't work, consensus doesn't work!

David
 
I mean, all the information in this thread leads me to a pretty radical conclusion.

How is modern science validated? We seem to be approaching the conclusion that apart from practical gadgets or techniques, it can't be validated - peer review doesn't work, consensus doesn't work!

David

There's also baseless extrapolation from simple cases - I suspect this is why Psychology has been at the center of the replication crisis.

That said, I think peer review does work in part - after all it's how we got to some of the applied technology/medicine we use today. Consensus...I think the inherent problem there is populations don't have the minimal knowledge necessary to judge many claims supposedly made in the name of science. I suspect a society properly educated about how science works, what limitations it (arguably) has, mistaken assumptions about what it's already shown, and so on would improve science-as-practiced immensely.
 
There's also baseless extrapolation from simple cases - I suspect this is why Psychology has been at the center of the replication crisis.
Some of the problems of psychology may well be due to ψ effects!
That said, I think peer review does work in part - after all it's how we got to some of the applied technology/medicine we use today.
Well we are talking mainly about modern science, where computer programs have been written to generate fake papers that then pass into the literature via the peer review process!

I mean if there was a trace of sanity, science institutions would fund a large program to create more and better software of this sort, and then stress test every journal regularly.
Consensus...I think the inherent problem there is populations don't have the minimal knowledge necessary to judge many claims supposedly made in the name of science. I suspect a society properly educated about how science works, what limitations it (arguably) has, mistaken assumptions about what it's already shown, and so on would improve science-as-practiced immensely.
The problem is that the vast majority of people are way behind the point where they can judge these issues. For example, if calculus is way above your head (and you don't like maths), how do you assess claims that high energy physics has become trapped by an obsession with 'beautiful' mathematics - as Roger Penrose (and many others) now seems to think.

When you look at the sheer breadth of evidence for science going off the rails, I can't see how it can be fixed - particularly when most scientists and institutions seem to want business as usual, even while all this evidence is coming out. Maybe we are entering a dark age. Maybe after that science has to be done in a place that is more like a monastery, where everyone has to listen to sermons about the evil practices that gave rise to the dark age!

Modern science rather resembles the EU! At first it looks as if it could be fixed and made to work again. However hardly anyone on the inside wants the pain of fixing it, so it goes on deteriorating so that in the end it simply has to break up.

David
 


When universities stonewall investigations of research misconduct

Colleagues had raised doubts about Paolo Macchiarini’s work since 2014, questioning whether he had obtained informed consent from patients, and alleging that he made up results. An initial outside inquiry found that he had, indeed, committed misconduct. But the Karolinska initially rejected that finding, saying that he had only been, well, slightly sloppy.

Then, in January, a story broke in Vanity Fair in which a former girlfriend recounted how Macchiarini claimed to be the personal physician to Pope Francis and to have treated the Obamas, Bill Clinton, and other world leaders. Combined with a very thorough Swedish documentary that raised other questions, suddenly Macchiarini’s oeuvre didn’t look so hot. Within a month, the Karolinska announced that it wouldn’t renew Macchiarini’s contract, and six weeks after that, they fired him, effective immediately.

But the narrative does look familiar. And it wasn’t the first time in which universities — who by US law are the ones that must open an investigation into misconduct — stonewalled the effort.

The other case we’re thinking of is that of former Duke University cancer specialist Anil Potti. Back in 2006, Potti led a team that published a paper in Nature Medicine about a way to tailor patients’ cancer treatments using their individual genetic signatures. In a glowing press release, Duke declared that its scientists “have developed a panel of genomic tests that analyzes the unique molecular traits of a cancerous tumor and determines which chemotherapy will most aggressively attack that patient’s cancer.”

Not everyone was so impressed. In 2007, a pair of statistics experts in Texas raised questions about Potti’s work. Upon analysis, they believed, Potti’s findings weren’t reliable. Potti’s — and Duke’s — response? Thanks for that interesting esoterica, but the results stand just fine. Anyone want to be in a clinical trial? And so hundreds of people with cancer lined up to be in the supposedly groundbreaking study, their treatment determined by Potti et al’s algorithm.

That study was published in The Lancet Oncology. Then, in 2010, Potti resigned from Duke in a misconduct scandal that continues to ripple even today. Last year, the Federal Office of Research Integrity (ORI) announced that Potti had faked data.

So what toppled the Blue Devils’ former golden boy? Not an internal investigation into the veracity of his research, since Duke steadfastly denied there were any problems. What brought him down was a report in a cancer newsletter that the Duke scientist had fabricated his resume to include, among other things, a bogus Rhodes scholarship. That revelation led to an unraveling of lies that, in the end, proved too great an embarrassment for the institution to ignore.

Rewrite the Potti script with new dates and a new research area, and you have the Macchiarini story. And vice versa.

Even if it were only these two cases in which institutions dragged their feet and ignored clear evidence of misconduct while patients suffered, it would be two too many, but it’s not. We see these sorts of cases play out all the time, with most flying under the public’s radar because they are not so high-profile.
 
https://www.sciencebasedmedicine.org/the-power-of-replication-bems-psi-research/

Criticisms of Bem

It’s possible for a study to “look good on paper” – meaning that the details that get reported in the published paper may make the study look more rigorous than it actually was. There may also be alternate ways to analyze the data that give a different picture Ritchie, Wiseman, and French outline several criticisms of Bem’s methods. They mention the Bayesian issue, but also that an analysis of the data shows an inverse relationship between effect size and subject number. In other words, the fewer the number of subjects the greater the effect size. This could imply a process called optional stopping.

This is potentially very problematic. Related to this is the admission by Bem, according to the article, that he peeked at the data as it was coming in. The reason peeking is frowned upon is precisely because it can result in things like optional stopping, which is stopping the collection of data in an experiment because the results so far are looking positive. This is a subtle way of cherry picking positive data. It is preferred that a predetermined stopping point is chosen to prevent this sort of subtle manipulation of data.

Another issue raised was the use of multiple analysis. Researchers can collect lots of data, by looking at many variables, and then making many comparisons among those variables. Sometimes they only publish the positive correlations, and may or may not disclose that they even looked at other comparisons. Sometimes they publish all the data, but the statistical analysis treats each comparison independently. In short what this means is that if you look at 20 comparisons with a 1/20 chance of reaching statistical significance, by chance one comparison would be significant. You can then declare a real effect. But what should happen is that the statistical analysis is adjusted to account for the fact that 20 different comparisons were made, which can potentially make the positive results negative.

Finally there was a serious issue raised with how the data was handled. Subjects occasionally made spelling error when listing the words they recall. The result may have been a non-word (like ctt for cat) or another word (like car for cat). Researchers had to go through and correct these misspellings manually.

The authors point out that these corrections were done in a non-blinded fashion, creating the opportunity to fudge the data toward the positive by how correction choices are made. Bem countered that even if you removed the corrected words the results would still be positive, but that is still methodologically sloppy and is likely still relevant, for reasons I will now get into...
 
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