Critiques of Science as Currently Praticed

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Science can't really be about consensus. If people need to rely on consensus, it would be more honest to say that there isn't really any clear evidence one way or the other, or that there is contradictory evidence - which itself implies that something isn't understood.

Consensus seems to have lead to some terrible mistakes. Think for a moment about the consensus that has existed for decades that high blood cholesterol is bad for you, and then read this:

http://vernerwheelock.com/179-cholesterol-and-all-cause-mortality/

Empirical study after study has shown that high cholesterol is beneficial. Is it any use talking about the consensus view of cholesterol? Note that some of those studies also looked at LDL cholesterol, and then then the result is the same!

This illustrates something that is common to a lot of really bad science - it couldn't exist if everyone was aware of all the currently available evidence. I mean, why would you target a molecule that is clearly required by the body, and seems from repeated studies to be correlated with long life? At the very least you would expect those wanting to reduce cholesterol levels to begin by describing those studies and then explain why they were somehow misleading!

Likewise, nobody in their right minds would set out to measure supposed changes in global temperature of tenths or hundredths of a degree using the data from weather stations:

https://wattsupwiththat.com/2011/01/22/the-metrology-of-thermometers/

Or to take the possible problems with vaccines, surely the place to start is with the CDC Insider who came out as a whistle-blower!

David
 
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If we want good science, we have to create better incentives

The Parasite is a new award for scientists who replicate the work of others. Started by Casey Greene and colleagues at the University of Pennsylvania Perelman School of Medicine, the Parasites competition is designed to "recognize outstanding contributions to the rigorous secondary analysis of data," its website says. What it secondarily does, though, is serve as a great example of an incentive for good behavior — which science could use more of.

The name of the prize is a jab at the editors of the New England Journal of Medicine, who used the expression "research parasites" to describe how some scientists feel about those who conduct studies using data other people have generated. Many scientists reacted with disbelief and disdain, and while the journal later clarified that it wasn't necessarily endorsing the idea, they also didn't come out and say the term sent the wrong message, either.


The award — which generated a fair amount of buzz on social media — is unlikely to significantly shift the opinions of the unnamed scientists for whom the NEJM purportedly spoke. But it speaks to the urgent need for incentives to reward those scientists doing what's best for their field. Unfortunately, our current incentive structure — based almost entirely onpublishing in prestigious journals, with large cash rewards in some countries — discourages sharing, replication, and, some might argue, careful science.

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The underbelly of simulation science: replicating the results

Replicating computer-simulated science is harder than you think, as a group of aerospace researchers from George Washington University have found.

In fact, without decent versioning, documentation, publication of data and rigorous evidence standards, simulations that attract headlines both in academic and general media should probably be consigned to the lamented Journal of Irreproducible Results.

Olivier Mesnard and Lorena Barba of the university's mechanical and aerospace engineering school have just spent three years trying to replicate computational fluid dynamics (CFD) results first published in 2014, and have published their travails here at Arxiv.

Different hardware, a newer operating system, and a newer compiler can all wreck reproducibility, they write: “In an iterative linear solver, any of these things could be related to lack of floating-point reproducibility. And in unsteady fluid dynamics, small floating-point differences can add up over thousands of time steps to eventually trigger a flow instability (like vortex merging).”

As they note, “computational science and engineering lacks an accepted standard of evidence”.

“When large simulations run on specific hardware with one-off compute allocations, they are unlikely to be reproduced. In this case, it is even more important that researchers advance towards these HPC applications on a solid progression of fully reproducible research at the smaller scales."
 
The War Inside Your Head: Researchers are battling over how to identify and treat mental illness — but the changes may help pharmaceutical companies more than patients.

....As anyone who has taken Intro to Psych knows, the DSM has been controversial from the start. Supporters argue that the medicalization of mental illness, as embodied by the DSM, is beneficial for those suffering from mental illness and their loved ones. It legitimates mental illness in the public discourse and undermines pervasive ideas that mental illness is not real or is exaggerated by patients — or that mental illness reflects a defect of moral character or a “weakness of will.”

Critics of the DSM have long argued that the medical model divorces mental illnesses from the social and historical conditions in which they arise. By assuming that the cause of mental illness lies entirely within the person and not in society, the medical model and the DSM depoliticize the distress of the disadvantaged and marginalized. At the same time, the business of codifying, and treating, mental illnesses is also quite lucrative, sparking concerns that the needs of those suffering often come second to the needs of the insurance and pharmaceutical industries.

Recently, however, the loudest critiques of the DSM have come not from the Left, or the anti-psychiatric movements, but from the major players in the mental health field itself. The National Institute of Mental Health (NIMH) — the largest funder of mental health research and a longtime stalwart of the DSM — has dramatically changed its position on the diagnostic manual over the past few years. Now sharply critical of the manual’s validity, the NIMH is calling for the field to move away from the diagnostic manual altogether and towards a new paradigm of mental illness....

Subjective experience is central to mental illness. So while the modest effects of psychopharmacological drugs discovered in the past decade could indicate that better biological research is needed, they could also mean that the key to understanding and addressing mental illnesses lies elsewhere. Obviously biology matters, but the field needs to study mental illness on its own terms, rather than uncritically emulate the logic of the so-called hard sciences for the legitimacy and funding it brings.

Questioning the medical model doesn’t mean mental illness is a myth. Far from it. People’s distress is very real, and the field can no longer ignore the problems in its current understanding of mental illness. But the RDoC’s exclusive focus on biomarkers to draw in pharmaceutical investment will not address these shortcomings.

Instead, the RDoC will further strengthen the field’s economic and ideological ties to the profit-driven private sector. Its focus on “cutting-edge” neuroscience biomarkers will tether psychologists ever tighter to psychopharmacology and the prerogatives of big pharmaceutical companies.

The RDoC also hurts those suffering the most by ignoring the connection between mental illness and societal structures. As Francessays, “NIMH has had its attention so distracted by glorious dreams of a future research revolution that it has completely lost touch with the desperate suffering of schizophrenic patients in the present. It pays no attention to, and takes no responsibility for, the mess that is US mental health care.”

Over the past fifty years, the number of public psychiatric hospital beds in the US has decreased from 340 to 17 beds per 100,000 people, leaving poor patients nowhere to turn for adequate care. Many become homeless or end up in the prison system for petty crimes that could have been easily prevented if they had the proper communitycare. “These patients are suffering greatly not so much for lack of knowledge on how to care for them, but because of a lack of attention and inadequate resources,” says Frances. RDoC is part of a growing trend in which state and community services are short-changed in favor of a psychopharmacological model for treatment.
 
Cosmologists should be more skeptical of dark matter

To get computer models to look similar to the Universe around us, cosmologists have assumed that around 96 per cent of matter and energy are in forms that we cannot directly detect. You might think that this would make cosmologists wary of relying on such hypothetical substances. Yet for the majority working today, dark matter and dark energy are every bit as real as the stars and galaxies that we can see.

Such corporate belief might work for business, but it has no place in science. Back in 1620, Francis Bacon published his Novum Organum (The New Method). In his description of how to investigate nature, he cautioned would-be scientists about four ‘idols of the mind’. Namely:

Idola tribus (idols of the tribe) – which occur when people try to feed new facts into their preconceived ideas. ‘The human understanding is like a false mirror,’ Bacon wrote, ‘which, receiving rays irregularly, distorts and discolours the nature of things by mingling its own nature with it.’

Idola specus (idols of the cave): ‘Everyone… has a cave or den of his own, which refracts and discolours the light of nature,’ writes Bacon. These individual likes and dislikes cloud judgment.

Idola fori (idols of the marketplace): in the exchange of ideas, Bacon writes, ‘the ill and unfit choice of words wonderfully obstructs the understanding’.

Idola theatri (idols of the theatre): the final idol comes about by blindly following academic dogma and not asking enough real questions about the world. Why theatre? ‘In my judgment,’ writes Bacon, ‘all the received systems are but so many stage plays, representing worlds of their own creation after an unreal and scenic fashion.’

Cosmology could well be falling foul of these idols. In the case of dark matter, the unquestioning belief is puzzling because the direct searches for these particles are coming up effectively empty‑handed. Yet observations are routinely interpreted as being the result of dark matter. No other avenues of approach are taken by the vast majority of researchers.

In reality, there are other possible solutions that at least warrant examination and comparison. In certain circumstances they fit the observations better than dark matter can. They usually involve a different approach, which is to alter how the force of gravity works or to relax an assumption about the way we think the Universe works, rather than add new constituents to the Universe...
 
Here is an interesting article about evolution. Towards the end, the author gives a graphic example of how conventional science tends to mismanage data!

http://www.evolutionnews.org/2016/05/toward_a_consen102879.html

David

From that article:
With all of this contradictory evidence, even evolutionists have realized in recent years that the traditional evolutionary tree model is failing. As one evolutionist explained, "The tree of life is being politely buried."

The whole concept of of a tree here is known to be flawed, sometimes after some re-evaluation, some species may suddenly be lifted from one branch and re-positioned on a completely separate branch. A mesh structure is more appropriate, with criss-crossings and interweaving of lines.

Why has this situation come about? I believe it is because underlying the whole structure are religious and moral underpinnings, with hellfire and damnation never far away. The idea that all creatures, throughout all of time, have only ever mated with their own kind has a strong moral undertone. To think otherwise would be heresy, Yet it is clearly wrong. Evolutionary theory needs to rid itself of its religious and moral basis if it is to arrive at a more scientific understanding.
 
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Brian Whitworth on why physics is a "Hollow Science", taken from Quantum Realism, Chapter 1: The physical world as a virtual reality

"It is important to realize that in physics today, we have no knowledge of what energy is. We do not have a picture that energy comes in little blobs of a definite amount. It is not that way. However, there are formulas for calculating some numerical quantity and when we add it together it gives “28″—always the same number. It is an abstract thing in that it does not tell us the mechanisms or the reasons for the various formulas."

-Feynman on Energy
 
Torture, APA, and the Hoffman Report: What Now?

If all of the elements of the Hoffman Report are accurate—and I have no reason to believe this Report is not accurate—then, several key points are quite clear:

  1. Members of the APA leadership/staff were indeed collusive with the torture policies of the Bush Administration following the attacks of 9/11 and the resulting wars.
  2. Before 2001, there was a push for the Ethics Office to be less aggressive in pursuing ethics policy and adjudication of ethics complaints. The failure of APA to maintain a rigorous Ethics policy paved the path for psychologist collusion in torture and other prisoner abuses.
  3. Key APA leaders/staff actively endeavored to weaken anti-torture Resolutions/Referendums through a pattern of manipulation, misdirection, and misinformation.
  4. Key APA leaders/staff engaged in a pattern of deception to hide their complicity in torture and abusive interrogation practices from other APA leaders, members volunteering in the Association, the broader membership, as well as the wider population.
  5. The fox appeared to be guarding the chicken coop. Under current APA procedures, all ethics- related policy and adjudication of ethics complaints must be coordinated with and through the Ethics Office. Yet, Dr. Stephen Behnke, Director of the APA Ethics office, was at times also on the Department of Defense (DoD) payroll. The Ethics Office should serve the membership of the APA and use the full resources of that office to maintain and promote ethics and the protection of human welfare and human rights. Unfortunately, it now appears that Dr. Behnke used that office to maintain and promote the goals of the DoD and, by extension, the government’s abusive interrogation policies.
Based on the findings of the Hoffman Independent Review and Report, APA Council of Representatives should undertake several actions immediately. These actions should be at minimum be three-pronged. First, and foremost, APA needs to further strengthen its policies related to torture, prisoner interrogations, and national security concerns. Second, the APA needs to clean house and address the wrongs of the past. Third, APA must review policies, procedures, and organizational structures to insure that human rights are moved to the forefront of APA values.
 
Undisclosed Financial Conflicts Endemic in Clinical Practice Guidelines

While there has been a recent push to account for financial conflicts of interest in medical research, less attention has been paid to organizations that produce clinical practice guidelines (CPGs) that offer official treatment recommendations to doctors and providers. A new analysis published this week in the journal PLOS Medicine reveals that such organizations are often rife with financial conflicts of interest with biomedical companies and that these conflicts are often undisclosed. According to the study, only one-percent of the guidelines disclosed the organization’s financial relationships with companies and only half of all guidelines disclosed the financial conflicts held by individual members of the organizations.

“These types of relationships can have undue influence because clinical practice guidelines are resource intensive to produce and are developed by a small number of expert clinicians who determine the scope of the guidelines, synthesize and interpret the published evidence base, and provide recommendations,” the researchers, Henry Stelfox and his colleagues from the University of Calgary in Canada, write.
 

Wow, this needs more exposure:
http://www.apa.org/independent-review/APA-FINAL-Report-7.2.15.pdf
Our investigation determined that key APA officials, principally the APA Ethics Director joined and supported at times by other APA officials, colluded with important DoD officials to have APA issue loose, high-level ethical guidelines that did not constrain DoD in any greater fashion than existing DoD interrogation guidelines. We concluded that APA’s principal motive in doing so was to align APA and curry favor with DoD. There were two other important motives: to create a good public-relations response, and to keep the growth of psychology unrestrained in this area.

We also found that in the three years following the adoption of the 2005 PENS Task Force report as APA policy, APA officials engaged in a pattern of secret collaboration with DoD officials to defeat efforts by the APA Council of Representatives to introduce and pass resolutions that would have definitively prohibited psychologists from participating in interrogations at Guantanamo Bay and other U.S. detention centers abroad. The principal APA official involved in these efforts was once again the APA Ethics Director, who effectively formed an undisclosed joint venture with a small number of DoD officials to ensure that APA’s
statements and actions fell squarely in line with DoD’s goals and preferences. In numerous confidential email exchanges and conversations, the APA Ethics Director regularly sought and received pre-clearance from an influential, senior psychology leader in the U.S. Army Special Operations Command before determining what APA’s position should be, what its public statements should say, and what strategy to pursue on this issue.
 
Study: Elite scientists can hold back science

What's interesting is that the deaths seemed to hurt the careers of the luminaries' junior collaborators, the ones who frequently co-authored papers with them but not in a senior role. "The death of an elite scientist has a negative and seemingly permanent impact on the productivity of their coauthors," the study reports. They published less, while outsiders flooded the void.

(The authors caution that gatekeeping by elite researchers isn't always a bad thing. "Gatekeeping activities could have beneficial properties when [a] field is in its inception," granting scientists more room to take risks.)

All of this is another example of how progress in science is confounded by human behavior. We see this in so many ways. Scientists lie about results. Or they discount insights derived from failures. Science is so obsessed with the rewards of solving complicated problems that it forgets about the simple ones. The field overwhelminglyis biased toward males (experiments have shown "John" gets more accolades than "Jennifer" with the identical résumé).

It's worth remembering: Science may be a noble discipline based on cold logic and rational observation; but humans are animals fueled by emotion and bias. As the NBER researchers conclude: "[T]he idiosyncratic stances of individual scientists can do much to alter, or at least delay, the course of scientific advance."

When Great Minds Think Unlike: Inside Science's 'Replication Crisis'

Psychology's Credibility Crisis: the Bad, the Good and the Ugly
 

That's a really good article! Very impressed that it went into the nuances of the issues involved.

Article highlights the importance of pre-registering. But also that care must be done when preregisteribf replications. They must take care to make sure the methodology is a suitable replication prior to registering or they can get stuck with suboptimal methods!
 
That's a really good article! Very impressed that it went into the nuances of the issues involved.

Article highlights the importance of pre-registering. But also that care must be done when preregisteribf replications. They must take care to make sure the methodology is a suitable replication prior to registering or they can get stuck with suboptimal methods!
There are an awful lot of excellent (but very sobering) articles in this thread.

David
 
There are an awful lot of excellent (but very sobering) articles in this thread.

David

You always seem to approach it with a glass half empty attitude. Sure there are some bad egg types in science, as there are in every area of life. And yes it can be disappointing when we find out certain findings weren't as firm as some once thought. But most of all what these articles show is that doing science in the most rigorous manner is damn hard!

So many articles about the flaws in past studies is indeed sobering, but on the plus side the reason there have been so many over the last few years is that our collective understanding of what makes the most - and least - reliable research practices has made significant progress in recent years. Particularly with the development of. The field of meta research.

The fact that there is so much focus on it is good news. It is important to review old studies with critical eyes, and no doubt we have not seen the last article documenting a series of findings that are now suspect. But the crucial thing to look at is how is the scientific community reacting to these findings. What efforts are being made to make things better. Are we learning our lessons. From what I can tell there is a heck of a lot of work going on across fields with this in mind. And that bodes well for the future of science.

Incidentally David, a few months ago I spotted IIRC a Cochrane review on statin use. I meant to draw it to your attention at the time. I didn't read it in detail but I thought you would probably find it interesting.
 
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