"Compromised science" news/opines (includes retractions, declining academic standards, pred-J, etc)

Continuation of updates in Wegs' retracted studies and papers thread, but under a broader title to better reflect the range of material that becomes contiguous with the narrower topic.

 

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Former cancer research center director plagiarized and faked data, feds say
https://retractionwatch.com/2023/04...giarized-and-faked-data-feds-say/#more-127006

The former director of a cancer research center faked data and presented others’ published data and text as his own in four grant applications to the National Institutes of Health (NIH) and one research record, according to a U.S. government watchdog.

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US-backed researchers in Colombia accused of experimenting on animals, humans without approval
https://retractionwatch.com/2023/04...-animals-humans-without-approval/#more-127001

On January 16, inspectors from an environmental agency in western Colombia made some troubling findings. At a U.S.-funded facility supposed to be doing cutting-edge malaria research, researchers were keeping dozens of monkeys in dirty cages in poorly ventilated, over-lit enclosures. Several animals were smeared with feces. Some looked sick, and one was missing an eye. A fetid smell hung in the air. On the floor of a cage, a baby monkey lay dead.

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‘Frankly abusive’: More questions about the journal that stole an author’s identity
https://retractionwatch.com/2023/04...l-that-stole-an-authors-identity/#more-126985

Last week, we brought you the story of a professor who found her name on an article she didn’t write, which also seemed to have been plagiarized. Since our story was published, we’ve learned a little more about the journal that published the article, the African Journal of Political Science.

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Torturing data to predict bitcoin prices: A book excerpt
https://retractionwatch.com/2023/04...ct-bitcoin-prices-a-book-excerpt/#more-126972

The fact that changes in bitcoin prices are driven by fear, greed, and manipulation has not stopped people from trying to crack their secret. Empirical models of bitcoin prices are a wonderful example of data torturing because bitcoins have no intrinsic value and, so, cannot be explained credibly by economic data.

Undaunted by this reality, a National Bureau of Economic Research (NBER) paper reported the mind-boggling efforts made by Yale University economics professor Aleh Tsyvinski and a graduate student, Yukun Liu, to find empirical patterns in bitcoin prices.
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Research Finds No Gender Bias in Academic Science
https://www.insidehighered.com/news...esearch-finds-no-gender-bias-academic-science

Reviewing decades of studies, researchers with “adversarial” perspectives conclude that tenure-track women and men in STEM receive comparable grant funding, journal acceptances and recommendation letters—and that women have an edge over men in hiring.

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The World Health Organization Has a Pseudoscience Problem (i.e., soul)
https://www.mcgill.ca/oss/article/c...health-organization-has-pseudoscience-problem

It is not technically theirs, but it appears in the glossary of one of their many official documents. The soul, according to the WHO, is derived from the astral organization, which is another term they have had to define. The astral organization, you see, is distinct from the etheric organization. That same document, coming out of the world’s foremost authority on global health, mentions such esoteric concepts as rhythmical embrocation, a type of energy healing that involves rhythmic strokes on the body.

At a time when the WHO is accused by conspiracy theorists of being in the pocket of Bill Gates and using mass vaccination as a nefarious scheme to control humanity, it’s easy to forget that there are genuine reasons to criticize the WHO. Its mission to ensure everyone on Earth has access to healthcare has led to its legitimization of prescientific belief systems and of thoroughly debunked practices. The WHO doesn’t stop at validating these pseudomedicines; it wants them integrated with evidence-based medicine.

RELATED: indigenous science (wikipedia) ........ We Need Indigenous Science ........ An uneasy alliance: Indigenous Traditional Knowledge enriches science

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Comparing scientific abstracts generated by ChatGPT to real abstracts with detectors and blinded human reviewers
https://www.nature.com/articles/s41746-023-00819-6

When given a mixture of original and general abstracts, blinded human reviewers correctly identified 68% of generated abstracts as being generated by ChatGPT, but incorrectly identified 14% of original abstracts as being generated. Reviewers indicated that it was surprisingly difficult to differentiate between the two, though abstracts they suspected were generated were vaguer and more formulaic. ChatGPT writes believable scientific abstracts, though with completely generated data. Depending on publisher-specific guidelines, AI output detectors may serve as an editorial tool to help maintain scientific standards. The boundaries of ethical and acceptable use of large language models to help scientific writing are still being discussed, and different journals and conferences are adopting varying policies.

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Double-blind peer review affects reviewer ratings and editor decisions at an ecology journal
https://besjournals.onlinelibrary.wiley.com/doi/ftr/10.1111/1365-2435.14259

For all the strengths of our peer review system, there are reasons to worry that it has flaws too. One important worry is that peer reviewers (or editors) might be biased in their assessment of manuscripts based on their knowledge, or guesses, about the identities of the authors. Might manuscripts by female authors be treated more harshly? What about manuscripts by authors from the Global South? How might things change (and would it be for the better) if reviewers didn’t know who the authors were?
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Climate reasoning, prior beliefs, and partisanship
https://academic.oup.com/pnasnexus/article/2/5/pgad100/7147350?login=false

PRESS RELEASE: A popular explanation for climate denialism is that humans will adopt beliefs that accord with their political orientation, using their cognitive abilities to explain away identity-inconsistent information in a process called “motivated reasoning.”

To test this hypothesis, Bence Bago and colleagues challenged volunteers’ ability to think rationally using time pressure and cognitive loads of varying intensity. The team recruited American participants from Lucid, a website that connects academics with online survey participant pools.

The authors found that people who had the ability to deliberate free of cognitive load or time restrictions showed greater coherence between their judgments about climate change and their prior beliefs about climate change. Controlling for this effect, there was no significant residual relationship between partisan identity and judgement.

For example, Republicans who believe in climate change were significantly more likely to disagree with arguments against the reality of climate change when they had adequate time to deliberate than when they were rushed and had divided attention.

Evaluating new evidence as more reliable if it accords with prior beliefs is sometimes called “confirmation bias,” but such reasoning can also be entirely rational from a Bayesian perspective: Broadly speaking, previously established facts are likely to be true and new contradictory information from an uncertain source is likely to be false.

The authors conclude that instead of trying to decouple discussion of climate change from politics, those who wish to communicate about the issue should primarily focus on providing accurate information.
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"Scientific American" argues that those who accept a binary do so out of bigotry, transphobia, & racism
https://whyevolutionistrue.com/2023...-do-so-out-of-bigotry-transphobia-and-racism/

INTRO (Jerry Coyne): If you want a combination of an author and a venue guaranteed to produce ideologically-motivated nonsense, it’s Agustin Fuentes writing at Scientific American. The combination of a badly misguided author, distorting biology for political reasons, with a magazine devoted to promulgating “authoritarian progressive” ideology disguised as science, gives me the same feeling I’d have if my mother called me to dinner and announced that we’d be having liver and Brussels sprouts.

The article at hand, a Scientific American op-ed that you can access by clicking the screenshot below, further erodes the reputation of this once-absorbing journal, which under editor Laura Helmuth has taken the route of becoming explicitly political, and political in a woke way. To many the journal has become almost worthless. Fuentes’s article doesn’t help, and we’ve seen the Princeton anthropologist before arguing about the racism of Charles Darwin.

I’m not going to argue again why sex in humans (and all animals, as well as most vascular plants) is binary. This is the “definition” (or “conception”, if you will) of sex: males have the reproductive apparatus to produce small, mobile gametes (sperm), while females have the reproductive apparatus to produce large, immobile gametes (eggs). There are no other sexes. If you want a justification and explanation of this, and why human hermaphrodites (vanishingly rare, and almost invariably sterile) or individuals with “disorders of sex development”(DSDs) are not members of distinct sexes, there are many sources... (MORE - details)
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A dangerous trend to decolonize the scientific method
https://skepticalinquirer.org/2023/...us-trend-to-decolonize-the-scientific-method/

EXCERPTS: In India, traditionalists are challenging the scientific method as a Western construct. This objection stems from the fact that Eastern methods of acquiring knowledge are not dependent on observational phenomena but rather on the methods involving the mind as indicated in ancient Vedic literature.

Attacks on existing scientific methods frequently leads to infamous nationalistic statements akin to the one made by a minister of Ayush [...] depicting all physicians prescribing non-ayurvedic medications as anti-nationals.

[...] We are faced with a movement that champions decoloniality over postmodernity. Decoloniality relates to delinking the source of knowledge from the ones laid down by colonizers. The work of prominent sociologists Walter D. Mignolo and Aníbal Quijano linking rationality and modernity with “coloniality”—the indoctrination of the indigenous mind with the principles of their colonial masters—provides the inspiration for this decolonization movement. From an Indian perspective, the aim seems to rid ourselves of the principles of modernity and rationality emerging out of the European Renaissance.

Several terminologies were introduced to indicate the direction that needs to be followed to achieve this decolonization. The recovery of geographical and political space from the colonizers do not immediately lead to a state of complete freedom. Rather it is a state of “post coloniality,” whereby the colonial mindset is still prevalent.

Hence, the final step to complete freedom is freeing the mindset from the Western construct, defined as decoloniality. Although we have freed ourselves from our Middle Eastern and European colonizers, we have not been able to get rid of the mentality ingrained in the Indian system of administration and education.

[...] This conflict is particularly visible in the field of medicine in India. Do we integrate our indigenous values into the prevalent system, which is global in nature, or do we dismantle all that is considered modern, rational, and progressive by the global definition and introduce a new system based on the cultural traditions dating back thousands of years? (MORE - missing details)
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Australian study supporting mask mandates earns expression of concern
https://retractionwatch.com/2023/05...ates-earns-expression-of-concern/#more-127062

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Leading primate researcher demoted after admitting he faked data
https://retractionwatch.com/2023/05...archer-demoted-after-admitting-he-faked-data/

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Hindawi shuttering four journals overrun by paper mills
https://retractionwatch.com/2023/05...-journals-overrun-by-paper-mills/#more-127039

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Chemist in India loses seven papers, blames outsourcing of images
https://retractionwatch.com/2023/05...ers-blames-outsourcing-of-images/#more-127013

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Nature editors retract influential cancer paper with “unreliable” data
https://retractionwatch.com/2023/05...ancer-paper-with-unreliable-data/#more-127019

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How to improve scientific peer review: Four schools of thought
https://onlinelibrary.wiley.com/doi/full/10.1002/leap.1544

To provide a more systematic understanding of the landscape of innovation in peer review, we suggest that the landscape is shaped by four schools of thought: The Quality & Reproducibility school, the Democracy & Transparency school, the Equity & Inclusion school, and the Efficiency & Incentives school...

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Researchers who agree to manipulate citations are more likely to get their papers published
https://www.nature.com/articles/d41586-023-01532-w

Researchers who are coerced by editors into adding superfluous citations in their manuscripts are more likely to succeed in publishing papers than are those who resist, finds a study published in "Research Policy".

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Research with integrity – referencing work is way more than just a tick-box exercise
https://news.cancerresearchuk.org/2...rk-is-way-more-than-just-a-tick-box-exercise/

One way to preserve the integrity of the scientific record is the retraction of work that contains significant errors, fraud or other types of research misconduct. However, a surprisingly large number of papers continue to be cited after they have been retracted.

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Retraction: “Microbiome-based hypothesis on Ivermectin’s mechanism in COVID-19: Ivermectin feeds Bifidobacterium to boost immunity”
https://www.frontiersin.org/articles/10.3389/fmicb.2023.1216170/full

Following publication, concerns were raised regarding the scientific validity of the article. An investigation was conducted in accordance with Frontiers’ policies. It was found that the complaints were valid...

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Grandpa McMooty: "It's not just for the social sciences, anymore... Those ideological and conspiracy fixation biases of the administrative level of science publications and institutions affecting and dictating research and dialogue." --stage skit
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"Whiteness" in physics: the Physical Review version of Catch-22
https://quillette.com/2023/05/05/the-unbearable-whiteness-of-being/

EXCERPTS (Lawrence M. Krauss): A little over a year ago, I tweeted about what seemed to be a ludicrous article that had just been published in the prestigious physics journal [...] The article claimed, among other things, that the use of whiteboards was an example of “whiteness” in physics.

It seemed so silly that [...] I thought it was a spoof paper ... to see whether this kind of content could now make it through the refereeing process today, even in hard science publications.

I wasn’t alone, and the paper generated a reasonably large negative outcry from the physics community [...] the editors stated, “we condemn the highly inappropriate and harassing emails and social media responses to the paper, some of which appear to have little basis in the content of the article.”

They then issued a threat: “The APS Ethics Committee regularly reviews and responds to allegations of harassment and related misconduct. In some cases, these behaviors may lead to the revocation of APS awards, prizes, leadership positions, and/or disqualify candidates from consideration....."

Shortly after that, several physicists wrote to the authors of the APSNews piece [...] expressing concerns about its tone, which seemed to suggest that any discussion of the paper on social media would be interpreted as harassment...

In June, four physicists from Los Alamos National Laboratory and Cal Poly Pomona submitted a Comment for publication. As per normal procedure, the journal sent this Comment to the original authors to review.

[...] the editor rejected the Comment on the grounds that it was “framed from the perspective of a research paradigm that is different from the one of the research being critiqued.”

[...] In a masterstroke of suppression of speech, the American Physical Society and Physical Review have together devised a strategy to ensure negative comments about this paper cannot appear officially anywhere in print. [...] a scientific critique of the paper was not appropriate for publication because the original paper wasn’t scientific.

This is what I meant by the Physical Review version of Catch-22. If you critique the scientific basis of a paper claiming that “White Privilege” exists in physics teaching, then you are being scientific; but if you are being scientific, you cannot critique a non-scientific paper!

[...] this gives additional ammunition to those who, without an otherwise firm scientific basis, continue to try to paint Physics as systemically racist... (MORE - missing details)
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Debunking the Dunning-Kruger effect – the least skilled people know how much they don’t know, but everyone thinks they are better than average
https://theconversation.com/debunki...ne-thinks-they-are-better-than-average-195527

INTRO: John Cleese, the British comedian, once summed up the idea of the Dunning–Kruger effect as, “If you are really, really stupid, then it’s impossible for you to know you are really, really stupid.” A quick search of the news brings up dozens of headlines connecting the Dunning–Kruger effect to everything from work to empathy and even to why Donald Trump was elected president.

As a math professor who teaches students to use data to make informed decisions, I am familiar with common mistakes people make when dealing with numbers. The Dunning-Kruger effect is the idea that the least skilled people overestimate their abilities more than anyone else. This sounds convincing on the surface and makes for excellent comedy. But in a recent paper, my colleagues and I suggest that the mathematical approach used to show this effect may be incorrect... (MORE - details)

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Jesse Singal critiques a new Scientific American article on puberty blockers, calls the piece “potentially harmful” and “negligent science journalism”
https://whyevolutionistrue.com/2023...lly-harmful-and-negligent-science-journalism/

INTRO (Jerry Coyne): . . . I’ve read a lot of Jesse Singal‘s writings on transgender issues, both before and after he started his Substack column, “Singal Minded.” I like to read him because he specializes in careful analysis of data to analyze (often erroneous) claims about sex and gender issues. [...]

A Critique of Scientific American's recent article "What Are Puberty Blockers, and How Do They Work?"

I’m not going to rail about the ideological bent of Scientific American, as I’ve mentioned that many times before, except to say that a once-admired magazine is now scientifically untrustworthy and ideologically motivated (the two are connected). Worse, because it’s a very popular magazine, on the issue of medical treatment for gender dysphoria its ideological bent, according to Singal, is implicitly harmful, for it purveys misleading information about drugs, behavior, and treatment of people that could lead to irreversible medical decisions.... (MORE - missing details)
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Ah, so most people think they are better than average, not necessarily the best, at something. I think that's a common misconception about the Dunning-Kruger effect. This reminds me of a quote from Bertrand Russell, “The whole problem with the world is that fools and fanatics are always so certain of themselves, and wiser people so full of doubts.''

 

Fake scientific papers are alarmingly common
https://www.science.org/content/article/fake-scientific-papers-are-alarmingly-common

EXCERPTS: When neuropsychologist Bernhard Sabel put his new fake-paper detector to work, he was “shocked” by what it found. After screening some 5000 papers, he estimates up to 34% of neuroscience papers published in 2020 were likely made up or plagiarized; in medicine, the figure was 24%. Both numbers, which he and colleagues report in a medRxiv preprint posted on 8 May, are well above levels they calculated for 2010—and far larger than the 2% baseline estimated in a 2022 publishers’ group report.

[...] His findings underscore what was widely suspected: Journals are awash in a rising tide of scientific manuscripts from paper mills—secretive businesses that allow researchers to pad their publication records by paying for fake papers or undeserved authorship. “Paper mills have made a fortune by basically attacking a system that has had no idea how to cope with this stuff,” says Dorothy Bishop, a University of Oxford psychologist who studies fraudulent publishing practices. A 2 May announcement from the publisher Hindawi underlined the threat: It shut down four of its journals it found were “heavily compromised” by articles from paper mills... (MORE - missing details)

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‘Too greedy’: mass walkout at global science journal over ‘unethical’ fees
https://www.theguardian.com/science...at-global-science-journal-over-unethical-fees

EXCERPTS: More than 40 leading scientists have resigned en masse from the editorial board of a top science journal in protest at what they describe as the “greed” of publishing giant Elsevier.

The entire academic board of the journal Neuroimage, including professors from Oxford University, King’s College London and Cardiff University resigned after Elsevier refused to reduce publication charges.

Academics around the world have applauded what many hope is the start of a rebellion against the huge profit margins in academic publishing, which outstrip those made by Apple, Google and Amazon.

[...] Professor Chris Chambers, head of brain stimulation at Cardiff University and one of the resigning team, said: “Elsevier preys on the academic community, claiming huge profits while adding little value to science.”

He has urged fellow scientists to [...] submit papers to a nonprofit open-access journal which the team is setting up instead... (MORE - missing details)
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Paper with authorship posted for sale retracted nearly two years after Retraction Watch report
https://retractionwatch.com/2023/05...arly-two-years-after-retraction-watch-report/

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Spider researcher Jonathan Pruitt faked data in multiple papers, university finds
https://retractionwatch.com/2023/05...ked-data-in-multiple-papers-university-finds/

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Retractions should not take longer than two months, says UK Parliament committee
https://retractionwatch.com/2023/05...than-two-months-says-uk-parliament-committee/

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Prominent nanoscientist retracts paper after PhD students flagged error
https://retractionwatch.com/2023/05...r-retracted-after-phd-students-flagged-error/

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Article that assessed MDPI journals as “predatory” retracted and replaced
https://retractionwatch.com/2023/05...journals-as-predatory-retracted-and-replaced/

A 2021 article that found journals from the open-access publisher MDPI had characteristics of predatory journals has been retracted and replaced with a version that softens its conclusions about the company. MDPI is still not satisfied, however.

Heh. Even watchdogs potentially afflicted with a "publish or perish" (hurry up) aspect to the job?

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Saudi universities entice top scientists to switch affiliations — sometimes with cash
https://www.nature.com/articles/d41586-023-01523-x

Some institutions arrange for highly cited researchers to change their main affiliations, which boosts their position in global university rankings.

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Flawed protocol for levodopa clinical trial brings retractions
https://www.spectrumnews.org/news/flawed-protocol-for-levodopa-clinical-trial-brings-retractions/

Two studies conducted at the New York State Psychiatric Institute in New York City have been withdrawn because the researchers violated their own study protocol. The studies were based on a clinical trial that began in 2016 and tested whether treatment with the Parkinson’s disease drug levodopa could improve mood and mobility in older adults with depression.

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Identifying spin bias of nonsignificant findings in biomedical studies
https://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-023-06321-2

ABSTRACT

Objective: The purpose of this research note is to share a technique for the identification of spin bias that we developed as part of a living systematic review on the cardiovascular testing of e-cigarette substitution for cigarette smoking. While some researchers have remarked on the subjective nature of ascertaining spin bias, our technique objectively documents forms of spin bias arising from the misrepresentation of nonsignificant findings and from the omission of data.

Results: We offer a two-step process for the identification of spin bias consisting of tracking data and findings and recording of data discrepancies by describing how the spin bias was produced in the text. In this research note, we give an example of the documentation of spin bias from our systematic review. Our experience was that nonsignificant results were presented as causal or even as significant in the Discussion of studies. Spin bias distorts scientific research and misleads readers; therefore it behooves peer reviewers and journal editors to make the effort to detect and correct it.
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If there's one sacred place in the entire universe, free from corruption, you'd think it'd be within science.

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Well, not really. It is after all a human activity and scientists are not saints. But at least scientists don't choose their profession for the money, so there is perhaps a reason to expect most of them to be more or less honest.

One of the current problems is the pressure to publish, in order to retain tenure and advance careers. This has become absurd and leads to a deluge of shit papers. A BBC radio programme I heard recently said that a significant proportion of the papers that emanate from Chin, in particular, are bogus, produced by "paper mills" that fake all or parts of the research and write it up for authors that are too busy or desperate. The deluge of papers is such that even the peer review process can be overwhelmed, so that reviewers are not able to fully examine the papers they sign off. It seems to be worst in the social sciences. There are now people who have devoted themselves to searching out dud papers, using sophisticated algorithms to spot data copied from elsewhere and so forth.

We need more gamekeepers to catch the poachers, and in my view a more intelligent, humane and respectful way to judge the value of research, rather than by sheer volume of stuff produced.

But having said all that, science is ultimately self-correcting. Bad research can't be reproduced and will eventually be smoked out. But it could have wasted a lot of people's time before that happens.

 

Yea, I’d like to believe that most scientists go into their profession for altruistic reasons, but science has become a business; look at the healthcare industry for example. Money is a powerful motivator to breed corruption, even in science. This isn’t to say scientists shouldn’t profit on their discoveries and experiments; we need good scientists for progressive inventions, therapies and medicines, for example. Unfortunately though, science isn’t immune to greed and corruption.

That’s true about science being “self correcting,” but to what end has the damage already been done, and you can’t lead the horse back into the barn. Like all of these retraction articles I’ve posted in my other thread and that C C has found - it’s great that retractions were made, but will anyone care? Once a story is out there, even science-based, it’s difficult to reel it back in and say “hey everyone, that was wrong and this is actually the correct data.” Mistakes happen, but some of these retractions aren’t due to mistakes.

 

Well no, actually, it does get reeled in and the horse does get back into the barn. It's not like politics, in which a lie can get traction and be impossible to snuff out. The distinguishing feature of science is it relies on reproducible observation. If someone writes a paper with poor research, and people do further work in that area assuming what is in the paper is correct, they will fail. And then they will find out, soon enough, that the paper they relied on was no good. Research claims are tested, in effect, because they become part of the structure on which further research is built. But it is true it can take a while and involve people wasting their time trying to do something that doesn't work.

 

That makes sense. I was comparing this with politics (in terms of how retractions are handled) - you’ve helped me see that the two are not the same. Scientists like anyone else, are fallible and mistakes can happen but, how is misconduct getting past peer reviews?

 

Usually it doesn't of course, but it depends on what the misconduct is. A reviewer can take apart conclusions that don't follow from the data presented, can criticise poor experimental methodology, or point out that results don't seem consistent with previous work in the field. But if someone chooses to fake actual data points, there's not much a reviewer can do to detect that. He or she can't be expected to repeat the actual research themselves, after all.