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

Is science’s dominant funding model broken?

EXCERPT: The team delved into the structure and outputs of academic research. To their horror, the researchers uncovered a system that, in their words, “ends up rewarding administrators and empire-builders, not creative scientists actively engaged in research and mentoring”. They have much more to say in their report, A New National Purpose: Leading the Biotech Revolution, but this quote demonstrates their shock over how academia is structured and how it operates. The structure of academia is also attracting attention from high-level policymakers because science is increasingly seen as a way to boost economic growth... (MORE - details)
 
What a database of more than a thousand dismissive literature reviews can tell us

EXCERPTS: In academia, declarations of a void in the research literature are rarely challenged. As long as a few unknowing, uncaring, or otherwise cooperative reviewers and editors let the statement slide, it passes unimpeded into the world of scholarship and becomes what I call a dismissive literature review. No one with a self or public interest in countering the claim is offered an opportunity to challenge.

[...] For the most part, the list includes statements made by “serial dismissers,” scholars who dismiss repeatedly on a variety of topics. This is done to help counter the argument that they might be innocent, did try to look for previous research, and simply could not find it. In some cases, they dismiss a research literature that is hundreds or thousands of studies deep. And, when they do that repeatedly across a variety of topics, the odds their dismissive behavior could be innocent fade to miniscule... (MORE - details)

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Authors – including a dean and a sleuth – correcting paper with duplicated image
https://retractionwatch.com/2024/06...leuth-correcting-paper-with-duplicated-image/

The corresponding author of a paper flagged on PubPeer for an apparently duplicated image will be asking the journal to publish a correction...

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Seventeen journals lose impact factors for suspected citation manipulation


Clarivate, the company that calculates Journal Impact Factors based on citations to articles, didn’t publish the metric for 17 journals this year due to suspected citation manipulation. That’s a substantial increase from last year, when only four were excluded...

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‘All authors agree’ to retraction of Nature article linking microbial DNA to cancer

A 2020 paper that claimed to find a link between microbial genomes in tissue and cancer has been retracted following an analysis that called the results into question...

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Journal retracts redundant case study of same patient from different authors
https://retractionwatch.com/2024/06...study-of-same-patient-from-different-authors/

Cureus has retracted a 2024 case study after learning it had published a piece about the identical patient, by authors from the same institution, just months earlier...

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Paper recommending vitamin D for COVID-19 retracted four years after expression of concern

A paper that purported to find vitamin D could reduce the severity of COVID-19 symptoms has been retracted from PLOS ONE, four years after the journal issued an expression of concern about the research...
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The Biden administration’s Scientific Integrity Task Force is rightly opposed by researchers on the ground.

EXCERPTS: In its first year, the Biden administration launched a fast-track Scientific Integrity Task Force, intended to “lift up the voices of Federal scientists of many perspectives and backgrounds” and put scientific integrity “paramount in Federal governance for years to come.” The task force took a “whole-of-government” approach to ensuring the scientific integrity of federally funded research and included representatives from the 21 federal agencies that maintain scientific-research programs. For those with a high pain threshold, the final report may be seen here.

Prominent among the move’s critics have been the Council on Governmental Relations (a consortium of research universities) and the Association of Research Integrity Officers...

[...] As with all things governmental, one looks at this spectacle and asks “why?” It’s not like anyone is in favor of scientific misconduct. ... Nor has there been an absence of means to detect and punish research misconduct...

[...] There is a bigger picture in play, however. As demoralizing as research misconduct is, we should hardly be surprised by its occurrence...

[...] Since 1950 ... the science ecosystem has morphed into a “big science cartel,” united through an interwoven network of self-aggrandizing actors who hold a common interest, not around science but around capturing research funds. University administrations are one such actor, but there are many others. ... includes universities who look with favor on representatives who can keep the research money flowing in.

Those 21 federal agencies represented on the task force constitute another crucial player: bureaucratic entities whose value and very existence is tied to capturing dollars from the federal budget.

[...] We can now begin to make sense of the dust-up between the bureaucracy-based Scientific Integrity Task Force and the university-based Council on Governmental Relations. Neither is concerned so much with protecting the integrity of science; they merely differ on who shall be the enforcers...

[...] while I’m no friend of the shenanigans of university administrations and the games they play, I’m far more concerned about the Biden administration’s move to complete the federalization of university science begun in 1950, which may finally squash the very people who are the most effective custodians of scientific integrity: scientists themselves.... (MORE - missing details)

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Federal funding for major science agencies is at a 25-year low

EXCERPTS: Government funding for science is usually immune from political gridlock and polarization in Congress. But, federal funding for science is slated to drop for 2025. [...] Federal funding for many programs is characterized by political polarization, meaning that partisanship and ideological divisions between the two main political parties can lead to gridlock. Science is usually a rare exception to this problem. [...] Ideally, all the best ideas for scientific research would receive federal funds. But limited support for scientific research in the United States means that for individual scientists, getting funding is a highly competitive process... (MORE - details)
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Two reasons I’m sceptical about psychedelic science (Michiel van Elk)

My initial optimism about psychedelics and their potential has changed into scepticism about the science behind much of the media hype. This is due to a closer scrutiny of the empirical evidence. Yes, at face value it seems as if psychedelic therapy can cure mental disease. But on closer inspection, the story is not that straightforward. The main reason? The empirical evidence for the efficacy of and the working mechanisms underlying psychedelic therapy is far from clear...
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How you can help improve the visibility of retractions: Introducing NISO’s Recommended Practice for Communication of Retractions, Removals, and Expressions of Concern (CREC)

In the majority of cases, retracted publications continue to be cited as if the retraction had not occurred. So how do we better disseminate the editorial status of retracted work?

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Elsevier withdraws plagiarized paper after original author calls journal out on LinkedIn

In late May, one of Sasan Sadrizadeh’s doctoral students stumbled upon a paper with data directly plagiarized from his previous work...

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‘A threat to the integrity of scientific publishing’: How often are retracted papers marked that way?

How well do databases flag retracted articles?

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Food science journal retracts 10 papers for compromised peer review
https://retractionwatch.com/2024/07...tracts-10-papers-for-compromised-peer-review/

A research group based in Pakistan has had 10 of their papers retracted from Wiley’s "Food Science & Nutrition" based on flaws in the peer review process...

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‘We authors paid a heavy price’: Journal retracts all 23 articles in special issue

A journal has retracted an entire special issue over concerns the guest-edited papers underwent a “compromised” peer review process...
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The misplaced incentives in academic publishing

EXCERPTS: Lamentations over the current models of academic publishing come from all corners of the scientific community. How does the system work?

[...] The arguments against it are many but tend to focus on dubious features of peer review, and the business model of journals that publish peer-reviewed reports of new research...

[...] Despite the fact that the public funds much of this work, much of it remain behind a paywall, freely accessible only to those with affiliations at institutions that can afford subscriptions (and the rare individual who can pay themselves), thus eliminating most of the citizen-science public...

[...] But as damning as these charges are, they only capture one aspect of the hypocrisy and irrationality in the academic publishing model. Some of this only became apparent to me after I began to see the process from the other side — that is, as an editor at several journals. And this has forced me to conclude that many of the largest, under-appreciated sins of publishing do not arise from the journals themselves, but from the professional ecosystem that defines modern academia. The incentive structure encourages behavior that reinforces the current broken publication model... (MORE - missing details)
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Journal retracts letter to the editor about predatory journals for ‘legal concerns’

A journal has retracted a letter to the editor and removed the online version from its website “because legal concerns were raised to the Publisher,” according to the notice. The retracted letter had referred to multiple journals as “predatory.” [/b]

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‘Rare’ criminal charges for data manipulation in Cassava case send a ‘powerful message’: lawyers

The recent criminal indictment of a medical school professor and former scientific advisor to Cassava Sciences on fraud charges for manipulating images in scientific papers and applications for federal funding is a “rare” outcome for such alleged actions that “sends a very, very powerful message.”

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Author blames retraction on ‘Chinese censorship’

A former assistant professor of international relations at Yibin University in Sichuan, China, said he was fired from his job and “forced” to retract a paper on COVID-19 because the article did not “paint a good picture of the Chinese government.”

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University president faces allegations of duplication, institution says no misconduct
https://retractionwatch.com/2024/07...f-duplication-institution-says-no-misconduct/

The president of the Kyoto Institute of Technology (KIT) has corrected two of his papers and is set to correct another amid allegations of duplication – sometimes inelegantly referred to as “self-plagiarism” – despite a university committee clearing him of misconduct...

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The wolf in Scopus’ clothing: Another hijacked journal has indexed nearly 900 articles

A prolific hijacked journal has managed to breach the defenses of Scopus, one of the world’s leading academic databases. This time, the target is the award-winning journal Community Practitioner, the official publication of the UK-based organization Unite-CPHVA...
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When scientific citations go rogue: Uncovering ‘sneaked references’

EXCERPTS: People are becoming more aware of scientific publications and how they work, including their potential flaws. Just last year more than 10,000 scientific articles were retracted. The issues around citation gaming and the harm it causes the scientific community, including damaging its credibility, are well documented.

[...] we found through a chance encounter that some unscrupulous actors have added extra references, invisible in the text but present in the articles’ metadata, when they submitted the articles to scientific databases. The result? Citation counts for certain researchers or journals have skyrocketed, even though these references were not cited by the authors in their articles... (MORE - details)
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‘Mistakes were made’: Paper by department chair earns expression of concern as more questioned
https://retractionwatch.com/2024/07...rns-expression-of-concern-as-more-questioned/

A 14-year-old paper has earned an expression of concern after an anonymous whistleblower found evidence of image duplication in the work. The authors have had images from several more papers flagged on PubPeer...

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Supplement maker sues critic for defamation, spurring removal of accepted abstract

A Frontiers journal has taken down the abstract of a “provisionally accepted” article about harms from an herbal supplement after the company that sells the products sued the first author for defamation.

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Scopus is broken – just look at its literature category
https://retractionwatch.com/2024/07/17/scopus-is-broken-just-look-at-its-literature-category/

As Retraction Watch recently reported, three of the top 10 philosophy journals in the highly influential Scopus database turned out to be fakes: Not only did these dubious journals manage to infiltrate the list, but they also rose to its top by trading citations. This news is embarrassing in itself, but it is hardly shocking. Our rankings-obsessed academic culture has proven time and again that it is prone to data manipulation. Rankings for both publications and institutions are routinely hacked by scholars, editors, and administrators who are ready to tweak or even falsify numbers as needed. The problems with the Scopus journal rankings, however, run much deeper...

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Exclusive: Kavli prize winner threatens to sue critic for defamation

One of the winners of the 2024 Kavli Prize in nanoscience has threatened to sue a longtime critic, Retraction Watch has learned. In a cease and desist letter, a lawyer representing Chad Mirkin, a chemist and director of the International Institute for Nanotechnology at Northwestern University in Chicago, accused Raphaël Lévy, a professor of physics at the Université Paris Sorbonne Nord, of making “patently false and defamatory” statements about Mirkin’s research.

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Did Flint water crisis set kids back in school? Paper saying so is ‘severely flawed,’ say critics \

A paper finding kids did worse in school following the Flint water crisis is “severely flawed and unreliable,” according to critics who were deeply involved in exposing the crisis. The paper has now earned an addendum from the authors, but the critics say it should be retracted...
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Is peer review failing its peer review?

INTRO: Ivan Oransky doesn’t sugar-coat his answer when asked about the state of academic peer review: “Things are pretty bad.”

As a distinguished journalist in residence at New York University and co-founder of Retraction Watch – a site that chronicles the growing number of papers being retracted from academic journals – Oransky is better positioned than just about anyone to make such a blunt assessment.

He elaborates further, citing a range of factors contributing to the current state of affairs. These include the publish-or-perish mentality, chatbot ghostwriting, predatory journals, plagiarism, an overload of papers, a shortage of reviewers, and weak incentives to attract and retain reviewers... (MORE - details)

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The history of peer review is more interesting than you think

EXCERPT: As with any human enterprise, peer review is far from foolproof. Errors and downright frauds have made it through the process. In addition, as Moxham and Fyfe note, there can be “inappropriate bias due to the social dynamics of the process.” (Some peer review types may introduce less bias than others.)

The term “peer review” was coined in the early 1970s, but the referee principle is usually assumed to be about as old as the scientific enterprise itself, dating to the Royal Society of London’s Philosophical Transactions, which began publication in 1665.

Moxham and Fyfe complicate this history, using the Royal Society’s “rich archives” to trace the evolution of editorial practices at one of the earliest scientific societies... (MORE - details)
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What is it like to attend a predatory conference?

TAKEAWAYS: The supposed 25th Global Nephrology, Urology and Kidney Failure Congress listed several “renowned speakers”.

A Nature reporter attended the event, and found it to be shambolic. It was facilitated by a PhD student, who said that she had been asked by e-mail just a couple of days beforehand to take on the extra, unpaid role of delivering a conference speech.

The number of predatory conferences continues to grow, and their organizers are swift to change their practices to evade detection. It's believed that ‘vulture conferences’, to use a Japanese term, are now more plentiful than legitimate ones.

A key reason that they persist is that “researchers, especially those eager to strengthen their publication records, are sometimes lured by the promise of subsequent publication indexed in reputable citation databases”, such as in conference proceedings or in journals published by the conference organizer... (MORE - missing details)
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Authors up past 60 retractions amid ongoing investigation
https://retractionwatch.com/2024/07/26/authors-up-past-60-retractions-amid-ongoing-investigation/

A group of researchers in Iran now have had more than 60 papers retracted for concerns about peer review and plagiarism as a publisher investigates its back catalog. One of the researchers, A. Salar Elahi, now ranks 7th on the Retraction Watch Leaderboard.

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‘A proper editor would be horrified’: Why did a pediatric journal publish articles on the elderly?

In June, a scientist researching sarcopenia came across a relevant paper about treatment for elderly patients with complications from the disease as well as type 2 diabetes. The paper was “very bad,” he told us. “It looked like someone just copied two or three times the same text."

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Exclusive: Prof plagiarized postdoc’s work in now-retracted paper, university found
https://retractionwatch.com/2024/07...work-in-now-retracted-paper-university-found/

A political scientist in Canada copied his postdoc’s work without credit in a paper, according to the retraction notice and a university inquiry report.

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Elsevier investigating geology journal after allegations of pal review

Elsevier is investigating the journal Geoscience Frontiers after a PubPeer thread flagged an editorial advisor whose articles in the journal were edited by his frequent co-authors.

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Giant rat penis redux: AI-generated diagram, errors lead to retraction

In an episode reminiscent of the AI-generated graphic of a rat with a giant penis, another paper with an anatomically incorrect image has been retracted after it attracted attention on social media. The authors admit using ChatGPT to make the diagram.
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Zombie theories: why so many false ideas stick around?

EXCERPTS: When I talk to friends or family members who do not work in academia, they have beliefs about how science works — beliefs that appear entirely sensible. [...] As I’ve shown in a recent blog post, none of this is the case.

I do not want to revisit this debate, but instead take a look at why this is: why do problematic studies get published in the first place? Why do ideas stick around even when they’re shown to be false? And what can we do about that? The main reasons are vicious cycles and self-sustaining feedback loops inherent in how academia and science operate.

[...] There are many other examples of zombie theories — theories that stick around and simply won’t die. ... A 2020 paper showed that retractions after misconduct basically have no impact on citation count. That means that retracted papers keep gathering citations in the same way they would if they were not retracted... (MORE - missing details)
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Seems to be a follow-up to some previous Nature output posted on the subject: What is it like to attend a predatory conference?
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Predatory conferences are on the rise. Here are five ways to tackle them

As Nature’s Careers team reports in a two-part investigation, researchers are paying commercial conference providers the equivalent of hundreds, even thousands, of US dollars to attend such ‘predatory conferences’. Institutions and funders don’t seem to be aware of the scale of these operations. They need to become so, and quickly. [...] What then, can be done? Here are five potential interventions...
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Journal retracts paper on chiropractic product after company complains
https://retractionwatch.com/2024/08...chiropractic-product-after-company-complains/

An article about the overuse of spinal imaging has been retracted after the owner of a chiropractic product it criticized in passing complained to the journal...

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Cancer paper retracted 11 years after reported plagiarism

In November 2013, Elisabeth Bik reported five papers containing what she thought was “pretty obvious” plagiarized text in Karger’s Digestive Diseases to the journal’s editor in chief...

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Science and the significant trend towards spin and fairytales

In science, publishers and editors of academic journals prefer to publish demonstrably new findings – gold – rather than replications or refutations of findings which have been published already. This “novelty pressure” requires presentation of results that are “significant” – usually that includes being “statistically significant.”

[...] How do researchers create the illusion of novelty in a result when the finding has a probability value close to, but on the wrong side of, the stated probability threshold – for example, a probability of 0.06? Talk it up, spin out a story! It’s the fairytale of Rumpelstiltskin in modern garb.

Here are more than 500 examples of pretzel logic researchers have used to make claims of significance despite p values higher than .05. It would be comical if not for the serious obfuscation of science which the stories cause...

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The Ruthless Politicization of Science Funding

EXCERPT: These requirements to incorporate DEI into each research proposal are alarming. They constitute compelled speech; they undermine the academic freedom of researchers; they dilute merit-based criteria for funding; they incentivize unethical — and, indeed, sometimes illegal — discriminatory hiring practices; they erode public trust in science; and they contribute to administrative overload and bloat.

Instructions to applicants and examples of successful proposals make it abundantly clear that DEI plans must adhere to a specific ideological doctrine. According to NASA, “the assessment of the Inclusion Plan will be based on […] the extent to which the Inclusion Plan demonstrated awareness of systemic barriers to creating inclusive working environments that are specific to the proposal team.”

Thus, to get funding, scientists must declare that their own institution and research groups are uninclusive and discriminatory, which is an offense to the many scientists who have worked hard to ensure fair and transparent hiring practices in their institutions. These requirements effectively constitute DEI loyalty oaths as prerequisite for funding... (MORE - details)
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A THB Follow Up: Climate Research Fails a Science Integrity Test

Today, I heard back from PNAS that the dataset and paper are without problems and the matter is now closed. I reproduce the full PNAS email to me below. Some highlights: Remarkably, PNAS did not actually examine the dataset in question...

[...] Don’t take my word for it — look at the evidence and the data and come to your own conclusions. For me, this episode is yet another example of how some (not all) climate science has a tendency to go off the rails. This is a particularly egregious example.


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In Texas, ‘Junk Science Law’ Is Not Keeping up With Science

EXCERPTS: When the state legislature passed the junk science law in 2013 after two previous failed attempts, the measure was hailed across the nation as the first of its kind, with several states following suit and passing their own version.

The law creates a procedural pathway for convicted people to obtain new trials if they can show that underlying forensic evidence in their case was flawed, and that without that flawed evidence, they likely would not have been convicted. Examples of science that has formed the linchpins of junk science claims include the now-debunked bite mark comparison theory, new DNA evidence, and faulty cause-of-death determinations.

“The intention was to accommodate evolving science,” said Bob Wicoff, chief of the wrongful convictions division in the Harris County Public Defender’s Office. “Whereas the criminal justice system demands finality — they want cases to come to a close, and they want a judgment entered and pronounced and finality to be enacted — science keeps evolving.”

[...] “The law isn’t working as people believed it would,” said Estelle Hebron-Jones, director of special projects at the Texas Defender Service. “I don’t think it’s something that we can really get a gold star for, even though on paper that’s how it’s been presented.” (MORE - details)

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Looking our limitations in the eye: A call for more thorough and honest reporting of study limitations

ABSTRACT: The replication crisis and subsequent credibility revolution in psychology have highlighted many suboptimal research practices such as p-hacking, overgeneralizing, and a lack of transparency. These practices may have been employed reflexively but upon reflection, they are hard to defend.

We suggest that current practices for reporting and discussing study limitations are another example of an area where there is much room for improvement. In this article, we call for more rigorous reporting of study limitations in social and personality psychology articles, and we offer advice for how to do this.

We recommend that authors consider what the best argument is against their conclusions (which we call the “steel-person principle”). We consider limitations as threats to construct, internal, external, and statistical conclusion validity (Shadish et al., 2002), and offer some examples for better practice reporting of common study limitations.

Our advice has its own limitations — both our representation of current practices and our recommendations are largely based on our own metaresearch and opinions. Nevertheless, we hope that we can prompt researchers to write more deeply and clearly about the limitations of their research, and to hold each other to higher standards when reviewing each other's work.
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31% of Republicans say vaccines are more dangerous than diseases they prevent

Public sentiment on the importance of safe, lifesaving childhood vaccines has significantly declined in the US since the pandemic—which appears to be solely due to a nosedive in support from people who are Republican or those who lean Republican, according to new polling data from Gallup.

[...] Perhaps most concerning, the data indicated that a growing number of Americans view vaccines as more dangerous than the diseases they prevent—including polio, measles, tetanus, rotavirus, diphtheria, whooping cough, meningitis, and RSV, among others. Now, 20 percent of Americans overall think vaccines are more of a threat than the dangerous diseases they effectively prevent.


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The cynical war on genetically engineered crops grinds on

There is one, and only one, solution that could work on a global scale: a vitamin A-enhanced rice known as Golden Rice. The only thing blocking this global treatment is a coalition of advocacy groups [...] that has intimidated the public and manipulated some regulators and courts into believing that obstructing the genetic engineering revolution is a more important cause than preserving the life of vulnerable children.

In April, a Philippine court, acting on a filing by Greenpeace, rescinded the country’s commercialization approval of Golden Rice — a ruling even the uber-liberal The Guardian/UK, long a dogged opponent of genetically modified crops and a former ally of Greenpeace on this issue, characterized as disgraceful.

Greenpeace’s opposition is grounded in misrepresentations of science. It has long claimed that GE crops are inherently dangerous and unpredictable because the process uses ‘foreign’ genes—obtained from a harmless bacterium from another species — to facilitate the modification.

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I think genetically modifying foods to have more nutrients and protein is a very good thing and benefits populations that are very limited in their dietary choices. Like this golden rice:

"Golden Rice is a new type of rice that contains beta carotene (provitamin A, a plant pigment that the body converts into vitamin A as needed). This compound is what gives this grain its yellow-orange or golden color, hence its name.

Golden Rice is developed through genetic engineering. While ordinary rice does produce beta carotene, it is not found in the grain. Thus, scientists used genetic engineering to add the compound to the grain - a minor tweak that improved the grain’s nutritive value. The beta carotene in Golden Rice, which was made possible by the addition of two new enzymes, is identical to the beta-carotene found in green leafy and yellow-colored vegetables, orange-colored fruit, and even in many vitamin supplements and food ingredients.

Like ordinary rice, Golden Rice does not require any special cultivation practices, and generally has the same yield and agronomic performance.

While vitamin A can be obtained from food products and supplements, challenges regarding their availability, accessibility, and affordability make it difficult to address the problem of vitamin A deficiency (VAD). As rice is a staple food in many vitamin A-deficient communities in Asia, Golden Rice can be a significant help in improving these areas’ vitamin A status once the grain becomes available for public consumption."---- https://www.irri.org/golden-rice-faqs
 
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‘Violated’: Engineering professor found her name on four papers she didn’t write

“I became angrier the more I found, and also started feeling really violated that someone had used my name and title to put forward something that wasn’t scientifically rigorous,” Schaefer, a professor of mechanical engineering at Rice University in Houston, said.

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‘No animosity between us’: Lungless frog finding retracted after 16 years

In May, another team of herpetologists, using more sophisticated tools, said they’ve found evidence of lungs – tiny but functional – in the creatures.

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Paper claiming to discover new pain syndrome retracted

Researchers who said they discovered a new disease akin to rheumatoid arthritis, but caused by pollution, are standing by their claim despite the retraction of their paper last month.

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PNAS corrects article by Kavli prize winner who threatened to sue critic

Readers will “be unaware that this correction results from my comment, which Chad Mirkin tried to silence with a legal threat, and that PNAS decided not to publish,” Lévy said. “They will also not know that the results are from an interim report of a clinical trial that stopped several years ago.Thus this correction does nothing to correct the main problem” of the article."

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Journal republishes chiropractic paper it had retracted after legal threats

A journal has republished an edited version of a paper it retracted after a distributor of a chiropractic product the paper criticized wrote in to complain.
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