Coffee Break: Science Agonistes, with Hope at the End

Part the First: Confirmation the Scientific Literature Has Entered Terminal Decline?  In an update from last week’s Coffee Break, Cabell’s Predatory Reports database passes 20,000-journal milestone:

The US-based information services company reports that Predatory

Reports has grown by more than 300% since its launch in 2017. Having reached 10,000 journals in 2019 and 15,000 in 2021, a recent upgrade to its underlying technology has enabled the addition of further titles in recent months. As of January 30, 2026, the database contains 20,274 journals.

Journals are included in Predatory Reports if they meet some of the 70-plus criteria used by Cabells’ team to assess whether a journal is deceptive. Predatory journals are often fake or misleading, frequently seeking to dupe authors into paying for publication by mimicking legitimate peer-reviewed outlets.

Predatory Reports is complemented by Journalytics Academic and Journalytics Medicine, curated databases covering more than 13,000 and 9,000 journals respectively that have been verified as reputable. Together, the three resources provide publication information, metrics and analytics to help researchers identify appropriate venues and maximise the impact of their work.

So – we have 20,000 predatory or predatory-adjacent journals versus 21,000 reputable journals. Does this mean that every scientific paper, just like every video on the interwebs, must be considered a deep fake until proven otherwise?  I think it does.  The older I get, the more I miss the Current Journals tables in the university libraries.  They were a better way to keep up with what one needed to know.  Science, natural and social, plus the humanities were smaller, but outside a very far and very thin margin, published material could be taken at face value.

Some of it would never matter, but a vanishingly small part of published work was fraudulent.  Mistaken, possibly, but that is true of all provisional knowledge.  Back in the day, the science journalists William J. Broad  and Nicholas Wade wrote a book called Betrayers of the Truth: Fraud and Deceit in the Halls of Science (1983).  Somewhere in a box in the basement rests my copy.  As I recall the examples were vivid but they were rare, very rare.  Incidentally, Nicholas Wade, has an interesting recent history.  He believes that race is a legitimate biological concept.  Eugenics is here to stay, especially among the few with the power.

Part the Second: Clinical Trials Can Be Unnecessary and Unethical.  The current head of the Federal Drug Administration is famous for saying “RCT or STFU.”  Civil, very civil, Dr. Prasad.  Lambert used to say that a Randomized-Controlled Trial for the utility of a parachute if one wanted to jump out of a plane was silly.  Ditto for the use of N95 masks when a lethal respiratory virus is on the loose.  We already know both work as intended, but for user error.  This is not difficult.  It is already well known that the HepB vaccine works and that vaccinated newborns is perfectly safe (which is not to say reactions to the vaccine are impossible).  This is why the Hepatitis B vaccine trial that has been proposed for Guinea-Bissau should not be done, and if it proceeds, the results should not be published, in a reputable journal:

The Committee on Publication Ethics (COPE), an international organization that establishes best practices for scholarly journals, has endorsed specific ethical standards for studies that involve vulnerable groups. Among these standards is this statement in the Declaration of Helsinki: “Reports of research not in accordance with this Declaration should not be accepted for publication.” The current controversy about the U.S. Centers for Disease Control and Prevention (CDC) funding for a proposed study of hepatitis B vaccines in Guinea-Bissau must serve as a reminder of this core requirement of publication ethics.

An unsolicited $1.6 million grant to the Bandim Health Project at the University of Southern Denmark (SDU) would randomly assign more than 14,000 newborns into two groups, those who would receive the vaccine at birth and those who would act as a control group with delayed vaccination. The purpose of the controversial study was to assess the “broader health effects” of the vaccine for the control group.

But we already know the most critical health effect beyond the 48-months of the study: Withholding vaccination will predictably result in an increased incidence of liver disease later in life, including liver failure, cirrhosis and cancer. Therefore, the true scale of the tragedy brought on by this study would never be fully be known.

Already patently unethical, the study design would also exploit one of the world’s poorest countries, where more than 50 percent of its population live in poverty, according to the World Bank. The Center for Infectious Disease Research and Policy of the University of Minnesota reports that about 1 in 5 people born in Guinea-Bissau has chronic hepatitis B, that 9 in 10 babies who are exposed at birth develop a chronic infection and that 1 out of 4 of them will die of hepatitis B-related liver disease.

There is a larger bizarre context surrounding this now paused study: The Trump administration’s Advisory Committee on Immunization Practices voted in December to abandon a 30-year recommendation that all babies born in the U.S. be vaccinated for hepatitis B at birth. This is a recommendation that flies in the face of the best available evidence about the dangers of failing to vaccinate. The World Health Organization and pediatric and infectious disease groups uniformly recommend hepatitis B vaccination at birth. It is only Kennedy and his cadre of anti-vaccination zealots who see harm from a beneficial vaccine where none has been shown and sought to initiate a study to vindicate their dangerous view.

…

To be sure, there are other ways to publish data these days, and there are plenty of disreputable outlets that might enjoy the attention that a prominent scandalous research project would attract (Part the First). But that does not change the duties of responsible publication outlets. The community of legitimate journal editors recognized by their peers as upholding moral standards must, to maintain their legitimacy, draw a bright line.

Whatever happens, as the article by Drs. Kaplan and Moreno points out, the leaders of the University of Southern Denmark should be ashamed of themselves for approving a “scientific” study that fairly reeks of another very well-known long-term study of untreated syphilis in an older but similarly disadvantaged population.  Eugenics, again.  Unsurprisingly.

Part the Third: All Is Not Lost All the Time.  There are organizations that, for now, work very hard at protecting the integrity of that which we read and depend on: Libraries, as explained in Libraries on the frontline: protecting research integrity:

You’d have to have a laser focus elsewhere not to notice the growing concern about research integrity. In recent months there have been many reports, conference sessions and webinars all looking at the risks institutions and researchers face when research is of uncertain quality or dubious provenance. Librarians are at the forefront of addressing this challenge: they lead their institutions in understanding its causes and confronting strategic risks to trust, reputation and funding.

It can be difficult for an inexperienced researcher to judge the quality of the resources they find and use. Unfortunately, unvalidated or free resources are often the easiest to find during a general internet search – and the open web is often the first port of call when starting discovery.

On the other hand, when institutional libraries clearly signpost routes to valuable sources and provide a seamless authentication infrastructure that makes the experience straightforward, researchers and library users can access curated, quality-assured content easily and quickly – and all within the terms of licence and subscription agreements. High quality research resources take time and experience to collect. They are a valuable and unique asset for institutions that create them.

The library at my institution is very good at identifying reliable sources.  This is especially important or student and clinicians who have not been immersed in the literature of scholarly disciplines.  This is true of the libraries at public colleges and universities, as well as the local public library that I can see across the street as I write this.  I can only hope it survives the onslaught from politicians whose children get their books content from Bezos and his Tech Bros.

Part the Fourth: Lysenkoism 2.0 Continues into Its Second Year.  Yes, it does, although (so far) without the Gulag and show trials complete with coerced confessions and terminal outcomes.  Policy-based science is all the rage today (Part the Second), as shown by recent actions that fulfill the dreams of our current political misleadership: Trump team’s new rule could make firing government scientists easier:

The administration of US President Donald Trump moved forwards last week with its plan to make it easier to fire some government workers — including scientists — overriding objections from the public that this would lead to further political interference in US science.

On 5 February, the US Office of Personnel and Management (OPM) finalized a rule that it proposed last year to create a new class of government employee called ‘Policy/Career’. This class would reassign career civil servants who influence government policy — a potentially broad category — and strip them of the job protections that they usually have under US law. (Career civil servants are hired through a competitive, merit-based system and hold their jobs for years, unlike political appointees who typically remain for one administration.)

According to the new rule, Policy/Career employees could be fired for “subverting Presidential directives”. Agencies in the US Executive Branch including the National Science Foundation (NSF) and the National Institutes of Health (NIH) — the main federal funders of science in the country — have already assembled lists of workers to convert to the new category. The OPM recommended considering positions involved in awarding research grants at such agencies. On the basis of those lists, the OPM estimates that the rule will reclassify around 50,000 federal employees.

Virtually all scientists in government labs are civil service employees.  They are hired after a rigorous search.  They must meet stringent expectations to make it past their probationary period.  They are not “in it for the money” or they would be working for Big Medicine, Big Pharma, Big Oil, or Big Tech.  They do not make policy.  And those scientists who do make policy are not much different from those who do the science.  Will the Administration succeed in procuring a scientific (sic) workforce that does its bidding?  Someone will have to ask Polymarket.  But I would not bet against them.

Part the Fifth: Yes, Virginia, It Really Is the Age of Policy-based Science.  This is the inescapable conclusion from EPA scraps the ‘endangerment finding’ that climate change harms human health from yesterday in Scientific American:

The Environmental Protection Agency scrapped the agency’s landmark 2009 global warming “endangerment finding” breaking with the long-standing scientific consensus that global warming poses a risk to human health. The finding played a critical role in regulating greenhouse gas emissions from cars and trucks. The transportation sector accounted for 28 percent of all U.S. emissions in 2022.

“As EPA Administrator, I am proud to deliver the single largest deregulatory action in U.S. history on behalf of American taxpayers and consumers,” said Lee Zeldin, head of the EPA on Thursday at a White House event alongside U.S. president Donald Trump.

As the press release from EPA (a creation of our last notionally liberal President, Richard Nixon) says, this will create policy based in reality.  Well, the endangerment finding is the natural outcome of the reality that led to the Clean Air Act, originally enacted more than sixty years ago.  This was discussed long form yesterday in The Daily from The New York Times.  The usual suspects are there, including one of Justice Lewis’s Powell’s creations.  Will the legal vultures carry the day?  Probably.  Will our children and grandchildren pay the price?  Certainly.

And that is a pity.  I grew up in a small industrial city that had become a waste dump on the marsh.  The Clean Air and Clean Water Acts changed all that, despite the rather weird beliefs of hometown friends who still maintain that the impacts of human behavior are too small to have an impact on something as large as climate.  I guess they just cannot believe their lyin’ eyes.  The irony is sharp.  If this subversion of the spirit of the Clean Air Act prevails, that one hundred miles of mostly unspoiled paradise between the Savannah River in the north and the St. Marys River to the south will certainly become uninhabitably underwater (please pardon the self-citation) during the lifetimes of their great grandchildren, if not their grandchildren.  Pity.

Part the Sixth: Economies of Meaning for the Current Age and the One Aborning.  Or from another little gem from The Front Porch Republic, “Gardening is cheaper than therapy.”  And it may be what makes a human life possible for our children and grandchildren:

We stoop at self-checkouts and hope meaning will arrive in two-day shipping, filling our carts to fill the hollow that community once held. Yet meaning can’t be manufactured, and our kind of hunger can’t be cured by more. When I walked the rows and beds of that half-forgotten garden, I was struck by how different its logic was from the market: the soil didn’t panic when I paused. It waited. It held the memory of rain not yet fallen. It knew growth rises from rest as much as labor. The economy measures transaction; the earth measures transformation. Some of the truest profit appears only when the frenzy pauses. We’re no longer sold products—we’re sold the signals of transformation. A car poses as freedom, a phone as connection, a brand becomes a tribe. Consumer culture doesn’t cultivate change; it packages the feeling of having changed. What we once became, we now buy.

(Victor E.) Frankl was a young Jewish psychiatrist from Vienna, trained in the long shadow of Freud and Adler. Where Freud sought pleasure and Adler sought power, Frankl sought purpose. He called his approach “logotherapy,” or healing through meaning. When the Nazis came, Freud fled to London. Frankl stayed, hoping to protect his family and his patients. He was sent to Theresienstadt, then to Auschwitz, and lived to write about both. Freud chose escape; Frankl chose abiding. Both choices were human. Only one taught us how meaning survives. Frankl lost his parents, his wife, and the child she carried. Yet from that abyss he brought back what our age keeps forgetting: the soul can bear almost any suffering except suffering stripped of purpose.

He came to see that people fail not from pain but from meaninglessness. In the camps he watched men endure starvation and cold, yet collapse when they lost the reason to continue. Those who lost their why could not bear the how. Our culture mistakes ease for salvation and trys to manage the ache of being human instead of honoring it. We treat silence as loneliness and waiting as failure, even though meaning grows in the very spaces we refuse to fill. When I returned to the garden, I thought of those camps – like Mount Sinai; they were places where endurance meant life.

Frankl reminds one of another Victor, Victor Klemperer.  Hope and optimism are not the same thing.

See you next week!