Part the First: Predatory or Not? Over the past six years the biomedical literature has accumulated 494,547 scientific “publications” with “COVID” (case insensitive) somewhere in the paper. A search using “AIDS HIV” as the query returns 204,559 papers over the past forty-five years. Something does not add up here. And that something is the nature of the scientific literature and the business of scientific publishing. We are now living in an open-access, pay-to-publish-anything world. A very large fraction of the COVID papers can be described using the technical term trash. It’s as simple as that, but no one will ever document this. I tried early in during pandemic and was overwhelmed. Life is too short.
How does one identify these predatory journals, when their typical website and downloaded pdfs are indistinguishable from the websites and pdfs from Journal of Heredity (1910) Journal of Biological Chemistry (1905) or Journal of General Physiology (1918, founded by Jacques Loeb, who was the model for the protagonist in Sinclair Lewis’s Arrowsmith)? For the non-scientist this can be a difficult question. For the typical Evaluation Committee in a university, whose only skill is counting much more often that it should be, this is not a problem but a solution (that tide might be turning, though, should universities survive). For working scientists with integrity, it is usually a simple matter of “I know it when I see it.” But perhaps for my younger successors under irresistible pressure to “publish” (and probably perish anyway, but I digress) this is more difficult. Still, they should be advised to be careful. And there is some help, as described in this news item in Nature by Matthew Hutson in Is this journal legitimate? This tool can help you decide.
Scientists are subject to scams, just as much as anyone else. Predatory journals take advantage of authors who submit papers and readers who access these papers; predatory conferences exploit speakers and attendees. But an innovative tool called Aletheia-Probe (named after the Greek word for truth) offers a simple way to check the ratings of journals and conferences, so users can better assess which ones to trust (“Aletheia” is essentially the antonym of Lethe, River of Forgetfulness).
Scientists often receive flattering e-mails (yes, we do, and the current scam is to entice unknowing medical students into this trap because they think this will “look good on their residency applications”) inviting them to submit their work to journals and conferences that are happy to take their money in return for a shoddy service. The publications might skimp on the peer-review process or disappear after a few months; the conferences might consist of empty meeting rooms or involve off-topic talks. Researchers who are deciding which journal to submit their papers to, or whether to include a specific paper in a systematic review, can check various lists of legitimate journals (such as the Directory of Open Access Journals) or predatory ones (such as Predatory Journals), as well as databases such as CrossRef that provide more nuanced information about journals. But the information is scattered across sources, and the lists don’t always agree. Aletheia-Probe is a one-stop shop.
The software collects data from a dozen databases and applies an algorithm to integrate the information. Users can download Aletheia-Probe from cloud-based repository GitHub and run it on a text-based command-line interface (for instance, the macOS Terminal or MobaXterm on Windows). The command ‘aletheia-probe journal “Nature”’ directs the software to scrutinize this journal. It’s conclusion “Result: LEGITIMATE (confidence: 0.95)” is offered alongside a summary of its reasoning. For other journals, it might reply, “PREDATORY (confidence: 0.90)” or “INSUFFICIENT_DATA (confidence: 0.45)”. “My idea of this is something like having a virus scanner,” Florath says.
Florath uploaded a paper about the tool to the preprint server arXiv on 15 January. In an ironic twist, a predatory publisher subsequently e-mailed him asking if he would publish it with them, he says.
I do not know how useful this will be to the interested citizen, but the tool is free. The arXive paper is here: Alethia–Probe: A Tool for Automated Journal Assessment. In the meantime, when an article in the media or a friend refers you to the latest and hottest scientific paper about COVID or Ozempic, several questions should be asked:
Does the journal have a Wikipedia page? I know, Wikipedia, but Wiki is good for basic facts and the three legacy journals listed above are described there.
Does the editor have an institutional address and email instead a Gmail address or equivalent?
Is the editorial board of a reasonable size (subjective, but if the list goes on forever the editors are there for a line on their CV) and have you heard of their institutions?
When was the first issue published? If the journal appeared in the last fifteen years, caveat emptor.
Have you heard of the publisher, and does it have a Wikipedia page?
A “no” answer to any of these questions is an invitation to scroll right on by. Perhaps this fetid swamp will be drained eventually, but it is difficult to remain hopeful.
Part the Second: The New Adventures of Podcast Jay. Those rascals (albeit board-certified physicians and scientists, unlike the current Director of the National Institutes of Health, who is all degreed up, but never completed his graduate medical education and therefore has no right to call himself “Doctor” if the implication is that he is a practicing physician) at Science-Based Medicine have been on a roll for a while now, and this post is particularly useful: Lysenkoism 2.0 continues: Podcast Jay wants to turn NIH into the ‘research arm” of MAHA.” Polymarket would agree. This began horribly and will not end well.
As noted, this has been somewhat under the radar given the visibility of RFKJr, but:
(T)he dismantling of the NIH and, with it, likely the dominance in biomedical research that the US has enjoyed for decades gets a lot less attention. Worse, when it does get attention, there’s an unfortunately good chance that it will be in the form of a fawning interview in the New York Times by a hack pundit like Ross Douthat about “restoring trust” in science, which is – among other things – what prodded me last week to get off my duff and write a post that I’ve been meaning to write for weeks now about how Dr. Bhattacharya is serving as the useful idiot and figurehead under which the NIH is being transformed into the “research arm” of MAHA. If that’s not Lysenkoism 2.0 (as I’ve been calling it), I don’t know what is.
Taken in context, the MAHA takeover of the NIH under the figurehead “direction” of Dr. Bhattacharya is, as I’ve written before, an extinction-level threat to public health and biomedical research in this country. Quite frankly, it could well mean the end of the relatively apolitical – or at least nonpartisan – research agenda of the NIH for a generation, with the NIH being turned into yet another patronage system under a profoundly transactional President.
…
Before a discussion of what Dr. Bhattacharya claims and says, it’s useful to compare whatever he says to an actual analysis published in Science a week ago, US government has lost more than 10,000 STEM Ph.D.s since Trump took office:
Some 10,109 doctoral-trained experts in science and related fields left their jobs last year as President Donald Trump dramatically shrank the overall federal workforce. That exodus was only 3% of the 335,192 federal workers who exited last year but represents 14% of the total number of Ph.D.s in science, technology, engineering, and math (STEM) or health fields employed at the end of 2024 as then-President Joe Biden prepared to leave office.
And they won’t be coming back, as PZ Myers has correctly observed. Science does not rebound like that. Nor does anything else, really, which is something my PMC peeps should keep in mind as the Neoliberal Dispensation now comes for them. Once stopped on a whim, a research program or project cannot be restarted by fiat. I can attest to that from my own professional life. Materials dissipate and decay and are soon lost because they often cannot be recovered absent the years of effort they took to build. Skills atrophy. Fiat ex lux worked only once. Could NIH and NSF have been improved, incrementally, from the margin to the core? Yes. Would that have improved American science? Undoubtedly. But improvement is not the objective. Policy-based science instead of science-based policy is the objective. Unfortunately, policy-based science has had a spectacularly bad run the past six years or so. But that is no good reason to discard it.
As they say, read it for yourself. Dr. David Gorski is always worth reading, and the story he tells on a weekly basis is grim. But I do want to emphasize something (italics below) from the discussion of Podcast Jay’s interview with the regrettable Ross Douthat:
As a board-certified practicing cancer surgeon with a PhD, I can’t help but reiterate that Podcast Jay never actually practiced medicine after medical school. He’s never taken care of patients except under the close supervision under which medical students take care of patients…As is the case with a lot of COVID “contrarians,” Podcast Jay likes to pretend that, just because COVID-19 was a new disease caused by a new virus (SARS-CoV-2), we didn’t know anything about it or anything about how to slow its spread. This ignores the simple fact that SARS-CoV-2 is a coronavirus, and we knew a lot about coronaviruses before COVID-19 appeared, so much so that it was obvious that a “natural herd immunity” solution as proposed in the GBD (Great Barrington Declaration) was highly unlikely to work because coronaviruses are known to mutate so quickly that they can evade “natural immunity” (more properly called postinfection immunity) and reinfect the same people. Cranks like Podcast Jay like to pretend that SARS-CoV-2 was a blank slate, something entirely new, and that we knew nothing about it or how to combat it, when decades of public health research and practice were there to draw upon and make inferences from. Tellingly, when public health officials inevitably got some things wrong, Podcast Jay routinely implied that we shouldn’t trust anything they said.
We have covered this before, repeatedly. Coronaviruses are “old” (first identified as infectious bronchitis virus, IBV, in chickens in the early 20th century) and scientists have known at least since World War II that they are “different,” especially in their evasion of the vertebrate immune system. A theme at SBM is that the COVID vaccines have been astonishing feats of biomedical science. This they were and are. They have saved millions of lives and prevented serious disease in just as many. But the scientific and political establishments oversold something that made billions of dollars for Big Pharma. They should have known better, especially the scientists who knew or should have known that durable immunity to coronaviruses has been a unicorn since the first IBV vaccines were produced. This is settled scientific knowledge that I first learned from a veterinarian colleague who died too young, perhaps from Long Covid.
If NIH, CDC, WHO and other organizations had pointed out that the SARS-CoV-2 vaccines, along with non-pharmaceutical interventions such as masking and improving ventilation in enclosed spaces like schools, would lessen the severity of the pandemic, there is every reason to believe the people have responded as citizens instead of partisans. This did not happen, and it turned relatively low-grade anti-vax nonsense into another epidemic. Some of the results of that are described above. In the meantime, biomedical mRNA technology, which has tremendous potential in rapid responses to other emerging diseases as well as cancer therapeutics, has been cast into the outer darkness, and only because it became “famous” as a false promise: “Get vaccinated and you will be safe!” As for MAHA, that trope is as absurd as durable immunity through infection or vaccination to coronaviruses.
Part the Third: Young Dr. Attia Faceplants. Continuing with the today’s theme, Dr. Peter Attia (MD, Stanford, along with Casey Means MD) is a star in the longevity medicine (sic) firmament that predates but is now undoubtedly a part of MAHA. Or he was a star, until the latest Epstein File dump:
The Epstein Files, while they still haven’t harpooned their biggest whales, continue to destroy reputations on the side. One of the most unusual scalps claimed last week was that of celebrity doctor and “longevity expert” Peter Attia, creator of the “Outlive” brand. Last month, CBS News named Attia one of 19 new essential contributors. Now it’s cutting ties with him. And they’re not the only ones.
Attia was born in Canada but graduated from Stanford University Medical School in 2001. He spent five years as a general surgery resident at Johns Hopkins Hospital, where he was named “Resident of the Year,” followed by a surgical oncology fellowship at the National Cancer Institute focusing on melanoma.
After a brief tenure at McKinsey and company, Attia founded a private clinic to implement “Medicine 3.0,” a proactive approach to health that emphasizes exercise, nutritional biochemistry, and emotional health to prevent chronic disease. His 2023 book, Outlive: The Science and Art of Longevity, became a #1 New York Times bestseller. One of his most famous concepts is the Centenarian Decathlon: a list of 10 physical tasks you want to be able to do in your last decade of life. One of those tasks, we assume, wasn’t hanging out with Jeffrey Epstein.
Again, you should read it yourself. At least one of the emails is absolutely not safe for work or fit for a family blog and others are ten exits past disgusting and worse. And it should be noted that, contra Neal Pollock of The Spectator, Peter Attia-MD, just like Casey Means-MD, never completed his surgical residency, unless this video two years ago from BolognaFishMD, about whom I know nothing, is an early deep fake. Regarding his career trajectory, I do wonder if Peter Attia-MD’s brief time at McKinsey was the result of one of their recruiting visits to Johns Hopkins University School of Medicine. He would be the second Johns Hopkins medical resident or postdoctoral fellow I have known who made that transition instead of becoming a licensed physician or scientist. Oh, and this “news” did make me laugh out loud the other morning when I was building a spreadsheet for a project and Saagar Enjeti of Breaking Points (first three minutes) expressed his utter dismay that one of his heroes had plopped down on the doorstep so ignominiously in the Epstein Files.
I’m a member of the home team, but this is one of the analyses of the Epstein Case I have read, in case you missed it. But we should also remember, as Caitlin Johnstone writes from Oz, nothing is likely to come of this. Their armor is strong.
Part the Fourth: The iPatient and the Good Doctor. Dr. Will Lyon is a geriatrician from Wauwatosa, Wisconsin (pop. ~48,000). From Front Porch Republic he writes of the practice of modern medicine in Doctoring and the Device Paradigm:
Before doctors see a patient, they perform a procedure called “chart review.” This involves reviewing the patient’s history, medications, lab or imaging data, and notes from any recent specialist visits or hospital stays. There is variation in how much chart review one prefers to perform before meeting a patient, but in general it is good and necessary to be sufficiently informed and prepared before the visit. But chart review can be a double-edged sword: it can save time and help put the history you obtain and the physical exam you perform into context, but it can also box you in to a false understanding of who the patient is. In the age of ubiquitous electronic health records, which promise an ostensibly more efficient method of chart review but also contain vast amounts of information, chart review can become daunting.
…
Several years ago, when my wife’s grandfather – “Opa” – presented to the ER with shortness of breath while I was on service in the hospital, I learned the value of meeting the real patient first.
I only learned of his arrival because I was notified by my family, and I could not access his medical record. Instead, I went straight to meet him in his emergency department room. On my elevator ride down, I thought about his shortness of breath. I knew that he had had a myocardial infarction earlier in the year, treated with the placement of a coronary stent.
When I walked in the room, he looked almost as pale as the bedsheets. When I shook his hands, I noticed that they were cool. He described feeling lightheaded whenever he stood up at home and was so short of breath that he wasn’t able to walk across his living room – a drastic change in his functional status. All of these signs suggested a common cause – anemia. However, the iPatient’s story suggested at a different suspected cause: new or recurrent heart problems. Or so I learned when the ER doctor stopped by.
Turns out it was anemia and not a heart attack, and according to Dr. Lyon “I still think of Opa’s case when I get lost in the weeds of chart review and need to remember that sometimes, the most valuable information is gathered from the patient by using our eyes, ears, and hands.” This is the lesson we try to teach our medical students from their first few weeks of medical school, even as they are consumed by biochemistry, genetics, and cell biology. From Dr. Lyon:
I do not intend to minimize the importance of reviewing the patient’s chart. Oftentimes, a thorough review provides critical information that guides your clinical approach (in the case I described, the fact that Opa was on blood thinners would increase the likelihood of blood loss as the cause of his anemia). Failing to identify key history on chart review can have devastating consequences, especially in the case of complex medical patients. The error comes when we mistake the iPatient for the flesh-and-blood human being in the exam room or hospital bed.
What I instead hope to illustrate is the tradeoff that occurs when doctors approach the EHR as their primary means of information-gathering and decision-making, and the patient as their secondary source. Sir William Osler, who revitalized and reshaped medicine and medical education in the late 19th century, famously requested that his epitaph include only the fact that he “taught medical students in the wards.” If he were choosing his epitaph today, he would likely include the qualification that he taught medical students at the bedside, and not just in a team room full of computers. While abstract data is important and indispensable, so is information from the history and physical exam. As Osler taught, “our fellow creatures can not be dealt with as man deals in corn and coal.” Instead, he advocated for an approach based on careful observation, wisdom acquired through experience, and the “education of the heart,” all in the service of the patient.
To counter the device paradigm and our over-reliance on the EHR, we need a renewal of confidence, competence, and wonder when it comes to the richness and depth of information available from a patient’s story and a physical examination. Many have already recognized this. Initiatives such as the Society of Bedside Medicine are working to educate and inspire clinicians to approach bedside evaluation with confidence and competence. As Brian Volck put it at the 2022 FPR conference, we need to return to practicing medicine “as if bodies actually mattered.”
I am not a clinician, but I have read Osler (pronounced Oh-slur) and so far I have gotten possibly two medical students to do the same in too many years. I like to believe they have become better physicians for that. And I never stop reminding our current students that electronic medical records are built for billing, with medical care left back down the track, maybe as far as last-place Sham behind Secretariat in the 1973 Belmont Stakes (still a thrilling few minutes after 52 years).
See you next week!
