(Roughly) Daily

Posts Tagged ‘medicine

“It is not the germs we need worry about. It is our inner terrain.”*…

Germs (source)

Background becomes foreground: Jean-Laurent Casanova on how we might better think about infectious diseases…

In 1955, René Dubos famously expressed his “second thoughts on the germ theory”, attributing infectious diseases to various “changing circumstances” that weaken the host by unknown mechanisms. He rightly stressed that only a small minority of individuals infected by almost any microbe develop clinical disease. Intriguingly, though, he did not mention the abundant and elegant findings reported from 1905 onward that unambiguously pointed to host genetic determinants of infection outcome in plants and animals, including human inborn errors of immunity. Diverse findings over the next 50 y[ears] corroborated and extended these earlier genetic and immunological observations that René Dubos had neglected. Meanwhile, the sequential advent of immunosuppression- and HIV–driven immunodeficiencies unexpectedly provided a mechanistic basis for his own views. Collectively, these two lines of evidence support a host theory of infectious diseases, with inherited and acquired immunodeficiencies as the key determinants of severe infection outcome, relegating the germ to an environmental trigger that reveals an underlying and preexisting cause of disease and death…

The full essay: “From second thoughts on the germ theory to a full-blown host theory,” from @PNASNews.

Pair with: “The World Is Toxic. Welcome to the Metabolic Era,” from @k_pendergrast in @WIRED.

* Louis Pasteur (who was clearly already having second thoughts)


As we contemplate the clinical, we might sending healing birthday greetings to Charles Mayo; he was born on this date in 1865. A medical doctor (surgeon) and philanthropist, he co-founded  the Mayo Clinic and it’s supporting/governing body, the Mayo Foundation. Within Mayo’s lifetime, it registered one million patients. As of today, Mayo Clinic has ranked number one in the United States for seven consecutive years in U.S. News & World Report‘s Best Hospitals Honor Roll, maintaining a position at or near the top for more than 35 years.


Written by (Roughly) Daily

July 19, 2023 at 1:00 am

“History repeats itself, in part because the genome repeats itself. And the genome repeats itself, in part because history does.”*…

The original Human Genome Project map of the human genome was largely based on the DNA of one mixed-race man from Buffalo, with inputs from a few dozen other individuals, mostly of European descent. Now, researchers have released draft results from an ongoing effort to capture the entirety of human genetic variation…

More than 20 years after the first draft genome from the landmark Human Genome Project was released, researchers have published a draft human ‘pangenome’ — a snapshot of what is poised to become a new reference for genetic research that captures more of human diversity than has been previously available. Geneticists have welcomed the milestone, while also highlighting key ethical considerations surrounding the effort to make genome research more inclusive…

The draft genome, published in Nature on 10 May, was produced by the Human Pangenome Reference Consortium. Launched in 2019, the international project aims to map the entirety of human genetic variation, to create a comprehensive reference against which geneticists will be able to compare other sequences. Such a reference would aid studies investigating potential links between genes and disease.

The draft pangenome follows the 2022 publication of the first complete sequence of the human genome, which filled gaps that had been left by the original Human Genome Project. But unlike the original draft human genome and its successor, both of which were derived mostly from the DNA of just one person, the draft pangenome represents a collection of sequences from a diverse selection of 47 people from around the globe, including individuals from Africa, the Americas, Asia and Europe…

More at “First human ‘pangenome’ aims to catalogue genetic diversity,” in @Nature.

See the paper on the Pangenome Project here; and for more background, “This new genome map tries to capture all human genetic variation.”

* Siddhartha Mukherjee, The Gene: An Intimate History


As we go wide on genetics, we might send microscopic birthday greetings to Christian Anfinsen; he was born on this date in 1916. A biochemist, he won the 1972 Nobel Prize for Chemistry for his research on the shape and primary structure of ribonuclease (the enzyme that hydrolyses RNA), in whihc he found that found that its shape and consequently its enzymatic power could be restored– leading him to conclude that ribonuclease must retain all of the information about its configuration within its amino acids.


Written by (Roughly) Daily

May 14, 2023 at 1:00 am

“Long life is welcome, agreeable, pleasant, and hard to obtain in the world”*…

… maybe, as recent research from Saul Justin Newman explains, even harder than we thought…

The observation of individuals attaining remarkable ages, and their concentration into geographic sub-regions or ‘blue zones’, has generated considerable scientific interest. Proposed drivers of remarkable longevity include high vegetable intake, strong social connections, and genetic markers. Here, we reveal new predictors of remarkable longevity and ‘supercentenarian’ status. In the United States supercentenarian status is predicted by the absence of vital registration. In the UK, Italy, Japan, and France remarkable longevity is instead predicted by regional poverty, old-age poverty, material deprivation, low incomes, high crime rates, a remote region of birth, worse health, and fewer 90+ year old people. In addition, supercentenarian birthdates are concentrated on the first of the month and days divisible by five: patterns indicative of widespread fraud and error. As such, relative poverty and missing vital documents constitute unexpected predictors of centenarian and supercentenarian status, and support a primary role of fraud and error in generating remarkable human age records…

The paper in full: “Supercentenarian and remarkable age records exhibit patterns indicative of clerical errors and pension fraud,” at @biorxivpreprint.

(Image above: source)

* Buddha


As we long for longevity, we might send healthy birthday greetings to William H. Welch; he was born on this date in 1850. A physician, pathologist, bacteriologist, and medical educator, He was one of the “Big Four” founding professors at the Johns Hopkins Hospital, the first dean of the Johns Hopkins School of Medicine, and the founder of the Johns Hopkins School of Hygiene and Public Health, the first school of public health in the country.

Welch revolutionized American medicine by demanding of its students a rigorous study of physical sciences and an active involvement in clinical duties and laboratory work. His students included Walter Reed, James Carroll and Simon Flexner.


“Psychedelic experiences are notoriously hard to render in words”*…

… to categorize them, even harder. But Josie Kins (@Josikinz) and her colleagues at Effect Index are putting in the work…

The Subjective Effect Index is a set of articles designed to serve as a comprehensive catalogue and reference for the range of subjective effects that may occur under the influence of psychoactive substances and other psychonautic techniques.

The effects listed here are accompanied by detailed descriptions on the subjective experiences of them. They are written in a consistent and formal writing style that avoids the use of flowery metaphors or analogy; instead, they strive to use simple and accessible language. This is done with the hope that they will eventually serve as a universal terminology set that enables people to better communicate and share experiences that are, by nature, difficult to convey.

The Index is separated into 233 effects, which are organised into categories based on the senses they affect and their behavior. Many of these are further broken down into leveling systems, subcomponents, and style variations that may occur across different substances. Detailed image, video, and audio replications [like the one above] have been included wherever possible to supplement text-based descriptions…

Stanislav Grof, M.D has argued that “LSD is a catalyst or amplifier of mental processes. If properly used it could become something like the microscope or telescope of psychiatry.” Effects Index is attempting to build a database to help that process along.

* Michael Pollan


As we tackle the taxonomy of trips, we might recall that it was on this date in 1842 that (modern) anesthesia was used for the first time in an operation– by Dr. Crawford Long.  Long, a physician and a pharmacist, used diethyl ether in the removal of a tumor from the neck of James Venable in Jefferson, GA; given success with Venable, Long then used ether in other surgeries and in childbirths.  He published the results of these trials in 1848 in The Southern Medical and Surgical Journal (an original copy of which is held in the U.S. National Library of Medicine).

It’s cool that Long is the subject of one of the two statues representing Georgia in the crypt of the U.S. Capitol.  It’s cooler that Long was the cousin of Doc Holliday.

Crawford Long (source)

Written by (Roughly) Daily

March 30, 2023 at 1:00 am

“For the sake of the science, it might be time for scientists to start trusting each other a little less”*…

We’ve looked at methodical problems in scientific and medical research before (see here, here, and here). Let us turn now to outright dishonesty. The rising number of retracted research papers suggests that either medical research fraud is on the rise or that efforts to spot it are getting better. Either way, it’s a problem …

… Partly or entirely fabricated papers are being found in ever-larger numbers, thanks to sleuths like Dr Mol. Retraction Watch, an online database, lists nearly 19,000 papers on biomedical-science topics that have been retracted (see chart 1). In 2022 there were about 2,600 retractions in this area—more than twice the number in 2018. Some were the results of honest mistakes, but misconduct of one sort or another is involved in the vast majority of them…

… Yet journals can take years to retract, if they ever do so. Going by these numbers, roughly one in 1,000 papers gets retracted. That does not sound too bad. However, Ivan Oransky, one of Retraction Watch’s founders, reckons, based on various studies of the matter and reports from sleuths, that something more like one in 50 papers has results which are unreliable because of fabrication, plagiarism or serious errors…

… It is often asserted that science is self-correcting. And it is true that, if a claimed result is important enough, an inability to replicate it or of subsequent work to conform to it will eventually be noticed. In the short term, though, it is easy to hide in the shadows. Even co-authors of a data-fabricating scientist—those, in other words, who are closest to him or her—may not notice what the culprit is up to. In complex studies of a particular disease, several types of researchers will be involved, who are, by definition, not experts in each other’s fields. As Dr Bishop observes, “You just tend to take on trust the bits of data that somebody else has given you.”…

In the end, however, keeping fakes out of the scientific record depends on the willingness of publishers to stump up more resources. Statistical checks of clinical-trial papers often involve laborious manual work, such as typing up specific data in spreadsheets. This would require journals to hire dedicated staff, cutting into profits.

Many academics who have spent years trying to get fabricated papers retracted are pessimistic that better ways to detect fraud will, alone, make a big difference. Dr Roberts and Dr Mol want journals to be regulated in the way that social media and the news business are in some countries, with standards on what they publish. Peter Wilmshurst, a British cardiologist who has raised the alarm about numerous cases of research misconduct in his field, thinks there should be criminal penalties for those who fabricate data. Dr Gunsalus wants universities to make public the reports from their research-fraud investigations. And everyone agrees that publish or perish is a recipe for disaster.

None of these solutions will be quick or straightforward. But it is now clear that choosing to look the other way is causing palpable harm to patients…

“There is a worrying amount of fraud in medical research- and a worrying unwillingness to do anything about it,” from @TheEconomist.

* Stuart Ritchie, Science Fictions


As we look harder, we might spare a thought for Alfred Habdank Skarbek Korzybski; he died on this date in 1950. Trained as an engineer, he developed a field called general semantics, which he viewed as both distinct from, and more encompassing than, the field of semantics. He argued that human knowledge of the world is limited both by the human nervous system and the languages humans have developed, and thus no one can have direct access to reality, given that the most we can know is that which is filtered through the brain’s responses to reality. (Korzybski assumed that the quest for knowledge was an authentic, honest one; that said, if “human nervous system” an be understood to extend to “human nature”…)

Korzybski was influential in fields across the sciences and humanities through the 1940s and 50s (perhaps most notably, gestalt therapists), and inspired science fiction writers (like Robery Heinlein and A.E. van Vogt) and philosophers like Alan Watts.

His best known dictum is “The map is not the territory.”


Written by (Roughly) Daily

March 1, 2023 at 1:00 am

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