(Roughly) Daily

Posts Tagged ‘disease

“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

“Smells are the fallen angels of the senses”*…

In an excerpt from his new book, Where We Meet the World: The Story of the Senses, Ashley Ward contemplates the oft-ignored and much-maligned olfactory sense…

Despite the wonderful contributions that smell makes to our lives, it’s undervalued in modern Western societies. Polls conducted in both the US and the UK reported that of our five main senses, smell was the one that people were least concerned about losing, while a study of British teenagers found that half would rather be without their sense of smell than their phone.

Despite the wonderful contributions that smell makes to our lives, it’s undervalued in modern Western societies. Polls conducted in both the US and the UK reported that of our five main senses, smell was the one that people were least concerned about losing, while a study of British teenagers found that half would rather be without their sense of smell than their phone.

It may have to do with olfaction’s checkered past. For much of human history, smells were things to be wary of. The idea that sickness was borne out of noxious smells was the prominent theory in disease propagation for centuries. Clouds of pungency, known as miasmas, released from unclean dwellings, filthy streets, and even the ploughing of soil, were blamed for contaminating the body, leading to any number of maladies. A debilitating fever emerging from marshes and swamps was named after the medieval Italian for bad air: mal’aria. Terrifying epidemics that haunted the world for centuries seemed to be induced by foul, corrupted air.

While odors themselves were regarded with distrust, it seems like every famous man in history who ever felt moved to write about our sense of smell had some derogatory point to make (there’s a notable shortage of opinions from the women of history). Most fall into one of two camps: those who regarded smell as relatively unimportant, and those who associated it with depravity. Plato considered that smell was linked to “base urges,” while others described it as degenerate and animalistic. Aristotle wrote that “man smells poorly” and Darwin asserted that “the sense of smell is of extremely slight service.”

The migration of primate eyes to the front of the face allows excellent stereoscopic vision, compared to the side-of-the-head arrangement favored by many other mammals, but limits the space available for the olfactory equipment. The loss of the snout in apes especially seems only to further restrict the capacity for smell.

Finally, primates in general and humans in particular seem to be losing genes associated with our sense of smell. We have something like 400 working olfactory genes, but sitting in our genetic code are close to 500 olfactory pseudogenes. These are the genetic equivalents of fossils; genes that used to contribute to our sense of smell but that no longer work. In other words, we’ve lost over half of our smell genes across evolutionary time…

Eminently worth reading in full: “How Smell—the Most Underrated Sense—Was Overpowered By Our Other Senses,” from @ashleyjwward in @lithub.

* Helen Keller


As we breathe in, we might we might recall that it was on this date in 1943 that Swiss chemist Albert Hofmann discovered the sensory- enhancing, even altering– that’s to say, psychedelic– properties of LSD.  Hofmann had synthesized the drug five years earlier, but its hoped-for use in treating respiratory problems didn’t pan out, and it was shelved.  On this day, he accidentally absorbed some of the drug through his skin (as he touched its container).  He became dizzy with hallucinations.  Three days later he took the first intentional dose of acid: 0.25 milligrams (250 micrograms), an amount he predicted to be a threshold dose (an actual threshold dose is 20 micrograms).  Less than an hour later, Hofmann experienced sudden and intense changes in perception.  He asked his laboratory assistant to escort him home and, as use of motor vehicles was prohibited because of wartime restrictions, they had to make the journey on a bicycle… which is why April 19 has been celebrated (since 1985) as “Bicycle Day.”


Written by (Roughly) Daily

April 16, 2023 at 1:00 am

“Many a person will forget the past for a present”*…

… and many won’t, as Benjamin Errett explains…

… Do consider where many gifts end up: The fulskåp, defined in The Gentle Art of Swedish Death Cleaning as “a cupboard full of gifts you can’t stand to look at, and which are impossible to regift. Usually these are presents from distant aunts and uncles that you put on display when the giver comes to visit.” 

The perfect gift for the person who has everything is either penicillin or a burglar alarm, as the old jokes have it. So there’s always the option of deliberately flubbing the gesture with a gag gift, which is what the British royal family reportedly does. Prince Harry once delighted the Queen with a shower cap that read “Ain’t life a bitch.”…

You shouldn’t have: “The Wit’s Guide to Gifts, ” from @benjaminerrett.

Gladys Parker


As we wrap it up, we might recall that it was on this date in 1946 that UNICEF (the United Nations International Children’s Emergency Fund) was launched. Among the most widespread and recognizable social welfare organizations in the world, with a presence in 192 countries and territories, it provides immunizations and disease prevention, administers treatment for children and mothers with HIV, enhances childhood and maternal nutrition, improves sanitation, promotes education, and provides emergency relief in response to disasters (most recently, e.g., the COVID epidemic and the invasion of the Ukraine).


Written by (Roughly) Daily

December 11, 2022 at 1:00 am

“The world is bound in secret knots”*…

Everyone knows what a knot is. But knots have special significance in math and science because their properties can help unlock secrets hidden within topics ranging as widely as the biochemistry of DNA, the synthesis of new materials, and the geometry of three-dimensional spaces. In his podcast, The Joy of Wh(Y), the sensational Steven Strogatz explores the mysteries of knots with his fellow mathematicians Colin Adams and Lisa Piccirillo

How do mathematicians distinguish different types of knots? How many different kinds of knots are there? And why do mathematicians and scientists care about knots anyway? Turns out, there’s lots of real-world applications for this branch of math, now called knot theory. It started out with the mystery of the chemical elements about 150 years ago, which were, at the time, thought to be different kinds of knots tied in the ether. Nowadays, knot theory is helping us understand how enzymes can disentangle strands of linked DNA. And also, knot theory has potential in basic research to create new kinds of medicines, including some chemotherapy drugs. But in math itself, knot theory is helping mathematicians work out the riddles of higher-dimensional spaces…

The study of knots unites the interests of researchers in fields from molecular biology to theoretical physics: “Untangling Why Knots Are Important,” from @stevenstrogatz in @QuantaMagazine. Listen here; read the transcript here.

Athanasius Kircher


As we take stock of tangles, we might might send nicely-tied birthday greetings to a beneficiary and user of knot theory, Francis Collins; he was born on this date in 1950. A physician and geneticist, he discovered the genes associated with a number of diseases, led the Human Genome Project, and served as the director of the National Institutes of Health.


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