burnsandallen

westbrookmaine1937.com: writings

IJH

Dear and Glorious Physician

Enigmata

PIERRE ROCHELEAU

2

By the second half of the nineteenth century, the dramatic achievements of the experimental and theoretical sciences had brought a certain prestige to science. Science in the middle decades of the [nineteenth] century becomes a major source of military, industrial, and economic strength. As a consequence, one sees a fundamental transformation in the political function of science. Science becomes increasingly a metaphor for the explanation of why things are as they are: people look to science to explain the origin of human character and institutions; science becomes an important part of ideological argumentation and a means of social control. ...

In many such cases [in which “science” is used to buttress what “many already believed”], the appeal to science lent a certain authority to ideological pronouncements. By the mid-nineteeth century, science had become an important metaphor in Anglo-European culture, and people looked to science for the answers to social problems. The science to which one looked, however, was of a very special kind. Science was appealed to, not in the abstract, but only insofar as it could be given a certain interpretation.

—Robert N. Proctor, Racial Hygiene (1988)

9:10 AM on the dot, on the nose, and I am tiptoeing out of my building. (I had wanted to leave earlier.) I am travelling alone. I have one bag. I am on my way to midtown, where I will pick up a rental. On the street I am whistling.

I have to get out. Have to get out. Because of the heat and humidity. Or that is what I tell everyone. “Oh I have to get out. Can’t stand the heat and humidity!” But that’s only part of it. I have to get away from the Covid mess, the Covid débâcle, the Covid nonsense. Or I will go mad. I will absolutely become cuckoo (a 1940s word, my parents’ word). Dr. Pam Popper in her writings refers to “the Covid hoax.” Well yes and no. Use of the word hoax (in this context) will land one in very hot water—sure as shootin. And yet I am basically in agreement (with Popper). It is a partial hoax. Misdiagnosis is endemic—but the illnesses are real. The deaths are real enough. (Hard to deny a death I think.)

Actually it is not in my view “the Covid hoax.” It is I believe the Covid hoaxes. Covid is among many other things a vast series of little hoaxes. (A few are moderate-sized.) But it is a series of little hoaxes—interconnected and (as we speak) interconnecting. Mutually reinforcing. (The interconnecting hoaxes are in addition inchoate and badly disordered.)

Hold that thought. To call Covid a series of hoaxes—that’s not quite right either. Somebody help me out please.

In my small apartment on West 4th Street often I wake up in the middle of the night. I grab my phone and get a taste of the news. It is an uneasy feeling.... sometimes a sick feeling. At 4 in the morning. I read headlines. I tap headlines and read first and second paragraphs. I am sweating—on most nights. I am hyperventilating. I say to myself: They’re changing the science, wholesale. And I say, on most nights: We’re being played.

I say to myself: Oh dear God what is going on? Almost every night it’s like a scene from Rosemary’s Baby. Where Rosemary begins to sense—something is afoot. Then it dissipates. It goes away.

Can’t blame what’s going on on Klaus Schwab. (I don’t know what’s going on.) Actually I know one thing that’s going on: the French Wars of Religion, all over again. That’s the aforementioned Latter Day French Wars of Religion.

New York State is gorgeous on this gorgeous day. They’ve given me a great car. The young woman officer at Alamo Rent a Car, 21 or 22 or thereabout, had been bubbly and bouncy, and nice. She was instantly my friend. She walked me to my car (I don’t think that is common practice, at Alamo, or at this particular Alamo) and we joked about the heat of that morning in Manhattan. I said, “It was 83 degrees when I left my apartment at 9 AM. What’s it going to be at 3 PM?” She answered, “150.” She laughed. I laughed. The car she has given me has a pretty good engine and is fun to drive. I sail up the Taconic Parkway. It is everywhere I look as green as Ireland.

I flee. I fly. The slightest pressure of the foot—and I am soaring. On the Taconic Parkway. It has a miraculous aspect. (I may be a medievalist at heart. I do not believe that driving a car is entirely licit.)

I know it is childish and childlike but I cannot contain my excitement. I sing songs, loud. (The power windows are up.) I sing a Martha Reeves and the Vandellas number, and a George Gershwin number. What’s wrong with George Gershwin on this morning I ask myself.

The way you changed my life
No, no, they can’t take that away from me
Nooooooooo they can’t take that away
Can’t take that away
They can’t take that away frommm meeeeeeeeeeeeeeee

What can’t they take away? My liberal and leftist and progressive bona fides. It has been my experience in New York (and in the state of Massachusetts) for above 4 months: when I have in any way, in a subtle way, in a slight way, challenged Covid policy, the (putative) Covid wisdom, the Covid narrative, the Covid groupthink I am summarily called “conspiracy theorist,” “Trump-lover,” and I am asked to go and put on my tin foil hat. (I am not always called conspiracy theorist, and Trump-lover. Sometimes I am told I “sound like a conspiracy theorist,” I “sound like a Trump-lover.”)

Sectarianism perhaps. Intense tribalism? In mixed company (in fall 2020) I said a few positive things (possibly glowing things) about Dr. Vladimir Zelenko (1973—2022) and his use of hydroxychloroquine to treat Covid illness and I was instantaneously “a QAnon conspiracy theorist” and “a QAnon believer.”

I am called “antiscience.” And it’s expanding.

HYT

Are we, right now in the United States [it is 2020], seeing a slow drift toward fascism? Or is that unduly alarmist? Maybe we are not seeing that. But somehow I am reminded: Emma Goldman said the “western democracies” do not possess democracy. But what they have got—fascism in disguise. (Imagine that one. A Trump-lover bringing up Emma Goldman.)

All very hypothetical of course—but in respect of all those who have fretted and stewed that the United States might one day become a de facto fascist state—how many envisaged that materia medica was going to be the delivery system?

I am from a liberal place—a liberal landscape, a liberal terrain, a liberal state, a liberal and progressive part of the country (southern Maine, Cumberland County in Maine), the most liberal of U.S. cities (Portland Maine). I grew up in a liberal and progressive household. My mother was instinctively and unerringly liberal. (It is possible to err in the practice of liberalism.)

For approx. 40 years (beginning in 1972) I went to political demonstrations and I hunted down, and read, biographies of “liberal” figures. That was what I did. For 40 years.

I did also work. And I had a social life. I hung out with members of the Catholic clergy, nuns and priests, mostly nuns, in Maine. Those were the days. Such great times I kid you not.... with Sister Maura (Murphy), Sister Maureen (Thornton), and Mother Dennis, and others, in Portland Maine.

When the Iraq War started (5:30 A.M. Baghdad time on March 20 2003) I was, for a while, in a perpetual state of rage. For 4 months in the first half of 2003, in New York, I was going to on average one demonstration per week. A motive for my attending all those demonstrations was the idea, from Simone Weil: “Sometimes the infinitesimal is decisive.” I was the infinitesimal. I understood of course that my presence at anything, at any event, was unlikely to be decisive. I guess I believed that if enough of us acceded to be infinitesimals we would be noticed (by Cheney, Rumsfeld, Wolfowitz et al.) and become a counterweight to the prevailing groupthink (centered on weapons of mass destruction, in February 2003). We were never noticed. By Cheney, Rumsfeld, Wolfowitz et al. We were never noticed (not really) by the New York Times. We were mocked by the New York Times. We were, collectively, never a counterweight.

I said I used to hunt down biographies. I craved and coveted lives, or the written histories of lives—of Marx, of Engels, of Lenin, of Mikhail Bakunin, of Leon Trotsky (to a certain extent). The lives of Eugene V. Debs, of Robert La Follette (to a greater extent). As well: Bernard Shaw, George Orwell, Bertolt Brecht, Upton Sinclair. Herbert Marcuse. Che Guevara, Saul Alinsky. Emma Goldman. I had a thing for Emma Goldman. Believe it. Rosa Luxembourg, Simone Weil. FDR. Michael Harrington. (My father knew Harrington at the College of the Holy Cross, Worcester Mass, in the late 1940s.) Bernie Sanders. Others.

But starting in mid April 2020, and counting, I am no longer liberal. I am just a regurgitator of right-wing talking points. Go figure & isn’t it rich.

I will mention in passing: “liberal” and “conservative” are meaningless presently (in May 2023). March 2020—the moment in history when everything started to slide. The Covid phenomenon is perhaps the largest episode, the largest political episode, in all of world history. The planet changed, it convulsed, and “right” and “left” seemed to trade places. Massive identity crises have arisen since the start of the pandemic. The identity crises continue. Constitutional rights, civil rights, and civil liberties all started to slide in March 2020 and (astoundingly, I thought) voices of authority and prestige on the left went silent.

In spring 2020 I became brittle and fidgety and neurasthenic every time I listened to or looked at media and kept saying to myself: “Never again.” (Never again what? I wasn’t sure.)

I worshipped Amy Goodman (for decades)—until the first week in April 2020. I would have killed for Rachel Maddow—until the first week in April 2020. (In March 2020 I was still forgiving.) They (and scores, or hundreds, of others in media) grabbed hold of junk science, pseudoscience, industrial science, industry-funded science—and they named it science. They shilled. They ran—they went to town. They became oppressors. They were alarmist—they were catastrophist. They promoted Covid misinformation whilst strongly accusing others (of promoting Covid misinformation). They censored. They (and “media elite”) were accomplices.

Spookily the liberal party became the proto-fascist party. The liberal party became the party of censorship.

Persons were injured—in more ways than one. Persons were injured—iatrogenically injured (which includes vaccine-injured). Persons were injured in hospitals. Persons were injured—sometimes catastrophically. Also: the largest transfer of wealth upward (the largest rapidly occurring transfer of wealth upward) in human history..... Still not a sound from prestigious figures on the left. (They were following the science.)

There was a narrative. They (media elite, seasoned immunologists Goodman and Maddow, hundreds of others) did not countenance dissenting opinions. They spurned and ridiculed dissenting opinions. And it continues—it is far from over.

Of the differences between “liberal” and “conservative”—I am without a clue (in May 2023).

_______________

Addendum. March 12 2025. Brain-ticklers.

1. How do you take your pandemic? Answer: Without nuance, thanks.

2. How do the large media companies prefer their pandemics? Answer: Without nuance.

3. How do the large media companies report on their pandemics? Answer: Without nuance.

4. How do you take your principles of immunology? Answer: Without nuance, thanks.

The anti-Covid shots: Landscape without nuance. (Nuance is pesky. One doesn’t need it.) The design was: one size fits all. The design was: the shots would make their way into (approx.) 7 billion arms. (In the end they made their way into fewer than 3 billion arms.) Operation Warp Speed was no appreciator of, no respecter of nuance. Guess not. The anti-Covid vaccine mandates (in many jurisdictions) encompassed the rejection of all vaccine exemptions. Expunging of all exemptions: Simplify, simplify.

In the United States. Vaccination was required of persons who wanted a job—or who wished to remain in a job. Vaccination was required of persons who wished to study. It was required of persons who wished to enter public buildings, public spaces. No exemptions. No exemptions.

No exemptions. Religious, philosophical, personal belief, medical.

The (human) immune system is nuanced. It is so hyper-nuanced—its complexity may not be imagined. Quite literally.

The immune system is, arguably, not a system. (Tom Cowan says: It is not.) Let’s assume it is. Let’s define it as a system.

Also. The immune system is more than “a system.” It is a system made up of systems. I regard the immune system as an alter ego. As a second self—as large and varied and complex as self # 1. I have sometimes called my own immune system my “super-self.”

It equals ceaseless movement, ceaseless change (in the body). It is everywhere (in the body). It goes everywhere. It surveils everywhere. It is one’s defense, one’s only defense, against cancers. (Eating right, resting right, moving about right, mitigation of stress, avoidance of alcohol etc. are “environmental” inputs, not natural defenses and not defenses.)

And immune cells are not just for defense... against pathogens (invaders)... against cancer cells and other “stressed” cells. They, immune cells, shape organ development. Some immune cell types have their roles to play, unrelated to or mostly unrelated to defense against invaders and cancers, in the (structural) development of some organs—incl. brain/CNS development—or most importantly brain/CNS development. Microglia, brain-resident macrophages, “sculpt” neural circuits during brain development for example. Microglia “prune” excess synapses during brain development. (RE this synapse pruning: something one would not want in any way to influence or mess with?)

That “immune system” has been evolving for greater than three and a half billion years. Homo sapiens of course has not been around for 3.5 billion years. But the species from which he is descended (and their evolving immune systems), collectedly, have. The up and running immune system that lives in the lone human being is a truly astonishingly accomplished and astonishingly “talented” adaptive apparatus.

That mighty sculptor, time. In my imagination at least—evolution has much to do with what we see at the outer surface (of the body). What we see has to do, finally, with the sexual selection (and natural selection) that occurred across eons of time (and continues). With the immune system more or less representing the (related) evolution that was going on in that same stretch of time—deep inside the body. It, the immune system, standing for the “sculpting” that was going on deep inside—in parallel with the sculpting going on at the surface.

The immune system is not: B cells (B lymphocytes), T cells (T lymphocytes) & antibodies. [Sorry, legacy media.]

I wrote (above): Dr. Gary Goldman has said, “We understand the immune system at its fringes.” We understand chunks of it, swaths of it.

There are things we know we don’t know—and things we don’t know we don’t know. The known unknown’s and the unknown unknown’s. (Per Donald Rumsfeld.)

“The immune system” is an umbrella term.

Coming under the umbrella—the things that have (at least some) physical structure, incl. some clusters of immune cells: bone marrow (often designated the “principal organ” of the immune system), thymus, spleen, lymph nodes. Coming under the heading mucosa-associated lymphoid tissue: gut-associated lymphoid tissue (incl. tonsils, pharyngeal tonsils, lingual tonsils, appendix, Peyer’s patches—the last one said to be 70 percent of the immune system); respiratory-associated lymphoid tissue; nasal-associated lymphoid tissue; cutaneous-associated lymphoid tissue (incl. epidermal and dermal immune cell clusters). Lymphatic vessels, lymphoid follicles, liver (which has immune-related functions), hematopoietic stem cell niches (in bone marrow), others.

Coming under the umbrella—immune cells with their varied functions, in circulation or residing in specific tissues. Classes of immune cells. Populations of immune cells. Monocytes, macrophages, mast cells. Innate lymphoid cells—“discovered” and classed ca. 2013. The field is young! Dendritic cells. Granulocytes: neutrophils (very abundant, very phagocytic), eosinophils, basophils. B cells. T cells. Helper T cells, cytotoxic T cells, gamma delta T cells, regulatory T cells. Natural killer cells. Platelets (which have immune function in addition to the clotting function). Many more.

Dendritic cells (meaning “tree-like” cells) for that matter were identified not that long ago (ca. 1974). Going along with the idea that the discipline is young... Dendritic cells are understood as, framed as—“a bridge” (or “the bridge”) between innate immunity and adaptive immunity. The “discovery” of dendritic cells revamped and recast then-existing understandings of immune cell interactions and intercommunication. (The discovery of any new immune cell type is likely to have that effect.) For me, the 1970s were recent. It’s all relative of course. When I was taking formal science courses in the 1970s there was no textbook I happened to get my hands on, or could’ve got my hands on, that contained the term dendritic cell (used in this context—to refer to an immune cell type).

Because an individual class of (immune) cells may have or is likely to have multiple and diverse functions, it is difficult—to come up with a concise and “universal” taxonomy of these cells. In fact it’s something of a mess. (Existing taxonomies are something of a mess.)

Immune cells show functional plasticity. There are immune cells that are hybrid cells. Many cell types have context-dependent functions. Many cells have the option: they can be pro-inflammatory or anti-inflammatory (or both—usually not simultaneously), depending on a range of factors.

Nuanced. Also mind-boggling.

New (cellular) subtypes are ever being discovered.

There are immune cells, discovered, identified, that cannot be put into any existing taxonomy of immune cells—that await “final” classification.

There are immune cells (along with their functions or putative functions) and immune proteins (along with their functions or putative functions) just being discovered—as we speak.

Immune cells are repurposed.

In the 1950s a man named Macfarlane Burnet was possibly the first to put forward the idea that falling and rising titers of (some) immune cells (in circulation) represent a process akin to natural selection. Concentrations of some cells tend to increase when they are needed, as they are needed. (It is not natural selection, it resembles natural selection.)

Macrophages for example are repurposed—can undergo radical functional shifts—according to “environmental” cues.

Exaptation (the word taking shape via back-formation from adaptation) is—when an organ or structure (animal or plant) begins its evolutionary “journey” as one item but later (across eons of time) manifests as a quite different item. (It is theorized that the wings of birds started out as fin-like structures purposed toward temperature homeostasis—not flight.)

The repurposing of immune cells resembles exaptation.

And then—the immune proteins (incl. the “complement system”) & immune signaling. Immune proteins: Antibodies/immunoglobulins. Interferons, interleukins, “major basic protein” (has 4 or 5 or 6 functions, released from eosinophils), tumor necrosis factor, chemokines. C-reactive protein. Antimicrobial peptides (I spoke of defensins, above). Immune receptors (proteins embedded in immune cell membranes that “recognize” antigens/pathogens).

The utility and end results of Major Histocompatibility Complex (MHC) proteins in the context of (human) immune responses to unwanted presences (let’s say): just shy of miraculous? (That were superstition. MHC proteins emerged, and are emerging, from a vast sequence of teeny tiny evolutionary refinements across hundreds of millions and billions of years.)

Ramp up. Then tamp down. Ramp up. Then tamp down. Immune proteins ramp them up (the body’s killing systems); they tamp them down. In general the immune system has as many “mechanisms” for tamping down as for ramping up. The human immune system is ever moving toward the Goldilocks principle.

The immune system has “regulatory” proteins, and “regulatory” cells. The immune system is an avatar of balance—of the idea of balance. Tamping down mechanisms have to do with the curtailing of autoimmunity. The rhythm of ramping up and tamping down is a basic element of survival.

Imagine perhaps these varied items all of them—more or less as parts of an interconnecting and coordinating whole.

___________________

I have switched over to Route 87. I am near Saugerties New York.

It is before noon. I stop at a highway travelers’ welcome center. (It has a food court, framed maps on the wall, and travel brochures.) Hills and mountains are in the distance but where I am stopped it is oddly flat. It looks like farmland. I am in rare form—just the small tract of flatness I am able to see from the parking lot fascinates me.

The parking lot, empty, has a single tree (at the far end) and I park under it—which means I have to traverse the parking lot on foot. It seems perverse—but the unimpeded sunlight and heat are in a way, for a few moments—magisterial, for lack of a better word. They are something to marvel at almost. I despise extreme heat and so I decide I’m going to revel in it as I walk from the car and to the entrance without any kind of shield. Inside I sit on a tall stool near a window and sip coffee.

At close to noon I visit my friend who lives just outside of Albany. She had wanted me to see her house. I am there for an hour and a half, and as I back out of her driveway, waving enthusiastically, and drive slowly away, I am conscious for the first time (on this day) of being alone. For the remainder of my retreat (just 5 days and 4 nights) I am alone and I discover that I love it, that I’m into it. (I am very used to being alone but not very used to traveling alone.)

I sweep past Saratoga Springs, past Glens Falls. I drive along the perimeter of Lake George—slightly less beautiful than Sebago Lake in Maine (in my view). 7 PM. I have arrived at my destination.

The large parking lot at the Best Western is empty. (Not my first empty parking lot on this day.) I am the only guest in the hotel. (I am told that by the desk clerk.)

In the parking lot the air is balmy—gorgeous perhaps. It is nonhumid. It is no longer hot.

The lobby is empty. The front desk has an immense plexiglass shield—possibly the biggest I’ve seen. It is one piece. It extends across the full length of the front desk and it is tall.

The lobby is empty—but a woman emerges from a room behind the front desk. I don’t wait for her to speak. I speak up immediately. “Hello. I have a reservation.” That’s what I think I said. The woman, younger than I, perhaps 47 years old, plump and absurdly healthy (in my judgment), is personalityless. Actually I discover on the following day that she is not personalityless. She is personalityless for starters. She speaks up. “Credit card and driver’s license please.” We are both masked by the way.

Between plexiglass shield and countertop there is “free space.” I start to slide my hand, holding credit card and driver’s license, under the shield and toward her hand. She lifts one arm and waves 2 fingers. As if she is saying, “Stop!” She starts to slide a small plastic basin toward me—similar to the kind of kidney-shaped basin one sees on height-adjustable bedside tables in hospital rooms. I place the 2 cards in the basin. She slides it back toward herself.

Atop the counter, at one end of the counter, a gleaming egg-yolk yellow plastic pail. There is a sign. It announces to hotel guests checking out that room “keys” (which resemble credit cards) must be placed in the pail. And: anyone who has used a hotel pen at the front desk must place the pen in the pail.

My room is on the 2nd floor. (The place has only 2 storeys.) I decide to climb the stairs. It is a beautiful staircase with beautiful carpeting—kind of a display staircase (not a stairwell). Carrying the one piece of luggage I climb, and walk, very slowly. All the way to my room I am asking myself, muttering to myself: “Who did this? Who is responsible for this? Who did this? Who is responsible for this?” But I know the answer. Well there’s the short answer and the long answer. This short answer is of course: media. Think: the gone to the dogs “mainstream media.” (CNN’s reach extends as far as the living rooms of Ticonderoga N.Y. I believe.)

The room is OK. It has nice fall colors. Terracotta, olive green, and so on. And it is home—for the next 4 days or so. I leave immediately to get coffee. There’s a McDonald’s about a mile away. McDonald’s, possibly counterintuitively, has great coffee. (They serve Paul Newman’s coffee.)

Everybody knows what’s next? The McDonald’s worker is behind a plexiglass shield & masked. She is tiny and has a tiny voice, she looks as if she’s all of 15 perhaps. She’s cute, she couldn’t be any cuter. Even with mask. She is darling. Customers muse on the idea of adopting her I think. I am masked. I give my order. She asks me to stand back. “Could you stand back a bit more?” There are signs, big signs, about “six feet apart” everywhere. (I had been standing back. I may have been standing just five and a half feet back.) I take a step back. It’s no big thing of course. I am happy as I walk out of the place.

But as I walk, once again, across the hotel parking lot and into the hotel, again I am muttering: “Who did this? Who is responsible for this?”

Le fort Carillon was built by French colonists (1755—1757) to protect the (St. Lawrence Valley) region from British invasion. In 1755 in that region American (soon to be American), Native American, British, and French military and paramilitary forces were embroiled in 4 or 5 or 6 or more wars. British seized possession of the fort in 1759 and renamed it. In 1760 it is becoming known as Fort Ticonderoga. In 1775, during the American Revolution, nascent Americans (Green Mountain Boys) grabbed it from the British, who grabbed it back in 1777.

In November 1775 in Boston, during the (11-month) Siege of Boston, George Washington despatches 25 yr. old Henry Knox and an army to Fort Ticonderoga to get its cannon and convey the cannon to Boston. Sixty ton of cannon are conveyed 300 miles, by ox-drawn sled, across frozen ground, through mountains, in dead of winter, to Boston—the “noble train of artillery.”

The noble train arrives in Cambridge Massachusetts January 24 1776. Its weapons are positioned forthwith at Dorchester Heights, overlooking Boston. British artillery fire cannot reach the heights. The liberation of Boston is begun.

After 1780 the political and strategic importance of Fort Ticonderoga nosedives.

I arrive breathless at Fort Ticonderoga, one morning. I want my tour and I get it. I hang out at Fort Ticonderoga for 3 hours on one day and for 2 hours on the following day. The price of admission ($19.00 in July 2020) allows for the 2nd visit.

There’s a commissary and a gift shop (“museum store”). I don’t go in, not even to nose around—which is somewhat unlike me.

On an afternoon I sit at a picnic table positioned on a grassy hummock underneath glorious sunshine and survey and take in. I sit and I survey and I try not to think of the Covid horror show—but it comes to mind agan and again. Like a goddamn homing pigeon it returns and returns and returns.

The world stands out on either side. I crane my neck. I take in. I notice, I just happen to notice—and it may have been artefact—a discrepancy. The peons (the workers) dashing about, going here and there, are entirely masked, and persons visiting the fort for educative purposes let’s say, many sitting at outdoor tables near mine, are entirely unmasked. It occurs to me that the men in costumay might also be workers—the men wearing tricorner hats, plumed hats, longcoats with immense cuffs, jabots, knee breeches etc. etc., sometimes carrying weapons. The men in costumay are not wearing masks. (So I guess not all workers were masked.)

I am not into the debate on masking and other social distancing. It feels lightweight perhaps, relative to other Covid-related debates. I believe that the efficacies of mask wearing and the 6-feet guideline (as Covid containment measures) are not at the zero level, but close to it. I believe that the urge to mask oneself, and to put masks on others, and the urge to social distance oneself, and to social distance others, have ancient, ancient roots—are atavistic and primitivist. (Personal motives and motivations undergirding urges to mask and social distance, and to mask and social distance others, are multiple and layered perhaps.)

Sigmund Freud in The Three Essays on the Theory of Sexuality speaks of the “emotion” of disgust. Disgust is an influencer. It plays a role in sexual development (per Freud). He stated that the lone human being must overcome feelings of disgust before he, or she, can engage in sexual activity. (He also said that these feelings are in part a product of the culture that surrounds him or her.) One may ask—if the emotion of disgust has something or anything to do with urges to mask up and to social distance, and is something that gives perennial oomph to the germ theory of disease.

Related to social distancing: there is a universal and perhaps inescapable belief (way down deep) that some folks are tainted, some less tainted, some folks are cleaner, some less clean. (It has ancient roots.) The urge to social distance and to social distance others is not entirely detached from the (universal) phenomena: 1. xenophobia and 2. caste (or class). (Or does one think that xenophobia and caste have zero relationship to social distancing in the year 2021?)

The deeply voltairean Glenn Greenwald—grenade thrower (like Voltaire)—needs no introduction. From Greenwald’s The Masking of the Servant Class [September 14 2021].

From the start of the pandemic, political elites have been repeatedly caught exempting themselves from the restrictive rules they impose on the lives of those over whom they rule. Governors, mayors, ministers, and Speakers of the House have been filmed violating their own COVID protocols in order to dine with their closest lobbyist friends, enjoy a coddled hair styling in chic salons, or unwind after signing new lockdown and quarantine orders by sneaking away for a weekend getaway with the family.

Further down:

Last month, a delightful event was hosted by Speaker of the House Nancy Pelosi (D-CA) for wealthy Democratic donors in Napa—the same wine region of choice for Governor Newsom’s notorious dinner party—at which the cheapest tickets were $100 each and a “chair” designation was available for $29,000. Video of the outdoor festivities showed an overwhelmingly white crowd of rich Democratic donors sitting maskless virtually on top of one another—not an iota of social distancing to be found—as Pelosi imparted her deep wisdom about public policy.

And:

Trying to find a cogent scientific rationale for any of this is, by design, virtually impossible. The rules are sufficiently convoluted and often [sufficiently] arbitrary that one can easily mount arguments to legally justify the Versailles-like conduct of one’s favorite liberal political leaders. Beyond the legalities, everything one does can be simultaneously declared to be responsible or reckless, depending on the political needs of the moment. But what was most striking about Pelosi’s donor event was not the possibility of legal infractions but rather the two-tiered system that was so viscerally and uncomfortably obvious.

All of “life,” all of “society,” all of “people” and “population” is stratified. Man itches to make strata. That populations and subpopulations should fall into strata: inevitable very likely, a universal phenomenon, as universal as the tendency toward religion, or toward the formation of family units.

Stratification, sure. But then there are the untouchables—taking one form or another. How does one explain that? How does one explain the concept of untouchables or untouchability? It is less amenable to analysis (than the concept of class stratification). There is no basis for it, no underpinning, no rationale—in “science,” in medicine, in molecular biology, in objective “fact.” No adequate explanation in “depth pyschology.” (Think: caste in India 2,000 years before the birth of Christ, Dalit in India, slaves in Greece and Rome, slaves in general, Cagots in France during the Middle Ages, Roma/Gypsies, blacks in the United States, blacks enslaved in the United States, blacks in the United States during Jim Crow, Jews, Jews as “spreaders of disease” in 20th century Europe, the War Against the Jews 1939—1945, Melungeons in the United States, “white trash,” “trailer trash” [2 terms I detest], Rohingya, Palestinians, others.)

Does one invoke the emotion of disgust? The idea of contamination—a visceral idea, experienced viscerally.

As an aside: ideas of contamination (emotion-dense, fundamentally nonscientific and antiscientific) have been—across 3 centuries—the impetus for much of, or most of, vaccine advocacy and promotion.

Related to Jews as spreaders of disease in 20th century Europe. So.... identification of spreaders of disease. Seems benign enough (to some). What follows? (Identification of spreaders of disease indeed.) Identification of spreaders of disease is inherently disturbing, inherently repugnant, it is crime, it is science fraud, and it is the beginning of very slippery slopes. (Population contact tracing, the World Health Organization and the use of vaccine passports come to mind perhaps.)

RRE

A virus goes viral. Pathologist Roger Hodkinson of Alberta Canada believes that all Covid-related social distancing practices have been futile. Hodkinson contends that nothing can be done to slow the spread of an upper respiratory virus “in society.”

Where Hodkinson has said nothing can be done to slow the spread of an upper respiratory virus in society, I think I would have said: nothing can be done to slow the spread of an upper respiratory virus in a staggeringly densely populated district—such as the “New York Metropolitan area.” 30 million people.

A minority view. I believe that the “Wuhan virus” was here (in the New York Metropolitan area) in the final 6 months of 2019, and that before the end of January 2020 in the 5 boroughs of New York City for example the virus had disseminated (almost) as widely as it was going to disseminate, and would disseminate only very slightly further. (Perfect wellness, in and around New York, in the first few months of 2020 did not mean one hadn’t had contact with the virus, or many contacts with the virus, or 100,000 contacts with the virus, or 100,000 contacts per day with the virus, or hadn’t experienced subclinical infection.)

Roger Hodkinson—holder of minority views. Roger Hodkinson, physician and scientist, speaking in August 2021.

More than anything this is a pandemic of fear. Fear that was intentionally driven by two major factors: the notorious PCR test, and the viciously effective silencing of any counternarrative. The PCR test creates over 95% false positives in perfectly well people and drives the graphs in the morning papers, where these false positives are called “cases.” They are no such thing! You are being lied to. The 2nd driver of fear is the brutal silencing of the truth, from the 3 sources you would normally rely on to form your own independent judgment: politicians, the media, and physicians....

Fear in turn became the excuse for politicians and unelected bureaucrats to enforce the ludicrous, totally arbitrary mandates that have no consensus for effectiveness in the medical literature. None. I’m talking about masks, social distancing, travel bans, and lockdowns. They [masks, social distancing, travel bans, lockdowns] couldn’t work, haven’t worked, and will not work.

Governments must get used to the fact that modern medicine is totally impotent at controlling the spread of respiratory viruses. We must simply accommodate to them, in ways we have done most effectively in past flu epidemics.

And just before, in June 2021.

You cannot solve the spread of an upper respiratory tract virus by any means known to medical science. It is simply not possible.

None of the mandates first of all is supported by any scientific consensus whatsoever. If there had been one [a consensus, as well as an effective upper respiratory virus containment measure], we would have used it in previous flu epidemics. And we never did.

8 AM. The penultimate morning in my little room in the mountains. My two sliding windows are wide open. The air rushing in is gorgeous, for lack of a better word. I have a plan to go driving in the Adirondack wilderness.

I am back at the McDonald’s at 8:30 AM. I buy an egg sandwich and a medium-sized coffee with cream, no sugar. I bring it back to my room.

The hotel offers a “modified continental breakfast during the pandemic.” Each morning there is a brown paper bag with my name on it (literally) atop the front desk, over to one side. The modified breakfast: a banana and a fancy nutrition bar. I love the stuff (the fancy bars), but they are weighted down with sugar and I decline them. I leave the nutrition bars on the counter.

[In 2021 I am remembering that fantastic and inspired morning, the penultimate morning at the hotel (in July 2020), when I moved slowly and did almost nothing for a few hours. I almost didn’t go exploring on that day. I thought of staying in the room and just existing, just being—like an animal. I like to putter, indoors, with music.]

Ava Gardner, sage:

The truth is that the only time I'm happy is when I'm doing absolutely nothing. Why is everyone praising hard work all the time? Doing nothing feels like floating on warm water to me. Delightful, perfect.

But at a quarter to noon I leave the hotel quickly, get in the car and drive and drive. And sightsee. (To not have done so would have seemed wasteful perhaps.) In the afternoon I stop in villages and walk their little streets. I sit at the edge of Lake Pleasant. I hike at the base of Speculator Mountain.

On the following day I am sad as I am getting ready to leave. I am leaving TICONDEROGA. On the following day I’m driving again—driving fast, driving south. I’m on my way back to NYC.

Again I sweep past Saratoga Springs. A great highway, uncongested. A great car. Again I am flying—it feels a bit like the ballet. I look for something on the radio. But it is slim pickings believe you me. I hit the scan radio button frenetically. Almost everything I come up with is NPR. (Every station is NPR?)

I am getting—it is literally every other signal the scanner “decides” has the appropriate signal-to-noise ratio—Governor Andrew Cuomo’s “coronavirus briefing” [from that day or from the day before]. I decide to listen. Governor Cuomo is taking questions from reporters. Under discussion at least for the moment is testing—testing for Covid illness. I am unable to listen for long. Cuomo wants to call PCR, or RT–PCR, “the diagnostic test” and insists it be called that (in that conversation, in that moment). A mistake. Not that big a thing actually (in that conversation, in that moment). Something for which we can forgive the man I think. (And yet it’s incorrect.)

I had written (above) that PCR is not a test:

It is a technique that enables a test. You’re looking for a particular something.... Finding it versus not finding it is the test. PCR just makes the something a lot easier to find.

Finding a particular something versus not finding it is then interpreted as follows: finding it equals illness present (you’ve got Covid); not finding it equals illness absent (you don’t have Covid).

There are many “PCR tests” and many manufacturers of the tests. The PCR tests should be named: tests for Covid illness that utilize PCR. Or perhaps: DNA hybridization tests that utilize PCR. Perhaps: tests for the presence of SARS CoV 2 fragments that utilize PCR.

I find it quite stunning. “The PCR test” was a main driver of the pandemic; a driver of—of things too inchoate to be conspiracies. A driver of (half-baked) ambitious, centralizing, all-centralizing, surveillance-expanding, globalist objectives and wishes, perhaps.

The medical arts are fundamentally ecological in nature (they take in the physical surroundings), they are dovetailed with highly specific environmental niches, they belong to the lives and landscapes upon which they act or impinge, they are inherently localized and local. What could be more absurd than globalist medical arts?

The PCR tests—the tests for Covid illness that use PCR (the tests themselves “authorized” rather than “approved”) use “next-generation” viral genome sequencing—which entails algorithmic/in silico whole genome or partial genome “assembly.” With next-generation (viral) whole genome or partial genome sequencing: DNA (sometimes DNA transcribed from RNA) is broken up, in the laboratory, into small segmants and the small segments are (rapidly) sequenced. In silico genome assembly refers to the computational [computer-based] process of putting those (sequenced) segments, or pieces, back together as it were.

The DNA hybridization portion of a PCR test (test for Covid illness) must bring together primer, or probe, and target nucleic acid (see above). Here, primer and target nucleic acid are polynucleotides—DNA segments (sometimes DNA segments derived from RNA segments). In the hybridization phase one tries to match to, and to match against. The target nucleic acid (obtained from patient specimen) one matches to something (a primer molecule or primer molecules), the primer one matches against.

The primer is (a synthetic, a manmade version of) a segment of viral genome—the genome of the (presumed) disease-causing agent. Again: the target nucleic acid is nucleic acid obtained from patient respiratory tract specimen.

All PCR chemistry centers on DNA chemistry. (Hence RNA must be “converted” to DNA.) In respect of potential identification of a Covid “case” or Covid illness: primer and target are single-stranded DNA. Captured RNA has been “transcribed” to DNA via the enzyme reverse transcriptase—yet another source of potential error I will say in passing.

C C G G A T G T G A A A A A C T A A A A G T G T A G G G C G G

C C C A A A A A G T G T A G G A T A A A A A G T G G G G G G G

Primer molecules are “sequence-specific.” Related to chromosomal sequencing tasks: a primer sequence (corresponding to pathogen genome, i.e. a segment of pathogen genome) they’re gonna have to get right—one intuits. Perhaps tens of thousands or hundreds of thousands of target nucleic acid molecules (belonging to patient specimens) are going to be gauged against it.

In the hybridization phase of PCR tests/Covid illness tests that use fluorescence-based compounds: following amplification of target DNA (corresponding to RNA culled from patient specimen), hybridization of primer and target will entail the throwing of a (fluorescent) signal—the larger the amount of target DNA (which as it happens has been amplified exponentially), the larger the signal.

With these tests for Covid illness: fluorescently labeled dyes (in the reaction mixture) bind to newly hybridized double-stranded DNA. The dyes, in binding to double-stranded DNA, exhibit large increases in fluorescence.

Hybridization of primer and target—what we call a match and perhaps subsequently a positive test result (depending on the magnitude of the signal)—occurs when the primer sequence and target sequence are perfectly complementary (or close to it).

Viral (whole genome) genetic sequencing that entails computational/in silico methods spells out a viral genome. An in silico viral genome?

The phrase in silico seems almost a deliberate joke, a deliberate wisecrack. Silicon the element is a semiconductor. It is the stuff of computer chips—the stuff of the digital revolution, the digital world.

Latin phrase in silico means more or less: performed on computer, performed by computer. It sprang into existence via back-formation from Latin phrases like in vivo and in vitro.

With genome sequencing that uses computational/in silico methods, computer software parses digital representations of nucleic acid fragments and “looks for” regions of identity—which may or may not correspond to regions of chromosomal overlap.

C C G G A T G T G A A A A A C T A A A A G T G T A G G G C

T G T A G G G C A A A C A A A

The software endeavors to link fragments—to put parts of a whole together again. Think perhaps: a very large and very complex jigsaw puzzle. (A partial analogy: the computer-generated nucleotide sequences are one-dimensional arrays.) It, the software, will come up with very large numbers (usually) of possible chromosomal sequences. One of these sequences is eventually selected (as template) and comes to occupy the holy spot. It is almost always the longest (the longest contiguous sequence) that is selected. The others are “computer-discarded.”

The Sanger method of DNA sequencing (1977) was the first. Supposed to be of perfect or near perfect accuracy. Sanger sequencing: the anti–warp speed method. Sanger sequencing is “first-generation” sequencing technology.

In Sanger sequencing DNA is broken up into smaller segments. DNA is then sequenced one segment at a time. One begins with a “piece” of single-stranded DNA, DNA that is to be sequenced—many copies of this piece actually; one proceeds to synthesize the complementary strands (they will be complementary to what is being sequenced).

Sanger sequencing is also known as the chain-termination method. DNA synthesis of the complementary strands is taking place: into the reaction mixture are put (fluorescently labeled) “chain-terminating nucleotides,” along with “standard” nucleotides. A chain-terminating nucelotide once incorporated into a growing DNA strand stops cold the synthesis (of the individual strand). At the end one has newly synthesized DNA strands of very varying lengths. Each newly synthesized fragment has a (fluorescently labeled) chain-terminating nucleotide at one terminus. Fragment sizes are compared via electrophoresis. The sequence of nucleotides (the sequence complementary to that of the original strand) is determined by “reading” the patterns of fluorescent signals—there are basically 4 signals, one for each of 4 kinds of nucleotides—and the full sequence is constructed from these data.

Sanger sequencing sequences one fragment at a time. Stunningly perhaps: next-generation sequencing (or 2nd-generation sequencing) allows for the simultaneous sequencing of millions to billions of DNA fragments.

I call it an uptick. (I’m trying to be funny.) It is a staggering, colossal increase. It is not an expansion (of the sequencing grunt work) by a factor of 5, 10, 20, 50, 100, 100,000, or even 500,000. One asks perhaps—what was the breakthrough that enabled such an increase?

For one thing—in next-generation sequencing (sometimes called parallel sequencing, and massively parallel sequencing): a large chromosomal segment is broken up into much smaller segments, millions of segments (often)—which are then attached to a solid surface. DNA molecules complementary to the attached strands are then synthesized, en masse and simultaneously. The varied building blocks (polymerase enzymes, other enzymes, [labeled] nucleotides—all the components needed for DNA synthesis) are added to the system: those building blocks swim in a solution that more or less bathes the strands attached to the solid surface. Massively parallel DNA synthesis occurs.

Next-generation systems also use “synchronous” nucleotide detection methods—they capture data for let’s say millions of DNA fragments coming into being, as they are coming into being, en masse and simultaneously. Individual nucleotides—these are the nucleotides swimming in solution—are fluorescently labeled, and as individual nucleotides are incorporated into the growing strands, cameras capture the fluorescent signals (there are 4 distinct signals, one for each: A, T, C, G). Each, each nucleotide, is identified—as it is being incorporated.

Would that be one camera or many, many cameras—capturing millions, or even billions, of synthetic events occurring simultaneously? Answer: one camera. One camera, multiple shots (in rapid succession). A single high-resolution camera captures the fluorescent signals emanating virtually simultaneously from millions, or billions, of synthetic sites. The imaging process requires the use of microscopy and algorithmic image analysis. I asked ChatGPT for help in envisioning... a camera (or cameras) recording millions of small events taking place simultaneously. (Is that kosher?) ChatGPT [January 18 2025]: “How to envision this? A good analogy is a satellite image of a city at night.”

There is presently third-generation DNA sequencing.

It is helpful sometimes to think of DNA sequencing as having two quite distinct groupings: 1. the sequencing of small chromosomal segments; and 2. the sequencing of very large chromosomal segments. It is also helpful sometimes to envision tests for Covid illness that utilize PCR as having two distinct parts: 1. DNA sequencing (the preliminary work); and 2. DNA hybridization (testing for illness).

In respect of sequencing the small DNA segments—both Sanger and second-generation algorithmic sequencing are recognized for their high accuracies.

I should mention—presently, virtually all genomic sequencing methods entail the breaking of DNA into smaller fragments and use of computer software for analysis of fragment sequences.

Next-generation sequencing, an exemplar: The first sequencing of the “Wuhan variant” generated 1,714,056 sequences—starting from 56,565,928 nucleic acid fragments harvested from a single patient—a 41 yr. old Wuhanese man, with symptoms, a worker at the open air food market in Wuhan (Wu et al., A new coronavirus associated with human respiratory disease in China; 2020). The close to 2 million sequences (“contigs”) were put together from (digital representations of) small, or short, nucleic acid fragments (150 nucleotides or less). Longer fragments were “discarded.” The longest contig (30,474 nucleotides) was selected—was anointed viral genome sequence.

There is the problem of specimen “contamination.”

In the sequencing of the Wuhan variant, fascinatingly—at no point—if I am not mistaken—was there isolation of virus particle or particles from tissue, tissue specimen, epithelial surface, or epithelial surface specimen (and then extraction of genetic material from said particle or particles).

RNA fragments were culled from bronchoalveolar spaces (in the lone participant in the study described just above) via bronchoalveolar lavage.

Lavage, a French word. Laver means “to wash.” Lavage means “washing,” the act of washing. In respect of the medical arts—a measured amount of water (essentially) is injected into a bodily space, or cavity, or tract, then suctioned or allowed to drain.

With bronchoalveolar lavage, the “return flow” is collected. It is not a homogeneous solution.... It is become a farrago—containing human cells, fungal cells, bacterial cells, cellular fragments, cellular detritus, viruses, viral fragments, nucleic acid fragments, “foreign” nucleic acid fragments, foreign proteins, foreign protein fragments, etc. etc.

From the return flow (from the lung fluid) RNA is extracted.

The familiar swabbing of nasopharyngeal mucus, in PCR-utilizing Covid testing, yields a similar farrago, or grab bag.

Science outlier and Covid skeptic/unbeliever Dr Andrew Kaufman has written that genetic material (RNA) culled from patient specimens (or lone specimen), to be used in viral genome sequencing tasks and testing for Covid illness, will represent “at least around 100 different organisms.”

There’s the narrative and the counternarrative.... The main narrative and the main counternarrative. There are perhaps 80 or so narratives (by my count)—but two main ones. Speaking generally or speaking approximately there are two sides. It is a worldwide phenomenon and a (simplistic) worldwide bifurcation—and it is ugly stuff.

January 16 2023. Can it be said that the main narrative (viz., a devastating pandemic; a devastating virus—having jumped species; insidious spread; high-level or highest-level viral genome sequencing and pristine vaccine clinical trials; use of RT–PCR test results per se to diagnose Covid illness; the stance that natural immunity is basically half-assed, or half-hearted, and is improved by vaccinating on top of it; vaccines safe and effective) is beginning to tend toward parody or self-parody? When I have talked about this I have been called “denialist” and “Covid-denialist.” I may be those things.

I would like to know actually: are viral whole genome or partial genome sequences as elucidated by (spelled out by) computational/in silico methods likely to be of highest-level reliability? Are the “sequencing products” in the end partly fictive? Partly specious? How long are they, the sequencing products, good for? What are the expiration dates? RNA viral genomes mutate considerably more readily than their DNA viral counterparts. How accurate/reliable are the genomic sequences of the SARS coronavirus 2 variants?

Les hommes distingués Jeremy R. Hammond and Dr Andrew Kaufman are adherents to the counternarrative—the main one. Kaufman and Hammond: on the same team, on the same side, in the same camp. But greatly at odds (are Kaufman and Hammond) on the subject of the aforementioned problem of “contamination” of materials being sequenced—i.e. the varied sources of genetic material in patient specimens.

Hammond sees the multiplicity of sources of RNA in patient specimens (or lone specimen) as not deleterious to the integrity of viral genome sequencing. (Kaufman sees the varied sources of RNA as deleterious and detrimental—to the integrity of viral genome sequencing.)

Jeremy Hammond [June 16 2022]:

Kaufman’s claims [an article by Kaufman, The Great Covid Virus Debate, April 17 2022] about whole genome sequencing are also wrong. Apart from falsely claiming that no purification process is undertaken during the process of virus isolation, the claim that whole genome sequencing cannot be done if there is more than one source of genetic material in a sample is also false. It’s called “metagenomic” genetic sequencing. (You could mix up the pieces to dozens of different puzzles and still reassemble each puzzle because each piece only fits one other piece. You can’t start with a puzzle of an elephant and a bear and mix up the pieces so that you end up with a puzzle of a woolly mammoth.)

There’s an argument here and Hammond has not (or has not entirely) quelled the argument. An invocation of metagenomic genetic sequencing or metagenomic analysis (of sequencing data) does not quell the argument.

Reading the passage... it feels like Hammond is thinking of the jigsaw puzzle—in which a picture that has been cut up (as if by a jigsaw) is reconstructed from puzzle pieces being fitted together. In respect of jigsaw puzzles—individual pieces have tabs, or knobs; and slots, or indents. (I mentioned jigsaw puzzles—above.) “A puzzle of an elephant and [one of] a bear” calls to mind—jigsaw puzzles.

Perfect analogies (or just good ones) are not to be found. In respect of algorithmic/in silico sequencing of whole genomes—pieces of a puzzle are not being put together exactly. Their stand-in’s are being put together. Their “ashes” are being put together.

RNA fragments are not being melded in the laboratory to form longer and longer RNA fragments (and then something that’s genome-length). It’s done on paper. Digital representations of nucleic acid fragments (one’s and zero’s) are being put together.

Hammond is quite correct: 2 distinct sets of puzzle pieces belonging to 2 distinct puzzles (and forming 2 distinct images) could never amalgamate so as to form a (coherent) 3rd image. But no one would think that were possible... (So I’m a tad confused.) And hence—polynucleotide sequences gleaned from multiple organisms could never turn up in or be represented in a single sequencing product?

Hammond is less correct when he writes: “[E]ach piece only fits one other piece.” A jigsaw puzzle is a kind of tiling puzzle. With the jigsaw puzzle—each puzzle piece is going to articulate with (lock in with) 2 to 4 other puzzle pieces (2 for corner pieces; 3 for edge pieces; 4 for interior pieces). Each puzzle piece “fits” [in] at one (and only one) spot, or site, or position—is what I think Hammond wanted to say.

If I am not mistaken—a digital representation of a given (chromosomal) nucleotide sequence may not “only fit one other piece” or may not fit [in] at only one spot.

And this is the point at which the analogy (between puzzle solving and genomic assembly) breaks down.

At any rate—it is a poor analogy overall. A jigsaw puzzle is a two-dimensional array. A genetic sequence (a linear nucleotide sequence) is a one-dimensional array.

Genomic nucleotide sequences (in all cells of all organisms across all species) tend to be highly repeating, or repetitive (greater than 50 percent of DNA in the human genome is repetitive DNA)—as well as highly “conserved” across species, including viral species. The presence of repeat sequences is “a universal.” Repeat sequences are abundant in: humans, other animals, plants (even more abundant in plants), fungi. For obvious reasons they are less common, or much less common, in viral genomes. (Viruses are very small.) But repeat sequences exist in viral genomes. The presence of repeat sequences and conserved sequences (in all species) suggests: use of nucleic acid fragments culled from patient specimen to assemble a given viral or other pathogen genome is always going to be—not easy.

The general belief, I believe, is: the computational software, ever-improving, is so good presently that—as the viral genome is being assembled, nonviral sequences (here, non–SARS coronavirus 2 sequences) are ferreted out (by the software). It takes a while—the “non-members,” the “reads” that don’t belong, are eventually jettisoned. And “each [SARS coronavirus 2] piece only fits one other piece” (or rather each piece locks in at one, and only one, spot or site). The general belief is: each SARS coronavirus 2 piece will eventually find its rightful place.

That is probably optimistic.

C C G G A T G T G A A A A A C T A A A A G T G T A G G G C G G

C C C A A A A A G T G T A G G A T A A A A A G T G G G G G G G

Metagenomics studies diversities and extents of diversity of microbes in their natural environments. (It studies symbioses.) Metagenomic investigations tend to show that extents of microbial diversity in natural environments are consistently underestimated.

In the context of genome sequencing, metagenomics is an adjunct. Next-generation in silico genome sequencing has its algorithms. A metagenomic analysis will have its algorithms. One is adjunct to the other. In combination they provide a better lens with which to probe environmental samples of all kinds or virtually all kinds—including patient nasopharyngeal and bronchoalveolar samples—insofar as one wishes to determine what’s actually there (in the samples). Other probative methods (apparently) find only a small fraction of the (microbial) species present in a sample. Metagenomic analyses (of antecedently existing sequences) will bring in new information on the composition of a specific microbiome. Metagenomics will sometimes deliver up some real surprises I understand.

Algorithmic metagenomic analyses are likely to be of assistance in differentiating among varied sources of target RNA or DNA. With “complex” samples, metagenomics is generally credited with being able to identify (and therefore separate out) nucleic acid fragments according to kingdom, to phylum..... and according to species. Metagenomics is credited with being able to separate human from bacterial, human from viral, bacterial from viral, and so on. It contributes to the simultaneous sequencing of genomes originating from the multiple organisms (including viruses) that comprise the sample.

All RNA fragments (or DNA fragments) harvested from patient specimen are going to look alike and “feel” alike.... In respect of complex specimens: RNA fragments belonging to one species will closely resemble RNA fragments belonging to other species. DNA fragments belonging to one species will closely resemble DNA fragments from other species. The computer software that does 99 percent of the sequencing work doesn’t know (at first—certainly not at first) which cells or organisms the individual fragments originated from. Nucleotide sequences that are identical (i.e. in which the sequences of the nitrogen bases are identical) are also species-indistinguishable. (Strictly speaking—entities that are “identical” would be indistinguishable by definition.)

Do metagenomic analyses “take in” physical and chemical properties (of the fragments)? Do metagenomic analyses of sequencing data take in for example electrical or density-related properties of the nucleic acid fragments—or for example the relative amounts of methyl groups in the fragments—as they assign the specific sequences (the “reads”) to taxonomic groups (human, fungal, viral, and so on)?

They do not. Metagenomic analyses rely entirely on the sequences themselves, the actual sequences of nitrogen bases. A metagenomic analysis in this context will “consult” the already sequenced, the antecedently sequenced—large databases of “reference” sequences and “reference” genomes.

Like Sanger sequencing, algorithmic/computational whole-genome sequencing is credited with high-level accuracy.

Virtually always a given (identifiable, isolable) microorgansim is the cause of a given (infectious) illness—per the germ theory of disease. In cases of viral respiratory infection it is (sometimes) possible to isolate/purify virus particles believed to be pathogenic from tissue specimens (and to extract viral genome from virus particle)—tho’ it isn’t easy and doesn’t comport with “warp speed” requirement.

In respect of viral whole-genome sequencing: the fact that one hasn’t extracted nucleic acid material from a purified virus is seen very broadly as—not a problem.

Would viral whole-genome sequencing that uses extraction of genetic material from purified virus yield more “authoritative” sequencing results in the end—versus computational sequencing (following the harvesting of RNA from patient specimens containing RNA from tens or hundreds of sources of RNA)?

Metagenomics data lend refinement to whole-genome sequencing processes. (The sequencing products themselves are refined.) Many things get better over time. The computer programs that do the sequencing grunt work get better over time. (There is still room for error.)

Determinism deals in certitudes, in certainties. The methods and logic of algorithmic/computational whole-genome sequencing are inherently more probabilistic than deterministic.

We can’t know for example that RNA segments culled from patient specimen (and from which Covid test DNA template sequences may be devised) belong to a specific virus (here SARS CoV 2) with certainty, or absent a certain doubt.

The algorithms must make probabilistic choices in putting together fragments/reads. It’s built into the (algorithmic decision-making) system.

Overlap—what is designated as overlap (see above)—is always inferred overlap. So the identification of (chromosomal) overlap is probabilistic. Computational methods of genome assembly sometimes struggle—particularly where there are abundant repeat and conserved (DNA) regions—as they “work” to assign reads to the appropriate species and the appropriate positions.

Some of the algorithms are error-correction algorithms. Computational genome assembly uses probabilistic methods and probabilistic algorithms to identify (probable) errors and correct them.

But probabilistic methods (used in computational genome sequencing), and the presence of statistical uncertainty—the possibility of error in the sequencing products, does not mean the sequencing products are lousy (i.e. unreliable). The (complex) algorithms are built on, founded in vast amounts of data (overwhelmingly sequencing data, the actual sequences collected from—what has already been sequenced).

There is a tradeoff. The tradeoff resides in computational/algorithmic genome assembly’s speed (verus the Sanger method’s precision).

The most conspicuous failing I would argue (I’m repeating myself): when Covid-19 PCR testing “works”—i.e. has (correctly) identified a fragment of SARS CoV 2 in a human specimen: that identification of viral detritus does not mean illness, or infection, or past illness, or past infection.

And so. What’s known as a hard sell. An official narrative that convinced—convinced a nation and a world—yet failed to entirely convince a single living soul. Its promulgators included. Fauci and Gates included. In respect of the anti-Covid vaccines: they all knew that something was wrong. They all had (most private) misgivings.

Choose a search engine. Search on “Kary Mullis” and you will receive word immediately that Mullis never said—Mullis never said that PCR should not be used for the diagnosis of Covid-19 (or the detection of SARS CoV 2 nucleic acid fragments in human specimens). I believe that Mullis never spoke in any way on PCR in connection with Covid-19. Hopefully he did not. Mullis died at age 74 on August 7 2019.

Mullis was the inventor of PCR—the inventor of the technique of copying/amplifying small segments of DNA. For this technique Mullis, along with Michael Smith, was awarded the 1993 Nobel Prize in Chemistry.

There was never the smallest argument between Mullis and Anthony Fauci on the subject of Covid-19. Again Mullis died in August 2019. Mullis and Fauci had been for years at loggerheads RE subjects, virtually all subjects, related to HIV/AIDS.

In the 1980s and 1990s Mullis was critical of Fauci for suppressing (alternative) views on the causes of AIDS. Mullis was ever the “controversial” one. Always Kary Mullis and never Anthony Fauci: the guy with the idea, the guy with the controversial view, the scientific outlier, the disputant. Always Anthony Fauci and never Mullis: they guy minus the idea, the scientific administrator, the bureaucrat, the adherent. Mullis fervently believed PCR was misused in HIV testing.

From “Reuters” [2020]:

FACT CHECK: Inventor of method used to test for Covid-19 didn’t say it can’t be used in virus detection.

By “Reuters Staff”

CORRECTION November 13 2020: The verdict of this fact check has been changed from false to misleading, to reflect that the quote examined may have been a fair reflection of Mullis’ views, even if not a direct quote.

...

Social media users have been sharing a quote attributed to the inventor of the Polymerase Chain Reaction (PCR) test [sic], currently being used to detect Covid-19, which says “PCR tests cannot detect free infectious viruses at all.” This quote appears not to be a direct quote from inventor Kary Mullis, has lost some context, and does not mean Covid-19 testing is fraudulent, as suggested by some social media posts.

[N.B. Mullis was not the inventor of the “Polymerase Chain Reaction test.” There are scores of Polymerase Chain Reaction tests being used presently—as part of the diagnosing of Covid illness. And polymerase chain reaction is just one component of those tests. Mullis was the inventor of the Polymerase Chain Reaction technique for amplifying DNA segments.]

...

However the quote is actually from an article written by John Lauritsen in December 1996 about HIV and AIDS, not Covid-19.

...

Even if Mullis had voiced a similar statement before his death in 2019, this quote does not mean the PCR test is unable to detect the presence of SARS-CoV-2—the virus that causes Covid-19—rather that it cannot determine whether the individual tested is infectious.

The PCR test is the preferred Covid-19 testing method in England. It detects the presence of the virus by amplifying the virus’ genetic material to a point where it can be detected by scientists.

A spokesperson for Public Health England told Reuters why PCR tests are being used widely in England: “Molecular diagnostic tests, such as real-time PCR, are the gold standard methods for identifying individuals with an active viral infection, such as SARS-CoV-2, in their respiratory tract. These tests are rapid and produce results in real time.”

So.... Mullis may have said something on the order of—PCR tests should not be used to diagnose viral illness. And (per the above) if he did say it he was dead wrong.

What is real-time PCR, the test that “produces results in real time”? In real time is very likely to signify: the experience of events or episodes (by attendants/onlookers), usually after the fact, at the same “velocities” at which the (original) events or episodes unfolded. Admittedly the phrase has some plasticity—as do most phrases and most words.

Is someone mistaken?—insofar as the technique that is used in a wide range of medical tests that recognize (or fail to recognize) DNA segments is actually RT–PCR. Wherein RT stands for reverse transcriptase. The enzyme that “writes backward” as it were. Are there persons who think it stands for real time?

Actually the phrase real-time PCR is used widely—by “media,” in science writing, in science journalism. That doesn’t make it correct.

What is the intended meaning of real-time PCR? I believe that what they, its varied authors, are straining after: one is getting test results—and an answer to the question: “Is the patient in question ill/infected?”—on the spot—as they, the results (the fluorescent signals), are happening.

It was part of a propaganda campaign: the patient who tested positive was “actively” infected or synchronously infected—synchronously with the test’s being administered.

That is false: a deliberate falsehood or an indeliberate one. And it is dismaying (whenever it occurs): discussion of active infection or current infection (vis-à-vis test results) in the absence of discussion of patient condition, patient symptoms or symptom.

Much reprised words of Mullis (much reprised for example if you happen to be a YouTube user)—speaking in 1997 on the subjects: PCR, PCR used in the diagnosis of viral infection, AIDS, cause(s) of AIDS.

I don’t think you can misuse PCR. The results, the interpretation of it [are dubious]. See, if they can find this virus in you at all—and with PCR, if you do it well you can find almost anything in anybody—it starts making you believe in the Buddhist notion that everything is contained in everything else. Because if you can amplify one single molecule up to something that you can really measure, which PCR can do, then there are just very few molecules you don’t have a single one of in your body. So that could be thought of as a misuse of it—just to claim that it’s meaningful.

And so—per Mullis: interpretation is the sticking point. What he is saying just above: In respect of the use of PCR results to diagnose viral infectious illness, it is the interpretation (of the results) that is the impasse. Identification, correct identification, of a given nucleotide sequence does not mean illness or infection.

In 2020 and 2021—of all the well-known media outlets, the most craven and the most enslaved to the (pandemic-related) main narrative (arguably) was NPR. Followed by the New York Times.

In May and June 2020 (right around the time I was making plans to go to Ticonderoga Land) I was reading consistently over at Health News from NPR [@ the NPR.org website]: “positive PCR” was proof positive of active Covid infection. I found it troubling. I believed that—over at Health News from NPR—they were making it up.

The journalistic pieces were short pieces—at Health News from NPR. They were never well-written or precisely written (in spring and summer 2020). That is OK. The Health News pieces were I believe geared toward “the bright high school student.” The bright high school student is (in my experience) the audience toward which science writers contributing to the pop science magazines are most often advised to aim.

An extract from How Reliable Are COVID-19 Tests? Depends Which One You Mean. [Health News from NPR May 1 2020]

Diagnostic or PCR Test

What it does: Doctors use this test to diagnose people who are currently sick with COVID-19. This is the one we’ve been hearing so much about.

How it works: The test uses a sample of mucus typically taken from a person’s nose or throat. The test may also work on saliva—that’s under investigation. It looks for the genetic material of the coronavirus. The test uses a technology called PCR (polymerase chain reaction), which greatly amplifies the viral genetic material if it is present. That material is detectable when a person is actively infected. [Emphasis mine.]

Why wouldn’t that material [DNA segments transcribed from RNA segments] be detectable if it has been amplified (increased, multiplied) literally by a factor of 1 billion (or more)?

Who was it that said—PCR testing in its sniffing out of specific nucleic acid fragments “turns up everything and nothing”?

Persons have strong tendencies toward binarist thinking. Very often a specific thought seems to attract, pull toward it, or conjure up out of thin air (almost): its inverse or opposite. If a given test (for infectious illness) does not uncover active infection at the time the test is administered, then there is one that does—or there must be one that does.

I believe that—in respect of the statement that a test for Covid illness (“PCR”) would yield a given result when the person in question had active infection—they made it up.

Continuing to glide. I put the pedal to the metal. I continue to soar over and across large swaths of New York State. I want to get the car back—before 6 PM or I may have to pay something extra. (I’m becoming a tightwad.) I am near Poughkeepsie. I pull off the highway and into a rest stop because I want to use my phone.

I have a text from my (conservative) brother Jimmy. It is a link. I am glad to get it. I tap.

It is Howie Carr. Words of Howie Carr. Not a video—it is just spoken words. Conservative radio talk-show host Howie Carr. I don’t really know who Carr is. I've heard of Carr. About the only thing I knew of Carr at that moment, in late July 2020: he was born in Portland Maine. (That is something I rather liked.) And I knew he wasn’t my type. (I don’t know a lot about Carr now, in December 2023.)

Carr is Jimmy’s type I think. Jimmy and I have not seen eye to eye—as adults. We are right now in transit, moving in opposite directions & meeting in the middle. Our paths are crossing. Since the start of the Covid phenomenon he has been moving leftward; I, rightward. (I had thought there wasn’t a force anywhere on Earth or in Heaven that could do that. We are becoming tight buddies. It is almost a miracle.)

When I say that my brother is migrating leftward: in mid 2020 he listens to and is much influenced by the official Covid propaganda (if you’ll excuse me) that pours forth almost continuously from CNN and MSNBC. He is lapping it up like a cat lapping up cream.

Carr is speaking of the “gaming of the numbers.” Numbers of cases and numbers of deaths. That’s Covid cases and Covid deaths. Carr seems quite amused at moments—by the media skulduggery (related to “case” counts) he delineates.

There is a superette, or mini-mart, adjacent to where I’m stopped. I go in and buy a hot tea with milk, no sugar. I sip it in the car and listen to the podcast (if that’s what it is). [?] I listen to it in its entirety, I rather enjoy it. This is pure bonding (between me and my brother), I say to myself.

In May 2023, at video-sharing sites that are free-speech alternatives to YouTube, doctors—doctors in alignment with “the opposing narrative”—talk about their treatment of patients “who have Covid.” Again and again I ask: How do they know? Flu and colds, which can be virulent (severe) and life-threatening, have never gone away.

For me, at this point, it is axiomatic that RT–PCR as the test used in the diagnosis of Covid illness—is worthless. (A point that is in debate, in May 2023.) I have written (above) that flu is hard to diagnose. (Persons told that they have flu may have illness that resembles flu caused by other respiratory viruses.) Covid-19 is similarly hard to diagnose—and for all the same reasons.