Reverse Engineering the source code of the BioNTech/Pfizer SARS-CoV-2 Vaccine

https://berthub.eu/articles/posts/reverse-engineering-source-code-of-the-biontech-pfizer-vaccine/

• The CAP to make sure the RNA looks like regular mRNA
• A known successful and optimized 5' untranslated region (UTR)
• A codon optimized signal peptide to send the Spike protein to the right place (amino acids copied 100% from the original virus)
• A codon optimized version of the original spike, with two ‘Proline’ substitutions to make sure the protein appears in the right form
• A known successful and optimized 3' untranslated region
• A poly-A tail with a ‘linker’ in there

 

If we look closely, we see that the majority of the changes happen in the third codon position, noted with a ‘3’ above. And if we check the universal codon table, we see that this third position indeed often does not matter for which amino acid is produced.

So, the changes are synonymous, but then why are they there? Looking closely, we see that all changes except one lead to more C and Gs.

So why would you do that? As noted above, our immune system takes a very dim view of ‘exogenous’ RNA, RNA code coming from outside the cell. To evade detection, the ‘U’ in the RNA was already replaced by a Ψ.

However, it turns out that RNA with a higher amount of Gs and Cs is also converted more efficiently into proteins,

And this has been achieved in the vaccine RNA by replacing many characters with Gs and Cs wherever this was possible.

This is one of the exceptionally clever bits about the vaccine. Our body runs a powerful antivirus system (“the original one”). For this reason, cells are extremely unenthusiastic about foreign RNA and try very hard to destroy it before it does anything.

This is somewhat of a problem for our vaccine - it needs to sneak past our immune system. Over many years of experimentation, it was found that if the U in RNA is replaced by a slightly modified molecule, our immune system loses interest. For real.

So in the BioNTech/Pfizer vaccine, every U has been replaced by 1-methyl-3'-pseudouridylyl, denoted by Ψ. The really clever bit is that although this replacement Ψ placates (calms) our immune system, it is accepted as a normal U by relevant parts of the cell.

Many people have asked, could viruses also use the Ψ technique to beat our immune systems? In short, this is extremely unlikely. Life simply does not have the machinery to build 1-methyl-3'-pseudouridylyl nucleotides. Viruses rely on the machinery of life to reproduce themselves, and this facility is simply not there. The mRNA vaccines quickly degrade in the human body, and there is no possibility of the Ψ-modified RNA replicating with the Ψ still in there. “No, Really, mRNA Vaccines Are Not Going To Affect Your DNA” is also a good read.

Lauren Groff - "Matrix"

"Matrix" for the Latin for Mother.

One of those exceptional books that tell the whole lifetime of a character and you actually believe it. Marie de France, unknown who she was according to wikipedia, but so influential in the 12th century....

But Goda needs to punish someone, and so the grave is dug in the unconsecrated ground outside the churchyard, without ceremony, Avice is lowered into it in her shroud facedown with her babe at her feet, so that in the Revelations her bones will never be able to rise to the hands of the Angels of the Resurrection. Such pitilessness, Marie thinks, for a sin of flesh.

At last, she shees a clump of darkness on a rise that, when Marie nears, revels the sheep saved, nuns running into the sodden fields waist deep to save more. Palenesses floating in the dark are drowned sheep. Marie wades out into the icy water to her waist, to her ribs. Cold sezies her and the wet habit grasps at her legs. She finds a ewe standing upon a dead sister, paddling with its front legs in panic, and though the beast is twice the size of an ordinary child and thashes in her frenzy, Marie picks her up in her arms and carriers her to the rise.

And her smell was strong, the soap of lemon balm and lavender at the heart of her braid, skin with honey and wild onions and leaf rot in it.

So hungry, the nun's faces are skulls skinned of flesh in the dark dortoir. There are soups in which meat is boiled and removed to save for future soups. Fingernails the cold blue of sky.

Tom Mueller - "Extra Virginity: the Sublime and Scandalous World of Olive Oil"

Nice little book about olive oil and particularly all the ways it gets adulterated and messed with. You don't dare to buy the stuff anymore after reading this book.

Finally, on November 13, 1960, the European Parliament passed a groundbreaking law on olive oil quality, which created several new oil grades. The highest of these had an odd-sounding name, with overtones of science and religious mystery: extra virgin. The law stipulated that extra virgin oil be made solely by mechanical methods, without chemical treatment, and set a number of chemical requirements, including a maximum of 1 percent free acidity.

In olive oil fraud, an EU investigator told me, "profits were comparable to cocaine trafficking, with none of the risks." Widespread adulteration and huge supplies of refined olive oil fueled a price war, which forced even the largest oil companies like Unilever and Nestle to seek ever cheaper sources of oil, with the risk of purchasing and reselling, knowingly or not, adulterated products themselves. While the quality of estate olive oils soared, supermarket extra virgins plummeted.

Nobody knows which cultivars the Spanish monks of New Norcia brought over from their homeland. Many trees died during the ocean journey, and as Gordon Smyth says, those which survived the salt air of the voyage "were as tough as old boots by the time they got here." Over the last 150 years, in the antipodean sunshine and the breezes off the Indian Ocean, these trees have grown apart from their Mediterranean ancestors and are now considered a separate cultivar, the West Australian mission olive.

The first olive oil importers to the New World were the conquistadors, for whom, as for their contemporaries in Spain, olive oil was a crucial food, fuel for lamps and engines, and active ingredient in medicine and religious rites. Spanish explorers packed quantities of olive oil, together with wine, salt pork, sardines, raisins, sandals and weapons, in each ship they sailed to the Americas. As in Roman times, when the legions planted olives wherever they were stationed, olive trees grew in the furrows of the conquistadors' swords, becoming a vivid symbol of conquest.

Congressional hearings on margarine began in the early 1880s and continued through 1950. In 1886, Congress enacted a Margarine Act, slapping stuff taxes and restrictions on margarines; when he signed the act into law, President Grover Cleveland remarked that one of its main benefits was "the defense accorded the consumer against the fraudulent substitution and sale of an imitation of the genuine article of food of very general use. I venture to say that hardly a pound of oleomargarine ever entered a poor man's home under its real name and in its real character." Around the turn of the century, the Supreme Court heard several cases concerning margarine. "We need insistent recognition of the fact of the interdependence of the human animal upon his cattle," Herbert Hoover intoned. "The white race can not survive without its dairy products and no child can be developed on short or bad milk supply." The world wars and butter rationing boosted teh margarine industry, but strong limits remained on the way the product could be marketed and sold: through the 1950s, federal taxes remained in effect on the product, and in many states margarine could only be sold as a white block, with a pellet of yellow coloring that the consumer had to knead in. In Wisconsin it was still illegal to sell yellow margarine until 1968, and in Quebec, the substance was only legalized in 2008, after Unilever brought suit against the provincial government.

This suggests another fundamental difference between wine and oil. Grapes contain not wine but grape juice, which must be transformed by the vintner's art. Oil is already there in the olive, if we can only coax it free. Wine in the final analysis is man-made, while oil is made by nature, through the medium of the strange tree-mysterious, because it comes from something greater than ourselves. Wine in a meal is the soloist, set apart in its gleaming glass, while oil permeates the food, losing itself but subtly changing everything. Wine's effects on us are vivid and swift, while oil works on the body in hidden ways, slow and lingering in the cells and in the mind, like myths. Wine is merry Dionysus; oil is Athena, solemn, wise, and unknowable.

Charlie Jane Anders - "The city in the middle of the night"

Amazing sci-fi about the planet January where a human spaceship arrived generations ago. Tidal locked, one side of the planet is always blazing, one in eternal dark.

Various people, Mouth, and Sophie, struggling between the two cities (Xiophant, strict rules, strict times) and Argelo (party, freedom, no responsibility) and the Citizens (Mouth is the only survivor) as well as the Resourceful Couriers, "crocodiles" or Gelet that Sophie can speak with...

Amazing stuff.

Alix E. Harrow - "A Spindle Splintered"

Modern retelling of Sleeping Beauty, where multiverse-beauties break out of their fate.

okay, but could not get used to the "gen-z" ish word and language, the continuous need to sound snappy and sharp. Tiresome.

Mouse Heaven or Mouse Hell?

https://www.sciencehistory.org/distillations/mouse-heaven-or-mouse-hell

Eventually other deviant behavior emerged. Mice who had been raised improperly or kicked out of the nest early often failed to develop healthy social bonds, and therefore struggled in adulthood with social interactions. Maladjusted females began isolating themselves like hermits in empty apartments - unusual behavior among mice. Maladjusted males, meanwhile, took to grooming all day-preening and licking themselves hour after hour. Calhoun called them "the beautiful ones." And yet, even while obsessing over their appearance, these males had zero interest in courting females, zero interest in sex.

Intriguingly, Calhoun had noticed in earlier utopias that such maladjusted behavior could spread like a contagion from mouse to mouse. He dubbed this phenomenon "the behavioral sink."

Between the lack of sex, which lowered the birth rate, and inability to raise pups properly, which sharply increased infant mortality, the population of Universe 25 began to plummet. By the 21st month, newborn pups rarely survived more than a few days. Soon, new births stopped altogether. Older mice lingered for a while-hiding like hermits or grooming all day-but eventually they died out as well. By spring 1973, less than five years after the experiment started, the population had crashed from 2,200 to 0. Mouse heaven had gone extinct.

Recently, however, human birth rates have dropped sharply in many developed countries-often below replacement levels- and young people in those places have reportedly lost interest in sex. The parallels to Universe 25 seem spooky.

The Sandman

Enjoyable enough, but a bit too much the overwhelming CGI action we all expect these days.

The "24/7" diner episode is great, although the separate episodes with their sub plots work less in a series than in the graphic novel.

The Humans

Slightly disturbing film of a family coming together for Thanksgiving in a dilapidated New York City apartment. Each family member, particularly the dad, has their problems and fixations.

Carter (2021)

Crazy action film, semi-one shot, Korean, of a guy protecting his family, with a bomb in his mouth and has forgotten his memory.

Crazy stuff, quite enjoyable.

The Northman

Impressive Viking tale of revenge. Music reminded me of "Once Upon A Time in the West" with its quickly vibrating hook.

Aurora

Norwegian folky synthpop, child voice.

The Innocents (De uskyldige)

Nice Scandi horror about a few children getting supernatural powers and battling each other while parents are unaware

Westworld s4

not sure where it's going, slow start, but might get interesting

The Boys s3

Wild rollercoaster ride. Fun stuff. Good (better?) character development than earlier seasons, maybe.

Mad God

If Harlan Ellison's "I have no mouth yet I must scream" was a trilogy, this was the fourth part written while on LSD.

Amazing stop motion. Not sure I'm getting the whole story yet. Babel. Rebirth. Circle. Empty gestures, empty living...

Kate

Fun action film where protagonist knows she will die and tries to take revenge on the yakuza.

The Gray Man

Enjoyable full-fight action film with Ryan Gosling as CIA "gray" man, full on action like John Wick etc.

Call of Juarez: Gunslinger

Enjoyable enough western shootout game.

Stray

Truly beautiful game where you play a soft-mewing stray cat trying to escape the post apocalyptic underground city.

Sophia Kennedy - misc

Good stuff. Some in German.

"People treat their problem as pet / feed it while it's hungry / mourn it when it's dead"