The Dangers of Hype and Bragging

When uncle Boris started talking about an irrevocable exit from pandemic, I thought to myself “that is a pretty stupid thing to say. Talk about setting potentially unrealistic expectations.”

Now people are talking about Freedom Day. Oh dear.

Unless you have worked extensively with non-linear equations it is really easy to misunderstand. Most people have linear only thinking.

Back when things started to kick off in the USA, I started doing a naïve, no assumption modelling of the incoming data. A simple exponential fit predicted very well the initial and fast ramp up in case numbers.

I have had a little play with the most recent UK case numbers.

This ultra-naïve model which does not as yet fit very well predicts over 7000 cases a day in a couple of weeks, rising reasonably quickly to over ten thousand.

The so-called irrevocability is very much in the balance…

Rainy Saturday and SARS-CoV Binding.

It is raining on and off here this afternoon, so I have been delving a little into the SARS literature. Below is a model highlighting {I think} where the spike glycoprotein is changed in the various variants. The ACE2 is the human lung receptor{brown spirally thing}, the three variants on the top right-hand side change close to where the virus protein binds to the human lung at the receptor binding domain {RBD}.

Below is the near molecular detail of how SARS-CoV and SARS-CoV-2 bind to the receptor {the green spirally thing}. The mechanism between the two viruses looks quite different with what looks like hydrogen bonding in the more recent virus.

How strong these bonds are along with the ease of conformational change will affect the virus binding {and release} rate constants. It must bind to replicate and must release at some stage in order to spread via coughing etc..

I wondered has anybody tried making a compound that preferentially binds to the ACE2 site in competition to the virus. Seems like a strategy for treating the disease. Add a high concentration of the ACE2 site blocker and outcompete the virus. If only a few hydrogen bonds enable the virus to bind it might be possible to design an antagonist molecule that is not toxic.

Hmnn…

Is Covid a Metaphor for Deforestation?

This is prompted by an article in Les Echos.

« Les poumons de la planète sont au bord de l’asphyxie

Qu’ils soient verts ou bleus, les puits de carbone et de régulation climatique se dégradent inexorablement. Leur mécanisme pourrait même se retourner contre l’équilibre atmosphérique global. »

This is a pair of years in which we heard the phrase “I can’t breathe” and when there is a shortage of oxygen, dephlogisticated air, where people have died struggling to breathe in their hundreds of thousands. A year in which the lungs of the planet, Brazil, have continued to be scorched and where the death toll of not breathing is very high. The leadership has done little to prevent deforestation and pooh-poohed the virus. It is a time of floods and fire. When the air has been filled with smoke.

As we stop the planet from breathing, is it stopping us from breathing too? Have a taste of your own medicine you nasty, greedy human beings. See what I feel like when I can’t breathe.

Is it our knee on the neck of the planet?

On the way back from the supermarket I suggested to the wife that we buy a dephlogisticator just in case. As the oxygen content in the atmosphere drops, we might be in dire need.

I don’t think we are paying sufficient attention to what the planet, the universe, is trying to teach us!

It seems people can only see the light at the end of the tunnel, so that they can get back to “normal”. Have drink in a bar and go on holiday. What we don’t perhaps realise is that the light is a TGV {Train à Grande Vitesse} heading in our general direction.

New Breton Coronavirus Variant

This from Le Figaro:

Covid-19 : un variant breton détecté, des investigations sont en cours

Détecté au sein du centre hospitalier de Lannion, dans les Côtes-d’Armor, ce variant ne présente pas, à ce stade, de gravité ou de transmissibilité accrues par rapport au virus historique.

Un nouveau variant du coronavirus SARS-CoV2 a été détecté en Bretagne, a annoncé lundi 15 mars la Direction générale de la santé (DGS), précisant que des investigations sont en cours pour en évaluer la transmissibilité et la sévérité.

En attendant, ce variant a été classé dans la catégorie « à suivre » par les autorités, celle qui regroupe la plupart des milliers de variants qui apparaissent naturellement dans le monde, et dont seule une petite proportion poseront finalement des problèmes particuliers de santé publique, par exemple s’ils s’avèrent plus transmissibles. Les autorités sanitaires ont tout d’abord détecté en Bretagne plusieurs cas de malades présentant les symptômes du Covid, « rattachés à un cluster » mais dont les tests PCR étaient négatifs.

Il s’agit d’un cluster au centre hospitalier de Lannion (Côtes-d’Armor). Le 13 mars, 79 cas y ont été identifiés, dont 8 cas porteurs du variant, confirmé par séquençage. Des analyses réalisées par l’Institut Pasteur ont mis « en évidence un nouveau variant (…) porteur de neuf mutations dans la région codant pour la protéine S mais également dans d’autres régions virales », a précisé la DGS dans un message aux professionnels de santé.

Pas de gravité accrue à ce stade

« Une évaluation est en cours afin d’apprécier l’impact possible de ces modifications génétiques sur un défaut de reconnaissance par les tests virologiques conduisant à un sous-diagnostic », poursuit-elle. « Les premières analyses de ce nouveau variant ne permettent de conclure ni à une gravité ni à une transmissibilité accrue par rapport au virus historique », indique un autre communiqué de la DGS lundi soir, ajoutant que « des investigations approfondies sont en cours afin de mieux connaitre ce variant ».

L’apparition de variants du virus est un processus naturel puisque celui-ci virus acquiert des mutations au fil du temps, pour assurer sa survie. A ce stade, trois variants dans le monde sont considérés comme particulièrement préoccupants, ceux qui ont d’abord été détectés en Angleterre, en Afrique du Sud et au Japon (mais sur des voyageurs venant du Brésil, d’où son nom commun de « variant brésilien »). Parallèlement, il existe une deuxième catégorie de variants, surveillés par la communauté scientifique internationale à cause de leurs caractéristiques génétiques potentiellement problématiques mais qui ne circulent encore qu’à moindre échelle.


This from the DG Santé

This new variant was found about 25 km from here and from what I have so far read it is sufficiently different to have been missed in some of the PCR testing. No doubt they will update the databases.

Because there are only 8 cases so far, they don’t know if it is more infectious or more grievous than the original virus. Nor do they know if it can elude the antibodies generated by the current vaccines.

Le Figaro is doing a poll to ask its readers if they approve of the suspension of the Astra Zeneca vaccine or not.

It looks like were are going to be getting some more confinements etc. on a departmental basis. Although the virus per person density is low here, this new development may mean that the Côtes-d’Armor, our department may have some additional restrictions. We shall have to wait and see. There are some strict quarantine protocols advised in the alert from the DGS.

Another twist and turn, much as I predicted.

Hmnn..

Vaccine – Gung Ho

Every time I hear a British Politician or read a British Newspaper bragging about how well the vaccine roll out is going, I think to myself what fools. Not only this they diss the EU. They are talking as if coronavirus is a done deal, it is sorted, and all will be fine and dandy. There is a part of me that thinks “do not tempt fate”.  They are very nearly promising that it is all over. This wishful thinking and bigging up is in marked contrast to the press here. But the fat lady has not yet sung, so to speak.

 The figures here are excerpted from a preprint , a not yet peer reviewed, article:

 “Circulating SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity.”

from medRxiv.

{humoral immunity is antibody-mediated immunity}

The virus continues to mutate, here the purple is the British strain, which is mutating a lot, the red is the South African strain, and the yellow and orange are Brazilian. The “British” virus is rampant in Europe now.

The Brazilian P.1 and P.2 strains can reinfect people who have already had the earlier version of covid 19. A couple of the vaccines in preliminary data have been shown to have less efficacy against these Brazilian and South African strains. But this elephant in the room is not mentioned. The wonderful surge testing will root them out! All hail the great vaccine roll-out we shall be free soon.

The two viruses on the right here are SARS-CoV-1 and a related bat coronavirus. These are different from SARS-CoV-2 only sharing about 75% of the make up with it.

The P.1 and P.2 mutants come from Manaus in the Amazon. There is a strange sense that we burn and destroy the Amazon rain forest. It is in our cells there that the virus mutates, perhaps as karma. Until there is no longer a significant number of infected people, there will be mutations. The more people infected the more mutations there will be. It is a numbers game.

So, the UK can brag about its roll-out, but the virus will “breed” and evolve all over the world.

Anyway, I saw the GP yesterday and I am now on her list to be vaccinated. She says that they might have some vaccine next week and she is checking who is willing to be vaccinated. Right next to the UK there is country in which willing vaccine take up may be only as high as 50%. Great the UK is vaccinated, but much of its goods pass through an unvaccinated neighbour.

I am sure there will be many more twists and turns to this situation.

Please do not tempt fate with braggadocio….

Over promising again?

dephlogisticated air

People are dying because they don’t have enough dephlogisticated air or in other words oxygen.

Oxygen has eight as its number and the most common isotope is 16 it is about 20% of the atmosphere and you can buy cylinders online.  Medical grade is not cheap.

8 is the jewel Harmony (though conflict) so a lack of harmony causes death.

Tarot 8 is la Justice

16 is liberation through the power of intent the tarot card Maison Dieu.

The oxygen molecule is 32 which is the dark jewel disharmony.

32 Disharmony

Active Shortcoming: Inertia
Behaviour: Anarchy, nihilism, discrediting, slander, gossip, interrupting
Passive Shortcoming: Entropy
Behaviour: Apathy, indifference, carelessness, negligence, slothful, confusion, laziness

Quite a potent mix of numerology

————–

I was really struck when I saw people queuing to get their tanks re filled in south America. They being poor, were trying to look after their loved ones at home.

Because I know how to handle gases, I could fit a regulator and the like. It will be a quick learning curve.

So COVID is showing us all the signs of inequality. We will have vaccine inequality for sure.

And those mutants will keep on coming.

 

 

In the, for now, rich countries the new vaccines will probably just about keep pace with the mutants.

There will be a lag.

Might be wise to buy some pharma shares… hmnn…

Difficulty breathing is the dreaming symbol for lack of personal power. In this sense it is accumulated vitality from following a spiritual path or in other words, knowledge.

Because of the ice, the road outside is ultra-quiet. The groovy icicles are groovy.

At last they have stopped going on about the light at the end of the tunnel, if only for a short while..

Now they are complaining about holidays again…

SARS-Ninja-CoV-3

The UK news is reporting that the virus is developing a “superpower”. Not sure that this is a good thing to be doing. It will freak some people out and others might even believe it. There is a lot of imagination out there. It might be changing so as to need different antibodies to counter it is perhaps a better way of saying it. Decoding complex scientific articles is not easy unless you are a specialist. I have a science background and from time to time I like to check the source materials:

Comprehensive mapping of mutations to the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human serum antibodies.

 

Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants.

 

mRNA-1273 vaccine induces neutralizing antibodies against spike mutants from global SARS-CoV-2 variants.

These articles are reduced into “one liners” for the news. I can get the gist because of my training but I do not get the details because it is not my field of expertise. It is pretty complicated stuff.

But it is a race. Every time the virus replicates it is prone to mutate. The more replications, the more mutations. The more hosts the more mutations. Several million hosts increases the likelihood of any mutation by sampling the possibilities. If I have understood it the RSA and the UK versions are suggesting that one type of mutation is more probable. Sooner or later the virus will mutate sufficiently that the current vaccines won’t be effective against it. Probably not a matter of if but when.

When will it have mutated sufficiently that it gets deemed a whole new virus? I don’t know how these things are classified.

I wish people would stop making reckless “good news” soundbites. If I hear “light at the end of the tunnel” again…yaargh..It is a marathon and not a sprint!!

Just when you thought it was safe to go out of lockdown along comes SARS-Ninja-CoV-3 and a whole new cycle of vaccine development and clinical trial begins. I suspect however that the work is already underway towards the next generation of vaccines.

2022 – SARS-CoV-3a and SARS-CoV-3b

Some satirical speculation on the new normal:

It was February 2022 and President Harris had just signed an executive order finally banning all interstate travel. Prime Minister Starmer was on the TV announcing the ninth national lockdown, this time with a 6pm to 6am curfew enforced by the army. The United Kingdom was to all intents and purposes in quarantine from the rest of the world. Trade with Europe was affected by lorry drivers parking trailers on ferries and then driving off. When the ferry docked continental drivers unloaded the trailers. Nobody would accept any people from the UK because it was there that the virus had mutated so much that it had been given new designations; SARS-CoV-3a and SARS-CoV-3b. The disease was now COVID 21.

The fleets of airplanes lay idle and rusting. Only the fighter jets flew patrolling the skies. Oil and gas were getting scarce. People shivered in their homes. Because of the travel ban most UK universities were in dire financial trouble. The shift to massively online learning did not go well. With no foreign students the finances began to dry up, students refused to pay the fees. No children had been at school for a year. Private tuition online became the norm for those with enough money.

The black-market supply in oxygen was thriving on the dark web. New oxygen separation facilities were springing up everywhere adding an increased strain to the national grid. AI sex robots a la Blade Runner were literally worth their weight in gold. The border conflict between China and India continued to escalate but had remained conventional so far.

In the United States the share price of Gilead had outstripped Apple. New ventures making hermetically sealed body bags were doing well on the Dow Jones. Big pharma was struggling to keep pace with the mutations. Volunteers for clinical trials fell away as it was becoming widely understood that many on a trial got only a placebo.  

The Sons of Alba were getting increasingly deadly. They had shifted from simply burning houses to planting car bombs notably in London and the South East. Meibion Glyndwr was also once again active, like Mebyon Kernow they had started destroying second homes to keep the infectious city dwellers out.

The Schengen area had evaporated once again the borders were up. Each country eyeing the data of others to confirm which has the most virulent rate of infection. Some countries had stop publishing their infection rates. Online trade in strong steroid medication outstripped the sales of cannabis for the very first time. Private labs which used to make MDMA were switching to steroid synthesis as it was becoming more profitable. The market was flooded with sub-standard medication and laboratory glassware was in very short supply.

Coming soon to a world near you…

Is Coronavirus an Agent of Karma?

A thing which is not actually living, and which is smaller than a human hair width by a factor of around one hundred is going “viral”. {We probably should not have invented this phrase.} It is propagating around the world like the latest trend or meme. Those countries in which it has not been respected have faired worse. It is infecting our computers (minds), there is no Norton or McAfee to keep it at bay. It a malware eating at our files.

People who have pooh-poohed have got a dose. Sir Boris The Most Decisive of Clarity City ended up at the O2 stadium so to speak. Orange man has been ousted by some tiny electrostatic time bomb bag of RNA and his unwillingness to listen to anyone other than his bigly genius hunches. Yup he did put America first and they are number one in the charts, he made ‘em great. Right now, several countries are movers and climbers, the UK will soon knock France of its current spot in the charts and become a top five hit, pop pickers.

People will kill their relatives because they want that Thanksgiving dinner and can’t go cold turkey on Xmas.

Like a teenage turtle it is starting to mutate into a ninja virus. But we must keep schools open even if it kills us all. Like van Helsing we now have our stakes, crosses, our precious phials of Holy Water {thanks to pharma}, with our medicinal garlic to keep the little bugger at bay. People keep going on about normal, forgetting the fact that elements of the economy will no longer exist. Right now, ‘tis winter and the virus is in the Northern Hemisphere, in a few months’ time it will head South. If it goes green, we will have SARS-Ninja-CoV-3. Sometimes art imitates life or predicts it.

 

It is really dangerous to get overconfident that the vaccine will cure the pandemic, because karma likes quirks of fate. Get all self-important, that karmic boomerang will be back quicker than a Terminator, hasta la vista baby.

The virus is getting many to “kneel”, which sounds a lot like karma to me. If we continue to mess up the planet it might well “retaliate” by manufacturing more surprises for us.

I think that this virus is an agent of karma, in that it does demonstrate quite well cause and effect. Procrastination causes death, will full behaviour causes infection. Sometimes karma teaches us by pain to ourselves, sometimes it takes away that which we love, but karma does eventually teach even the deniers.

We could learn or we could continue to imagine ourselves Masters of the Universe, Sovereign Lords over the most Beautiful Blue Planet full of tears (sic). Maybe we should listen to what the planet is trying to tell us…