Science, Experts, Commentators

 Science is filled with uncertainty. Paradigms, namely the basic "example", shift from day to day, and absolute science just does not exist. Take COVID, the most recent variant and say glycans. The most recent one has lots of new glycans and we know they can dramatically change protein structure. But not exactly, not even approximately.

Then we have erstwhile "experts" in the NY Times who tell us what to do. Some alleged academic sociologist having apparently no demonstrated expertise in virology or related fields espouses how we as a country must act stating:

We need stricter testing regimens involving several tests over time and even quarantine requirements for all travelers according to the incubation period determined by epidemiological data. We also need more intensive and widespread testing and tracing to cut off the spread of the variant. This means finally getting the sort of mass testing program that the United States has avoided and which has been part of successful responses to Covid in other countries.

The writer continues:

It’s possible Omicron developed through a persistent infection in an immunocompromised patient, such as someone who may not have been treated properly to control an H.I.V. infection. Such lengthy infections are suspected of having allowed other variants to develop as well. This is all the more reason that if the developed world is going to impose restrictions on South Africa, and other countries, it should provide them with financial support.In about two to three weeks, lab research and epidemiological data should start to provide a clearer picture of how transmissible this variant is, how it affects the severity of illness, and whether and how much it can evade some vaccine protection.

 Now here is someone who on paper in my opinion seems clueless telling the rest of us what to do. We wrote extensively about these variants over the past almost two years yet we know that we still have major gaps. 

So why should we even listen to someone who is clueless?

Omicron, Glycans and Aggressiveness

 

We wrote about glycans and their effect on the COVID Spike protein and aggressiveness. All the other variants have little if any glycan changes. Omicron has the above, namely 11 out of a total of about 30. Namely one third of the protein sites will be affected by glycan activity, which we now know lends itself to aggressive behavior. Even though we do not yet know the folding and binding sites the glycan profile is worrisome.

Fox is Back!

 

My friendly local fox wandering around at 2 AM!

NJ 2021 11 27

 Now we have the new variant but the old one seems to doing the job quite well. Almost all break through cases. Assuming the same gross incompetence of the Government folks again we will most likely see an explosion some time in January!

First deaths are flat which is good. LTC still present.

County per day still rising. Wonder who they are as usual. Most appear to think this is over. Just like before the Battle of the Bulge. The German Tigers are assembling at out airports and southern borders.

State wide it is not as bad.

It is clear nationally as to the breakthroughs.

Whereas we have improved vaccinations.

We can see that below even better

The county seems to be exploding where as the town is ok

Noting that the town doubling is on the rise.

It's Loose!

 The Guardian notes:

The first suspected cases of the Omicron Covid variant in Germany and the Czech Republic are being investigated, as Dutch authorities scramble to see if 61 passengers from South Africa who tested positive for Covid-19 have the new variant. Omicron, first identified in South Africa and known officially as B.1.1.529, has already been detected in travellers in Belgium, Hong Kong and Israel, according to reports. Australia and several other countries joined those imposing restrictions on travel from southern Africa on Saturday after the discovery of the variant – described by the World Health Organization as “of concern” – triggered a selloff on global stock markets. In Germany, a minister in the state of Hesse said on Saturday the variant had probably arrived in a traveller returning from South Africa.

And our medical wizards in Washington have delayed our restrictions until Monday, how many will get in by then, and leave the southern border wide open for massive influx and then distribute them across the country. 

 Two years ago if we had acted we would not be in this mess. Unfortunately we seem to have the same life time employment folks in control worsened by politics.

It Is Now Officially "Omicron"

 Looks like the WHO skipped over a few letters so now it is "Omicron". It is now officially on the WHO Variants of Concern (VOCs) list, namely the "most wanted". 

One now awaits the determination of vaccine efficacy and a new vaccine targeted at this.

Some Perspective

 For those who cannot grasp the problem with this variant I have depicted the changes from the original below. The red boxes are mutations in amino acids and the grey are deletions and blue insertions. This is what I feared almost 18 months ago and discussed early this year. This is a massive change.

The related table of amino acids is shown below. Many of the mutations in this variant are significant and mitigate any vaccine protection.

This becomes a "Wildfire" event as Michael Crichton had noted some fifty plus years ago. Allowing uncontrolled flow of putatively infected persons makes this a population killer bomb. Again our folks in DC are asleep at the switch. Close the borders, test and sequence, and if necessary quarantine aggressively. We need another Ellis Island, it worked a century ago, so why not again.

The New Nu Variant Can be a Killer

 The Nu variant which we discussed earlier well before the NY Times took notice, presents a clear and present danger. I have examined the spike protein and it may be a much more aggressive version. As the BBC notes:

UK Health Secretary Sajid Javid said from 12:00 GMT on Friday six countries would be added to the red list, with flights being temporarily banned.One expert described the variant, known as B.1.1.529, as "the worst one we've seen so far", and there is concern it has the potential to evade immunity.No cases have been confirmed in the UK.Only 59 confirmed cases have been identified in South Africa, Hong Kong and Botswana so far.

The cases have exploded in just a few hours. They continue:

It is the most heavily mutated variant so far and is now radically different to the form that emerged in Wuhan, China.That means vaccines, which were designed using the original, may not be as effective. And some of its mutations are known to increase the ability of coronaviruses to spread. But there have been many variants that looked bad on paper before, but haven't taken off. There are early signs this virus is spreading in South Africa and may already be in every province in the country. 

As such it may readily "leak" into the US via the open southern border. It spreads like wild fire and can during the winter season take over from Delta. They continue:

Scientists say the variant has 50 mutations overall and more than 30 on the spike protein, which is the target of most vaccines and the key the virus uses to unlock the doorway into our body's cells. Experts in South Africa have said the variant is "very different" to others that have circulated, with concerns that it could be more transmissible but also able to get around parts of the immune system.

We showed this earlier today. Thusfar there has been no response from the CDC and the NIH. It appears the CDC has taken a four day holiday! We know what happened last time when these bumblers saw the first locomotive coming on the tracks. This, folks, is a real problem, especially as we see the massive increases in vaccinated people.

Thanks for This?

 

The County is exploding with infections. Back to the peak last winter but now 95% are allegedly immune. So what is up? These are all Delta variants which look as if they bypass the Ab from the vaccine. The variant we showed earlier from Africa is a hundred times worse. As we noted a year ago now the vaccines should be tracking these variants. They are NOT. Thanks to the CDC! I never thought I would be commenting on this six months ago.

New Variant

 A new and significant COVID variant from Africa has emerged, B.1.1.529. The Guardian notes:

Scientists have said a new Covid variant that carries an “extremely high number” of mutations may drive further waves of disease by evading the body’s defences. Only 10 cases in three countries have been confirmed by genomic sequencing, but the variant has sparked serious concern among some researchers because a number of the mutations may help the virus evade immunity. The B.1.1.529 variant has 32 mutations in the spike protein, the part of the virus that most vaccines use to prime the immune system against Covid. Mutations in the spike protein can affect the virus’s ability to infect cells and spread, but also make it harder for immune cells to attack the pathogen.

The putative spike variants are:

 A67V, Δ69-70, T95I, G142D/Δ143-145, Δ211/L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493K, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F

These are very troubling. The spike protein now has a dramatically different conformation but does attach to ACE2 receptor but may most likely not be attached to the Ab generated by any vaccine. 

The only current action is to immediately quarantine the countries of outbreak. Otherwise we start all over again.

Nature notes:

Researchers in South Africa are racing to track the concerning rise of a new variant of the coronavirus that causes COVID-19. The variant harbours a large number of mutations found in other variants, including Delta, and it seems to be spreading quickly across South Africa. A top priority is to track the variant more closely as it spreads: it was first identified in Botswana this month and has turned up in travellers to Hong Kong from South Africa. Scientists are also trying to understand the variant’s properties, such as whether it can evade immune responses triggered by vaccines and whether it causes more or less severe disease than other variants do. “We’re flying at warp speed,” says Penny Moore, a virologist at the University of Witwatersrand in Johannesburg, whose lab is gauging the variant’s potential to dodge immunity from vaccines and previous infections. There are anecdotal reports of reinfections and cases in vaccinated individuals, but “at this stage it’s too early to tell anything,” Moore adds. “There’s a lot we don’t understand about this variant,” Richard Lessells, an infectious disease physician at the University of KwaZulu-Natal in Durban, South Africa, said at a press briefing organized by South Africa’s health department on 25 November. “The mutation profile gives us concern, but now we need to do the work to understand the significance of this variant and what it means for the response to the pandemic.”A World Health Organization (WHO) expert group will meet on 26 November, and will likely label the strain — currently known as B.1.1.529 — as a variant of concern or variant of interest...

 We really do not understand what this mutation does but it has been highly anticipated. As Nature notes:

The variant would likely be named Nu — the next available letter in the Greek naming system for coronavirus variants — if it is flagged by the WHO group.

 

NJ 2021 11 20

 Things are getting worse by the hour. There has been an explosion of cases almost all break through cases. So much for herd immunity and the vaccine. Why? We really do not know. That is the problem. Based upon what we do know this should not be happening. When things like this occur we get the chance to better understand the dynamics.

Let us start with the county. It is exploding and the prevalence is increasing fast. This is amazing given that we have exceptionally high immunization.

The State prevalence is also showing the same.

The incidence is on a hyper increase curve. In fact it appears to have exploded. Why? We really have no clue and almost all are immune!

The State shows a similar effect.

The doubling time is dropping demonstrating the effect as above.

Here is the doubling time per county. Strange Hudson is so high since it is the least vaccinated! Warren has high vaccination and low pop density. Makes no sense.

Town prevalence shows similar increase. These are ALL immunized people. Why do we now hear about this. I suggest re-instituting self precautions as we did at the beginning.

Town and County show similar results.

With comparable doubling times.

National vaccinations are running at good level.

Yet new infections to vulnerable remains high

This is my new curve. We discussed this before but now we have some data to show the immune are not immune and now dominate the infection base.

An Interesting Graph

 We have been examining the break through cases. So I thought that if we looked back using the CDC data and assuming:

1. The vulnerable have an incidence of 600 per 100,000 per week and the immune have a rate of 100 per 100,000 per week. That was the CDC data points. We also assume that this has held true since the beginning of this year.

2. We then calculated the number in each class and converted down to per day numbers.

3. We then plotted the 7 day running average of the CDC reported cases.

This is what we get:

Now this is confusing. 

1. First, the number of projected cases per day for the immune exceeds the number of cases per day for the vulnerable. Consistent with our prior observation. Immune people are NOT immune. Just not as bad as vulnerable. 

2. The actual daily 7 day averages equal what we see with the model only since about 1 September 2021. Before that there is a total miss. Why? Must be lower transmission rates. Namely 600 and 100 were lower.

3. So why do we see higher transmission rates as we get more vaccinated? No idea.

4. This vaccine/virus behaves like no other. In 1943 I got my smallpox immunization. Never went back. I have rabies, yellow fever, polio, and the list goes on. This virus however does not follow norms of virus/vaccine/immune system. Why?

5. Could one engineer a virus to act this way? Working on that question. Shame the Jesuitical Sophist has not addressed these issues.

Economics: Science, Art, Religion? Choose One

 I have dabbled in economics from time to time. The first thing I noted is that it uses mathematics to hide gross ignorance. Macroeconomics is especially prone to this. Lots of hand waving and assuming elephants had wings and then one is off to the circus.

Skidelsky has written an interesting piece. He notes:

The problem with quantitative easing (QE), quipped then-US Federal Reserve Chair Ben Bernanke in 2014 about the Fed’s bond-buying program, “is it works in practice but it doesn’t work in theory.” One could say the same about macroeconomic policy in general, in the sense that there is no robust theory behind it. Governments routinely “stimulate” the economy to “fight” unemployment, but with a theory that denies there is any unemployment to fight. 

 Macros generate tons of large scale data and then they try to understand this data via modela which may or may not be verifiable. Their models assume human behavior models which all too often are wanting. He continues:

The key assumption here is that everyone optimizes: they choose the best available option for themselves. Work is always available at some price. Therefore, unemployment is optimal for the unemployed. Given the assumption, the logic is unassailable. 

He proceeds as follows:

The relationship between theory and practice is thus not as Bernanke saw it. Monetary policy works in theory but not in practice; fiscal policy works in practice but not in theory. Fiscal Keynesianism is still a policy in search of a theory. Acemoglu, Laibson, and List supply a piece of the missing theory when they note that shocks are “hard to predict.” Keynes would have said they are impossible to predict, which is why he rejected the standard view that economies are cyclically stable in the absence of shocks (which is as useless as saying that leaves don’t flutter in the absence of wind). 

Theories after theories. We are now facing and  massive macro upheaval and it appears that having no rudder, compass, and not even seeing the sunlight, we sail ahead possibly over the abyss. 

Amazon: Down the River in a Leaky Boat

 Some wizard ( read in my world "moron") at Amazon has introduced a double security system where they send you a code on your cell. First it assume you have one. Second, I have tried fifty times to get the code but no luck. No call back to mobile! Blocked out of Amazon just at the start of shopping. And no way to remedy. That is what happens when a company does not care a wit about its customers! Shame...

Breakthroughs and the CDC

 The CDC kind of gives some insight to breakthroughs. Here goes. It is a bit confusing but it reads something like this.

1. Incidence in unvaccinated is about 600 per 100,000 per week? 

2. Incidence in vaccinated is about 100 per 100,000 per week. Not really but that is what they say, I think. 

Also this is mid September data listed mid October and it is now mid November. Horrible way to steer a ship! But alas it is the FEDs.

Now a quick calculation:

1. Assume 500,000 people, say Morris County

2. Assume 80% vaccinated and 10% previously infected. Close and you may win a cigar!

3. Then we would have 90% "immune" and 10% vulnerable

4. Thus we have 100 times 4.5 per week from the immune pool or 450 and 600 times 0.5 from the vulnerable pool or 300. Thus we have 1.5 times the infections from those immune than from vulnerable. 

This calculation tells us a great deal as to how to handle the current plague. It is NOT the vulnerable it is the "immune". 

This virus almost seems engineered to be evasive. Wonder why?

More Breakthrough

 

The State finally released data. Above is the County showing massive breakthrough infections. Frankly we really do not understand the breakthroughs. Vaccinated and previously infected should have antibodies but still we see infections. Death rates in this class are 2-3%. It appears the only remedy is post-infection antivirals, almost over the counter treatments. In many ways this is unlike other viral infections. Wonder why? Engineered that way? Stay tuned.......

NJ 2021 11 13

 We do not have today's NJ data. I guess they are asleep again in Trenton.Let us start with deaths. Frankly they are high given the base of vaccinated and naturally immune. Not at bad as when they were killing off the LTC residents but still nothing to pass off.

The county incidence is exploding. One suspects that most are breakthroughs! But as with the State and worse with the CDC there is no data! A Public Health disaster.

The State incidence also is increasing.

Strangely vaccinations are increasing but that is most likely the Feds demands. Wait till people find out the lack of efficacy.

The normalized incidence is still high. This should be the canary in the coal mine measure. I suspect we shall see this increase as well.

The town is also exploding. 80% of the people over 12 are vaccinated in the town. Plus 12% previously infected. There MUST be reinfections! Given the death rates they are also just as deadly despite what the powers to be say.

One can see the town doubling time drop.

and the town prevalence increase. I see people walking around as if it is all over. It has just begun AGAIN!

Rosa Luxemburg: A Hagiography

Mills book on Luxemburg is a bit of a challenge. I first got introduced to Rosa Luxemburg in the late 60s in Cambridge when I was first teaching at MIT. My office was in the old wooden Building 20, and one night allegedly the Rosa Luxemburg chapter of SDS attempted to burn the building down, with me in it. My second exposure was in the late 90s with my Polish partners in Warsaw, several early Solidarity members who had been imprisoned by the Soviets, and there I was lectured about Luxemburg’s less that sterling image. Later my Russian partners had similar feelings. Thus it became important to better understand this person. Who was this person that could become the flag bearer of those seeking to overthrow governments and yet be so despised by regular Poles and former Communists.

There are many bios of Luxemburg and Mills adds to this pile. Unlike all other bios, which follow the tried and true path of facts and time, Mills is a combination hagiography and polemic. Her book is one of unending praise for Luxemburg while at the same time telling the reader what they should believe. For example, on p 180 in the very last sentence she states:

“See that you join Rosa Luxemburg’s march.”

I have never seen a biography ending with commands! But that appears to be the way of Mills.

Now as to the book itself.

P 33 The author makes the assertion that there was a false claim regarding the success of capitalism in Germany in the late 19^th century. There seems to be no basis for this claim other that the author’s assertion of it being factual. In reality is demands a clear definition of what capitalism meant, then and now, and then in Germany at that time one would question it given the overbearing political environment. Germany was not England.

Pp 36-37 Here the authors spends time inserting Marxist historical determinism. This concept has always been a difficult one and in fact it often got Soviet mathematicians in trouble when dealing with stochastic processes. Reality is uncertain and deterministic historical movements, Marxism being one, have been challenged by the random occurrence of events. History is neither preordained nor predictable.

P 95 The author asserts a statement by Luxemburg that capitalism is the first form of economy with propagandist power. It is not readily obvious that such is the case. One may argue that the rule of the Church under the two swords construct for almost a millennium was an exercise of a propagandist and a structured economy. I admit that may be a bridge too far but it may have some merit in the underlying historical facts.

P 140 The author presents classic Luxemburg polemic when she quotes: “Imperialism or Socialism. War or Revolution. There is no third way.” This is a classic example of Luxemburg and her treatment of extremes. Luxemburg was also a pure internationalist, eschewing any form of nationalism. That was also one the sore points between her and the Soviets.

P 142 The author provides one of the more interesting quotes of Luxemburg. Namely, “Freedom is always and exclusively freedom for one who thinks differently.”  This has been a challenge for many who differed from Luxemburg, for she asserts that freedom of thought is sine qua non, but then again ….

P 151 The authors presents a brief discussion of the Spartacus League. Frankly it may be worth a full chapter.

P 173 The author conflates Luxemburg and Arendt. I find that a difficult match. If one reads Arendt and Revolutions one perceives a great appreciation for the American revolution and her disdain for the French and in turn for the Russian.

To provide a personal bent on this book, one should know that my grandmother was the head of the Socialist Party in New York, ran for Congress in 1916, jailed and tortured by Wilson’s people in 1917 for seeking women’s right to vote and continued active through 1922. I grew up with her so I have first hand knowledge of Socialists. However, she was neither a Communist nor a Marxist. Thus, I find the author’s intertwining of Socialist ideas and Marxist rhetoric a further complication in reading this book.

The book is less a biography and more a person’s journey understanding Luxemburg. If it had been presented as such then there would not have been such an ambiguity of expectations on the part of the reader.