CDC Headquarters in Atlanta by Ribastank courtesy of pixabay.com
What happened to the CDC (Centers for Disease Control and Prevention)? It appears that political loyalty to the person of the Commander in Chief has elbowed aside scientific expertise and is causing terminal dysfunction in an organization that should be at the spear-tip of the global response to the SARS-CoV-2 pandemic. American cooperation with the WHO (World Health Organization) is in jeopardy due to a political calculation by a chief executive with his eyes on re-election in November instead of on a robust response to a global pandemic that has already killed nearly 100,000 Americans and is sure to exceed that total by the first of June.
First, just so you know: scientists at Harvard Medical School in Boston (with nine monkeys) replicated a Chinese study published in March (with four monkeys) that shows rhesus macaque monkeys definitely develop complete immunity to re-infection with SARS-CoV-2. The scattered reports of “re-occurrence” of infection appear to be in error.
I apologize in advance for the length of this post. Please be seated and have a stimulating beverage on your table.
It is not widely known among Americans, but the US-CDC has been a model for government agencies in countries around the world. The US government agency was so widely revered that its organization has been copied everywhere. The agency proudly states that they support other countries in their efforts against many serious diseases, particularly Ebola, HIV, tuberculosis, and malaria (the latter two are the diseases that kill the most people around the world every year, just not in the US).
According to the Wall Street Journal (WSJ) in 2018, “The CDC currently works in 49 countries as part of an initiative called the global health security agenda, to prevent, detect and respond to dangerous infectious disease threats. … The package included $582 million in funds to work with countries around the world after the Ebola crisis in 2014 and 2015.” Obviously that changed with the current administration and its emphasis on “America First”. That leads directly to the answer to our question, “What happened at the CDC?”
The obvious problems in this pandemic started with the CDC’s decision not to use the SARS-CoV-2 antigen test that had been developed by the World Health Organization (WHO) and is being used in virtually every other country in the world. Instead, they decided to develop their own test. The test was first announced on February 3, and received Food and Drug Agency (FDA) Emergency Use Authorization (EUA) on February 4. The EUA followed the announcement of a public health emergency on January 31.
At first, they did everything right: they created a real-time reverse transcriptase polymerase chain reaction (RT-PCR) test that had three components: one to identify the virus’ nucleocapsid gene one, one for nucleocapsid gene two, and one to identify human RNA-ase gene P. Problems arose with the third component, which was contaminated when the test was scaled up for production by a separate lab.
The problems with contamination in the mass-produced kit made by International Reagent Resource (IRR) made the test unusable. Apparently, appropriate procedures were not followed in production and the same isolation hood was used for two separate processes, contaminating a reagent with human DNA. These problems were not corrected for weeks. Since this test was the only one authorized by the FDA, no other clinical lab (even the ones that created their own tests) could legally test for COVID-19 during this period– most of the month of February, a critical blind spot, as it turned out.
The absence of a test made it appear as if there were no cases of COVID-19 in the US– despite the fact that labs knew full well that there were many patients who had the infection, due to their use of unapproved tests (but could not legally say so). Research labs that did testing on non-clinical specimens, that is, tests that didn’t identify the patients that the samples came from, knew that there were cases. At this time, there was plenty of influenza-like illness (ILI or just “flu”) to be had at clinics and emergency rooms, so early cases were dismissed as “flu”.
Only when the patient tested negative for actual influenza and other respiratory viruses did doctors have any notion that they were dealing with a new entity (although they suspected exactly that). If you’ve gone to the doctor for the flu, you know that ordinarily little or no testing is done. If you’re lucky, you’ll get a rapid test for strep throat (which you should because ten percent of sore throats are strep). You won’t get a test for influenza, although they are available. Nor will you get a test for the common coronaviruses that cause “colds” even thought these are also available. You most certainly won’t get an acute serum blood test drawn to be saved for comparison to a test two weeks from now when you recover– how is the doctor going to justify that to the insurance company?? (I used to do that when I worked at a government clinic for Native Americans– but I was the only one.)
Now we have information that makes this month of February appear appear truly critical. The first known case of COVID-19 in the US was in a patient who self-identified as being a novel coronavirus case (he read about the WHO alert in the paper) and came directly from Wuhan (the source of the outbreak)– he was hospitalized on January 21 and his case appeared in the New England Journal of Medicine (NEJM) on January 31. The first known death from the new virus in the USA occurred in Santa Clara County, California on February 6 and was retrospectively identified by autopsy (which also showed the terminal event to be a massive myocardial infarction, a heart attack) — but this wasn’t announced until April 22.
Thousands of travellers to and from Wuhan, China entered and left the US between December and the end of January (when flights from China were stopped by presidential order, except for US citizens and their dependents). We now suspect that many of these travellers were carriers of the new virus. Travellers from the epicenter also went to Europe and seeded the infection there; the outbreak in New York actually began with a European variant of the virus rather than directly from China.
In the meantime, the CDC was asleep at the switch. I suspect that the agency had been neutered by political appointees from the present administration, who sabotaged its functioning. I have no evidence for this suspicion, just a feeling. Of course, I trust my own feelings so much more than I trust the feelings of our current Commander in Chief. This is because my feelings are informed by scientific information instead of real-estate information (whatever real-estate information is, or whatever Fred transmitted to his son and heir).
I could be wrong. Judge for yourself.
The CDC created a “guide to re-opening” which wasn’t acceptable to the Commander because it was “overly prescriptive”. It wasn’t released. Instead, a pared-down, dumbed-down version consisting mostly of pictures and simple diagrams was given out, missing a critical component: advice to houses of worship. Even this watered-down guide is being misapplied and isn’t being followed. Apparently the Commander’s real objection to the CDC’s guide was that it told churches what to do– a no-no to his evangelical base, who only take orders from G_d.
Worst of all: I learned today, in a highly critical article from the Atlantic (titled “How could the CDC make that mistake?”) that the CDC has been conflating (mixing together) two different types of tests for the new virus: the antigen test, described above, and the newer antibody test. The two tests give completely different information and have different levels of sensitivity and specificity. The antigen test identifies acutely infected people starting a couple of days before symptoms begin (if symptoms occur at all): when contagiousness starts. The antigen test continues to show positive for variable periods, generally about two weeks after infection has begun. The antibody test, on the other hand, only becomes positive roughly two weeks after infection and stays positive for months, probably a year or more.
The antigen test is extremely specific, in part due to its careful makeup: it tests for two different parts of the new virus’ genome and controls for the presence of human genes. It should be extremely sensitive, due to its inherent nature: a polymerase chain reaction is able to magnify and identify incredibly tiny quantities of genetic material. Reports available early in the pandemic revealed that, in actual use, the test only identified 72% of actually infected patients when compared to tests using fluid obtained directly from the bronchi and lungs. This fact has been glossed over, but has re-surfaced in criticism of the new rapid test used in the White House. Claims appeared after two aides tested positive that the rapid test missed as much as half of the actually infected patients. Those claims may be exaggerated, but it has not been widely understood that the antigen test is not as sensitive as we would wish it to be.
The antibody test is not as specific as the antigen test: there are circumstances, particularly when the infection is rare, in which the antibody test will be false-positive. The antibody test also may not be as sensitive as we would want: some patients who have recovered may never show antibodies. The antibody test is probably more sensitive than the antigen test. We are also not sure that the presence of antibodies (or recovery from the infection) confers immunity to a repeat infection, although studies in rhesus macaque monkeys both in China and here in Boston do show immunity.
The problem with conflating these two tests in announcements is that they measure two different things. They should be announced separately so we can have a clear idea that “this is the number of acute cases we have identified” and “this is the number of resolved cases we have identified”. The problem with the CDC appears to be that some naive individuals involved in compiling test results for announcement don’t understand the difference and want to inflate the number of tests performed at the same time as they reduce the percentage of positive tests– for the publicity. The same is true of several states that are doing the same thing (although some states corrected this when it was pointed out to them) — see the Atlantic article for details.
A separate problem, in Georgia, appears highly motivated: on a day they announced “re-opening”, Georgian officials displayed a graph that showed the dates all mixed up– with the result that the positive test results appeared to be going down daily when in fact they were fluctuating randomly.
This problem, the presence of naive individuals who clearly don’t know what they are doing, is typical of the current administration. People are being selected for jobs based on their particular political loyalties rather than their expertise. There is a shortage of people with actual expertise who have the desired loyalties. The result is that people who have no experience in the needed areas are doing jobs for which they are not qualified and they are, to put it bluntly, screwing up.
I apologize again for the length of this post, but I have tried to put the point in the first paragraph: the CDC is being sidelined in a crisis when the expertise of their nonpolitical employees is really needed. People who know what they are doing are being fired or transferred, almost literally, to the Aleutians (America’s Siberia, if you will). Richard Bright, who has filed a “whistleblower complaint”, is only one example.
Need I go on? I believe I have made my point.
photo by AtlantaMomoFive courtesy of pixabay.com
Franklin Delano Roosevelt (the president we need now) was a famous sufferer of paralytic poliomyelitis. He lost the ability to walk and spent years recuperating. He was an adult when he came down with the disease, unlike the average patient, who is usually under five years of age. He also took up stamp collecting because of his illness… but that’s another story.
There are some odd, little known parallels between poliovirus and the novel coronavirus– Sars-CoV-2 (which causes CoViD-19)– parallels with which I was unaware until I looked up the symptoms of polio while watching the movie about Sister Kenny, an Australian nurse who revolutionized the treatment of polio before and after WW I. First, polio is “defined” as “paralytic poliomyelitis”, which excludes asymptomatic and nonparalytic infections with the poliovirus. Second, polio infection is actually asymptomatic in most cases. If I remember correctly after perusing the various sources available to Google on my phone while watching the movie (OK, not the best way to retain the information, I grant): only about 0.5 percent of polio cases involve weakness or paralysis.
Most commonly, polio weakness affects the legs, but then it can also affect the head, neck, and diaphragm. “In those with muscle weakness, about 2 to 5 percent of children and 15 to 30 percent of adults die” (based on an authoritative textbook, as quoted from Wikipedia). Some 70 to 75 percent of people with polio infection have no symptoms; most of the rest have “minor” effects such as fever, chills, sore throat; “up to 5 percent have headache, neck stiffness and pains in the arms and legs.”
Thus, the picture presented in the movie of children moaning with pain and having stiffness is accurate; most of these patients will recover fully within two weeks. Again, only half of one percent of infected patients (say, ten percent of those with headache, stiffness, and pain) will go on to develop weakness or paralysis. One of the more lately realized effects of polio is called “post-polio syndrome” in which patients with stable weakness develop additional problems many years later (5 to 20 or more years). These patients will have increasing weakness in the same areas as before, with spreading of the weakness and concomitant fatigue and depression.
Parenthetically, my father suffered from polio when he was about 18; he was left with a withered calf and later developed osteoporosis in the affected lower leg. He tried to hide the condition but no longer was able to participate in vigorous sports. Previously, he had gained his high school diploma by playing tight end on a football team in Texas for one season (this was despite never having attended high school). He had also participated in professional boxing at a low level as a teenager. This was one reason why he never played catch with me or taught me to bat.
Anyway, to the comparison with the novel coronavirus: as you should know by now, it appears that many cases of this virus are asymptomatic. The exact percentage is not yet known, but may be between 25 and 50 percent, or more– we just don’t know. The milder manifestations of the new virus are also similar: fever, headache, sore throat. Here the differences begin: polio doesn’t appear to ever cause a cough. Polio apparently can cause diarrhea, abdominal pain, nausea, and vomiting, although this is not prominent. The new virus can sometimes cause gastrointestinal symptoms as well.
Transmission of polio is primarily by the fecal-oral route, that is, the virus is passed in stool and infects others through contamination of water supplies. The new virus is also passed in stool, but this doesn’t appear to be a primary method of transmission, perhaps because sanitation is so much better now than it was in the heyday of polio. The new virus is primarily passed from person to person by breathing in the oral/tracheal secretions of others, passed in the air through coughing and even talking or just breathing. The new virus survives on surfaces for a time and can be passed in this way, although I doubt if this is a major route if everyone washes their hands and refrains from touching their faces every five minutes (I’m joking, ok?)
So here we have two viral infections that are or were epidemic; both are primarily asymptomatic (although this was not known in years past), making it appear that paralytic polio was a rare disease. The harmful effects of polio are well known, and the stereotype is that of an affected person left with permanent paralysis and a withered leg or surviving in an “iron lung”. I wonder how long it will be before we see persons affected by severe coronavirus living in iron lungs for a month or more… a while, because there just aren’t too many iron lungs available. In all this work at building makeshift ventilators, I have not seen anyone just go back to the old iron lungs; perhaps they don’t remember.
That’s enough about polio. Except that there are two excellent vaccines available, one a killed/inactivated virus, the other a mutated live virus. The live virus vaccine is used in developing countries where the incidence of polio is higher and sanitary water facilities are hard to come by. The advantage of the live virus vaccine is that it spreads through the same route as the wild virus and thus can afford protection to people who drink contaminated water and are thus exposed. The disadvantage is that sometimes the virus mutates back to a more harmful form and then causes the same disease it was designed to protect against. Polio is so rare in this country (the US) that the mutation event is considered more harmful, and more common, than exposure to the wild virus– thus it is safer to give the killed virus vaccine despite its weaker protection levels.
As yet there is no vaccine available against the novel coronavirus. That will change, probably in less than a year. There was opposition to the polio vaccine, too, but it has been forgotten– I don’t think the opposition to the CoViD vaccine will be forgotten.
Coronavirus by Engin Akyurt via pixabay.com (open access)
From the New York Times: “On Facebook, “Plandemic” was liked, commented on or shared nearly 2.5 million times, according to the CrowdTangle data.” The NYT counted over 8 million views of the video. This is absurd and dangerous. Judy Mikovits went from being a graduate student to tending bar, to working for a Las Vegas millionaire who wanted to research chronic fatigue syndrome because she had a relative with the disorder. She was fired from that position, arrested for stealing her lab notebooks from work, and released without charges after the multi-millionaire husband was investigated for fraudulently contributing to a political campaign.
At loose ends, she cast about for a new way to make ends meet. She discovered fringe publishing, writing two books which she arranged for a self-publishing firm to produce. She hit the jackpot with the second book, in part because of the pandemic. She used her expertise in virology to advance a fringe theory about vaccines: that they were contaminated with retroviruses. This idea fit the agendas of “anti-vaxxers”– a group of people opposed to the use of vaccination to prevent (mostly) childhood scourges such as measles, mumps, and polio.
This idea took root in her research for the millionaire family that wanted to find a cause for chronic fatigue syndrome (also known as “myalgic encephalomyelitis”). This poorly understood syndrome has a series of baffling and disabling symptoms that wax and wane over years: fatigue, weakness, intolerance to exercise with exacerbation of symptoms, muscle pain (myalgia), and other relapsing symptoms such as fever, sore throat, swelling of lymph nodes in the neck, and so on. Many of these symptoms are shared with other disorders of known cause. For example, mononucleosis (caused by a known virus) causes fever, sore throat, and marked cervical (neck) lymph node swellings, followed by weeks or months of fatigue, especially in teenagers, and is popularly known as “the kissing disease” because it is particularly prevalent in early adolescence.
Here is a list of symptoms, from health.harvard.edu:
The most prominent symptom of chronic fatigue syndrome is an unexplained feeling of fatigue, which is not relieved by rest. This fatigue is severe enough to decrease a person’s activity level at home, work or school by 50% or more. In addition, the diagnosis requires that patients should have at least four of the following symptoms that also are present for at least six months:
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Impaired concentration or short-term memory, severe enough to affect routine activities at home, work, school or social functions
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Sore throat
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Enlarged lymph nodes (swollen glands) in the neck or underarm area
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Muscle pain
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Pain in several joints, with no redness or swelling
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Headaches that are different in some way: a new type of headache pain, a new pattern of headaches or headaches that are more severe than before
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Sleep that doesn’t refresh, or not feeling rested on waking
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An extreme reaction to exertion: feeling sick after exercise or strenuous activity, often not starting until the next day
The syndrome of “myalgic encephalomyelitis” has been much-studied, with little result. Ms. Mikovits’ contribution, published in 2011 but later retracted, was to blame a mouse retrovirus. The paper was retracted because all of her samples were contaminated with this virus, for unknown reasons. (Retroviruses are known to be an abstruse type of virus that integrates its genome into the DNA of its host, ensuring that it is transmitted to all descendants of the infected cell. Retroviruses do not directly cause cell death and are compatible with long-term survival of the host. They can cause cancer in some cases.) To date, no known cause for “myalgic encephalomyelitis” has been established with any certainty, and the condition remains frustratingly real but beyond the grasp of medical science to unravel.
Enter the pandemic. The video “Plandemic” was produced by a hitherto little-known videographer who shall remain nameless here. It was widely publicized and struck a nerve because it made some serious (but unfounded) charges in regard to both the novel coronavirus and vaccination. As mentioned, it has been viewed over eight million times, before and since being taken down from Facebook as being full of misinformation. Other authors have refuted its charges point by point; factcheck.org pops up first when I Google “refutation of plandemic” but there are many others. One of the reasons for the video’s popularity is that it includes just enough truth and half-truth to resound with skeptics and people with low information levels.
I don’t know how much money Ms. Mikovits has made off of this second book or the video but I’m sure it’s substantial, more than me. I can’t help but feel a little envious of her “success” and worse than that, it comes at the expense of truth and perhaps some people’s health. Karma will certainly catch up, but don’t hold your breath waiting.
Gandhara Buddha circa 1900 years ago, courtesy of wikimedia commons
Wikipedia: “In Buddhism, the three marks of existence are three characteristics (Pali: tilakkhaṇa; Sanskrit: त्रिलक्षण, trilakṣaṇa) of all existence and beings, namely impermanence (aniccā), unsatisfactoriness or suffering (duḥkha),and non-self (anattā).”
- Impermanence: simply, this means that everything changes. There is nothing which is constant. We want things to stay the same, but we know that they always change.
- Suffering: all that exists is “unsatisfactory” or “incapable of satisfying” or marked by suffering. We know that when we reach a goal, we find it unsatisfactory; most people set new goals when they discover that the ones they have reached are not satisfying. Most people do not stand back and realize that all their goals, the ones they have reached and the ones that they set, will not satisfy. If you were to realize that any goal could not satisfy you, perhaps you would stop making goals and decide to just live with it. Most people could not tolerate the idea of just living with the suffering; toleration is not in their nature. Instead, I will decide to tolerate the lack of satisfactoriness and live with suffering.
- Non-self: this means that there is no permanent, unchanging soul. We ourselves feel as if we are always the same person, but we are not. This is liberating if we can really feel it– if we do not change, we will feel regret for what we have done wrong in the past.
Each of these three “marks of existence” is characterized by change: nothing stays the same, no goal can satisfy you, and you are not a permanent, unchanging person.
Change is difficult to live with. We want things to stay the same. If things were always the same, they would be easier to understand and work with. Instead, we are forced to live with change against our wills.
The Four Noble Truths:
- Suffering is an innate characteristic of the world.
- Suffering results from attachment to the world or desire/craving.
- Suffering can be ended by renouncing attachment or desire.
- The Noble Eightfold Path leads to renouncement of desire and the end of suffering.
The Noble Eightfold Path:
- Right view. Our actions have consequences into the next life; death is not the end– there is rebirth (there are three worlds in Buddhism: life, hell/underworld, heaven).
- Right resolve. (Intention/aspiration/motivation) Here the monastic gives up home and adopts the life of a mendicant.
- RIght speech. No lying, no rudeness, no gossip (telling one person what another says about him to cause discord or harm their relationship with one another).
- Right conduct. No killing, no stealing, no sexual misconduct. Here the monastic gives up sex altogether.
- Right livelihood. Gain your livelihood by benefiting others; don’t sell weapons, poisons, or intoxicants. The monastic lives by begging and accepts only what he/she needs.
- Right effort. Try to restrain your senses; generate wholesome states (the seven factors of awakening) and prevent unwholesome states (including the five hindrances).
- Right mindfulness. Never be absent-minded; always be conscious of what you are doing.
- Right meditation. Concentrate on one point and aim at insight.
These practices are said to lead you to liberation from the painful cycle of death and rebirth. Working on this makes you a Bodhisattva on the path to Buddhahood (a very, very, very long path).
The seven factors of awakening that lead to enlightenment:
- Mindfulness. Maintain awareness of reality (dharma).
- Investigation. Investigate the nature of reality.
- Energy or determination/effort.
- Joy or rapture.
- Relaxation or tranquility.
- Concentration. A calm, one-pointed state of mind or clear awareness.
- Equanimity. To accept reality as it is without craving or aversion.
Wikipedia: “In the Samyutta Nikaya’s “Fire Discourse,” the Buddha identifies that mindfulness is “always useful” (sabbatthika); while, when one’s mind is sluggish, one should develop the enlightenment factors of investigation, energy and joy; and, when one’s mind is excited, one should develop the enlightenment factors of tranquility, concentration and equanimity.”
The five hindrances:
- Sensual pleasure.
- Ill-will.
- Sloth or torpor.
- Restlessness or worry.
- Doubt.
The four Virtues, immeasurables or infinite minds:
- Loving kindness.
- Compassion.
- Sympathetic joy.
- Equanimity.
There is clearly some overlap here: equanimity is listed as one of the seven factors that lead to enlightenment as well as one of the four Virtues. I think that there may be two or more senses of the word equanimity. “Joy or rapture” as one of the seven factors is also listed under “Sympathetic joy” for, I think, similar reasons.
I’m giving these lists as a shorthand way to explain what the Buddhists were trying to convey and what Buddha said; words are never sufficient to convey the concepts that are described. The path of liberation from the cycle of birth and death is subtle and complex, and mere descriptions are not enough to set you on that path.
There is also room for argument: there is no clear evidence for such a thing as a cycle, no evidence for rebirth, no evidence for heaven or hell. Our lives lead in a straight line from birth to death, and death appears to be the end of everything for each one of us. If one is a Buddhist, one accepts on faith that there is a cycle.
There is also logic in rolling everything up this way: otherwise, one would be free to do evil and try to get away with it– and doing good without getting a benefit means there’s no reward. Adding the cycle into one’s reckoning means that one can never “get away” with anything, and if one’s good deeds are not rewarded now, they will be later.
Those are my thoughts on the subject, briefly. I’m getting close to my self-imposed one-thousand-word limit, so I’ll have to continue this later.
pollution by marcinjozwiak courtesy of pixabay.com
From Nature Climate Change on May 19:
Daily global CO2 emissions decreased by –17% (–11 to –25% for ±1σ) by early April 2020 compared with the mean 2019 levels, just under half from changes in surface transport. At their peak, emissions in individual countries decreased by –26% on average. The impact on 2020 annual emissions depends on the duration of the confinement, with a low estimate of –4% (–2 to –7%) if prepandemic [sic] conditions return by mid-June, and a high estimate of –7% (–3 to –13%) if some restrictions remain worldwide until the end of 2020.
We see a lesson here. Surface transportation is responsible for a large proportion of climate-changing gases emitted into the atmosphere. If we were to transition to electric-powered (or even hydrogen-powered) vehicles for getting about, we would see a dramatic decrease in greenhouse gas emissions. If not, we will continue to suffer the effects.
Another problem: fires in the sub-arctic regions of Russia (Siberia) are increasing this spring. According to EcoWatch, 5 million acres are currently burning in Siberia and Eastern Russia. Last year saw an enormous number and size of fires as the permafrost thawed and humans were unable to control ignitions. Many of these fires are spontaneous, the result of lightning hitting dry vegetation. The existing fire control systems are not up to the task of stopping these fires, and the Russian economy is in such bad condition that it is unrealistic to expect any reinforcements. The remoteness of most of these fires also militates against control. These circumstances (the cratering Russian economy) are a result of the pandemic weakening oil prices, on which the Russians depend for foreign exchange. Thus, there is a negative effect of the pandemic on greenhouse gases as well as a positive effect from reduced vehicular activity.
(fiddler by Moshe Harosh courtesy of pixabay.com)
Today, the revival of “Comment of the Day” because I’m too lazy to write another post about the virus:
(By “noappforthat” in Washington Post, commenting on a column about the firing of the Inspector General for the State Department– which column appears to pin the firing on investigations that the IG has been doing about the $8 billion arms sale to the Kingdom of Saudi Arabia, OK’d by the State Department despite the murder and dismemberment of the renegade Kashoggi in the Saudi Embassy in Turkey… )
These petty details don’t matter. How about the illegal wars waged against Iran, China and Venezuela? How about the systematic undermining of international institutions from WHO, to the EU to NATO to the WTO? How about the 100,000+ dead Americans attributable to a combination of incompetence and deepening social inequalities? How about an administration loaded up with sycophants that openly engages in the worst forms of nepotism and cronyism, making even the worst tinpot dictatorships look like paragons of democracy and accountability? How about routine violations of the rule of law? Patent corruption? Abuse of powers? Undermining the independence of the judiciary? Radical worsening of income disparities and racism in America fuelled by toxic politics and right-wing policies? The debased and puerile reporting of it all? The US media and the political opposition wax indignant over various follies, insults and misdemeanours, opine on matters partisan and personal, and turn blind eyes to the complete failure of US democratic institutions, the vulgarity and venality of president and congress alike, and the disgraces that both the Democratic and Republic political parties have become. It isn’t the presidency in America that’s been taken ill; the entire nation is deeply diseased. Americans may not regard matters this way, but assuredly the rest of the world looking on does. A deeply flawed electoral process pitting an inept, decrepit and disgraced Biden against a buffoon incumbent will scarcely put things right. The presidential election is another symptom, not a cure.
That’s some pretty harsh sentiments! I would not go so hard on ex-Vice President Joe Biden, as he is the only electable alternative to He-who-must-not-be-named. Mr. Biden may not be a highly competent young man with vigor and verve, but he is an alternative. If you can’t see a difference, you are not paying attention. Remember that personalities count (that’s about the only thing that distinguishes the candidates, in fact). Mr. Biden’s personality is sweet and tolerant, whereas the other one is a sociopathic, malignant narcissist… and the “Democratic Socialist” Sanders is almost as much a narcissist as our buffoon-in-chief.
photo by WikiImages courtesy of pixabay.com
The sun goes through a more or less regular cycle of sunspots, from minimum to maximum and back again every eleven years. Sunspots are directly related to solar flares, in which gigantic balls of charged particles come shooting off the surface hundreds of millions of miles into space, right past and through the Earth in many cases. These balls of charged particles interfere with electrical systems on Earth, although they are somewhat attenuated by the atmosphere. These flares result in auroral displays– and the aurora borealis is something you should try to watch when you get the chance. Unfortunately, you won’t see any auroras for quite a while, as we are in a deep minimum right now.
Here’s a release from NASA in June 2017 that includes a nice picture of a solar maximum and minimum. It’s no longer being updated so it’s not of much help this year. Shouldn’t there be a story on NASA’s website about the solar minimum? You would think so, but then you’d be wrong.
Today, Newsweek ran a story describing the current minimum as a deep solar minimum– but referred to spaceweather.com, so going to that site, we find: a post from March 31 reminding us that we will not be able to determine when the solar minimum occurred for six months after it has passed. Although it was predicted for April 2020, we will not know for sure until October. By then, sunspots should have picked up at least a little. So far this year, according to Newsweek, there have been 104 days without sunspots– including the last five days, according to SILSO (Sunspot Index and Long term Solar Observations) (not secure site). Here’s the daily plot, which shows nothing since the first of May.
The last great solar minimum occurred between 1645 and 1715 and is known as the Maunder Minimum (see Wikipedia: solar minimum). “The Maunder Minimum occurred with a much longer period of lower-than-average European temperatures which is likely to have been primarily caused by volcanic activity.”
Solar “insolation” is reduced by 0.1% or so during a minimum and has no effect on Earth temperatures. Although sunspot activity was relatively high during the twentieth century, it had nothing to do with anthropogenic warming. What’s more, the current solar minimum has nothing to do with the current, uh, you know.
This post is intended as a distraction. I suggest, in particular, that you visit the NASA site linked above and spend some time looking at the sun (not directly, you understand, that would be unwise and certainly unpresidential) (can’t we leave Him out of at least one post? No.).
Coronavirus by Engin Akyurt via pixabay.com (open access)
Moderna announced results of Phase I clinical trials of a COVID-19 vaccine, resulting in a 700 point rise in the Dow stock market index. The announcement was carried on all the online news networks as well as print and television. A total of 45 humans received the vaccine, in three dosages: low, at 25 micrograms, medium, at 100 micrograms, and high, at 250 micrograms of lipid nanoparticles bearing mRNA transcripts for the coronavirus spike protein. The vaccine was given twice, at two-week intervals, with the first dose given in late March.
Two weeks after the second dose, 8 patients were tested at the low and medium doses for “neutralizing” antibodies (antibodies which were able to stop the virus from infecting human cells in a test tube), and all had sufficient levels. The antibody levels in four patients who received the 25 mcg dose were described as similar to the levels found in patients who had recovered from the natural illness caused by SARS-COV-2, and antibody levels in four patients who received 100 mcg exceeded those found in natural infection.
According to some media reports, a significant proportion of patients developed fever and other symptoms after receiving the vaccine. Three out of four patients who received the second 250 mcg dose had grade three (out of four) “systemic” reactions (serious but not “life-threatening”). Such adverse reactions are typical for vaccines but their frequency is concerning and will probably eliminate the 250 mcg dose from consideration.
Higher frequencies of such “systemic” adverse reactions militate against higher doses of the vaccine, which in turn limit its effectiveness. However, if a lower dose is settled on finally, more of the vaccine would be available for more patients.
These results clear Moderna to continue on to Phase II of clinical trials. These trials will be done in a larger group of patients– some 600. They will determine which dose is optimal for widespread adoption in Phase III, which will begin in July if all goes well in Phase II. The final phase will determine whether the vaccine is really effective in stopping natural infections and the illness COVID-19 in the wild.
A news release from NIH (the National Institutes of Health) on March 16 announced the commencement of phase I clinical trials for this vaccine, mRNA-1273. The news release described it as being a fruit of previous research with coronaviruses, specifically the ones which caused SARS and MERS. The vaccine consists of messenger RNA (mRNA), which is actually the cell’s own normal method for producing proteins; mRNA is translated within the cell into the spike protein of the virus’ envelope with which it attaches to the outside of cells.
The mRNA is enclosed within a lipid nanoparticle; this lipid is like the cell’s own envelope and allows the mRNA to enter a cell. Injecting this will induce the person’s cells to produce the spike protein, which will in turn stimulate an antibody response. The antibody will attach to any spike proteins in circulation; if the affected spike protein is attached to a virus the antibody will physically block the virus from invading cells.
When inducing immunity in this fashion, there is always a risk that the presence of circulating spike protein will cause a reaction identical to that which occurs during a natural infection: fever, chills, body-aches, and so on. The scientists would be surprised if there were not at least some level of “systemic” reaction of this nature.
Due to the exigent circumstances, a greatly accelerated program has been planned which will include a much smaller number of patients than is usually recruited for Phase III studies. Once Phase III is completed– which will take 6 months– general distribution of the vaccine can begin. This is planned for January 2021. I expect that this timetable will be adhered to, for political reasons: the president has promised a vaccine by this date. Whether the results of the Phase III trials are good or not, the vaccine will be given out as scheduled.
A second vaccine was reported in an NIH release on May 15: a single dose of ChAdOx1 nCoV-19, an investigational vaccine against SARS-CoV-2, has protected six rhesus macaques from pneumonia caused by the virus. This vaccine was created at the University of Oxford. Human trials began on April 23. This vaccine uses a “replication-deficient” (unable to grow) adenovirus to carry a SARS-COV-2 protein, which induces an immune response. The results were reported on BioRxIv on May 13.
Another report, in Biospace on May 18, states that AstraZeneca will produce 30 million doses of this vaccine for the UK by September and 100 million by the end of the year. This would represent an example of a vaccine limited to a specific country– a thing that has been deplored by some.
There are over a hundred different vaccines somewhere in the pipeline, but only a total of eight have advanced far enough for clinical trials. According to Kyodo News on May 16, these eight vaccines include: Inovio in the US, Pfizer and BioNTech SE in Germany, and four in China. Another six vaccines are in preclinical evaluation in Japan.
Global News of Canada reported that Phase I trials of a Chinese vaccine produced by CanSino Biologics had begun on March 16 and that Phase II trials are underway; further trials in Canada had been approved by Prime Minister Trudeau as of the article’s date, May 16. The vaccine is called Ad5-nCoV and uses an adenovirus as well, like the one called ChAdOx1 nCoV-19. According to CTV News, this vaccine could be produced in Canada and China.
Apparently, vaccines of several types could be in use by early next year. Which vaccines are most successful remains to be seen, but the number of cases worldwide by then will be at least ten and possibly a hundred million.
Lancet: Investigation of an early outbreak of COVID-19 in Germany: their patients zero through five
Electron micrograph of SARS-COV-2 virions in vitro
Read this study in the Lancet from May 15: Investigation of a COVID-19 outbreak in Germany resulting from a single travel-associated primary case: a case series. Or, better yet, read the summary in the Medium coronavirus blog from this morning. This looks like a great coronavirus blog, and it has 18,000 followers, but I just found it today. So far behind.
Coronavirus by Engin Akyurt via pixabay.com (open access)
We earlier reported on a Stanford antibody prevalence study performed in early April and published on MedRxiv on April 14. This study, which included 3,300 people who had blood tests attempting to discern antibody to SARS-COV-2 (the agent which causes COVID-19), claimed that there were as many as 85 times as many infections as nasopharyngeal swab tests had ascertained. The greater number of infections reduced the case fatality rate (the proportion of infected people who die) to roughly 0.1%, closer to the rate observed with seasonal influenza (which has a case fatality rate of less than 0.1%).
The results of this study are a little hard to swallow because they seem to exaggerate the number of infections somewhat. Now, a whistleblower complains, as reported by Buzzfeed News on May 15, that the test used to detect the antibodies had a significant false-positive rate, making its estimates suspect. With the small percentage of subjects found to have positive results, the number of false-positive tests could have been double the number of true positives. In addition, the people who volunteered for the study likely thought they had been infected and wanted to be tested to confirm this: the recruitment information emphasized this.
The whistleblower states that the study was partially funded by the JetBlue Airways founder David Neeleman, and that he “sought out the study authors for their congruent policy views” and funded their work accordingly. They further state that Neeleman was in contact with the authors during the study, in part to encourage them to make conclusions that he supported (not a good way to do science). The research wound up being cited by those on the right wing (link to NYT opinion piece) who claimed that the severity of the novel coronavirus infection was overstated and that the period of shutdown was unwarranted. Some of those who used the study for support aired their views on Fox Business News.
If we use the study’s results more carefully, we discover that the actual number of people infected with the new virus in Santa Clara County is probably much smaller than they stated. The study states that 1.5% of the people studied had positive antibody tests, with a sensitivity of 82.8% and specificity of 99.5%, and after adjustment it calculated that 1.2% of the study’s patients were positive. After weighting for the population characteristics of the county, it states that approximately 2.8% (between 1.3 and 4.7%) of the people in the county had been infected with the virus. Since there were only 1,000 confirmed cases at that time and the test implied that there had been between 14,000 and 91,000 cases, the study concluded that there had been a vast undercount of cases.
While there had certainly been a dramatic undercount of virus cases for numerous reasons, including lack of access to tests and asymptomatic infections, the conclusion that was made was an exaggeration. Those who wanted the new virus to be less lethal jumped to the conclusion that, with the confirmed number of deaths, the death rate was as low as 0.1%. This is wrong because of the reasons mentioned before, as well as another reason: the confirmed number of deaths was also too low.
Since that study was released, the county coroner made news by indicating that the earliest known COVID-19 death had occurred in early February. This was based on tests conducted on autopsy cases of people who had died at home, and is, again, “only the tip of the iceberg.” Only a few of those at-home deaths have even been evaluated for the virus. Some of those who died were thought to have had “obvious” heart attacks or strokes, but we now know that SARS-COV-2 can actually bring on these terminal events.
A study of the Spanish population was recently released, as reported in El Pais on May 14. This study (with nearly 70,000 people tested) indicates that, overall, about 5% of the population of Spain, or 2.3 million people, have been infected with SARS-COV-2. The antibody prevalence ranged from 14.2% in Soria province, to 11.3% in Madrid, down to less than 2% in isolated regions. Since the confirmed number of cases was only about 230,000 (as of the date of the article), this means that 90% of the cases went uncounted. Based on the antibody percentage, the actual death rate, with 27,000 deaths, is between 1 and 1.2%.
In truth, we have seriously undercounted both the number of cases (by a factor of ten or more, not a factor of 50-85 times) and the number of deaths (by an unknown factor, but possibly less than double). Putting all this together, we can estimate that the real death rate is between 0.4 and 1.2%– less than the 6% previously suggested, but certainly far more than the rate we find with seasonal influenza (less than 0.1%).
There’s a lot of uncertainty surrounding the number of people who have had the virus, and some people are exploiting the uncertainty for political reasons. Those who want the death rate to be low so that we can stop “social distancing” and “safer at home” policies and “jump start” the economy are probably wrong. Most Americans sense this and are justifiably afraid to venture forth without more information about who has the virus and what we can do to avoid getting sick. We hope that the delusional optimists (who seem to be on the right-wing end of the political spectrum) do not consolidate control of the country.
Conrad Theodore Seitz 