Solipsist's Switcheroo

 Hi Loyal Readers of Solipsist's Soiree and hope you both are well,

Soso is moving to a more dependable (paying) gig at the Genetic Literacy Project (GLP), providing its formidable editing skills to that website, with additional possibilities of podcast creation in which case you will be treated to raspy Brooklyneese and snide commentary. If time remains, these unreliable posts will continue at blogspot, so keep tuned to this channel and please subscribe to GLP.  GLP, creation of Jon Entine, has an interesting slant on things, positioning itself to support science and inquiry against both left-wing and right-wing criticism.

Meantimes....

https://www.nytimes.com/2021/04/23/opinion/covid-germs-health.html

This is a link to a commentary from the Sunday Review section of the NYT and a worthy and relevant topic at this time noting the ascendancy to the Pantheon of hand sanitizers, Lysol fights for the remaining wipes at ShopRite and hoarding of cleaning supplies. Fomites is a fancy name for surfaces and research has shown that Covid-19 is unlikely to be transmitted by surfaces but that is not stopping people from clinging to pseudo-science and propagating false information. How will we feel safe every again? According to the commentary, "Some health experts are watching this ongoing onslaught with a mounting sense of dread. They fear that many of the measures we've employed to stop the virus, even some that are helpful and necessary, may pose a threat to human health in the long run if they continue." What they are referring to is our microbiota, the microbes that constitute our normal flora, which are probably more susceptible to this cleaning frenzy, than many viruses are.

B. Brett Finlay, author of the PNAS paper cited in the commentary calls getting rid of the good microbes (baby bacteria with bathwater) "collateral damage" and laments the major consequences to our health and immune systems if we do not start to live with germs again. This microbiome research is fairly recent and warrants keeping up with. There has been research indicating that children who grow up on farms and play in dirt have immune systems more resistant to challenges than those that play in sanitized environments. Auto-immune diseases are also being reevaluated in this context. The commentary concludes that the body is an ecosystem, "home to a vast and symbiotic ecosystem of organisms", which, when disrupted, suffers consequences. Reference is also made to the overuse of antibiotics in the pandemic, which they also attribute to "hygiene zealotry".

 

Vaccine Interregnum

 https://www.nytimes.com/2021/02/04/opinion/owling-nature.html

 SoSo back and half-vaxxed. Here is an op-ed piece about owls. An author finding owls for her owl-obsessed son using a mouse decoy. "Owling teaches patience: Rarely do we actually connect with an owl." Having read about the extermination of passenger pigeons, this is probably of great benefit to owls. The article introduced me to the word "crepuscular", meaning active at twilight, which was not a good movie.  "When we owl we return to our truest selves."  This is great prose. Coincidentally, Soso will be volunteering to lead an owl watch this month. "To owl is to have an experience that cannot be bought, cannot be imitated."

https://www.nytimes.com/2021/02/06/opinion/epidemic-invasive-species-trees.html

Still on the theme of the beauty of nature and sorrow at its loss or desecration, another op-ed piece from the NYT, this time about tree disease. I used to ask my students, "Which tree is dying of Dutch Elm Disease?" Invariably, the answer would be chestnut, oak or maple. The article is about diseases of chestnut, elm, ash and hemlock. Many of these trees are anchors of ecosystems. Rotting, sick trees release CO2 in the atmosphere at the same rate as wildfires do and they are thusly accelerating climate change. Trees cannot be immunized or move. They do have a sort of immune system, which explains how they can harbor many insect pests and still produce leaves. (I wish I could produce leaves.) And there is a lag period between the time tree plagues take hold and become noticeable. The spotted lanternfly, a non-native species of this area, has decimated orchards and vineyards.

 

VAXXED!

 https://www.nytimes.com/2021/01/12/opinion/world-covid-vaccines.html

This NYT OP-ED piece is about mismanagement in the pandemic. It is written by AIDS activists. Dr. Fauci has been getting a lot of credit, which may to some degree be deserved, for "telling it like it is" but I was around (and processing bloods from HIV patients) when the AIDS activists held his feet to the fire to get wide access to, and speed distribution of, experimental drugs . They were right and they won the war, although so many young people died that they lost the battle. The point now (as then) is that Biden (Bush, 20 years ago) should commandeer the government's resources to "make sure that countries with limited resources get medication" at that time to treat HIV, now to treat Covid-19.  Biden can establish an emergency organization to build vaccine-manufacturing plants and their components at scale. According to the article, it is easier to manufacture mRNA vaccines than other vaccine technologies. We should not only be relying on private industry's version of scaling but use public-private partnerships to build more manufacturing capacity. Authors say this can be done for less than $4 billion, which is less than the US government spends each day on Covid-relief, and averages out to $2 per dose. Viruses do not recognize borders and everyone must be protected. Where are our Covid- activists?

https://www.nytimes.com/2021/01/11/opinion/death-penalty-mental-disability.html

Another OP-ED NYT piece about death sentences for intellectually disabled people. This is illegal in the US yet judges and juries, clinicians and defense attorneys often do not understand intellectual disability. The writers reference Corey Johnson, whose abilities were that of an average elementary school student at age 24. It is complex. IQ tests measure intelligence in comparison to age-based reference groups and they have, curiously, risen over time. So older versions of tests can have inflated results when compared with population norms from times past. So the numbers should be normalized for this, which would indicate that Mr. Johnson is intellectually disabled. But the Appeals Court rejected the appeal to present evidence in court and if a stay is not granted he may. although intellectually disabled, be killed. 

https://www.nytimes.com/2021/01/16/world/europe/uk-coronavirus-variant.html

Back to Covid-19. Article in NYT about viral mutations in Britain. Mutations have been detected in the spike protein, which the virus uses to access cells which it can use to generate more viruses. A mutation was also identified in South African and Brazilian patients, which is supposedly making the virus able to more easily access cells and be transmitted from person to person. In March Britain began a viral sequencing effort. Up until that time it was assumed that it had a relatively slower mutation rate, which would lead one to think that virus might be defeated based on this characteristic. Brits are producing nearly half of the world's inventory of coronavirus sequences, which at this time is 165,000 genomes. Our country has to do better at sequencing. It can give us a better idea how the virus is spreading and also how to design new and better vaccines to defeat it. One mutation changes the shape of the spike protein; another makes the protein bind more tightly to human cells. B.1.1.7 is considered to be a new variant and it is possibly more transmissible. But it is not necessarily more lethal at least so far as research has shown. It is also possible that the  variant weakens the potency of vaccines. It is speculation but scientists imagine that this will be predominant version of the virus in US by March. 

Perihelion

 https://www.nytimes.com/2020/12/23/well/live/pulse-oximeter-black.html

A NYT article about a letter to the NEJM reporting on widespread inaccuracies in the determination of blood oxygenation using pulse oximeters in black patients. Pulse oximeters, which are widely used and which home-based Covid patients use to keep track of the level of oxygen in their blood detect oxygen  by shining light through the finger. Darker skin pigmentation affects the results. Oxygenated blood is bright cherry red and deoxygenated blood is darker, almost purple. Pigments are compounds that absorb light to varying extents. According to the article, the pigment in darker patients' skin "scatters the light around", reducing the signal. (When I did this with my students, one with black nail polish had an aberrant result.) This mainstay tool is used to determine how much oxygen a patient requires and whether they should be put into intensive care. There was an article in The Boston Review in August about racial disparities in pulse oximetry readings. In the article in the NYT, the reporter writes that the pulse oximeter indicated that the oxygen saturation level was between 92 and 96 percent when it was as low as 88%.

 

https://www.inquirer.com/health/coronavirus/covid19-mutation-british-colorado-spread-easily-vaccine-20201230.html

Article from the Inquirer about the new variants of Sars-CoV2 which are monopolizing the attention of the media. The hysteria in the headlines "70% more transmissible" belie the fact that the measures we are taking, some successful, some not in different cases, to avoid becoming infected and ill are the same in stopping the new variant as the strains of the virus we have been dealing with all year. And, we have dealt with other variants. The increase in transmission rate could also have been produced by human movement and random chance. Viruses mutate all of the time due to the selection pressure on the virus. Some of the mutations can make the virus more successful and some less so. Some mutations in the DNA do not produce any change in the amino acids of the viral proteins or change the viral characteristics, which include transmissibility. And only 50,000 cases in the US have had genomic sequencing of the virus. A problem would be if there is a mutation that causes a change in the amino acids in the spike protein. One reason is that the pcr, which tests for various DNA regions of the virus would not get a readout in this region, but another problem would be if the vaccines are made against the spike protein and the virus therefore evades the human immune response invoked by the vaccine. The article also quotes Susan Weiss, a coronavirus researcher at Penn. The number of mutations detected so far represent only 1% of the total 30,000 DNA bases in the virus.

https://www.nytimes.com/2020/12/23/science/covid-mink-animals.html

NYT article about the mink industry in Denmark, which killed all of its 17 million mink. Mink are the only non-human animal known to become severely ill and die from the virus. They have caught the virus from humans and passed it back. It was initially thought that the virus, which spilled over from people to minks and back seemed to carry mutations that made it more transmissible. Mink are unusual in their susceptibility to the virus. Stan Perlman, a coronavirus expert at the U of Iowa who does research with genetically engineered mice noted that ferrets, which like mink are members of the weasel family, get very mild disease, which wouldn't predict the severity of the disease in mink. The article notes that livestock kept in close proximity to humans have always been a source of disease exchange, both ways. Diphtheria, Influenza A, measles, mumps, pertussis, rotavirus, smallpox and TB are all diseases of temperate regions (like ours) that jumped to humans from animals.

https://www.nytimes.com/2020/12/15/todayspaper/quotation-of-the-day-rush-by-rich-countries-to-reserve-early-doses-leaves-the-poor-behind.html

NYT article about the wealthy countries having laid claim to more than half of the doses of the vaccine that came to market by the end of the year. This exposes the great inequality in the health system. According to the article, many poor nations expect to be able to vaccinate possibly 20% of their population during 2021 but the rich countries have reserved enough doses to immunize their population multiple times over. And it could take until 2024 for many nations in the developing world  to immunize their entire population. India will produce many more doses of the vaccine next year than any other county. The Serum Institute of India has contracts with AZ and Novavax vaccines and has promised India half of its output. The AZ vaccine is well-suited for poorer countries because it is less expensive and easier to store. Figure is from Nature magazine.

 

https://www.nytimes.com/2020/12/24/health/herd-immunity-covid-coronavirus.html

Herd immunity is a concept I teach in my writing class. This is an article by Don McNeil Jr about the adjustment of the figure calculated by experts from 60-70% upwards to a possible 85%. How is this explained?  Herd immunity is the proportion of the population that must acquire resistance to  Sars-Co-V2 either through infection or vaccination in order for the disease to fade away. At this proportion, vulnerable people (children who are not yet immunizable or immune-compromised people) are protected from infection or so it goes with measles, which has a high herd immunity (93%). Dr Fauci is now revealing that, since some people intend to refuse the vaccine, that it is near the figure for measles, or between 75-90%. Actual herd immunity numbers come from measuring how quickly in herds a disease spreads from one animal to another.  The Rnaught number reveals how many new victims each carrier of the virus infects and for Sars-Co-V2, it was estimated that this number was 3 from studies in China. From this calculation 2 out of 3 potential victims (67%) would have to be immunized in order for the carrier to infect fewer than 1 and the virus not propagate itself. This number was revised upwards in Wuhan because the number of victims of the first wave was undercounted. WHO scientists do not know which number is correct.  This experiment (meaning us) is ongoing.

https://www.nytimes.com/2020/12/29/health/dietary-guidelines-alcohol-sugar.html

A non-Covid article from NYT. This article describes a revision of scientists' dietary advice that Americans forgo sugar and alcohol. Dietary guidelines for Americans are revisited every 5 years. I had not heard of the "quarantine 15", which has to do with people drinking more alcohol and eating more junk food and therefore gaining weight. These new guidelines don't address this or the advice that since chronic diseases are on the increase, sugar and alcohol consumption should be reduced in order for people to remain healthy. More than 2/3 of Americans are overweight or obese and obesity, diabetes and other chronic conditions also increase the risk of developing severe Covid-19. The one drink a day recommendation from the Obama years does remain in place. And the new guidelines also say for the first time that children under two should avoid consuming added sugars, such as those in cereals and beverages. Marian Nestle, a food expert from NYU is "stunned" that the committee ignored the recommendations of the scientific committee they had appointed.

https://www.nytimes.com/2020/12/23/opinion/dna-caribbean-genocide.html

Another non-Covid article, this one is by David Reich, who is a genetics researcher at Harvard. Christopher Columbus (a non-scientist) estimated the population of Hispaniola (DR and Haiti) to be about 1.1 million people, but this figure has been contested. A publication in Nature magazine analyzing the DNA of ancient indigenous Caribbean people shows that there were no more than tens of thousands of people and that the estimates were off by an order of magnitude at least. In order to do this the DNA was obtained from skeletal remains. Reich analyzed the genomes of more than 260 people of the ancient Caribbean. A new scientific advance allowed "DNA cousins" in ancient genomes to be identified, figuring out whether two people share large segments of DNA inherited from a recent ancestor, like 23andMe and Ancestry.com do with living people. Reich's group found that within the 91 people whose genomes he sequenced there were 19 pairs of DNA cousins on different large islands, meaning that the entire population had to be very small: it would be impossible to find that random pairs of people had such a high probability of being related if the population were large. 

A Big Year of Science

Soso wishes the readers of The Solipsist's Soiree a Happy Christmas and New Year, masked, distant, virtual, etc. Elbow rubs and Soso's version of an oldie for you, updated, gratis a Petula Clark to the tune of "Downtown":

When you're alone and life is making you lonely 

You should never go downtown

When you've got worries, all the noise and the hurry
Seems to stress you out, stay home
Just listen to the music of the traffic in the city

Please avoid the sidewalks where the neon signs are pretty
Please wear a mask
The lights are much brighter here
You can forget all your troubles, forget all your cares

So stay home
Things will be great when there’s a vaccine
No finer place for sure, at home
Everything's waiting for you

Don't hang around and let your problems surround you
There are movie shows online
Maybe you know some little places to go to
Where they never close: don’t go

Just listen to the rhythm of a gentle bossa nova
You'll be Zooming too until the Spring is over
You'll get your shot
The lights are much brighter here
You can forget all your troubles, forget all your cares

https://www.nytimes.com/2020/12/23/health/covid-antibody-treatment.html

Instead of antibody treatments needing to be rationed, they are going unused. How is that explained? The federal government has 532,000 doses of the two Eli Lilly and Regeneron treatments but it is only being given to 20% of patients. Some of this has to do with people's perception that the treatment was only for wealthy people; some don't want to venture out to healthcare settings; some physicians are skeptical of the evidence and want to see stronger data. At Mass General/Brigham, patients are chosen by lottery and many patients refuse the treatment. The data behind these treatments led to the conclusion that the number of patients at risk for severe Covid-disease  who required hospitalization was shorted, even though it was not, as Trump reported, a cure.

. 

https://www.nytimes.com/2020/12/21/us/politics/stimulus-law-education.html

A NYT article about restoring Pell grants for incarcerated students, a provision included in the higher-education law provisions which are part of the stimulus package. Decades of punitive practices are about to be rescinded with these new bipartisan measures which are meant to restore Pell grants removed during the Clinton administration. President-elect Biden supported the removal of financial aid for convicted felons; now he claims that this was a mistake. I taught in a state prison and fully support the restoration of Pell grants and the expansion of higher educational opportunities in federal, state and county prisons.  The expansion of the Pell grants will make an additional 55,000 students newly eligible for grants. These programs are a lifeline for students and will more than pay for themselves in reducing recidivism, as data has shown. Orange lives matter.

https://www.nytimes.com/2020/12/21/world/europe/eu-coronavirus-vaccine.html

A NYT article about the EU approval of the Pfizer-BioNTech vaccine. Most of the EU is in the stranglehold grip of the second wave of the pandemic. Publication of the identification of what is described as a "more transmissible" variant of Sars-CoV2 earlier this week led to the borders being closed between Britain and the EU although it is admitted that this variant had already reached the continent. Pfizer will assist with the transport and storage of the vaccine in each country and then each of the countries will be responsible for distributing the vaccine based on the priorities of the individual country. The EU this summer pooled resources to negotiate the best deal with Pfizer, this they are paying less than the US for the vaccine. France and Germany will start shots by the end of the month weeks after England began vaccine administration. The inoculation campaign will get going in earnest in the EU in the first quarter of 2021. Pfizer is working on a schedule for future vaccine deliveries but many European governments are worried that supplies will dwindle.

 

https://www.inquirer.com/opinion/commentary/english-classes-curriculum-classic-literature-20201221.html

An Inquirer op-ed about a debate on Twitter whether literary classics like The Great Gatsby and Wuthering Heights are still relevant and should be taught in the classroom. From a justice standpoint, educators are recommending more inclusion of literature that is relevant to the Black experience and Black and brown audiences who want to see themselves represented in the literature they read in school. The op-ed writer agrees with this viewpoint but insists that classics do not become such based on their old, white appeal but because of beautiful writing about the trials of human beings. The writer references Shakespeare as the "first secular writer of fiction in Western history". Writers like Chinua Achebe, Tony Morrison and Ralph Ellison are already included in grade school curricula. A good quote: "If we want our students to be prepared for college, and the world, we should not only update our canon...to hold a mirror to their experiences but hold onto classics for what they are: works of beauty that help us understand each other."

https://www.nytimes.com/2020/12/20/health/coronavirus-britain-variant.html

Sigh, another coronavirus article, this time about a variant which has acquired properties of increased transmissibility. Evidence that was provided was the rapid spread of the virus through London. The UK went into a deep lockdown and the EU closed its borders to Britain. Was this necessary? Well, the idea of a variant, meaning a mutation in the DNA is common to the understanding of viruses. Within an individual with HIV, many variants exist due to the fast mutation rate of the virus, but every mutant is not successful.  Some DNA mutations do not change the virus' proteins (like the spike, which gets the virus into cells) at all. And some may be selected to increase transmission from person to person. The British variant has about 20 mutations, some of which may make the virus get into cells more easily and also may make it transmit more easily between people. Another concern is that one change, which is a deletion mutation could make the virus more able to avoid the body's own immune defenses. But according to the article, the number being bandied around and tweeted around of 70% more transmissible comes from modeling studies and not actual experiments. It is also possible that human behavior, meaning movement of infected people, could have caused the increases. Experiments have to be done and replicated before such conclusions can be safely reached. The deletion mutants have also been around for months and been identified independently in Thailand and Germany in early 2020. A conclusion mentioned was that immunizing 60% of the population in a year and keeping case numbers down will help minimizing the chances of the virus mutating significantly.

https://www.inquirer.com/wires/ap/scientists-focus-bats-clues-prevent-next-pandemic-20201214.html

An Inquirer article about researchers in Argentina, Brazil and India attempting to minimize the possibility of another global pandemic. It is called a "spillover" when an animal disease jumps from its animal to a human host. Bats are thought to be the intermediary hosts of multiple viruses that have spawned pandemics such as Covid-19, SARS, MERS Ebola, Nipah virus, Hendra and Marburg viruses. Bats have a very high metabolic rate and are very resilient and long-lived. Raina Plowright, an epidemiologist who studies bats suggest that evolution, which provided them with these three advantages also  gave them protection against pathogens. Let's remind ourselves that it is human invasion into bat habitats such as tropical forests that creates the possibility of spillover.