Solipsist Epidemiologist

 https://www.nytimes.com/2020/11/20/health/covid-vaccine-95-effective.html

Hold on a minute, please. 95% efficacy sounds good and boosted Pfizer's and Moderna's stock, as if they weren't getting enough shekels from the US government.  I may have reported on this article before but I wanted to stress, with my solipsist's hat off and my epidemiologist's hat on (full disclosure, my epi is self-taught) that they should be testing all people who got either the vaccine or the placebo for Covid-19 by pcr analysis. According to the article (and convention), researchers wait for participants to develop symptoms and then figure out which  group the illnesses came from. But it seems that in the case of the virus caused by Sars-Co-V2 many asymptomatic cases have been identified by widespread testing of people who are believed to have been in contact with an infected or symptomatic individual. It would be the right and correct thing to do to test everyone who received a treatment, which may represent a revision of practice.  A quote from the article, and worth reiterating, "And so it’s possible that a number of people who got vaccinated in the clinical trials got infected, too, without ever realizing it. If those cases indeed exist, none of them are reflected in the 95 percent efficacy rate."

 

 

 

https://www.nytimes.com/2020/12/02/world/europe/cannabis-united-nations-drug-policy.html

This is a NYT article about the reclassification of cannabis used for medical purposes by the UN Commission for Narcotic Drugs from  a category of drugs including dangerous, addictive drugs like heroin, which will pave the way for its use for medical purposes as has been done safely throughout history, and allow countries to widen patients' access to treatment using this drug.  Products containing cannabis derivatives like CBD are a cornerstone of the wellness industry. One of the implications of this change is a potential change in the reliance on opiates for pain relief. 

 

https://science.sciencemag.org/content/370/6520/1023

This is an article from Science magazine about the various ways schools are stretching their mandates to cope with the Coronavirus crisis. It reflects the changes from when New Zealand, Norway and Japan, having dealt with the crisis, moved cautiously at first then threw open the school doors, with the idea that the need for in-person schooling superseded the danger due to the virus. But things are different now, as the article notes. The virus has revealed disparities between wealthy and poorer communities, some of the latter being unable to provide quality distance education. Some countries are closing bars and restaurants, while keeping schools open. The Czech Republic, Austria and Russia finally gave in and closed schools recently. Outbreaks in schools are not common....Duke U reports on the cases identified in 6 N. Carolina school districts in the first 9 weeks of school (50,000 students and staff)  (197 identified cases acquired outside of school by community spread and 8 cases spread from one person to another within schools, which were determined to be "secondary transmission"). There are asymptomatic cases missing from this data. Sequencing the virus could provide important information about whether the cases within a school are even related. Whether schools should remain open is going to be a continuing question possibly through the end of the school year and an epidemiological, medical and political, moving target.

https://www.nytimes.com/2020/12/02/style/can-these-period-underwear-crusaders-convert-you.html

A NYT article about fashion, unusual for the SoSo. Let's talk periods that don't end sentences. Bleeding into your underwear. Or, the meeting where you are scheduled to talk and your handbag is at your desk and then you uh-oh. There is a company called The Period Company that sells period underwear. (I just like writing that word.) They want us (well, not me anymore) to break with tradition and consider buying "period panties." A marketing survey revealed that the younger cohort, aged 18-34 would be interest in reusables in order to protect the environment. The older group, 30s and 40s were against this type of product. It is like a type of shapewear with a pad sewn into the crotch. The product is washed and reused. It is time to move on to Period underwear for "that time of the month".

https://www.nytimes.com/2020/12/04/upshot/epidemiologists-virus-survey-.html

A NYT survey from The Upshot about how 700 epidemiologists are living now.  24 activities were included in the survey and those answering in the affirmative ranged from 90 to 2%. What things are they doing or avoiding. And when might that change. Going grocery shopping 90%. Seeing friends indoors depends on circumstances (in home of elderly relative or friend 10%, attended small dinner party 9%, church service, 4%). 30% would expect to change after they themselves were vaccinated. A minority said that if highly effective vaccines were distributed it would be safe for Americans to live freely this summer. Most agreed that indoor venues with lots of people present the most danger. At least one of the epidemiologists expects it to be at least the next 12 to 18 months and maybe a few years of masking, which will begin to be "the new normal".

 

December spiking, surging, and zooming towards the solstice

 https://www.nytimes.com/2020/11/30/technology/deepmind-ai-protein-folding.html

I did my master's thesis on chaperone proteins, which are essential for proper protein folding. When protein folding goes awry, you have diseases like Mad Cow Disease, or when I first met it (we go way back) it was Bovine Spongiform Encephalopathy (BSE). The article in today's NYT is about how artificial intelligence (AI) is going about solving the shape of proteins in our bodies. Carbohydrates and lipids and even nucleic acids are found in canonical shapes. By that we mean 3-dimensional shapes, since our bodies are not dimensionless aggregates as shown in textbooks. The company DeepMind, with its system AlphaFold is able to predict a protein's 3-D shape, too late, as the author reveals, to help with our obsession du jour, Sars-Co-V2. DeepMind uses a system modeled, more or less on neural networks, or the network of neurons in the human brain. It identifies patterns in huge quantities of data, such as being able to identify a cat after looking at patterns in photos of cats.  Drugs bind to proteins in our bodies and alter their acitvities, like penicillin binding proteins in bacterial membranes bind to penicillin. If DeepMind can  find proteins and identify their shapes this can be a driver in drug development. It can do this 2/3 of the time, according to one of the developers. Its mistakes are smaller than the width of an atom. This technology can also be used to predict the outcomes of clinical trials. In the past this lab has built systems that outperformed humans at Starcraft video game and the ancient game Go.

https://www.nytimes.com/2020/11/30/health/coronavirus-vaccine-prisons.html

Another NYT article about how the vaccine, when it comes, will be prioritized. When I worked at SouthWoods state prison, my classroom was next to Medical. I was surprised at how many wheel-chair-bound inmates were arriving and departing. Not the usual George-Raft-Humphrey Bogart scenario of tough inmates in the yard plotting escapes, more of a realization that people spend scores of years, decades locked behind prison walls, invisible, isolated, hopeless and vulnerable. In the case of Sars-Co-V2 which causes the coronavirus, these inmates disproportionately African-American and Latino are in the direct path of disaster. The men in their wheelchairs are often suffering from chronic disease such as high blood pressure, diabetes and various mental illnesses. How would it not be in the interests of humanity to release them or at least to vaccinate them? The article discusses whether the inmate population should be prioritized for administration of some of the first doses of vaccines but they are not ranked by the CDC in the "top tiers". The CDC did prioritize prison guards and others who work in jails. During the summer more than 2200 inmates were sickened and 28 people died at San Quentin SP in California. 

https://www.nytimes.com/2020/12/01/climate/georgina-mace-dead.html

NYT obit for Georgina Mace, who no one has heard of, who was responsible for building the scientific basis for recording endangered species and member of the International Union of Conservation Biologists. In 1990 she was a member of the Zoological Society of London and she solidified the Red List to make it applicable in a rigorous way to be "rapidly applicable to thousands of species." The list incorporates climate change as a danger threat.  From the article "The list has grown to include more than 120,000 species of animals, plants and fungi; some 32,000 are currently listed as endangered."

 

 

 

 

https://www.nytimes.com/2020/12/01/science/leaf-stick-insects-phyllium-asekiense.html 

This from the NYT is about eggs received by the Montreal Insectarium supposedly from a leaf insect, Phyllium asekiense. The Covid-19 hiatus from real life is as good a time as any to fulfill your childhood fantasy of breeding insects. Eggs hatch into nymphs, if you remember your insect life cycles. One of the eggs grew and looked like its mom but the other was thin and stick-like (not leaf-like) and had wings. It turned out the two insects, which had been classified as different species,were actually the same species. This is called sexual dimorphism, where the males and females appear totally different. Since the females appear differently from the males (and since this is a descriptive science) how can the puzzle of relating the two sexes be solved, besides of course, the infrequent event that was written about here? What a cool job!                                                                                                                                                                                  

                                                                                                                                                                                                                                   

 

 

 

https://www.nytimes.com/2020/12/02/business/singapore-lab-meat.html    

A NYT article about lab-grown meat.  Eat Just is an American start-up based in SF which would permit you to satisfy your carnivorous instincts without an animal having to be killed. Although having to pay $50 for a single nugget may seem excessive for conscience-salving, it doesn't seem that this product will be quick to market since regulatory agencies in the US and Europe have not regulated it yet. (Let's focus on a vaccine, shall we?)  The nuggets have been approved by the regulatory agencies in Singapore.

                                             

Hand Sanitizer-Brined Turkey Recipes

 https://cn.nytimes.com/china/20201118/china-fat-shaming-rmart-rotten/en-us/

Sorry that this is the Hong Kong version of an article in NYT that describes the Taiwanese merchant RT-Mart having relabeled its "large" women's line "Rotten", "Extra Rotten", and "Rotten to the Core." It is called "fat-shaming" because smaller-sized women get to select from "Slim" and "Beautiful" sizes. I just wonder are they going to do this with men's clothing also, "John Deere", "18-Wheeler", "Butt Crack", etc. A nice trend.

 

 

 

 

 https://www.nytimes.com/2020/11/24/world/covid-mutation.html

A NYT article about  the controversial mutation 614G, which makes the coronavirus or Sars-Co-V2 more contagious. Earlier reports about this mutation said the virus had become "more virulent". Viruses do mutate at alarming rates and not all mutations increase either the virulence or the contagiousness. The first reports of this mutation were from tissue cultures and experts were dubious but this new research involving genetic analysis of human lung tissue, showed that the 614G variant may infect people more easily than the original isolate from Wuhan. A quote from David Engelthaler, a geneticist at the Translational Genomics Research Institute in Arizona, "It could be that this mutation is what made the pandemic."

https://www.nytimes.com/2020/11/23/opinion/brain-neuroscience-stress.html

This is an Op-Ed by a psychiatry professor at HMS, MGH and Northeastern introducing the idea of "brain-budgeting". She posits the idea that your brain runs the body using a budget, allocating resources where they are needed. (Glucose, water, salt.) Spending resources withdraws from your bodily account and replenishing resources involves sleeping, eating, etc. Even though this is sort of a simplistic version and the brain in more complex than that, she maintains that "every thought you have, every feeling.....is part of your brain's calculations as it allocates and budgets you metabolic needs." This is kind of a reductionist argument, because your brains does more than direct metabolism but this argument beats the Triune brain argument that the brain is made by the deposition of layers like sedimentary rock, representing a reptilian, mammalian and human layering. That to me seemed like a Just So story.

She has a new book "71/2 Lessons About the Brain"

 

https://www.nytimes.com/2020/11/20/health/covid-vaccine-95-effective.html

This is a Carl Zimmer article about the recent reports by Pfizer, Moderna and now A-Z about the amazingly successful efficacy rates of their vaccines. Since the data wasn't presented at the time and there was only a press release, it seems like it was addressed to the stock market, which is irresponsible. 95% sounds great but as the article says it doesn't tell you your chances of getting sick if you get vaccinated (do get vaccinated).  Efficacy and effectiveness are different and effectiveness is what we care about, not just clinical trial results, even though they are encouraging. This has to do with the fact that people who sign up for the trials are not a great reflection of the population. The actual population will include people with chronic health problems and cohorts that do not sign up for trials as has been seen historically (children, African-Americans, elderly.)

One of the great talents of this virus is the asymptomatic spread. Possibly people who got vaccinated got infected without realizing it. So, there's the rub. Also, if these asymptomatic people get vaccinated and stop wearing masks or being safe, they could spread the virus to others. And, the endpoints that these pharmas are measuring in the trials are also important and whether they test all vaccinated people for virus or just people who are symptomatic. Long story long.

https://www.nytimes.com/2020/11/20/health/tuberculosis-ai-apps.html

Another NYT article but NOT about Sars-Co-V2! This is a report about the use of algorithms to battle TB. A new app on a phone is able to scan an x-ray for signs of TB, Covid-19 (I lied) and 27 other conditions.  TB is the most deadly infectious disease in the world, killing 1.5 million people last year. The app is called qXR and is an important AI-based tool for screening and diagnosing TB. It uses an algorithm instead of a radiologist, although the machine plus the clinician is the best at diagnosing.  This app will be useful in underserved areas but the x-rays also carry signs that  are too subtle for a non-expert to diagnose. qXR scans the x-rays and assigns the patient a score. Doctors then perform further tests. This app will also help diagnose pediatric TB, which is difficult to diagnose.

Post-Election-Stress-Disorder (PESD)

 https://www.inquirer.com/wires/ap/forensic-genealogy-cracks-cold-cases-amid-privacy-concerns-20201114.html#loaded

 This is a Philly Inquirer article about the possibility of law enforcement using your Ancestry.com or 23andme data to solve unsolved crimes. The DNA kits have become increasingly popular and are given as Christmas gifts to the consumer, unaware that this information, possibly of greater consequence than other information, such as social security numbers or medical information which is guarded. The article makes the point that, with 26 million people using this "service" as of 2019, a trend which may increase the number to 100 million by 2021, whether or not you have provided your DNA, your relatives may have done this for you. The writer describes a cold case, that of the Golden State Killer, in which DNA evidence from the crime scene was uploaded into a genealogy website, which then linked the sequence to a relative of the killer and led to his capture. Some states have laws specifically addressing the privacy of biometric  information.

https://www.nytimes.com/2020/11/14/at-home/insomnia-advice.html

This is from the NYT, speaking directly into our Suprachiasmatic Nuclei about sleep. Are you not safely enveloped in the arms of Morpheus but instead nervously prowling around your apartment at 3AM? The author suggests that Covid-trauma may be the cause and mentions various approaches including Cognitive Behavioral Therapy, meditation, mindfulness and muscle relaxation, cutting off screen contact, reducing alcohol, chocolate and caffeine, exercising during the day and not thinking of the bed as fraught with anxiety (get out of bed). And maybe none of the above will work for you. We are all waiting for Godot-vaccine after all is said and done.

https://www.nytimes.com/2020/11/16/world/asia/china-fat-shaming-rmart-rotten.html

This had to go in my blog. RT-Mart has relabeled its large women's clothing as "rotten", "extra-rotten" and "rotten to the core."

Pandemic Fatigue

https://www.nytimes.com/2020/08/17/well/live/mammograms-older-women.html

A NYT article about whether women 75 years old and older should receive screening mammograms. It is known that breast cancer becomes extremely more common as women age. Therefore it would seem of utmost importance to screen in order to catch cancer in its early stages so treatment can be more effective  and simpler. The caveat here is, since this population is more likely to die of other causes before untreated and undiagnosed breast cancer becomes a threat to their health and lives. It is also impossible to determine which cancers detected on a mammogram might be slow-growing and therefore not warrant treatment. There is also some evidence that breast cancers detected in older women tend to be less aggressive and resolve favorably. The ACS guidelines specify that women with an average risk of developing breast cancer should have yearly mammograms after age 45, changing to every other year after age 55 and continuing every year or two for as long as they have a life expectancy of ten years or more. This conflicts with the US Preventative Services Task Force, which recommends stopping routine screening mammograms at age 75 regardless of life expectancy.

 

https://www.nytimes.com/2020/08/17/health/coronavirus-herd-immunity.html

An article from the NYT about how to determine what level of infection can provide herd immunity. At this level, the virus will be unable to find susceptible individuals in order to survive. Scientists suggest that the magic number is 70% but it could be only 50%. Sophisticated modeling has  shown that it is possible that there is no community in the word with enough immune residents to resist a second wave. There are some communities that do have significant immunity. This is calculated by the r-naught, which indicates how many people each infected person passes the virus to. The initial calculations assumed that every person in the community mixed randomly with each other person in the community and passed the virus with the same likelihood, which has been shown to be incorrect., since susceptibility could vary from community to community. Researchers in Mumbai did a random household survey to take blood for antibody testing. The results indicated a wide disparity between the city's richest and poorest neighborhoods. One conclusion about London and NYC was that these cities may have reached herd immunity, possibly because of pre-existing immunity to common cold coronaviruses or memory cells which recognize the new coronaviruses, but other experts reject this theory.

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https://www.nytimes.com/2020/08/14/nyregion/freshkills-garbage-dump-nyc.html

An article from the NYT about the recovery of the Fresh Kills Landfill. The Arthur Kill is a tidal straight that separates Staten Island from New Jersey. Twenty years ago barges routinely left College Point, Queens loaded with garbage headed for Fresh Kills but this voyage is made no longer since Fresh Kills has been rebranded as Freshkills and a park has been build at the site of the old dump which will receive its first visitors next Spring. The idea for this transformation came from Major Bloomberg during his first term. A problem in the transition from dump to park is adapting 150 million tons of garbage, which involves capping it with plastic, covering it with fresh soil and planting native grasses in the soil and transforming the four mountains of garbage into soft green hills "straddling the convergence of creeks". Henry David Thoreau lived on Staten Island and walked the shore, climbed the hills and may have boated in the wide open streams of Fresh Kills.  Tidal creeks and salt marshes like Fresh Kills are, according to the author, "the lifeblood of the giant Hudson-Raritan estuary, which includes the lower Passaic and Hackensack watershed referred to as the Meadowlands."

Solipsist's Soiree Social Distance

 https://www.sciencemag.org/careers/2020/07/pandemic-hitting-scientist-parents-hard-and-some-solutions-may-backfire

This article in Science mag reports data in Nature Human Behavior about the problems scientist parents have that they always have had but that now have increased logarithmically, if not exponentially, or maybe those are the same thing.  How can a scientist balance professional and parental pressure? This has always been a problem for women, as the peak time for childbirth/rearing corresponds with career expectations. Scientists with children below 5 years of age report working 38% fewer research hours than normal; those raising children between ages 6 and 11 worked 32% fewer hours. The article suggests that teaching loads be redistributed away from professors with small children. One of the professors interviewed said that she is unable to mentor junior colleagues since she is barely surviving with young children at home. What occurs to this writer is: what is going to happen to the development and advancement of scientific thought? 

https://www.nytimes.com/2020/08/13/climate/trump-methane.html 

This is a NYT article about the weakening by the EPA of a major climate change regulation, rolling back the last major Obama-era climate rule. New studies, in fact, have indicated that the scale of methane pollution "could  be driving the planet toward a climate crisi faster than expected."  The discontinuance of these regulations, viewed by the Trump administrations as "burdensome and ineffective" will garner $100 million a year through 2030 and lead to the release of more than 850,000 tons of methane into the atmosphere concurrently. Robert Howarth, an earth systems scientist at Cornell, last year published a study blaming North American gas production for 1/2 of the global increase in methane emissions of the past decade.  And the next ten will be worse.  The bad news is that emissions are probably higher than what the EPA says they are due to the reliance on self-reported company data by the EPA and some testing that is not comprehensive. 

https://www.npr.org/2020/08/12/901775768/eagles-and-mockingbirds-catch-a-break-as-judge-strikes-down-trump-bird-opinion

This is an article from NPR about a NY federal judge striking down a Trump administration decision to roll back protections for migratory birds. In the ruling that was rolled back, with the judge citing a quote from "To Kill a Mockingbird", companies that killed a migratory bird during their work would no longer face threats of prosecution, The Audubon Society and other conservation groups filed complaints against the Trump administration in 2018. "For decades this law has been a proven incentive to remind companies to do the right thing for wildlife," interim chief conservation officer for the National Audubon Society, Sarah Greenberger said. The Migratory Bird Treaty Act was enacted in 1918. Today, a violation of the act is a misdemeanor punishable by a fine of up to $15,000 and imprisonment for up to six months. The birds protected by this law include eagles, owls, mockingbirds and vultures.

Dining for Dummies

https://science.sciencemag.org/content/369/6503/510

This is an article from Science magazine about viruses and their cellular receptors. This is complex because  various factors determine entry of substances into cells, like receptors and transporters, which are proteins. Proteins are encoded by genes, so a particular gene sequence regulates these receptors and transporters which control which tissues in the body are infected. We know that this virus infects various bodily tissues, and not uniformly. The article mentions the Spike protein, by which the virus latches on to the Angiotensin-Converting-Enzyme (ACE) 2 to enter cells. ACE2 also functions in things like blood pressure and inflammation. So there you go. This is a pretty technical article but worth getting through. The enzyme ACE (a different enzyme) performs a chemical function, changing the hormone precursor (not the active hormone) Angiotensin I to Angiotensin, which is an antagonist of Angiotensin II. ACE2 is balanced by ACE. Both ACE and ACE2 are highly present in the pulmonary (lung) endothelial cells and blood vessels. ACE2 is also expressed in the intestine, which explains some of the GI symptoms.

The article also goes into the deterioration that causes severe systemic COVID-19. And the immune system involvement in the disease. Immune-mediated damage might involve complement-activation, antibody-dependent enhancement or cytokine release or all of the above. The conclusion is always the same, and sadly not within reach at this point: 

I quote: Therefore, it is essential to identify individuals with early SARS-CoV-2 infection who are at high risk of progression to severe disease, and test antiviral therapies to prevent viral entry and replication. It should not be too difficult to identify these “at risk” patients who are in danger of progressing to severe disease through contact tracing and testing, even prior to symptom onset.

 https://www.nytimes.com/2020/07/30/health/covid-19-vaccine-monkeys.htmThis is an article by Carl Zimmer in the NYT about clinical trials which are proceeding with the J and J vaccine and one made by the Moderna company. An important quality of a vaccine is whether it protects from infection, which is called a challenge. And how long the protection lasts. There is no getting around the protection, but if the duration of the immunity is shorter than necessary, boosting the protection with a second vaccination is the usual course of events. The J and J vaccine uses a vector to carry the Spike protein gene into the body and there the gene makes the coronavirus proteins, which  provoke an immune response. After a single injection of one vaccine, scientists waited for a week, then injected animals with the coronavirus and looked at the amount of protection offered. In 6 out of the 7 vaccines variants, partial protection was provided and the seventh was more powerful because no virus was detected in the challenged, vaccinated monkeys.  J and J is advancing this seventh vaccine into a Phase I human safety trial, which is preliminary to the Phase III efficacy trial.

https://www.nytimes.com/2020/08/09/business/coronavirus-vaccine-.htm

This is a NYT article about the warp speed fallacy. It is actually about how clinical trials' new audience seems to be Wall St, with the stock price of one small biotech company in Pennsylvania surging based on promising early results. The article points out that this same company announced "encouraging news" about malaria, Zika and cancer vaccines but has never brought a vaccine to market. Shares went up as much as 963%. Insiders trading on the stock, made a big profit. The vaccine needs to be administered by what sounds like a version of an electroporator, which moves DNA into cells.  A 36-person trial was done in April, with reports that the vaccine was well-tolerated and generated an immune response. But no data was presented, meaning that there is no way to tell if it works to protect people against the coronavirus.  

  https://www.nytimes.com/2020/08/05/arts/design/bronx-virtual-tour.html This is an article from the NYT about the home of the Bronx Bombers in antiquity. Not in 1967, when I lived there; saw James Brown at the stadium as well as the bombers, ate ice cream at Addie Vallens. The Lenape name for the Bronx is Minnewits. The Bronx is the only part of NYC that is actually attached to the rest of North America (Manhattan and Staten are islands, Brooklyn and Queens are part of Long Island.) The article format is interview with Eric Sanderson, senior conservation ecologist of the Wildlife Conservation Society, who holds my ideal job and is based at the NY Zoological Gardens. To those of my audience who remember the Yanks' transit from the Polo Grounds in Manhattan across the Hudson, salutations. Mr. Sanderson quotes a paper (unnamed) which speculates that during the Pleistocene Era, about 1.5 million years ago, the Hudson River flowed the path of what is now the Harlem River, not along the west side of Manhattan, past the future Polo Grounds and Yankee Stadium, through Flushing Meadows, and carved out the valley under Jamaica Bay.  Later glaciations rearranged everything. The interviewer's conclusion is that the city's rivers, like its inhabitants, have changed neighborhoods and assumed new identities.