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.

It Takes a Pandemic to Raise a Child

https://www.nytimes.com/2020/07/24/nyregion/climate-change-nyc.html
This is a NYT article about the effect of increased temperatures in the metro area on the number of new species. NYC, once classified as a humid subtropical climate, has achieved the distinction of residing in the humid continental category, summers averaging above 72 degrees F and winters above 27, on average. Forget about wrapping your fruit trees in burlap in the winter, for example, not that I have ever done this. Enjoy one of the 15 sultry tropical nights every summer when temperatures stay above 75: it used to be 10. The article doesn't suggest growing palmetto palms in Central Park: Georgia, Florida and South Carolina still retain that distinction. The downside is that invasive weeds, such as knotweed and porcelain berry are running rampant. In the fauna department, bugs that died off in the winter are surviving and multiplying, such as the hemlock woolly adelgid.

https://www.sciencemag.org/news/2020/07/scientists-pull-living-microbes-100-million-years-beneath-sea
Here is a Science magazine article, which I would subtitle, "So you think you have sleep issues?"
It describes 100 million year old microbes which, when brought back to the lab, revived and multiplied. A geomicrobiologist at the Japan Institute for Marine Earth Science and Technology launched a drilling expedition at a site in Australia, at a confluence of ocean currents that is considered the deadest part of the world's oceans. They extracted samples from the mud cores and fed them with nitrogen and carbon compounds. There were 100x fewer samples than in ordinary sea mud and they had to develop special techniques to analyze the small numbers of cells. In terms of geological time, this is very impressive.

https://www.nytimes.com/2020/07/28/health/alzheimers-blood-test.html A NYT article to remind people that non-Covid research continues. although there might be some advantage to our forgetting at least the first half of 2020. Looking for diagnostic tests for AD has been proceeding apace for years. This is a great result. The test can distinguish whether people with dementia had Alzheimer’s instead of another condition. And can identify signs of the degenerative, deadly disease 20 years before memory and thinking problems are expected in people with a genetic mutation that causes Alzheimer’s. The test is inexpensive and should be available in 2-3 years. This research was published in JAMA.

Black Deaths Matter

https://www.nytimes.com/2020/07/02/health/santillana-coronavirus-model-forecast.html
This is a NYT article about using social media to predict outbreaks. An international team of scientists has developed an algorithm that could be predictive and get a two0week head start from Twitter, Google searches and mobility data from smartphones that would guide whether to relax or ramp up public health interventions. This is from a prepub from arXiv.org and the commentary is by the director of Machine Intelligence Lab at Boston Children's Hospital. With the caveat that the Google Flu Trends Algorithm from 2008 didn't work as expected but researchers have made adjustments to the program combining Google searches with other kinds of data. It is called a "harmonized" algorithm because it weights the data sources depending on how strongly it correlated to a coming increase in cases.

https://www.nytimes.com/2020/07/02/opinion/coronavirus-jail.html
This is a commentary from an anthropology  Ph.D. candidate and medical student about the increase in the number of Covid-19 cases in jails. His research deals with the Cook County (Chicago) jails and was published in the Journal of Health Affairs (not a premier journal from the sound of the title). The study showed that "the cycle of arrests, jailings and releases was the most significant predictor of the spread of the coronavirus in Chicago and the rest of Illinois." A sixth of all of the cases in the city and state were linked to people who jailed and released from a single prison, according to data through April 19th. Nonviolent offenses account for 95% of the more than 10 million arrests in America every year. The conclusion from this data is that standard policing and incarceration policies are driving preventable spread of the virus. People are being released from prison daily with the belief they are negative  when in reality the virus has begun to spread in their bodies.  The authors suggest that policymakers should stop the daily cycling of thousands of people in and out of jails. During the pandemic issues of criminal justice reform should not be determined by partisan politics.

https://www.nytimes.com/2020/06/30/upshot/coronavirus-economists-dexamethasone.html
This is the Upshot and a discussion of the Recovery trial, a randomized controlled trial in Britain. It showed that natural experiments, such as when a shortage of one particular drug that was used to treat sepsis gave scientists the unique ability to assess the effects of the drug on mortality rates. Apparently, natural experiments allow a more causal interpretation of data, while associational studies, typical in medicine, do not.  This points out the sometimes-abritary clinical cutoffs made to allocate particular treatments. For example, a hospital decides whether to provide a ventilator to patients based on whether they use 6 liters of oxygen per minute, but actually a 5-liter-per minute patient is pretty much the same. The commentary suggests that these questions must be asked and  thresholds must be known and interrogated. Differences in treatment around the threshold must be examined to see whether they correspond to differences in clinical outcomes. In terms of the Recovery trial, after the results were announced, the data for critically ill Covid-19 patients were examined, with the expectation that patients hospitalized before the Recovery trail results were announced would fare worse than those hospitalized in the days afterward, assuming that doctors started using DEXA.

https://www.nytimes.com/2020/07/14/us/politics/trump-cdc-coronavirus.html
Article in NYT detailing the  protracted rape of the CDC by the administration. So the HHS is now being tasked with collecting daily reports about the patients that each hospital is treating, number of available beds/ventilators, and other information vital to tracking the pandemic. S'posed to make it easier for decisions about allocating short-supply items like remdesivir, but in all likelihood this new policy will make it hard to access new information not open to the public, potentially affecting the work of scores of researchers, modelers and health officials who rely on data formerly sent to the CDC to make projections and crucial decisions. Just another "trump" in the road. Will this also be true of the Weather Bureau, the US Geological Service, NASA, FDA? Will the federal government be hiring new data "remodelers" trained to suppress information? What will be their civil service grades?
 








https://www.statnews.com/2020/07/16/hospital-data-reporting-covid-19/

This is from StatNews about an alarming new change in the way real-time Covid-19 data is reported. Accurate and timely reporting of data informs stop-on-a-dime policy changes. Covid-19 data,rather than being reported to CDC and HHS is now only being reported to the HHS, leading to concerns that the data would be eliminated, manipulated, falsified or all three. The rationale is data consolidation in order to make decisions about allocation of scarce resources, such as remdesivir.  “In the midst of the worst public health crisis in a century, it is counter-productive to create a new mechanism which will be extremely complicated to build and implement,” public health officials, including former CDC director Tom Frieden, wrote.  The data is openly available on the CDC’s website and allows some of the most consulted Covid-19 tracking sites, like covidexitstrategy.org, to provide numbers on how many hospital beds hospitals are open in different states.

Real men wear masks

https://science.sciencemag.org/content/368/6498/1414
This is a science mag article about our favorite whipping boy and my former employer, ETS.  As bad luck would have it, just when unis are thinking of not requiring the GREs, along comes Covid-19, requiring tests to be administered online. According to Science, the specifications for students who take the online GREs include being alone in a room, having a computer with a webcam, having a whiteboard if they take notes, sitting in a standard, not overstuffed chair, and ensuring no one will enter the room for the entire 3 hours. How hard/easy is this? I read about a school that had to set up a hotspot in a school bus so the profs could get the internet for teaching. We are talking about high school students here. For schools that had been considering disconnecting from the GRE as a requirement for graduate school. Covid-19 may be the camel's-back-breaker. Good riddance to high stakes testing. There is proctoring software (examsoft) that universities make available for giving exams but probably also a readily available-to-students industry for getting around it.

A Walk in the Park

https://www.nytimes.com/2020/06/27/opinion/prison-coronavirus.html
This is a link to a Sunday Review (NYT) article from a former prisoner in Ohio, who has since been released. He remarks on the prison's overcrowding, poor sanitation arrangements (8 showers for 160 inmates), proximity of bunks, among other complaints. Parole hearings were delayed and law libraries closed due to health concerns, at least this was the reason offered. Mealtimes were staggered to have fewer inmates dining than regular practice, which required dinners to be offered to some as late as 8PM. Masks were offered to prisoners but some corrections officers refused to wear them. I saw a broadcast in which one state's governor, when confronted by the concerning statistics about prison infections, reassured the public that the prison is a "closed system", which it is not by any means. Prisoners in the state the governor was from were kept in solitary upon diagnosis. And, how would the threat of solitary confinement encourage reporting of symptoms? Reduce the prison population: it is too severe a penalty to die of Covid-19 as punishment for a parole violation, non-violent crime or first offense. Some of the prisoners I saw at Southwoods were elderly and in wheel chairs.  The correctional system's system's chaotic and ill-thought out response makes as little sense as the public health philosophy guiding the nation's response to the virus.

https://science.sciencemag.org/content/368/6497/1317/tab-pdf
This is a link to a Science mag article about the gender gap in STEM fields. The research was done at Dept of Applied Statistics, Social Sciences and Humanities at NYU. Male to female ratios in US college majors in Bio, Chem, Math and other STEM fields as 1:1, while Physics, Engineering and Technology ratios are 4:1. But they take it further to show that low achieving males (high school) major in the latter fields  (PECS)  at a higher rate than the same-achieving females.  Prior research has shown that females have less confidence in their math abilities, value societal goals and a work-life balance more than salary, take different high school STEM classes and have different career aspirations.  Their model took into account both high achieving and low achieving students and comes up with analyses. Interestingly, of students not intending to major in PECS in high school, males are more likely to major in PECS than females. They conclude that, interventions such as coding camps, role models and peer networks to encourage PECS majoring in college, may work for only a select group of high-achieving women and that "to raise the quality of students in PECS, it must be recognized that the gender imbalance varies through the achievement distribution and is  perpetuated by male-favoring cultures that disproportionately attract low achieving men to the fields."
 
https://www.theguardian.com/world/2020/jun/30/new-swine-flu-with-pandemic-potential-identified-by-china-researchers
This is a Guardian article about a new swine flu that has been detected in China that has "pandemic potential", meaning it is auditioning for the next Covid-19. As published in PNAS, it is genetically descended from the H1N1 strain that caused a pandemic in 2009.  Quoting from the report, this strain, called G4 "was observed to be highly infectious, replicating in human cells and causing more serious symptoms in ferrets than other viruses do. Tests also showed that any immunity humans gain from exposure to seasonal flu does not provide protection from G4." Science has shown that this strain can pass from pigs to humans but has not shown a human to human transmission.

https://www.nytimes.com/2020/06/18/climate/trump-epa-perchlorate.html
An article in the NYT about a Trump administration decision not to limit perchorate in drinking water. Perchlorate is a toxic chemical in rocket fuel linked to fetal brain damage.  The EPA also overturned the scientific finding (how do you overturn a scientific finding?) that declared perchlorate a serious health risk for 5-16 million people in the US. The reason offered was that the "one size fits all" standard is less effective (federal control) versus state and local control. The National Resources Defense Council opposed the decision saying that this reversal threatens the health of pregnant moms and young children. Perchlorate can cause loss of IQ.

The House That Covid-19 Built

https://www.nytimes.com/2020/06/11/climate/airborne-plastic-pollution.html
This is a report of a study done at Utah State University on microplastics in places like national parks and wilderness areas. The PI in the investigation suspected that the calculations, which reported microplastics in 98% of the samples and 4% of the dust particles that were tested, were incorrect, but upon retesting, the results were confirmed. In fact, the smaller particles that were detected, were surmised to have been carried  extremely long distances on air currents as part of the cycles of global dust transport.  Although previous papers have reported on microplastics in atmospheric deposition, this paper was the first to ask  "why and how is this happening."  Fine plastic particles in the air means that we are breathing them in, which may have health effects.









https://www.nytimes.com/2020/06/10/arts/music/bats-field-works-ultrasonic.html
This is a NYT article about bats, Stuart Hyatt's neighborhood bats. The composer and producer of the album "Ultrasonic" records bats, whose songs are so high in frequency that humans cannot hear them, makes them audible and sends them to composers. He has also made "field recordings" of  Scientology ceremonies and the Indiana State Fair and began to consider animals as his source material in 2018 on a trip to the Great Smoky Mountains State Park, where he recorded bats and translated their sounds to audible electronic signals. Then he actually found bats roosting 40 minutes from his home along wetlands near the Indianapolis airport. The tracks of "Ultrasonic" include "A Place Both Wonderful and Strange." His next library of sound will include poems from Arabic and English about cedar trees, read and sung over hypnotic instruments and accompanied by a comic book. And, yes, I ordered "Ultrasonic."