Thoughts From Inside

https://www.nytimes.com/2020/05/03/world/europe/coronavirus-antibodies-italy.html
This NYT article describes the "antibody passport", meaning that if it is determined by a blood test that one has mounted an IgG antibody response to the Sars-CoV-2, one may go about one's daily business. This might require, I imagine, a sort of antibody police and the possession of an antibody license, without which one would be returned to sequestration, upon threat of a more severe penalty  than sequestration. The sticking point here is that people develop different quantities of antibodies, which may last different amounts of time and may or may not be protective. So, it is complicated. The article says that an IgG antibody would neutralize the virus, but in my experience, the mere existence of an IgG subclass doesn't mean that the antibody is neutralizing, which means that it inactivates the virus.  Levels of complexity.




https://www.nytimes.com/2020/05/03/opinion/dave-eggers-coronavirus-questions.html
This is a NYT article by Dave Eggers about the actual versus the public space perception of our risk of  contracting the coronavirus (Covid-19), the disease caused by Sars-CoV-2. Is it dangerous or "low risk"?  If we stay inside, will it go away? Is it less potent in the summer? The virology, immunology and vaccinology qualifications of the deliverers of the erratic and contradictory media messages are questionable. And the history of the 1918-1919, which infected 500 million people is a potent reference in the literature, if not public memory.





https://www.nytimes.com/2020/05/04/climate/heat-temperatures-climate-change.html
Moving away from Covid-19 for a millisecond,  this NYT article reminds us that, with the rise in global population expected to rise by 10 million by 2070, as many as 3.5 billion people will live in conditions considered unsuitable for human habitation. These numbers are admittedly the "worst case scenario",  according to climate scientists but there are a lot of worst case scenarios that are playing out now in our current environment. According to the article, history shows that the vast majority of people has always been concentrated in a narrow temperature range.



https://www.nytimes.com/2020/05/04/health/gene-therapy-harvard-coronavirus.html
Back to the main topic of interest: Covid-19.  This NYT article describes work at Mass Eye and Ear and another hospital which use an AAV or adeno-associated virus to deliver DNA in a vaccine. This AAV is a harmless virus that has been approved and is safe. Using this technique requires miniscule amounts of material, so the yield would be high in manufacturing the vaccine. What happens is that,the virus, also known as a vector, gets the coronavirus' DNA into cells, which is transcribed and translated (jargon-y words) in the cell to eventually crank out a protein to put the immune system on alert.

 https://science.sciencemag.org/content/368/6490/476
This is a super-great AAAS policy-forum observation of a pivoting in practices and a caution against compromising the rigorous standards of scientific research in a time of crisis, as we are living through now. Examples are not conducting randomized controlled clinical trials. Are "fastidious research standards" a luxury in a pandemic, when death is knocking? Should "sub-optimal" study design be acceptable?  Are small sample sizes and lack of blinding in an age of urgency practices that will accomplish the desired end: a treatment and a vaccine? The article makes the point that "the challenges that rigorous methods address don't disappear in the face of urgent need."



https://www.youtube.com/watch?v=XlnUt9vK3-Q&feature=youtu.be
This is a great youtube video from Penn done by a researcher who has worked on coronaviruses for 30 years. It is part of a symposium.


https://www.nytimes.com/2020/05/05/health/crispr-coronavirus-covid-test.html
This article is about how to use the Crispr/Cas9 system to report on the presence of the virus in a sample. Is is called SHERLOCK and works a little like the pregnancy test in that thepositive results develop on a paper and can be read as a y/n. It was developed at the MIT McGovern Institute and there are similar tests being developed at the U of Buenos Aires and CASPR Biotech in San Fransisco. The components would be cheaper than the pcr-based test, which also involves more steps. This new test is in a preprint and it has also to be determined whether it is scalable.

Saturday, Looking Like Sunday

https://www.nytimes.com/2018/08/08/upshot/chores-girls-research-social-science.html  This is from The Upshot, which was based on American Time Use Survey diaries from 2003 to 2014 by 6,358 high school students ages 15-19. Maybe this is even too late (this writer's opinion). Boys ages 15-19 do about half and hour of housework and girls about 45 minutes. According to the article, girls' chores take a little less time than a decade ago, but boys' allocation hasn't changed. This also varied with parents' education but the difference was mostly seen in girls. Boys were also paid more allowance for their time, based on an APP called BusyKid, twice what girls earned. The gender gap in pay for chores and time spent was worldwide. In terms of caring for other family members, boys ans girls spend the same amount of time; researchers expect that this could result in these boys becoming more engaged fathers.




https://www.nytimes.com/2018/08/07/opinion/stem-girls-math-practice.html
A commentary from the NYT about STEM and girls and the importance of math skills. Not practicing math, even if you are good at it, can turn into a lack of competence, according to several research studies. Becoming an expert at anything, according to K. Anders Ericsson, requires developing neural patterns and honing them (my addition here) through practice and repetition. The commentary critiques modern methods that attempt to "make learning more fun" by avoiding drill and practice. In the international PISA study  the US ranks near the bottom of the 35 industrialized nations in math and that's not just girls. All learning shouldn't be "fun" (a quote).  I agree but it is hard to convince the students that there is something in it for them when the screens stop flashing and the equations appear.


https://njenvironmentnews.com/2018/07/23/n-j-finds-pfnas-chemicals-of-emerging-concern-in-some-recreational-fishing-waters/ This is an article from the NJ Environment News about PFAs, including PFOA, PFOS and PFNA, compounds that were used to make non-stick cookware, in NJ recreational waters.  Exposure to PFAs can lead to adverse health effects in humans, including high cholesterol.
The report was by theAgency for Toxic Substances and Disease Registry (ATSDR). The DEP sampled water, fish tissue and sediment.  The DEP cautioned anglers to eat very limited amounts of certain species found in waters where PFAS was detected.

Birthday Blog

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0200103 This is a PLOS ONE research article in which researchers weighted data from two independent surveys with census data to come up with the conclusion that 65% of Americans think that they are "above average" in intelligence. There have been problems with the generalizability of data collections in surveys showing the :greater than average" effect. Intelligence is normally distributed throughout the population and not skewed like other desirable traits. Researchers used a bunch of different types of surveys (telephone, online) weighted to the US census (2010). 65% agreed wih statement "I am more intelligent than the average person" as a conservative estimate. The survey concluded that college graduates slightly underestimated their relative intelligence whereas undereducated  people overestimated thier relative intelligence.








 https://www.statnews.com/2018/07/20/fda-approves-agios-first-in-class-leukemia-treatment/
This is an article from STAT news about a first-in-class leukemia drug approved by the FDA. It treats refractory AML sufferers from whhich possess a mutation in the gene IDH1. The drug received "orphan drug" status and the price for a monthly supply is about  $26,000. 30% of people in clinical trails saw their disease go into complete remission.





https://www.nytimes.com/2018/07/23/well/chemicals-food-children-health.html An article from NYT reporting on an AAP issuance of new guidelines for exposure of young children to plastics in food containers, exposure of pregnant women to processed meats and consumption of fresh foods and vegetables over processed food. This revision of guidelines has been influence by other professional groups in response to scientific evidence pointing to exposure to certain chemicals in foods as a culprit in interfering with development. Nitrates and nitrites in meat products, phthalates in plastics and bisphenols in metal cans have been identified as well as PFCs used in grease-proof  paper and perchlorates, used in plastic packaging.  Wrap foods in wax paper instead of plastic wrap and avoid canned and processed food is a take-home from the article. Some of these chemicals interfere with or block hormone function.


https://www.nytimes.com/2018/07/23/science/genes-education.html An article in NYT about a study reported in Nature Genetics on how genes affect how people do in school. The study found that many of the genetic variants implicated in educational attainment are involved in how neurons communicate in the brain. Genetic sequencing was done on over 1 million people, mostly white and of European descent. One of the study's finding were that certain genetic variants were found among found in people who finished school compared with those who left school early and those variants were involved with helping neurons form connections in the brain. The researchers figured out how to calculated a "genetic score" for educational success.


https://www.nytimes.com/2018/07/23/opinion/spider-in-my-life.html This is an opinion of sorts by Margaret Renkl in the NYT about the spider in her family room. When your "world has lost its center" the spider provides a source of stability. Surprise; we are talking about politics. Ms. Renkl takes comfort in one small spider in a well-written piece reminiscent of many writers using nature metaphorically.




https://www.nytimes.com/2018/07/25/style/sperm-count.html This is an article in the STYLE section of the NYT about the declining numbers of sperm in American males. A metaanalysis of 185 st. udies last summer concluded that sperm numbers have declined in a generation. Are men being feminized? Does lifestyle matter? Is there birth control in the water supply? A fertility start up company sells a sperm activity test because, in terms of fertilization, the sperm's ability to move is critical. There is also an app to watch your sperm move under a microscope live streamed on your phone. (I guess that's why it is in the style section.) Call this article "Semen Variations".







https://www.nytimes.com/2018/07/19/climate/endangered-species-act-changes.html Article from the NYT about the proposed changes to the Endangered Species Act. The 1973 law had seen few changes in 30 years. The deputy Secretary of the Interior claims that the changes to the law will streamline it, improving the regulatory process and providing more protection thereby. Environmental activists protest that the changes will set more species on the path to extinction. The Trump administration is also set to roll back the National Environmental Policy Act which lays out the policy that federal agencies must follow when planing infrastructure projects.





http://www.philly.com/philly/health/depression-treatment-blood-test-acetyl-l-carnatine-20180731.html Article in the inquirer about a new biomarker for depression which may be used in drug development to come up with a new mechanism. The biomarker is acetyl-L-carnitine, which is a product of cellular metabolism. Allegedly, things like childhood neglect contribute to the level of acetyl-L-carnitine and the publication indicates a correlation between the biomarker and severity of depression. I will need to be convinced of this before believing it.


https://www.sciencealert.com/having-children-makes-women-s-dna-cells-age-equivalent-11-years-telomeres  From Science Alert a report of a study in Human Reproduction about a sampling of DNA from nearly 2000 reproductive aged women which showed that that women who had given birth to at least one child had telomeres that were 4.2 percent shorter on average than those of women who had not borne children.e who had given birth had altered telomeres, a mark of cellular aging. It could mean that giving birth to one child is equivalent to 4.5 years of cellular aging.

99 degrees and counting

http://www.philly.com/philly/health/fear-of-math-is-harmful-to-your-health-this-woman-wants-to-help-20180629.html  An article from the Philadelphia Inquirer from a scholar at the Annenberg Public Policy Center at the University of Pennsylvania who is writing a book about the effects of innumeracy. Quoted from the article, "According to data reported in 2013, almost a third of the U.S. adult population can do only simple operations with numbers — they can count, sort, and do simple arithmetic. If you translate that into the current U.S. adult population, there are about 73 million people who can do up to only basic problems with numbers."  That means they also understand less in terms of how to take a missed dose of medicine (it says to do so on some medications), and also tends to mean that they rely on anecdotal information, which could have no bearing on their own circumstances. People who have diabetes also have to modify their insulin dosages based on their glucose levels and innumeracy make it complex. They also must read meters and other devices. Many people don't know what relative risk is compared to absolute risk and not understand that doubling one's risk could mean 20% to 40% or mean 0.01% to 0.02%, which is negligible.

https://www.nytimes.com/2018/07/13/science/youtube-science-women.html An article from the NYT about  comments left on youtube videos made by women. In a paper published in the JOurnal for the Public Understanding of Science women depicted drew more comments per view than men and more critical comments on their appearance. Some of the researchers' findings echoed a 2014 TED talks study in which it was reported that "when the presenter was a woman, 15.28 percent of comments were about her as opposed to the talk, when the speaker was a man, only 9.84 percent of comments were about him." This is having a discouraging effect on women who wish to make videos on a professional of semiprofessional level, according to the article and study.




http://www.philly.com/philly/health/depression-medication-genetic-test-genomind-anxiety-adhd-20171026.html This is an article in the Philadelphia Inquirer about a new genetic test for resistance to depression medications. It is called the Genomid Genecept  Assay test. It is better at predicting whether a medication will not work. It uses a proprietary algorithm to analyse 12 different genes to weight their combined effects on patient response to more than 55 different medications.  Some pharmacists will be trained to counsel patients if they see a pattern of unresponsiveness to treatments. There is a type of treatment called TMS (transcranial magnetic stimulation) or else electrocution therapy (ECT) is used typically used for patients unresponsive to medication.

Junesomething

https://www.nytimes.com/2018/05/30/well/cancer-group-calls-for-colorectal-cancer-screening-starting-at-age-45.html An article from the NYT about the new guidelines from the American Cancer Society recommending that people age 45 and above receive colorectal cancer screening. There will be six options offered for screening, including stool sample collection at home to be brought to a lab for tests, to colonoscopy, the most invasive test. This screening is necessary because it is expected that 16.450 new cases of colon cancer will be diagnosed in the age group 45-49 Americans under the age of 50 this year. There has been a 50% increase in cases of colon cancer in adults under the  age of 50 from 1994 to 2014. I have had students (college) who have had more than one colonoscopy so I am only partly surprised by this.



https://www.theguardian.com/lifeandstyle/2018/jun/06/broccoli-coffee-scientists-create-new-way-to-eat-more-greens  From The Guardian, Scientists have made powdered broccoli, which can be added to foods to increase the amount of greens in one's diet.  This was done by the Australian science agency CSIRO. But I don't think of broccoli as "ugly" produce.


https://www.nytimes.com/2018/06/09/opinion/protected-area-myth.html This is an opinion in the NYT about areas devoted to wildlife protection according to the 1993 Convention on Biological Diversity. The author asks us to examine what he calls the "delusions" that accompany this type of project. Apparently, designating these areas is easy but protecting them hard. In Australia's Barrow Island Marine Park, a designated protected area due to the richness of wildlife there, the government allowed construction of a vast energy complex. There is something called Paddd, protected area downgrading, downsizing and degazettement (?) because this is such a common occurrence.





https://www.nytimes.com/2018/06/09/climate/trump-administration-science.html An article from NYT about the fact that, even now as Trump meets with North Korea, when denuclearization is sure to come up as a topic of conversation, Trump has no science advisor. Past advisors to presidents  say that the absence of such high level expertise could put Mr. Trump at a disadvantage. (I would have said "is sure to"). This indicates the marginalization of science is shaping US policy. Neither the State Department nor the Department of Agriculture have chief scientists, for example. Even as we speak, Scott Pruitt, head of the EPA, is rolling back legislation designed to protect the environment.



https://www.nytimes.com/2018/06/13/health/mediterranean-diet-heart-disease.html An article in NYT about the Mediterranean Diet Study, much-cited, reporting that the Mediterranean diet, containing more vegetables and fruits, cuts risk of heart attacks/strokes, was not randomized. The paper was reanalyzed and, according to Barnett Kramer, director of cancer prevention studies at NCI. contains the same flaws.






https://www.nytimes.com/2018/06/13/climate/antarctica-ice-melting-faster.html This goes into the Antarctica is Melting column. 0.3 inch doesn't sound like a lot for the sea level to rise but this is the statistic for the years 2112-2117 as published in the journal Nature. By 2100 it is expected that there will be a rise of another 6 inches as estimated by the  Intergovernmental Panel on Climate Change. Oh, not to mention that Greenland also lost one trillion tons of ice between 2011 and 2014.

 

https://www.nytimes.com/2018/06/12/science/crispr-cancer-gene-editing.html

An article in the NYT by Carl Zimmer about obstacles that have surfaced in Crispr-Cas9 gene editing as reported in Nature Medicine.  In a study of cancer cells, Crispr was used to cut genes out of cancer cells to find the cause of their aggressive growth. Their control was human retinal cells but Crispr didn't work in these cells.  It is hoped that these obstacles can be worked out so that cell lines can be created and then implanted in the body to treat diseases.

 

https://www.nytimes.com/2018/06/15/health/alcohol-nih-drinking.html This is a NYT article reporting the discontinuing of a federally-funded study of drinking.  The study dealt with whether a daily beer or cocktail can prevent stokes and cardiovascular disease. It was recently determined that major funding for the study as provided by the alcohol industry, solicited by the NIAAA, a federal agency.
 

https://www.sciencedaily.com/releases/2018/06/180614213608.htm
This is an article from Science Daily reporting on a finding discussed in Science about a new type of photosynthesis that uses near-infrared light. Cyanobacteria (blue-green algae) when they grow near bacterial mats.  Chlorophyll a is normally used for photosynthesis but in near-infrared light chlorophyll f takes over.  It used to be thought that light damage would be severe beyond the "red limit", that is longer than near-infrared, but this changes the textbook understanding of the energy requirements for photosynthesis. Our understanding of life pushed incrementally forward....
 

https://www.nytimes.com/2018/06/21/health/alzheimers-virus-herpes.html An article from the NYT about  a new study in the journal Neuron suggesting that by analyzing brains some with Alzheimer’s, some with other types of neurological problems, and some without cognitive impairment, two hypes of herpes viruses, 6A and 7, were found in Alzheimers brains. People with elevated APOE4 had more 6A. This is a controversial and not a new theory and by no means has wide agreement in the Alzheimers field. But peole could be screened who have susceptibility to these viruses.  The question, "Do infections contribute to the development of Alzheimers?"



https://www.nytimes.com/2018/05/25/health/fetal-bone-marrow-transplant.html An article from NYT about a patient who received 5 blood transfusions in the womb. This was for treatment of alpha thalassemia, a genetic blood disorder which causes red blood cells to be unable to carry oxygen, causing severe anemia, heart failure and brain damage. Stem cells in the bone marrow, which is being tranferred with the transfusion, could replace cells which have the genetic defect.  It is a recessive disease, but when two carriers have children, an offspring could have 2 copies and therefore have the disease. Pregnant women are usually advised to abort. The donor in the case of this transplant is the mother, since the mother and the fetus' blood streams are in contact and there is little chance of rejection.This can work even if the mother is a carrier.




https://www.nytimes.com/2018/05/28/science/sea-spiders-oxygen.html This is a fascinating article about the Antarctic sea spider in the NYT. They have a small heart, but no lungs or gills. A fluid called heterolymph  carries oxygen. And pores on their legs bring sea water thtough their exoskeletons.  This work is reported in the Journal of Experimental Biology. There is also a video accompanying the article.
https://www.youtube.com/watch?v=Ojmvz5kLN5M

https://www.nytimes.com/2018/06/07/science/mars-nasa-life.html This is an article in the NYT from an article in the journal Science about the discovery by the Mars Rover of carbon molecules which could have originated from living material.  These molecules could have also been produced by chemical reactions that were not biological. In the same issue of Science it was reported that Mars' atmosphere contains a low amount, less than 0.5 parts per billion, by volume, of methane. This methane also may be the product of geological interactions (non-biological) or could have been produced by microbes as a waste product.  Future missions could provide additional clues.




https://www.nytimes.com/2018/06/07/us/politics/epa-toxic-chemicals.html A NYT article about the reevaluation of rules by the EPA that were passed  to ensure worker safety from toxic chemicals used in dry cleaning, paint strippers, cosmetics and other beauty products. The EPA is narrowing its scope in reviewing the use of these chemicals and removing from consideration the possible improper disposal of these chemicals. This has been the result of heavy lobbying by the chemical industry.





https://www.nytimes.com/2018/06/05/health/immunotherapy-lymphoma.html An article from the NYT from a study reported in NEJM about patients with adult T-Cell leukemia-lymphoma who received immunotherapy with the drug Opdivo and whose disease became worse after treatment. This drug, a monoclonal antibody is from a class of therapies called "Checkpoint Inhibitors"  and is not specifically approved for this type of cancer. After the third patient's disease became worse, the trial was stopped. These checkpoint inhibitors work by activating a type of white blood cell called T-cells, which should be mobilized to attack tumors but this didn't happen. It is thought that maybe disease T-cells became activated as well.

Cinco de Mayo

https://www.nytimes.com/2018/05/01/health/ticks-mosquitoes-diseases.html
This is an article from the NYT reporting the CDC recommendations for protection against tick-bearing diseases now that the hot weather is upon us. There are new tickborne diseases such as the Heartland virus and the number of cases of Lyme disease is growing. The CDC study did not attribute the increase in these and other diseases like dengue and Zika (in island territories) to climate change.  To protect yourself wear long pants, long sleeves, pants tucked into socks, hat and bandana, use DEET on feet and insect repellent on exposed skin.




https://www.nytimes.com/2018/05/23/climate/rice-global-warming.html
This is a NYT article reporting the results of a study published in Science Advances by plant physiologists at the USDA that concluded that 18 varieties of rice grown in experimental rice fields which were exposed to the elevated levels of CO2 that are expected  to occur later on this century contained fewer nutrients than rice that is grown today. The nutrients examined were protein, iron, zinc, Vitamin B1, B2, B5, and B9. For people in wealthier countries who consume a diverse diet this may not matter but for people who rely on rice as a primary food source, this is a significant decrease. Although this seems counterintuitive, higher levels of CO2 may cause plants to produce more carbohydrates, diluting other components.





https://www.nytimes.com/2018/05/25/opinion/sunday/meat-antibiotics-organic-farming.html This is a link to a NYT article about the use of antibiotics in the meat industry, in animal farms, and ultimately in our food.  Antibiotics are added to animal feed not just to prevent microbial diseases but also to improve rates of growth. In 2017, the FDA enacted legislation to ban the use of human antibiotics for growth promotion due the the increase in the numbers of humans infected with antibiotic-resistant bacteria. According to the CDC, more than 400,000 people in the US become ill due to infection with food-borne antibiotic resistant bacteria every year. Recent studies of gut microbiota have determined that antibiotics were take as medication can disrupt our native microbiota and lead to the increase in chronic diseases and allergies. Antibiotic misuse in livestock and people may be destroying our ability to fight certain diseases and infections. Handwriting on the wall department.


A book the solipsistssoiree wants to heartily recommend is "She Has Her Mother's Laugh" by eminent science writer Carl Zimmer. Mr. Zimmer writes amusingly, personally and elegantly about the history, understandings and, more frequently, misunderstandings of heredity in a way that moves genetics out of the Punnet Square realm into the force it has become in modern society since the deciphering of the human genome.





https://www.nytimes.com/2018/05/26/opinion/sunday/insects-bugs-naturalists-scientists.html?login=email&auth=login-email This opinion piece in the NYT is by a professor of natural science about the reduction in biomass of flying insects. A recent study of 63 locations in Germany over the past four seasons concluded that there was 76% decline in the total biomass of insects.  Why should we care? Insects are pesky critters. The author, a "lake scientist", who examines sediment cores from lake bottoms and has published about the loss of plankton communities, suggests that agricultural chemicals may be poisoning aquatic organisms such as plankton and insects that begin their lives as aquatic larva.

April Finally

https://www.nytimes.com/2018/03/31/opinion/sunday/nazi-history-asperger.html This is a link to the NYT article about the German researcher who the disorder Asperger Syndrome is named for. Hans Asperger has contributed to the diagnoses and ideas around people who have :limited social skills and narrow interests", similar to autism, but also was seen as a resister to the Third Reich and its ideas. The writer of the article practiced psychiatry at the University of Vienna in the Nazi era and introduced the diagnosis of "autistic psychopathology" for some of the disturbed children he treated. Some of his categorizations of their behaviors would result in their being euthanized. Children who were classified as "drains on the state", were killed in special wards and Asperger worked closely with the top figures in Vienna's euthanasia program. In 1994, Asperger disorder was added to the American manual of mental disorders to be reclassied in 2013 as autism spectrum disorder.