Posts Tagged ‘quote’

Opinion | The Pandemic, from the Coronavirus’s Perspective – The New York Times

November 21, 2020

Joshua Lederberg, a Nobel Prize laureate in 1958, at age 33, wrote: “The future of humanity and microbes likely will unfold as episodes of a suspense thriller that could be titled ‘Our Wits Versus Their Genes.’ ”

Wits are fundamentally a product of genes, and in the end, genes beat wits. QT:{{”
Chimpanzees were a species in decline, alas, because of habitat loss and killing by humans; humans were a species in ascendance. The SIVcpz virus reversed its own evolutionary prospects by getting into us and adapting well to the new host. It jumped from a sinking lifeboat onto a luxury cruise ship.

SARS-CoV-2 has done likewise, though its success has occurred much more quickly. It has now infected more than 30 million people, just under half as many as the number of people infected by H.I.V., and in 10 months rather than 10 decades. It’s not the most successful human-infecting virus on the planet — that distinction lies elsewhere, possibly with the Epstein-Barr virus, a very transmissible species of herpesvirus, which may reside within at least 90 percent of all humans, causing syndromes in some and lying latent in most. But SARS-CoV-2 is off to a roaring start.

Now, for purposes of illustration, imagine a different scenario, involving a different virus. In the mountain forests of Rwanda lives a small, insectivorous bat known as Hill’s horseshoe bat (Rhinolophus hilli). This bat is real, but it has been glimpsed only rarely and is classified as critically endangered. Posit a coronavirus, for which this bat serves as reservoir host. Call the virus RhRW19 (a coded abbreviation of the sort biologists use), because it was detected within the species Rhinolophus hilli (Rh), in Rwanda (RW), in 2019 (19).

The Children Never Had Covid. So Why Did They Have Coronavirus Antibodies? – The New York Times

November 19, 2020

Wonder whether the chronic inflammation in asthmatic patients also has similar effects & if this explains why #COVID19 didn’t hit asthmatics quite as hard as was expected.

After examining blood taken from 190 people before the pandemic emerged, Dr. Elledge and his colleagues concluded that many already had antibodies, including the one targeting the base of the spike — presumably from infections with related coronaviruses that cause colds.

But while adults might get one or two colds a year, Dr. Elledge said, children may get up to a dozen. As a result, many develop floods of coronavirus antibodies that are present almost continuously; they may lessen cold symptoms, or even leave children with colds that are symptomless but still infectious.

Making the leap | C&EN Global Enterprise

November 16, 2020

So far, though, efforts to find other mutations that might power the virus’s pandemic prowess have largely fallen short. Starr, Bloom, and their colleagues set out to mutate every position in the
201-amino-acid RBD one by one and then examine how each mutation affects the protein’s folding pattern and capacity to bind ACE2. They found that the region has a high tolerance for mutations. “It can handle a high number of mutations and do its job just fine,” Starr says. The team even found dozens of mutations that boosted the RBD’s ability to bind the ACE2 receptor, but the virus seems to have not adopted any of them (Cell 2020, DOI: 10.1016/j.cell.2020.08.012). That finding suggests that the virus functions effectively with the binding affinity it has, and that there’s no strong selective pressure pushing for mutations that might increase it, Starr says. He wonders if that’s because the virus is tearing through a population that has never encountered it and has no immune defenses against it. “Right now, the virus has basically found a buffet table of susceptible [hosts].”
As the COVID-19 pandemic has progressed, one virus mutation does appear to have become a permanent feature of SARS-CoV-2’s genome. Researchers collecting virus samples from infected patients have been sequencing viral genomes and analyzing the strains spreading in different parts of the world. They have found that one mutation, a change from an aspartic acid (D614) to a glycine (G614), is now present in the majority of SARS-CoV-2 viral sequences. People infected with strains carrying this mutation tend to shed more virus than those infected with strains that don’t, hinting that this mutation may make the virus more infectious (Cell 2020, DOI:
10.1016/j.cell.2020.06.043). Farzan’s team has conducted cell studies with the lab-made viruses carrying SARS-CoV-2 spike proteins and found that the mutation causes the virus to more readily infect human cells, perhaps because there are more spike proteins on the virus’s surface (bioRxiv 2020, DOI: 10.1101/2020.06.12.148726v1). The data from those studies have not yet been peer reviewed.

Covid-19 vaccine distribution agreement with pharmacies, measles cases hit 23-year high, & participation in cancer trials

November 15, 2020

Lab Chat: Cleaning up genetic data to protect privacy but get maximum use

As research using genetic data has accelerated in recent decades, scientists are trying to find ways to get the most out of the data while still preserving individuals’ privacy. In a new study, experts describe a program that allows them to “sanitize” and blur out any identifying genetic variants in available data. I spoke with Mark Gerstein and Gamze Gursoy, two authors of the study and bioinformatics researchers at Yale, to learn more:

What is the current problem with privacy, and which datasets have this problem? Gerstein: There is this binary view of privacy — either the data is locked or not locked. It’s hard to aggregate data when it’s locked down and what we’re trying to do in the paper is measure the amount of private information in there so we can just remove that [and access the rest].
Gursoy: Some examples of databases with this problem are the Cancer Genome Atlas, and even the one we manage, called PsychENCODE [for understanding the genetics of psychiatric disorders].

How did you cover up the private data?
Gursoy: We have a reference genome that represents everyone — but there is 1% that’s unique to each of us. So, if you see an “A” in the genetic code of the reference genome, but a “G” in the data you have, you change it to the “A.”
Gerstein: When you use Google’s Street View, the people on the street are unimportant to the information you’re trying to get about stores, etc. The Google car takes pictures of people’s faces, but then finds people in the images and blurs them out. Our process is similar. “}}

Why Polling on The 2020 Presidential Election Missed the Mark – The New York Times

November 14, 2020


Senator Susan Collins did not lead in a single publicly released poll during the final four months of her re-election campaign in Maine. But Ms. Collins, a Republican, won the election comfortably.

Senator Thom Tillis, a North Carolina Republican, trailed in almost every poll conducted in his race. He won, too.

And most polls underestimated President Trump’s strength, in Iowa, Florida, Michigan, Texas, Wisconsin and elsewhere. Instead of winning a landslide, as the polls suggested, Joseph R. Biden Jr. beat Mr. Trump by less than two percentage points in the states that decided the election.

This year’s misleading polls had real-world effects, for both political parties. The Trump campaign pulled back from campaigning in Michigan and Wisconsin, reducing visits and advertising, and lost both only narrowly. In Arizona, a Republican strategist who worked on Senator Martha McSally’s re-election campaign said that public polling showing her far behind “probably cost us $4 or $5 million” in donations. Ms. McSally lost to Mark Kelly by less than three percentage points.

A separate set of changes may involve how the media present polling and whether publications spend as much money on it in the future. “The media that sponsor polls should demand better results because their reputations are on the line,” James A. Baker III, the former secretary of state, wrote in The Wall Street Journal this week.


By David Leonhardt
Nov. 12, 2020

When You Can be Around Others After You Had or Likely Had COVID-19 | CDC

November 8, 2020,viral%20test%20for%20COVID%2D19.


You can be around others after:

10 days since symptoms first appeared and
24 hours with no fever without the use of fever-reducing medications and Other symptoms of COVID-19 are improving*

*Loss of taste and smell may persist for weeks or months after recovery and need not delay the end of isolation

If you continue to have no symptoms, you can be with others after 10 days have passed since you had a positive viral test for COVID-19. “}}

How to Keep the Coronavirus at Bay Indoors – The New York Times

October 4, 2020

thought this was useful…

Tips for dodging the virus as Americans retreat from colder weather: Open the windows, buy an air filter — and forget the UV lights. …
For a classroom or office, a portable air cleaner suited to the room’s size “is a great low-cost plug-and-play strategy to give you several air changes per hour of clean air,” Dr. Allen said. These are compact devices that can be plugged into any outlet; effective models are available for less than $200.
Some people mistakenly think that the average air filter, portable or part of a larger system, is no match for the microscopic virus. But “the virus is not naked in the air,” Dr. Marr said. “It comes out in respiratory droplets.”


Wearing a mask but not covering your nose? You’re doing it all wrong | The Star

October 3, 2020

anosmia & sniff tests

While it’s well established that the primary way people get infected with COVID-19 is from inhaling aerosol droplets, Kennedy said there is emerging evidence it’s “a lot easier” for the virus to get a grip on our internal system when it enters through the nasal passage versus the mouth.

That’s because the nasal passage tissue is rich in cells that have a certain receptor the virus attaches to.

“There’s more cells in the upper airway in the nasal passages that have high levels of receptor expression,” Kennedy explained. “So the virus is more likely to find the cell to infect, and it’s easier for the virus to infect cells sort of in the upper airway in the nasal passages than it is down in the lungs.”
It’s evident the nose and our sense of smell hold many answers to understanding COVID-19. It’s now clear a loss of sense of smell, known as anosmia, is one of the most common symptoms of COVID-19. Valentina Parma, chair of the Global Consortium for Chemosensory Research, said her organization’s data seems to show that anosmia is a better indicator of COVID-19 than fever.

For this reason, she’s an advocate of objective tests to measure sense of smell, such as sniff tests. To that end, her organization has developed an online smell and sniff test which can be completed by people by using scents in their own home, such as banana or shampoo. “}}

Kids Can’t Go to School. Should They Play Youth Sports? – WSJ

October 3, 2020

Sahil is sticking with tennis and golf.

The Elusive Peril of Space Junk | The New Yorker

October 3, 2020

““Imagine how dangerous sailing the high seas would be if all the ships ever lost in history were still drifting on top of the water,” ESA’s director general said at the time. “That is the current situation in orbit, and it cannot be allowed to continue.””
The Elusive Peril of Space Junk