Lies, Damned Lies, and Statistics…

Which states have dropped mask mandates and why, Marlene Lenthang, Yahoo News

Topics: Biology, COVID-19, Dark Humor, Existentialism, Mathematics, Politics

Figures often beguile me, particularly when I have the arranging of them myself; in which case the remark attributed to Disraeli would often apply with justice and force: “There are three kinds of lies: lies, damned lies, and statistics.”

Mark Twain, also: https://en.wikipedia.org/wiki/Lies,_damned_lies,_and_statistics

A follow-up to Tuesday’s post: VOC…

‘No Thank You, Mr. President’: GOP States Still End Mask Mandates Despite Covid-19 Rise And Warnings From Biden, CDC, Alison Durkee, Forbes Business, April 2, 2021

Having some “fun” with mathematics. It’s dark humor for all you young libertarians.

The current US COVID deaths are 573, 988 from https://ncov2019.live/.

The current US population is 332,494,997 from Worldometers.info. Each link updates minute-by-minute, so by the time you read this, these figures will have changed.

(US COVID deaths/current US population) x 100 = 0.17%. Round up to 0.2%.

That’s pretty low.

For the “freedom-loving libertarians” spring breaking in Miami, or Fort Lauderdale, Florida, and Corpus Christi, Texas – a thought experiment:

100,000 of you are about to dive in the ocean.

There is a 0.2% = 0.2/100 chance some of you will get devoured by sharks.

100,000 x (0.2/100) = 200 dead spring breakers.

So, out of 100,000 – 200 = 99,800, or 99.8% have a very good chance of not becoming “chicken of the sea,” and surviving your spring break. The dilemma is, there will still be blood in the water. Blood that carries pathogens that despite your “Y” swimming lessons and the saline environment, you might ingest red tide, and suffer the consequences.

The problem is, your 0.2% chance is not zero. Under normal circumstances (and pandemics are once-in-a-century “not normal”), there’s no libertarian case for this:

Ingenuity…

NASA’s Ingenuity Mars helicopter is seen in a close-up taken by Mastcam-Z, a pair of zoomable cameras aboard the Perseverance rover. This image was taken on April 5, 2021, the 45th Martian day, or sol, of the mission.
Credits: NASA/JPL-Caltech/ASU

Topics: Mars, NASA, Space Exploration, Spaceflight

NASA is targeting no earlier than Sunday, April 11, for Ingenuity Mars Helicopter’s first attempt at powered, controlled flight on another planet. To mark a month of Ingenuity flights, the agency will host several events to bring people along for the ride.

A livestream confirming Ingenuity’s first flight is targeted to begin around 3:30 a.m. EDT Monday, April 12, on NASA Television, the NASA app, and the agency’s website, and will livestream on multiple agency social media platforms, including the JPL YouTube and Facebook channels.

Ingenuity arrived at Mars’ Jezero Crater Feb. 18, attached to the belly of NASA’s Perseverance rover. The helicopter is a technology demonstration with a planned test flight duration of up to 31 days (30 Mars days, or sols). The rover will provide support during flight operations, taking images, collecting environmental data, and hosting the base station that enables the helicopter to communicate with mission controllers on Earth.

The flight date may shift as engineers work on the deployments, preflight checks, and vehicle positioning of both Perseverance and Ingenuity. Timing for events will be updated as needed, and the latest schedule will be available on the helicopter’s Watch Online webpage:

https://mars.nasa.gov/technology/helicopter/#Watch-Online

News Briefing and Televised Event Schedule

Virtual media briefings before and after Ingenuity’s first flight attempt and the livestream coverage of the flight attempt will originate from NASA’s Jet Propulsion Laboratory in Southern California.

A preflight briefing at 1 p.m. EDT (10 a.m. PDT) Friday, April 9, will provide the latest details on the helicopter’s operations and what to expect on the first flight day.

NASA Invites Public to Take Flight With Ingenuity Mars Helicopter

VOC…

Inside the B.1.1.7 Coronavirus Variant, By Jonathan Corum and Carl ZimmerJan, The New York Times, January 18, 2021

Topics: Biology, COVID-19, DNA, Research

VariantReported cases in USNumber of Jurisdictions Reporting
B.1.1.716,27552
B.1.35138636
P.135625
Source: CDC

Download Accessible Data [XLS – 738 B]

CDC is closely monitoring these variants of concern (VOC). These variants have mutations in the virus genome that alter the characteristics and cause the virus to act differently in ways that are significant to public health (e.g., causes more severe disease, spreads more easily between humans, requires different treatments, changes the effectiveness of current vaccines).

CDC: US COVID-19 Cases Caused by Variants

Weather Prediction…

Observations of clouds, sunbeams, and birds—like those seen in this photo taken in Salisbury, UK—were important elements of classical weather forecasting. (Image courtesy of Peter Lawrence.)

Topics: History, Meteorology, Research

In August 1861 the London-based newspaper The Times published the world’s first “daily weather forecast.” The term itself was created by the enterprising meteorologist Robert FitzRoy, who wanted to distance his work from astrological “prognostications.” That story has led to a widespread assumption that weather forecasting is an entirely modern phenomenon and that in earlier periods only quackery or folklore-based weather signs were available.

However, more recent research has demonstrated that astronomers and astrologers in the medieval Islamic world drew widely on Greek, Indian, Persian, and Roman knowledge to create a new science termed astrometeorology. Central to the new science was the universal belief that the planets and their movements around Earth affected atmospheric conditions and weather. It was enthusiastically received in Christian Latin Europe and was further developed by Tycho Brahe, Johannes Kepler, and other astronomers. The drive to produce reliable weather forecasts led scientists to believe that astrometeorological forecasting could be more accurate if they used precise observations and records of weather to refine predictions for specific localities. Such records were kept across Europe beginning in the 13th century and were correlated with astronomical data, which paved the way for the data-driven forecasts produced by FitzRoy.1

Islamicate astrometeorologists were the first to replace the ancient practice of observing only short-term signs, such as clouds and the flight of birds, to predict weather. They based their action on the hypothesis that weather is caused by the movements of planets and mediated by regional and seasonal climate conditions. Improved calculations of planetary orbits and updated geographical and meteorological information made the new science possible and compelling.

The prospect of acquiring reliable weather forecasts, closely linked to predictions of coming trends in human health and agricultural production, made the new meteorology attractive in Christian Europe too. Considerable pride shines through medieval Christian accounts of the weather questions that they could now start to answer. Central among them was one that classical meteorologists had failed to figure out: How can weather vary so much from one year to the next when the seasons are caused by regular, repeating patterns produced by Earth’s spherical shape and its interactions with the Sun?

Medieval weather prediction, Anne Lawrence-Mathers is a professor of history at the University of Reading in the UK. Physics Today

Asteroids, Dinosaurs, and Rain Forests…

Topics: Asteroids, Biology, Evolution, Existentialism, Research

Note: Working on two reviews, and my research proposal. It’s a very busy writing semester.

Dinosaur and fossil aficionados are intimately familiar with the meteorite strike that drove Tyrannosaurus rex and all nonavian dinosaurs to extinction around 66 million years ago. But it is often overlooked that the impact also wiped out entire ecosystems. A new study shows how those casualties, in turn, led to another particularly profound evolutionary outcome: the emergence of the Amazon rain forest of South America, the most spectacularly diverse environment on the planet. Yet the Amazon’s bounty of tropical species and habitats now face their own existential threat because of unprecedented destruction from human activity, including land clearing for agriculture.

The new study, published on Thursday in Science, analyzed tens of thousands of plant fossils and represents “a fundamental advance in knowledge,” says Peter Wilf, a geoscientist at Pennsylvania State University, who was not involved in the research. “The authors demonstrate that the dinosaur extinction was also a massive reset event for neotropical ecosystems, putting their evolution on an entirely new path leading directly to the extraordinary, diverse, spectacular and gravely threatened rain forests in the region today.”

These insights, Wilf adds, “provide new impetus for the conservation of the living evolutionary heritage in the tropics that supports human life, along with millions of living species.”

The Asteroid That Killed the Dinosaurs Created the Amazon Rain Forest, Rachel Nuwer, Scientific American

Women’s History Month, and CRISPR…

Topics: Biology, Chemistry, DNA, Nobel Prize, Research, Women in Science

This year’s (2020) Nobel Prize in Chemistry has been awarded to two scientists who transformed an obscure bacterial immune mechanism, commonly called CRISPR, into a tool that can simply and cheaply edit the genomes of everything from wheat to mosquitoes to humans. 

The award went jointly to Emmanuelle Charpentier of the Max Planck Unit for the Science of Pathogens and Jennifer Doudna of the University of California, Berkeley, “for the development of a method for genome editing.” They first showed that CRISPR—which stands for clustered regularly interspaced short palindromic repeats—could edit DNA in an in vitro system in a paper published in the 28 June 2012 issue of Science. Their discovery was rapidly expanded on by many others and soon made CRISPR a common tool in labs around the world. The genome editor spawned industries working on making new medicines, agricultural products, and ways to control pests.

Many scientists anticipated that Feng Zhang of the Broad Institute, who showed 6 months later that CRISPR worked in mammalian cells, would share the prize. The institutions of the three scientists are locked in a fierce patent battle over who deserves the intellectual property rights to CRISPR’s discovery, which some estimate could be worth billions of dollars.

“The ability to cut DNA where you want has revolutionized the life sciences. The genetic scissors were discovered 8 years ago, but have already benefited humankind greatly,” Pernilla Wittung Stafshede, a chemical biologist at the Chalmers University of Technology, said at the prize briefing.

CRISPR was also used in one of the most controversial biomedical experiments of the past decade, when a Chinese scientist edited the genomes of human embryos, resulting in the birth of three babies with altered genes. He was widely condemned and eventually sentenced to jail in China, a country that has become a leader in other areas of CRISPR research.

Although scientists were not surprised Doudna and Charpentier won the prize, Charpentier was stunned. “As much as I have been awarded a number of prizes, it’s something you hear, but you don’t completely connect,” she said in a phone call with the Nobel Prize officials. “I was told a number of times that when it happens, you’re very surprised and feel that it’s not real.”

At a press briefing today, Doudna noted she was asleep and missed the initial calls from Sweden, only waking up to answer the phone finally when a Nature reporter called. “She wanted to know if I could comment on the Nobel and I said, Well, who won it? And she was shocked that she was the person to tell me.”

CRISPR, the revolutionary genetic ‘scissors,’ honored by Chemistry Nobel, Jon Cohen, Science Magazine, AAAS

Mask Mandates and Starships…

Topics: Civics, Civil Rights, Climate Change, COVID-19, Democracy, Existentialism, Human Rights

Thank you, Reginald!

You’re all signed up for “(1st Dose) COVID – 19 Vaccine Clinic.”

Vaccine Appointment

03/11/2021 (Thu.) 1:45pm – 2:00pm EST

Location: NC A&T Alumni Foundation Building (200 N. Benbow Rd.)

My Comment: Older graduate student, 58 years.

Thank you for registering to receive dose 1 of the COVID-19 vaccine. Please note the following:

The instructions noted the address (I knew), where to park in proximity to the NC A&T Alumni Foundation building, instructions to enter the building from N. Benbow Road, and to bring a valid student ID. The same building I’ve celebrated the Greensboro Four every first of February, kicking off African American/Black History Month at the nation’s largest HBCU.

My wife received her first dose of the Pfizer vaccine last Saturday at the Greensboro Coliseum. It’s the ten-year anniversary of the Fukushima Daichi accident. I received my first dose of the Moderna vaccine on also ironically, the first anniversary the World Health Organization declared SARS-CoV-2, the Novel Coronavirus, a worldwide pandemic.

Every STEM major student at a primary or historically black college suddenly was thrust into a world of “I Am Legend” protocols against an invisible zombie apocalypse. Navigating research to attain a Master’s, or Ph.D. is challenging enough: add to it KN95 masks, 3.66 meters of social distance (12 feet, for the British unit crowd), washing hands, hand sanitizers every 10 meters, and protocol-driven digital, and analog sign-in/sign-out for contact tracing. There’s also been isolation, the lack of banter with classmates, no lunches between experiments, or card games. Science is from our hunter-gatherer ancestors: it’s a social exercise. Our worlds have been reduced to the dimensions of our laptop monitors, the visual cues common to hominids in conversation reduced to two-dimensional “Zoom fatigue.”

To cope with the angst of “sameness,” I retreated, or returned more apt and accurately, to spoken word poetry: STEM extended by one vowel is STEAM, the “A” for art, and Einstein played the violin. On Sundays, I perform for a venue in Austin, Texas that’s called “Spoken and Heard,” started by a friend going by the stage name “Element 615” (don’t bother looking it up: it doesn’t exist), managed by some poetry friends, and streamed on Facebook and YouTube via Skype. Our poetry tends to center on the topics of the recent week’s news.

Mask Mandates and Starships” was my reaction to the day before, the state of Texas lifted their statewide mask mandate. The news for Greg Abbott’s re-election looked grim after botched handling of a once-in-a-hundred-years climate change event (that seems to be occurring annually). If Abbott didn’t learn anything from the last administration when you can’t solve a problem: bluff, blame, and deflect to something else. Gaslighting 101. It solves nothing but shows his disdain for the citizens of Texas: he really thinks they’re stupid. No one rows a boat, or pilots a light sail in multiple directions. It gets you nowhere fast.

The thesis of the piece is, it will take extreme and global cooperation to build ONE vehicle capable of interstellar travel, let alone a fleet of them. The same cooperation we’re going to need to get out of this pandemic. Though there is much writing of papers on the Alcubierre Drive, a breakthrough to superluminal speeds taking us to other worlds is highly unlikely. We’re born, will live, and die on this one. Hopefully, so will our progeny. We still have radiation poisoning, the current, and future pandemics, climate disasters that are occurring with the frequency of subway lines in New York, or Philly. Continuation of any civilization isn’t guaranteed, and discontinuations have many precedents in history.

Zoonotic diseases aren’t new, and they tend to strike every one hundred years. The Great Dying was due to the introduction of things like measles, smallpox, influenza, typhus, and tuberculosis to Native American populations by the invasion of Spain and Portugal to the Americas. It is naïve, and ignorant to name any pathogen after its point of origin; racist and xenophobic to center it on one culture. It is also placing whole populations not responsible for the spread in danger of physical violence, which solves nothing. The first piece of legislation on immigration was the Chinese Exclusion Act of 1882, meant to curb the rise in their population for ten years, signed into law by President Chester A. Arthur on May 6, 1882. This is in America’s DNA. Tribalism and any other narcissistic “ism” will not save us.

Asian Americans scapegoated. Black Lives (obviously don’t) Matter. The LGBT are human beings, not scarecrows hung like Matthew Shepard. “Women’s Rights ARE Human rights.” Unless the pathogen was dropped on us from Alpha Centauri, it, and we all live here.

We either live together or die miserably, and sadly into extinction.

What if this pandemic, / Is Gia’s test / Before we leave the nest? / “In space, no one can hear [you]r screams,” / No matter replicators or Uber Eats, / No 911 to call for assistance, / No tribes to define oneself with, / No conservatives, liberals, republicans, or democrats, / The only question is, “no rescue is coming; can WE fix it?” / No poetic Latin words E Pluribus Unum, / The only governing philosophy boiled down to three letters: GSD, equaling “get shit done!” / More “final frontier” than we’ve ever been,.. from “Mask Mandates and Starships.”

We conclusively know now we cannot gaslight a pandemic. 543,690 deaths, and counting. If we can’t do the simple things, are we mature enough to become a space-faring species?

What if? Are we?

We all know the truth: more connects us than separates us. But in times of crisis, the wise build bridges, while the foolish build barriers. We must find a way to look after one another as if we were one single tribe. Chadwick Boseman, as King T’Challa in the movie, “Black Panther” (Rest In Power), from Internet Movie Database.

Snaps From Perseverance…

Combining two images, this mosaic shows a close-up view of the rock target named “Yeehgo” from the SuperCam instrument on NASA’s Perseverance rover on Mars. The component images were taken by SuperCam’s Remote Micro-Imager (RMI). To be compatible with the rover’s software, “Yeehgo” is an alternative spelling of “Yéigo,” the Navajo word for diligent.
Credits: NASA/JPL-Caltech/LANL/CNES/CNRS/ASU/MSSS
Annotated version

Topics: Mars, NASA, Space Exploration, Spaceflight

Data from the powerful science tool includes sounds of its laser zapping a rock in order to test what it’s made of.  

The first readings from the SuperCam instrument aboard NASA’s Perseverance rover have arrived on Earth. SuperCam was developed jointly by the Los Alamos National Laboratory (LANL) in New Mexico and a consortium of French research laboratories under the auspices of the Centre National d’Etudes Spatiales (CNES). The instrument delivered data to the French Space Agency’s operations center in Toulouse that includes the first audio of laser zaps on another planet.

“It is amazing to see SuperCam working so well on Mars,” said Roger Wiens, the principal investigator for Perseverance’s SuperCam instrument from Los Alamos National Laboratory in New Mexico. “When we first dreamed up this instrument eight years ago, we worried that we were being way too ambitious. Now it is up there working like a charm.”

Perched atop the rover’s mast, SuperCam’s 12-pound (5.6-kilogram) sensor head can perform five types of analyses to study Mars’ geology and help scientists choose which rocks the rover should sample in its search for signs of ancient microbial life. Since the rover’s Feb. 18 touchdown, the mission has been performing health checks on all of its systems and subsystems. Early data from SuperCam tests – including sounds from the Red Planet – have been intriguing.

“The sounds acquired are remarkable quality says Naomi Murdoch, a research scientist and lecturer at the ISAE-SUPAERO aerospace engineering school in Toulouse. “It’s incredible to think that we’re going to do science with the first sounds ever recorded on the surface of Mars!”

Perseverance Rover’s SuperCam Science Instrument Delivers First Results

Our Flexible Molecule…

1 Soap, shampoo and worm-like micelles a Soaps and shampoos are made from amphiphilic molecules with water-loving (red) and water-hating (blue) parts that arrange themselves to form long tubes known as “worm-like micelles”. Entanglements between the tubes give these materials their pleasant, sticky feel. b The micelles can, however, disentangle themselves, just as entangled long-chain polymer molecules can slide apart too. In polymers, this process can be modelled by imagining the molecule sliding, like a snake, out of an imaginary tube formed by the surrounding spatial constraints. c Worm-like micelles can also morph their architecture by performing reconnections (left), breakages (down) and fusions (right). These operations occur randomly along the backbone, are in thermal equilibrium and reversible. (Courtesy: Davide Michieletto)

Topics: Biology, DNA, Physics, Polymer Science, Research

DNA molecules are not fixed objects – they are constantly getting broken up and glued back together to adopt new shapes. Davide Michieletto explains how this process can be harnessed to create a new generation of “topologically active” materials.

Call me naïve, but until a few years ago I had never realized you can actually buy DNA. As a physicist, I’d been familiar with DNA as the “molecule of life” – something that carries genetic information and allows complex organisms, such as you and me, to be created. But I was surprised to find that biotech firms purify DNA from viruses and will ship concentrated solutions in the post. In fact, you can just go online and order DNA, which is exactly what I did. Only there was another surprise in store.

When the DNA solution arrived at my lab in Edinburgh, it came in a tube with about half a milligram of DNA per centimeter cube of water. Keen to experiment on it, I tried to pipette some of the solution out, but it didn’t run freely into my plastic tube. Instead, it was all gloopy and resisted the suction of my pipette. I rushed over to a colleague in my lab, eagerly announcing my amazing “discovery”. They just looked at me like I was an idiot. Of course, solutions of DNA are gloopy.

I should have known better. It’s easy to idealize DNA as some kind of magic material, but it’s essentially just a long-chain double-helical polymer consisting of four different types of monomers – the nucleotides A, T, C and G, which stack together into base pairs. And like all polymers at high concentrations, the DNA chains can get entangled. In fact, they get so tied up that a single human cell can have up to 2 m of DNA crammed into an object just 10 μm in size. Scaled up, it’s like storing 20 km of hair-thin wire in a box no bigger than your mobile phone.

Make or break: building soft materials with DNA, Davide Michieletto is a Royal Society university research fellow in the School of Physics and Astronomy, University of Edinburgh

Haplotypes and Neanderthals…

a, Manhattan plot of a genome-wide association study of 3,199 hospitalized patients with COVID-19 and 897,488 population controls. The dashed line indicates genome-wide significance (P = 5 × 10−8). Data were modified from the COVID-19 Host Genetics Initiative2 (https://www.covid19hg.org/). b, Linkage disequilibrium between the index risk variant (rs35044562) and genetic variants in the 1000 Genomes Project. Red circles indicate genetic variants for which the alleles are correlated to the risk variant (r2 > 0.1) and the risk alleles match the Vindija 33.19 Neanderthal genome. The core Neanderthal haplotype (r2 > 0.98) is indicated by a black bar. Some individuals carry longer Neanderthal-like haplotypes. The location of the genes in the region are indicated below using standard gene symbols. The x axis shows hg19 coordinates.

Topics: Biology, COVID-19, Genetics, Research

Abstract

A recent genetic association study1 identified a gene cluster on chromosome 3 as a risk locus for respiratory failure after infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A separate study (COVID-19 Host Genetics Initiative)2 comprising 3,199 hospitalized patients with coronavirus disease 2019 (COVID-19) and control individuals showed that this cluster is the major genetic risk factor for severe symptoms after SARS-CoV-2 infection and hospitalization. Here we show that the risk is conferred by a genomic segment of around 50 kilobases in size that is inherited from Neanderthals and is carried by around 50% of people in south Asia and around 16% of people in Europe.

Main

The COVID-19 pandemic has caused considerable morbidity and mortality, and has resulted in the death of over a million people to date3. The clinical manifestations of the disease caused by the virus, SARS-CoV-2, vary widely in severity, ranging from no or mild symptoms to rapid progression to respiratory failure4. Early in the pandemic, it became clear that advanced age is a major risk factor, as well as being male and some co-morbidities5. These risk factors, however, do not fully explain why some people have no or mild symptoms whereas others have severe symptoms. Thus, genetic risk factors may have a role in disease progression. A previous study1 identified two genomic regions that are associated with severe COVID-19: one region on chromosome 3, which contains six genes, and one region on chromosome 9 that determines ABO blood groups. Recently, a dataset was released by the COVID-19 Host Genetics Initiative in which the region on chromosome 3 is the only region that is significantly associated with severe COVID-19 at the genome-wide level (Fig. 1a). The risk variant in this region confers an odds ratio for requiring hospitalization of 1.6 (95% confidence interval, 1.42–1.79) (Extended Data Fig. 1).

The genetic variants that are most associated with severe COVID-19 on chromosome 3 (45,859,651–45,909,024 (hg19)) are all in high linkage disequilibrium (LD)—that is, they are all strongly associated with each other in the population (r2 > 0.98)—and span 49.4 thousand bases (kb) (Fig. 1b). This ‘core’ haplotype is furthermore in weaker linkage disequilibrium with longer haplotypes of up to 333.8 kb (r2 > 0.32) (Extended Data Fig. 2). Some such long haplotypes have entered the human population by gene flow from Neanderthals or Denisovans, extinct hominins that contributed genetic variants to the ancestors of present-day humans around 40,000–60,000 years ago6,7. We therefore investigated whether the haplotype may have come from Neanderthals or Denisovans.

The major genetic risk factor for severe COVID-19 is inherited from Neanderthals, Hugo Zeberg, & Svante Pääbo, Nature