Ricki Lewis's Blog, page 9

On the Third Anniversary of the Pandemic, My 100th COVID Article, With Links to All

Three years ago, health officials in China announced the first cases of infection with a "novel coronavirus."

 

Dr. Zhang Jixian reported the first case on December 26, 2019 in a senior couple living in the residential community near her hospital in Wuhan. An expert in SARS, she recognized the triad of fever, cough, and an unusual pneumonia.

 

The earliest events remain a bit murky.

 

"On December 30th, China reported an outbreak of respiratory disease in Wuhan City, a major transportation hub about 700 miles south of Beijing with a population of more than 11 million people," declared Nancy Messonnier, director of CDC's National Center for Immunization and Respiratory Diseases, on January 17, 2020.

 

But I heard about it on NPR shortly after New Years.

 

My first COVID post was January 23: "I'm astonished at the speed with which geneticists and epidemiologists are zeroing in on the Wuhan coronavirus," referring to the first viral genome sequence announced January 15. Sequencing viral genomes would evolve into a powerful tool of, well, viral evolution, with the US caught behind.

 

It's been a hellish roller coaster ride, with terrible tragedy juxtaposed against some of the most astonishingly brilliant science I've ever encountered. I switched from covering rare genetic disease to following the erupting pandemic, reporting news, interpreting technical reports, and delving into the history of epidemiology.

 

To continue reading, go to DNA Science, where this post first appeared.

‘Lessons in Chemistry’: New Apple TV series based on best-selling book has opportunity to skewer sexism while challenging the ‘nerd stereotype’

I loved Lessons in Chemistry, the hit novel by Bonnie Garmus, and I'm thrilled that Apple TV+ picked it up "straight-to-series" more than a year before it was published in March 2022. Executive Producer Brie Larson, of "Room" and "Captain Marvel" fame, stars as chemist-turned-TV-cook Elizabeth Zott.

The book is hilarious, fast-paced, and expertly plotted. But while the feminist message is obvious, the subtext simmers with a disturbing "othering" of scientists. Let's see what happens with the TV version, which debuts in 2023.

 

Book synopsis

In 1956 Elizabeth Zott works at the Hastings Research Institute in Commons, California, "EZ" emblazoned on her lab coat. She has a master's in chemistry, which in science generally means failing to pass qualifying exams — sometimes it's even called a "terminal masters," like a cancer. 

 

When she hunts for spare beakers in the lab of star chemist Calvin Evans, he assumes she's a secretary. Two weeks later, they bump into each other at an operetta and Calvin, sick from something he ate and after his date bolts, promptly barfs on her. 

 

The two share interests, traumatic upbringings, and a physical attraction that neither at first wants to acknowledge. But they bond (more a covalent sharing than an ionic exchange). She tends to get on her soapbox, lamenting the system that keeps women out of science. 

 

"'You're saying,' he said slowly, 'that more women actually want to be in science,'" Calvin probes incredulously. 

 

To continue reading, go to Genetic Literacy Project, where this post first appeared. 

Ten Lessons from COVID: A Round-up of Experts

Planning for the next pandemic begins with acknowledging what we did wrong for COVID-19. As the situation has calmed, experts are weighing in on what we did, and didn't do, as the months unfolded. I've distilled and organized their comments from the medical literature and webinars. Several of the opinions are from Preventing the Next Pandemic: New Tools for Global Surveillance, which the Harvard T. H. Chan School of Public Health held for journalists October 17, 2022.

 

Next time, we should:

 

1. Recognize the field of ethics as practical, not just an academic discipline.
Determining the 'right' course of action in many circumstances proved more vexing and controversial than solving the technical challenges, such as developing vaccines and treatments, wrote Ezekiel Emanuel, Vice Provost for Global Initiatives at the University of Pennsylvania and colleagues, in The New England Journal of Medicine ("What COVID Has Taught the World About Ethics").

 

To continue reading, go to DNA Science, where this post first appeared.

On COVID Origin and Omicron Persistence: This Geneticist’s View

The latest phrase borrowed from biology in COVID conversations is convergent evolution. It refers to pairs of unrelated species that look similar because their ancestors evolved under similar environmental conditions. Natural selection favored adaptive (helpful) inherited traits, and millennia later, two unrelated species of mammals or birds look remarkably alike.

 

Convergent evolution happens to viruses, too. It is unspooling right now as SARS-CoV-2 genome evolution coalesces into variations on the Omicron theme.

 

The natural history of SARS-CoV-2 began with the wild type, another term from classical genetics. It means "most common," not "normal" as the media often misuses it.

 

As the virus changed, we grouped sets of new mutations, which substitute one RNA base of the genome at a time, into "variants." We named them, which biologists tend to do.

 

Alpha, recognized in November 2020, begat beta, gamma, and delta, all of which stayed with us for a bit. The next few versions were fleeting. The International Committee on Taxonomy of Viruses and WHO skipped Nu (because it sounds like "new") and Xi (a common surname), landing on Omicron. And natural selection has favored its collection of mutations. No new Greek letters necessary.

 

When Species Look Alike

 

Biologists term traits that are alike in two species that arise from recent shared ancestors homologous, while similar structures or behaviors that arise from similar environmental exposures are analogous. Convergent evolution reflects responses to similar environments (analogy), rather than descent from recent shared ancestors (homology).

 

Striking examples of convergent evolution are pairs of placental mammals and Australian marsupials. These include anteaters, moles, wolves, ocelots and native cats, flying squirrels and flying phalangers, and groundhogs and wombats.

 

To continue reading, go to DNA Science, where this post first appeared.

A 2-Million-Year-Old Ecosystem in the Throes of Climate Change Revealed in Environmental DNA

The reconstruction of a once-living landscape in northern Greenland from 2 million years ago, deduced from bits of DNA bound to minerals, reveals an Ice Age ecosystem in the throes of climate change that may suggest ways to mitigate rising global temperatures today. The collection, analysis, and interpretation of environmental DNA from this distant time and place provides a "genetic roadmap" for how organisms can adapt to a warming climate. The work is the cover story in Nature this week. Six of the 40-member multinational team discussed the findings at a news conference.

 

eDNA

 

Environmental DNA – eDNA – is used to describe habitats both ancient and contemporary. Until now, the oldest eDNA was from a mammoth that lived in Siberia one million years ago.

 

To continue reading, go to DNA Science, where this post first appeared. Image credit Beth Zaiken.

Men Can't Do Zumba. Is It In Their Genes?

Zumba saved me during the pandemic. Prior to COVID, I took 3 or 4 of the ATP-burning classes a week (for the uninitiated, ATP stands for adenosine triphosphate, the molecule that cells split to release energy). But in March 2020, when the world shut down, my beloved dance classes suddenly ceased. I remember my last class. Only ten people attended, because so many were already too scared to venture out. 

 

As lockdown continued, I found thousands of dance videos online, favoring a blond woman instructor from Germany and groups of teens from the Philippines and South Korea. It felt worldly while being trapped. My local Zumba instructors quickly reinvented themselves for zooming. Then when the world started to open up again, I returned to classes, masked until that, too, was dropped.

 

The one thing that stood out, especially during COVID, was how few men participated. Part of the reason may be a reaction to what some may have felt was a 'girly' exercise. But is something else going on here?

 

To continue reading, go to Genetic Literacy Project, where this post first appeared.

Halloween Evokes Thoughts on Organoids

When the jello brains and gummy organs of Halloween come out, my thoughts turn to organoids. These are tiny organs, or parts of them, grown in lab dishes or transplanted into rodents, so we can watch a disease begin and maybe even test a candidate drug. Organoid technology isn't a headline hog like CRISPR, but it's intriguing, and certainly easier to envision.

 

Organoids that appear from dividing stem cells offer a landscape of early development – the process of organogenesis. A heart, liver, or kidney takes form from dividing, folding, and interacting cells, a little like watching a photographic image emerge and sharpen in a pan of developer, for those who remember that technology.

 

To continue reading. go to DNA Science, where this post first appeared.

My Five-Year Breast Cancerversary

Five years ago today, I learned that I had breast cancer.

 

I didn't find out in the usual way, an alarmingly ambiguous phone call and then a sit-down with my doctor. The radiologist knew I saw patients in the office for genetic counseling, so while I was getting dressed after my annual mammogram, she beckoned me to her nearby office.

"Take a look at the two screens, Ricki. The left one is last year's image."

 

It didn't take training in radiology to see that something had happened since last year's mammogram. On the right screen, a small mass blocked a narrow passageway, a milk duct.

 

When the radiologist enlarged the image, the clump of cells was not only blocking the duct, but pushing against one wall. I realized instantly that if I had skipped my mammogram that year, the next year's scan would have shown invasive cancer.

 

 

To continue reading, go to DNA Science, where this post first appeared.

Nobel Prize to Paleogenetics Rockstar Svante Pääbo Evokes Memories of Being Drawn to Science

One of my favorite places as a child was the American Museum of Natural History. While most kids would rush to the towering dinosaur skeletons, I'd stand, transfixed, at a small glass-enclosed display of skulls and try to envision what their owners had looked like – australopithecines, Neanderthals, a few others. I remember that part of the museum as The Hall of Man; it's now the Hall of Human Origins.

 

Discovering My First Fossil

 

I loved the museum, but yearned to discover things myself. That happened when I was in the fourth grade, and my parents took my sister and me to the Baseball Hall of Fame in Cooperstown, NY. We couldn't have cared less about baseball. But behind the motel, we waded in a stream, where the angle of the sun on the wet rocks revealed striking patterns of stripes. I picked one up, and realized that it wasn't an ordinary rock.

 

It was a fossil. Edith and I spent the weekend collecting.

 

To continue reading, go to DNA Science, where this post first appeared.

The Age of the Pangenome Dawns

"Pan" has several meanings.

 

As a noun, it refers to "a round metal container that often has a long handle and a lid."

 

As a verb, it means criticism, like panning a film.

 

Peter Pan refers to an adult who doesn't want to behave like one, from Sir James Barrie's play about the boy who didn't want to grow up

 

As a prefix, "pan," from the Greek, means "all, every, whole, and all-inclusive."

 

Sigmund Freud reportedly used the term pan-sexualism in 1914, to mean "sex as a motivator of all things."

 

In genetics, the human pangenome is a complete reference of human genome diversity. It is envisioned as a new type of map that represents all of the ways that the sequence of 3,054,832 billion DNA base pairs – the building blocks of a genome – vary, plus or minus a few from short repeated sequences. The depiction is so densely packed that it resembles a map of the New York City subway system.

 

The Human Pangenome Reference Consortium is spearheading creation of a "genome reference representation that can capture all human genome variation and support research on the full diversity of populations."

 

 

To continue reading, go to DNA Science, where this post first appeared.