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Genetic Linkage

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.

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In Search of a Religiosity Gene

Do our genes predispose us to follow a religion? I searched Google Scholar for reports on the inheritance of religiosity.


I sought something scientific – does being religious favor the survival-to-reproduce that fuels natural selection of an adaptive inherited trait?


I skipped regular Google and mainstream media, seeking data and not opinions, and included "inheritance" and "religiosity" in my search. To me inheritance means genes that encode proteins that affect the phenotype (trait or illness). But inheritance also means passing something from parents to offspring – such as money, property, possessions, or ideals.


Surely someone had done a genome-wide association study for "religiosity." A "GWAS" is a survey of single-DNA-base positions (SNPs) in a genome where individuals vary, having any of the four DNA bases. These studies have been around for two decades, seeking evidence for genetic underpinnings of such traits as antisocial behavior, loneliness, and even political ideologies.


Today researchers use an abbreviated "polygenic risk score" to describe so-called complex traits – those influenced by several genes as well as environmental factors. In contrast to an either-or diagnosis like cystic fibrosis, a PRS tallies variants of many genes that contribute to a trait or illness.

The investigations that Google Scholar returned came more from the social sciences, using language with which I am admittedly unfamiliar. Here's a brief chronology of five studies that probed whether religiosity is in our genes.


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

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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.




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.

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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.

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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.

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‘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. 

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