Ricki Lewis

It's been a strange and busy 15 months for science journalists.

Each day, throughout the day, our inboxes overflow with the latest from the technical medical and science journals – tables-of-contents, abstracts, news releases, and the never-ending stream of article preprints. We jumpstart the journals by going straight to medRxiv and bioRxiv, aka "med-archive" and "bio-archive," where investigators post articles before peer review.

Where We Get Information

It's a deluge, an unrelenting barrage of new reports from the Science and Nature family of journals; the medical journals like JAMA, the Lancet group, and the NEJM; and publications that cover more basic science, like Cell and the journals from Public Library of Science, which has sponsored this blog since 2012. The journals send wrap-ups on the weekends, in case we've missed anything.

The clearinghouse for news releases for journalists, Eurekalert, provides information from a wide range of publications, government agencies, academic institutions, research centers, nonprofits, and companies, with quotes from experts and images and videos we can use. Eurekalert added a COVID tab to the topics menu early in the pandemic. Much appreciated!

As we try to stay ahead of our inboxes, we're invited to webinars, zooms, and podcasts, all wonderfully helpful in crafting our stories.

To continue reading, go to my DNA Science blog at Public Library of Science, where this post first appeared.

A year ago, the Director General of the World Health Organization, Tedros Adhanom Ghebreyesus, delivered the message that would divide time:

"WHO has been assessing this outbreak around the clock and we are deeply concerned both by the alarming levels of spread and severity, and by the alarming levels of inaction. We have therefore made the assessment that COVID-19 can be characterized as a pandemic."

What followed was a call to action to all. "We have rung the alarm bell loud and clear." And instantly, the redundant "global pandemic" ricocheted across the media, reverberating still.

The name of the enemy had changed quickly as 2020 began, from the "Wuhan coronavirus" to "2019 novel coronavirus" shortened to "2019-nCoV," and finally to SARS-CoV-2, acknowledging similarity to SARS, circa 2003-2004.

Whatever it's name, did SARS-CoV-2 have an older guise, perhaps in a lab?

The Bioweapon Hypothesis

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

Glimmers of hope are beginning to shine through the gloom of the past year. That was evident in a recent webinar that the Massachusetts Consortium on Pathogen Readiness (MassCPR) held to "demystify" the new viral variants. Each consists of several mutations.

Will the variants fuel "a novel stage of contagion, COVID 2.0?" opened George Daley, MD, PhD, dean of Harvard Medical School. "What has been unsettling is how many times mutations have cropped up independently in infected patients across the globe and in petri dishes. This is a consequence of Darwinian evolution by natural selection in real time," he added. The fact that the virus, SARS-CoV-2, has mutated in the same ways at different times and places suggests that the changes benefit the virus.

Also disturbing is that once variants appear, they proliferate. "That suggests the virus is more contagious, or replicates faster, so that it takes over the outbreak," said Jeremy Luban, MD, from the University of Massachusetts Medical School. Most mutations are neutral; we need to worry when they combine into "variants of concern," aka VOC. "They could permit the virus to escape immune control that's been established in a person from prior infection or from a vaccine," Luban added.

The "big three" variants of most concern now have hard-to-remember numerical names, which avoid stigmatizing a place: B.1.3.5.1 variant (South Africa), B.1.1.7 (UK), and P.1 (Brazil). The last one may be the worst to arise, so far. It first came to attention in Manaus, Amazonia. "Up to 70% of the population had been infected and they had developed what we'd consider herd immunity that would prevent new infection," Luban explained. The explosion of hospitalizations and deaths in December, a second wave, coincided with the appearance of the P.1 variant. "Many mutations in it raise concerns about whether the virus is resistant to the immune response against the first virus," he added.

Tackling variants requires asking three questions, Luban said:
• Do they enhance transmission?
• Do they permit reinfection?
• Do they decrease vaccine efficacy?

Fortunately, the vaccines so far are doing their job. Here are 6 pieces of good news.

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

I can't believe it's been a decade since I researched and wrote The Forever Fix: Gene Therapy and the Boy Who Saved It. Since then I've shared stories of other families doing amazing things to help researchers develop treatments for their loved ones' rare diseases. The need is all the more compelling in these days of the pandemic.

Now entering its fourth decade, gene therapy continues along what seems at times a never-ending rocky road, riding the waves of fantastic success and plunging setbacks.

A Slow Start

The US has approved just two gene therapies. Luxturna has provided vision to patients with a form of retinal blindness (the basis of The Forever Fix), while Zolgemsa treats spinal muscular atrophy, a disease typically lethal in young children.

The latest in a series of setbacks, beginning in 1999 with the death of 18-year-old Jesse Gelsinger, came just yesterday. The FDA placed a clinical hold on two gene therapy trials for sickle cell disease, following reports of blood cancer in two trial participants. But that's not all.

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

Bits of human brain growing in a lab dish can reveal a great deal about how a disease begins and unfolds. But because the brain is also the seat of our consciousness and individuality, does disembodying it for science's sake pose bioethical challenges? 

That's what Stanford Law School researcher Henry (Hank) T. Greely addressed in "Human Brain Surrogates Research: The Onrushing Ethical Dilemma" in the January issue of The American Journal of Bioethics. Will the technology reach a stage at which the brain model is perhaps too close a mimic for comfort?

"If it looks like a human brain and acts like a human brain, at what point do we have to treat it like a human brain — or a human being?" he asks.

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

An international team has assembled billions of DNA snippets from molars that three mammoths left in the permafrost of northeastern Siberia, at widely different times. The research reveals an unrecognized ancestor that contributed half of the genome of the mammoth species that came to North America some 1.5 million years ago. The report appears in Nature.

The timescale of the study paints a portrait of mammoth evolution, perhaps even capturing a glimmer of speciation. The finding also sets back the clock of ancient DNA analysis; a horse that lived 780,000 to 560,000 years ago holds the record.

The three mammoth specimens were excavated in the 1970s from different locations in Siberia, dating from half a million to roughly 1.2 million years ago. They reside at the Geological Institute, Russian Academy of Sciences, in Moscow. The permafrost helped to preserve the DNA.

The Land Bridge Where It Happened

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

I wrote "The Making of a Mutant" in 1978. Then a PhD student in the lab of Thom Kaufman at Indiana University, I snuck the story into a draft of a manuscript we were submitting to the journal Genetics – just to see if the boss was paying attention. The tale was about our research on the mutation Antennapedia in the fruit fly Drosophila melanogaster, which reroutes development so that legs grow where antennae normally extend.

My story was passed down to generations of graduate students, and read aloud at Thom's 60th birthday party many years later. I published "The Making of a Mutant" at Scientific American blogs in 2012, and then here at DNA Science in 2013. It's a geneticist's love story for Valentine's Day.

But never in a million years could I have imagined that my vision of a mutation that takes over a population would echo in the form of a novel coronavirus that is continually reinventing itself as it tears through human bodies and populations.

My story chronicles how the abnormal becomes the normal, and the new normal eventually spawns a new abnormal. That's what evolution is, change at the molecular level that reverberates up through populations of organisms – and viruses. The mutations in my imagined world in a milk bottle, home to the flies, were induced – in contrast to the situation for SARS-CoV-2.

We can't stop evolution. Mutation is a fundamental characteristic of a genetic material, endowing it with the plasticity that underlies adaptation, which fuels evolutionary change.

Evolution of SARS-CoV-2 in a Single Patient

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

"So, you've been eatin' hot dogs and chicken nuggets all your life and you don't want the vaccine 'cuz you don't know what's in it??" asks a befuddled chicken in a meme.

Actually, plenty of information is out there about "what's in it."

Upon entering a vaccination center, you're handed a multi-page fact sheet that, among many other things, lists the chemicals about to be plunged into your arm.

The first two COVID vaccines are roughly the same recipe, adjusted for proportions and tiny details: mRNA, 4 fats (including cholesterol), a pinch of sugar, and a few salts. No eggs, preservatives, ricin, or leechee nut extract. (See The First COVID-19 Vaccines: What's mRNA Got to do With it?) Ingredient lists for hot dogs and chicken nuggets are far longer and complex.

Yet the comparative transparency of vaccine ingredient lists isn't enough to dispel the fear of something new and unfamiliar being jabbed into your body. For many people that fear arises against a backdrop of the history of dishonesty in medicine that has misled and mistreated marginalized groups, as well as the record of unethical clinical trials for some vaccines, notably influenza.

To continue reading go to my DNA Science blog at Public Library of Science, where this post first appeared.

Vaccines against COVID-19 were developed in record-smashing time, and now that the rollout has begun, attention is returning to herd immunity, in a real rather than hypothetical sense.

Herd immunity refers to the protection against an infectious disease that arises when a critical mass of individuals in a population becomes immune. The pathogen can't find welcoming bodies, and the epidemic dies out. Once herd immunity is attained, mitigation measures can be relaxed. But if society opens too soon, a second and even third wave of disease can ensue – as we've seen.

A vaccine, engineered to evoke a strong and diverse antibody response, is more likely to build herd immunity than is natural infection.

Establishing herd immunity against COVID-19 requires that a whole bunch of ducks align. The variables include:

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

A woman lingers at a display of coffeemakers. Soon after, images of the very same contraptions festoon her Facebook feed, courtesy of her phone's GPS and store cameras.

A man diagnosed with a blood clot gets TV ads for a drug to prevent further episodes.

A person peruses ads for indoor herb gardens for a gift and is later bombarded with botanical options on social media.

People turn 65, and suddenly Joe Namath interrupts their favorite TV shows, with unending descriptions of Medicare Supplement plans.

Coincidences? Hardly. In this age of TMI, it can feel as if our very brains are being intrusively picked, constantly.

Even our DNA can be trolled for embedded preferences and habits, if we (sometimes unknowingly) provide permission.

How foreboding is the 'privacy crisis'?
Remi Daviet, Gideon Nave, and Jerry Wind, from the Wharton School of the University of Pennsylvania, dissect "Genetic Data: Potential Uses and Misuses in Marketing," in a report in a special issue of the Journal of Marketing.

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