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kottke.org posts about medicine

Vaccines: “The Greatest Benefit Conferred on Humankind”

From The Economist on the occasion of the award of the Nobel Prize for Medicine to Katalin Karikó and Drew Weissman for their work that led to the development of the Covid-19 mRNA vaccines, a lovely short appreciation of vaccines.

The World Health Organisation (WHO) says that vaccines have saved more from death than any other medical invention. It is a hard claim to gainsay. Vaccines protect people from disease cheaply, reliably and in remarkable numbers. And their capacity to do so continues to grow. In 2021 the who approved a first vaccine against malaria; this week it approved a second.

Vaccines are not only immensely useful; they also embody something beautifully human in their combination of care and communication. Vaccines do not trick the immune system, as is sometimes said; they educate and train it. As a resource of good public health, they allow doctors to whisper words of warning into the cells of their patients. In an age short of trust, this intimacy between government policy and an individual’s immune system is easily misconstrued as a threat. But vaccines are not conspiracies or tools of control: they are molecular loving-kindness.

The WHO says that vaccines currently prevent 4-5 million deaths per year. The CDC points to a paper that says that more than 50 million death can be prevented between 2021 and 2030. Vaccination is nothing short of a scientific miracle. (via eric topol)


Madeline Miller: “Long Covid Has Derailed My Life”

Madeline Miller (Circe, Song of Achilles) got sick in February 2020 with what turned out to be Covid, which then turned into Long Covid. It has profoundly affected her life (gift link).

I reached out to doctors. One told me I was “deconditioned” and needed to exercise more. But my usual jog left me doubled over, and when I tried to lift weights, I ended up in the ER with chest pains and tachycardia. My tests were normal, which alarmed me further. How could they be normal? Every morning, I woke breathless, leaden, utterly depleted.

Worst of all, I couldn’t concentrate enough to compose sentences. Writing had been my haven since I was 6. Now, it was my family’s livelihood. I kept looking through my pre-covid novel drafts, desperately trying to prod my sticky, limp brain forward. But I was too tired to answer email, let alone grapple with my book.

When people asked how I was, I gave an airy answer. Inside, I was in a cold sweat. My whole future was dropping away. Looking at old photos, I was overwhelmed with grief and bitterness. I didn’t recognize myself. On my best days, I was 30 percent of that person.

I turned to the internet and discovered others with similar experiences. In fact, my symptoms were textbook — a textbook being written in real time by “first wavers” like me, comparing notes and giving our condition a name: long covid.

Even if Miller were physically able to get back to some semblance of “normal life”, the current policies and attitudes w/r/t Covid make it next to impossible.

Despite the crystal-clear science on the damage covid-19 does to our bodies, medical settings have dropped mask requirements, so patients now gamble their health to receive care. Those of us who are high-risk or immunocompromised, or who just don’t want to roll the dice on death and misery, have not only been left behind — we’re being actively mocked and pathologized.

I’ve personally been ridiculed, heckled and coughed on for wearing my N95. Acquaintances who were understanding in the beginning are now irritated, even offended. One demanded: How long are you going to do this? As if trying to avoid covid was an attack on her, rather than an attempt to keep myself from sliding further into an abyss that threatens to swallow my family.

I cannot remember where I read this (it was likely more than a year ago), but it would be more accurate/helpful if we thought of the disease caused by the SARS-CoV-2 virus as a chronic vascular disease (aka Long Covid) that often comes with short-term symptoms and acute, life-threatening effects instead of the other way around.


The Reason Why Cancer Is So Hard to Beat

Using the metaphor of a cancerous tumor as an unruly village, Kurzgesagt explains how cancer develops in the human body, how the body fights against it, and how, sometimes, the cancer develops into something unmanageable.

In a sense this tiny tumor is like a rogue town. Imagine a group of rebels in Brooklyn decided that they were no longer part of New York but started a new settlement called Tumor Town, which happens to occupy the same space. The new city wants to grow, so it orders tons of steel beams, cement and drywall. New buildings follow no logic, are badly planned, ugly and dangerously crooked. They are built right in the middle of streets, on top of playgrounds and on existing infrastructure. The old neighborhood is torn down or overbuilt to make room for new stuff. Many of the former residents are trapped in the middle of it and begin to starve. This goes on for a while until the smell of death finally attracts attention. Building inspectors and police show up.


How Does Humor Intersect With Grief and Fear?

Last week, popular YouTuber, author, and science communicator Hank Green announced that he had cancer (very treatable Hodgkin’s lymphoma). His video announcement was part of a series of back-and-forth videos he does with his brother John Green, popular YouTuber and novelist. John replied to Hank’s video with a short one of his own, noting that humor is one way that people deal with grief but also a way in which we can accompany people through tough times.

To work, the humor has to feel like love rather than judgment, like inclusion rather than stigma, and like celebration rather than dismissal. And that’s a tough balance. Sometimes well-intentioned people, including me, get it wrong. And it also depends on, like, who’s saying it and the context.

Good luck and my warmest thoughts to the Greens and their family as they navigate this difficult time. And, you know, fuck cancer.


Is Ozempic an Anti-Addiction Drug?

Writing for The Atlantic, Sarah Zhang details how some people taking Ozempic for weight loss are reporting that the drug has also curbed their addictive impulses (to drink, to shop, to smoke).

Earlier this year, she began taking semaglutide, also known as Wegovy, after being prescribed the drug for weight loss. (Colloquially, it is often referred to as Ozempic, though that is technically just the brand name for semaglutide that is marketed for diabetes treatment.) Her food thoughts quieted down. She lost weight. But most surprisingly, she walked out of Target one day and realized her cart contained only the four things she came to buy. “I’ve never done that before,” she said. The desire to shop had slipped away. The desire to drink, extinguished once, did not rush in as a replacement either. For the first time — perhaps the first time in her whole life — all of her cravings and impulses were gone. It was like a switch had flipped in her brain.

Not everyone experiences these effects, but there’s enough anecdotal evidence at this point that scientists are interested and investigating.


The Future Pandemic Playbook: What the US Got Right

From The Atlantic, 23 Pandemic Decisions That Actually Went Right, the result of interviews with more than a dozen pandemic experts.

17. Basic research spending matters. The COVID vaccines wouldn’t have been ready for the public nearly as quickly without a number of existing advances in immunology, Anthony Fauci, the former head of the National Institute of Allergy and Infectious Diseases, told us. Scientists had known for years that mRNA had immense potential as a delivery platform for vaccines, but before SARS-CoV-2 appeared, they hadn’t had quite the means or urgency to move the shots to market. And research into vaccines against other viruses, such as RSV and MERS, had already offered hints about the sorts of genetic modifications that might be needed to stabilize the coronavirus’s spike protein into a form that would marshal a strong, lasting immune response.


What Happens When You Get Sick?

From Kurzgesagt, an accessible explanation of what happens to the human body when you get sick.

Your brain activates sickness behavior and reorganizes your body’s priorities to defense. The first thing you notice is that your energy level drops and you get sleepy. You feel apathetic, often anxious or down and you lose your appetite. Your sensitivity to pain is heightened and you seek out rest. All of this serves to save your energy and reroute it into your immune response.

They also reveal the best way to boost your immune system to protect yourself against disease. I don’t want to spoil it but it’s vaccines. Vaccines are one of the best things humans have ever invented.


What’s the Deal with Ozempic, the “Breakthrough” Diabetes and Weight-Loss Drug?

In the last several months, semaglutide, a drug originally developed to help manage type 2 diabetes, has been in the news for its “breakthrough” weight loss abilities. This video from Vox is a good overview of what the drug does and the interest & controversy around it.

Both Ozempic and Wegovy, Ozempic’s counterpart approved specifically for weight loss by the FDA, are brand names of a drug called semaglutide. Semaglutide is one of several drugs that mimics a crucial digestive hormone called glucagon-like peptide 1, or GLP-1. It amplifies a process our bodies perform naturally.

GLP-1 is released in our intestines when we eat, and there are receptors for the hormone in cells all over the body. In the pancreas, GLP-1 promotes the production of insulin and suppresses the production of glucagon. This helps insulin-resistant bodies, like those with type 2 diabetes or obesity, manage blood sugar levels. In the stomach, GLP-1 slows gastric emptying, extending the feeling of being full. In the brain, GLP-1 suppresses appetite, which also promotes satiety and curbs hunger, so we eat less.

Jia Tolentino wrote a long piece about semaglutide for the New Yorker this week: Will Ozempic Change How We Think About Being Fat and Being Thin?

But, as I kept reminding Ozempic-curious friends, these medications were designed for chronic conditions, obesity and diabetes. For people who are dealing with those conditions, Ozempic appears to create a path toward a healthy relationship to food. For those who aren’t, it might function more like an injectable eating disorder. As the side effects make clear, it’s not a casual thing to drastically alter your body’s metabolic process, and there is no large-scale data about the safety of these drugs when taken by people who are mainly interested in treating another chronic condition, the desire to be thin.

Julia Belluz wrote a piece for Vox on Obesity in the age of Ozempic and Eric Topol wrote about The New Obesity Breakthrough Drugs.

Update: In the shuffle of the last few months, I’d missed reading Paul Ford’s piece about “the post-hunger age”, A New Drug Switched Off My Appetite. What’s Left?

I can see my anxiety mirrored in the wave of reactions starting to appear — op-eds, TV segments, people explaining why it’s good, actually, that the vast majority of those using this drug lose a quarter of their body weight. On social media, fat activists are pointing out that our lives were worthy even without this drug. The wave of opinion will not crest for years.

And that’s fair because this is new — not just the drug, but the idea of the drug. There’s no API or software to download, but this is nonetheless a technology that will reorder society. I have been the living embodiment of the deadly sin of gluttony, judged as greedy and weak since I was 10 years old-and now the sin is washed away. Baptism by injection. But I have no more virtue than I did a few months ago. I just prefer broccoli to gloopy chicken. Is this who I am?

Even outside the context of drugs, I find the tension between accepting who you are versus trying to change some behavior you find unappealing is challenging to navigate — it’s something that comes up in therapy a lot. (thx, anil)


New Synthetic Antibiotic “Cures Superbugs Without Bacterial Resistance”

Well, this is potentially a huge deal:

In a potential game changer for the treatment of superbugs, a new class of antibiotics was developed that cured mice infected with bacteria deemed nearly “untreatable” in humans — and resistance to the drug was virtually undetectable.

Developed by a research team of UC Santa Barbara scientists, the study was published in the journal eBioMedicine. The drug works by disrupting many bacterial functions simultaneously — which may explain how it killed every pathogen tested and why low-level of bacterial resistance was observed after prolonged drug exposure.

Huge if true, etc. What really caught my attention is how they discovered this in the first place…they were working on a way to charge cell phones:

The discovery was serendipitous. The U.S. Army had a pressing need to charge cell phones while in the field — essential for soldier survival. Because bacteria are miniature power plants, compounds were designed by Bazan’s group to harness bacterial energy as a “‘microbial”’ battery. Later the idea arose to re-purpose these compounds as potential antibiotics.

“When asked to determine if the chemical compounds could serve as antibiotics, we thought they would be highly toxic to human cells similar to bleach,” said Mahan, the project lead investigator. “Most were toxic — but one was not — and it could kill every bacterial pathogen we tested.”

Here’s the original paper if you’d like to take a look.


H5N1 Bird Flu: “An Even Deadlier Pandemic Could Soon Be Here”

Zeynep Tufekci on the H5N1 strain of the avian influenza, which is showing some recent signs of spreading in mammals.

Bird flu — known more formally as avian influenza — has long hovered on the horizons of scientists’ fears. This pathogen, especially the H5N1 strain, hasn’t often infected humans, but when it has, 56 percent of those known to have contracted it have died. Its inability to spread easily, if at all, from one person to another has kept it from causing a pandemic.

But things are changing. The virus, which has long caused outbreaks among poultry, is infecting more and more migratory birds, allowing it to spread more widely, even to various mammals, raising the risk that a new variant could spread to and among people.

Alarmingly, it was recently reported that a mutant H5N1 strain was not only infecting minks at a fur farm in Spain but also most likely spreading among them, unprecedented among mammals. Even worse, the mink’s upper respiratory tract is exceptionally well suited to act as a conduit to humans, Thomas Peacock, a virologist who has studied avian influenza, told me.

The three relevant facts here are: 56% of humans who’ve contracted H5N1 have died, there are signs of spreading among mammals, and that particular mammal is “exceptionally well suited” to pass viral infections along to humans. Tufekci, who attempted to sound the alarm relatively early-on about Covid-19, goes on to urge the world to action about H5N1, before it’s too late. Will we act? (No. The answer is no.)

*sigh*

You know, it’s a little shocking to read about a potential solution to the Fermi paradox on a random February Monday, but here we are.


Letter of Recommendation: Get a Vasectomy

Men in the US typically do not talk about or worry about birth control that much, to the detriment of the health and safety of women. In the spirit of trying to change that a little, I’m going to talk to you about my experience. About a decade ago, knowing that I did not want to have any more children, I had a vasectomy. And let me tell you, it’s been great. Quickly, here’s what a vasectomy is, via the Mayo Clinic:

Vasectomy is a form of male birth control that cuts the supply of sperm to your semen. It’s done by cutting and sealing the tubes that carry sperm. Vasectomy has a low risk of problems and can usually be performed in an outpatient setting under local anesthesia.

Whether you’re in a committed relationship or a more casual one, knowing that you’re rolling up to sexual encounters with the birth control handled is a really good feeling for everyone concerned.1 Women have typically (and unfairly) had to be the responsible ones about birth control, in large part because it’s ultimately their body, health, and well-being that’s on the line if a sexual act results in pregnancy, but there are benefits of birth control that accrue to both parties (and to society) and taking over that important responsibility from your sexual partner is way more than equitable.

(Here’s the part where I need to come clean: getting a vasectomy was not my idea. I had to be talked into it. It seemed scary and birth control was not something I thought about as much as I should have. I’m ashamed of this; I wish I’d been more proactive and taken more responsibility about it. Guys, we should be talking about and thinking about this shit just as much as women do! I hope you’ve figured this out earlier than I did. Ok, back to the matter at hand.)

Vasectomies are often covered by health insurance and are (somewhat) reversible. These issues can be legitimate dealbreakers for some people. Some folks cannot afford the cost of the procedure or can’t take the necessary time off of work to recover (heavy lifting is verboten for a few days afterwards). And if you get a vasectomy in your 20s for the purpose of 10-15 years of birth control before deciding to start a family, the lack of guarantee around reversal might be unappealing. Talk to your doctor, insurance company, and place of employment about these concerns!

Does the procedure hurt? This is a concern that many men have and the answer is yes: it hurts a little bit during and for a few days afterwards. For most people, you’re in and out in an hour or two, you ice your crotch, pop some Advil, take it easy for a few days, and you’re good to go.1 It’s a small price to pay and honestly if you don’t want to get a vasectomy because you’re worried about your balls aching for 48 hours, I’m going to suggest that you are a whiny little baby — and I’m telling you this as someone who is quite uncomfortable and sometimes faints during even routine medical procedures.

So, if you’re a sperm-producing person who has sex with people who can get pregnant and do not wish for pregnancy to occur, you should consider getting a vasectomy. It’s a minor procedure with few side effects that results in an almost iron-clad guarantee against unwanted pregnancy. At the very least, know that this is an option you have and that you can talk to your partner and doctor about it. Good luck!

  1. Just to be clear, you still have to worry about sexually transmitted infections — a vasectomy obviously does not provide any protection against that.

  2. There also is a follow-up about 6-12 weeks later to make sure the procedure worked. You masturbate into a cup and they check to see that there’s no sperm in the sample. Part of this follow-up, if my experience is any guide, includes checking that the doctor’s office bathroom door is locked about 50 times while watching very outdated porn on a small TV mounted up in the corner of the tiny room. It’s fine though! And you have a fun story to tell later.


Abortion Protects the Lives of Women

Dr. Dipti S. Barot writing for HuffPost, My 11-Year-Old Patient Was Pregnant. Here’s What I Want You To Know About Being ‘Pro-Life.’ (Content warning: rape.)

Sophia is in her 20s now. I wonder how she has healed, how she has processed that trauma. Did she get to go to college? Has she been able to trust an intimate partner? Has she been pregnant on her own terms at the time of her choosing? Does she have a child? I can see her wide face and her soft smile in my mind’s eye and I know now, just as I knew then, that the decision to terminate Sophia’s pregnancy, supported by the ones who loved her the most, was a pro-life decision.

And:

I remember how tiny that clinic room felt. There was no room for politicians signing evil bills flanked by child props as old as Sophia, no room for Supreme Court justices who claim to value life while wondering aloud how pregnancy can be an undue burden. No room for those extraneous, unnecessary, useless others in that most intimate of spaces. Our clinic rooms will always be too small for anybody but providers and our patients.


A History of Birth Control

From Lindsay Holiday, an engaging history of birth control, covering the ineffective and often dangerous methods used in the ancient world, the rhythm method, proto-condoms, actual condoms, Lysol (!!), and of course one of the modern world’s most impactful inventions, the hormonal birth control pill.

Through most of history pregnancy and childbirth were a very dangerous undertaking for women. In medieval Europe 1 in 3 women died in their child-bearing years and 1 in 4 children did not live to see their first birthday. Even when both mother and child survived the ordeal of birth women were not always able to provide for a child. And in most cultures pregnancy outside of wedlock was considered a great sin and often resulted in the shunning of the woman and child while the man often got away scot-free. It is no surprise therefore that women throughout history have been trying a wide variety of methods to prevent conception.

(via open culture)


How Did This Many Deaths Become Normal?

In his newest piece for The Atlantic, Ed Yong explores why, despite more than 6 million official deaths worldwide and almost a million official deaths in the US, the toll of the pandemic isn’t provoking a massive social reckoning. This is a hell of an opening paragraph:

The United States reported more deaths from COVID-19 last Friday than deaths from Hurricane Katrina, more on any two recent weekdays than deaths during the 9/11 terrorist attacks, more last month than deaths from flu in a bad season, and more in two years than deaths from HIV during the four decades of the AIDS epidemic. At least 953,000 Americans have died from COVID, and the true toll is likely even higher because many deaths went uncounted. COVID is now the third leading cause of death in the U.S., after only heart disease and cancer, which are both catchall terms for many distinct diseases. The sheer scale of the tragedy strains the moral imagination. On May 24, 2020, as the United States passed 100,000 recorded deaths, The New York Times filled its front page with the names of the dead, describing their loss as “incalculable.” Now the nation hurtles toward a milestone of 1 million. What is 10 times incalculable?

And it just keeps going from there — this is one of those articles so well written and packed with so much information and insight that it’s difficult not to quote the whole thing, even though it paints a bleak picture of America. Read the whole thing here. See also Yong’s accompanying Twitter thread.


Measles Makes Your Immune System Forget Its Protections Against Past Illness

Historically, contracting the measles has been linked to subsequent illness (and possibly death) from other causes. In the past few years, scientists have discovered why this is: measles causes “immune amnesia”.

Enter “immune amnesia”, a mysterious phenomenon that’s been with us for millennia, though it was only discovered in 2012. Essentially, when you’re infected with measles, your immune system abruptly forgets every pathogen it’s ever encountered before — every cold, every bout of flu, every exposure to bacteria or viruses in the environment, every vaccination. The loss is near-total and permanent. Once the measles infection is over, current evidence suggests that your body has to re-learn what’s good and what’s bad almost from scratch.

“In a way, infection of the measles virus basically sets the immune system to default mode,” says Mansour Haeryfar, a professor of immunology at Western University, Canada, “as if it has never encountered any microbes in the past”.

This re-learning process takes up to three years, which “around the time it takes infants to acquire immunity to everyday pathogens in the first place”. In the meantime…

It’s not surprising, then, that measles doesn’t just increase the risk of illness, but also death. In fact, childhood mortality from other viruses is strongly linked to the incidence of measles. The 2015 study showed that when childhood mortality in the UK, US, or Denmark goes up, this is usually because measles has become more prevalent.

The findings explain why vaccinating children against measles has the unexpected, beneficial side-effect of reducing deaths among children, way beyond the numbers who were ever at risk of dying from measles itself.

Of course, an extremely effective and safe vaccine offers protection against both measles and the immune amnesia it causes. But with the steep rise in anti-vaccination sentiment during the pandemic and the increasing willingness of conservative leaders to disregard public health protections in favor of “individual freedom”, widely vaccinating against this dangerous pathogen in the US & elsewhere will be more difficult than in the past.


Haematopoiesis

a colorful pattern by Rubén Álvarez

a colorful pattern by Rubén Álvarez

a colorful pattern by Rubén Álvarez

a colorful pattern by Rubén Álvarez

a colorful pattern by Rubén Álvarez

During the course of battling salivary gland tumors over many years, photographer and artist Rubén Álvarez discovered hematopoiesis (the process by which blood cells & blood plasma are formed in the body) as a possible treatment option. The treatment didn’t end up being applicable to his situation, but the process became the inspiration for a very personal project called Haematopoiesis.

This project was inspired by my very personal experiences so I discovered the Hematopoiesis process, while I was looking for treatments for more than 15 pleomorphic adenomas that were located around my head and neck. I went through several surgeries to remove them and reconstruct my facial nerve, as well as almost thirty radiotherapy sessions to prevent these adenomas to appear again.

Álvarez used paint, ferrofluid, and magnets to produce his interpretation of the actual hematopoiesis process. (via moss & fog)


CDC Report Shows Steep Drop in US Life Expectancy in 2020

The CDC recently released their report on Mortality in the United States, 2020 and this graph of US life expectancy at birth since 1950 by Christopher Ingraham dramatically summarizes the report’s main finding:

graph showing US life expectancy at birth since 1950, featuring a steep drop in 2020

That’s a decrease in life expectancy of 1.8 years from 2019. Here are some more of the report’s significant findings:

In 2020, life expectancy at birth was 77.0 years for the total U.S. population — a decrease of 1.8 years from 78.8 years in 2019. For males, life expectancy decreased 2.1 years from 76.3 in 2019 to 74.2 in 2020. For females, life expectancy decreased 1.5 years from 81.4 in 2019 to 79.9 in 2020.

In 2020, the difference in life expectancy between females and males was 5.7 years, an increase of 0.6 year from 2019.

graph of the death rates in the US for 2020

The age-adjusted death rate for the total population increased 16.8% from 715.2 per 100,000 standard population in 2019 to 835.4 in 2020. Age-adjusted death rates increased in 2020 from 2019 for all race-ethnicity-sex groups, increasing 42.7% for Hispanic males, 32.4% for Hispanic females, 28.0% for non-Hispanic Black males, 24.9% for non-Hispanic Black females, 13.4% for non-Hispanic White males, and 12.1% for non-Hispanic White females.

graph of the leading causes of death in the US in 2020

In 2020, 9 of the 10 leading causes of death remained the same as in 2019. The top leading cause was heart disease, followed by cancer. COVID-19, newly added as a cause of death in 2020, became the 3rd leading cause of death. Of the remaining leading causes in 2020 (unintentional injuries, stroke, chronic lower respiratory diseases, Alzheimer disease, diabetes, influenza and pneumonia, and kidney disease), 5 causes changed ranks from 2019. Unintentional injuries, the 3rd leading cause in 2019, became the 4th leading cause in 2020. Chronic lower respiratory diseases, the 4th leading cause in 2019, became the 6th. Alzheimer disease, the 6th leading cause in 2019, became the 7th. Diabetes, the 7th leading cause in 2019, became the 8th. Kidney disease, the 8th leading cause in 2019, became the 10th leading cause in 2020. Stroke, and influenza and pneumonia, remained the 5th and 9th leading causes, respectively. Suicide dropped from the list of 10 leading causes in 2020.

And from the report’s summary:

From 2019 to 2020, the age-adjusted death rate for the total population increased 16.8%. This single-year increase is the largest since the first year that annual mortality data for the entire United States became available. The decrease in life expectancy for the total population of 1.8 years from 2019 to 2020 is the largest single-year decrease in more than 75 years.

Since more people in the US died of Covid in 2021 than in 2020, I’d expect the decline life expectancy and the rise in death rate to continue.


America Is Not Ready for Omicron

This piece, from Ed Yong, is not at all surprising: America Is Not Ready for Omicron.

America was not prepared for COVID-19 when it arrived. It was not prepared for last winter’s surge. It was not prepared for Delta’s arrival in the summer or its current winter assault. More than 1,000 Americans are still dying of COVID every day, and more have died this year than last. Hospitalizations are rising in 42 states. The University of Nebraska Medical Center in Omaha, which entered the pandemic as arguably the best-prepared hospital in the country, recently went from 70 COVID patients to 110 in four days, leaving its staff “grasping for resolve,” the virologist John Lowe told me. And now comes Omicron.

Will the new and rapidly spreading variant overwhelm the U.S. health-care system? The question is moot because the system is already overwhelmed, in a way that is affecting all patients, COVID or otherwise. “The level of care that we’ve come to expect in our hospitals no longer exists,” Lowe said.

The real unknown is what an Omicron cross will do when it follows a Delta hook. Given what scientists have learned in the three weeks since Omicron’s discovery, “some of the absolute worst-case scenarios that were possible when we saw its genome are off the table, but so are some of the most hopeful scenarios,” Dylan Morris, an evolutionary biologist at UCLA, told me. In any case, America is not prepared for Omicron. The variant’s threat is far greater at the societal level than at the personal one, and policy makers have already cut themselves off from the tools needed to protect the populations they serve. Like the variants that preceded it, Omicron requires individuals to think and act for the collective good — which is to say, it poses a heightened version of the same challenge that the U.S. has failed for two straight years, in bipartisan fashion.

The main point:

Here, then, is the problem: People who are unlikely to be hospitalized by Omicron might still feel reasonably protected, but they can spread the virus to those who are more vulnerable, quickly enough to seriously batter an already collapsing health-care system that will then struggle to care for anyone — vaccinated, boosted, or otherwise. The collective threat is substantially greater than the individual one. And the U.S. is ill-poised to meet it.

Also from Yong: he recently cancelled his 40th birthday party because of Omicron and wrote about how he thought through the decision.

If someone got sick, I know others could too. A week later, many of my friends will spend Christmas with their own families. At best, a cluster of infections at the birthday party would derail those plans, creating days of anxious quarantine or isolation, and forcing the people I love to spend time away from their loved ones. At worst, people might unknowingly carry the virus to their respective families, which might include elderly, immunocompromised, unvaccinated, partially vaccinated, or otherwise vulnerable people. Being born eight days before Christmas creates almost the perfect conditions for one potential super-spreader event to set off many more.

As has been the case the entire pandemic, our political and public health systems are not equipped to collectively combat this virus, so it falls to individuals to make good choices for our communities. It’s a nearly impossible thing to ask to pandemic-weary folks to focus in again on making good personal choices and even harder to achieve if few are willing to do it, but goddammit we have to try.


The Omicron Variant

Last week, a worrisome variant of SARS-CoV-2 burst into the public consciousness: the Omicron variant. The concern among scientists and the public at large is substantial, but it is unfortunately going to take a few weeks to figure out whether those concerns are warranted. For a measured take on what we know now and what we can expect, read these two posts by epidemiologist Dr. Katelyn Jetelina (as well as this one on vaccines).

B.1.1.529 has 32 mutations on the spike protein alone. This is an insane amount of change. As a comparison, Delta had 9 changes on the spike protein. We know that B.1.1.529 is not a “Delta plus” variant. The figure below shows a really long line, with no previous Delta ancestors. So this likely means it mutated over time in one, likely immunocompromised, individual.

Of these, some mutations have properties to escape antibody protection (i.e. outsmart our vaccines and vaccine-induced immunity). There are several mutations association with increased transmissibility. There is a mutation associated with increased infectivity.

That sounds bad but again, we presently do not have enough information to know for sure about any of this. As Jetelina concludes in one of the posts:

We still have more questions than answers. But we will get them soon. Do not take Omicron lightly, but don’t abandon hope either. Our immune systems are incredible.

None of this changes what you can to do right now: Ventilate spaces. Use masks. Test if you have symptoms. Isolate if positive. Get vaccinated. Get boosted.

This Science piece by Kai Kupferschmidt also provides a great overview about where we’re at with Omicron, without the sensationalism.

Whether or not Omicron turns out to be another pandemic gamechanger, the lesson we should take from it (but probably won’t) is that grave danger is lurking in that virus and we need to get *everyone* *everywhere* vaccinated, we need free and ubiquitous rapid testing *everywhere*, we need to focus on indoor ventilation, we need to continue to use measures like distancing and mask-wearing, and we need to keep doing all of the other things in the Swiss cheese model of pandemic defense. Anything else is just continuing our idiotic streak with this virus of fucking around and then finding out. (via jodi ettenberg & eric topol)


Entering the Acceptance Phase of the Pandemic

In the United States and in many other countries around the world, we’re slowly shifting away from the Covid-19 pandemic to SARS-CoV-2 being endemic (like the flu), Dr. Lucy McBride argues that we need to recalibrate our risk calculations and expectations of what’s safe & dangerous. From A COVID Serenity Prayer in The Atlantic:

For the past 18 months, my patients have craved straightforward answers: a simple “Yes-it’s perfectly safe” or “Go for it. Have fun!” or even a “No, you absolutely cannot” to quiet the endless loops of risk calculations. But medicine is not about certainty. It never has been.

The two things that patients want-reassurance that they won’t get COVID-19 and permission to engage in life-I cannot deliver, and I never will be able to. SARS-CoV-2 is here to stay. The virus will be woven into our everyday existence much like RSV, influenza, and other common coronaviruses are. The question isn’t whether we’ll be exposed to the novel coronavirus; it’s when.

And although many of us will inevitably get COVID-19, for the majority of vaccinated people, it won’t be so bad. The vaccines weren’t designed to wholly prevent COVID-19; they transformed it into a manageable illness like the flu.

That means that, from a decision-making perspective, we’re starting to reach the acceptance phase of the pandemic: a time when we must recalibrate our individual risk gauges, which have been completely thrown out of whack. The approach I’m embracing with patients boils down to a secular version of the serenity prayer. We need “the serenity to accept the things [we] cannot change, courage to change the things [we] can, and the wisdom to know the difference.”


How to Solve Thorny Global Problems

Within the past 50 years, the global community has solved two huge problems that had the potential to harm every person on Earth. Smallpox once killed 30% of the people who contracted the disease but through the invention of an effective, safe vaccine and an intense effort that began in the 1960s, smallpox was completely eradicated by 1980. In the 1980s, scientists discovered a hole in the ozone layer that protects the Earth from UV radiation; further depletion would have caused major problems with the world’s food supply and an epidemic of skin cancer. Forty years later, we’ve virtually eliminated the chemicals causing the depletion and ozone losses have stabilized and have recently shown improvement.

So how did we do it? The short video above talks through each of challenges, how they were met (science + politics + a bit of luck), and how we might apply these lessons to the big problems of today (climate emergency, the pandemic).


Doctor Explains Why He Violated Texas’s Extremist Abortion Ban

Dr. Alan Braid, a practicing OB/GYN in the state of Texas for 45 years, explains why he provided medical care in the form of an abortion to a woman in violation of the state’s absurd and dangerous new law.

A new Texas law, known as S.B. 8, virtually banned any abortion beyond about the sixth week of pregnancy. It shut down about 80 percent of the abortion services we provide. Anyone who suspects I have violated the new law can sue me for at least $10,000. They could also sue anybody who helps a person obtain an abortion past the new limit, including, apparently, the driver who brings a patient to my clinic.

For me, it is 1972 all over again.

And that is why, on the morning of Sept. 6, I provided an abortion to a woman who, though still in her first trimester, was beyond the state’s new limit. I acted because I had a duty of care to this patient, as I do for all patients, and because she has a fundamental right to receive this care.

I fully understood that there could be legal consequences — but I wanted to make sure that Texas didn’t get away with its bid to prevent this blatantly unconstitutional law from being tested.

Braid concluded his piece: “I believe abortion is an essential part of health care.” Absolutely.


Even with Delta Variant, the Amazing Vaccines Are Saving Lives

It may seem like sometimes that with the pandemic, we’re back to square one. With the much more contagious Delta variant in play and an increasing number of breakthrough infections, the efficacy of these vaccines that we thought were amazing maybe aren’t? (Or maybe we just need to readjust our expectations?) But in terms of what these vaccines were specifically developed for — reducing & preventing severe disease and death — they are still very much doing their job. Just take a look at this graph from a White House Covid-19 press briefing yesterday:

a graph of Covid-19-associated hospitalizations among unvaccinated and fully vaccinated in the US

Even with Delta endemic in the country, the vaccines are providing extraordinary protection against infections severe enough to land folks in the hospital. In a recent CDC study of infections and hospitalizations in Los Angeles County, they report that on July 25, the hospitalization rate of unvaccinated people was 29.2 times that of fully vaccinated persons. 29 times the protection is astounding for a medical intervention. These vaccines work, we’re lucky to have them, and we need to get as many people worldwide as we can vaccinated as quickly as we can. Period.


Dying in the Name of Vaccine Freedom

You might want to take a deep breath or do a couple of laps around the house before watching this video about a community in the Ozarks with a very low Covid-19 vaccination rate. Here’s a sample. An ICU patient wearing an oxygen mask on why he didn’t get vaccinated:

I’m more of a libertarian and I don’t like being told what I have to do. I’m still not completely 100% sold on the inoculation.

Video narrator:

It was eerie to hear Christopher insist on his individual freedoms even as he struggled to breathe.

Can you hear me screaming all the way from my desk to wherever you are? I don’t like being told what I have to do?! Fucking hell. And this:

There’s no better place to see the impact of this political rhetoric than in the hospital. Only about 50 percent of the staff are vaccinated. None of the unvaccinated staffers were willing to talk.

Absolutely maddening. I want off this ride.


What’s the Proper Metaphor for the Covid Vaccine?

For The Atlantic, Katherine Wu writes about the difficulty of communicating how vaccines work and how they protect individuals and communities from disease: Vaccines Are Like Sunscreen… No, Wait, Airbags… No, Wait…

Unfortunately, communal benefit is harder to define, harder to quantify, and harder to describe than individual protection, because “it’s not the way Americans are used to thinking about things,” Neil Lewis, a behavioral scientist and communications expert at Cornell, told me. That’s in part because communal risk isn’t characteristic of the health perils people in wealthy countries are accustomed to facing: heart disease, stroke, diabetes, cancer. Maybe that’s part of why we gravitate toward individual-focused comparisons. Slipping into a pandemic-compatible, population-based frame of mind is a big shift. In the age of COVID-19, “there’s been a lot of focus on the individual,” Lewis told me. That’s pretty at odds “with how infection works.”

As someone who has struggled with analogizing the virus & vaccines, I was nodding my head a lot while reading this. Something I’ve noticed in recent years that Wu didn’t get into is that readers desire precision in metaphors and analogies, even though metaphor is — by definition! — not supposed to be taken literally. People seem much more interested in taking analogies apart, identifying what doesn’t work, and discarding them rather than — more generously and constructively IMO — using them as the author intended to better understand the subject matter. The perfect metaphor doesn’t exist because then it wouldn’t be a metaphor.


Getting into the Delta Variant Mindset

I’m just going to go ahead and say it right up front here: if you had certain expectations in May/June about how the pandemic was going to end in the US (or was even thinking it was over), you need to throw much of that mindset in the trash and start again because the Delta variant of SARS-CoV-2 has changed the game. I know this sucks to hear,1 but Delta is sufficiently different that we need to reset and stop assuming we can solely rely on the vaccines to stop Covid-19 from spreading. Ed Yong’s typically excellent piece on how delta has changed the pandemic’s endgame is helping me wrap my head around this.

But something is different now — the virus. “The models in late spring were pretty consistent that we were going to have a ‘normal’ summer,” Samuel Scarpino of the Rockefeller Foundation, who studies infectious-disease dynamics, told me. “Obviously, that’s not where we are.” In part, he says, people underestimated how transmissible Delta is, or what that would mean. The original SARS-CoV-2 virus had a basic reproduction number, or R0, of 2 to 3, meaning that each infected person spreads it to two or three people. Those are average figures: In practice, the virus spread in uneven bursts, with relatively few people infecting large clusters in super-spreading events. But the CDC estimates that Delta’s R0 lies between 5 and 9, which “is shockingly high,” Eleanor Murray, an epidemiologist at Boston University, told me. At that level, “its reliance on super-spreading events basically goes away,” Scarpino said.

In simple terms, many people who caught the original virus didn’t pass it to anyone, but most people who catch Delta create clusters of infection. That partly explains why cases have risen so explosively. It also means that the virus will almost certainly be a permanent part of our lives, even as vaccines blunt its ability to cause death and severe disease.

And a reminder, as we “argue over small measures” here in the US, that most of the world is in a much worse place:

Pandemics end. But this one is not yet over, and especially not globally. Just 16 percent of the world’s population is fully vaccinated. Many countries, where barely 1 percent of people have received a single dose, are “in for a tough year of either lockdowns or catastrophic epidemics,” Adam Kucharski, the infectious-disease modeler, told me. The U.S. and the U.K. are further along the path to endemicity, “but they’re not there yet, and that last slog is often the toughest,” he added. “I have limited sympathy for people who are arguing over small measures in rich countries when we have uncontrolled epidemics in large parts of the world.”

Where I think Yong’s piece stumbles a little is in its emphasis of the current vaccines’ protection against infection from Delta. As David Wallace-Wells explains in his piece Don’t Panic, But Breakthrough Cases May Be a Bigger Problem Than You’ve Been Told, vaccines still offer excellent protection against severe infection, hospitalization, and death, but there is evidence that breakthrough infections are more common than many public health officials are saying. The problem lies with the use of statistics from before vaccines and Delta were prevalent:

Almost all of these calculations about the share of breakthrough cases have been made using year-to-date 2021 data, which include several months before mass vaccination (when by definition vanishingly few breakthrough cases could have occurred) during which time the vast majority of the year’s total cases and deaths took place (during the winter surge). This is a corollary to the reassuring principle you might’ve heard, over the last few weeks, that as vaccination levels grow we would expect the percentage of vaccinated cases will, too — the implication being that we shouldn’t worry too much over panicked headlines about the relative share of vaccinated cases in a state or ICU but instead focus on the absolute number of those cases in making a judgment about vaccine protection across a population. This is true. But it also means that when vaccination levels were very low, there were inevitably very few breakthrough cases, too. That means that to calculate a prevalence ratio for cases or deaths using the full year’s data requires you to effectively divide a numerator of four months of data by a denominator of seven months of data. And because those first few brutal months of the year were exceptional ones that do not reflect anything like the present state of vaccination or the disease, they throw off the ratios even further. Two-thirds of 2021 cases and 80 percent of deaths came before April 1, when only 15 percent of the country was fully vaccinated, which means calculating year-to-date ratios means possibly underestimating the prevalence of breakthrough cases by a factor of three and breakthrough deaths by a factor of five. And if the ratios are calculated using data sets that end before the Delta surge, as many have been, that adds an additional distortion, since both breakthrough cases and severe illness among the vaccinated appear to be significantly more common with this variant than with previous ones.

Vaccines are still the best way to protect yourself and your community from Covid-19. The vaccines are still really good, better than we could have hoped for. But they’re not magic and with the rise of Delta (and potentially worse variants on the horizon if the virus is allowed to continue to spread unchecked and mutate), we need to keep doing the other things (masking, distancing, ventilation, etc.) in order to keep the virus in check and avoid lockdowns, school closings, outbreaks, and mass death. We’ve got the tools; we just need to summon the will and be in the right mindset.

  1. In a tweet introducing his piece, Yong says “Many folks are upset & confused by the last month” and that’s right where I am with this. Maybe you are too. I’m expecting to get angry email about this post, calling it alarmist. But Covid is different now and thinking our same March 2021 thoughts about it isn’t going to help ourselves, our families, or our communities. The sooner we can regroup, the better.


One Woman’s Mission to Get Vaccines to Her Rural Alabama Town

The Panola Project is a short film by Rachael DeCruz and Jeremy Levine that follows the efforts of local convenience store owner Dorothy Oliver to get the people in her small Alabama community vaccinated against Covid-19. A trusted member of her community, Oliver teams up with county commissioner Drucilla Russ-Jackson to call & go door-to-door, talking with people one-on-one, cajoling and telling personal stories of loss to get folks signed up for a mobile vaccination clinic.

In the film, Oliver and Russ-Jackson arrange for a hospital to set up a pop-up site in Panola, but the site will only be established if they get at least forty people to sign up to take the vaccine. We follow Oliver as she goes door to door, talking people into signing up, lightly cajoling them about their fears and concerns. When I asked her how she does it, her answer was disarmingly simple: “I just be nice to them,” she said. “I don’t go at them saying, ‘You gotta do that.’” DeCruz, too, was struck by the way Oliver and Jackson talked to people who were on the fence about the vaccine, an issue more often discussed with stridency of various types. “There’s this very warm and kind of loving and caring way that Dorothy and Ms. Jackson approached those conversations, even when people aren’t in agreement. And it wasn’t done in a way that’s, like, ‘I know better than you.’ “

Oliver’s charm with the skeptics is remarkable, but so is her determination to bring the vaccine to her underserved town. Most of the women and men Oliver talked to leaped at the opportunity to sign up for the vaccine. On vaccine day, they rolled down their car windows to thank her. “We appreciate y’all giving it to us, because a lot of people don’t really know where to go to take these vaccines,” one woman tells her. Vaccine hesitancy in Black communities has been harped on in the media, but those conversations can gloss over questions of availability. Levine told me that they were struck by how many people had put off vaccination for logistical rather than ideological reasons. In Panola, he says, they regularly heard people say, “I want the shot. How do I get this? I don’t have a car; how am I going to get forty miles to the closest hospital and back?”

The result? In a state with one of the lowest vaccination rates in the country, 94% of adults in Panola have been vaccinated, due in part to Oliver’s and Russ-Jackson’s efforts.


Living with Delta

This piece by Susan Matthews is really helpful for those of us who are vaccinated and trying to figure out what their risks are regarding the much more transmissible delta variant of SARS-CoV-2. Covid-19 is endemic now — how do we live with that? What reasonable actions should we take to keep ourselves, our communities, and our loved ones safe?

All of this is making people — yes, probably mostly vaccinated people — rethink the basic questions they thought their vaccine had answered for them: Can I go to restaurants and bars unmasked? Can I go back to the office? Can I see my grandma? Can I go on vacation? Can I unmask at my people-facing job? Can I have a wedding, or a party? The answer to those questions is not quite as easy as “yes, if you’re vaccinated.” It depends partly on how many in your group are vaccinated, but the actual answer is basically the same as it’s been all pandemic: It depends on your risk tolerance, it depends on what is happening with case counts locally (though, as more people travel, this might become a less reliable tool), and it depends on any unique risk factors in your group. Kass’ perspective felt novel to me: She said she suspects that in the end, a lot of people are going to end up boosting their immunity by suffering through a mild case of COVID. So no one should feel that bad about getting sick after they’re vaxxed. What matters is getting the order right: “If everyone who gets vaccinated still gets COVID but doesn’t die, that’s a success,” she said. The issue is that it doesn’t feel like a success for vaccinated people. Plus, “if you get infected after you’re vaxxed, it’s all you talk about,” she said. And right now, that’s understandably freaking out a lot of vaccinated people who thought they were in the clear.

Long Covid isn’t mentioned anywhere in here though — surely that has to be part of the conversation here (although anecdotally it doesn’t seem like too much of a worry).


“It’s Too Late”

Dr. Brytney Cobia treats Covid-19 patients at the Grandview Medical Center in Birmingham, Alabama, a state that ranks last in the US in fully vaccinated adults. In a recent Facebook post, Cobia shares that people are willing to get vaccinated after having to watch an unvaccinated member of their family die from Covid.

I’ve made a LOT of progress encouraging people to get vaccinated lately!!! Do you want to know how? I’m admitting young healthy people to the hospital with very serious COVID infections. One of the last things they do before they’re intubated is beg me for the vaccine. I hold their hand and tell them that I’m sorry, but it’s too late. A few days later when I call time of death, I hug their family members and I tell them the best way to honor their loved one is to go get vaccinated and encourage everyone they know to do the same. They cry. And they tell me they didn’t know. They thought it was a hoax. They thought it was political. They thought because they had a certain blood type or a certain skin color they wouldn’t get as sick. They thought it was ‘just the flu’. But they were wrong. And they wish they could go back. But they can’t. So they thank me and they go get the vaccine. And I go back to my office, write their death note, and say a small prayer that this loss will save more lives.

Heartbreaking.


The US Isn’t Ready for Another Pandemic

Olga Khazan writing for The Atlantic:

After an inept coronavirus response, will the United States do better when the next pandemic strikes? Experts generally agree that America learned from the past year, and that the next public-health crisis won’t be quite as bewildering. But America’s pandemic preparedness still has major gaps, some of which are too big for any one administration to fix. In recent weeks, I’ve called back many of the experts I interviewed over the past 18 months about masks, testing, contact tracing, quarantine, and more. I asked them, “Are we ready for another one?” The short answer is “Not quite.” The long answer is that being truly “ready” will be harder than anyone realizes.

The Trump administration mishandled the American response to Covid-19 so completely that it’s tempting to pin most of the pandemic carnage on him. But the more I read about the pandemic (Michael Lewis’s The Premonition is a recent example), the more I have come to believe that the majority of the American pandemic deaths were baked in, no matter who was President. Trump was definitely a worst-case scenario, but even a more competent person in the White House in Jan 2020 (like Clinton or Sanders or Romney) would not have done so much better. Poor public health infrastructure, politicized government agencies, no mandatory paid leave, an overpriced healthcare system that only works for some, uncoordinated national response (+ federalism), years of defunding government programs, a reactive (rather than proactive) CDC, unhealthy populace, poverty, systemic racism in medicine, entitled individualism, high rate of uninsured people, growing anti-science sentiment — the pandemic was destined to race through the United States like a brush fire no matter what.

Even the European Union, whose member nations do not share many of America’s aforementioned challenges (but have other issues), did only marginally better than the US in preventing Covid deaths. The UK did worse:

a chart showing the cumulative covid deaths per million of the US, UK, EU, and world