Category Archives: science

Delta Blues, or how I spent my summer not being able to take a vacation

We still need all of these layers.

When I started writing this post, I was planning on a straightforward update on the current situation with the delta variant (sorry, I couldn’t resist the obvious title). And then a 13-year-old killed a classmate at a local middle school for no discernible reason. And then the Taliban took back Afghanistan.

The murdered boy was trying to talk his killer out of continuing to bully his friends. He stood up to him with words, doing exactly what most of us would teach our kids to do, what my daughter would do, what I would do. The right thing.

Going into Afghanistan was never the right thing. I remember writing “Can you say ‘quagmire’?” back then. Three quarters of Americans thought this war was a great idea. I was part of the other quarter. I take no pleasure in being right in this case. Afghanistan continues its reputation as the “graveyard of empires.”

In order to avenge the deaths of 3000 Americans, we killed or maimed tens of thousands more, plus tens of thousands of Afghans and then Iraqis, naturally including myriad children. We spent 20 years and a couple of trillion dollars and we accomplished what looks right now to be little or nothing.

And to begin with, the perpetrators of 9/11 were Saudis, and we never gave Saudi Arabia the slightest grief over that. We always fought the wrong battles for the wrong reasons. For so many years we, that is, our leaders knew we were failing and we just kept on going, perhaps in the belief that whenever we left things would be exactly as bad as they are now. And things were always worse than we realized.
https://www.washingtonpost.com/investigations/2021/08/10/afghanistan-papers-book-dick-cheney-attack/

I suppose I should not be surprised that instead of effectively fighting this pandemic and its wide-ranging ills, we spend so much of our energy fighting each other.

Pulling the Fangs Back

Anger at the unvaccinated and the irresponsible among us is real. While a more-transmissible strain like delta was bound to come along, wider uptake of vaccines and more stringent adherence to public health common sense would have helped limit the damage, and would still damp down the development of newer variants. Our US deniers and anti-vaxxers are only one aspect of this; many governments have been too poor or too inefficient to get vaccines out to the majority of their people. But seeing Americans die or cause others to get sick because they haven’t taken the most obvious steps to avoid it is maddening.

Dr. John Lapook said, on the Stephen Colbert show on 8/16, “We come into these conversations coiled.” He suggested “pulling the fangs back” when trying to convince someone that getting vaccinated would be a good idea. I didn’t realize how “coiled” I was until I ran into a certain friend at an outdoor event in July. She announced that she wasn’t hugging anyone because she wasn’t vaccinated, which she said was because of her health condition. She really does have a condition in which it’s reasonable to be extremely cautious about medications, but it could just as easily be said that she needs the vaccine all the more because of it— her situation is honestly a bit fuzzy and it’s not crazy that she has hesitated. She has also fallen for a lot of the misinformation, though, and that has been frustrating to deal with. Anyway, I lit into her. Without knowing I was going to do it, I snapped at her. That is, I snapped. She reacted just as badly. Not a productive exchange.

A doctor in Alabama has even refused to see patients who are not vaccinated. ‘“If they asked why, I told them covid is a miserable way to die and I can’t watch them die like that,” wrote Valentine, who has specialized in family medicine with Diagnostic and Medical Clinic since 2008.’ Alabama has the lowest vaccination rate in the US and a high number of residents hospitalized with COVID.


Summer Non-Vacation— Why Is This Happening?

What did you want to do this summer? I wanted to have the party I didn’t get for my 60th birthday last year. (Oh, well— at least I was alive to have another birthday!) It’s very unclear what to do now. Nothing involving a large group of people, certainly. Is it OK to have a small outdoor gathering with vaccinated family and friends? And should we stop attending any non-crucial indoor events of any kind, even with masks and good ventilation? How much have things changed now that delta has taken over?

Amanda Mull wrote a compassionate piece about where we stand with these questions, “Delta Has Changed the Pandemic Risk Calculus.”
‘Assessing risk pre-vaccination was often bleak, but at least the variables at play were somewhat limited: ventilation, masks, crowds, local spread. Now the number of additional, usually hyper-specific questions that people must ask themselves is itself a barrier to good decision making, says Jennifer Taber, a psychologist at Kent State University who studies health risk assessment. “When people feel like things are uncertain, they engage in avoidance,” Taber told me. That can manifest in disparate ways. An unwillingness to acknowledge that many new things are safe for the average vaccinated person is avoidance. So is a refusal to continue taking even minor precautions for the benefit of others.’
https://www.theatlantic.com/health/archive/2021/08/delta-variant-pandemic-risk-safety/619798/

A big part of my job as a clinician is helping patients to sort through all the available information to answer health questions like this, and it’s not easy these days. Just as we’ve been through the entire pandemic, we’re still flying by the seat of our pants, trying to keep up with ever-changing conditions and advice. The rise of delta has been a predictable but chaotic and confusing development that hit us with a bait and switch just when we thought we were getting our lives back. It’s still new and we’re still figuring it out.

What I mean by predictable is that this is normal virus behavior. A more transmissible variant will obviously outcompete others, and it would have been a surprise had we not seen a variant like this eventually. Viruses “want” to produce as many copies of themselves as possible, and any mutation that leads to more chances to replicate is great for them.

In general, causing less illness and death is also good for viruses, because having hosts walking around spreading viral particles results in far more replication than having hosts lying isolated in hospital beds, or in graves. So over time a viral species is likely to become more transmissible but less deadly. Sadly, delta seems to cause at least as much and as severe disease as earlier forms of COVID, maybe more.
https://www.cdc.gov/coronavirus/2019-ncov/variants/delta-variant.html

We had some small hope of getting enough people vaccinated quickly enough, as a planet, to limit the possibility of worse new variants popping up. We didn’t make it, and that too was predictable. Viruses can adapt much faster than we can. We can still hope to escape without a far more dangerous variant coming along, but time is not on our side. The more humans there are who cannot access or will not accept vaccines, and the more who refuse to take other precautions, the more opportunities the virus has to mutate.

Here’s a good way of putting it:
‘You might think of viral replication as buying lottery tickets, in which the virus accumulates random mutations that very occasionally help it spread. And the fewer lottery tickets the virus has, the less likely it is to hit the mutation jackpot. The appearance of troubling new variants may slow down.’*

The now-famous Provincetown outbreak around the 4th of July has taught us a great deal.
https://www.washingtonpost.com/health/2021/08/05/provincetown-covid-outbreak/
The area population was so highly vaccinated that the tens of thousands of visitors who descended on the place didn’t worry about getting sick. They even packed cheek by jowl into indoor venues, without a mask in sight. No one expected to need them. Here you can get a sense of just how packed together the revelers got:
https://theboatslip.com/tea-dance
Then some folks noticed they were feeling unwell or had lost their sense of smell. By that time it was dawning on us all that delta was different and that we had been wrenched into a yet another new reality where we had to learn the rules all over again.

The misinformation mill has seized on Provincetown’s experience as an example of vaccines not working. That’s not remotely the case. Yes, 74% of the infections were in vaccinated people, but with over 900 infections, there were only 7 hospitalizations and zero deaths. An unvaccinated population would have a very, very different outcome. This article explains everything you need to know about the outbreak and what it means for the rest of us:
https://www.factcheck.org/2021/08/scicheck-posts-misinterpret-cdcs-provincetown-covid-19-outbreak-report/

You could just read the article, and you should, but I’m going to summarize some key points:

— Imagine a population that was 100% vaccinated. Vaccines are not perfect, so there would be some infections, and 100% of them would occur in vaccinated people.
— Infections in vaccinated people are rare, but since the vaccinated population consists of hundreds of millions of people, a significant number of people do get infected.
— The most important thing: With current strains of the virus, even if one does become infected, vaccination means essentially no chance of dying and very little chance of becoming severely ill.
— It looks like vaccinated people may harbor as much viral material in their noses as unvaccinated ones if they get infected, but infection doesn’t get as far into the body and the viral load goes down quickly as the immune system responds.

Research is ongoing to try to determine how likely an infected vaccinated person is to transmit the virus. That may be less than some studies suggest. From the same article:
‘For one, these sorts of PCR tests are good at identifying viral RNA, but they can’t tell whether that genetic material is in an intact, infectious virus particle or not. That becomes especially relevant for vaccinated people, Deepta Bhattacharya, an immunologist at the University of Arizona College of Medicine, said.
‘“Antibodies from a vaccinated person can coat the released virus and keep it from infecting other cells,” he told us. “And T cells can kill infected cells, releasing viral genetic material but not infectious particles.”
‘Second, the tests are only looking for RNA present in the nose and throat, not the lungs — even though vaccines are likely to have more of an impact there, according to previous research.
‘“Though it isn’t entirely clear how much of transmission comes from the lungs vs. the nose and throat,” Bhattacharya said in an email, “it is almost certainly some.” That would also suggest a vaccinated person with a similar cycle threshold as an unvaccinated person would be less infectious.
‘Vaccinated people also likely aren’t infected as long, since their immune systems are quicker to respond to the virus, which would also make them less likely to infect as many people as an unimmunized person.’

Here is a similar explainer, with data from the UK, where delta has run rampant:
https://theconversation.com/covid-the-reason-cases-are-rising-among-the-double-vaccinated-its-not-because-vaccines-arent-working-164797

Another highly vaccinated place that’s weathered a recent surge is Iceland.
‘Iceland, the experts say, is providing valuable information about breakthrough infections in the fully inoculated. Yet it also remains a vaccine success story.’
https://www.msn.com/en-us/news/world/iceland-has-been-a-vaccination-success-why-is-it-seeing-a-coronavirus-surge/ar-AANl2dx +

As with the surge in England, soccer was involved. ‘The country’s top health officials linked most of the cases to nightclubs and to residents who traveled to London to attend Euro 2020 soccer matches that some warned would be “a recipe for disaster.”’

Epidemiologist Brandon Guthrie gave some perspective in the Iceland article:
‘“We’ve handicapped ourselves in what the definition of success is,” he said. Scientists originally hoped for vaccines that were 50 percent effective, he said, and the goal was to prevent death and severe disease — not to provide blanket protection against any chance of infection.’
That is, the current reduced effectiveness of the vaccines is about as good as we hoped vaccines would be in the first place. Keep that in mind whenever you feel like despairing.

Even if it’s been quite a while since you were vaccinated, and you don’t have a lot of antibodies circulating in your blood, your T and B cells still remember how to recognize and fight SARS-CoV-2. Infection won’t get into your lungs because it will have been fought off by that time. It may take as much as 5-6 days for the body to marshal a good crop of antibodies, but generally it would take 10 or more days for a COVID infection to get as far as the lungs.

But meanwhile, kids are getting sick and being hospitalized, and some of them are dying of this disease that too many adults insist is no big deal for them. Vaccines for the under-12 cohort are on the way, but at this point the behavior of adults is the only real protection younger kids have, and in too many places adults are doing a crappy job.

“This new variant is a major contributor, but a major issue is that people’s behavior has changed,” said Gigi Gronvall, a senior scholar at the Johns Hopkins Center for Health Security. “I don’t think we can absolve people and leaders of responsibility for this because it gives them a pass. The reason kids are getting infected is because we don’t have those precautions and parents and households are getting infected.”
https://www.nbcnews.com/news/us-news/kids-sick-covid-are-filling-children-s-hospitals-areas-seeing-n1276238

‘Kline said it is unclear what kind of long-term effects babies and children will face.
‘Specifically, Kline referenced the brain fog adults see after contracting the virus.
‘”How does that affect a baby who is still having a developing brain? We just don’t know.”
‘Kline said another concern is cardiac issues in children.
‘”It worries me a lot that people say sure, kids can get COVID-19 but most of them recover uneventfully,” said Kline. “We know almost nothing about what those infections could produce down the line. I think there is a real risk that a proportion of these kids will have some long-term effects.”’
https://www.wdsu.com/article/new-orleans-louisiana-children-sick-covid-19-unvaccianted-adults-responsible/37259391

And all this is before school starts in a lot of the country.

Conspiracy Theory Roundup

For the sake of readers who live in a bright future where this craziness is forgotten: Droves of parents are currently following right-wing leaders and fighting requirements to wear masks in schools, sometimes with physical violence against teachers, principles, health care providers, and other parents.

As far as I’m concerned, there is no excuse for willful failure to protect children; I suppose it relates to that tendency toward avoidance when things feel uncertain. Yet, even the parents who give the most insane reasons for refusing to let their kids wear masks believe they are doing their best for them. Some may have thought things through and come up with vaguely rational justifications, but most have surely spent too much time in the conspiracy-verse, where they find an endlessly creative cornucopia of crap being produced every day.

The funniest example going around is the claim that vaccinated people will grow tails. My first reaction to that was Cool!  Unlike the claim that we become magnetic, this one cleverly avoids being immediately disproven by saying that the tails will grow at some point in the future. At least that’s how I heard it. I hope it doesn’t take too long….

For a while we were hearing that women would become infertile if they were vaccinated. Now the same scary disinformation is being aimed at men.
https://www.factcheck.org/2021/06/scicheck-research-rebuts-baseless-claims-linking-covid-19-vaccines-to-male-infertility/

Oddly enough, sperm counts have actually been found to increase after vaccination! The reason is unclear, but it’s been a consistent effect.
https://jamanetwork.com/journals/jama/fullarticle/2781360
“Sperm Parameters Before and After COVID-19 mRNA Vaccination”

President Former Guy rejected masks and publicly visible vaccinations as making him look less manly, but hey, maybe vaccines make for more manliness. I think we should really hammer on this selling point!

(Stephen Colbert pointed out that the conspiracy theory that vaccines cause a drop in fertility must be true— all those elderly people were vaccinated first, and sure enough none of them have had kids since.)

A more insidious claim is the one that COVID is being brought in by people coming over the border from Mexico; this is in line with centuries of blaming “foreigners” for disease. And of course it neatly deflects blame from the GOP fearmongers and unvaccinated Americans who are actually driving the high case counts. But this too is easily disprovable. We know that the bulk of transmission is coming from people within the US, not those coming from elsewhere, because we can track the genomes of various strains of the virus and see who is carrying which and where those strains are prevalent.

The lieutenant governor of Texas, Dan Patrick, added further venom to this trope by disgustingly blaming Black Texans for the state’s horrific rise in COVID illness and deaths. Patrick is the same guy who last year said people over 70, like him, should be willing to sacrifice their lives in order to keep the economy going. And he’s only doubled down in the face of criticism of his racist statements, which again are easily disproven.
‘Patrick acknowledged Texas’ public-health crisis — rising cases, hospitalizations, and fatalities — and said he’s aware of the criticisms of the state’s Republican leadership. But the lieutenant governor insisted the blame be directed at unvaccinated African Americans, not the GOP officials who remain passive toward the pandemic.
‘”The Democrats like to blame Republicans,” Patrick said. “Well, the biggest groups in most states is African Americans who are not vaccinated. Last time I checked, over 90 percent of them vote for Democrats in their major cities and major counties.”’
‘…In fact, the latest data suggests unvaccinated White Texans outnumber unvaccinated Black Texans by a roughly three-to-one margin.’
https://www.msnbc.com/rachel-maddow-show/dan-patrick-falsely-blames-covid-surge-unvaccinated-black-texans-n1277307

Meanwhile, Patrick’s cohort Governor Greg Abbott continues to interfere with requirements for masks around the state in the name of “freedom.” He’s getting plenty of pushback, but why should anyone have to use up their energy— or money— fighting for the right to protect their or their children’s health? Meanwhile taxpayers’ funds are drained away in court battles the state need never have started, instead of meeting real human needs. If only we could immunize against stupidity and self-serving political posturing.

One way out of the mess is to make masking voluntary, but as pediatrician Dr. Danny Benjamin said, a voluntary masking policy is “like having a no-peeing section in a pool.”

Onward with Delta Force

A major development just occurred: the FDA approved the Pfizer vaccine, so it is no longer being given under an Emergency Use Authorization. Moderna was later to submit data but its approval will be coming along soon. Many of the vaccine-hesitant have said this would make a difference in their acceptance of the shots.

The biggest question among my patients right now is when and where boosters will be available. I’m in the camp that wonders whether large numbers of us privileged sorts should be getting a third dose when so much of the world hasn’t even had a first one. We’re told that there are plenty of doses to go around in the US and that we can both give extra protection to Americans and send vaccines to poorer countries, but I personally don’t feel great about using a dose someone else may desperately need, and I recognize that the only way to protect everyone is to protect everyone.**

Giving a third dose to organ transplant recipients on immunosuppressants and others who have not been able to mount a strong response to their original vaccination is a different matter and a clear benefit as far as we know. For the rest of us, we’re told that we should probably get a booster about 8 months after our second shot. For me and a lot of health care workers, that’s early October, so we’ll need to decide pretty soon.

Surprisingly, it appears that flu shots give some protective effect against a range of severe symptoms of COVID. I was figuring that since I would likely stay masked this winter, and that if pandemic limitations continued we might have little or no flu season last year, a flu shot would be pretty worthless. The risk/benefit calculation has changed again. The authors suggest that for populations that have not had access to COVID vaccines, flu vaccine might be better than nothing.
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0255541
“Examining the potential benefits of the influenza vaccine against SARS-CoV-2: A retrospective cohort analysis of 74,754 patients”

What about those who have already had COVID? Aren’t they immune? They do have some protection, though we aren’t sure how long it lasts. However, since the virus has ways to evade the immune system as part of its normal strategy, natural infection doesn’t confer immunity as well as the vaccine. If you have both a history of natural infection and the vaccine, you have the highest possible level of immune response. For you, a vaccine is essentially a booster. (Similarly, if you become infected despite being vaccinated, the disease has a booster effect.)
https://www.cidrap.umn.edu/news-perspective/2021/03/covid-19-survivors-may-be-able-skip-2nd-vaccine-dose

Last year when vaccines were being developed, there were breezy assurances that we would be able to tweak them to take new variants into account. Can’t we do that for delta? Well, yes, but no. The practical problem with creating vaccines against specific variants is that by the time studies are done and the product approved, that variant may be gone and another may be ascendant. If a variant comes along that completely evades current vaccines, though, we will need to meet that challenge.

Intranasal vaccines are being developed. Injecting a vaccine into the arm doesn’t teach the body to be on the lookout specifically for a respiratory virus. That is, giving a vaccine in the nose tells the body that the virus involved is going to enter through the nose and that’s where defenses need to be placed, so it’s a more efficient strategy. It should also be a bit easier on the needle-squeamish.

‘Charneau and a group of scientists in Paris have shown that natural SARS-CoV-2 infections trigger both systemic and mucosal immunity. But our current crop of COVID-19 vaccines offer only systemic protection. Developing vaccines that are sprayed up the nose, rather than injected into the arm, could change that, Charneau says. Mucosal immunity in our noses could be like a guard at the door, potentially helping stop even small infections of SARS-CoV-2 right where they start.’
https://cen.acs.org/pharmaceuticals/vaccines/Intranasal-nose-vaccines-stop-COVID/99/i21

I’ll leave you with another hopeful note, a story about former pastor Curtis Chang, who has been working within the vaccine-resistant evangelical community to dispel common myths.
https://www.motherjones.com/politics/2021/08/this-former-pastor-is-changing-evangelicals-minds-on-covid-vaccines/

‘Historically, the evangelical movement has baked into it a certain wariness of dominant secular institutions. And this can be captured in the saying that Jesus called us to be in the world, not of the world. We’re not of the world in the sense of just conforming automatically to the assumptions and beliefs the world. But what’s happened is that this orientation of being wary has gotten weaponized.

‘‘There’s been three main forces that I think have done that. One is that you can actually gain a lot of ratings by playing up those fears of what Washington is doing or what the left is doing. Christians are being bombarded by so much conservative media that they automatically just assume they’re out to get us. Another one is that conservative politicians have realized that you can gain a lot of votes by playing up these fears. And then the third is sort of outside conspiracy movements. QAnon, the anti-vaxxer movement—they have realized that evangelicals are fertile hunting grounds for their theories, because they are already primed to be distrustful of institutions, and so they can be easily kind of recruited into their deep conspiracies of distrust.’

Pastors, Chang says, are in a difficult position. Most of them are in favor of vaccination, but they risk backlash from their congregations if they speak too strongly about it— same problem GOP politicians have. (I would argue that both have helped create this problem.)

‘I understand that people are frustrated, that they’re losing patience, that they just want to make things via mandate, and give up trying to persuade these people. I think that’s short-sighted, for a couple of reasons. One, if you just resort to sheer coercion, it just confirms the narrative that they’re out to get us, that they are shoving things down our throat. You’re just laying the groundwork for a deepening divide. The second reason is that you have to realize that we’re still in the first or second inning of vaccine outreach, globally. You have to realize that parts of Africa and Asia are heavily influenced by Christian culture. A country like Uganda is like 90 percent Christian. Those churches, those places in Africa, they actually take their cultural cues to a great extent from American evangelicals, especially leading white evangelical voices. So America is—unfortunately, through evangelical culture—exporting its vaccine hesitancy. A lot of the same conspiracy theories and doubts and fears that we’ve been battling here, we are definitely seeing emerge and being replicated in the rest of the world. Changing American culture is not just about getting more American evangelicals to take the vaccine, it’s going to be critical to getting the rest of the world vaccinated. And ultimately, for all of us, if we don’t get the entire world vaccinated, we’re all at risk. ’

‘…What’s going to be really important is for Christians to convey to other Christians is that it’s okay to change your mind. The Christian virtues of grace and acceptance are going to be paramount here because people are going to be even more resistant if they think that in changing their mind they are going to be shamed.’

Grace and acceptance… those sure sound good right now.

***************************************************************
TAKEAWAYS for the Delta Era:
— You can still get infected even if you’re vaccinated, though most likely you won’t.
— Remember the Swiss cheese layer concept and take multiple precautions as reasonable and available.
— Be good to yourself and others and acknowledge the effects of the unrelenting pain and uncertainty of our time.
— WEAR THE DAMN MASK!

************************************************************

Original source: https://www.washingtonpost.com/world/europe/iceland-covid-surge-vaccines/2021/08/14/bdd88d04-fabd-11eb-911c-524bc8b68f17_story.html

Data from the UK, May to July 2021: 
https://spiral.imperial.ac.uk/bitstream/10044/1/90800/2/react1_r13_final_preprint_final.pdf

*https://www.theatlantic.com/science/archive/2021/08/how-we-live-coronavirus-forever/619783/
“The Coronavirus Is Here Forever. This Is How We Live With It.”

***https://www.npr.org/sections/goatsandsoda/2021/08/04/1019780576/why-who-is-calling-for-a-moratorium-on-covid-vaccine-boosters
Meanwhile, Israel is not waiting and has already given third doses to around 600,000 of their citizens— while Palestinians next door in Gaza and the West Bank have had so much trouble even getting a first dose. Here’s part of that sad tale, in which they were offered nearly-expired doses, for which Israel would have received fresh replacements:
 https://mondoweiss.net/2021/06/we-returned-them-palestinians-axe-1-million-pfizer-dose-deal-with-israel/

A new examination of the possible origins of COVID-19:
https://science.sciencemag.org/content/early/2021/08/16/science.abh0117
“The animal origin of SARS-CoV-2”

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Filed under health and healing, history, nature, psychology, science

I Don’t Know How the Pandemic Started, But I Do Know These Things

I got to thinking about what we do know for sure about this and other pandemics, trying to clarify it all in my mind. Here is the list I made for myself.

— New diseases arise all the time; most of them don’t spread far so most people don’t pay much attention.
— The warming climate has pushed disease-carrying insects and other creatures farther north. 
— The growth of the human population has pushed humans into new territories with more contact with animals in their habitats, and pushed the animals to migrate. Both of these movements make transmission of diseases more likely.
— It’s crucial that we study zoonotic diseases and their vectors, and do everything we can to prepare for the next ones that will come along.
— Tick-borne diseases are emerging as an issue of huge importance, again exacerbated by climate change.

— Plagues and pandemics of many kinds have happened commonly throughout history.
— The origins of most pandemics, including the 1918 flu, have never been definitively determined.
— More pandemics will arise in the future. This is the one fact of which we can be absolutely certain.

— Accidents happen, mistakes are made, and anything that can go wrong eventually will.
— Humans are tremendously creative and awfully smart in terms of developing things like new technologies, but also incredibly stupid in many important ways, and common sense is not common.
— Facilities such as microbiology labs are run by humans.
— More humans and more facilities mean more possibilities for error.

— People don’t like to be wrong, and they like admitting it even less.
— Mother Nature always has the last laugh.

***********************************************************************

Meanwhile, I was involved in discussions with a colleague who outlined some questions about the effects of the SARS-CoV-2 spike protein, both the natural version and the inactivated version coded for by the mRNA vaccines.  I tried to chase down some solid information and found a lot of fascinating stuff, which I’ve collected for you here:

 

https://www.theatlantic.com/science/archive/2021/05/spike-protein-vaccines-covid/618954/
“COVID-19 Vaccine Makers Are Looking Beyond the Spike Protein”

 

https://www.snopes.com/fact-check/vaccine-lung-damage/
“Will mRNA COVID-19 Vaccines Wreak ‘Havoc on The Lungs’ in 4 to 14 Months?” [Spoiler: NO.]

 

https://healthfeedback.org/claimreview/byram-bridles-claim-that-covid-19-vaccines-are-toxic-fails-to-account-for-key-differences-between-the-spike-protein-produced-during-infection-and-vaccination-misrepresents-studies/
“Byram Bridle’s claim that COVID-19 vaccines are toxic fails to account for key differences between the spike protein produced during infection and vaccination, misrepresents studies”
[Worth reading carefully.]
‘Ogata et al. found extremely low levels of the spike protein compared to the harmful levels reported in animal studies, as Uri Manor, one of the authors of the study in hamsters, pointed out on Twitter. The blog Deplatform Disease calculated that the amount of spike protein that the authors found in vaccinated people was about 100,000 times lower than the levels of viral spike protein shown to cause harm. This is “a situation that could hypothetically occur in severe COVID-19 patients, pending studies confirming it, but not achievable in vaccinated people, at least for those who received the Moderna vaccine, and unlikely to occur for the other vaccines”, explained Al-Ahmad.

‘While some of the vaccine might end up in the bloodstream, the body breaks it down over time. The European Medicines Agency (EMA) explained in a 23 March 2021 letter that the proportion of vaccine that enters the bloodstream is very small and almost all of that ends up in the liver:’

‘…I have personally discussed these biodistribution data (as obtained by Bridle and colleagues) on my blog, as I teach pharmacokinetics to pharmacy students. The data is pretty clear: the number of vaccines needed to be injected in a 12-year old to reproduce the findings observed in rats and reported as “terrifying” would be equivalent to 60,000 doses given at once, to reproduce the number of nanoparticles used in that study.’


https://www.sciencedaily.com/releases/2020/10/201029141941.htm
“SARS-CoV-2 spike proteins disrupt the blood-brain barrier, new research shows”  [Can this explain some or all of the neurological symptoms?]


https://www.sciencedirect.com/science/article/pii/S2211124720302928
“Route of Vaccine Administration Alters Antigen Trafficking but Not Innate or Adaptive Immunity”  [Where the vaccine goes after injection]
‘The transport of vaccine antigen to the local LNs [lymph nodes] is crucial for priming of T and B cell responses (Liang et al., 2017b). We and others have shown, using both flow cytometry and positron emission tomography (PET)/computed tomography (CT), that vaccine transport after i.m. injection is restricted to the local LNs and is not disseminated systemically (Liang et al., 2017a, Liang et al., 2017b, Lindsay et al., 2019).’


https://www.science20.com/w_glen_pyle/the_thorny_problem_of_covid19_vaccines_and_spike_proteins-254373
“The Thorny Problem Of COVID-19 Vaccines And Spike Proteins”
‘In addition to engineering the spike protein so it can not be fully activated, the protein is tagged with an extra piece called a “transmembrane anchor”. The transmembrane anchor allows the spike protein to appear on the surface – or membrane – of the cell, but it is held in place by the anchor. This prevents the spike protein from drifting away and creates a fixed target for the immune system to recognize the foreign protein.’
‘…Lei and colleagues conclude their paper by noting that their study “suggests that vaccination-generated antibody and/or exogenous antibody against [spike] protein not only protects the host from SARS-CoV-2 infectivity but also inhibits [spike] protein imposed endothelial injury.” In other words, the spike proteins used by currently available vaccines actually offer a double layer of protection.’


https://cen.acs.org/pharmaceuticals/vaccines/tiny-tweak-behind-COVID-19/98/i38
“The tiny tweak behind COVID-19 vaccines
Prepandemic coronavirus research by Jason McLellan and Barney Graham led to a trick for stabilizing the prefusion form of spike proteins”
[This one, linked in the article above, has drawings of the molecular structures of the natural and inactivated spike proteins to help us understand what was changed and why– good to nerd out on]


https://magazine.ucsf.edu/what-covid-doing-our-hearts
“What Is COVID Doing to Our Hearts?”
‘Healthy heart muscle (left) created from adult stem cells has long fibers that allow them to contract. SARS-CoV-2 infection causes these fibers to break apart into small pieces (right), which can cut off the cells’ ability to beat and may explain lasting cardiac defects in COVID-19 patients.’

 

 

 

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Don’t “Panic,” But We’re Not Done with This Yet. Not Even Close.

 

Best New Mexican conspiracy theory. The booster has microguacamole.

 

Last week we got the news that a little girl, under 10 years of age, died of COVID-19 in our state. Because of privacy concerns, all we know is that she had underlying conditions and was hospitalized. Kids her age are of course not being vaccinated as yet, one more reason we still need to be careful. This is not over, not by a long shot.

I started writing this post in early April, then ended up working on other matters and putting it off for an unconscionably long time. Many things about the pandemic have become clearer since then, while others have become muddier still.

At that time a few months ago, COVID-19 was doing its maximum damage in India, and Brazil was not far behind. There were still influential voices referring to the pandemic as a “panic,” implying that it is overblown and not really so bad. One of these voices belonged to someone I respect a great deal; you could actually hear the quotation marks when he said “panic,” and I was deeply disappointed to witness that. (Anyway, if you lived in India, wasn’t panic a pretty reasonable response?) That was what got me stirred up to write about the current state of play, and how things look from the perspective of a holistic health care provider.

That is, how things look from my own perspective. Quite a few people in my profession and other areas of “alternative” medicine have been caught up in conspirituality thinking. In general, these people are sincere, and they are promoting some empowering ideas: that the human body has the capability of fighting any disease on its own, and that what appears to be illness in the material world is not really what it seems and has causes quite different from the pathogens we (sort of) understand.

They’re not wrong.

However, I submit that they are impractical and that material-world measures still need to be taken at this point. Humanity as a whole is nowhere near a time when we can all throw off disease with a thought, and this pandemic is a very, very large field of reality-stuff, a huge mass to contend with. I note that some very aware and enlightened health-care gurus have themselves become infected, some with long-term consequences. Yes, I know that the material world isn’t what it seems*, but in consensus reality, if you jump off a cliff you are going to go splat. And in consensus reality, a pathogen your body has never learned to recognize has an excellent chance of making you very sick.

The V Word

I spend a lot of time somewhere other than consensus reality, myself, and don’t put a lot of stock in it for the most part. I’m so alternative that I often treat people from a distance, essentially by just thinking about them. Yet I am still saying that as things stand, our best chance of reducing transmission of this virus and the rise of worse variants is… the dreaded V word.

My best take on the whole situation is that whether we are infected ourselves, dealing with the illness or death of loved ones, affected by the biological challenges of vaccines, or “only” experiencing the heavy pall lowered over the planet by the pandemic and its economic fallout, we WILL be affected. To an extent you can choose your response, but you will necessarily respond in some way. You can’t isolate yourself from it.

As I write this, I’m doing something that until recently was a forbidden pleasure, sitting inside at Michael Thomas Coffee, nibbling a piece of spinach quiche and sipping some nice fair-trade light roast, with other humans in the same room. I owe this enjoyable hour first and foremost to the people who developed the Pfizer vaccine.

When I last wrote about pandemic issues and those who refuse to see reason, around Halloween 2020, COVID vaccines were still only theoretical. We did not expect the degree of efficacy that we’ve had, and for a while there was more room to debate about whether it was worthwhile for any given person to get their “Fauci ouchie.” Now there’s no more question. Cases among vaccinated Americans are practically nil, while among others the virus rages on at similar levels to what it was doing months ago.

A news story that went by as I was working on this concerned an outbreak with deaths and hospitalizations, all of unvaxxed folk, at a government office building in Florida. The vaccinated guy who was exposed didn’t get it.

https://www.cnn.com/2021/06/23/us/manatee-county-outbreak-spread/index.html

The wife of one of the deceased said she and her husband had considered the vaccine, but “we just wasn’t ready yet.” The virus refused to wait for them. So sad, so frustrating, so unnecessary!

And meanwhile, more transmissible variants take over. At this moment, the winner in the evolutionary race is the delta variant, the one that’s given India so much grief. It has even caused an outbreak in Australia, where the virus had seemed to be beaten— and where only a few percent of the population are fully vaccinated.

I wasn’t totally crazy about being among the first wave of vaccinees myself, both because I might have liked to see more about how the side effects played out and because a lot of other people were at higher risk than I. But as a health care provider, I was given the opportunity early on, in January, and I felt that I’d better take it while I could, for my patients’ sake as well as mine.

After I received my first shot, I experienced a major psychological boost, a sense of greater safety and freedom— along with a very sore arm that felt heavy and was difficult to use for a day or so. Since then I’ve treated some pretty significant vaccine side effects among my patients. With my patient population being small, I must conclude that they are common. Most of my patients reported no ill effects at all, though, and most of those who did got over them very quickly. Two who already had skin issues had increased inflammation and itching, which also resolved, but more slowly. Two others who had longer-lasting effects appeared to have lurking underlying illnesses which were brought to the surface. That was uncomfortable but not necessarily a bad thing, as those conditions could then be treated.

What bothers me most is that the majority people who do have significant ill effects will be left without meaningful treatment on the energetic level or even the deeper physical levels, as mainstream medicine may only apply band-aids like steroids. It’s been heartening to see that mainstream medicine has taken the matter very seriously, especially in the rare but quite dangerous cases of odd blood clots associated with the Astra-Zeneca vaccine. (For those who pointed out that birth control pills are more likely to cause clots than these vaccines, meaning it’s no big deal: these are very unusual clots and in more dangerous locations.)

‘In the new study, his team found that 15 weeks after the first vaccination, immune cells in the body were still organizing — becoming increasingly sophisticated and learning to recognize a growing set of viral genetic sequences.
“The longer these cells have to practice, the more likely they are to thwart variants of the coronavirus that may emerge. The results suggest that the vast majority of vaccinated people will be protected over the long term — at least, against the existing coronavirus variants.”
https://www.nytimes.com/2021/06/28/health/coronavirus-vaccine-immunity.html

An area of great interest is the interaction between immunity after infection and that after vaccination. It looks like people who have had both get the most robust and long-lasting immunity.

There has been a surprising and wonderful development in which COVID vaccination actually becomes a treatment. A significant percentage of people with “long COVID”— the ones who never get better— are improved or even cured after receiving a vaccine. And fascinatingly enough, the vaccine put a lymphoma patient into remission (which can also happen with a viral infection). I have seen reports of Lyme disease, lupus and other conditions improving as well.

https://www.forbes.com/sites/victoriaforster/2021/02/08/did-covid-19-cure-this-persons-cancer/?sh=7d18df674217

At the same time, people with autoimmune conditions and others who are on immunosuppressant drugs may not mount a sufficient immune reaction to a vaccine. Giving an extra dose to those people is an option currently being studied, and it looks like it helps.

Myocarditis has been seen, rarely but enough to worry, in young men after vaccination. So far we have been seeing it resolve and not cause a long-term problem. Myocarditis is also caused by COVID itself, so the vaccine is not causing an increased risk of it as far as I know.
https://jamanetwork.com/journals/jamacardiology/fullarticle/2780548
Note that this study concerned healthy college athletes, not a population whose health had already been compromised.  Heart damage from the virus is a real risk.

It should go without saying that vaccines aren’t 100% safe for every person every single time. No effective form of medicine is without problems when applied to millions of people. My guiding star is always the risk/benefit ratio. In the case of COVID vaccines, for most people, the benefits far, far outweigh the risks. I would contrast this with the annual flu shot, which I usually avoid on the basis of: its relatively poor efficacy, the existence of at least some immunity to these viruses and the ability to treat the illness, the small but nonzero risk of Guillain-Barre syndrome, and the fact that it has to be given over and over, putting more toxic crap in the system each time. I’m not laughing off flu in the least— I’ve had some really nasty cases. From what I know, and that’s always changing, I simply want to limit vaccines to those that make a serious difference.

In any case, we can’t vaccinate our way out of every conceivable epidemic. New pathogens come along all the time, as their nature is to evolve quickly and to evolve toward more transmissibility. It’s still crucial to continue all our basic public health measures such as tracking and isolating cases of outbreaks; that was how Ebola was contained, well before a vaccine was developed. Vigilance is still needed, all around the world. And that’s why those who demonize or laugh at laboratories that study potentially devastating viruses, like the one in Wuhan (I’m talking to YOU, Jon Stewart!) are doing great damage.

Disinformation (and some honest confusion)

A British gentleman, Chris Woollams, who publishes a very useful website that aggregates current information about cancer treatments is among those who fell into the current fashion of vilifying these efforts and Dr. Anthony Fauci personally. He was easily taken in by the right-wing campaign that paints Dr. Fauci as a liar who is somehow responsible for all we’ve been through in the past year and a half, which nicely deflects attention from the failures of the administration that was in power at the time. He even quoted Rand Paul as a reliable source of information in his article about this. (I’ll wait while you finish laughing. Take your time.) When I attempted to inject some facts into the discussion, he email-yelled at me, “Dr. Fauci is endangering me and my family!” Sadly, I can no longer consider him to be a reliable source himself, as he’s shown that his BS detector is malfunctioning.

The other day Woollams also insinuated on his website that some new research on DNA repair in human cells means that the mRNA in vaccines can become part of your DNA. That’s extremely irresponsible at best. Here’s where he got the idea:
 https://advances.sciencemag.org/content/7/24/eabf1771

The human genome is full of sections derived from viral RNA anyway; HIV famously uses its reverse transcriptase to write itself into our DNA. That’s normal biology. The question being explored recently is whether this mechanism might help explain why some people continue to test positive for COVID after recovery. So far, no.

Some researchers thought they did see evidence of SARS-CoV-2 integrating into the human genome:
https://www.pnas.org/content/118/21/e2105968118
“Reverse-transcribed SARS-CoV-2 RNA can integrate into the genome of cultured human cells and can be expressed in patient-derived tissues”
However that appears to be incorrect: https://journals.asm.org/doi/abs/10.1128/JVI.00294-21
“Host-virus chimeric events in SARS-CoV-2 infected cells are infrequent and artifactual”

From this last article: ‘”If the virus was able to integrate its genetic material into the human genome, that could have meant that any other mRNA could do the same. But because we have shown that this is not supported by current data, this should allay any concerns about the safety of mRNA vaccines,” he said.
‘It is possible for the genetic material of some viruses to be incorporated into the DNA of humans and other animals, resulting in what scientists call “chimeric events.” Human DNA contains approximately 100,000 pieces of DNA from viruses that our species have accumulated over millions of years of evolution. In total, this lost-and-found DNA from viruses makes up a bit less than 10% of the genetic material in our cells.’

So although research continues, you don’t have to worry about the mRNA in vaccines becoming part of your DNA. (If you really want to keep worrying about that, just get a different type of vaccine.)

At least Woollams’ contention is based in some sort of reality, and the underlying biology is important and fascinating, as well as confusing to the non-virologist. That can’t be said of the wacked-out statements we’ve heard from some other internet pundits.

I don’t know if anyone will ever exceed the, um, whimsy of Dr. Sherri Tenpenny’s insistence that vaccines make you magnetic, nor if any anti-vaccine concept will ever be easier to disprove. (I’m sitting on a chair made of ferrous metal right now. Nothing.) Yet, this got as far as testimony before the Ohio state legislature. Think about that for a moment. Lord, I’m glad I don’t live in Ohio anymore.

Second prize goes to the person who dreamed up the idea that the viral spike protein in the vaccine penetrates the uterine wall, thus explaining increased menstrual bleeding. Just how big do they think viruses are?

Sadly, a lot of the worst misleading statements, aka lies, about vaccines are coming from real health care providers who used to be trustworthy sources of solid medical information. I grieve particularly to see Christiane Northrup, MD in this group; I used to recommend her women’s health books to my patients. Some of these were called out by the Center for Countering Digital Hate under the title “The Disinformation Dozen,” in a presentation calling for more policing of misinformation by social media corporations. Some might find CCDH a little strident, but a number of the memes they collected are truly eye-popping and nearly at the level of the “magnetic” claim. Tenpenny, a DO, is included.
https://252f2edd-1c8b-49f5-9bb2-cb57bb47e4ba.filesusr.com/ugd/f4d9b9_b7cedc0553604720b7137f8663366ee5.pdf

There is not a hint here of sober consideration of potential side effects or of the risks of the disease itself. Instead there is idiocy like “masks make you get sick” and “vaccines have killed more people than the disease itself” and even “if you are getting tested you are part of the problem.” Huh? And if you sift through crap like this long enough, eventually you get to the hoary old “it’s the Rothschilds.”

I want to emphasize again that their claims are easily disprovable.

 

 

Just plain not true. 

 

Some of these folks, like Sayer Ji, have promulgated solid information about nutrition and other aspects of health in the past, before they went so far off the deep end. On the other hand, the Bollingers, of “The Truth about Cancer” fame, not only put out statements about cancer that don’t hold water, but now they also promote Mr. 45’s election fraud lies. Anyone who believes T. won the 2020 election has some obvious issues with critical thinking, and “truth” is not their strong suit.

Still, a lot of people have been burned by the medical establishment in one way or another, and they have reasons to be leery. They have trouble trusting anybody who tries to advise them about their health. So I was heartened to see that one’s personal doctor does still get named as a trustworthy source:

 

 

 

And trust is slowly ticking up.

 

 

These graphics come from the Zoom updates the UNM infectious disease department holds every week. The kind and supportive community of doctors and other health care personnel helps me stay on top of the latest developments in COVID prevention and treatment— including aspects like nutrition and exercise— and answer the many questions my patients bring up. It also helps me keep some semblance of sanity. The presenters put in a lot of effort to do this on top of their very demanding jobs. It’s clear to me that all these providers are doing everything they can to understand and act upon the best information they can get. When people talk trash about doctors, these are the people I think of, and it hurts my heart.

Unnecessary Deaths and Long-Term Debility

Those who refuse to take the pandemic seriously, and there still are plenty of those, often state that “only” 1% of those who are infected die. Leaving aside the question of whether that percentage is accurate, who would they like to choose for those unnecessary deaths? For a thought experiment, let’s take Albuquerque Public Schools, which has about 4000 employees. That’s a population you can probably imagine, and an appropriate one since schools have always been great places to pass diseases around. Now imagine them as 4000 people who get COVID. Imagine that 40 will die— 40 moms, dads, sisters, brothers, friends. And they’ll die miserably.

Are you OK with that? I’m not, not if we can prevent it.

But while relatively few may die, a great many who contract COVID will have long-term consequences. You know about the devastation of “long COVID,” but you may not have heard that an increased incidence of a variety of health problems and even a greater likelihood of death are seen in the months after infection, even in those who appear to recover normally.

“We show that beyond the first 30 days of illness, people with COVID-19 exhibit a higher risk of death and use of health resources. Our high-dimensional approach identifies incident sequelae in the respiratory system, as well as several other sequelae that include nervous system and neurocognitive disorders, mental health disorders, metabolic disorders, cardiovascular disorders, gastrointestinal disorders, malaise, fatigue, musculoskeletal pain and anaemia. We show increased incident use of several therapeutic agents—including pain medications (opioids and non-opioids) as well as antidepressant, anxiolytic, antihypertensive and oral hypoglycaemic agents—as well as evidence of laboratory abnormalities in several organ systems. Our analysis of an array of prespecified outcomes reveals a risk gradient that increases according to the severity of the acute COVID-19 infection (that is, whether patients were not hospitalized, hospitalized or admitted to intensive care). Our findings show that a substantial burden of health loss that spans pulmonary and several extrapulmonary organ systems is experienced by patients who survive after the acute phase of COVID-19.”
https://www.nature.com/articles/s41586-021-03553-9

Long COVID is something you do not want. It’s still poorly understood, it’s difficult to treat, and it can completely disable you. It often follows mild cases that had seemed to be of little consequence, and it happens even to young, athletic people with no previous health issues. Take it seriously!

The best article I have seen about long COVID is not from a medical journal, but in The Atlantic. I hope you can read it and not be paywalled away. (The Atlantic is superb and worth subscribing to in any case.) The gist is that long COVID involves a derangement of the autonomic nervous system that doesn’t fix itself, but that the brain and body can be retrained with measures as simple as breathing exercises. The cases described are terrifying, but the conclusion is hopeful. I am confident that studying long COVID is helping us to better understand other post-infection syndromes like chronic fatigue syndrome/myalgic encephalitis, something else you definitely do not want.
https://www.theatlantic.com/magazine/archive/2021/04/unlocking-the-mysteries-of-long-covid/618076/

Panic may not be helpful, but a certain degree of alarm is still appropriate. This is no time for complacency. Though a lot of us in the more-vaxxed parts of the USA are sitting pretty right now, with transmission still so high in so much of the world, the virus has millions upon millions of chances to mutate, and we have literally no idea what may happen. At this writing, the delta variant is taking over and causing havoc in a number of countries. Reducing the rate of transmission is the only way to prevent the development of variants that could resist our best efforts and prevention and treatment. And we are a long, long way off from knocking transmission down to a low level in a lot of places. Even Australia has started lockdowns again. Until everyone is safe, no one is really safe.

 

*”How I Know the Material World Isn’t”  https://elenedom.wordpress.com/2010/05/16/how-i-know-the-material-world

Related: “Sorting Medical Fact from Fiction, Part IV: Vaccination, Variolation, and What Doctors Do Tell You”  https://elenedom.wordpress.com/2020/11/01/sorting-medical-fact-from-fiction-part-iv-vaccination-variolation-and-what-doctors-do-tell-you/

 

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