Eggs are Expensive Because Producers Won't Vaccinate Because of Trade Agreements

There are a lot of complexities around influenza, but this particular causal relationship of influenza and egg prices is very straightforward:

We have international poultry product trade agreements that stipulate that the chickens will not have been vaccinated for Highly Pathogenic Avian Influenza [1]. When influenza breaks within a poultry flock, U.S. producers would rather kill all of the chickens and start over than risk losing access to international markets by vaccinating to prevent or minimize disease in the first place. The H5N1 strain of influenza has been hitting U.S. flocks lately (in part spread by migratory birds), and so egg production has gone down. And when supply goes down in the face of strong demand, price goes up.

There's not much Biden could have done about this, and there's not much Trump can do about it either, short of re-negotiating those trade agreements.

So we're all at the mercy of nature and economics. Sorry!

Here's a great article from last year that goes into a little more detail [Link].

By the way, the same strain of influenza got into dairy cattle last year (nobody saw that coming), and even though the same trade agreements don't exist for cattle, jitteriness about international trade has been one factor stopping aggressive action there as well. It's unknown whether this will all eventually impact humans in a significant way (there have only been isolated cases thus far), but money is clearly in the driver's seat.

Notes:
1. This is not because of concerns about vaccination, per se. Chickens already receive a number of vaccinations, and frankly the industry would be destroyed if they didn't vaccinate for some diseases. It is intended to protect the importing country from accidentially introducing a foreign strain of influenza. The approach is basically, "We don't want you to vaccinate because we want total assurance that H5N1 hasn't been in your flock at all." That may not the best approach, but it is what it is.

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Project 2025 Drags Vaccines into the Abortion Wars

Just for fun (of a sorts), I decided to see what the infamous Project 2025 document has to say about abortion. My curiousity was piqued by a news article wherein someone from the Heritage Foundation said that the claim of Democrats that Project 2025 calls for banning abortion nationwide is a lie. Sometimes I like to do spot checks to see who is telling the truth.

The first thing I will say is that if you download a copy and do a word search on the word "abortion," there are a LOT of hits. In fact, if all you did is click through each hit, you could be forgiven for thinking that abortion is the main topic addressed in the document. Anyway, right up front on page 6 the document says this:

But the Dobbs decision is just the beginning. Conservatives in the states and in Washington, including in the next conservative Administration, should push as hard as possible to protect the unborn in every jurisdiction in America. In particular, the next conservative President should work with Congress to enact the most robust protections for the unborn that Congress will support while deploying existing federal powers to protect innocent life and vigorously complying with statutory bans on the federal funding of abortion.

I'll let you decide if that sounds like a call for a national ban. In spite of the many references to abortion, I was unable to find any position on what limits there should be or whether there should be any exceptions to abortion bans [1]. Just this follow-up sentence:

Conservatives should ardently pursue these pro-life and pro-family policies while recognizing the many women who find themselves in immensely difficult and often tragic situations and the heroism of every choice to become a mother.

Sounds a bit like empty "thoughts and prayers" to me [2], but maybe I'm being too cynical.

As I browsed further, I was disheartened to see this kind of inflammatory language about vaccines.

The CDC oversaw and funded the development and testing of the COVID-19 vaccines with aborted fetal cell lines, insensitive to the consciences of tens of thousands to hundreds of thousands of people who objected to taking a vaccine with such a link to abortion....There is never any justification for ending a child’s life as part of research, and the research benefits from splicing or growing aborted fetal cells and aborted baby body parts can easily be provided by alternative sources.

And later, this:

Thousands of Americans of faith and conscience wish to receive various childhood vaccinations for themselves and their families but are not allowed to receive vaccines that are derived through or tested on aborted fetal cells. For example, the chickenpox, Hepatitis, and MMR vaccines in the U.S. are all linked to abortion in this way. There are ethically derived alternatives abroad that have been used safely there for decades, but the FDA makes it exceedingly difficult for Americans to import them....To avoid future moral coercion of the sort experienced with the COVID-19 vaccines, the FDA and NIH should require the development of drugs and biologics that are free from moral taint and switch to cell lines that are not derived from aborted fetal cell lines or aborted baby body parts.

There is a lot to say about this, but I will try to be brief.

1. It is true that a handful of cell lines (like, four) in vaccine production and research were originally derived from aborted fetuses in the 1960s, 70s, and 80s. Importantly, these fetuses were not aborted for the purpose of obtaining cells. Rather, the abortions were happening anyway and the fetal tissues were donated to medical use. The cells derived from these fetuses were useful because they were unlikely to be contaminated with any other undetectable viruses, they were human-derived and supported the growth of the vaccine strains of virus well, and they could be propagated and expanded to meet production needs for the foreseeable future. Two of those cell lines were further genetically modified to better support virus growth and transformed such that they can propagate indefinitely--at this point you could think of them as cancer cells. One of them is ubquitous in biomedical research.

2. There is no need for new human fetal cells for the production of these vaccines. We are talking about cell lines that have been in use for decades. And the references to "ending a child's life for research" and "aborted baby body parts" are just prejudical inflammatory language.

3. The vaccines produced from these cell lines have benefited millions of children by saving them from death and disability resulting from these diseases. Moreover, since rubella (the "R" in MMR) can cross the placenta and damage a fetus, we can also say that a great many fetuses have been protected as well.

4. The Catholic Church is famously conservative on reproductive issues (even more so than our Church), and even the Vatican has considered this history and repeatedly affirmed that these vaccines are acceptable for use. Obviously we don't all take our marching orders from the Vatican, but it shows that Project 2025 is not entitled to the presumption of moral superiority on this issue.

5. The most popular COVID-19 vaccines (mRNA vaccines from Pfizer and Moderna) were not produced using these cell lines. So the complaint that conscientious objectors to the COVID-19 vaccines, on the grounds of abortion, were morally coerced is weak at best. (Too bad rightwingers stirred up prejudice and distrust against mRNA vaccines [3]. Nothing seems to make them happy.)

6. Switching cell lines for mass production of vaccines, especially vaccines that have decades of safety and efficacy data behind them, is not a casual decision. It would be a lengthy and costly process. For the adenovirus-based COVID-19 vaccines, in fact there are no other options that I am aware of. And while it's nice and easy to blame FDA for making it difficult, if FDA were to relax their process I have a feeling that the Heritage Foundation would be right there to criticize them on the other side for lowering standards and approving insufficently tested vaccines.

7. I get the feeling that Project 2025 is not the work of serious, responsible thought.

Like I've said previously, people generally view the donation of bodies, organs, and tissues to medical science favorably, but for some reason the word "fetus" gives people the vapors and conjures up all kinds of lurid imagry. We need not celebrate the abortions that made these vaccines possible, but we can be greatful for the immeasurable good that has come from the cells they produced. Attempts to taint vaccines in the eyes of people will only end up multiplying harm.

Notes:
1. To their credit, they do not consider removing an ectopic pregnancy to be an abortion. On the other hand, emergency contraception gets sort of lumped in with abortion. The reasons are not air tight, but it's the same contradiction that plagues those who want to declare a fertilized egg to be fully human and somehow avoid the problematic ramifications that flow from that.
2. Maybe we could honor them at football games or something.
3. You can sense a trace of this in a different section of the document where it refers to the COVID-19 "vaccine", complete with quotes as if the fact that it is a vaccine is questionable.

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Remembering and Honoring Anti-Miracles

During my recent sickness with COVID [1], I had some time to contemplate the amount of collective misery infectious diseases have inflicted on humans throughout history. My conclusion is, A LOT. An incomprehensible amount of suffering and misery. And that's not even counting the misery inflicted by infectious diseases of livestock or crops that result in hunger and economic loss. Amazingly, it has only been in the last 150 years or so that we have understood the causes of such diseases, and even more recently how to combat (some of) them effectively. Such knowledge and progress has been hard-won, and yet I am sometimes alarmed at how little value some people place on that knowledge. Clean water and sanitation, vaccines, and antibiotics have changed our world. I am especially disturbed when people think that faith in God can substitue for effective public health policies and medical care. It's like they are entirely ignorant of history--even recent history--and more to the point, Church history.

I've been reading through the Church's new Saints series on the history of the Church. The books describe a number of miraculous experiences in the history of the restoration, but I have been impressed that they also tell of what we might call anti-miracles. Many of these involve infectious diseases. Here are some examples I've collected.

Volume 1:

As the Camp of Israel disbanded, a devastating outbreak of cholera attacked its ranks. Saints who had been healthy only hours before collapsed, unable to move. They vomited again and again and suffered intense stomach pains. The cries of the sick filled the camp, and many men were too weak for guard duty... Joseph and the elders in camp gave blessings to the sick, but the disease soon struck many of them as well. Joseph fell ill after a few days and languished in his tent, unsure if he would survive. When people began to die, Heber Kimball, Brigham Young, and others wrapped the bodies in blankets and buried them along a nearby stream. The cholera ran its course after several days, clearing up in early July. By that time, more than sixty Saints had fallen sick. Joseph recovered, as did Nancy, Eunice, and most people in the camp. But more than a dozen Saints died during the outbreak, including Sidney Gilbert and Betsy Parrish, one of the few women in the camp. [p. 198-199]

Malaria was a problem in Illinois. After describing Joseph's miraculous healing of Elijah Fordham:

Joseph’s efforts to bless and heal the sick did not end the spread of disease in Commerce and Montrose, and some Saints perished. [p.376]

Volume 2:

Some of the challenges at Winter Quarters and other temporary settlements were impossible to avoid. By the time cold weather set in, over nine thousand Saints lived in the area, including thirty-five hundred who lived in Winter Quarters. Accidents, sickness, and death plagued every settlement. Malaria, tuberculosis, scurvy, and other illnesses claimed about one person in ten. About half of the deceased were infants and children. [p. 37]

During one of the westward migrations:

The elders in the camp fasted and gave blessings of healing and comfort to the sick, but cholera continued to claim more lives. Near the end of June, Jacob himself became too sick to keep up with the wagons. Other company leaders sent a carriage back for him, and when he rejoined the camp, the elders blessed him. His health continued to worsen, however, and he died on the afternoon of July 2. [p. 193]

In Hawaii:

One morning in February 1887, little Jay came down with a fever and a cough. At first, Susa and Jacob assumed it was a cold, but the symptoms got worse over the next week. They cared for Jay as best they could and called in Joseph F. Smith and others to bless him. Susa marveled at the faith exercised in behalf of her son. But Jay did not get any better... Jay did not improve, and that afternoon, he fell peacefully asleep and then passed away just before two o’clock. Susa’s grief was inexpressible, but she had barely begun mourning when Karl came down with the same sickness. As he grew worse, the Saints from around Laie fasted and prayed, but nothing helped. The family was placed under quarantine to prevent the spread of the disease, and Karl died soon after. [p. 493]

Volume 3:
This is a tragic but instructive story that I first encountered in Thomas Alexander's Mormonism in Transition. It's not about infectious disease, per se, but still involves microbes. I was pleasantly surprised to see it included in Saints. It involves Hyrum M. Smith, an Apostle and son of President Joseph F. Smith (and grandfather to M. Russell Ballard, current Acting President of the Quorum of the Twelve Apostles).

Hyrum’s sickness became more serious with each passing day. He felt severe pain in his abdomen, a sign he had appendicitis. His friends urged him to go to the hospital for an operation, but he refused. “I have kept the Word of Wisdom,” he said, “and the Lord will take care of me.” On January 19, the pain became almost unbearable. Hyrum’s wife, Ida, notified Joseph immediately, and he prayed earnestly for his son’s recovery. Apostles Orson F. Whitney and James E. Talmage, meanwhile, joined Hyrum at his bedside and watched over him during the night. A group of doctors and specialists, including Dr. Ralph T. Richards, Joseph’s nephew, also attended him...[Eventually he was pursuaded to go the hospital.] At the hospital, the doctors took two x-rays and decided to remove Hyrum’s appendix. During the procedure, Dr. Richards discovered that the appendix had ruptured, spreading toxic bacteria throughout Hyrum’s abdomen...

Hyrum survived the procedure, but Joseph remained weak with anxiety and spent the afternoon lying down, unable to eat. Hyrum seemed to gain strength that evening, which lifted Joseph’s spirits. Filled with gratitude and relief, he returned to his duties as Church president. Then, three days after Hyrum’s surgery, Joseph received a telephone call from the hospital. Despite many prayers and the careful work of the doctors, Hyrum had passed away... A cloud of sorrow hung over the Smith family in the days after Hyrum’s death. There were Saints questioning his decision not to go immediately to the hospital. “If he had gone when first spoken to,” some said, “he might have lived.” Presiding bishop Charles Nibley, a close friend of the family, agreed. Hyrum’s faith in the Word of Wisdom was well intentioned, he noted, but the Lord had also provided skilled men and women who were scientifically trained to care for the body. [p. 272-273]

The lesson of these anti-miracles, in my opinion, was once expressed by Elder Boyd K. Packer.

The very purpose for which the world was created, and man introduced to live upon it, requires that the laws of nature operate in cold disregard for human feelings. We must work out our salvation without expecting the laws of nature to be exempted for us. Natural law is, on rare occasions, suspended in a miracle.

We can choose to be wise and use our knowledge and technology to help protect us from negative effects of natural laws, or we can leave ourselves vulnerable to their operations. But what we cannot do is expect or believe that faith in God, alone, will save us from their consequences. The few examples above illustrate that much. Remembering such anti-miracles reminds us that health is naturally fragile, and we honor them when we choose wise practices and policies that weren't available to our forebearers.

Notes:
1. If you want gory details of my illness, continue reading. I was fully vaccinated and boosted previously, but the updated vaccines weren't yet available. I had a few days of feeling something going on in my nasopharynx, but figured it was just allergy or a light cold. That changed when I woke up in the middle of the night with a fever of 101 F. I did a rapid antigen test, which was positive for COVID. The next 36 hours were miserable. I had to take ibuprofin every 6 hours to keep the fever somewhat in check, otherwise I was cold and feverish. I fortunately did not have a headache or lose smell/taste, but I had various aches within my abdomen. I also pretty quickly developed a sore throat, which made it painful to swallow. That's bad enough for eating and drinking, but when you are coughing up phlegm and having to swallow it, it's insult to injury. My abdomen made all kinds of noises. The collected misery, pains, and noises made it difficult to sleep. Fortunately, the worst of the fever symptoms ended after about 36 hours. I thought about people earlier in the pandemic who suffered fever for days on end, and I recalled news articles about people who were cavalier about the disease and ended up in the hospital surprised at how very sick they were. I felt fortunate that wasn't me, but at times the warning in D&C 19 went through my mind, "how hard to bear you know not." I speculate that the acute fever was relatively short due to prior vaccination, but I wasn't out of the woods. All of that abdominal activity progressed to diarrhea that lasted several days. Meanwhile, my cough, sore throat, and general fatigue and sickness continued. Although I was out of the acute fever, it seemed like any place of pressure on my body would cause sweating and I had some impressive night sweats. I awoke one night astounded at how soaked my pajama bottoms were below the knee. It was almost as if I had been wading in a stream. Sleep was not entirely restful, as I would usually wake up in the night and have trouble going back to sleep. Sometime after the acute fever, I developed a decent cough that made sleep more difficult. Along the way I had variable appetite and tried to keep myself hydrated, but the persistent sore throat didn't help. Theoretically I was able to stop isolating after 5 days, but I was still strongly positive by rapid antigen test. I finally tested negative at 10 days, at which point my sore throat finally let up. By then I had lost 10 lbs. When I looked at how the CDC defined mild, moderate, and severe cases, I was surprised to find that I seemed to fit the mild definition. Mild is not the word I would use to describe my experience, especially the first couple of days, but I never needed to seek medical care so I guess from that perspective it's appropriate. Fortunately, I'm mostly recovered. I still have a bit of a lingering cough, but otherwise I feel fine and have returned to my exercise routine. I lived in isolation from the time I tested positive to testing negative, so was able to keep it to myself. While I guess all's well that ends well, it was not a fun journey and I recommend trying to avoid it.

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Bateman's Only Real Sin Was Blaming the Jews

Dave Bateman, founder and (now former) chairman of a Utah tech company, made a splash this week when he sent out an email to Utah tech and political leaders blaiming Jews for the pandemic and accusing them of trying to kill the American people (apparently with both the virus and the vaccine). I haven't been able to find the full text of the email, but various reports quote the following excerpts.

I write this email knowing that many of you will think I'm crazy after reading it. I believe there is a sadistic effort underway to euthanize the American people. It's obvious now. It's undeniable, yet no one is doing anything. Everyone is discounting their own judgment, and dismissing their intuition.

I believe the Jews are behind this. For 300 years the Jews have been trying to infiltrate the Catholic Church and place a Jew covertly at the top. It happened in 2013 with Pope Francis. I believe the pandemic and systematic extermination of billions of people will lead to an effort to consolidate all the countries in the world under a single flag with totalitarian rule. I know, it sounds bonkers. No one is reporting on it, but the Hasidic Jews in the US instituted a law for their people that they are not to be vaccinated for any reason.

The spike protein in both the vaccine and the illness are [sic] attacking the reproductive systems of women, and will eventually erode the number of T cells in our bodies that can ward off infections. Don’t get the illness and don’t get vaccinated.

I pray that I'm wrong on this. Utah has got to stop the vaccination drive. Warn your employees. Warn your friends. Prepare. Stay safe.

When the local FOX station followed up with him, he responded:

"Yes. I sent it. I have nothing but love for the Jewish people. Some of my closest friends are Jews. My heart breaks for their 2500 years they’ve been mistreated by nearly every country on earth. But I do believe Scottish Rite Freemasons are behind the pandemic (overwhelmingly Jewish)," he wrote. "And I fear billions of people around the globe right now are being exterminated."

That Bateman would believe this, not to mention broadcast it, is horrifying and he deserves all the public denunciation that he is receiving, which is primarily focused on his antisemitism. But I couldn't help but notice that most of what he said is fairly non-controversial in right-wing circles [1]. His downfall (thus far) was blaming "the Jews". That's still a bridge too far (for now), so it's the easiest part to denounce. But if he had only blamed a single Jewish person (e.g. George Soros), his ideas wouldn't be any more controversial than what is said by right-wing commentators and politicians every day.

Bateman may seem down and out at the moment, but if he hangs in there and plays his cards right [2], he will go from pariah to right-wing hero with surprising speed.

Notes:
1. Maybe not the Catholic part, but I don't know. There are fundamentalist strains of protestantism that don't accept that Catholics are even Christian, and there are conservative Catholics who don't like Pope Francis, so it's possible the Catholic part is more widesrpead than I realize. But the rest is pretty garden-variety and easy to find. Examples on this blog alone are here and here.
2. Don't apologize; get on a speaking/media tour; narrow to a single prominent Jewish person or family; blame the whole controversy on the liberal media and cancel culture; remind everyone that HE is the victim.

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Initial Thoughts on Omicron and Vaccines

You've no doubt seen discussion in the news and social media about the emerging coronavirus variant called Omicron. It was first detected in South Africa, but is now in many countries including the U.S. Because it is fairly new, it's hard to say much definitive about it. I recommend keeping an eye on knowledgable commentators (a few links below).

Initial data from South Africa suggest that it is spreading very fast, and that prior infection with COVID does not give protection (at least robust protection) against Omicron. How well the vaccines protect remains to be seen, but we will likely see a lot more breakthrough cases than with Delta. The reason, simply put, is that the Omicron spike protein has changes that will prevent some of the antibodies that were previously generated from recognizing the Omicron spike. It's not all or nothing; rather, it's degradation by degree.

I made the following figure to illustrate how I think about COVID vaccines. Ideally, most people stay in the first stage, and very few people proceed to the bottom stages. With Omicron, we will probably see more people (either vaccinated or previously infected) go further down than they would if this was just another Delta wave. People with no COVID or vaccination history are simply at the mercy of nature.

What can you do? The same kinds of things you've already been doing. However, you need to be fully vaccinated, including the booster. For one thing, the Delta variant is still very prevelant and we are heading into winter [1]. So you want to be as protected as possible against it. But even if the vaccine isn't as potent against Omicron, there is every reason to expect that it will still be helpful. Whether you have previously had COIVD or not, get fully vaccinated so that your immune system is as prepared as possible for Omicron. Even if the antibodies are not as good as they could be, having them at higher concentration will help. Also, there's more to the immune system than antibodies (namely, T cells), and they need to be on high alert too.

A Few Suggested Information Sources [2]:
Your Local Epidemiologist (Katelyn Jetelina) (Twitter / Substack)
Scott Gottlieb (former FDA commissioner)
Carl Zimmer (science reporter - one of the best in the business)

Notes:
1. As our family was leaving for our Thanksgiving trip, we learned of deaths in the extended family of some friends. The friends were vaccinated, but their rural relatives refused to get vaccinated (for the reasons you can imagine), even though an uncle had died of COVID. A birthday party for the father became a superspreader event, resulting in four hospitalizations. The father died, and at the last update a 31 year-old cousin was on a ventilator and expected to die [update: confirmed dead]. You make your choices, but you don't choose the consequences.
2. I've chosen a few relatively non-technical resources. Keep your eyes on these professionals and those they recommend. Beware of contrarians.

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Sure, Go Ahead and Undo Your Vaccine

I have to admit that I got a bit of a chuckle from an NBC News article about people giving in and getting vaccinated, and then "undoing" it.

In a TikTok video that has garnered hundreds of thousands of views, Dr. Carrie Madej outlined the ingredients for a bath she said will “detox the vaxx” for people who have given into Covid-19 vaccine mandates.

The ingredients in the bath are mostly not harmful, although the supposed benefits attached to them are entirely fictional. Baking soda and epsom salts, she falsely claims, will provide a “radiation detox” to remove radiation Madej falsely believes is activated by the vaccine. Bentonite clay will add a “major pull of poison,” she says, based on a mistaken idea in anti-vaccine communities that toxins can be removed from the body with certain therapies.

Look, unless you are under the care of a physician--probably at the emergency room, it's a virtual guarantee that anything that claims to 'detox' you is utter baloney. In fact, I'll go so far as to say that the word 'detox' is a bright red signal that you are probably dealing with a charlatan.

That's why I thought the article was funny. People who are into 'detoxing' themselves have already left the realm of medical/scientific reality. Why would they care about a news article that tells them that they can't undo or "detox the vaxx"? Excuse me, TikTok says otherwise.

But, since getting a high proportion of the population vaccinated is a good thing, there's a part of me that wants to go along with this. Here's what I might say:

Oh, no! Don't you dare get the vaccine and then take a bath and smear mud on your skin! You'll ruin everything, and the government can't do anything about it! Now you know why doctors are so mad and don't want you to know about this one wierd trick!

That kind of marketing has to be good for something.

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Anti-Vaccine Sentiment is Not Uncommon Among Chiropractors

Following my last post on anti-vaccine lies told by a chiropractor, I came across two news articles (one new, the other from last May) that highlight that chiropractors seem to be a concentrated source of vaccine mis-information, something that existed before COVID but that has become more prominent in the wake of COVID.

AP News: Anti-vaccine chiropractors rising force of misinformation
The Atlanta Journal-Constitution: Some Ga. chiropractors are stoking fears of COVID vaccines

Both articles state that anti-vaccine sentiment comes from a minority of chiropractors, but they seem to have outsized influence. How much of a minority? It's hard to say, but the AP News article offers this:

AP could find no national numbers of vaccination rates among chiropractors, but Oregon tracks vaccine uptake among all licensed health providers, and the numbers show chiropractors and their assistants are by far the least likely to be vaccinated -- and far less than the general public.

Just 58% of licensed chiropractors and 55% of chiropractic assistants in Oregon were vaccinated as of Sept. 5. That’s compared to 96% of dentists, 92% of MDs, 83% of registered nurses, 68% of naturopathic physicians, and 75% of the general public.

Of course, mainstream medicine has its share of quacks and hucksters, and although I have never sought treatment from a chiropractor, I am willing to believe that most of them provide useful medical services [1] in the vein of physical therapy. The problem is that pseudoscience is baked into the history, philosophy, and sometimes the training of chiropractic. The AJC article is particularly interesting here because the largest chiropractic school, Life University, is in Georgia and it is still rooted in outdated 19th century medical ideas.

Such beliefs trace back to the founder of chiropractic, D.D. Palmer, who postulated in the late 19th century that most diseases and maladies are caused by spinal or joint misalignments, and therefore chiropractic adjustments can boost immunity.

Life University still embraces this concept of “vertebral subluxation,” though there is no scientific basis for it. During the height of the pandemic, the school’s guidance for faculty and students on how to prevent getting coronavirus included, “Get your spine checked and adjusted regularly to ensure your nerve system is able to optimally adapt to these external stressors.”

This is such unadulterated horse crap. The notion that an adjusted spine could protect you from contracting COVID is just as stupid as if I were to tell you that the COVID vaccine can protect you from getting a herniated disc. The problem here is that if your beliefs about health are wrapped around notions of mystical energies and "natural healing," then your diagnoses and treatments are going to be primarily concerned with unlocking said mystical energies [2] and promoting "natural healing". But healthy living, good nutrition, and great posture can only take you so far [3].

And yet, graduates of Life University who absorb these views are seen as doctors (with accompanying authority) in the eyes of the public, which is reinforced by their licensure by the state. This in spite of the fact that they are not licensed to prescribe drugs or perform surgeries. In Georgia, they aren't allowed to puncture the skin, so they presumably couldn't offer vaccination even if they wanted to.

Look, I'm not trying to demean any chiropractors out there in my readership, or their friends and loved ones. If they provide genuinely useful treatments to people and stick to their sphere of training and licensure, then God bless them. But the public should know that a chiropractor's sphere of medical authority is rather narrow, and the opinions of chiropractors on vaccines should hold commensurate weight.

Notes:
1. Some patients may also find social/psychological benefit from their visits.
2. An old chiropractor I knew once said that he had to understand quantum mechanics for his job. I was too dumbfounded and incredulous to ask questions.
3. As an extreme example, rabies virus travels up the peripheral nerves to the central nervous system. Once there, it is virtually always fatal in humans. No vitamin juice to aid "natural healing" or spinal adjustment to optimize nerve adaptation to such an "external stressor" has changed that. Vaccination or passive antibody treatment after a bite is your only real hope.

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Example of a COVID Chart Crime

A chart crime is when a chart is used in a misleading way [1]. It could be that the data are manipulated, cherry-picked, or the chart is simply designed such that true data lacks correct context.

Recently the cynical side of me was imagining how I could use COVID data to commit a chart crime. Here is what I came up with.

This chart showing U.S. COVID deaths per capita is extremely misleading, but I haven't monkeyed with the data at all. Can you tell why it is misleading?

Think about it this way: who are the people dying in this chart--especially in the peak on the right? Are they vaccinated or unvaccinated? If you are reading the news at all, you know the answer is that the vast majority of people dying of COVID have not been vaccinated. In fact, according to CDC data, as of Sep 13 there have been 3,040 total fatal breakthrough cases (i.e. vaccinated people who nevertheless died of COVID). By comparison, just since Aug 1 there have been about 60K COVID deaths (U.S. data only). So the mere fact that there is a spike in COVID deaths occuring in the face of the vaccine rollout means nothing for whether vaccines are efficacious or who is at risk of dying. You need more granular data to draw those conclusions.

Assuming the data are good, population-level data are useful for making comparisons between populations, and for developing hypotheses for further investigation. But you need to be careful about what conclusions you draw about particulars from population data alone because even if it is accurate, it masks complications in sub-groups going on underneath.

A word to the wise.

Notes:
1. The term was coined in the finance industry, where apparently chart crimes are common.

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COVID Vaccines: Letter to a Friend

An old friend recently contacted me with some questions about the COVID vaccines. I spent enough time composing my response that I thought I would post it here in case anyone finds it useful. Below is a lightly edited copy of my emailed reply.

---------------------------------------

These are good questions. Instead of taking them point by point, I think it makes sense to address them in the course of a longer discussion. (Probably too long, but I can’t help it.) First, I should state that I am only giving general information and not specific medical advice. Ultimately, I would follow whatever your kids' doctors advise.

Messenger RNA (mRNA) is an intermediary between the genome and the cellular machinery that makes proteins. It essentially tells cells which amino acids to link together in order to make a protein. All proteins in the body (specifically in cells) are made using mRNA. When a virus infects a cell, it starts making its own viral mRNAs, which causes the cell to start making viral proteins. The spike protein is one of a number of proteins that the coronavirus makes. The spike protein is important because it is responsible for attachment to cells, and then entry into the cells. From an immunology and vaccine perspective, it is the most important protein because if you can make antibodies that bind to it in the right spot, the spike protein is unable to attach to or enter new cells. Thus, the virus is neutralized.

Right now there are two basic classes of approved coronavirus vaccines.

1. Moderna and Pfizer use mRNA technology. They take chemically synthesized mRNA (coding for spike) and formulate it with some lipids and cholesterol to form a nanoparticle that can be taken up by cells. mRNA is easily degraded, which is why it can't be simply injected by itself. It needs that lipid nanoparticle to protect it until it is delivered into cells. Cells have various mechanisms of sensing RNA that is out of place, so to speak, so the vaccine mRNA has slight chemical modifications to help avoid alerting cells to its presence. This is done in order to help maximize the amount of protein produced; otherwise the cell would try to shut down protein production, which would negatively impact the ability to generate a good immune response. Currently, two doses are considered fully vaccinated.

2. Johnson & Johnson and AstraZeneca (Europe) take a different approach. They use a different kind of virus called adenovirus as a delivery vehicle (a 'vector'). (They actually use different adenoviruses, but the principles are the same.) The adenovirus is modified in two basic ways. First, it is missing some key parts of its genome such that it can only replicate in special laboratory cells, but not in people. Second, the gene for the coronavirus spike protein has been added into its genome. When the adenovirus is injected, it can "infect" cells, but it can't make copies of itself. However, it does make spike mRNAs, which are then turned into the spike protein by the cell. Currently one dose is considered fully vaccinated.

Aside from a small mutation in the spike protein that helps keep it in the optimal shape for an immune response, there is no difference between the spike protein made by the vaccine vs spike made by the virus. The production of spike by both vaccines is transient. Ultimately, the mRNA and/or adenovirus are degraded, as is the spike protein that was produced. How long does the spike protein stick around? One study of some people who got the Moderna vaccine detected spike in blood for about 7-10 days after the first vaccination, and then barely at all after the second vaccination--presumably because the immune system was poised to deal with it quickly. I don't know whether comparable data has been generated for the adenovirus vaccines, but it would probably be something similar (but only one dose). There could be some trace amounts retained in lymph nodes for longer, which is normal and allows further honing of antibodies, but for all practical purposes I think it's safe to say that vaccine-produced spike is gone by 2-3 weeks. There is nothing about the vaccines that would make spike a permanent part of your body any more than natural infection would.

Any new vaccine or drug is tested in animals (if possible) and then gradually introduced into humans. First, 10s of people are tested for safety. Then a few hundred or thousand are tested for efficacy. Any obvious problems should be apparent at this point. However, in a genetically and biologically diverse population, it is impossible to predict whether more rare problems will arise. This is further complicated by the fact that weird and unexpected medical events happen every day. Sorting out coincidences from causal connections is a challenge, and the more rare the adverse event, the larger the population is needed in order to reach statistical certainty. Even when there is statistical certainty, the adverse events need to be weighed against the benefits.

I'm not intimately familiar with the FDA licensing process, but several factors came together that enabled the quick development of the COVID vaccines. First, the delivery systems (mRNA or adenovirus) already had a lot of research behind them. Second, previous coronavirus research made the choice of targeting the spike protein a natural one. Third, the expanding pandemic made it easier to generate the needed data to compare vaccinated vs non-vaccinated. It takes a lot longer to do this when a disease is less common. Finally, the federal government took on a lot of the financial risk. Ordinarily vaccine companies would wait until near the end of the process to invest in manufacturing facilities. In this case, the federal government essentially said, "Go ahead and start preparing for manufacturing while collecting the data from the early phases of evaluation. If it turns out that the vaccine fails safety or efficacy standards, we will cover the cost of having prematurely invested in manufacturing."

There are a few garden-variety side effects that often occur with vaccines. Things like fevers, aches, and so forth--basic flu-like symptoms that are really just automatic parts of an immune response. Other side effects become apparent over time and with larger populations. The CDC and FDA monitor these other side effects and provide updates on the most important ones here: LINK

As you noted, the adenovirus-based vaccines (J&J in the U.S.; Astrazeneca in Europe) have been associated with a rare clotting issue, resulting in a pause in their use earlier this year in both Europe and the U.S. I think the exact mechanism behind this isn't known for sure, but it doesn't seem to be as simple as the presence of the spike protein because the same thing has not been seen with the mRNA vaccines. Clotting issues of this type need to be treated differently than other clotting issues. Part of the reason for the pause was so that the word could get out to physicians that they needed to be aware of this association so that they did not inadvertently use the wrong treatment. The J&J vaccine has also been associated with a rare nerve issue.

The mRNA vaccines (Pfizer and Moderna), on the other hand, have been associated with rare cases of myocarditis, especially in young men after the second dose. The majority of these rare cases have resolved with minimal treatment. It is also worth noting that COVID infection itself can also cause myocarditis.

The duration and effectiveness of natural immunity vs vaccine immunity is still a developing story. It does appear that people with natural immunity have good protection against re-infection. Some studies suggest that they are better protected against re-infection than vaccinated people, and there are good immunological reasons to think that would be the case. However, studies also indicate that natural immunity can be further improved with one dose of vaccine, including better ability to neutralize variants. So as a generalization, I would say that when it comes to re-infection, natural immunity + 1 dose of vaccine is superior to either natural immunity alone or fully vaccinated without prior infection. (For people who have been previously infected, the second dose doesn't seem to add much additional benefit. On the other hand, keeping it at 2 doses (mRNA only) helps to ensure that all people are fully vaccinated.) To be clear, that doesn't mean that natural immunity is preferred, since that implies getting infected and likely having disease, something we want to avoid. It is impossible to predict what future variants may come our way. However, it looks increasingly likely that they will be sub-variants of the current delta variant. Presumably, future booster shots will incorporate updated variant spikes.

But let's come back to natural immunity for a moment. Like most things biological, there is a spectrum. Some people develop fantastic immunity, and others develop mediocre immunity, which is borne out by documented cases of re-infection. Although antibodies are only one part of the immune response, studies suggest that antibody levels correlate pretty well with protection. As far as I know, current commerically available antibody tests cannot be interpreted to indicate the level of antibodies or level of protection. They only indicate that antibodies are present. (The FDA warned about this in May.) If I had to guess where someone who never had symptoms falls on the spectrum of natural immunity, my guess would be on the weak, less durable side. My reasoning is that if the virus didn't cause symptoms, then it probably didn't replicate enough to really get the attention of the immune system. (The scientific literature is a little bit conflicted on this point, but some studies support my view.) Unfortunately, absent a more robust test designed to assess the levels and/or neutralizing capacity of antibodies, there's no way to know where any individual stands. This is part of the reason why people who have recovered from COVID are still encouraged to be vaccinated.

I take your point about long-term safety. (Although I would note that the long-term consequences of COVID aren't known yet either.) We obviously can’t see into the future, but I think this framework might help. Virtually all of the adverse events—even the rare ones—that have been observed have occurred within days to a couple of weeks of vaccination. That is the time when vaccine components are present, spike is being made, and the immune system is most active. So let’s call these acute adverse events. As I explained earlier, the vaccine and spike protein are gone within 2-3 weeks. After that point, any adverse events would have to either be leftover consequences of the acute adverse events, or some aberrant immune activity—like maybe the vaccine provoked the immune system to start attacking some part of the body (autoimmunity). With the possible exception of rare cases of Guillain-Barré Syndrome, I’m not aware of any such thing having been observed. There’s a sense in which anything is possible in nature, but it is hard for me to imagine how there could be any long-term adverse events—not connected to the acute events--that would spontaneously arise months/years after vaccination. Moreover, inasmuch as virus infection and vaccination both stimulate an immune response against the spike protein, it is hard for me to imagine how such a long-term adverse event could be specific to vaccination. That’s not a guarantee of long-term safety, but I think we should have every expectation of long-term safety for the vast majority of vaccinates.

I think I have taxed your patience enough for now. I hope this helps. I am happy to answer any follow-up questions, provide references, or explore other sources of information as you may desire.

Jared

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Time to Clean Up Some Vaccine Information Pollution

There is a viral video going around of a pathologist claiming that the COVID vaccines are toxic. It is a compeling talk, but it is garbage...in a sort of glorious way. Time for cleanup.

First, who is this guy? Dr. Ryan Cole is apparently an independent pathologist in Idaho who has previously attracted the attention of FactCheck.org, and has affiliated with a group called America's Frontline Doctors, which is a group of doctors with...let's say a contrarian take on COVID and public health. The video is of a presentation he apparently gave on July 27 to his like-minded colleagues.

Cole's basic claim seems to be that the Spike protein of the virus is responsible for most of the pathology and disease manifestations of COVID. Therefore, we should not be pushing vaccines that use the Spike protein on people, and especially children, since we don't know what the long-term effects will be. (As if we do know the long term effects of COVID infection?) Also, we should be doing more autopsies of people who die after having had the vaccine in order to determine whether there is a causal connection.

I've stated his thesis using calmer and more neutral language than Cole, and put this way it seems like a reasonable position. When watching the video, I quickly determined that this was a guy with an axe to grind. There's nothing wrong with being passionate, but the way that he derided the vaccines made it clear that this wasn't just a doctor with some scientific concerns. It was almost like he was trying to come up with his best insult. At one point he said, "these are not vaccines," which is kind of a stupid thing to say because they are, in fact, vaccines. (Maybe he has his own special definition?)

Before I address his claims, I need to do a spoiler alert. Just like knowing how a magic trick is done or how a mystery ends can take away the feeling of wonder, what I am about to explain may deny you the opportunity to feel the same sense of fear and indignation toward the vaccines and medical establishment that you might otherwise feel. So if you want to feel the tension build and wonder how it could possibly be resolved, go watch now and do not read further.

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OK, I'm going to do the big reveal up front, but we'll still go through the journey. Here it is: NONE of the scary pictures of inflammation that Cole shows are from a vaccine. Even worse, some of them are actually from COVID patients. You may find that hard to believe, but stay with me.

Inflammation
If you haven't watched it, much of the talk consists of Cole showing slides of tissues and commenting on the inflammation. You could be excused for thinking that these were from cases that he investigated or experiments that he did. In fact, at the 4:45 mark he says, "We did studies in lab animals." He must have meant the royal 'we' because there's no evidence, that I can find, that he has been involved with any animal studies dealing with COVID. None of the image slides contain references, but thanks to the magic of Google I was able to track them all down. They are all pulled from the scientific/medical literature, or from medical news articles.

I'm going to go through each of them and comment on his claims. Because I am lazy, I don't feel like reproducing all of the images here, so I'll just give a description, where in the talk they can be found, and provide links to the image sources so you can check them out for yourself.

1. (5:20) Endothelial cell mitochondria (black, purple, and rainbow colors) - Claim: The damage is caused by Spike alone from the vaccine, not the virus. Fact: This is wrong. No vaccine was involved. What the researchers did is to make inert viral particles that have the Spike protein and treated endothelial cells (in the lab) with these particles. Yes, they attributed the observed, effects to Spike, but it is a logical leap to say that the vaccine would do the same thing--or be biologically meaningful if it did. In fact, the article suggests that a vaccine would be protective.

2. (6:57) Lung tissue (the image appears to come from news articles, like this one, that describe results that were later published) - Claim: disease is from the vaccine. Fact: Again, no vaccine was involved in the study. The researchers injected part of the Spike protein directly into the trachea of mice. Perhaps it shouldn't be surprising that putting a foreign protein directly into the airway caused inflammation. It's an interesting finding that helps inform us about the disease process, but it's another logical leap to say that the vaccines would cause the same effect. More about this later, but for now the practical takeaway is don't snort Spike powder.

3. (8:16) Brain cells - Claim: inflammation from Spike. Fact: This comes from the autopsy of a man who had the first Pfizer dose but caught COVID 3 weeks later while at the hospital for other health problems. His death was ruled not to be due to COVID infection, since they did not see typical signs of COIVD, but many of the tissues sampled (including brain) had viral RNA and he was well past the point when Spike would have been present from the vaccine. At any rate, it's no surprise that having virus in the brain would lead to inflammation.

4. (8:28) Heart images, myocarditis (scroll down) - Claim: "That's after a shot." Fact: These images are from a public database of radiology images. The case description does not mention COVID or the vaccine. It's true that there are some rare cases of myocarditis associated with mRNA vaccination (but not the Johnson and Johnson vaccine), and it could be that this image is representative of such cases (I'm not qualified to say), but this image is not from someone who had a vaccine. Cole probably pulled it from an online news article that used it as a stock image (like this one) and mistakenly thought it was actually from a vaccine patient.

5. (8:55) Heart tissue - This image does not have anything to do with COVID at all. The top pictures are from an entirely different virus, enterovirus A71.

6. (9:50) Kidney - The rest of the images are shown in rapid succession and can be addressed together since they can all be found in the same article. Fact: All of these images are from people who actually had COVID.
7. (10:05) Liver
8. (10:15) Testes

If you are wondering why Cole would show tissue slides of people who had the disease (or even a different disease) and then claim that this is what the vaccine does, you're asking a good question! I think the most charitable answer I can give is that Cole has taken the data from the mice with Spike injected in their airway and extrapolated to the conclusion that all COVID inflammation comes from Spike and therefore the vaccines (which cause your cells to make Spike protein) cause pathology equivalent to COVID disease. That's quite the extrapolation! And it's plainly false just from a clinical perspective. (Are vaccinated people having to monitor their oxygen levels?) So if you follow Cole's logic, you should avoid the vaccines and instead leave yourself open to becoming infected and getting the types of pathology that he has shown in his slides. (Joke: maybe it's best that Cole's patients are already dead.)

Miscellaneous
The images are really the main story, but there are a variety of other claims and issues that need to be addressed.

First, let's go back to the mice that had Spike protein (actually only part of the Spike protein, S1) injected in their airway. Consulting the paper, the scientists gave the mice 400 micrograms of Spike per kg of the mouse weight. Cole mentioned a Harvard study that measured the circulation of Spike in the blood of people given the Moderna mRNA vaccine. Spike (S1) was only detectable for 9 days or so after the first shot, and virtually not at all after the second shot (consistent with the rise of antibodies). At the peak of S1 circulation, the average amount was 68 picograms/mL. Let's do some math. The Internet tells me that an average adult human has about 5 liters of blood. Let's make it 6 L, which is equal to 6,000 mL. 6,000 mL x 68 pg/mL = 408,000 pg = 0.408 micrograms total. Let's assume a weight of 90 kg (~198 lbs). Divide 0.408 micrograms by 90 kg = 0.0045 micrograms/kg. Do I need to continue in order to make the point that the mouse study used WAY more S1 protein than was found in the blood of vaccinated people?

(7:43) Spike crosses blood brain barrier (BBB). The slide accompanying this claim contains the only references provided in the whole presentation. Note that the slide title, "Spike as Toxin" comes from Cole, not the referenced articles (here and here). Poking around the literature, the focus seems to be on the ability of the virus to invade the central nervous system. I am unable to find any literature that addresses the BBB in the context of vaccination. However, I think you would be hard pressed to show that neurological outcomes of vaccinates are worse than COVID patients, and that's putting it lightly. Perhaps there's a kernal of truth here that could improve the next generation of COVID vaccines, in terms of tolerability or side effects. But that's just me trying to be charitable.

(10:30) Pfizer biodistribution study submitted to Japanese regulators shows accumulation in ovaries of rats, with a 16% decrease in fertility. Fact: First, the study shows that the percent of nanoparticle lipid that goes to the ovary is less than 0.1% of the dose, compared to the injection site (roughly 25%) or liver (~15%). As for the decrease in fertility, I was unable to find a source for this claim in the limited searching I did. But I DID find a recently published study from Pfizer showing that female rats given four doses of vaccine were not different in any way from non-vaccinated rats in terms of fertility, including estrous cycle.

(15:00) Cole makes a variety of claims about immune dysregulation leading to reactivation of other viruses and increase in cancer. These claims are purely anecdotal so they are difficult to address. He mentions a study from Germany and the Netherlands, but that's not much to go on. I suspect that, like his other examples, he is extrapolating data from COVID patients and inappropriately applying it to vaccinated people.

Finally, the CDC asked me to hide this from you, but I'm going to let you in on the secret if you promise not to tell. You can find information on COVID vaccine adverse events here and here, among other places.

Conclusion
I have shown that Dr. Cole's claims about vaccines are not connected to any of the images that he showed in his presentation, and that others of his claims are either false or missing important context. It is plainly dishonest to use images of tissues damaged by the virus in order to argue that the current vaccines are dangerous. I think it is reprehensible, and even unethical, that he would claim that vaccines are ruining the hearts of children, while showing a picture of a heart that was damaged for unrelated reasons. Never does he say that these are just examples of the kind of thing he is worried about. And it is worth stating again: following Cole's argument to its logical conclusion leads to the idea that people are better off facing the virus than being vaccinated. On a population level that is clearly false.

Buried in his screed are some questions and issues that perhaps have scientific merit, but he has overshadowed and distorted them with his sensationalism and misdirection. At a certain point we leave the domain of scientific debate and enter information pollution.

Now that you've taken all of this in, go back and watch the video again and see if it still has the same punch. Hopefully, my cleanup has been worthwhile.

P.S. I've tried to make sure my ducks are all in a row in this, but please bring any errors to my attention.

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Worries about COVID vaccines and infertility are ridiculous

Public Service Announcement: Claims that the COVID vaccine could cause infertility are somewhere between misguided and malicious. There is no more reason to think that COVID vaccines can cause infertility than that they could cause diabetes, or heart attacks, or arthritis, or irritable bowel sydrome, or anything else.

Vaccines are not entirely irrelevant to pregnancy. As a general rule, pregnant women are advised against vaccines that consist of a live attenuated virus or bacteria, out of abundance of caution. The the MMR (measles, mumps, rubella) vaccine stands out as one example. However, women are sometimes vaccinated before they know that they are pregnant and, fortunately, adverse effects on the fetus have not been demonstrated. Thus, the risk to pregnancy seems to be more theoretical than real. (And just for clarity, COVID vaccines do not contain live attenuated virus.)

Pregnancy aside, in the history of vaccination there have been a few vaccines that were pulled from the market due to safety problems. In the 1960s, an RSV vaccine for children was found to actually exacerbate disease [1]. In the late 1990s a vaccine against rotavirus was pulled after it was associated with a small risk of intestinal intussusception (where a segment of the intestine folds back on itself). Other vaccines have special safety considerations. The live polio vaccine, for example, is no longer used in countries with low polio risk because the virus can sometimes revert to virulence due to mutation in its genome [2]. As another example, the smallpox vaccine is still used in certain laboratory situations even though smallpox has been eradicated [3]. However, skin conditions like eczema and psoriasis pose a safety risk for this particular vaccine. The kinds of issues that I have described are well known among vaccine researchers and clinicians.

It is one thing to worry about how a live vaccine might theoretically affect a fetus, which doesn't have a functioning immune system. Similarly, I can understand being cautious when there are no safety data on pregnancy. But I cannot think of any vaccine used in the U.S. or internationally that is even suspected of causing infertility. It just isn't a thing.

There certainly are infectious diseases that can cause infertility, which leads me to a question: Why would you be more worried about a vaccine causing infertility than about the disease itself? It makes no sense. But that's probably because it isn't supposed to make sense; it's just supposed to scare.

Notes:
1. That a vaccine could make a disease worse is counter-intuitive at first glance, but there are exceptions to most rules in biology.
2. The live polio vaccine is superior to the killed vaccine in several respects, which is why it is still used in certain geographies where health infrastructure is poor.
3. It's not because they are doing smallpox research. It's because the virus that was used as the smallpox vaccine--called vaccinia--is a useful laboratory tool. Inadvertant infections can be nasty, so lab workers may be vaccinated as a precaution.

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Vaccination: What If I Already Had COVID?

Current recommendations are that people who had COVID should still get vaccinated. Does it do any good? In looking into this, I found two recently published papers (there may, of course, be others) that address this question with interesting results [1].

First, yes, the first dose of the mRNA vaccines significantly boosted the level of antibodies of people who previously had COVID. But interestingly, the second dose didn't seem to add much additional benefit.

At the same time, systemic reactions (fever, chills, fatigue, et.) to the first dose were more common in people who previously had COVID than in people with no prior exposure. Reactions to the second dose were similar irrespective of exposure history.

Does this mean that if you've already had COVID you can skip the second mRNA dose? Well, on average the data seem to point that way, although there will always be variability in the population. We don't know what the longer-term effects would be, like how long the antibody levels stay elevated. But if you previously had COVID and were miserable from the first mRNA dose, you might talk with your doctor and/or health department to see what they think.

I don't know whether or not recommendations will change based on these data. One problem is that people are often not reliable in recounting their health history. I know people who think they had COVID very early in 2020--so early that it is unlikely to be true. One person was convinced they had it in the fall of 2019! So if health officials said, "If you had COVID you only need one dose," there is a legitimate fear that we would end up with a bunch of half-vaccinated people because they self-diagnosed themselves as having had COVID. So I can't blame health officials if they just stick to two doses to help ensure everyone is fully vaccinated. But if you are really sure that you had COVID, then it might be a conversation worth having with your doctor and/or health department.

Notes:
1. Pre-print versions of these papers came out in February. However, official publication was within the last two weeks, and both can be viewed for free: here and here.

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Vaccine #2 Achieved

This week I received my second dose of the Pfizer COVID vaccine. Hooray! The next day was no big deal for me. I had some minor aching in my back and legs, and of course a sore shoulder, but if I had woken up with amnesia I wouldn't have had any reason to think that day was out of the ordinary (except for the shoulder, which was fine by the second day). Soon I will be considered fully vaccinated (i.e. second dose plus 10-14 days).

I'll be honest that things weren't as smooth for my wife. She started feeling increasingly ill the next day and developed a fever that got as high as 100.8 degrees F, along with a lot of aching (she said even her toes hurt) and chills. It hit hardest about 24 hrs after the vaccine, but after another 7 hrs the fever broke. On the second day she was feeling better, but still recovering from the soreness. By the third day she was pretty much fine [1].

It's impossible to know, but I can't help but wonder whether our respective responses to the second dose would have any correlation to severity of disease. If so, my wife would have been in pretty bad shape. Or, if it were an inverse correlation, I would have been in bad shape. Fortunately, we'll never know.

Some may think, "Well if I have a chance of getting sick with or without the vaccine, then why get the vaccine?" That's the wrong way to look at it. First of all there is the simple matter of duration. My wife was miserable for 1 day, and then it was over. People who get COVID are miserable for many days. Second, although my wife felt ill as a result of her immune system kicking into gear, there was no underlying disease. There was no virus causing damage to various organs, no loss of smell, no coughing, no extreme fatigue, and no breathlessness from simply going up the stairs. There was also no wondering when (or whether) recovery would come, worrying about whether a trip to the hospital would be needed, worrying about whether anyone else in the family would be next, or worrying about long-term effects. Other than some special cases, there is no rational risk assessment that would suggest that it's better (or neutral) to not get vaccinated.

We can't completely throw caution to the wind yet, since our 13-year-old is still vulnerable. But Pfizer has reported 100% efficacy in his age range, so I think it's probably only a matter of days before it is approved for him. At any rate, our family is close to being immune (our daughter was previously vaccinated due to some lucky circumstances--with no side effects), and I can soon go out to lunch with coworkers without worrying about getting sick myself or bringing the virus home to my family.

So my advice is to get vaccinated, but if you get the Moderna or Pfizer vaccines [2], just assume that you may need a sick day after the second dose. If your experience is more like mine, then great! But if your experience is more like my wife's, then at least you will be prepared.

Notes:
1. My wife had/has a bulging disk in her neck, so if she's not careful with her posture there is a domino cascade of muscle cramping in her upper back and a resulting headache. We think that the hunching and shivering set off that cascade, so technically on the third day she was still recovering from that.
2. I'm not as familiar with the Johnson & Johnson side effects. My wife's social media intelligence is that they are less severe, but last longer.

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Vaccine #1 Achieved

This week I received my first dose of the Pfizer COVID vaccine. Hooray! Right now, cells in my body have taken up the mRNA that was delivered by the vaccine and are producing the Spike protein of the coronavirus. Dendritic cells are starting to notice, and will make their way to lymph nodes to alert B cells and T cells that this foreign protein is in my body. Soon B cells that recognize the Spike protein will start to make antibodies--little proteins that bind onto the Spike protein whenever they come in contact with it.

In three weeks, I will receive my second dose, and the process will repeat except that the B cells that were activated the first time will really kick into high gear. At that point, my assimilation into the Bill Gates--Tony Fauci--George Soros conspiracy will be complete! (Also, I'll be immune to COVID.)

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How the New COVID Vaccines Compare to Other Viral Vaccines

The leading vaccines against SARS-CoV-2 are based on a new technology that delivers mRNA to cells. This novelty, combined with political and social division, has resulted in a fair amount of nonsense commentary about them. The AstraZeneca and Johnson & Johnson vaccines are also somewhat novel. I thought I would quickly put these new technologies into perspective by comparing them to other viral vaccine technologies.

The first thing you need to know is that the principal purpose of a genome is to store the sequence information for all kinds of different proteins. Our genome is made of DNA, but it does not directly make the proteins. Rather, a similar intermediate molecule called messenger RNA (mRNA) is produced from DNA, and it is the mRNA that is directly read by the cell's machinery to make proteins. DNA -> mRNA -> protein. (Additional variation on this scheme can be found among viruses, but RNA -> protein always holds.)

Next, the immune system can be conceptually divided into two arms that work together: innate and adaptive. The innate system responds in ways that are not specific to a pathogen (disease-causing microbe). It's what makes you feel lousy and gives you a fever, and it kicks in quick. The adaptive immune system takes longer to respond, but produces antibodies and other cells that specifically target a pathogen. The value of vaccines comes from their ability to engage the adaptive immune system such that it is ready to go when the actual pathogen shows up. When we talk about being immune to something, we're really talking about the adaptive immune response.

In order to gain immunity, the immune system needs to come in contact with components (usually proteins) of the pathogen. There are several ways of doing this. I've listed the basic strategies for viruses along with some well-known examples in human medicine. Almost all of them are also used in veterinary medicine. There are some further variations to these strategies, but I think this captures the major themes.

1. Infect someone with a weakened virus that does not cause disease. The virus commandeers the cells to produce viral proteins (via viral mRNAs). This is the oldest and classic strategy. (Examples: smallpox, measles, mumps, rubella, yellow fever, and oral polio.)

2. Inject a virulent virus that has been inactivated such that it cannot replicate. This is also a relatively old method. (Example: injected polio, hepatitis A)

3. Inject purified viral proteins. (Example: hepatitis B)

4. Inject virus-like particles (VLPs). These are essentially virus particles that do not have any genome, and thus no ability to replicate or produce more viral protein. (Example: HPV)

5. Use a different non-pathogenic virus as a Trojan horse to make proteins of the virus of interest. (Examples: the AstraZeneca and Johnson & Johnson COVID-19 vaccines are, I believe, the first approved human vaccines of this type. However, this strategy is used in a number of veterinary vaccines.)

6. Inject DNA that codes for viral proteins. DNA -> mRNA -> protein. (Doesn't seem to work well in humans, so it is not used in human vaccines. But there are a few examples in veterinary use.)

7. Inject mRNA that codes for viral proteins. This is the newest technology, first used by Moderna and Pfizer/BioNTech. The challenge of this method has been to deliver RNA to cells, since RNA is easily degraded. The technology advancement has been figuring out how to encapsulate the RNA in lipid nanoparticles such that the RNA is protected until it is delivered inside the cell.

In each of these cases, the adaptive immune system is exposed to viral proteins--proteins that were either produced by the body's cells, or were produced by cell culture prior to injection. mRNA vaccines are the cleanest vaccines in the sense that they don't involve any extraneous viral proteins or genetic material. They really get to the heart of the process: mRNA -> protein, and it's exciting to envision how they might be applied to other diseases.

Each method has pros and cons, and has to be matched to the biology of the virus and the resulting immune response. For example, in some cases antibodies directed against a single protein are sufficient to give you immunity. In other cases it's not that simple, so you wouldn't use a strategy that only delivers a single protein. But in every case, it really boils down to exposing the immune system to the right viral proteins in the right way.

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Vaccination is Not a Partisan Issue...Yet

During the last U.S. presidential election cycle, Michelle Bachmann was briefly seen as the Republican primary front-runner. Her downfall from that position was catalyzed when she claimed during a debate that the HPV vaccine could cause "mental retardation." Earlier this year a measles outbreak at Disneyland brought the issue of childhood vaccination to the public attention, resulting in California passing one of the strictest school vaccination laws in the country. Meanwhile, in the immediate aftermath of the measles outbreak, a variety of politicians, including some (then) potential Republican candidates, expressed less than solid support for vaccination.

Donald Trump has believed, since at least 2007, that childhood vaccinations cause autism. The issue was raised in the second Republican primary debate earlier this week.



Ben Carson gently and correctly noted that studies have not found any connection between autism and vaccines. Unfortunately, he and Rand Paul, the other physician in the debate, ultimately indulged Trump's idea of spreading vaccinations out. This led the New Yorker's Jon Chait to complain,

It is depressing that a presidential field with two doctors cannot even produce sensible views on medicine, let alone anything else. The party’s decades-long flight from empiricism and reason shows no sign of abating.

But in the Washington Post two graduate students of political science write that CNN should not have raised the question at all.

We fear that if party elites continue to polarize, the cues present in the press could begin to undermine the societal consensus on childhood vaccinations. Why are we reasonably sure this is the case? Because we have seen this movie before, with global warming....

We fear we may begin to witness a similar dynamic on vaccines. Republican elites are increasingly voicing skepticism of the medical science consensus. The media sees this as fitting a pre-established narrative that Republicans are hostile to science, and thus CNN asked the GOP field a question about vaccines in front of a record breaking national audience of 23 million people.

It would not be surprising if Democratic elites leap at this opportunity to solidify their own science-based credentials and make it a campaign issue, particularly if someone like Donald Trump wins the Republican nomination. These cues are then communicated to the public through the press, and we may be off to the polarization races.

I'm not sure what to make of this. On the one hand, the public ought to be informed that a leading contender for the U.S. presidency has crackpot views about vaccination. In normal times such views would bring a chorus of condemnation that would endanger presidential ambitions, as seen with Bachmann in the previous cycle. However, Donald Trump has shown himself to be impervious to shame. Apparently he cannot say anything ridiculous enough that would cause his supporters to abandon him, and attempts of the media--even Fox News(!)--to hold him accountable for his antics are, in the minds of supporters, more evidence that elitists are trying to manipulate the masses and keep a bold truth-teller from succeeding. Thus, whether they wanted to or not, Carson and Paul soft-peddled their criticism of Trump and ended up legitimizing his views.

I have a hard time seeing why CNN is responsible for that...other than the way the debate questions were constantly framed around Trump's views. If the media avoided this and other topics for fear of politicization, well wouldn't that just be interpreted as another manifestation of media elitism (i.e. that the simpletons of America are too dumb to risk discussing an issue in a political context)?

I do not think that vaccination will ever be as polarizing as climate change. Whereas addressing climate change is perceived by many as a threat to prosperity, vaccination is generally viewed as an enabler of prosperity. And whereas the consequences of error in judgment for climate change are delayed or almost imperceptibly gradual, the consequences for error in vaccination are more immediate and severe. However, vaccination is more sensitive to dissent; successful vaccination policies require a high degree of compliance.

Ultimately, if vaccination becomes a politicized issue Republicans will have nobody else to truly blame but themselves. If they and their outlets will give full support to vaccination, then by definition it won't be a political issue--at least between Republicans and Democrats. But if they voice skepticism, I don't think you can blame CNN for reporting it.

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Vaccine-Autism Link Fraudulent from Beginning

The vaccine-autism controversy began with a 1998 paper in the Lancet, by British doctor Andrew Wakefield, that suggested an association between MMR (measles, mumps, rubella) vaccine and autism in 12 children. Although the alleged vaccine component responsible, in the minds of anti-vaccine advocates, has shifted over time (eg. thimerosal, which has since been removed from childhood vaccines), it was Wakefield and MMR that started the ball rolling. The paper was finally retracted by Lancet last year and Wakefield lost his medical license over ethical problems with the study.

Now the BMJ (British Medical Journal) is publishing the results of journalist Brian Deer's investigation into the paper. The BMJ's judgment is unflinching: fraud.

Below I reproduce their summary for part 1 and provide relevant links.

How the link was fixed

The Lancet paper was a case series of 12 child patients; it reported a proposed “new syndrome” of enterocolitis and regressive autism and associated this with MMR as an “apparent precipitating event.” But in fact:

*Three of nine children reported with regressive autism did not have autism diagnosed at all. Only one child clearly had regressive autism

*Despite the paper claiming that all 12 children were “previously normal,” five had documented pre-existing developmental concerns

*Some children were reported to have experienced first behavioural symptoms within days of MMR, but the records documented these as starting some months after vaccination

*In nine cases, unremarkable colonic histopathology results—noting no or minimal fluctuations in inflammatory cell populations—were changed after a medical school “research review” to “non-specific colitis”

*The parents of eight children were reported as blaming MMR, but 11 families made this allegation at the hospital. The exclusion of three allegations—all giving times to onset of problems in months—helped to create the appearance of a 14 day temporal link

*Patients were recruited through anti-MMR campaigners, and the study was commissioned and funded for planned litigation

For more details:

BMJ news summary

Secrets of the MMR scare: Part 1, Part 2, and Part 3.

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The Vaccine-Autism Wars

There is an article in this month's PloS Biology titled, "A Broken Trust: Lessons from the Vaccine–Autism Wars." It does a nice job of explaining how the recent controversy over vaccines and autism came to be.

Now, more than ten years after unfounded doubts about vaccine safety first emerged, scientists and public health officials are still struggling to set the record straight. But as climate scientists know all too well, simply relating the facts of science isn't enough. No matter that the overwhelming weight of evidence shows that climate change is real, or that vaccines don't cause autism. When scientists find themselves just one more voice in a sea of “opinions” about a complex scientific issue, misinformation takes on a life of its own.

The article would have been even better if it had listed the main studies addressing the autism question along with summaries of the findings. But since it didn't, I found a site that has at least some of them: The National Network for Immunization Information.

• Studies on MMR and autism
• Studies on thimerosal and autism

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Autism's False Prophets

"Book Is Rallying Resistance to the Antivaccine Crusade" is a New York Times article about Paul Offit's book, "Autism's False Prophets." Dr. Offit is a pediatrician and chief of infectious diseases at the Children’s Hospital of Philadelphia.

Dr. Offit’s book traces the history of autism theories, starting with the child psychologist Bruno Bettelheim’s blaming “refrigerator mothers.” It describes early false cures, including “facilitated communication,” in which assistants helped mute children type their thoughts; head-squeezing by osteopaths; cod liver oil; diets; and a 1998 fad for secretin, a pig hormone. It sums up 16 epidemiological studies showing no link between autism and either measles or thimerosal, a vaccine preservative [which was removed from most vaccines as a precaution in 2001 -- LDSSR].

To the newer argument that vaccines overwhelm babies’ immune systems, Dr. Offit notes that current shots against 14 diseases contain 153 proteins, while babies cope with thousands of new foreign proteins daily in food, dirt and animal hair, and that the smallpox vaccine that nearly every American over age 30 got as a child contained 200 proteins.

I'll be putting this on my to-read list. I've followed the controversy at a more popular level, and my own training is in microbiology and immunology, so I am pretty familiar with the concept of vaccines and how they work. However, I am not a physician so I don't know the clinical side well, and I could use some more information on the history of the movement as well as the epidemiological studies.

You can read an excerpt from the book here. Also, Dr. Offit was interviewed on the podcast, "The Skeptic's Guide to the Universe," which is available here.

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Measles Up in the U.S.

The CDC released a report this week detailing an increase in measles cases this year. From January to July there have been 131 cases all around the U.S. One hundred twenty three of those are U.S. residents and 112 were unvaccinated--63 of them for religious or philosophical reasons.


The report reminds us of the importance of immunization.

In the United States, measles caused 450 reported deaths and 4,000 cases of encephalitis annually before measles vaccine became available in the mid-1960s (1). Through a successful measles vaccination program, the United States eliminated endemic measles transmission (1). Sustaining elimination requires maintaining high MMR vaccine coverage rates, particularly among preschool (>90% 1-dose coverage) and school-aged children (>95% 2-dose coverage) (7). High coverage levels provide herd immunity, decreasing everyone's risk for measles exposure and affording protection to persons who cannot be vaccinated. However, herd immunity does not provide 100% protection, especially in communities with large numbers of unvaccinated persons. For the foreseeable future, measles importations into the United States will continue to occur because measles is still common in Europe and other regions of the world. Within the United States, the current national MMR vaccine coverage rate is adequate to prevent the sustained spread of measles. However, importations of measles likely will continue to cause outbreaks in communities that have sizeable clusters of unvaccinated persons.

It's also important to remember that vaccination does not always confer immunity; a certain percentage of vaccinated people fail to mount a protective immune response. In fact, recently a co-worker told me that they had to get the MMR vaccine as an adult because even though they were vaccinated as a child, lab tests failed to find antibodies against measles.

MMWR Weekly: August 22, 2008 / 57(33);893-896

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