Category: pandemic

Andrew Sullivan compares wearing masks to gay men wearing condoms

April 25, 2021 • 12:00 pm

In his latest piece on Substack (click on screenshot, though you may have to be a subscriber), Andrew Sullivan, who is HIV positive, compares condom use by gay men to prevent HIV viral transmission with masks worn by people to prevent transmission of a different virus: Covid 19.

Sullivan, who’s been taking the HIV drug cocktail for years, and says his viral load is undetectable, has also been vaccinated against Covid.  In his view, mask-wearing around similarly vaccinated people is now optional. He maintains that the chance of getting the virus while wearing a mask, or of spreading it to others, is virtually nil. And this, he says, is also true for HIV: if your viral load is sufficiently low because you’re taking anti-retroviral drugs, condom-less sex with a similarly low-HIV partner taking the cocktail is virtually risk free. Therefore, just as gay men feel that they can have sex “bareback”, as Sullivan calls it, so we should be able to go maskless around people if both we and they are vaccinated.

A few quotes:

In this way, gay men became as attached to condoms during AIDS as many of us have to masks during Covid. They remained a reflexive totem of responsibility, a sign of continued vigilance, a virtue-signal to oneself and your partner — long after they made no sense as a way to avoid HIV if you and your partner were already being treated. From those of us with zero viral loads at the start to those today taking the newer “prep” pill that prevents HIV infection, bit by bit, the condom rule has disappeared.

And yet not using a condom for sex — though the overwhelming norm for humans in history — felt weird and scary for a while in the late 1990s, like going into a restaurant without a mask now. Walking my dog in the park mask-free last weekend, I felt the same jitters as when I first stopped using condoms. I felt naked, and a bit daring. But I really had nothing to worry about in either case. I almost certainly couldn’t transmit either HIV or Covid and if I ever somehow got Covid again, it wouldn’t kill me. Just as there is nothing to fear if a few fully vaccinated friends come over for a cozy smoke sesh and chill in 2021, there was nothing rationally to fear in 1997 if two men, fully treated for HIV, had sex without a condom. The moral panic long outlasted its viral reason.

And this:

. . .we are in a similar phase in which reasonable people are being irrationally demonized for going back to normal and going mask-free. It makes no sense, but the truth is we get attached to rituals of safety, even after they have become redundant. Look at airport TSA screening, twenty years after 9/11. We so identify with safety protocols that it can feel dangerous simply to follow reason when circumstances change. The fear of Covid somehow gets internalized and perpetuated, just as HIV was. Even today, for example, a diagnosis of HIV feels far more terrifying than, say, diabetes. But diabetes is much, much more problematic now than AIDS, over a lifetime. Covid now seems much scarier than the flu. But if you’ve been vaccinated, that’s exactly how we should think of it. Nasty, but not fatal. So live!

It is true that Covid is not over; that we should not totally relax; that many who refuse vaccines could be a problem; that mutations matter. For what it’s worth I have nothing personal against masks. I wore them from early February of last year and was punctilious about them. But the situation has changed, and as more and more get vaccinated, and the human “herd” of the vaccinated grows larger, the odds of infection will decline. Bottom line: this viral motherfucker is on the ropes and we do not need to be in a state of permanent terror.

Sullivan hastens to add that he’ll probably continue to wear a mask on planes and trains forever, and he has no problem with bars and restaurants demanding proof of vaccination for entry. But he adds that the argument for wearing masks to be a “role model” also has a cost: “if people see no-one being liberated by the vaccine, they’ll be less likely to get one. And if leaving masks behind is the fruit of vaccination, the more people in the party the more will want to join.”

But is not wearing a mask easily interpreted as a sign of being “liberated by the vaccine”? I don’t think so.  Most maskless people, I suspect, are simply those who object to masks and have not been vaccinated. Remember, only half of Americans have now received at least one shot.

He ends like this:

So get vaccinated. Then use reason. The point is to get back to normal life, not to perpetuate the damaging patterns of plague life. So take off your masks, if you want. Plan parties for vaccinated friends. Get your vacation plans ready. And stop the constant judging and moralizing of people with masks and those without. Summer is coming. Let’s celebrate it.

But there’s a difference between masks and condoms that Sullivan doesn’t mention—or at least a possible difference. We still do not know if you can infect someone else if you’ve been vaccinated against Covid—as an asymptomatic carrier. We already know that you can get infected if you’ve been vaccinated; after all, the protection afforded by even the most efficacious vaccines is 95%, which means that there’s still a chance you could get Covid if you’ve had the jab(s). Granted, it’s a much reduced chance, and the vaccinations reduce the chance to about zero of your being hospitalized or dying, but getting infected still means that you might be able to spread the virus even if you’ve been vaccinated.

The only question I have is whether, if you get infected post-vaccination, you would be an asymptomatic carrier, not knowing you could carry the virus. And we also don’t know whether, even if you’re an asymptomatic carrier, you could carry enough virus to infect others. If all this is in fact the case, then there could be a large number of vaccinated people who should wear masks because they could spread the virus. If they were asymptomatic, we wouldn’t know who they were unless they got a Covid test, and even then you could get infected after the test.

Here’s the difference between condoms with HIV and masks with a vaccination. Those you could infect if you’re vaccinated are not your sex partners who are aware of any risks. They are clueless people you come in contact with. That’s not the same as having HIV, possessing a very low virus titer, and not using condoms when having sex with a similar person. In that case the two informed adults make a judgment. For someone vaccinated against Covid who doesn’t wear a mask, that person alone makes the judgment, putting other non-consenting people at risk.

Surprisingly, though, we still don’t know if vaccinated people can be asymptomatic carriers. According to NBC News Boston (my emphasis):

Dr. Kimi Kobayashi, the chief quality officer at UMass Memorial, said it is important for everyone to wait the full two weeks after the second shot for the body to build up immunity. However, he also said everyone needs to keep taking precautions until more of the population is vaccinated.

“We’re in a complicated stage where some are vaccinated and some aren’t,” Kobayashi said. “It is really important to remember – even as vaccines become available – it doesn’t mean everyone is vaccinated. We still have to wait for a large number of population to be vaccinated.”

Kobayashi noted that experts still don’t know if someone who is vaccinated can transmit the virus or not.

Now how this translates into the big question—should you still wear a mask if vaccinated?—is more or less a judgment call. Personally, I still wear a mask when I’m around others. It’s still required at my university, in planes and on public transportation, and in stores in Chicago, so there’s no dilemma. The only time I don’t wear a mask is when I’m at home, in my office when nobody’s around, and when I’m exercising outside and far from other people. In these cases there is no chance that I could infect anybody.

Now I may be kvetching for no reason, as Sullivan doesn’t say that we should go maskless around people who may be unvaccinated. And he does say “use reason”. But he also says that we should “get back to normal life”.

Until we know whether vaccinated people can be asymptomatic carriers, I don’t see a reason to stop wearing masks. I suspect that the answer will be “no”, but I’ll wait for the science before I start debating whether I discard my mask—when it’s legal to do so.

And remember that in some places in East Asia, people always wear masks in public. There’s an argument for this, as it protects you against various respiratory ailments. I notice that since the pandemic hit over a year ago, I have had neither a cold nor the flu. I’m sure that my compulsive hand-washing and mask-wearing (and my flu shots) explain the lack of illness. But I’m not sure that I want to continue wearing a mask when the danger of Covid has largely passed. I am going to keep washing my hands more often, and I’ve learned how to do that properly.

What is your feeling on mask wearing? When will you stop, if ever?

New post by Dr. Alex Lickerman: Should you get the Johnson & Johnson vaccine?

April 2, 2021 • 10:00 am

Dr. Alex Lickerman, my GP, has a new post on his website about the coronavirus and vaccines, the twelfth since he began posting during the pandemic. Click on the screenshot below to read it (it’s free).

The short answer to the title question is “yes”, but there are lots of other questions answered (and some raised without known answers). One is whether you can be an asymptomatic carrier if you’ve been vaccinated. Alex’s answer:

The study didn’t present enough data to prove the vaccine prevents asymptomatic infection. Nor did it assess whether subjects who developed COVID-19 despite vaccination are less likely to transmit the virus. Thus, it’s not yet clear how effective the vaccine will be in containing the spread of the infection. (A recent study from the CDC, however, strongly suggests that both mRNA vaccines—Pfizer’s and Moderna’s—do indeed prevent even asymptomatic COVID-19 infection by 90 percent in real-world circumstances, which is great news. We need more studies to learn if this is also the case for J & J’s vaccine.)

The coronavirus and some basic evolutionary genetics

February 7, 2021 • 9:15 am

by Greg Mayer

Jerry and I were both working independently on posts about the coronavirus. When we realized this, we conferred and decided to continue our efforts, but with some coordination and cross-fertilization. Jerry’s piece was posted on Friday. 

[JAC: Greg has a “technical notes” section at the end which clarifies terms in the text that might confuse nonbiologists.]

1). Getting people vaccinated will impede the origin of new variants, because adaptive evolution is faster in larger populations. Widespread vaccination, by reducing the number of cases, will reduce the population size of the virus. Adaptive evolution is faster in large populations because selection is more effective in large populations; this is a well-known population-genetical result. And it’s also faster because large populations, by having a greater total number of mutations, explore more of the total mutational space—including the possibility of favorable double (or more) mutations in which the component single mutations are not favored but the combinations are. This is, in part, the principle behind the AIDS “cocktail” treatments: by attacking HIV in multiple ways at once, no single resistance-conferring mutation will allow the virus to escape, because if one drug doesn’t get it, another one will. Only having multiple mutations will confer resistance to the whole “cocktail”, but this is very improbable because the individual mutations, not being favored, will not accumulate. But in a very large sample (i.e., a large population), improbable things can happen.

There are also interesting issues of components of fitness or levels of selection in the evolution of viruses (or any disease-causing micro-organism, for that matter). Jerry discussed this in his piece, contrasting the evolution of virulence within an infected host versus transmissibility between hosts. These can be viewed as two components of reproductive fitness: competition to reproduce within the host, and competition to move to new hosts. Or it can be viewed as different levels of selection—individual selection among virus particles within hosts, and group selection between the populations of viruses between the hosts—they all get sneezed out to the next host as a group. The evolution of myxoma virus in rabbits in Australia, which Jerry discusses, has been interpreted from both points of view. The interest comes from the potential conflict between what’s “good” within the host (reproducing very rapidly), and getting to the next host. If you are too good at “taking over” the host, you might kill off the host before you can spread to the next host. And if you don’t spread, you go extinct. So, what’s good in the host may not be good for getting to the next host.

There’s also an interesting issue of what is the proper estimate of population size for the virus. Is it the number of viral particles? The number of hosts? For within-host selection, it would be the number of viral particles in that host. For selection between host populations, it might be nearer to the number of hosts. (I would guess that the theory for this has already been developed in the context of group selection theory.) Either way, fewer hosts, with lower viral loads within hosts, lowers the rate of adaptive evolution of the virus.

2.)  By a *very* crude analysis, the UK variant does not show evidence of selection on its protein sequences. The ratio of Nonsynonymous (N) to Synonymous (S) mutations is 13/6 = 2.17, which is very close to the expected ratio of 2.66 for neutral (i.e., unselected) mutation in a completely *random* genome. The defect of this analysis is that the virus’s genome is of course not random. I would expect that someone with the genomic sequence and the right software is already carrying out a proper analysis using the actual nucleotide and codon distribution of the virus. (In fact, I wouldn’t be surprised if it’s already been done; not being a virologist, I don’t follow that literature.) A second, and perhaps more important defect, which would apply even to a proper analysis, is that nonsynonymous/synonmymous ratios average over sites for a whole protein or genomic sequence, so even strong selection at one or a few sites in a protein can be lost in a sea of neutral change in the rest of the protein. (See Technical note below for more details.)

There are other ways of inferring selection, and Jerry stressed one of those: if the virus evolves in parallel in multiple locations, that suggests the action of selection. We seem to be seeing that, independently, in several different locations, the same variant is spreading widely and increasing in frequency. If the variants were neutral, their frequencies would change only due to chances of sampling and which variant happened to get somewhere first, so we wouldn’t expect the same variant to “get lucky” and take over all the time.

Another hint of selection would be if substitutions affecting function (such as nonsynonymous mutations and deletions) are concentrated in a part of the genome known to be of adaptive significance, such as the spike protein. That protein is a highly functional part of the virus, for it’s the part it uses to stick to host cells. The UK variant shows at least two nonsynonymous mutations and one deletion in the spike protein, but without full data, I can’t say if this is a greater than expected number for the spike protein (which forms ca. 10% of the genome).

3). The variants are differentiated strains, not “mutations”. The identified variants differ by multiple substitutions, and thus are not a mutation, but the accumulation of multiple mutations. Some substitutions in a strain may be subject to selection, but others will not be. If we think of the virus as a “species” (which, being a collection of asexual lineages, is not quite what the virus is), then the variants or strains are like “subspecies”: differentiated descendants of a common ancestor, differing in a number of ways, some of which may be adaptive, while others may not be. (In biological species, subspecies interbreed, and thus are a form of geographical variation; in viruses, however, the variants can exist without interbreeding in the same geographic area, including inside the same host, so the analogy to subspecies is inexact.)

4).  Some of the media, or at least reporter Apoorva Mandavilli of the NY Times, are grasping that virus evolution is key to the course of the pandemic. Words and phrases in her article include: “selection pressure”, “evolve” (4 times!), “evolving”, “evolutionary biologist”, “adaptation”, and “coronavirus can evolve to avoid recognition”. And here’s a statement in the article of the distinction between genetic drift and selection:

Some variants become more common in a population simply by luck, not because the changes somehow supercharge the virus. But as it becomes more difficult for the pathogen to survive — because of vaccinations and growing immunity in human populations — researchers also expect the virus to gain useful mutations enabling it to spread more easily or to escape detection by the immune system.

This article is a pretty direct affirmation of the importance of understanding how evolution works when dealing with viral diseases.

5).  After the AIDS epidemic, we all should have learned the importance of evolutionary biology for transmissible diseases. The lessons learned during the spread, evolution, and control of HIV and other viruses are so clear that they have become textbook examples of evolutionary principles, from elementary grades to college texts. Epidemics are all about evolution.

6.)  You should call it the “UK variant”. The article at Ars Technica from which I got the (limited) genomic data I used above, falls over itself trying not to use geographic terms because they cause “stigma”. This is stupid. One of the oldest practices in taxonomy is to name species after the place they are found. The native anole of the southern United States is named Anolis carolinensis, because the description was based on lizards supposed to be from Carolina. It was later found to occur all over the southeastern United States, with closely related forms (sometimes considered conspecific) on a number of West Indian islands. It has also been introduced all over the world, from California to Hawaii to Japan. It is still Anolis carolinensis. Stability of names is important, and names related to place are a useful mnemonic, since they require no knowledge of Latin or an arcane numbering system. (The article refers to the UK variant as “B.1.1.7”. If there’s only one variant this might do, but with multiple ones it becomes an exercise in memorization.) 

Technical note. “Nonsynonymous” mutations are mutations of the DNA sequence which change the amino acid structure of the resulting protein. Because the genetic code is redundant (DNA codes for the same amino acid in more than one way), some mutations are “synonymous”, resulting in an unchanged protein. There are 549 possible mutations of the 61 amino acid coding codons (61 codons X 3 nucleotides per codon X 3 possible nucleotides to change into). Of these possible mutations, 399 are nonsynonymous and 150 are synonymous. (I couldn’t find these numbers anywhere, so I counted them up myself from the table in Muse and Gaut (1994); my count could be off, but, I hope, not by much.) If a protein coding DNA sequence has a completely random sequence (i.e. all 61 protein coding codons are equally represented), then mutations occurring at random will occur with a nonsynonymous to synoymous ratio of

N/S = 399/150 = 2.66

and, if the mutations are neutral, will be fixed (i.e. will reach a frequency of 100%) in the same ratio, which is where I got the expected N/S ratio of 2.66 for evolution by neutral mutation.

However, the DNA sequence is not random, so we usually express the nonsynonymous/synonymous ratio by looking at the rate of substitution per site. Thus, we divide the the number of nonsynonymous mutations by the number of nonsynonymous sites (i.e. the number of nucleotide positions which would give rise to a nonsynonymous amino acid if mutated), and similarly for synonymous mutations. This gives us the dN/dS ratio, which is expected to be 1 under neutrality, because we have normalized by the expected rates of each type of mutation. It is greater than 1 when there is positive selection in favor of new mutations. In calculating dN/dS, adjustments can be made for known biases in the process of mutation (e.g. the different rates at which mutations which change the ring structure of the nucleotides occur).

dN/dS ratios are subject to some of the same limitations as raw N/S ratios, including the averaging effect noted above. Yang and Bielawski (2000) is a modestly readable introduction to using rates of nonsynonymous versus synonymous substitution to detect selection.

Charlesworth, B. and D. Charlesworth. 2010. Elements of Evolutionary Genetics. Roberts, Greenwood Village Colorado. An upper level text, but not as daunting as some. Amazon

Diamond, J., ed. Virus and the Whale: Exploring Evolution in Creatures Small and Large. NSTA Press, Arlington, Va. Uses HIV as an example of viral evolution. Amazon

Emlen, D. J. and C. Zimmer. 2020. Evolution: Making Sense of Life. 3rd ed. Macmillan, New York. Uses influenza as an example of viral evolution. Amazon

Herron, J.C. and S. Freeman. 2014. Evolutionary Analysis. 5th ed. Pearson. Uses HIV as an example of viral evolution. publisher

Muse, S.V. and B.S. Gaut. 1994. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Molecular Biology and Evolution 11:715-724. pdf

Yang, Z. and J.P. Bielawski. 2000. Statistical methods for detecting molecular adaptation. Trends in Ecology and Evolution 15:496-503. pdf

h/t Brian Leiter for the Ars Technica piece.

My Pfizer jabs

January 27, 2021 • 10:45 am

As I’ve mentioned in passing, I’ve had two coronavirus shots; these used the Pfizer vaccine. The university hospital has been vaccinating a gazillion people, starting with healthcare workers on the front line, hospital employees, local oldsters (like me) and then residents of the South Side, mostly black, as well as healthcare workers who aren’t affiliated with the hospital but work on the South Side. It was heartening to go to the Covid clinic, an efficient and dedicated facility in the hospital, and wait in line with a cross-section of Chicago, including healthcare workers in their scrubs, all of us “in it together.” I have nothing but praise for that organization and its efficiency, and everyone was uber-friendly. I even got a “congratulations” after my second shot.

And as I stood in line, I realized what a fantastic thing these vaccines are, and, indeed, what all vaccines are.  If our immune system had no memory, if scientists hadn’t figured out that you could stave off disease by tweaking that memory, and if they hadn’t figured out how to do it without causing the disease, humanity would have been driven down over and over again.

The Pfizer vaccine is even more marvelous: a vaccine made by injecting into your arm a liquid solution of RNA “code” for the virus’s spike protein, with that code encapsulated in little fat bubbles. Once in your arm, the specially designed code makes its way to your cells, which then use the code to make many copies of the virus’s spike protein. Those free-floating copies are themselves harmless, but are the parts of the virus that adhere to cells when you get Covid-19. The immune system then recognizes the spike proteins as foreign, goes to work destroying them, and then the memory of those proteins is stored in our immune system (this is the way that all vaccines work). When you get a second shot, the immune system recognizes the spike proteins that it’s seen before, and mounts a huge defense against them, creating not only greater memory but often producing some side effects for the second jab. When you’ve mounted two defenses, your immune system is ready to go when it sees the spike protein on a virus that infects you.

In late December I wrote a post about how scientists had tweaked the spike protein’s RNA code to get it into our cells intact and make it produce many copies of the protein. That tweaking itself rested on years of molecular-genetic work done without the goal of making a vaccine. It’s a testament to the power of pure research and human curiosity.

All in all, I consider the mRNA vaccines, like the Pfizer and Moderna ones, as “miracles”—except I don’t like the word because it smacks of religion. But they do show what our evolved neurons are capable of doing when faced with a medical problem. I don’t know a secular word for “miracle”, but if there is one then it should be used with these vaccines. And remember, jabs went into arms less than a year after the virus first began its depredations in China. Further, the vaccine was designed within just a few days after the genome of the virus was decoded, which itself took less than a week.

But people want to know what the shots were like.  The first one was a piece of cake: it was a simple jab (they manage to get six doses out of a vial at the hospital, increasing the number of jabs by 20%), and I didn’t even have a sore arm. The only side effect was a very slight soreness at the injection site, but a soreness that could be detected only by pressing on the site.

It was 18 days between jab 1 and jab 2, though the usual period is 21 days. I took the shorter period because it was within CDC and Pfizer recommendations, and I was eager to become immune. I’m not sure how they know that 13-21 days is the right interval, and I don’t think they really did a lot of tests about that.

The second jab went into my arm on Monday. I was informed in great detail, and given an instruction sheet, that this jab was likely to cause more side effects, including chills, fever, muscle aches, and even vomiting. I was prepared for that: it’s better to suffer for a day or so than to get infected! I felt fine throughout Monday, but my arm was a little bit more sore than after the first jab. On Tuesday morning I also felt pretty good, and, because they said symptoms may begin within 12-24 hours, I thought I was home free.

That was not to be. At about noon yesterday (28 hours after my second jab), I begin feeling muscle aches, overall tiredness, and a general malaise, as if I were getting the flu. I recognized this as side effects and went home, dosing myself with Tylenol. My temperature, which is normally low (about 97.3° F, went up a bit, to 99.5°F). I did not lose either my appetite or sense of taste or smell, and I had a decent dinner but abjured the vino. I went to bed still feeling out of it.

But I woke up this morning feeling right as rain. As the instructions said, the side effects pass within 48 hours.  One has to wait two weeks, I understand, to acquire the vaunted 95% immunity that comes with this vaccine. From this my advice would be “when you get your injection, schedule it for late in the afternoon, go home, and then be prepared to not go to work the next day.” A Friday afternoon would be ideal for that second shot.

I asked the nurse who gave me the second jab if there was any correlation between the severity of one’s side effects and the effectiveness of the immunization. One would think that a vigorous immune response to the second dose, indicating that your immune response was quite active against the protein, would mean that you’d be better protected against the real virus. In other words, the worse the side effects, the better off you are. She said there was no correlation, as did the instruction sheet I got. I still am a bit dubious, but if there is a correlation, that I’m good to go against the virus.

Of course I urge everyone to get their jab. I asked a staff member on campus with whom I’m friends if she got the jab. I was surprised when she said “no.” When I asked why, she said because “people had died from the vaccine.” She was afraid of it, which I think is a fairly common feeling. But I looked up the deaths associated with the Pfizer vaccine, and, as we know, it’s not risky. There were six deaths during the phase 3 trials, but four of those were in the control group. Two died in the vaccine (experimental) group, one from arteriosclerosis and the other from a heart attack. Those deaths were probably the results not of the vaccine, but of underlying conditions. Of course some people will die after being vaccinated: as the control group shows, that will happen in any large group of people! On balance, though, all the experts say it’s better for your own welfare to get vaccinated than to risk Covid-19. And it’s better for society as well, since the more people who get vaccinated, the quicker we’ll attain herd immunity.

I went back to my friend and told her the statistics, but she was unmoved, and clearly didn’t want to discuss the point. Although I was concerned with her health, I realized that there was no point in arguing, as vaccination avoidance is almost a form of religion, and certainly a type of faith. I won’t bring up the subject again.

I’m sure all readers here are eager to get their shots, and it’s frustrating to watch while others get them but you can’t get an appointment. Biden and his administration are working hard on the issue. But we should be cognizant of the vaccine shortages in other countries, which are far more severe than in America or Europe. The news last night reported that America will have five times the number of doses necessary to vaccinate the entire population, and Canada six times. Couldn’t the excess be used in places like Latin America, where the Covid rate is high but vaccines rare?  I know that Bill Gates and others are donating lots of dosh to buy vaccines for poor countries, but we will need about 18 billion dollars to do that job. This is not a U.S. or European issue, but a world issue, and with the vaccine we should be far more concerned about other countries than we usually are. Even from a selfish point of view, if you don’t go after Covid everywhere, the whole world remains in danger.

I didn’t take a “vaccine selfie”; here’s the best I can do:

Summary paper on the vaccines with Fauci as senior author

January 20, 2021 • 10:45 am

Reader Simon sent me a link to this free paper about coronavirus vaccines written by several researchers, including Anthony Fauci (“senior author” means “last author”, and the convention that this spot is occupied by the Boss or lab head). It’s a useful summary of where we are, which other vaccines are coming, and what we don’t know, and is understandable by the layperson. (Here’s a link to one term you might not know: “mucosal immunity“, while “parenterally” refers to medicines taken outside the digestive tract, usually through injection.)

Click on the screenshot to read:

There’s a useful table of vaccines already used compared to those in development. Of the five remaining vaccines, three involve viruses: mostly inactivated viruses that can’t replicate but can produce the spike protein that activates your antibodies, while two others involve injecting spike proteins themselves, made in insect cells. Click to enlarge:

 

Here’s a figure I’ve posted before showing the protection you get from the two vaccines in use in America now: the Pfizer/BioNTech and Moderna formulations.

Note that you’ve already gotten substantial protection before you get to the second jab. For both vaccines the efficacy (the reduction in the chance you’ll catch the virus if exposed) is about 95%.

The paper raises several concerns about the vaccines and people’s willingness to take them.

A.)  What are the side effects? Monitoring of those injected has only taken place for several months, and there may be long-term effects we don’t know about. The authors note, though, that some of the vaccinated would have had stuff like cancer and heart attacks anyway—effects having nothing to do with the injection. The frequencies of such incidents and diseases need to be compared to those in unvaccinated groups or base rates already known.

B.) We don’t know the efficacy in some important groups, including “children, pregnant women, individuals with underlying illnesses, and those taking medications that might influence the immune response to a disease.”

C.) The duration of protection provided by the vaccines. We know that the efficacy of flu vaccines wanes substantially between six months and a year after injection. Will we have to get yearly injections of coronavirus vaccines as we do with flu shots?  Of course they will continue developing vaccines, so they will get better over time.

D.) How well do the vaccines protect against (asymptomatic) infection and transmission of the virus? We should have the answer to this question in a while, and the authors consider this the most important unknown in trying to stem the pandemic. If after injection you can get infected and not show symptoms, as well as transmit the virus, this will dramatically curtail efforts to stop the pandemic cold, and mandate different strategies, like testing those already injected.

And a paragraph from the paper, which is disturbing given that roughly half of Americans plan to get vaccinated. That is INSANE! Tell your worried friends to get their jabs, as it’s better than getting coronavirus.

The point made is that the vaccines currently in use don’t provide immunity in the mucosal membranes (as in the nose), while polio vaccine did bestow that immunity, but only if made with live weakened virus. (Current flu vaccines don’t provide it either.) Active immunity in the mucosa kills the virus in the respiratory system before it has a chance to get into the blood. The coronavirus vaccines now available don’t seem to provide mucosal immunity and, as the authors say, we need vaccines that will do that. A summary:

Given that recent polling suggests that only 40% to 60% of people in the United States are currently planning to get vaccinated, it is conceivable that without some impact on transmission, the virus will continue to circulate, infect, and cause serious disease in certain segments of the unvaccinated population. Administration of parenterally administered vaccines alone typically does not result in potent mucosal immunity that might interrupt infection or transmission. In the case of poliovirus, induction of mucosal immunity through vaccination with the live attenuated oral polio vaccine, in contrast to the parenterally administered inactivated vaccine, was thought to have played a critical role in interruption of transmission and control of poliovirus epidemics. For these reasons, additional data regarding protection from infection should be generated as soon as possible. If these vaccines do not provide durable, high levels of protection from infection, and do not drive the prevalence of virus in the community to near zero, a thorough analysis of shedding and transmission will need to be done through additional study. Armed with such data, public health officials can make decisions regarding prioritization of populations to receive the vaccine, and researchers could potentially improve upon the first wave of vaccines.

Misguided journalist argues that science—and wearing of facemasks—are based on a quasi-religious faith

January 12, 2021 • 10:15 am

Despite what I consider my strong refutation of the idea that “faith” is pervasive in both science and religion, that idea persists. I won’t go through the arguments that I made in Faith Versus Fact or, more concisely, in an article in Slate, “No Faith in Science,” but people nevertheless persist in their nescience. The latest attempt to argue that science is faith-based is in the pages of The Post Millennial, a conservative Canadian news magazine. It’s just so tiresome in every way that I get no pleasure from putting fingers to keys. But since that rag is fairly widely read, I’ll say a few words.

The article is really a disguised harangue about how mandates to wear face masks during the coronavirus pandemic are infringements on our liberty. In other words, it’s the right-wing libertarian argument against masks that we see so often in the U.S. And, says Andrew Mahon—identified as “a Canadian-British writer based in London who has written for the Spectator, the Daily Wire, Conservative Woman, New English Review, Brexit Central, Catholic Journal and others”—the notion that masks reduce Covid-19 transmission is based on faith, because there’s supposedly no evidence behind it.

Click on the screenshot to read and weep:

You can read my Slate piece to see that when scientists use the word “faith”, they use it differently from believers. Scientists use it to mean “confidence born of experience.” And when people say “I have faith in my doctor” or “I have faith in Anthony Fauci’s views”, they mean that they trust authority figures who have a good track record. That’s not the same as religious faith, characterized by philosopher Walter Kaufmann as ” “intense, usually confident, belief that is not based on evidence sufficient to command assent from every reasonable person.”

Read my piece if you want more. The upshot is that the scientific notion of “faith” does not turn science into a religion, as Mahon implies in his headline. If you look up “religion” in the Oxford English Dictionary, you find this definition:

 Action or conduct indicating belief in, obedience to, and reverence for a god, gods, or similar superhuman power; the performance of religious rites or observances.

Even if science were based on a religious-like faith, which it isn’t, it couldn’t be described as a religion. We have no obedience to or reverence for gods or the supernatural. End of story.

Mahon, who I suspect is a believer, has a weird notion of religion, claiming that it is not based on evidence or claims about reality. That’s of course untrue, but it does adhere to the Gouldian “Non-overlapping magisteria” view of science and religion:

The religious impulse cannot be avoided. Alongside faith, everyone participates in ritual and follows prohibitions in one form or another. We do it in every human interaction, and we certainly notice whenever anyone doesn’t follow conventional norms. The question becomes where to direct the religious impulse. And, leaving aside the truth or falsehood of its claims, what Christianity achieved was to direct man’s religious impulse to the ideal place, away from the empirically knowable. Unlike other religions, Christianity directed it wholly towards things unknowable, unprovable and unfalsifiable. This effectively freed up the knowable world, severing it from the realm of faith, and allowed the scientific method to step in and transform human civilization.

Away from the empirically knowable? But if you’re a Christian, don’t you have to have some “knowledge” about the existence of Jesus and God,  and of their powers and their plans? In fact, empiricism is the only way to know about these things, making the term “empirically knowable” a bit of an redundancy. I guess he’s talking about “other ways of knowing,” i.e., revelation, authority, and sacred books, which are non-empirical. Neither are they a way to arrive at the truth, as we know from all the contradictory claims of the world’s diverse religions. As Mike Aus, a pastor who quit the church, said:

When I was working as a pastor I would often gloss over the clash between the scientific world view and the perspective of religion. I would say that the insights of science were no threat to faith because science and religion are “different ways of knowing” and are not in conflict because they are trying to answer different questions. Science focuses on “how” the world came to be and religion addresses the question of “why” we are here. I was dead wrong. There are not different ways of knowing. There is knowing and not knowing, and those are the only two options in this world.

So, although Mahon gives credit for science to religion’s wise decision to step away from empirical claims, I can’t be all that grateful. And I wish that religion would keep its mitts off evolution.  But of course Mahon’s claim bespeaks a profound ignorance of religion, many of whose proponents really do make claims about reality that they believe absolutely, and are constantly trying to buttress with evidence (viz. Biblical archaeology, miracles, and so on).

But the “religious impulse” that “can’t be avoided” is now, argues Mahon, directed towards the pandemic, in particularly those nasty mandates to wear masks. He gets into his anti-mask argument slowly, as he doesn’t want to look like a crazy right-winger at the very beginning.

Step 1: A general assertion:

The rush to accept the claims of scientists with blind faith rather than insisting on proof is a distinct sign of our times, as is the demand for proof of unprovable tenets of Christianity. In thrall to this topsy-turvydom, many scientists expect politicians to trust them in the absence of evidence and many Christians try to construe the book of Genesis as if it were a scientific treatise.

Step 2: Mahon gets more specific:

Surely, given the unprecedented disruption to people’s lives, the suppression of basic liberties and the destruction of the economy, the decision to shut down society ought to have been evidence-based rather than faith-based. But with few exceptions, our politicians didn’t insist upon evidence, choosing instead to defer to (or should we say, hide behind) their scientific advisors, who presented them with predictions, models, worst-case estimates and beliefs.

And of course those scientific advisors, who were blindsided like many of us, initially went on the best guesses they could make from evidence derived from previous coronavirus epidemics and from epidemiology. In other words, they went on evidence, scanty as it was at the beginning of 2020. They weren’t always right, but they did not rely on revelation, sacred books, or mere unevidenced pronouncements of authorities. And of course those scientists eventually presented the politicians with a vaccine. That vaccine wasn’t, of course, based on faith.

Step 3: Mahon reveals his real animus:

Take mask mandates. People who believe in wearing masks think that they’re basing those beliefs on science. But if that were true, they’d be able to show evidence. What you get instead is a patronizing cartoon of people peeing on each other, or Paul Rudd trying to be funny and then yelling at you from his celebrity pedestal. “It’s science!” he shouts. But is it?

Wearing masks makes some people feel better. It also satisfies a naive intuition. The mask is clearly a barrier that will at some level prevent fluids travelling through fabric, just like your pants. But that doesn’t constitute scientific proof that masks prevent the spread of a virus. Scientific proof in this case would take the form of randomized controlled trials. There was one five years ago which compared medical masks to cloth masks and found that “Moisture retention, reuse of cloth masks and poor filtration may result in increased risk of infection.” This was the line that most governments were taking at first, in the absence of any evidence to the contrary. But then they altered course without any new evidence, and the vast majority of people now accept it as an article of faith that masks save lives.

There has been a grand total of one randomized controlled trial conducted to determine the efficacy of masks in preventing the spread of SARS-CoV-2. The Danish study that initially struggled to find a publisher conclusively showed that there is a statistically insignificant difference between wearing a mask and not wearing a mask. Add to this the fact that masks are disgusting, unhygienic sneeze receptacles that in practice are rarely washed or replaced, that people touch their masks and faces constantly before feeling up avocados in the supermarket, that because of the false sense of security, people wearing masks are less likely to do other, more effective things, like wash their hands, and finally, that there is little to no evidence of asymptomatic transmission, and we have to wonder why all these healthy people are still walking around with their faces covered. The answer is quite simply that their faith is misplaced.

Now let’s grant that we lack the direct controlled, randomized trials that we need to show with absolute certainty that masks are useful in helping contain the epidemic. (Of course other things are very useful as well: hand-washing, avoiding big social gatherings, quarantining, and so on.) Doing those types of experiments would be unethical.  But we have correlational evidence that show mask wearing by symptomatic and asymptomic people, whether the latter be infected or not, reduces the incidence of transmission; that masks contain respiratory droplets, a source of infection; and so on. All the evidence is summarized in this post on the website of my doctor, Alex Lickerman—a post I’ve mentioned before (click on screenshot to read it):

You won’t find any faith in the post above, just data—data sufficient to buttress the argument that we should all be wearing masks.

At the end, Mahon reprises his claim that mask-wearing is a religious act, and makes what I call “The Argument from the Norm”:

Not wearing masks is the norm, freedom to visit family and friends is the norm, freedom to conduct business is the norm, and evidence should be required to displace by legal compulsion each and every one of these norms. But too many people aren’t interested in that, preferring instead to trust in the government’s claim to be following “the science,” and if challenged, they often react the way a religious person reacts when his beliefs are criticized — offended and scandalized.

Well, read Alex’s post above and see if you think there’s no “science” behind mask mandates.

But the best part of Mahon’s argument is his claim, at the very end, that because the erosion of Christianity in our society has also eroded the distinction between “the knowable and the unknowable”, then perhaps a return of Christianity will actually help revive science! I kid you not:

I’m not sure whether a return to Christianity is necessary to salvage the unknowable/knowable partition and preserve the utility of the scientific method. But whatever direction our society chooses to go in future, one thing’s for sure: we will have a religion. We may not have science.

Can you believe that? Mahon’s not even wrong here. Eventually religion will largely disappear from Western society, but science never will because it cannot. In the modern world, we don’t really need religion that much, but we’ll always need science. How else would we have gotten a vaccine? Science is the only good way to materially improve humanity, whether it be through technology, nutrition, or health. And, of course, it’s the only way to satisfy our insatiable curiosity about the cosmos.

The Post Millennial was in fact irresponsible in printing this piece, implying as it does that mask-wearing has no effect on viral infection rates. Mahon may have the right to endanger Canadians with his pabulum, but the paper should exercise better judgement in allowing columnists to make misleading statements about science, particularly when they affect public health. If this column were on Twitter, it would have gotten one of those “false tweets” warnings.

h/t: Paul

p.s. If you saw a mattress ad, ignore it. I had to turn off adblocker to get the article, and accidentally copied that ad. It should be removed now.

Stanford’s faculty senate condemns a colleague for exercising free (but misguided) speech

January 6, 2021 • 9:15 am

Once again we have a professor who said stupid stuff—not hateful this time, but medically wonky and potentially dangerous—and was officially condemned by his University.

Hot off the press from The Stanford News (click on screenshot): Scott Atlas, a senior fellow at Stanford’s Hoover Institution—and formerly a professor and chief of neuroradiology at the Stanford University Medical Center—became a coronavirus advisor in the Trump administration, and proceeded to make a number of pronouncements about the pandemic that contravened medical wisdom.  Last Thursday he was condemned in a Stanford faculty resolution, with 85% of the faculty voting for that resolution.

So here we have the usual conflict between freedom of speech and the “harm” imputed to that speech. And once again, while condemning the speaker, I defend Atlas’s right to say what he wants without institutional condemnation.

From the report:

A resolution, introduced by members of the Faculty Senate Steering Committee and approved by 85 percent of the senate membership, specified six actions that Atlas has taken that “promote a view of COVID-19 that contradicts medical science.”

Among the actions cited are: discouraging the use of masks and other protective measures, misrepresenting knowledge and opinion regarding the management of pandemics, endangering citizens and public officials, showing disdain for established medical knowledge and damaging Stanford’s reputation and academic standing. The resolution states that Atlas’ behavior is “anathema to our community, our values and our belief that we should use knowledge for good.”

The resolution singles out for criticism Atlas’ recent Twitter call to the people of Michigan to “rise up” against new public health measures introduced by Gov. Gretchen Whitmer to curb disease spread.

“As elected representatives of the Stanford faculty, we strongly condemn his behavior,” the resolution states. “It violates the core values of our faculty and the expectations under the Stanford Code of Conduct, which states that we all ‘are responsible for sustaining the high ethical standards of this institution.’”

In approving the resolution, members of the senate called on university leadership to “forcefully disavow Atlas’ actions as objectionable on the basis of the university’s core values and at odds with our own policies and guidelines concerning COVID-19 and campus life.”

The indictment goes beyond simply damning Atlas for misrepresenting the scientific consensus in a potentially harmful way (presumably if he misrepresented continental drift there would have been no faculty resolution), but criticizes him for giving the imprimatur of Stanford and the Hoover Institution to his words. This is a common way to criticize speech: by saying that the speaker is an authority figure and puts the weight of his/her position behind the words.

In discussion, David Spiegel, the Jack, Samuel and Lulu Willson Professor in Medicine, who has been among Atlas’ most vocal critics, reiterated his belief that the university has an obligation to act because Atlas has inappropriately used his position at the Hoover Institution to give credibility to his COVID-19 positions.

“What Atlas has done is an embarrassment to the university,” Spiegel said. “He is using his real affiliation with Hoover to provide credibility in issues he has no professional expertise to discuss in a professional way.”

Yes, of course what Atlas said was dumb, and would have potentially harmful effects on those who followed his public statements. (But be mindful that there have been dissenters from the received wisdom about how to control the pandemic. Sweden, for instance, initially (and fruitlessly) sought to stem the pandemic through herd immunity—one of Atlas’s recommendations.)

But stupid pronouncements, even when made as an official of the Trump administration (and a fellow on leave from Hoover) constitute free speech. Atlas’s intent, or so he said in his response to the resolution, was neither intended to cause harm (the guy was just clueless), nor, if harmful, did it cause immediate harm. Ergo it’s free speech under the First Amendment.

And it doesn’t violate freedom of speech to make a pronouncement as an individual affiliated with Stanford. As far as I know, if I tweeted, as Professor Jerry Coyne, “Face masks are useless for preventing spread of the virus,” I would not be violating the First Amendment simply because I mentioned my position.  I might be violating a company’s regulations, or Stanford’s regulations (though I don’t know if that’s the case), but Stanford, although a private university, should not have rules that prevent free speech among its faculty.

Indeed, faculty who voted against Atlas recognized the tension between free speech and “harmful speech”, but resolved it in favor of preventing harm. It’s a case of “we favor free speech BUT. . . ”

In his comments on the issue, [Stanford] President Marc Tessier-Lavigne said he was “deeply troubled by the views by Dr. Atlas, including his call to ‘rise up’ in Michigan.” Tessier-Lavigne noted that Atlas later clarified his statements, but he said that the tweet “was widely interpreted as an undermining of local health authorities, and even a call to violence.”

Tessier-Lavigne reiterated Stanford’s commitment to free speech and academic freedom. Atlas, he asserted, remains free to express his opinions.

“But we also believe that inflammatory remarks of the kind at issue here by someone with the prominence and influence of Dr. Atlas have no place in the context of the current global health emergency,” he said. “We’re therefore compelled to distance the university from Dr. Atlas’s views in the strongest possible terms.”

No, President Tessier-Lavigne, Atlas’s misguided statements were NOT a “call to violence”, at least of the immediate and predictable kind that does violate the First Amendment. Atlas even made that clear. How a statement is interpreted by people is not important; what’s important, if you’re seeking to damn someone for free speech, is what they intended to do. 

The University didn’t have to pass a resolution “distancing itself” from Atlas, and that wouldn’t have happened at the University of Chicago. For passing such resolutions chills speech, and, as our Kalven report emphasizes, says these wise words:

The instrument of dissent and criticism is the individual faculty member or the individual student. The university is the home and sponsor of critics; it is not itself the critic. It is, to go back once again to the classic phrase, a community of scholars. To perform its mission in the society, a university must sustain an extraordinary environment of freedom of inquiry and maintain an independence from political fashions, passions, and pressures. A university, if it is to be true to its faith in intellectual inquiry, must embrace, be hospitable to, and encourage the widest diversity of views within its own community. It is a community but only for the limited, albeit great, purposes of teaching and research. It is not a club, it is not a trade association, it is not a lobby.

In this case the University (Stanford) is the critic, making public pronouncements so it looks good. And by so doing, it chills the speech of those faculty who would advance renegade views. Some of the faculty even recognized this:

The discussion of Atlas’ actions raised issues of academic freedom and freedom of speech, as it has in the past. Among those expressing concern about the resolution’s effect on freedom of speech and academic freedom was John Etchemendy, former provost, the Patrick Suppes Family Professor in the School of Humanities and Sciences and the Denning Family Co-Director of the Stanford Institute for Human-Centered Artificial Intelligence.

Etchemendy said that the resolution could be interpreted as suggesting Stanford faculty members have less freedom of speech rights than members of society in general.

But Etchemendy said, “As far as the statements that have been made by Atlas, as a private citizen he has the right to make those statements. I am troubled by the idea that a person who has those rights to speak and to assert certain things – however outrageous – have fewer rights to speak, given that they are Stanford faculty. I find that to be contrary to what is, I think, the highest value of the university, which is the value and promotion of free speech and open dialogue.”

I agree wholly with Etchemendy. But clearly most faculty, even if they do favor free speech and academic freedom, favor the “free speech BUT. . .” variety. One more quote:

Debra Satz, dean of the School of Humanities and Sciences, said she believes the resolution has reminded the university of the importance of leading with its values.

“In our messaging, we have sometimes been more focused on the legal issues rather than the value issues,” she said. “This brings the value issues front and center. We have been pretty good at pointing to the value of freedom of speech and freedom of inquiry, which I believe are central. But there are other values at stake. As a university, we have a commitment to push back against the undermining of expertise and knowledge. That is one of the great threats to our democracy at the moment.”

In my view (others may differ), those “other values”, which constitute misinformation—even potentially harmful misinformation—do not outweigh the great value of freedom of speech, especially at a university. Stanford should have kept its collective mouth shut.

Now you might be asking, “Well, what’s the difference between what Atlas said and false advertising, which DOES violate the First Amendment?”  After all, Atlas’s statement, like false advertising of drugs, could be harmful to people’s health.

As far as I know, commercial advertising has a bit less leeway than other forms of speech, and what has been prohibited by the courts is deceptive commercial advertising, when a firm makes claims it knows to be wrong. That is not the case for Atlas, who believed what he said. But even if he knew what he said was wrong, he should be damned and excoriated for it by counterspeech, not subject to official university condemnation. Universities, after all, should be kept as unsullied as possible by the chilling of speech, for they are places where ideas should be freely expressed and debated.

Atlas is a moron, but even morons get to say dumb things under the First Amendment.

I was going to put a poll here, “Do you agree that Stanford should have had a vote on condemning Atlas?” But I’d rather hear what you have to say in the comments, so speak up.