Category: pandemic

Is now the winter of our discontent?

July 31, 2021 • 12:15 pm

I was talking to a friend last night who told me how worn out she was from the pandemic—and she has family all around her, including two grandkids. That made me realize how worn out we all our from our more-than-a-year sequestration. Nobody has been immune.

And now the specter looms of yet another lockdown and mask festival, this time caused by the delta variant of Covid, which can not only infect those who are doubly vaccinated, but can live in huge numbers in their nasal passages and infect other vaccinated people.  A huge number of Americans are resisting not only getting vaccinated, but also to wearing masks. Some yahoo governmental officials have declared that they won’t even consider mask mandates. All of this this presages another tough time this fall and winter. These are my predictions, and I dearly hope I’m wrong.

a.) There will be another surge in infections, which in fact is starting now, and breakthrough infections will start happening with the vaccinated. Other variants may arise even more dangerous than the delta. Kids will start getting the virus.

b.)  Booster shots will be instituted by the fall, and the smart folks will get them. In fact, I think we’ll need at least an annual COVID shot because immunity is wearing off faster than many thought.

c.) Perhaps more Americans will start wising up about vaccination and masking, but not enough of them. On Thursday heard four healthcare workers on the NBC Evening News explain why they didn’t want to get vaccinated. Healthcare workers! One said she didn’t trust the CDC. Another, confronted with the “facts” about vaccine efficacy, said she didn’t believe them.

d.) We will start having more lockdowns and mask mandates, and people, worn out from the last ones, will be even more resistant than before. Eight of the fifty states have indoor mask mandates. As of now, only two of of them (Nevada and Hawaii), as well as Washington, D.C., include the vaccinated. But of course we know now that the vaccinated can not only get infected, but spread the virus. (The just don’t get as sick as the unvaccinated.)

d.) As schools start to open, and the concert/entertainment festivals start, superpreader events will occur.  (The giant Lollapalooza Music Festival is going on right now in Chicago. You can get in if you wear a mask, but if you’re unmasked, you’re required to show a negative Covid test in the last three days or your vaccination card. But which masked people will  be keeping them on in the huge crowd?)  This all will lead to more lockdowns and other restrictions.

e.) Schools will open soon. Many kids have not been vaccinated, and nobody under 12 is even eligible. What with the Delta variant about, which makes younger people sicker than the previous variants, proper social distancing, air filtering, and mask wearing are essential for live classes. Everybody connected with school is sick of virtual teaching, so schools will desperately try to stay open “live”. This will cause problems, and many schools may go back to virtual classes.

The upshot: the “Summer of freedom” we all expected is dissolving fast, and I suspect we’re facing another wearing Fall and Winter of Restrictions. Many more people in the U.S. will die than would have had they gotten their jabs, and we’re all in for more restrictions, masking, and travel bans.

In short, it’s going to be tough until well into 2022. Such is my prediction, which is mine. It’s depressing. And you don’t have to be a rocket scientist to see it coming.

 

The Delta variant of COVID-19 (caption from NPR), which is more dangerous because it proliferates faster in the respiratory tract and reaches higher numbers: 1,000 times higher than previous variants.

The numerals in this illustration show the main mutation sites of the delta variant of the coronavirus, which is likely the most contagious version. Here, the virus’s spike protein (red) binds to a receptor on a human cell (blue). Juan Gaertner/Science Source

“Here we believe science is real”. . . . well, not everyone

May 11, 2021 • 1:15 pm

Ah, yes, here’s the sign one sees everywhere in good liberal communities. Notice the phrase at the top:

And yet, as “science” now tells us we can begin in many cases to resume some aspects of our pre-pandemic life, Emma Green at The Atlantic tells us that there are some liberals apparently so wedded to the provisions of the lockdown that they can’t let go of any of them.

I plead partially guilty here. I still wear a mask when walking outside, even when I’m not near anybody, as when I’m walking along the lakefront.  And yes, I’ve had my two Pfizer jabs. When I pass someone on the street with my mask pulled down, I pull it up over my mouth and nose.  Of course they don’t know that I’m vaccinated, so to me that’s okay—it reassures them. But the fact is that the chance that I could infect anyone is pretty close to zero percent, unless I’m an asymptomatic carrier. Still, even friends who have been vaccinated are wary of having me over—for no good reason I can determine. (Maybe I’m odious!) Click on the screenshot:

A few excerpts:

Lurking among the jubilant Americans venturing back out to bars and planning their summer-wedding travel is a different group: liberals who aren’t quite ready to let go of pandemic restrictions. For this subset, diligence against COVID-19 remains an expression of political identity—even when that means overestimating the disease’s risks or setting limits far more strict than what public-health guidelines permit. In surveys, Democrats express more worry about the pandemic than Republicans do. People who describe themselves as “very liberal” are distinctly anxious. This spring, after the vaccine rollout had started, a third of very liberal people were “very concerned” about becoming seriously ill from COVID-19, compared with a quarter of both liberals and moderates, according to a study conducted by the University of North Carolina political scientist Marc Hetherington. And 43 percent of very liberal respondents believed that getting the coronavirus would have a “very bad” effect on their life, compared with a third of liberals and moderates.

. . . . Even as the very effective covid-19 vaccines have become widely accessible, many progressives continue to listen to voices preaching caution over relaxation. Anthony Fauci recently said he wouldn’t travel or eat at restaurants even though he’s fully vaccinated, despite CDC guidance that these activities can be safe for vaccinated people who take precautions. California Governor Gavin Newsom refused in April to guarantee that the state’s schools would fully reopen in the fall, even though studies have demonstrated for months that modified in-person instruction is safe. Leaders in Brookline, Massachusetts, decided this week to keep a local outdoor mask mandate in place, even though the CDC recently relaxed its guidance for outdoor mask use. And scolding is still a popular pastime. “At least in San Francisco, a lot of people are glaring at each other if they don’t wear masks outside,” Gandhi said, even though the risk of outdoor transmission is very low.

Believe me, I have seen those glares, even when I’m six feet away from someone and I’m not wearing a mask. It’s almost a form of mask-shaming. In fact, it IS a form of mask-shaming.

Green recounts the tale of Somerville Massachusetts, a good liberal neighbor of Cambridge, and a place where “SCIENCE IS REAL.” Except when it comes to reopening schools. Lots of work and research, including installation of UV sterilization units and automatic toilet flushers, determined that Somerville schools could now re-open. But they won’t, because, well, “maybe science isn’t real.”  Finally they opened kindergartens and middle schools, but high schools are still locked tight. People are afraid because they’re afraid that science isn’t real.  Of course the risk is not 0%, but it’s good enough for the experts, as is the CDC recommendation that dining without a mask in a restaurant, for people who are fully vaccinated, is fine with proper precautions. My own physician tells me this. Why is Dr. Fauci resistant?

No, some people are just wedded to the idea that safety trumps everything, which isn’t realistic in a world where there are risks.  I understand this, and do not dislike those who cling to their masks and rituals. But it’s very odd that those of us who waited for vaccinations to free us in some ways are now reluctant to take advantage of that freedom. As Green says:

Policy makers’ decisions about how to fight the pandemic are fraught because they have such an impact on people’s lives. But personal decisions during the coronavirus crisis are fraught because they seem symbolic of people’s broader value systems. When vaccinated adults refuse to see friends indoors, they’re working through the trauma of the past year, in which the brokenness of America’s medical system was so evident. When they keep their kids out of playgrounds and urge friends to stay distanced at small outdoor picnics, they are continuing the spirit of the past year, when civic duty has been expressed through lonely asceticism. For many people, this kind of behavior is a form of good citizenship. That’s a hard idea to give up.

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:

Guest post: The New Yorker suggests that “other ways of knowing” can cure Covid-19

December 17, 2020 • 9:15 am

A few years ago I got an email from a colleague who was disturbed about the anti-science attitudes of the New Yorker, which include an emphasis on “other ways of knowing” —often through the arts and literature. But first I’ll repeat my colleague’s analysis:

The New Yorker is fine with science that either serves a literary purpose (doctors’ portraits of interesting patients) or a political purpose (environmental writing with its implicit critique of modern technology and capitalism). But the subtext of most of its coverage (there are exceptions) is that scientists are just a self-interested tribe with their own narrative and no claim to finding the truth, and that science must concede the supremacy of literary culture when it comes to anything human, and never try to submit human affairs to quantification or consilience with biology. Because the magazine is undoubtedly sophisticated in its writing and editing they don’t flaunt their postmodernism or their literary-intellectual proprietariness, but once you notice it you can make sense of a lot of their material.

. . . Obviously there are exceptions – Atul Gawande is consistently superb – but as soon as you notice it, their guild war on behalf of cultural critics and literary intellectuals against scientists, technologists, and analytic scholars becomes apparent.

Today’s topic, though, is “other ways of knowing through folk wisdom“. In particular: ways of healing used by indigenous people. Now this shouldn’t be rejected out of hand; after all, many modern remedies, like quinine, derive from plants used by locals. But that doesn’t imply a wholesale endorsement of “the collective lived experience” touted in this video about plant-based healing. For the “collective lived experience”, after all, sometimes includes shamanism and, in the example below, “spiritual elements” as a way of curing disease. And here the disease that “lived experience” tackles is something the Siekipai of Ecuador have never experienced: Covid-19.

Reader Jeff Gawthorpe saw a New Yorker video at the link below; I’m not sure whether you’ll have free access, but you will using the yahoo! finance link at the bottom, where the video was republished.

Jeff is about as distressed as I by the fulminating wokeness of the magazine and delivered his critical “review” of the video, which I asked if I could put up in full, including his name. (I don’t like paraphrasing other people’s words, especially when they’re as good as the analysis below). Jeff said that was fine, and so here is his take, indented. I have to say that I agree with it, and have a few comments of my own at the bottom.

Around 30 minutes ago I happened across a dreadful video on the New Yorker‘s website, which drove my temptation to meet head with keyboard through the roof. This piece of ‘journalism’ was entitled: “Fighting COVID-19 with Ancestral Wisdom in the Amazon”. And yes, It’s as bad as it sounds: unscientific, irresponsible nonsense. Complete tosh.

The message which the piece attempts to convey is that COVID-19 can be dealt with by ‘lived experience’, ancient ‘ways of knowing’, and a few bits of boiled tree bark. Then, if you hadn’t had enough already, Just before the end, a caption pops up saying: “With a new stock of plants, the Siekopai are prepared to address future outbreaks of the virus according to their traditions.” Urrrhhgg.

You’ll notice that they are canny enough to maintain a degree of plausible deniability by making no definite claims. To me this demonstrates the very worst of journalism:

  • Conveying mistruths to support an ideology
  • Lacking the courage to commit to claims by asserting them as supportable facts

That’s bottom of the barrel journalism at the best of times, but now it’s irresponsible, reckless even. It presents a clear message that indigenous knowledge and ancient wisdom are perfectly acceptable ways of dealing with the pandemic. At no point is it mentioned that these ‘remedies’ are not backed by evidence, clinical or otherwise.

As you know, many western societies have huge anti-vax movements which often distrust and denounce mainstream medicine. Unfortunately, this video just adds fuel to the anti-vaxers fire. By failing to mention that these plant ‘remedies’ have zero efficacy, they are providing implicit support to the anti-science, anti-vax groups. Worse still, they are acting like digital snake oil salesmen, imbuing members of the public with false confidence that that they can avoid or fight off this virus with a couple of well chosen tree bark specimens. It’s dangerous, irresponsible nonsense.

Click below to see the video:

My own comments are few. First, it looks like the “remedy” includes cinchona bark, the source of quinine, as a palliative (the remedy seems directed at symptomatic relief rather than a cure).

Second, even “lived experience”, while useful, is no substitute for double-blind clinical trials. Granted, the Siekipai can’t do that, but they sure as hell should take the vaccination when it gets to them.  And, like Jeff, I think it’s totally irresponsible of The New Yorker to present this video without any kind of caveat. After all, when Trump skirts the truth, they don’t hesitate to correct him.  I guess “lived experience of indigenous people” is a different matter—it’s not as if they’re recommending drinking bleach or anything.