Did the Covid-19 virus come from a Wuhan lab? It’s looking increasingly likely.

June 4, 2021 • 1:15 pm

You surely remember last year when the “conspiracy theory” was broached that the coronavirus, which was thought by nearly all the media to have come from a Wuhan wet market, might have actually come from a virology lab in Wuhan, with some even suggesting that it might have been released on purpose.

Well the “deliberate release” scenario is dumb, since how could one contain an easily-spread virus targeted at an enemy? But the “accidental release” theory is gaining more and more credibility, with the Biden administration deciding to launch its own investigation. The story below, from Newsweek (yes, a conservative site), recounts how a group of amateur Internet sleuths pieced together from publicly available data what is the most likely story: an accidental release of a virus stored in the Wuhan Institute of Virology (WIV). That virus seems to have come from a Chinese cave in which 3 men shoveling bat guano died in 2012, and died from a virus that was remarkably similar to the coronavirus responsible for the pandemic.

It’s thus likely that the Chinese repeatedly lied about the origins of the virus and the U.S. government, suckered in, didn’t do due diligence in following up. After all, if a bunch of amateurs can piece together this tale (and I emphasize that we don’t know if it’s true for sure), why couldn’t the government?

Click screenshot to read the story:

It was a group of amateurs, following the lead of an young Indian called “The Seeker,” who determined that the sequence of the pandemic virus was almost identical to that of the virus stored in the WIV (they managed to get the latter sequence), and that that virus was likely the one who killed the three men nine years ago. They also found out, through diligent labor, that the WIV was actually studying the virus despite their denial, and had made seven trips to the guano mine to collect samples. The amateurs found grant proposals from the WIV, which was apparently testing the infectivity of the collected viruses, possibly with the hope of producing a vaccine against them.

As Newsweek notes, “The ongoing effort to cover this up implies that something may have gone wrong.” What went wrong, if the story is indeed true, might never be known, as the Chinese either might not know themselves and at any rate haven’t been exactly forthcoming about what they do know. Now professional journalists and epidemiologists are on the case, so we should get some answers—at least about whether the virus came from the WIV.

The episode of course makes China look bad (the article is replete with the WIV’s and Chinese government’s lies), but it also makes the U.S. look bad. It makes the press look bad: newspapers and websites had to go back and change months-old headlines that the lab-escape theory had been debunked. And it makes science look bad. To dismiss a theory without having investigated it first, and dismiss it so, well, dismissively, is only going to make people trust scientists less.  It’s even worse when you realize that had the Chinese been open about what they were doing, and were studying the sequences of viruses related to the pandemic organism, a vaccination might have been developed—or at least been in the works years before the outbreak.

Again, this is just a theory, but it’s a theory that’s become so plausible that nobody dismisses it as lunacy any more, and our own government is taking it seriously. If it turns out to be true, what will be the upshot? We’ll know to trust Chinese assurances even less (apparently the U.S. government was too credulous), and perhaps this can ensure more cooperation with the Chinese in future cases. But I wouldn’t count on it. At least we know that science works best when it’s at its most open.

At any rate, you owe it to yourself to read this fascinating amateur detective story.

h/t: Luana

Why evangelical Christians fear Covid vaccination

May 16, 2021 • 11:30 am

It’s pretty well known that some of the people most hesitant to get vaccinated against Covid are evangelical Christians. In the NYT article below (click on screenshot), two of them do a good thing, urging their fellow evangelicals to get their jabs. Here’s a plot showing that while Jews and white Catholics are pretty down with getting their shots, Protestants, particularly white evangelical and Hispanic ones, are resistant, with fewer than half being “accepters”. (Evangelicals are also less likely to wear masks.)

Why is this? Chang and Carter explain:

The decision to get vaccinated is essentially a decision to trust institutions. Many people do not understand the vaccines’ scientific complexities, regardless of religion. That means getting immunized is a decision to trust “them” — the constellation of scientific and government institutions offering assurances that the vaccines are safe and effective.

But American evangelicals are historically prone to ambivalence toward dominant secular institutions. In fact, a posture of critical evaluation is built into the fabric of our faith. Evangelicals interpret Jesus’ teaching that his followers are in the world but not “of the world” (John 17:16) to mean we should engage with secular institutions with a certain measure of wariness. Some amount of caution is healthy for all communities, not just for evangelicals. No institution is infallible, and critical thinking can be a civic virtue.

What ever happened to “render unto Caesar the things that are Caesar’s“? For surely the vaccine is Caesar’s!

But there are other reasons as well:

Unfortunately, in recent years, the evangelical approach to engaging with secular institutions has morphed from caution into outright fear and hostility. Three forces have exploited this inherent ambivalence toward secular institutions. First, conservative media has mastered the art of sowing evangelical suspicion of the establishment to increase ratings. Second, politicians — some Christian and some not — have used evangelicals’ distrust of so-called elite institutions to gain our votes. Third, conspiracy movements such as QAnon and antivaccine campaigns have targeted evangelicals, conjuring fictional enemies intent on destroying our values and, in the case of the vaccines, our actual bodies. All of these forces shape how large segments of the evangelical community perceive the Covid vaccines.

In our vaccination outreach, evangelicals have told us they’re suspicious of the shots for a variety of reasons. Many worry that the development process was rushed, that the vaccines contain a microchip or that they are the “the mark of the beast,” a reference from the Book of Revelation that some Christians associate with a future Antichrist figure. A sharpened distrust of institutions underlies these fears.

But did you note the explanation above, which I’ll repeat:

In fact, a posture of critical evaluation is built into the fabric of our faith. Evangelicals interpret Jesus’ teaching that his followers are in the world but not “of the world” (John 17:16) to mean we should engage with secular institutions with a certain measure of wariness. Some amount of caution is healthy for all communities, not just for evangelicals. No institution is infallible, and critical thinking can be a civic virtue.

You can already see the dissonance here, and I’ll quote reader Philip, who sent me this link, who has a few questions:

As if critical thinking and “critical evaluation” (based on rational evidence and the desire to acquire it) constitute the foundation of evangelical skepticism.  Does he include “The Church” in his “No institution is infallible . . . .”?  Would he tell evangelicals that?  And when is critical thinking not a civic virtue?

The first sentence, “In fact, a posture of critical evaluation is built into the fabric of our faith” evoked a guffaw, if not a horse laugh. True critical evaluation by evangelical Christians would lead to the disappearance of the faith, if for no other reason than no Christian, evangelical or otherwise, if sufficiently critical, could demonstrate that their religion—as opposed to the gazillion others on the planet—is the right one. And if you don’t choose the right one, you’re going to fry for eternity.

Kudos to Chang and Carter for trying; theirs is an admirable though an uphill battle. But they really shouldn’t have claimed that critical evaluation and caution are healthy and “built into the fabric of their faith.”

“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.

Effectiveness of coronavirus vaccines

May 2, 2021 • 11:00 am

My doctor, Alex Lickerman, has put up post #13 in his continuing series on the medical science of coronavirus and the pandemic. This short but informative post (click on screenshot below) deals with a question we all have:

First, the effectiveness. Alex summarizes numerous studies showing how effective a vaccine is. Remember, though, what that number, expressed as a percentage, means. If a vaccine is 95% effective, it means that in a situation in which a certain percentage of people get infected, say 30%, then the chance you will get in infected is (100% – 95%) X 30%, or 1.7%.  Note that this does not mean that your chance of getting infected is 5%: it’s lower than that because not everybody gets infected when they’re not vaccinated.

Here are some effectiveness estimates taken by Alex from the literature:

Single dose Pfizer: 70%
Double dose Pfizer: 85%
Single dose Pfizer and Modern considered together, single dose: 80%
Double dose   ”            ”                   ”                 ”            double dose: 90%
The two above figures are also the same in another study not specifying vaccination

The 80%-90% holds for both symptomatic and asymptomatic infections; this means that yes, you can be an asymptomatic carrier if you have been fully vaccinated, but the chances are very small.

 Pfizer and Moderna combined (both mRNA vaccines): effectiveness: over 96%

Now remember again what these figures mean, because people get that meaning wrong all the time. Here’s one example I quote from the article:

A CNN article was skeptical of this data, arguing that “real-world studies of the Pfizer-BioNTech and Moderna vaccines show they are only 90% protective against the coronavirus, not 95% as reported in clinical trials. Translated into reality, that means for every million fully vaccinated people who fly, some 100,000 could still become infected.” Importantly, this is not what 90 percent effectiveness means! Ninety percent effectiveness means the vaccines reduce the rate of infection by 90%. To calculate a person’s absolute risk of getting infected after having been vaccinated, you have to start with the base rate of infection, which is different in different contexts. It would be true that “for every million fully vaccinated people who fly, some 100,000 could still become infected” if the base rate of infection for those million people was 100 percent. Yet the highest rate of infection we’ve seen in published contact tracing studies was around 30 percent (for spouses of infected people). This means that post-vaccination rates of COVID-19 infection in the vaccinated population are at most 90 percent less than 30 percent, or 3 percent. And that only if everyone who’s been vaccinated has an infected spouse.

In fact, the CDC reported that, as of April 20, 2021, out of 87 million fully vaccinated people there were only 7,157 breakthrough infections (0.008 percent), only 498 hospitalizations (0.0006 percent) related to COVID-19, and only 88 deaths (0.0001 percent) related to COVID-19.

Alex’s bottom line:

The mRNA vaccines are extraordinarily effective at preventing both symptomatic and asymptomatic infection and therefore at preventing transmission of SARS-CoV-2. Most importantly, if you’re fully vaccinated, your risk of dying from COVID-19 is 0.0001 percent.

What about the variants?. In answer to the question of whether the vaccines work against the variants, Alex says “yes”, at least for variants currently circulating. He adds that more data are to come.

Here’s Alex’s conclusion, which happens to echo the same conclusions reached by Bari Weiss in a piece published on her site this morning:

CONCLUSION: Given the incredible effectiveness of the vaccines at preventing both symptomatic and asymptomatic disease, and therefore disease transmission, and given that the rates of death from COVID-19 in vaccinated people is 0.0001 percent among all vaccinated people in the U.S. (an analysis that also included the J&J vaccine), if you’ve been vaccinated, we consider it reasonably safe to dine indoors, travel, and gather with even unvaccinated people. Living in the world has, of course, never been risk-free. Yet we can now say that with the advent of effective vaccines against SARS-CoV-2, the risk of living as you did before the pandemic has returned to what it was before the pandemic.

Here’s Weiss’s piece, which I think is free, though I’ve now subscribed. Click on the screenshot:

The hell that India has become

April 29, 2021 • 11:00 am

The Guardian has a “long read” piece by Arundhati Roy, a famous writer who lives in Delhi (you may have read her Booker-Prize-winning book The God of Small Things). If you have any interest in India (or let’s just say “humanity”), it is well worth reading.  Click on the screenshot to do so.

Roy deals with two connected topics, the pandemic that’s now ravaging India (the infection rate may soon rise to half a million per day), and the diffidence of the Modi government, which is corrupt, anti-Muslim and Hindu-centric, and absolutely without empathy.

I’ve written about both these things before, but Roy, being “on the ground” in Delhi, has a horrific account of what it’s like to live in the center of the maelstrom. She notes that deaths and infections are likely to be grossly underreported given the largely rural population of India, and that 78% of healthcare in urban areas and 71% in rural areas is handled by the private sector, which means that the poor are simply unable to afford healthcare, much less vaccinations or oxygen. The black market that has sprung up around these things, while typical of India in a desperate situation, is further hitting the poor, and, as you may have seen from photographs, the poor are being refused hospital admission (or asked to bring their own oxygen tanks), or are left to die on the sidewalks. There are so many bodies that there’s a shortage of wood to cremate them.

(From Guardian) People with breathing problems caused by Covid-19 wait to receive oxygen in Ghaziabad. Photograph: Adnan Abidi/Reuters

The Modi government under the Bharatiya Janata Party (BJP) isn’t positioned to help, either materially or psychologically. The fact is that Narendra Modi is basically an evil man—the kind of man who encourages or allows Hindus to kill Muslims. I consider him even worse than Trump, since he doesn’t even pretend to care about the plight that’s destroying India. Yet he’s still too popular to be deposed.  And while earlier he assured the world that India, the world’s second most populous country, had the virus under control, that proved to be untrue.  It’s clear that, like me, Roy is a bitter opponent of Modi and his minions, but you can read about that in the article. I’ll give just one quote:

As this epic catastrophe plays out on our Modi-aligned Indian television channels, you’ll notice how they all speak in one tutored voice. The “system” has collapsed, they say, again and again. The virus has overwhelmed India’s health care “system”.

The system has not collapsed. The “system” barely existed. The government – this one, as well as the Congress government that preceded it – deliberately dismantled what little medical infrastructure there was. This is what happens when a pandemic hits a country with an almost nonexistent public healthcare system. India spends about 1.25% of its gross domestic product on health, far lower than most countries in the world, even the poorest ones. Even that figure is thought to be inflated, because things that are important but do not strictly qualify as healthcare have been slipped into it. So the real figure is estimated to be more like 0.34%. The tragedy is that in this devastatingly poor country, as a 2016 Lancet study shows, 78% of the healthcare in urban areas and 71% in rural areas is now handled by the private sector. The resources that remain in the public sector are systematically siphoned into the private sector by a nexus of corrupt administrators and medical practitioners, corrupt referrals and insurance rackets.

Healthcare is a fundamental right. The private sector will not cater to starving, sick, dying people who don’t have money. This massive privatisation of India’s healthcare is a crime.

The system hasn’t collapsed. The government has failed. Perhaps “failed” is an inaccurate word, because what we are witnessing is not criminal negligence, but an outright crime against humanity. Virologists predict that the number of cases in India will grow exponentially to more than 500,000 a day. They predict the death of many hundreds of thousands in the coming months, perhaps more. My friends and I have agreed to call each other every day just to mark ourselves present, like roll call in our school classrooms. We speak to those we love in tears, and with trepidation, not knowing if we will ever see each other again. We write, we work, not knowing if we will live to finish what we started. Not knowing what horror and humiliation awaits us. The indignity of it all. That is what breaks us.

Oh, and a cry for help:

The crisis-generating machine that we call our government is incapable of leading us out of this disaster. Not least because one man makes all the decisions in this government, and that man is dangerous – and not very bright. This virus is an international problem. To deal with it, decision-making, at least on the control and administration of the pandemic, will need to pass into the hands of some sort of non-partisan body consisting of members of the ruling party, members of the opposition, and health and public policy experts.

As for Modi, is resigning from your crimes a feasible proposition? Perhaps he could just take a break from them – a break from all his hard work. There’s that $564m Boeing 777, Air India One, customised for VVIP travel – for him, actually – that’s been sitting idle on the runway for a while now. He and his men could just leave. The rest of us will do all we can to clean up their mess.

No, India cannot be isolated. We need help.

And here’s how to help: consult these articles, which give many links about how and where to give:

New York Times

Washington Post

Remember, India is the world’s biggest democracy, and despite the execrable government, the country and its people need our help. Please donate if you can.
h/t: David

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.