Responses to “On testing.”

Responses to “On testing.”

My spouse posted my previous essay on social media, and I’d like to address some of people’s comments.  There were some excellent points! 

My apologies if I failed to address everything that people said, but I tried my best.

Scroll to find my responses to:

  1. A shutdown could have prevented the Covid-19 epidemic.
  2. We know that the current shutdown is either delaying or preventing deaths due to Covid-19. 
  3. Ending this epidemic with a vaccine would be ideal. 
  4. Ending the shutdown while requesting that at-risk people continue to self-isolate would save lives.
  5. Why is it urgent to end the shutdown soon?
  6. Why might more people die of Covid-19 just because we are slowing the spread of the virus?
  7. How is the shutdown causing harm?
  8. What about the rate at which people get sick?  Isn’t the shutdown worthwhile, despite the risks described above, if it keeps our hospitals from being overwhelmed?
  9. Don’t the antibody tests have a lot of false positives?
  10. What about the political ramifications of ending the shutdown?

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1: “A shutdown could have prevented the Covid-19 epidemic.”

If we’d acted early enough, we could have isolated all cases of Covid-19 and prevented this whole debacle.

But we didn’t.

Covid-19 is highly infectious, and we made no effort toward containment or quarantine until the virus was already widespread.  We took action in March, but we already had community transmission of Covid-19 by January.  Given where we are now, current models predict that the epidemic will continue until the level of immunity reaches somewhere near 70%.

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2: “We know that the current shutdown is either delaying or preventing deaths due to Covid-19.”

To date, the data suggests that the virus has only reached saturation inside a few closed environments, such as prisons.  In Italy, both the timecourse of mortality and the results of antibody studies suggest that infections were still rising at the time of their lockdown. 

Among the passengers of the Diamond Princess cruise ship, deaths peaked 21 days after infections peaked – if the virus had already reached saturation in Italy, we’d expect to see deaths peak sooner than 21 days after the lockdown began.  They did not.

So, again, this much is clear: worldwide, there was a significant new cause of death.  When we look at mortality data, we see the curves suddenly rise in many locations.  Some researchers, such as John Ioannidis, have speculated that Covid-19 causes death primarily in people with low life expectancy, in which case we would expect to see these mortality curves drop to lower-than-average levels after the epidemic ends.  But even then, it’s unprecedented to see a number of deaths that would usually occur over the course of a year all within a matter of weeks.

Covid-19 is killing people, and the shutdown is either delaying or preventing people’s death from Covid-19.

For the shutdown to actually prevent death, one of the following needs to happen:

1.) We create a vaccine, allowing our population to reach 70% immunity without as many people contracting the illness.

2.) We take action to change which segment of the population is exposed to the virus, allowing us to reach 70% immunity without as many at-risk people being exposed.

See #3 and #4, below.

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3: “Ending this epidemic with a vaccine would be ideal.”

Vaccination is great science.  Both my spouse and I love teaching about vaccines, in part because teaching the history of vaccine use is a good component of anti-racist science class.

Developing vaccines often takes a long time.  I’ve read predictions of a year or two; my father, an infectious disease doctor, epidemiologist, research physician who runs vaccine trials, and co-developer of Merck’s HPV vaccine, guesses that it will take about five years.

And then, for the vaccine to end this epidemic, enough people will need to choose to be vaccinated that we reach approximately 70% immunity.

The reason it’s worthwhile to compare Covid-19 to seasonal influenza is that a vaccine will only end the epidemic if enough people choose to get it.  Many people’s personal risk from Covid-19 is lower than their risk from seasonal influenza.  Will those people choose to be vaccinated?

Obviously, I would be thrilled if the answer were “yes.”  I’d love to live in a nation where people’s sense of altruism and civic duty compelled them to get vaccinated.  My family is up-to-date on all of ours.

But many privileged families in the United States have elected to be freeloaders, declining the (well tested, quite safe) measles vaccine with the expectation that other people’s immunity will keep them safe.  And, despite the well-documented dangers of influenza, only 40% of our population gets each year’s influenza vaccine.

Yes, the influenza vaccine tends to be less effective than many others – some years it gives as little as ten percent protection, other years about sixty percent protection.  By way of comparison, the HPV vaccine has over 90% efficacy.

A vaccine with low efficacy will still offer better protection when more people get it.  If a higher percentage of our population were vaccinated against influenza, then influenza transmission would drop, and so each person’s immunity, whether high or low, would be less likely to be challenged.

Also, the efficacy of influenza vaccines is measured in terms of the likelihood that vaccination prevents infection.  The influenza vaccine is not great at keeping people from getting sick.  But vaccination also tends to reduce the severity of your illness, even if you do catch influenza.  Because you got sick, it seems as though the vaccine “failed,” but your case might have been far more severe if you hadn’t been vaccinated.

The influenza vaccine saves lives.  In Italy, where fewer people choose to get vaccinated against influenza (about 15% compared to our 40% of the population), the death rate from influenza is higher.  Although it’s worth noting that this comparison is complicated by the fact that our health care system is so bad, with poor people especially having limited access to health care.  In the United States, people between the ages of 18 and 49 comprise a higher proportion of influenza deaths than anywhere in Europe.  Either our obesity epidemic or limited access to health care is probably to blame; possibly a combination of both.

In summary, for this plan to help us save lives, we will need to develop an effective vaccine, and then people will have to get it. 

I am quite confident that we can eventually develop a vaccine against Covid-19.  The virus includes a proofreading enzyme, so it should mutate more slowly than most RNA viruses.  We don’t know how long it will take, but we can do it.

I am unfortunately pessimistic that people will choose to get the vaccine.  And, unfortunately, when a low-risk person chooses to forgo vaccination, they’re not just putting themselves in harm’s way, they are endangering others.  Most vaccines elicit a weaker immune response in elderly or immunocompromised recipients – exactly the group most at risk from Covid-19 – which is why we spend so much time harping about herd immunity.

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4: “Ending the shutdown while requesting that at-risk people continue to self-isolate would save lives.

This plan has major downsides, too.  Because we didn’t take action soon enough, every plan we have now is bad.

Low-risk people can still die of Covid-19.  Even if they don’t die, Covid-19 can cause permanent health effects.  Covid-19 reduces your ability to get oxygen to your body and brain.  Even a “mild” case can leave your breathing labored for weeks – you’re not getting enough oxygen.  Your muscles will ache.  Your thoughts will be sluggish.

With a more severe case, people can be looking at heart damage.  Renal failure.  It would be cruel to look at all these long-term consequences and blithely call them “recovery.”

If our health care system were better, we’d treat people sooner.  The earlier you intervene, helping to boost people’s oxygen levels, the better outcome you’ll have.  There’s a great editorial from medical doctor Richard Levitan recommending that people monitor their health with a pulse oximeter during this epidemic.

If you notice your oxygen levels declining, get help right away.  Early intervention can prevent organ damage.  And you’ll be helping everyone else, too – the sooner you intervene, the less medical care you will need.

Because medical debt can derail lives, many people in this country delay treatment as long as possible, hoping that their problems will go away naturally.  That’s why people are often so sick when they show up at the ER.  I imagine that this is yet another reason – alongside air pollution, food deserts, sleep loss, and persistent stress exacerbated by racism – that poor communities have had such a high proportion of people with severe cases of Covid-19.

And I imagine – although we don’t yet have enough data to know – that financial insecurity caused by the shutdown is making this worse.  It’s a rotten situation: you have a segment of population that has to continue working during the shutdown, which means they now have the highest likelihood to be exposed to the virus, and they’re now under more financial strain, which might increase the chance that they’ll delay treatment.

We know that early treatment saves lives, and not everyone is sufficiently privileged to access that.

All this sounds awful.  And it is.  But, if we took action to shift exposure away from high risk groups, the likelihood that any individual suffers severe consequences is lower.

And there is another caveat with this plan – some people may be at high risk of complications for Covid-19 and not even realize it.  In the United States, a lot of people either have type 2 diabetes or are pre-diabetic and don’t yet realize.  These people have elevated risk.  Both smoking and air pollution elevate risk, but people don’t always know which airborn pollutants they’ve been exposed to.  (Which, again, is why it’s particularly awful that our administration is weakening air quality standards during this epidemic.)

Even if we recommended continued self-isolation for only those people who know themselves to have high risk from Covid-19, though, we would be saving lives.  The more we can protect people in this group from being exposed to the virus – not just now, but ever – the more lives we will save.

We won’t be able to do this perfectly.  It’ll be a logistical nightmare trying to do it at all.  People at high risk from Covid-19 needs goods and services just like everybody else.  We might have to give daily Covid-19 PCR tests to anyone visiting their homes, like doctors, dentists, and even delivery workers. 

At that point, the false negative rate from Covid-19 PCR tests becomes a much bigger problem – currently, these false negatives reduce the quality of our data (but who cares?) and delay treatment (which can be deadly).  A false negative that causes inadvertent exposure could cost lives.

Stores will need to set aside morning hours for at-risk shoppers, and undertake rigorous cleaning at night.  We know that infectious viral particles can persist for days on a variety of surfaces.

Some people will be unable to work, either because they or a close relative has high risk of Covid-19.  Some children will be unable to go to school.  We will need a plan to help these people.

We will have to work very hard to keep people safe even after the shutdown ends for some. 

But, again, if everyone does the same thing, then the demographics of people infected with Covid-19 will reflect our population demographics.  We can save lives by skewing the demographics of the subset of our population that is exposed to Covid-19 to include more low-risk individuals, which will require that we stratify our recommendations by risk (at least as well as we can assess it).

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5: “Why is it urgent to end the shutdown soon?

1.) By delaying Covid-19 deaths, we run to risk of causing more total people to die of Covid-19.

2.) The shutdown itself is causing harm.

See #6 and #7, below.

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6: “Why might more people die of Covid-19 just because we are slowing the spread of the virus?

[EDIT: I wrote a more careful explanation of the takeaways of the Harvard study. That’s here if you would like to take a look!]

This is due to the interplay between duration of immunity and duration of the epidemic.  At one point in time, seasonal influenza was a novel zoogenic disease.  Human behavior allowed the influenza virus to become a perpetual burden on our species.  No one wants for humans to still be dying of Covid-19 in ten or twenty years.  (Luckily, because the virus that causes Covid-19 seems to mutate more slowly than influenza, it should be easier to design a single vaccine that protects people.)

In the Harvard model, we can see that there are many scenarios in which a single, finite shutdown leads to more deaths from Covid-19 than if we’d done nothing. Note the scenarios for which the colored cumulative incidence curves (shown on the right) exceed the black line representing how many critical cases we’d have if we had done nothing.

Furthermore, their model does not account for people’s immunity potentially waning over time.  Currently, we do not know how long people’s immunity to Covid-19 will last.  We won’t know whether people’s immunity will last at least a year until a year from now.  There’s no way to test this preemptively.

We’ve seen that immunity to other coronaviruses fades within a year.  If immunity to Covid-19 is similar, we really don’t want to prolong the epidemic past a year.

If we could all go into stasis and simply not move for about a month, there’d be no new cases of Covid-19, and this virus would be gone forever.  But people still need to eat during the shutdown.  Many people are still working.  So the virus is still spreading, and we have simply slowed the rate of transmission.

This seems good, because we’re slowing the rate at which people enter the hospital, but it’s actually bad if we’re increasing the number of people who will eventually enter the hospital.

Based on our research with other coronaviruses, we expect that re-infection will cause a person to experience symptoms less severe than their first case of Covid-19.  But a re-infected person can still spread the disease to others.  And we don’t know what will happen if a person’s risk factors – such as age, smoking status, diabetes status, etc. – have increased in the time since their last infection.

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7: “How is the shutdown causing harm?

If you turn on Fox News, I imagine you’d hear people talking about the damage we’re doing to our economy.  They might discuss stock market numbers.

Who gives a shit?  In my opinion, you’d have to be pretty callous to think that maintaining the Nasdaq bubble is more important than saving lives.

At the same time, I think you’d have to be pretty callous to not feel extremely concerned by the United Nations’ policy brief, “The impact of Covid-19 on children.”

In this report, they estimate that the shutdown we’ve had so far will cause hundreds of thousands of children to die, many from malnutrition and the other health impacts of poverty.  The longer the shutdown continues, the more children will die.

That’s a worldwide number, and most of those children live outside the United States.  But I’d like to think that their lives matter, too.

The report also discusses the lifelong harm that will be inflicted on children from five months (or more!) of school closure.  Drop-outs, teen pregnancy, drug abuse, recruitment of child soldiers, and the myriad health consequences of low educational attainment.

I live in a wealthy college town, but even here there is a significant population of students who don’t have internet access.  Students with special needs aren’t getting the services they deserve.  Food insecurity is worse.

You’re lucky that privacy protections prevent me from sharing a story about what can happen to poor kids when all the dentists’ offices are closed.  I felt ashamed that this was the best my country had to offer.

As the shutdown continues, domestic violence is rising.  We can assume that child abuse is rising, also, but we won’t know until later, when we finally have a chance to save children from it.  In the past, levels of child abuse have been correlated with the amount of time that children spend in the presence of their abusers (usually close family), and reporting tends to happen during tense in-person conversations at school.

We know that online sex work has increased during the shutdown.  There is an increased supply of sex workers who are experiencing increasing financial insecurity.  We don’t yet have data on this, but I’d be shocked if the shutdown hasn’t led many to feel pressured into riskier acts for lower amounts of money, including meeting clients in isolated (and therefore unsafe) spaces.

The shutdown has probably made our drug epidemic worse (and this was already killing about 70,000 people per year in the U.S.).  When people are in recovery, one of the best strategies to stay sober is to spend a lot of time working, out of the house, and meeting with a supportive group in communal space.  Luckily, many of the people I know who are in recovery have been categorized as essential workers.

But any slip can kill someone recovering from addiction.  One of my friends froze to death last year.

A neighbor recently sent me a cartoon suggesting that the biggest harm caused by the shutdown is boredom.  (I’m going to include it, below, but don’t worry: I won’t spend too much time rattling sabers with a straw man.) And, for privileged families like mine, it is.  We’re safe, we’re healthy, we get to eat.  My kids are still learning – we live in a house full of computers and books.

But many of the 75 million children in the United States don’t live in homes like mine, with the privilege we have.  Many of our 50 million primary and secondary school students are not still learning academically during the shutdown.

Whether the shutdown is preventing or merely delaying the deaths of people at risk of serious complications from Covid-19, we have to remember that the benefit comes at a cost.  What we’ve done already will negatively impact children for the rest of their lives.  And the longer this goes on, the more we’re hurting them.

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8: “What about the rate at which people get sick?  Isn’t the shutdown worthwhile, despite the risks described above, if it keeps our hospitals from being overwhelmed?

In writing this, I struggled with how best to organize the various responses.  I hope it doesn’t seem too ingenuous to address this near the end, because slowing the rate of infection so that our hospitals don’t get overwhelmed is the BEST motivation for the shutdown.  More than the hope that a delay will yield a new vaccine, or new therapies to treat severe cases, or even new diagnostics to catch people before they develop severe symptoms, we don’t want to overwhelm our hospitals.

If our physicians have to triage care, more people will die.

And I care a lot about what this epidemic will be like for our physicians.  My father is a 67-year-old infectious disease doctor who just finished another week of clinical service treating Covid-19 patients at the low-income hospital in Indianapolis.  My brother-in-law is an ER surgeon in Minneapolis.  These cities have not yet had anything like the influx of severe cases in New York City – for demographic and environmental reasons, it’s possible they never will.  But they might. 

Based on the case fatality rate measured elsewhere, I’d estimate that only 10% of the population in Minneapolis has already been infected with Covid-19, so the epidemic may have a long way yet to go.

If we ended the shutdown today for everyone, with no recommendation that at-risk groups continue to isolate and no new measures to protect them, we would see a spike in severe cases.

If we ended the shutdown for low-risk groups, and did a better job of monitoring people’s health to catch Covid-19 at early, more-easily-treatable stages (through either PCR testing or oxygen levels), we can avoid overwhelming hospitals.

And the shutdown itself is contributing toward chaos at hospitals.  Despite being on the front lines of this epidemic, ER doctors in Minneapolis have received a 30% pay cut.  I imagine my brother-in-law is not the only physician who could no longer afford day care for his children after the pay cut.  (Because so many people are delaying care out of fear of Covid-19, hospitals are running out of money.)  Precisely when we should be doing everything in our power to make physicians’ lives easier, we’re making things more stressful.

We could end the shutdown without even needing to evoke the horrible trolley-problem-esque calculations of triage.  Arguments could be made that even if it led to triage it might be worthwhile to end the shutdown – the increase in mortality would be the percentage of triaged cases that could have survived if they’d been treated, and we as a nation might decide that this number was acceptable to prevent the harms described above – but with a careful plan, we need not come to that.

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9: “Don’t the antibody tests have a lot of false positives?

False positives are a big problem when a signal is small.  I happen to like a lot of John Ioannidis’s work – I think his paper “Why Most Published Research Findings Are False” is an important contribution to the literature – but I agree that the Santa Clara study isn’t particularly convincing. 

When I read the Santa Clara paper, I nodded and thought “That sounds about right,” but I knew my reaction was most likely confirmation bias at work.

Which is why, in the essay, I mostly discussed antibody studies that found high percentages of the population had been infected with Covid-19, like the study in Germany and the study in the Italian town of Robbio.  In these studies, the signal was sufficiently high that false positives aren’t as worrisome. 

In Santa Clara, when they reported a 2% infection rate, the real number might’ve been as low as zero.  When researchers in Germany reported a 15% infection rate, the real number might’ve been anywhere in the range of 13% to 17% – or perhaps double that, if the particular chips they used had a false negative rate similar to the chips manufactured by Premier Biotech in Minneapolis.

I’m aware that German response to Covid-19 has been far superior to our bungled effort in the United States, but an antibody tests is just a basic ELISA.  We’ve been doing these for years.

Luckily for us, we should soon have data from good antibody studies here in the United States.  And I think it’s perfectly reasonable to want to see the results of those.  I’m not a sociopath – I haven’t gone out and joined the gun-toting protesters.

But we’ll have this data in a matter of weeks, so that’s the time frame we should be talking about here.  Not months.  Not years.  And I’ll be shocked if these antibody studies don’t show widespread past infection and recovery from Covid-19.

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10: “What about the political ramifications of ending the shutdown?

I am, by nature, an extremely cautious person.  And I have a really dire fear.

I’m inclined to believe that ending the shutdown is the right thing to do.  I’ve tried to explain why.  I’ve tried to explain what I think would be the best way to do it.

But also, I’m a scientist.  You’re not allowed to be a scientist unless you’re willing to be proven wrong.

So, yes.  I might be wrong.  New data might indicate that writing this essay was a horrible mistake.

Still, please bear with me for a moment.  If ending the shutdown soon turns out to be the correct thing to do, and if only horrible right-wing fanatics have been saying that we should end the shutdown soon, won’t that help our current president get re-elected?

There is a very high probability that his re-election would cause even more deaths than Covid-19.

Failing to address climate change could kill billions.  Immigration controls against migrants fleeing war zones could kill millions.  Weakened EPA protections could kill hundreds of thousands.  Reduced access to health care could kill tens of thousands.

And, yes, there are horrible developments that neither major political party in the United States has talked about, like the risk that our antibiotics stop working, but I think it’s difficult to argue that one political party isn’t more dangerous than the other, here.

I feel pretty confident about all the scientific data I’ve discussed above.  Not as confident as I’d like, which would require more data, but pretty confident.

I feel extremely confident that we need to avoid a situation in which the far right takes ownership of an idea that turns out to have been correct.  And it’ll be dumb luck, just a bad coincidence.  The only “data” they’re looking at are stock market numbers, or maybe the revenue at Trump-owned hotels.

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EDIT: I also wrote a more careful explanation of the takeaways of the Harvard study. That’s here if you would like to take a look!

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Header image by Goran Paunovic.

On testing.

On testing.

UPDATE: Wow, this got a lot of readers! Honestly, though, I wrote a response to common questions and comments about this essay and it is probably a better read.

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My spouse recently sent me a link to the article “Concerns with that Stanford study of coronavirus prevalence” by Andrew Gelman, a statistician at Columbia University.  From reading this article, I got the impression that Gelman is a good mathematician.  And he raises some legitimate concerns. 

But I’ve noticed that many of the people criticizing the work coming out of the Ioannidis group – such as the study of how many people in Santa Clara county might have antibodies to Covid-19 – don’t seem to understand the biology underlying the numbers.

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First, some background: in case you haven’t noticed, most of the United States is operating under a half-assed lockdown.  In theory, there are stay-at-home orders, but many people, such as grocery store clerks, janitors, health care workers, construction workers, restaurant chefs, delivery drivers, etc., are still going to work as normal.  However, schools have been closed, and most people are trying to stand at least six feet away from strangers.

We’re doing this out of fear that Covid-19 is an extremely dangerous new viral disease.  Our initial data suggested that as many as 10% of people infected with Covid-19 would die.

That’s terrifying!  We would be looking at tens of millions of deaths in the United States alone!  A virus like this will spread until a majority of people have immunity to it – a ballpark estimate is that 70% of the population needs immunity before the epidemic stops.  And our early data suggested that one in ten would die.

My family was scared.  We washed our hands compulsively.  We changed into clean clothes as soon as we came into the house.  The kids didn’t leave our home for a week.  My spouse went to the grocery store and bought hundreds of dollars of canned beans and cleaning supplies.

And, to make matters worse, our president was on the news saying that Covid-19 was no big deal.  His nonchalance made me freak out more.  Our ass-hat-in-chief has been wrong about basically everything, in my opinion.  His environmental policies are basically designed to make more people die.  If he claimed we had nothing to worry about, then Covid-19 was probably more deadly than I expected.

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Five weeks have passed, and we now have much more data.  It seems that Covid-19 is much less dangerous than we initially feared.  For someone my age (37), Covid-19 is less dangerous than seasonal influenza.

Last year, seasonal influenza killed several thousand people between the ages of 18 and 49 in the United States – most likely 2,500 people, but perhaps as many as 5,800.  People in this age demographic account for about 10% of total flu deaths in the United States, year after year.

Seasonal influenza also killed several hundred children last year – perhaps over a thousand.

There’s a vaccine against influenza, but most people don’t bother. 

That’s shocking. 

Seasonal influenza is more dangerous than Covid-19 for people between the ages of 18 and 49, but only 35% of them chose to be vaccinated in the most recently reported year (2018).  And because the vaccination rate is so low, our society doesn’t have herd immunity.  By choosing not to get the influenza vaccine, these people are endangering themselves and others.

Some people hope that the Covid-19 epidemic will end once a vaccine is released.  I am extremely skeptical.  The biggest problem, to my mind, isn’t that years might pass before there’s a vaccine.  I just can’t imagine that a sufficient percentage of our population would choose to get a Covid-19 vaccine when most people’s personal risk is lower than their risk from influenza.

When I teach classes in jail, dudes often tell me about which vaccines they think are too dangerous for their kids to get.  I launch into a tirade about how safe most vaccines are, and how deadly the diseases they prevent. 

Seriously, get your kids vaccinated.  You don’t want to watch your child die of measles.

And, seriously, dear reader – get a flu vaccine each year.  Even if you’re too selfish to worry about the other people whom your mild case of influenza might kill, do it for yourself. 

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We already know how dangerous seasonal influenza is.  But what about Covid-19?

To answer that, we need data.  And one set of data is unmistakable – many people have died.  Hospitals around the world have experienced an influx of patients with a common set of symptoms.  They struggle to breathe; their bodies weaken from oxygen deprivation; their lungs accumulate liquid; they die.

Many people have been put on ventilators, but that’s often the beginning of the end.  Most people put on ventilators will die.  Among patients over 70 years old, three quarters who are put on ventilators will die

For each of these patients saved, three others are consigned to an agonizing death in the hospital, intubated among the flashing lights, the ceaseless blips and bleeps.  At home, they’d die in a day; in the hospital, their deaths will take three weeks.

And the sheer quantity of deaths sounds scary – especially for people who don’t realize how many tens of thousands die from influenza in the United States each year.

Or, consider: cigarette smoking causes 480,000 deaths per year in the United States, including 41,000 people who die from second-hand smoke exposure.  Those 41,000 aren’t even choosing to smoke!  But cigarettes kill them anyway.

Indeed, when people die of Covid-19, it’s often because their lungs fail.  Smoking is obviously a major risk factor for dying of Covid-19 – a significant portion of reported Covid-19 deaths could be considered cigarette deaths instead.  Or as air pollution deaths – and yet, our current president is using this crisis as an opportunity to weaken EPA air quality regulations.

Air pollution is a huge problem for a lot of Black communities in the United States.  Our racist housing policies have placed a lot of minority neighborhoods near heavily polluting factories.  Now Covid-19 is turning what is already a lifelong struggle for breath into a death sentence.

I would enthusiastically support a shutdown motivated by the battle for clean air.

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So, Covid-19.  We know how many people have died – already (CORRECTION AS OF APRIL 21) forty-two thousand in the United States

But if we want to know how scary this virus is, we need to know how many people were infected.  If that many people died after everyone in the country had it, then Covid-19 would be less dangerous than influenza.  If that many people died after only a hundred thousand had been infected, then this would be terrifying, and far more dangerous than influenza.

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Initially, our data came from PCR testing.

These are good tests.  Polymerase chain reaction is highly specific.  If you want to amplify a certain genetic sequence, you can design short DNA primers that will bind only to that sequence.  Put the whole mess in a thermocycler and you get a bunch of your target, as long as the gene is present in the test tube in the first place.  If the gene isn’t there, you’ll get nothing.

PCR works great.  Even our lovely but amnesiac lab tech never once screwed it up.

So, do the PCR test and you’ll know whether a certain gene is present in your test tube.  Target a viral gene and you’ll know whether the virus is present in your test tube.  Scoop out some nose glop from somebody to put into the test tube and you’ll know whether the virus is present in that nose glop.

The PCR test is a great test that measures whether someone is actively shedding virus.  It answers, is there virus present in the nose glop?

This is not the same question as, has this person ever been infected with Covid-19? 

It’s a similar question – most people infected with a coronavirus will have at least a brief period of viral shedding – but it’s a much more specific question.  When a healthy person is infected with a coronavirus, the period of viral shedding can be as short as a single day.

A person can get infected with a coronavirus, and if you do the PCR test either before or after that single day, the PCR test will give a negative result.  Nope, no viral RNA is in this nose glop!

And so we know that the PCR test will undercount the true number of infections.

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When we look at the age demographics for Covid-19 infections as measured by PCR test, the undercount becomes glaringly obvious.

Consider the PCR test data from the Diamond Princess cruise ship.  To date, this is our most complete set of PCR data – everyone on board was tested multiple times.  And from this data, it appears that very few children were exposed to the virus.

Friends, it is exceedingly unlikely that such a low percentage of children were exposed to this virus.  Children are disgusting.  I believe this is common knowledge.  Parents of small children are pretty much always sick because children are so disgusting. 

Seriously, my family has been doing the whole “social distancing” thing for over a month, and yet my nose is dripping while I type this.

Children are always touching everything, and then they rub their eyeballs or chew on their fingers.  If you take them someplace, they grubble around on the floor.  They pick up discarded tissues and ask, “What’s this?”

“That’s somebody’s gross kleenex, is what it is!  Just, just drop it.  I know it’s trash, I know we’re not supposed to leave trash on the ground, but just, just drop it, okay?  Somebody will come throw it away later.”

The next day: “Dad, you said somebody would throw that kleenex away, but it’s still there!”

Bloody hell.  Children are little monsters.

It seems fairly obvious that at least as high a percentage of children would be infected as any other age demographic.

But they’re not showing up from the PCR data.  On the Diamond Princess cruise ship, the lockdown began on February 5th, but PCR testing didn’t begin until February 11th.  Anyone who was infected but quickly recovered will be invisible to that PCR test.  And even people who are actively shedding viral particles can feel totally well.  People can get infected and recover without noticing a thing.

We see the same thing when we look at the PCR data from Italy.  If we mistakenly assumed that the PCR data was measuring the number of infections, and not measuring the number of people who were given a PCR test while shedding viral particles, we’d conclude that elderly people went out and socialized widely, getting each other sick, and only occasionally infected their great-grandchildren at home.

Here in the United States, children are disgusting little monsters.  I bet kids are disgusting in Italy, too.  They’re disgusting all over the world.

A much more likely scenario is that children spread this virus at school.  Many probably felt totally fine; some might’ve had a bad fever or the sniffles for a few days.  But then they recovered.

When they got their great-grandparents sick – which can happen easily since so many Italian families live in multigenerational homes – elderly people began to die.

So we know that the PCR test is undercounting the true number of infections.  Unless you’re testing every person, every day, regardless of whether or not they have symptoms, you’re going to undercount the number of infections.

In a moment, we can work through a way to get a more accurate count.  But perhaps it’s worth mentioning that, for someone my age, Covid-19 would seem to be about as dangerous as influenza even if we assumed that the PCR data matched the true number of infections.

If you’re a healthy middle-aged or young person, you should not feel personally afraid. 

That alone would not be an excuse to go out and start dancing in the street, though.  Your actions might cause other people to die. 

(NOTE & CORRECTION: After this post went up, my father recommended that I add something more about personal risk. No one has collected enough data on this yet, but he suspects that the next most important risk factor, after smoking and age, will be type 2 diabetes. And he reminded me that many people in their 30s & 40s in this country are diabetic or prediabetic and don’t even realize it yet. Everyone in this category probably has elevated risk of complications from Covid-19.)

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After you’ve been infected with a virus, your body will start making antibodies.  These protect you from being infected again.

Have you read Shel Silverstein’s Missing Piece book?  Antibodies work kind of like that.  They have a particular shape, and so they’ll glom onto a virus only if that virus has outcroppings that match the antibody’s shape.  Then your body sees the antibodies hanging out on a virus like a GPS tracker and proceeds to destroy the virus.

So to make an antibody test, you take some stuff that looks like the outcroppings on the virus and you put it on a chip.  Wash somebody’s blood over it, and if that blood contains antibodies that have the right shape to glom onto the virus, they’ll stick to the chip.  All your other antibodies, the ones that recognize different viruses, will float away.

An antibody test is going to be worse than a PCR test.  It’s easier to get a false positive result – antibodies are made of proteins, and they can unfold if you treat them roughly, and then they’ll stick to anything.  Then you’ll think that somebody has the right antibodies, but they don’t.  That’s bad.

You have to be much more careful when you’re doing an antibody test. I wouldn’t have asked our lab tech to do them for me.

An antibody test is also going to have false negatives.  A viral particle is a big honking thing, and there are lots of places on its surface where an antibody might bind.  If your antibodies recognize some aspect of the virus that’s different from what the test manufacturers included on their chip, your antibodies will float away.  Even though they’d protect you from the actual virus if you happened to be exposed to it.

If you’re a cautious person, though – and I consider myself to be pretty cautious – you’d much rather have an antibody test with a bunch of false negatives than false positives.  If you’re actually immune to Covid-19 but keep being cautious, well, so what?  You’re safe either way.  But if you think you’re immune when you’re not, then you might get sick.  That’s bad.

Because antibody tests are designed to give more false negatives than false positives, you should know that it’d be really foolish to use them to track an infection.  Like, if you’re testing people to see who is safe to work as a delivery person today, use the PCR test!  The antibody test has a bunch of false negatives, and there’s a time lag between the onset of infection and when your body will start making antibodies.

It can be dangerous to use antibody tests to address the wrong questions.

If you use the antibody test on a bunch of people, though, you can tell how many were infected.  And that’s useful information, too.

In the town of Robbio in Italy (pop. 6,000), the PCR test showed that only 23 people had been infected with Covid-19.  But then the mayor implored everyone to get an antibody test, and 10% of people had actually been infected with – and had recovered from – Covid-19.  Most of them couldn’t even recall having been sick.

The PCR test measured 23 cases.  The antibody test suggested there’d been at least 600.  And antibody tests, by design, will generally have a bunch of false negatives.  When a team at Stanford assessed the antibody tests manufactured by Premier Biotech in Minneapolis, they found that for every 3 people who’d been infected with Covid-19, the tests registered only 2 positives.

I don’t know who made the tests used in Robbio – maybe they were a little better, maybe they were a little worse.  Based on my experience, I wouldn’t be so surprised if the true infection rate with Covid-19 in that town was really just 10% – nor would I be surprised to hear that the chips had a high false-negative rate and that the infection rate was 20% or more.

If you calculate the fatality rate of Covid-19 in Italy by assuming that the PCR tests caught every infection, you’d get a terrifying 10%.

If you instead assume that many other towns had a similar infection rate to Robbio, you’ll instead calculate that the fatality rate was well under one percent. 

Italy has higher risk than the United States due to age demographics, smoking rates, and multigenerational households – and even in Italy, the fatality rate was probably well under one percent.

When researchers in Germany randomly chose people to take a Covid-19 PCR test (many of whom had no symptoms), they found that 2% of the population was actively shedding virus – a much higher number of cases than they would have found if they tested only sick people.  And when they randomly chose people to take an antibody test, they found that 15% had already recovered from the infection (again, many of whom had never felt sick).  According to these numbers – which are expected to be an undercount, due to false negatives and the time lag before antibody production – they calculated a case fatality rate of 0.37%

That would be about three-fold more dangerous than seasonal influenza.

In the United States, our bungling president gutted the CDC, leaving us without the expertise needed to address Covid-19 (or myriad other problems that might arise).  During the first few months of this epidemic, very few people managed to get a PCR test.  That’s why our data from the PCR tests is likely to be a dramatic undercount – indeed, when we finally started producing accurate tests, the apparent growth in Covid-19 caseload superimposed with the growth in test availability.

In the absence of good PCR data, we have to rely on antibody data to track infections after the fact.  Which is why a town in Colorado with zero reported infections, as measured by PCR, had sufficiently widespread exposure that 2% of the population had already recovered from Covid-19.

And it’s why the data from the Stanford Santa Clara county study is so unsurprising. 

Yes, there were problems with the Stanford study’s data collection – they displayed advertisements to a random selection of people, but then a self-selected subset responded.  The pool of respondents were enriched for white women, but Santa Clara’s outbreak probably began among Asian-Americans.  And we all know that random sampling doesn’t always give you an accurate depiction of the population at large – after all, random polling predicted that a competent president would be elected in 2016.

Now look at us.

It’s also likely that people with a poor understanding of the biology could misinterpret the result of the Stanford study.  They found that PCR tests had undercounted the infection rate in Santa Clara county, at the time of this study, by 85-fold.

It would be absurd to assume that you could simply multiply all PCR results by 85 to determine the true infection rate, but some people did.  And then pointed out the absurdity of their own bad math.

In places where more people are being tested by PCR, and they’re being tested more often, the PCR results will be closer to the true infection rate.  If you gave everyone in the United States a PCR test, and did it every day, then the PCR data would be exactly equal to the true infection rate.

If we had data like that from the beginning, we wouldn’t have been scared.  We would’ve known the true case fatality rate early on, and, also, at-risk people could’ve been treated as soon as they got infected.  We’d be able to save many more lives.

If access to health care were considered a basic right in the United States, we might’ve done something like this. 

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In Italy, it seems like Covid-19 is three- or four-fold more dangerous than seasonal influenza.  My guess is that Italy might have had about 50,000 deaths if they hadn’t enacted the lockdown.

In the United States, on a population level, Covid-19 is probably also more dangerous than seasonal influenza.  But there’s a big difference in terms of the distribution of risk.

The New York Times is running a series with short biographies of people who’ve died of Covid-19.  As of noon on April 17, about 10% of the people profiled were younger than 35.

10% is roughly the proportion of young people who die of seasonal influenza.  But only 1% of Covid-19 deaths are people younger than 35.  The news reports don’t always make clear how much the risk of Covid-19 is clustered in a small segment of the population.

This has serious implications for what we should do next.  If we were dealing with a virus that was about three-fold more dangerous than seasonal influenza for everyone, we might just return to life as normal.  (Indeed, we carried on as normal during the bad years when seasonal influenza killed 90,000 people instead of last year’s 30,000.)

Because the risk from Covid-19 is so concentrated, though, we can come up with a plan that will save a lot of lives. 

Healthy people under retirement age should resume most parts of their lives as normal.  Schools should re-open: for students, Covid-19 is much less dangerous than seasonal influenza.  I think that people should still try to work from home when possible, because it’s the right thing to do to fight climate change.

At-risk people should continue to isolate themselves as much as possible.

This sounds crummy, but at-risk people would just continue to do the thing that everyone is doing currently.  And the plan would save many lives because the epidemic would end in about 3 months, after the virus had spread to saturation among our nation’s low-risk cohort. 

Indeed, when a team of researchers from Harvard’s School of Public Health modeled the Covid-19 epidemic, they found that social distancing was generally unhelpful.  That’s what their data show, at least – but in their abstract, they instead recommend that we continue social distancing for the better part of two years.

Their data are easy enough to understand.  In each of these graphs, they show a blue box for how long social distancing would last, and then four colored lines to represent how many infections we’d see if we did no social distancing (black), medium quality social distancing (red), good social distancing (blue), or excellent social distancing (green).

So, from top to bottom, you’re looking at the graphs of what happens if we do a month of social distancing … or two months … or three, or four … or forever.

And you can see the outcomes in the panels on the right-hand side.  The black line shows what would happen if we did nothing.  Infections rise fast, then level off after the virus has reached saturation.  There are two important features of this graph – the final height that it reaches, which is the total number of severe cases (and so a good proxy for the number of deaths), and the slope of the line, which is how fast the severe cases appear.  A steeper hill means many people getting sick at the same time, which means hospitals might be overwhelmed.

So, okay.  Looking at their graphs, we see that social distancing saves lives … if we do it forever.  If you never leave your house again, you won’t die of Covid-19.

But if social distancing ends, it doesn’t help.  The slopes are nearly as steep as if we’d done nothing, and the final height – the total number of people who die – is higher.

(Often, one of their curves will have a gentler slope than the others — usually the good-but-not-excellent social distancing seems best. So you’d have to pray that you were doing a precisely mediocre job of not infecting strangers. Do it a little better or a little worse and you cause people to die. This isn’t an artifact — it’s based on the density of uninfected people when social distancing ends — but let’s just say “mathematical models are wonky” and leave it at that.)

In a subsequent figure, the Harvard team tried to model what might happen if we occasionally resumed our lives for a month or so at a time, but then had another shutdown.  This is the only scenario in which their model predicts that social distancing would be helpful.

But, unfortunately, there’s a problem.  Research done with other coronaviruses shows that immunity fades within a year.  Because the Harvard model would cause the epidemic to last longer than a year, people would have time to lose their immunity and get infected again.

Even in the extreme case that we mostly stayed in our homes for the better part of two years, social distancing would case more deaths from Covid-19 than if we had done nothing.

That’s not even accounting for all the people who would die from a greater risk of domestic violence, hunger, drug addiction, suicide, and sedentary behavior during the shutdown.  

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When our data was limited, the shutdown seemed reasonable.  We wouldn’t be able to undo the damage we’d done by waiting.

Except, whoops, we waited anyway.  We didn’t quarantine travelers in January.  The shutdown didn’t begin March, when the epidemic was well underway in many places. 

Now that we have more data, we should re-open schools, though.  For most people, Covid-19 is no more dangerous than seasonal influenza.  We already have enough data from antibody testing to be pretty confident about this, and even if we want to be extremely cautious, we should continue the shutdown for a matter of weeks while we conduct a few more antibody studies.  Not months, and certainly not years.

At the same time, we need to do a better job of protecting at-risk people.  This means providing health care for everyone.  This means cleaning our air, staunching the pollution that plagues low-income neighborhoods.  This might mean daily medical checkups and PCR tests for people who work closely with at-risk populations.

Our country will have to be different in the future, but mostly because we, as a people, have done such a shitty job of creating justice and liberty for all.  We need to focus on addressing the inequities that we’ve let fester for generations.  That’ll help far more than using a bandanna to cover up your smile.

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UPDATE: Wow, this got a lot of readers! Thanks if you made it this far. I’ve also written a response to common questions and comments about this essay.

On the sacred.

On the sacred.

In jail, we were discussing isolation when somebody mentioned the plummeting price of marijuana.  We’d read a quote from quantum physicist Richard Feynman about sensory deprivation:

I went into isolation tanks and got many hours of hallucinations, so I know something about that.  Ordinarily it would take me about fifteen minutes to get a hallucination going, but on a few occasions, when I smoked some marijuana beforehand, it came very quickly.  But fifteen minutes was fast enough for me.

The guys asked me when these experiments had happened. 

“Late 1950s, early 60s,” I told them.

“Man, marijuana must have been so expensive then!  Just in the last few years, the prices fell so hard.  Like now you can get five pounds for fifteen hundred bucks.”

I was shaking my head.  “Five pounds?  The most I ever bought at once was half an ounce, back when I lived in California.  Even then, I think I paid two hundred for it.”

“Two hundred dollars?  You got ripped off!”

I laughed.  “Yeah, but I probably deserved it.”

“Let me tell you,” the guy sitting next to me said, “next time you see me on the streets, I could hook you up with some good stuff.”

I demurred.  “I haven’t smoked in so long, you could probably sell me a baggie of oregano, I’d hardly know the difference.”

The guy’s face fell.  The room grew silent.  Until somebody shouted, “Oregano?  He just called you a major asshole!”

I felt pretty bad.  I’d really hurt his feelings.

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As it happens, this guy – the one whose feelings I’d hurt – is in jail for robbing me.

Unsuccessfully.  Possibly by accident.  But still.

There was a dropped wallet.  His attempt to use my family’s Health Savings Account debit card to buy two sandwiches and a pack of cigarettes.  Some yelling at whomever was working the counter at Village Pantry when the card wouldn’t go through.  Then an arrest.

That whole episode transpired almost three years ago.  But I didn’t learn who it was until last month, when the prosecutor sent a letter to us asking for a victim statement.

The guy has been in my class several times before.  I like him – he reminds me of an old friend of mine, enthusiastically participates in our classes, and always bikes over to say “hi” when I see him on the street.  Apparently they’d put him on probation after the debit card incident, but now, after another slip up, they’re trying to slap him with all his backup time.

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Everybody in class laughed when I told him he was there for robbing me.  He said he hadn’t known whose card it was.  I shrugged and asked him to write an apology to my spouse.  Then we sent letters to his prosecutor and the judge, asking for leniency.

Money isn’t sacred.

Photo by Todd Huffman on Flickr.

I’ve heard guys tell stories about taking money from each other.  The story might end with somebody getting punched in the face, but there aren’t hard feelings.  Money comes and money goes.  It’s just paper.  Or less: numbers inside a machine.

That HSA account only has money in it through a fiction agreed upon by my family, the pharmacy, and the bank.  We scan a card and the value of our account goes down.  Nothing physically happens.

Financial trickery seems so hollow compared to sandwiches or cigarettes.

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But passing off drugs as something they’re not?  That violates something sacred.  Inside the jail, people’s possessions are stripped away – all they have left are their reputations.

You don’t have to be honest all the time.  You can embellish stories about cops you’ve evaded, people you’ve slept with, money that’s slipped through your fingers.  That’s all harmless talk.  Passing the time, shooting the shit.

If you’re there for hitting a girlfriend, you can say you failed a drug test.  Or admit you’re in for domestic, but say that you didn’t do it.  For the sake of your future, maybe it’s best you tell an alternate story often to believe it.

When you’re talking about drugs, though, people can get hurt.  If you say it’s dope, it’d better be dope.  Not pot dipped in embalming fluid.  Not heroin spiked with fentanyl.

I won’t tell another joke about oregano.

Indeed, the guy who’s in jail for trying to use our HSA card isn’t too upset about most of his charges.  But one really rankles him:

“Do you remember that time, summer of that ‘Occupy Bloomington’ thing, when all those people kept going to the hospital cause they were ODing on bad spice?  The cops tried to pin that whole thing on me!  They put my picture on Fox News.  I was so fucking pissed!  I’ve done some stuff, but I didn’t do none of that.”

On meditation.

On meditation.

More is different.

In the beginning, subatomic particles careened too quickly to connect.  The universe was “hot.”  (Temperature is a measure of average speed as objects jiggle.  When physics people say that our universe was “hot,” they mean that everything was moving just shy of the speed of light.)

In the beginning, our universe wasn’t very interesting.  But then the homogeneous cloud of fast-moving particles cooled as it expanded.  Speeds slowed.  Soon, particles dawdled long enough in each others’ vicinity that they could interact.  Hydrogen atoms formed, then hydrogen gas, then stars. 

Stars are interesting – when a cloud of gas is big enough, its net gravity can pull everything inward until the density becomes so high that nuclear fusion begins.  This raging cascade of explosions counteracts the force of gravity and the star reaches an unsteady equilibrium until, eventually, it runs out of fuel and collapses or explodes.

An exploding star scatters heavier atoms across the sky.  When these are incorporated into a new star, they can participate in nuclear fusion events in turn, producing even heavier atoms. 

Then that star might explode, too.

Eventually, there were enough heavy atoms floating about the universe that a condensing cloud could form both a star and a set of orbiting satellites.  On these satellites – planets – atoms combine in more interesting ways than inside the bellies of stars. 

After all, the infernal core of a star is pretty hot, too.  Inside that blazing oven, particles can form atoms, and atoms can combine to form heavier atoms, but these are too frantic to form molecules – long strings of atoms bonded together.

The chemical bonds that hold a molecule together are much weaker than the electrostatic and nuclear forces that maintain an atom.  But planets – even broiling, meteor-bombarded ones – are peaceful places compared to stars.  On the primordial earth, lightning strikes or UV radiation probably catalyzed the formation of complex molecules like amino acids and nucleic acids.

These molecules are just big amalgams of subatomic particles.  The underlying stuff is the same … but there’s more of it.

More is different.

Consider the behaviors of a single amino acid.  An amino acid is complex compared to a quark or electron.  It can do acid-base chemistry!  Its mix of charged and neutral surfaces lets it interact in neat ways with various solvents. 

But if you compare that single amino acid to a protein – and a protein is just more amino acids joined together – you’ll realize that the single amino acid is total snoresville.

Proteins, though … wow!  They can fold into fantastical shapes.  They can function as molecular machines, their parts churning and twisting and flipping as they shuttle other molecules from place to place, or even create whole new molecules.

When you glom more and more and more subatomic particles together, eventually you create things that are complex enough to imprint patterns on the world.  They create more things like themselves.  Proteins and RNA make new proteins and RNA.

And then, a cell!  A cell is an amalgam of molecules all dissolved inside a bubble of fat.  If you thought proteins were cool, check this out!  Cells can swim, they can eat, they can live and die.

Or, what if there were more cells?  Then you can make us!  With many cells, you can make brains, which makes consciousness, which can give all those subatomic particles the ability to work together and realize that they are subatomic particles.

Well, no. One single human animal, in isolation, probably wouldn’t figure that out.  Each human, as an individual, can be pretty great – but to form a culture complex enough to study particle physics, you’ll need more people.  Contemporary physics papers list hundreds of authors, and that doesn’t even credit everybody who worked to build the equipment, and or worked to grow the food, and took care for the children, or taught the physicists, when they were young, allowing them to one day become physicists …

And each of those physicists, and engineers, and farmers, and caregivers, and teachers … each is a collection of cells, which are collections of molecules, which are collections of atoms, which are collections of subatomic particles.  As we transition between scales, we see qualitative differences in behavior from adding more.

This essay is made from a set of just 26 letters, but these can be combined to form a few hundred thousand different words, and those can be combined to convey an infinite number of different ideas.

We blink many thousands of times each day.  Our eyes close, pause, and then open again.  We need to blink.  Staring at screens – as I’m doing now, typing this essay, and as are you, reading it – causes us to blink less frequently, and that can lead to headaches.  But the quality of each blink doesn’t affect us much.  Most blinks pass by without our even noticing.

Meditation is just a long blink.  Close your eyes and let more time elapse before you open them again.

But more is different.  A blink doesn’t disrupt your thoughts.  Meditation, however, can be a psychedelic experience.

Many religions praise the value of meditation, especially in their origin stories.  Before he began his ministry, Jesus meditated in the Judaean Desert – he saw all the world’s kingdoms before him, but rejected that vision of power in order to spread a philosophy of love and charity.  Before he began his ministry, Buddha meditated beneath the Bodhi tree – he saw a path unfurl, a journey that would let travelers escape our world’s cycle of suffering.  Buddha decided to share that vision with others.

Before teaching his fellows to reshape the world with words, Odin meditated from a tree branch – he felt that he had died, transcended life, and could see the secret language of the universe shimmering before him.

I’ve been preparing anti-racist material about paganism and spirituality so that we have more things to send to people who contact Pages to Prisoners.  As part of this project, I’d like to include information about meditation.  After all, neo-paganism is invented – typically quite recently – and, as above, many religions have preserved stories suggesting that their founders’ meditation inspired their faith.  These religions don’t always prioritize meditation as a contemporary practice, but many do: Christian monks repeat prayers in a way that’s strikingly similar to mantra meditation, Hindu adherents are advised to sit and experience a simulacrum of Shiva’s asceticism, and even warrior cultures have prized pre-battle stillness as a way to focus attention and more fully inhabit the present.

The scientific literature is also replete with papers about meditation — but most of these are junk. It’s fairly easy to find published studies claiming that mindfulness training can confer disease resistance, immunity to aging, or even paranormal abilities like extra-sensory perception.  Scientific papers aren’t inherently more trustworthy than the internet.

But it’s true that your mind is plastic, and your moods can dramatically alter the way you perceive the world.  Conditions that affect our nervous system – like depression, insomnia, and even chronic paincan be treated through meditation.  The experiments that scientists use to assess things like “creativity” or “attentiveness” are often open to interpretation, but it’s not unreasonable to imagine that meditation would help.

All people are creative.  Our problem, often, is that our ideas can flit away before we fully grasp them.  Like dreams, they fade, and we’re left with the irksome sensation that “I feel like I just had a good idea, but …”

Meditation can clear the turbid waters of your mind.  Like gazing into a pellucid lake, it could become easier to spot your good ideas when they come.

I’ve never been inside a prison, so I’ll have to collaborate with friends who have spent time there as I make the pamphlets.  But everything I’ve read suggests that most prisons are loud, chaotic, stressful, and dangerous.  Which has obvious implications for how easily people can meditate.  If you live near a beautiful glen, you could probably do well by your brain by simply taking some time each day to sit peacefully beside some flowing water.

Instead, I’ve been learning about mantra meditation.  By silently intoning the same phrase over and over – even if it’s just a nonsense word – you can overcome a fair bit of external distraction.  To test, I’ve tried meditating at the YMCA.  This place is very calm compared to our county jail, which I’ve heard is itself calmer than a prison, but where I sit, people are usually conversing, and there are a variety of rattling exercise machines.

Several of the guide books I’ve read recommend that you pay somebody a bunch of money to teach you transcendental meditation.  During your training, you’ll be given a secret Sanskrit word or phrase.  People who’ve taken these training courses have posted a bunch of the words online, and apparently a mantra is selected based upon your age and gender. 

That seems silly to me – although it’s possible that different people’s minds would respond best to different mantras, my gender isn’t a big component of my identity, nor is my age. 

I did pick out a Sanskrit phrase, which is perhaps a silly choice in and of itself.  After all, I can’t speak Sanskrit.  But I thought it might be nice to have a set of sounds that didn’t carry a lot of semantic meaning in the rest of my daily life.  Although Sanskrit mantras would have held meaning to the original practitioners of this style of meditation, Sanskrit is generally considered a formal, ritual language, not something that people speak at home with their families.  Even for native speakers, the chance of crossed wires, in which people were inadvertently saying their special mantras at other times of day, was probably pretty low.

While meditating, there are times when I’m pretty oblivious to my environs, even though I’m sitting in a crowded, noisy place.  I assume that I should recommend, for people meditating in prison, that they use a buddy system.  Unless somebody you trust immensely was sitting nearby, I assume it would feel too unsafe to allow yourself to completely let go in the way that deep meditation requires.

In case you’re interested in trying, I can tell you what’s worked so far for me.  I’ve been thinking the phrase “sat nam.”  I liked the translation when I looked it up online, and it’s felt convenient to have two discrete sounds – I think the “sat” while breathing in, and “nam” while breathing out.  I’ve read that people aim to spend about six seconds each on inhalation and exhalation, but I breath much more rapidly than that. 

If nothing too distracting is going on nearby – maybe just some clanking from the ellipticals, treadmills, and stairmasters – I breath in and out once every four to eight seconds.  But when people are having a conversation right next to me, I take a breath every one or two seconds, which means I’m intoning my little mantra more often and can do a better job of isolating myself from what’s going on around me.

As far as I can tell, that isolation is the goal of meditation.  Our minds evolved to expect constant stimulus during our waking lives.  If you reduce the degree of outside stimulation, like with a sensory deprivation chamber, you invite your mind to conjure strange thoughts, visions, and sounds to replace the inputs that it expects.  But you have to keep at it long enough.

When particle physicist Richard Feynman described his experience with sensory deprivation tanks, he wrote:

Ordinarily it would take me about fifteen minutes to get a hallucination going, but on a few occasions, when I smoked some marijuana beforehand, it came very quickly.  But fifteen minutes was fast enough for me.

Mr. Lilly had a number of different tanks, and we tried a number of different experiments.  It didn’t seem to make much difference as far as hallucinations were concerned, and I became convinced that the tank was unnecessary.  Now that I saw what to do, I realized that all you have to do is sit quietly.

I would like to have done it at home, and I don’t doubt that you could meditate and do it if you practice, but I didn’t practice.

I’ve only had a bit of practice, but when I sit still with my eyes closed and block out the outside world with a repeated phrase, my mind will sometimes drift.  I’ve been trying to sit for twenty minutes, although I often inadvertently rouse myself after about fifteen – which hasn’t seemed to be quite enough, for either me or Dr. Feynman.  But I get the feeling that it has to be continuous.  Once I’ve opened my eyes and glanced at the clock, I stop for the day.  Even if nothing much has happened.

On these days, I console myself with a quote from Maharishi Mahesh Yogi that I learned from Bob Roth’s Strength in Stillness:Even in a shallow dive, you still get wet.

I begin by stretching – although I’m practicing in a relatively distracting environment, it seems reasonable to minimize the distractions of my own body.  I try not to move while meditating, and it’d be harder to maintain a single posture if I could feel my body ache.

After I close my eyes, the first few minutes typically feel like a waste of time.  I’m sitting there repeating a nonsense phrase and I can’t help but think of the myriad other things that I ought to be doing.

As long as I can force myself to keep at it, though, the experience changes.  More becomes different.  Undulating phosphenes blossom in the umber field of my closed eyes.  Sometimes I slip into reverie; if I catch myself daydreaming, I’ll resume intoning my bit of Sanskrit, which helps me set aside whatever vein of thought led me astray.

Nobody is totally sure why we need sleep, but recent results have suggested that nitrogenous waste and other metabolic toxins can only be cleared from brain cells while we’re snoozing.  If you stay awake too long, trash piles up along the roadways of your mind, and all that junk prevents learning, memory formation, and attentiveness. 

During my classes in jail, I often work with men who have stayed awake for weeks at a time by taking methamphetamine – they’ve experienced a wide variety of hallucinations, paranoia, and mental turmoil.  Amphetamines aren’t very toxic, but loss of sleep can seriously damage a person’s brain.

One day without sleep won’t kill you.  Luckily so – since having kids, there have been many nights when a little one wakes up screaming and I never get to rest.  But more is different.  After three days without sleep, the shadow people start talking.  After eight days, my students have started talking back: “I knew they weren’t real … but I still didn’t want to be rude.  But we got into all these arguments.

Sleep washes away the argumentative shadow people.

When meditation goes well, I sometimes imagine my mind being cleansed – I’ll sit there thinking sat nam, sat nam and envision a cascade of water flowing over me like Heracles used to clean King Augeas’s stables.  But meditation might not help with keeping a brain tidy – those experiments on the waste-clearing function of sleep were done with mice, and (to the best of my knowledge) nobody has taught mice to meditate.

If you trust my spouse’s subjective evaluation, though, meditation seems to help.  I’ve apparently been more pleasant to live with since I started practicing. 

If you’re going to try, aim for at least twenty minutes, maybe once or twice a day for a few weeks.  My apologies if it seems pointless at first.  I’d recommend you keep at it – just like a single minute won’t give you the same benefit as twenty, it seems reasonable to expect that a single day wouldn’t have the same benefit as a month’s daily practice.

After all, more is different.

.

Featured image by Mitchell Joyce on Flickr.

On artificial intelligence and solitary confinement.

On artificial intelligence and solitary confinement.

512px-Ludwig_WittgensteinIn Philosophical Investigations (translated by G. E. M. Anscombe), Ludwig Wittgenstein argues that something strange occurs when we learn a language.  As an example, he cites the problems that could arise when you point at something and describe what you see:

The definition of the number two, “That is called ‘two’ “ – pointing to two nuts – is perfectly exact.  But how can two be defined like that?  The person one gives the definition to doesn’t know what one wants to call “two”; he will suppose that “two” is the name given to this group of nuts!

I laughed aloud when I read this statement.  I borrowed Philosophical Investigations a few months after the birth of our second child, and I had spent most of his first day pointing at various objects in the hospital maternity ward and saying to him, “This is red.”  “This is red.”

“This is red.”

Of course, the little guy didn’t understand language yet, so he probably just thought, the warm carry-me object is babbling again.

IMG_5919
Red, you say?

Over time, though, this is how humans learn.  Wittgenstein’s mistake here is to compress the experience of learning a language into a single interaction (philosophers have a bad habit of forgetting about the passage of time – a similar fallacy explains Zeno’s paradox).  Instead of pointing only at two nuts, a parent will point to two blocks – “This is two!” and two pillows – “See the pillows?  There are two!” – and so on.

As a child begins to speak, it becomes even easier to learn – the kid can ask “Is this two?”, which is an incredibly powerful tool for people sufficiently comfortable making mistakes that they can dodge confirmation bias.

y648(When we read the children’s story “In a Dark Dark Room,” I tried to add levity to the ending by making a silly blulululu sound to accompany the ghost, shown to the left of the door on this cover. Then our youngest began pointing to other ghost-like things and asking, “blulululu?”  Is that skeleton a ghost?  What about this possum?)

When people first programmed computers, they provided definitions for everything.  A ghost is an object with a rounded head that has a face and looks very pale.  This was a very arduous process – my definition of a ghost, for instance, is leaving out a lot of important features.  A rigorous definition might require pages of text. 

Now, programmers are letting computers learn the same way we do.  To teach a computer about ghosts, we provide it with many pictures and say, “Each of these pictures has a ghost.”  Just like a child, the computer decides for itself what features qualify something for ghost-hood.

In the beginning, this process was inscrutable.  A trained algorithm could say “This is a ghost!”, but it couldn’t explain why it thought so.

From Philosophical Investigations: 

Screen Shot 2018-03-22 at 8.40.41 AMAnd what does ‘pointing to the shape’, ‘pointing to the color’ consist in?  Point to a piece of paper.  – And now point to its shape – now to its color – now to its number (that sounds queer). – How did you do it?  – You will say that you ‘meant’ a different thing each time you pointed.  And if I ask how that is done, you will say you concentrated your attention on the color, the shape, etc.  But I ask again: how is that done?

After this passage, Wittgenstein speculates on what might be going through a person’s head when pointing at different features of an object.  A team at Google working on automated image analysis asked the same question of their algorithm, and made an output for the algorithm to show what it did when it “concentrated its attention.” 

Here’s a beautiful image from a recent New York Times article about the project, “Google Researchers Are Learning How Machines Learn.”  When the algorithm is specifically instructed to “point to its shape,” it generates a bizarre image of an upward-facing fish flanked by human eyes (shown bottom center, just below the purple rectangle).  That is what the algorithm is thinking of when it “concentrates its attention” on the vase’s shape.

new york times image.jpg

At this point, we humans could quibble.  We might disagree that the fish face really represents the platonic ideal of a vase.  But at least we know what the algorithm is basing its decision on.

Usually, that’s not the case.  After all, it took a lot of work for Google’s team to make their algorithm spit out images showing what it was thinking about.  With most self-trained neural networks, we know only its success rate – even the designers will have no idea why or how it works.

Which can lead to some stunningly bizarre failures.

artificial-intelligence-2228610_1280It’s possible to create images that most humans recognize as one thing, and that an image-analysis algorithm recognizes as something else.  This is a rather scary opportunity for terrorism in a world of self-driving cars; street signs could be defaced in such a way that most human onlookers would find the graffiti unremarkable, but an autonomous car would interpret in a totally new way.

In the world of criminal justice, inscrutable algorithms are already used to determine where police officers should patrol.  The initial hope was that this system would be less biased – except that the algorithm was trained on data that came from years of racially-motivated enforcement.  Minorities are still more likely to be apprehended for equivalent infractions.

And a new artificial intelligence algorithm could be used to determine whether a crime was “gang related.”  The consequences of error can be terrible, here: in California, prisoners could be shunted to solitary for decades if they were suspected of gang affiliation.  Ambiguous photographs on somebody’s social media site were enough to subject a person to decades of torture.

Solitary_Confinement_(4692414179)When an algorithm thinks that the shape of a vase is a fish flanked by human eyes, it’s funny.  But it’s a little less comedic when an algorithm’s mistake ruins somebody’s life – if an incident is designated as a “gang-related crime”, prison sentences can be egregiously long, or send someone to solitary for long enough to cause “anxiety, depression, and hallucinations until their personality is completely destroyed.

Here’s a poem I received in the mail recently:

LOCKDOWN

by Pouncho

For 30 days and 30 nights

I stare at four walls with hate written

         over them.

Falling to my knees from the body blows

         of words.

It damages the mind.

I haven’t had no sleep. 

How can you stop mental blows, torture,

         and names –

         They spread.

I just wanted to scream:

         Why?

For 30 days and 30 nights

My mind was in isolation.

On loneliness.

On loneliness.

Most laboratory animals live in bleak environs.  With mice, each cage typically contains a single animal.  There is bedding, food, and water.  There is very little space.

A lab mouse will be illuminated for many hours each day – sometimes twenty-four, sometimes slightly fewer – by fluorescent lights.  It will hear the constant thrum of ventilation fans and refrigerator compressors.  At least once a week, an apex predator – wafting stress-inducing smells, especially if it’s male – will reach into its home and grab it.

Chances are, it will see other mice.  A rotating cadre will fill adjacent cages during its tenure in the lab.  They will never touch.

Our cruelty makes for bad science, too.

When social animals are stored in isolation, their bodies and brains decay.  Neuron growth slows, which impedes learning.  Lifespan is curtailed.  Obesity rates increase.

Lab_animal_careIf we stop mistreating laboratory animals, though, new research might be inconsistent with past results.  When describing mice, scientists don’t say that deprivation stunts brain development.  Instead we write things like, “If a lab is studying the impact of stress on the growth of new neurons, for example, and then it lets mice exercise on a running wheel – which has been shown to spark neuron growth – the study could be jeopardized” (from David Grimm’s recent news article for Science magazine).

4117496025_8024f879d6_zWe give ourselves a very skewed view of neurology if we let ourselves think that a creature’s normal habits are stimulating neuron growth, rather than admitting that deprivation stops it.  For decades, most researchers thought that neuron growth ceased in adults.  Even in the 2005 paper demonstrating structural plasticity, the authors wrote that “such changes are only seen in response to external perturbation,” because brain development is sluggish in lab mice housed in normal conditions, i.e. those little cages.

Of course, some scientists do care about the well-being of their furry test tubes.  For instance, biologist Daniel Weary, who told Grimm “Our dream is that our animals live a better life with us than if they had never been born.”  Animals in Weary’s lab get to touch actual dirt.

Maybe not the highest bar, but the lives of most animals on our planet are worse than if they’d never been born.

Vivek_Murthy_nomination_hearing_February_4,_2014Most social animals – like mice, rabbits, and humans – aren’t going to be very happy when they’re housed in isolation.  Former U.S. Surgeon General Vivek Murthy considers loneliness to be a public health crisis, leading to health risks as bad as smoking or obesity.

Unfortunately, most biomedical research is done with research animals amongst whom pervasive loneliness is standard.  And our political system gives outsize influence to wealthy corporations that earn more money when people feel lonely.

We shunt humans into jail when we feel that their behaviors are unacceptable for the world at large.  Incarceration sends a message: don’t beat your family; don’t steal; don’t sell drugs; don’t take drugs; don’t be late for an appointment with your parole officer; don’t be too poor to pay your court fees.  To my mind, some of these offenses are worse than others.

The hope is that either the threat of incarceration deters people from these things, or that the experience of being incarceration cures them of the inclination.  (Or a third rationale – that seeing offenders punished will pacify others’ sense of fairness – which seems to encourage the evolution of cooperation, but, like many other evolved behaviors, seems unnecessarily vicious for the modern world.)

We’ve known for years that punishment doesn’t work well as a criminal deterrent.  And the experience of incarceration seems to make most people worse, not better.

Instead, we’re imposing loneliness on people who most need the help of friends and neighbors to turn their lives around.  Somebody screws up?  We store that person like a lab mouse.

10490113913_e3a697bdca_zI was recently chatting with somebody who’s done nine months so far for a parole violation – and is still waiting for his court date, which keeps being rescheduled.  (He’s already told the judge that he’ll plead guilty, and the prosecutor wanted to send him to rehab, but his PO nixed the deal.)

“It’s a lot better now, in J block.  Everybody said, you don’t wanna move from A block, you’ll get no bingo, you’ll get no … I don’t care about any of that.  We can look out the window, see people walking on the street.

“I spent almost an hour, the other day, watching this leaf blowing back and forth in the wind.  I was staring, thinking I’d say to the judge, ‘you can pile on whatever other charges you want, I’ll still plead guilty, I’ll plead guilty to all of it if you just let me out there to look at that leaf blowing around up close.  Just five minutes, just lemme see something!

“In D block, that was the worst.  All we could see was the parking garage.  On weekends, we’d see nothing, not even cars.  So I was starting fights every day.  I’d be like, hey, turn the TV to, I don’t know, some channel I don’t even like, just so I can start something with somebody.  Cause a fight would at least be something to do.”

John-Michael Bloomquist’s poem “The Prodigal’s Return,” about teaching poetry in jail, ends:

                                      Each day that I visit

the jail full of men, who hug me the way

their families cannot, write poems about childhoods

I couldn’t imagine, I feel the love of my father.

After nine months inside – un-touched, un-hugged, un-loved, under-slept – perhaps our man will finally be released.  Surely his time there will have cured him of his addiction!