Category Archives: Education

I write this book from the point of view of a career educator. My aim is to teach myself and others. These posts will relate to educational materials and issues. I will include material that I produced myself.

Coronavirus Primer, Part 5: So What Should We Do Now?

A full solution requires many pieces: health, economy, politics, and teamwork. Click here for attribution 1

I am researching and writing this primer to take a big-picture look at the COVID-19 epidemic.  What I originally envisioned as a single essay has now developed into an ongoing series of indefinite duration! Now that I have examined the pandemic from biological, medical, epidemiological, and social perspectives, today I consider the upshot:  “So … what should we do now?!”  How shall we resolve the three-way tug of war involving public health, the economy, and political peace?  How should we conduct our lives until the virus is under control?        

I. A Tricky Balance

President Trump tweeted, “We cannot let the cure be worse than the problem itself.” 2

Most people would agree with President Trump’s rationale.  The keyword in this sentiment is “worse”, which is frustratingly hard to define.  It depends on the costs and benefits of action vs. inaction. 

Let’s suppose at its simplest level that cost is measured strictly in terms of human lives lost.  One research team estimates that strict public health measures could save about a million American lives this year while causing around 100,000 poverty-related deaths.  That is a nightmarish ethical dilemma.  On balance, though, playing it safe with public health measures like stay-at-home orders would be justified. 3 The problem is that prevented deaths are invisible.  Virtually nobody would celebrate the million lives saved, while the actual recession-related deaths would make headlines daily. 

I got curious to look up the countries that had done best at protecting their economies, those that had done best to minimize infections, and those that had struck the best balance.  The results surprised me.  In the long run, there is no tradeoff.  The countries that have done best at keeping their COVID-19 deaths down are actually those with the most successful economies now. 4 Although “lockdown” is a difficult short-term process, it allows for an earlier return to normalcy and therefore greater long-term recovery.

If numbers were the only consideration, the solution would seem “obvious”.  With a truly rigorous, highly-enforced social lockdown for 2 – 4 weeks, we could put this pandemic behind us.  That scenario alarmed us in March, but by now another 2 – 4 weeks would not feel shocking. 

There’s another factor, though: political will.  I’d be willing to horde groceries and stay home for a couple more weeks.  I know that many of you would too, even some conservatives in small states.  But we also know how ferocious the resistance would be.  People would refuse to comply; the stricter the order, the harder it would be to enforce.  The short-term pain would be undeniable.  Some people would feel so angry and oppressed that they would develop permanent vendettas or even go Rambo on us.  The emotional costs of such drastic action would simply be too high.  Unfortunately, the longer this goes on, the more time the pandemic has to grow exponentially. 

If the short-term and long-term solutions are at odds with each other, how else can we find the right balance?

II. Suggestions from the Left and Right

I seem to see two competing visions emerging.

A. The “Experts'” or “Liberal” Solution

  • Monitor hotspots
  • Locally tailor protocols, including face mask mandates, business closures, and prohibitions of mass gatherings, where and when appropriate
  • Increase the number and speed of tests where needed
  • Improve contact tracing and quarantine procedures
  • Wait for a vaccine

A good example of this model is California’s stay-at-home order, which was one of the first statewide responses in the United States and which is regularly updated.  California counties are ranked on a heat spectrum (yellow < orange < red < purple < blue) which is now defined by availability of ICU beds.  Business activities and freedom of movement are more strictly restricted in hotter spots.  The state also recently launched the CA Notify app.  When someone who uses the app tests positive for SARS-CoV-2, she can alert the app.  Users who spend extended periods of time in proximity to her will then get notifications on their phones. 

B. The “People’s” or “Conservative” Solution

  • Preemptively quarantine the vulnerable
  • Let everyone else get back to life as usual
  • Face masks and social distancing up to personal conscience
  • Wait for herd immunity

The conservative model is expressed in the Great Barrington Declaration.  The preamble to this declaration indicates that its proponents are more concerned about government orders than the virus.  The plan calls itself “Focused Protection” because it would focus on protecting nursing home residents and other vulnerable patients, while keeping children in school because they are much less susceptible.  Many experts do not find focused protection to be feasible; flu pandemics illustrate that is not possible to effectively identify or quarantine the vulnerable population. 5 In fact, the apparent mass appeal of the Great Barrington Declaration is that it is extremely simple.  The declaration is short and abstract, more a set of goals than a plan of execution.    

III. My Humble Suggestions

A. Principles and Guidelines

In my coronavirus primer, I have discussed benefits and drawbacks to various prongs of the liberal and conservative approaches.  Business lockdowns cause their own pain, and mandates lead to political friction.  A vaccine could be years away in some parts of the world.  With indiscriminate reopenings, we might reach herd immunity before a vaccine is available, but that process would kill tens of millions of people and would overwhelm hospitals to the point of causing millions more non-COVID deaths.

Some compromise will be necessary and optimal. 6 Compromise requires looking at this pandemic as a political problem, not strictly a medical or economic one.  The political controversy is the main factor that tends to be left out when people discuss solutions.  No single plan will be perfectly acceptable to everyone.  But the status quo approach, which has led to violence and deep societal rifts, is outright unacceptable.           

Here are some abstract political principles that guide my thoughts.

  • “I’ll explain my position and respect yours.” 
  • In a democracy, we define what is “right” by the people’s choice, even when it’s based on false premises.  That is frustrating, but it’s a price we pay.
  • The more controversial a decision is, the more locally it should be made.
  • Consider externalities

Externalities are a fancy way of saying costs or benefits that one person’s decisions have on society around him.  Most economics classes teach that an economy is most efficient when people are charged for the messes they make or rewarded for the messes they clean up.  I’m a little surprised that I haven’t heard this topic being discussed widely this year in response to the pandemic.   

When I consider these principles in sum, I conclude that each person, family, business, and government should assume the right and the responsibility for its own decisions.  Here are some applications that would follow from this existential approach.

The people’s primary freedom is the right to decide how to carry out their lives.  Face masks, social gatherings, and business closures should mostly be individual decisions.  In fact, this already is true in reality.  It’s difficult to enforce mandates on individuals, so people already are acting according to their own judgment. 

In order to guide people’s actions, governments have a responsibility to educate: to provide data, science, and recommendations with justifications.  Most people will choose to do the right thing and respect sensible recommendations.  For instance, governments everywhere have been consistent about their advice to wear face masks.  Even without a mandate, 85% of Americans already report that they regularly wear face masks voluntarily, including 76% of Republicans. 7 For conservatives, it’s that last step of the requirement that gets the blood boiling.  Thus, the benefits of requiring face masks probably does not greatly outweigh the political ill-will.  

There are a few more COVID-specific principles to help us make common sense decisions.

  • A higher current level of infections justifies more restricted behavior.  
  • Stricter regulations are only sustainable over smaller places or shorter times.
  • Vulnerable people require greater protection.

States differentiate counties depending on their rates of new cases, rates of positive tests, percentage of ICU capacity available, etc.  Personally, I made a 1% rule of thumb for myself.  When the pandemic started, I vowed to stay out of areas where more than 1% of the population is actively infected.  Today, it so happens that my neighborhood, city, county, state, and country are all 2 – 6% actively infected.  These levels tell me that it’s time to stay in as much as possible. While I can commit to locking down at home for a couple of days, it’s unreasonable to expect self-quarantine for months on end.  It’s completely unrealistic to expect the whole world to hunker down for a year.   I did find it reasonable to stay home for last year’s holidays.  It’s a sacrifice I was willing to make because it felt like the right thing to do. I’m sure that you have your own standards to suit your own lifestyle.  No matter how young or healthy you are, though, be mindful that this disease can be fatal to the oldest generation in your family.     

Below, I detail a few more specific recommendations that follow from my principles.                        

B. Spreading the Liability for Spreading the Disease

COVID-19 liability is a hot topic this year, and it should play an important part in our response.  A pure economist might suggest that people, and especially businesses, should be held liable for medical costs if they cause infections by high-risk behavior.  We all know that’s an impractical solution.  For starters, it’s almost impossible to trace the origins of each transmission.  Furthermore, most germ-spreaders couldn’t afford the medical costs.  The ensuing lawsuits would not exactly help lighten up the atmosphere either. 

A practical middle-ground would be a “liability spreading” system, where the costs are spread out among the whole risk-sharing population.  The closest analogy would be a toll road:  those who use it pay for it.  A similar cost-reward system with tolls and subsidies could be set up by a city or county that chose to participate.  Just to throw an example out there, a city could sell foot traffic permits to businesses.  Pricing could be based on population density, with a discount for businesses that require on-site rapid testing.  The business could pass the cost on to customers.   Perhaps customers could pay a little extra by the minute or the mile to enter stores, ride buses, and the like.  The proceeds from these tolls could fund medical treatment, vaccine and face mask giveaways, and rapid tests.

Nobody likes tolls, but they’re better than outright bans.  Government directives to “stay at home” have been highly contentious – they are largely to blame for the rise of right-wing militarism in the last year.  Worse yet, these bans aren’t even enforceable.  Most governments are relying on an honor system with their citizenry.  The liability spreading system would

  • keep businesses open,
  • effectively discourage frivolous outings with an added cost (perhaps movie ticket prices would double)    
  • still allow citizens freedom of movement according to their own judgment and budget,
  • not cost anything for citizens who stay home,
  • raise money for COVID-19 treatment,
  • and be flexible.  It’s easier to adjust tolls than to expect citizens to keep up with an ever-shifting front of regulations.

C. Just Compensation and Focused Bailouts

If a government does force a business to close, it ought to compensate for lost profits.  In fact, in the United States, there is a constitutional argument in favor of such compensation.  The 5th Amendment states in part:

nor shall private property be taken for public use, without just compensation.” 

This “Takings Clause” applies to state and local governments as well as the federal government. 

In this pandemic, closing a business to mitigate the spread of a virus is a “public use”, and forcing an establishment to close is arguably “taking” the property for that use.  Under this theory, a government that ordered a business to close for a month would compensate that business for one month’s lost profits or payroll. 

This argument is not likely to be legally enforceable.  COVID-19 closures fall under a government’s police powers, which are legally exempt from the 5th Amendment.  (Such compensation was not made for Spanish Flu closures).  At least one legal scholar argues that some compensation would be the morally right thing to do, a responsibility that I argue for here.  This must be balanced by cost.  It would be prohibitively expensive to cover the widespread closures that have been mandated.  In fact, coronavirus bailouts like the PPP program have been the largest stimulus bills in US history. 

The liability-spreading system would mitigate such costs by allowing all but the worst super-spreader businesses to remain open.  In fact, it would be a mechanism for funding any such compensatory payments.  If a government were committed to covering profits for businesses that it forced to shut down, that government would have incentive to become extremely judicious with its closures.      

D. Conservative Messaging for Conservative Communities

Aristotle described three forms of persuasion:  logos, pathos, and ethos.  As someone trained in the sciences, I respond to logos: facts and logic.  However, I recognize that most people base their values primarily on ethos (who is delivering the message) supported secondarily by pathos (emotions), then perhaps justified after the fact by heavily filtered evidence.  In the United States, for instance, 1/3 to ½ of the nation is conservative.  Many people in this constituency have made up their minds that Democrats or even scientists are bad guys.  Those folks won’t listen to a word that Dr. Fauci, Governor Whitmer, or President Biden says, no matter how well it is supported by science. 

To reach conservative citizens, public health agencies must recruit conservative spokespersons.  I can hardly think of a better example than Dolly Parton.  This beloved red-state icon donated $1 million to the Moderna vaccine.  In fact, federal agents have already suggested enlisting her as a spokesperson to encourage mask wearing in Knox County, TN. 8 If Dolly and other conservative heroes encouraged people to stay at home and avoid gatherings as a patriotic call of duty, conservatives just might take it more seriously.  Let’s start comparing the sacrifices that we ordinary citizens make to those of soldiers and policemen, part of a higher cause. These are the arguments that resonate with conservatives.     

E. Anti-Curfews

I don’t understand the rationale behind curfews, and I’m not sure anyone has evidence that they do any good.  In fact, I would propose that businesses in high-risk zones should stay open 24 hours.  Then customers could spread themselves out throughout the day instead of packing themselves into limited business hours.  Hell, stores could even offer graveyard shift discounts. 

IV. Conclusions

It would be possible to end this pandemic within a month, but only with a coordinated and strictly enforced worldwide shutdown.  If the pandemic were strictly a medical issue, or even a long-term economic issue, this solution would be the sensible one.  But we all know it’s draconian and unrealistic.  Some people would suffer great loss, some would resent the lockdown for the rest of their lives.  Different people are swayed by different emotions or evidence, and some pay no heed to evidence at all.  But they are all part of the democratic decision-making machine.

There is room for individualized response.  In fact, that may be the only way to keep political tensions under control.  We must allow some latitude for people and businesses to make their own choices. 

On the flipside, freedom bears responsibility.  Charge an extra $10 for a movie ticket or 25% for bus fare, and then let people decide what they’re willing to pay for.  Use the proceeds for COVID-related medical expenses and to support businesses that have closed their doors.   

As I said, no solution is perfect, and this proposal is no exception.  Some people would object to paying extra to congregate.  Others would complain about a system that permits gatherings at all.  What can I say – life can not be perfect in times of pandemic.  That’s the hand we’re dealt right now.  The best we can do is respond efficiently and holistically.  Let’s seek the greatest medical, economic, and emotional good for the greatest number.   

V. Citations

  1. lumaxart, CC BY-SA 2.0 https://creativecommons.org/licenses/by-sa/2.0, via Wikimedia Commons, https://commons.wikimedia.org/wiki/File:Working_Together_Teamwork_Puzzle_Concept.jpg (accessed 12/17/20).
  2. Donald Trump, Twitter, 3/22/20, 8:50 PM, https://twitter.com/realDonaldTrump/status/1241935285916782593
  3. Olga Yakusheva, “The Cure is Not Worse than the Disease – A Humanitarian Perspective”, SSRN (8/07/2020, pre-print awaiting peer review), https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3638575 (accessed and saved 10/01/20).
  4. Joe Hasell, Which countries have protected both health and the economy in the pandemic? – Our World in Data (9/01/2020; accessed, saved, and archived 11/27/20).
  5. Julian Tang et al., “Expert reaction to Barrington Declaration, an open letter arguing against lockdown policies and for ‘Focused Protection’”, Science Media Centre (10/06/2020), expert reaction to Barrington Declaration, an open letter arguing against lockdown policies and for ‘Focused Protection’ | Science Media Centre (accessed, saved, and archived 12/16/20).
  6. Dr. Sandro Galea as quoted by Amelia Thomson-DeVeaux, “Republicans And Democrats See COVID-19 Very Differently.  Is That Making People Sick?” Five Thirty-Eight (8/27/2020),  https://fivethirtyeight.com/features/republicans-and-democrats-see-covid-19-very-differently-is-that-making-people-sick/ (accessed, saved, and archived 10/23/20).
  7. Stephanie Kramer, “More Americans say they are regularly wearing masks in stores and other businesses”, Pew Research Center (8/27/2020), https://www.pewresearch.org/fact-tank/2020/08/27/more-americans-say-they-are-regularly-wearing-masks-in-stores-and-other-businesses/ (accessed, saved, and archived 10/22/20).
  8. Cole Sullivan, “Federal report: Tennessee needs mask mandate, should enlist Dolly Parton to help”, WBIR News (7/21/2020), https://www.wbir.com/article/news/health/coronavirus/federal-report-tennessee-needs-mask-mandate-should-enlist-dolly-parton-to-help/51-7a3c938a-6f82-4760-ae91-963e4f0c66d3 (accessed, saved, and archived 12/29/20).
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Coronavirus Primer, Part 3: Epidemiology

“Pandemic”, the board game, was inspired by SARS. Now life imitates the art that imitated life. 1

About This Primer

I am researching and writing this series to take a big-picture look at COVID-19.  I’m taking a step back from the daily news information overload and fact-checking the (even larger) load of misinformation.  I announced this project in June and invited questions from my friends.  Part 1 covered the basics of viruses and coronaviruses.  Part 2 dealt with SARS-CoV-2 on the level of individual health. 

In today’s installment, I start out with a discussion of COVID-19 data: how it is collected and what it can and cannot tell us.  In section II, I discuss efforts to pin numbers on the virus to summarize this outbreak or compare it to others.  Section III recaps the history of this pandemic and human responses to it in the first several months.

I. Data

II. Viral Vitals

III. Medical Impact And Response

IV. Citations

I. Data

A. Where the Data Comes from

B. Sources of Uncertainty

A. Where the Data Comes from

As you can imagine, no single agency could count every case, illness, or death.  It’s a grassroots reporting effort.  When you get your nose swabbed, your sample is sent to a lab for processing.  Hospitals have labs as well as doctors who make personal diagnoses.  Labs and hospitals report to local governments, which report to state or national governments.  In the United States, the CDC issues reporting guidelines about who must report data, what they must report, and to whom. 2

Finally, national totals are reported to the World Health Organization for a global count.  The most commonly reported vital statistics are the daily SARS-CoV-2-positive test results (“cases”), hospitalizations, hospitalizations requiring intensive care, and deaths.  Private websites such as Johns Hopkins gather the data published by local and national governments.  The data in most media articles will be drawn from a major consolidated database such as the COVID Tracking Project. 

I have always felt partial to Worldometer.  This website honed its census skills estimating real-time populations. 1 3 Worldometer reports daily coronavirus figures for all US states and many counties, each nation, and the world.  It explains its methodology to account for a lag in the reporting system. 4 Local counts are the most complete and current, so Worldometer relies on local data to supplement national information as much as possible.    

B. Sources of Uncertainty

We could not possibly expect a decentralized, worldwide tabulation in a time of crisis to be 100% perfect.  Some tests are more accurate than others.  Cases might get lost or duplicated in the reporting system.  The cases and deaths are usually categorized as “probable” or “confirmed.” 2 Changes or differences in these definitions can lead to disagreements between databases.       

The greatest limitation of official data is that it only applies to reported cases.  Since COVID-19 is mild for most people, and since testing hasn’t kept up with viral contagion, many infections will never enter the reporting system.  Therefore, official records will under-report infections and over-report their death rate.  This is a big topic that will be detailed further below.    

Meanwhile, the death rate tends to be under-reported when we are tracking recent infections.  For cases that are less than a month old, the data will show that they are non-fatal just because these patients haven’t died yet.  While the number of infections continues to rise, a high percentage of cases are new and therefore unresolved.  The most accurate death rates will come from the data of months past.

The point is not to conclude that official figures are useless.  With numerous factors that both overestimate and underestimate reality, we can regard the reported numbers as middle-ground ballpark figures that are as precise as reasonably possible.  Even if absolute figures are murky, they can still be useful for drawing comparisons across times and places.  However, the most accurate information will not be available until the pandemic is over. 

You may see references to an “excess deaths” statistic, which is appealing in its simplicity.  The thought is that if we just count all deaths in 2020 and then subtract the baseline number of deaths in 2019, we will get the magic number of coronavirus-caused deaths.  The excess death measurement was useful at the beginning of the outbreak before people had time to respond to it.  However, this year’s social distancing and recession have affected death rates in so many other ways, such as the impact on accidents, medical practice, and other infectious diseases, that they drown out the impact of COVID-19 deaths.  Excess deaths are no longer informative.

II. Viral Vitals

Reid S. asked, “Please determine the death rate!”

We are all anxious for clear-cut answers about this bug’s vital statistics.  Unfortunately, if you want honest answers, you’re going to get complicated answers.  Virtually every measure of a virus is impacted by human activity.  The numbers vary greatly across time, place, and circumstance.

A. Reproduction Numbers

B. Fatality Ratios

C. Case-Infection Ratios

A. Reproduction Numbers

Some diseases are more contagious than others.  The reproduction number, R, counts how many healthy people an average sick person will infect.  The most disease-specific measure of R occurs at the very onset before people have time to respond to it.  That value is called R0.  The goal of preventive programs is to subdue R below 1 so that infections decrease.  While R is above 1, even slightly, infections will continue to increase exponentially. 

SARS-CoV-2 studies from Europe 5 and China 6 estimate R0 in the range of 2 to 9, most likely 4 to 6.  This is much higher than seasonal flu, a little higher than SARS, and lower than chickenpox or measles.  As of early August, R is estimated at 1.1 globally.  Roughly half of the world’s countries are still above 1.  The US has just reached R = 1, suggesting that this country is nearing its peak number of daily new infections. 7

B. Fatality Ratios

Brad B. asked about the impact of senior centers on death rates. 

Of all reported cases of COVID-19 that have had time to run their course, 5% of them have been fatal as of mid-August. 8 The confirmed case-fatality ratio ranges from 0% in Vietnam (yep) to 15% in the UK!  Singapore and other small countries like Qatar and the U.A.E. have young populations because they have large immigrant work forces.  They are also rich countries with good hospital facilities.  Despite major outbreaks, these countries have kept their death rates below 1%.  The UK is a standout with its 15% case-fatality ratio. 9 The high British rate is largely due to slow and feeble government response to testing, tracing, and imposing public health standards. 10 

By far the two most vulnerable populations are smokers and the elderly.  Nursing homes are ground zero in this pandemic.  With 1% of the US population, nursing homes report almost 25% of COVID-19 cases and 40% of its deaths. 11 Smokers are 14 times as likely as non-smokers to develop critical symptoms. 12 The death rate is higher in men than women.  This pattern probably reflects the fact that most smokers are men.

C. Case-Infection Ratios

Brad B. asked, “What is the estimate of the number of asymptomatic and mild cases?”

Mitzi M-H. asked about the discrepancy between virus swabs and antibody tests

“Silent spreaders” are a big part of the COVID-19 story.  The disease is contagious during an incubation period before symptoms appear.  Many people carry the virus without ever knowing it.  There is a great deal of interest in determining the “true” number of infections, for medical and political reasons alike. 

The best way to detect whether a person has ever been exposed to a virus is with an antibody test.  Although some antibody tests have had highly publicized flaws, there have been more reliable trials, and they yield a similar result.  In April, lab analysis of randomly drawn blood samples estimated that there were about ten times as many infections as confirmed cases. 13 This ratio is variable too, as it depends on the quality and especially the quantity of swab tests.

Meanwhile, mathematical epidemiologists are working with the most reliable data (death toll and the best-measured infection-fatality ratios) and are running SIR algorithms to estimate the true number of infections.  One sophisticated mathematical model in May estimated that infections are about four times more prevalent than reported cases worldwide, with a possible range of 2 – 12. 14

Many people argue that coronavirus is “less deadly than we thought” because of all the previously unreported infections that did not develop into serious cases.  That is true in the sense of a death rate, although it obviously does not reduce the sheer number of deaths.  In fact, the number of COVID-19 deaths is under-reported too, by a factor of up to 2. 15

Put it all together, and what do you get?  I’ve done the math for you; you’re welcome.  For a random person infected with the virus today, the probability of death is probably closer to 1% than 5%.  Whatever that means for your peace of mind is up to you!

The good news is balanced by bad news anyway.  The large pool of untested infections means that for every case that is followed up with quarantine and contact tracing, there are about ten others who go undetected.  This highlights the need for much, much more testing, and not just for sick people. 

By the way, even accounting for the unreported infections, still only about 1% of the human population has the antibody.  We’d need a prevalence of about 80% for herd immunity. 16 Letting the disease play itself out to herd immunity would therefore multiply the death count by 80, to about 50,000,000.  Needless to say, that’s an unacceptable solution. 

III. Medical Impact And Response

A. Devastation by Concentrated Impact

B. Effectiveness of Social Measures

C. What to Look for Next

A. Devastation by Concentrated Impact

Like many social ills – poverty, crime, overpopulation – the impact of COVID-19 is not distributed evenly throughout the world but is spotty.  It has devastating impact on a few localities like dense cities and senior centers.  In those localities, it hits the weakest links in the medical supplies and services chain. 

When WHO declared COVID-19 a global health emergency on January 30, the disease had killed only 200 people.  If those deaths had been spread around the world, nobody would have noticed.  They would have been a drop in the bucket of 5,000,000 normal deaths that month.  But those deaths, as well as 10,000 non-fatal cases, were concentrated around one city.  Wuhan probably could have handled them if they had been spread out over a year.  It was the concentrated impact of 10,000 cases in one city in one month that was so exceptionally stressful.  Wuhan hospitals were so short on beds and ventilators that the government erected a new hospital in two weeks.  Similar stories of overwhelmed resources occurred in Milan, Tehran, and New York City by early March.  Ventilators were the scarcest need.  Not every hospital has them; some countries have only a few. 17 By March, demand was already ten times the global supply. 18 Making new ventilators requires a massive global supply chain; it’s not easy to crank them out. 19 Medical personnel and ICU beds are other resources that got exhausted quickly.    

B. Effectiveness of Social Measures

Brad B. asked if there has been a change in the hospitalization rate.

The early urban hotspots were warnings.  If left to spread out of control, the virus had the potential to strike every city like that eventually.  WHO upgraded the disease to a pandemic on March 11, and governments around the world took measures shortly afterward.  This led to some enlightening experimentation.  Two countries that had exemplary success curbing COVID-19, South Korea and Iceland, did so by immediately implementing rigorous programs of testing, contact tracing, and quarantining.  Iceland finished assembling its coronavirus task force literally hours before the country’s first reported case. 20 Meanwhile, China and Italy each put 60,000,000 people on lockdown.  Italy’s outbreak has been on a steep decline since late March.  China enforced its lockdown more strictly, and its wave was effectively over before Italy’s began.  

Facemasks and social distancing have been effective at slowing the spread everywhere and bringing it under control in half the world.  Masks reduce transmission by up to 50% when used widely. 21 The countries that see masks worn most faithfully, in Asia, have low transmission rates. 22 Without any mitigating behavior, this virus could have infected 7,000,000,000 people and killed 40,000,000 this year. 23 Good job, us!

The number of daily deaths took a significant dip in April despite rising case counts. 24  This can’t be explained away with rates or miscounts, so it seems to reflect genuine improvement in public health.  Maybe defenses got tightened up at nursing homes or the most vulnerable people got more serious about staying home.  Perhaps doctors learned from experience, or hospitalizations got spread out more evenly across geography and time. 

Global data showing the impact of human activity after March 11, when WHO declared COVID-19 a pandemic.  Note how the “Daily New Cases” curve slows down abruptly around March 30, and “Daily Deaths” plummet around April 16.

The biggest problem this year has been lack of preparedness, coordination, and resolve.  That is showcased by the approaches of the United States, United Kingdom, and Sweden.  These are countries that like to flout government orders, 25 and their governments were slow to acceptance anyway.  Now, the US has the world’s largest case load, the UK has the highest death rate, and Sweden has one of the highest reproduction numbers. 

However, very few countries were as prepared as they should have been.  A 2019 study ranked countries on their pandemic preparedness.  Its report card gave a global average of 40%. 26 “Few countries pay for action plans out of national budgets,” the report found.  That explains why everybody had to scramble to legislate aid packages this year.

C. What to Look for Next

1. Africa

2. Reopening

1. Africa

Africa’s fate is one of the greatest unresolved questions.  Although many African nations are woefully unprepared, so far, numbers are low across the continent.  This is correlated to low testing, but the case-fatality ratio is low too.  Africa is the youngest continent, so it could be that its population is truly resilient. 27 Cases are just starting to blow up in a few hotspots like Congo, Djibouti, and South Africa.

2. Reopening

Lockdowns cannot continue forever.  However, when full mobility resumes, this pandemic will start all over again, a “second wave”.  The only way to get the outbreak under control without a vaccine is to continue lockdowns until new cases are reduced to a trickle, then have a testing / tracing / isolation system ready at the starting line when the economy reopens. 28

We face challenges this fall as schools resume, pneumonia season begins, and sectors of the economy simply must reopen out of necessity.  The hope is that we’ll be more prepared this time.  Let’s hear it for second chances.  

Continue to Coronavirus Primer Part 4: Coronavirus and Society    

IV. Citations

  1. Game photo by Padaguan / CC BY-SA (https://creativecommons.org/licenses/by-sa/4.0), https://commons.wikimedia.org/wiki/File:Pandemic_board_game.jpg (accessed and saved 8/17/20).
  2. Staff writer, “How to Report COVID-19 Laboratory Data”, US CDC (2020), https://www.cdc.gov/coronavirus/2019-ncov/lab/reporting-lab-data.html (accessed and saved 7/27/20).
  3. https://www.worldometers.info/watch/world-population/
  4. Staff writer, “Worldometer COVID-19 Data”, Worldometer (2020), https://www.worldometers.info/coronavirus/about/ (accessed, saved, and archived 7/27/20).
  5. Kevin Linka, Mathias Peirlinck, and Ellen Kuhl, “The reproduction number of COVID-19 and its correlation with public health interventions”, medRxiv (submitted 5/01/2020, peer review in progress), https://www.medrxiv.org/content/10.1101/2020.05.01.20088047v3 (accessed and saved 8/03/20).
  6. Steven Sanche et al., “High Contagiousness and Rapid Spread of Severe Acute Respiratory Syndrome Coronavirus 2”, Emerging Infectious Diseases 26(7):1470-1477 (Jul., 2020), https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7323562/ (accessed and saved 8/04/20).
  7. Garegin Papoian et al., “The Covid-19 Accelerometer Dashboard:  World Statistics of Rt (Effective Reproduction Number) (continuously updated), https://covid19-r0.com/ (accessed 8/04/20).
  8. Global Worldometer data as of 8/16/20:  Out of 15.6 million closed cases to date, 777,000 have resulted in death.  
  9. Staff writer, “Mortality Analyses”, Johns Hopkins University (continuously updated), https://coronavirus.jhu.edu/data/mortality (accessed and saved 8/04/20).
  10. Jasmina Panovska-Griffiths, “Coronavirus: five reasons why the UK death toll is so high”, The Conversation (6/10/2020), https://theconversation.com/coronavirus-five-reasons-why-the-uk-death-toll-is-so-high-140005 (accessed and saved 8/03/20).
  11. Jon Kamp and Anna Wilde Mathews, “As U.S. Nursing-Home Deaths Reach 50,000, States Ease Lockdowns”, Wall Street Journal (6/16/2020), https://www.wsj.com/articles/coronavirus-deaths-in-u-s-nursing-long-term-care-facilities-top-50-000-11592306919 (paywall).  Summarized e.g. by Stephanie Soucheray, “Nursing homes might account for 40% of US COVID-19 deaths”, Center for Infectious Disease Research and Policy (6/16/2020),  at https://www.cidrap.umn.edu/news-perspective/2020/06/nursing-homes-might-account-40-us-covid-19-deaths (accessed and saved 8/05/20).
  12. Wei Liu et al., “Analysis of factors associated with disease outcomes in hospitalized patients with 2019 novel coronavirus disease”, Chinese Medical Journal (5/05/2020), https://journals.lww.com/cmj/Fulltext/2020/05050/Analysis_of_factors_associated_with_disease.5.aspx (accessed and saved 8/04/20).
  13. See e.g. staff writer, “Commercial Laboratory Seroprevalence Survey Data”, US CDC (last updated 7/21/2020), https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/commercial-lab-surveys.html (accessed 8/05/20).  A survey of samples from ten US sites found actual infections mostly 6 – 12 times more prevalent than previously reported cases, with an outlier at 24 times. 
  14. Christina Bohk-Ewald, Christian Dudel, and Mikko Myrskyla, “A demographic scaling model for estimating the total number of COVID-19 infections”, medRxiv (5/26/2020), https://www.medrxiv.org/content/10.1101/2020.04.23.20077719v3 (accessed and saved 7/28/20).
  15. Bohk-Ewald, op. cit.
  16. Linka op. cit. at 8 (given more precisely as 78%).
  17. Emma Smith, “These countries have only a Handful of ventilators”, Devex (4/09/2020), https://www.devex.com/news/these-countries-have-only-a-handful-of-ventilators-96970 (accessed and saved 8/05/20).
  18. Jinshan Hong and Dong Lyu, “World Ventilator Demand Now 10 Times What’s Available, Says Maker”, Bloomberg (3/25/2020), https://www.bloomberg.com/news/articles/2020-03-25/world-ventilator-demand-now-10-fold-what-s-available-says-maker (accessed and saved 8/05/20).
  19. Torbjorn Netland, “A better answer to the ventilator shortage as the pandemic rages on”, World Economic Forum (4/03/2020), https://www.weforum.org/agenda/2020/04/covid-19-ventilator-shortage-manufacturing-solution/ (accessed and saved 8/05/20).
  20. Elizabeth Kolbert, “How Iceland Beat the Coronavirus”, The New Yorker (June 8 – 15, 2020), https://www.newyorker.com/magazine/2020/06/08/how-iceland-beat-the-coronavirus (accessed and saved 7/19/20).
  21. Staff writer, “IHME models show second wave of COVID-19 beginning September 15 in US”, Institute for Health Metrics and Evaluation (6/11/2020), http://www.healthdata.org/news-release/ihme-models-show-second-wave-covid-19-beginning-september-15-us (accessed and saved 8/05/20).
  22. Katharina Buchholz, “Asians Still Most Likely to Wear Face Masks Due to COVID-19”, Statista (4/21/2020), https://www.statista.com/chart/21452/share-of-people-wearing-face-masks-per-country-covid-19/ (accessed, saved, and archived 8/17/20).
  23. Patrick G.T. Walker et al., “Report 12 – The global impact of COVID-19 and strategies for mitigation and suppression”, Imperial College London (3/26/2020), https://www.imperial.ac.uk/mrc-global-infectious-disease-analysis/covid-19/report-12-global-impact-covid-19/ (accessed and saved 8/05/20).
  24. Graphs from Worldometer data, https://www.worldometers.info/coronavirus/ (accessed 8/06/20).
  25. Vicky McKeever, “Most Brits just won’t wear face masks – here’s why”, CNBC (7/15/2020), https://www.cnbc.com/2020/07/15/most-brits-just-wont-wear-face-masks-heres-why.html (accessed, saved, and archived 8/17/20).
  26. Michelle Nalabandian et al., Global Health Security Index, Nuclear Threat Initiative (Oct., 2019), https://www.ghsindex.org/ (accessed 8/05/20).
  27. Uwagbale Edward-Ekpu, “The pandemic’s spread across Africa is being tempered by a young population, for now”, Quartz Africa (7/09/2020), https://qz.com/africa/1878885/africas-pandemics-spread-is-being-slowed-by-young-population/ (accessed and saved 8/05/20).
  28. Sanche, op. cit. at 1470.
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Coronavirus Primer, Part 2: SARS-CoV-2, COVID-19, and the Individual

For most of us, 2020 is a year of masks, gloves, temperature checks, and social distancing. 1

I began this three-part series with background information, zooming in from the domain of viruses to  the genus of coronaviruses.  Today’s post specifically introduces this year’s novel coronavirus.  We’ll cover the topics of the virus’s origins and evolution, its effects, person-to-person transmission, and possibilities for a cure.    

I. Biology

II. Medicine

III. Citations

I. Biology

A. Origins

B. Evolution

A. Origins

The current pandemic is the third wave of deadly human coronavirus infections.  The new virus is officially called SARS-CoV-2, and the disease that it causes is COVID-19.  COVID simply stands for COrona VIrus Disease.

This year’s virus is so closely related to the 2002 SARS virus that virologists classify it as a new strain of the same species. 2 SARS-CoV-2 is not a descendant of SARS-CoV but a “cousin” that shares a recent common ancestor.  Though conspiracy theorists will believe what they will, genetic evidence shows with high confidence that the SARS-CoV-2 virus evolved naturally and was not engineered in a lab. 3 

The path of transmission, from bat to intermediate host to human, is uncertain.  The pangolin or “spiky anteater” was an early prime suspect because pangolins carry a coronavirus similar to SARS-CoV-2.  The current human and pangolin coronaviruses turned out to be, again, only cousins. 4 Nevertheless, they are similar enough to raise concerns about pangolins as potential carriers for future outbreaks, especially since the pangolin is a heavily trafficked wild animal.

The earliest confirmed human case of SARS-CoV-2 was reported on November 17 in Hubei Province, China (where Wuhan is located). 5 Interestingly, traces of the virus have been found in samples collected from Europe in December.  One was in Italian wastewater 6 and another in the bodily fluids of a French man who was tested for pneumonia. 7

The first mass outbreak came in late December.  It was traced to the Huanan Seafood Wholesale Market in Wuhan, China.  Because the market sells exotic animals, and because similar markets had been implicated in zoonotic transmission of SARS, people quickly jumped to the conclusion that Huanan Market was the site where the virus made its first jump into humans.  However, we now know that some early cases were not associated with Huanan Market 8 and that none of the animals at that market were infected. 9 It seems that a person who already had the virus brought it to the market, and it spread simply because of the crowded conditions.  The spike in Wuhan hospitalizations started to make headlines right around the first day of the decade.

B. Evolution

Taletha D. asked:  “How many versions are there? How fast did they mutate?  Why might they have mutated?” 

After SARS-CoV-2 infected people, its evolution was then guided by its human cell environment.  The virus has at least two variants, the “G” and “D” varieties.  They differ by only one “letter” in their RNA code, but the G version is much more effective at latching onto human cells. 10 Hence, the virus has been evolving strongly toward the G variety this year, especially in Europe and the United States.  Unfortunately for us, G’s gain is our loss.  The G virus is ten times as transmissible as D.  In other words, a sneeze requires only 10% as many G viruses as D viruses in order to spread equally to people nearby.  This explains why the epidemic is spreading through the US more rapidly than through China.   

Mutations, or genetic changes, happen randomly.  The G and D varieties might even have existed before human infection.  The part that’s not so random now is the evolution, the competition between G and D in human cells.  Since G is so much more effective, it will come to dominate the viral population. 

II. Medicine

A. Effects

B. Transmission

C. The Race for a Cure

A. Effects

Mitzi M-H. asked about the causes of death

Taletha D. asked:  “Why are some people asymptomatic?”

Karen K. asked, “I’m interested in the research on long-term kidney and lung damage.”

Individuals display a tremendous range of responses to SARS-CoV-2 infection.  The typical manifestation is normal flu-like symptoms.  Some patients experience severe symptoms like shortness of breath, low blood oxygen, or moderate pneumonia. The most critical cases involve respiratory failure, shock, or multiorgan system dysfunction, 11 which can of course be fatal.  Some of the damage comes from the virus itself, and some from cytokine storm, the immune system’s overreaction.  On the other extreme, some cases present no symptoms or signs at all. 12 The percentages of these categories are still in flux, and will be discussed further in Part 3.

The spike protein of SARS-CoV-2, like its cousin SARS-CoV, binds to a protein called ACE2.  ACE2 is distributed unevenly in the human body.  It is present in our lungs, heart, blood vessels, kidneys, liver, GI tract, and the lining of the mouth and nose.  Early COVID-19 reports show that damage to the heart, kidneys, and liver are a serious concern in the worst cases. 13 However, ACE2 is more abundant in the lungs, and that’s where the worst impact will be. 14 Even some asymptomatic carriers get lung damage! 15 The lining of the nose is especially rich with ACE2. 16 That explains those highly invasive nose swabs.  The only true long-term data we have is from SARS-CoV.  A small percentage of SARS survivors suffered long-term lung and kidney damage.  Fortunately, most have recovered completely. 17

The severity of symptoms is correlated to the intensity of viral infection as well as underlying medical factors.  Those with the most critical symptoms tend to be those who had pre-existing conditions commonly associated with old age, obesity, and smoking. 3 18 We still don’t know why some people don’t develop symptoms at all.

The long-term immune response is another great unknown.  We know that the human immune system synthesizes antibodies; almost 30 varieties are currently cataloged. 19 We haven’t had enough time to tell how long a SARS-CoV-2-specific antibody will remain in a survivor’s bloodstream.  As a reasonable comparison, SARS survivors maintained SARS-CoV-1 antibodies in their systems for an average of two years, with significant reduction after three years. 20 Preliminary results seem to show that SARS-CoV-2 exhibits a similar pattern. 21 If so, then we might have to rely on annual shots to avoid getting overwhelmed by future outbreaks.

B. Transmission

Julie W. asked if (and why) food really presents lower risk than surfaces.

SARS-CoV-2 is almost entirely transmitted directly from person to person through exhaled airborne water droplets.  Factors that increase transmissibility include the concentration of virus in a sick person’s system, proximity, crowd density, and duration of contact.  The six-foot rule is based on the distance that the largest cough / sneeze droplets will travel.  This distance is also chosen as a reasonable compromise between medical precaution and social necessities.  However, the dynamics of a sneeze are startlingly effective at spreading germs far and wide, especially because “sneeze clouds” tend to rise and get picked up by ventilation systems. 22

The virus usually incubates in a person for a day to a week before onset of symptoms.  Contagion peaks from two days before to two days after the onset of symptoms. 23 Although we hear a lot of debate about asymptomatic spread, the greater concern is in fact presymptomatic spread.  Of course, someone without symptoms doesn’t know whether she’s uninfected, asymptomatic, or presymptomatic until she starts coming down with symptoms, when it is too late to prevent transmission.  After she develops symptoms, she may be contagious for another week, 24 but by that time she knows she’s sick and is more likely to be quarantined.  The recommended two-week quarantine period comes from adding a week of incubation plus one more week of contagion.              

The makeshift face masks that we ordinary people wear out in public are meant to minimize the spread of water droplets from our own mouths.  These masks protect those around us (in case we are presymptomatic).  No, they are not 100% cough-proof, but they are pretty effective at slowing down water droplets 25 and reducing microbial spread. 26 The respirators reserved for medical workers are engineered for nearly complete two-way filtering; they protect doctors and nurses from infected patients.

We are often warned about touching things – surfaces, other people’s hands, or our own faces.  These are secondary precautions against indirect transmission.  The pathway here is that a sick person coughs or sneezes, his viruses land on a surface (which might be his own hand), a healthy person touches that surface and picks up the virus, and then the healthy person touches her face.  The virus doesn’t penetrate skin, but the eyes, mouth, and nose are vulnerable points of entry.  Since viruses don’t last long on surfaces, they don’t spread as readily this way.  That’s why gloves are not mandated nearly as much as face masks and distancing.   

Best-practice signs in Los Angeles, CA, 6/24/20. 27

The virus can remain on some surfaces for up to three days, though not in great numbers. 28 An exposed surface is not a hospitable place for a virus, so the risk is proportional to how often people touch the surface.  It’s a safe bet that many more people have handled the subway pole than your Subway sandwich! 

Since viruses don’t “eat”, food to them is just another surface.  They could theoretically infect bacteria on the food, but that is not a good route for viral proliferation.  It’s not likely that SARS-CoV-2 would find the right receptors in bacteria cells anyway.  There have been no known reports of people catching COVID-19 through food packaging. 29 Although the virus could theoretically live on produce, that has not been demonstrated as a known vector either. 30

C. The Race for a Cure

1. Vaccine

2. Antiviral

3. Symptomatic treatments

4. Cocktails and computer-aided concoctions

1. Vaccine

Over 40 vaccine trials are in progress. 31 Vaccine development, testing, and approval is an arduous process that normally takes a decade.  Testing occurs in three phases, with a larger and more vulnerable cohort in each phase.  Regulatory agencies are now permitting “fast track” approval processes that could theoretically accelerate the SARS-CoV-2 process to as short as 1 – 2 years.  This would be an unprecedented pace. 

The United States’ Operation Warp Speed is a major collaborative vaccine effort between the federal government and private labs.  OWS has selected three top contenders for Phase 3 testing this summer.  All three teams – Moderna 32 , Oxford / AstraZeneca 33 , and Pfizer / BioNTech 34 – have reported encouraging results in their Phase 1 trials. The Oxford vaccine is especially promising because it stimulates T cells, special white blood cells that would last longer than antibodies.

The road ahead is not guaranteed to be smooth and easy.  Some of the leading competitors in this race, including Moderna and Oxford, have never commercialized a vaccine before.  Proper dosages are still unknown.  The sterile plastic vials that contain vaccine doses will be a major bottleneck in distribution. 35 Nevertheless, these firms continue to speak optimistically of vaccine production beginning this year.

2. Antiviral

There are five or ten viable candidates for anti-coronaviral medications.  Most of them were created years ago for other viruses.  Antivirals are known to have strong side effects, so they are usually reserved for the worst cases until they’ve had adequate testing to prove them safe. 

One of the most promising drugs is called remdesivir, by Gilead.  This was a failed candidate for treatment of Ebola.  One trial has shown that it appreciably reduces the recovery time for surviving patients hospitalized with COVID-19. 36 The FDA has now issued Emergency Use Authorization for remdesivir to treat severe cases. 37

Eli Lilly has taken a new approach to an old remedy, the old “antidote from a survivor’s blood” trick.  After drawing antibodies directly from the blood of a COVID-19 survivor, this company formulated them into a medication called LY-CoV555.  It has been effective in the lab, and is currently being tested on human subjects. 38

3. Symptomatic treatments

The worst cases of COVID-19 result in low blood oxygen and inflamed air passageways.  Ventilators, highly invasive and cumbersome machines, have been the last resort in this fight.  Ventilators present numerous problems of their own.  They can infect patients and damage lungs.  Intubating a patient can eject virus-infected bodily fluid into the air, endangering healthcare workers.  It turns out that COVID-19 patients have surprisingly high tolerance for low blood oxygen.  Researchers now recommend simpler devices such as oxygen tanks and even CPAP machines for patients who have low oxygen as long as they’re still breathing comfortably. 39

Dexamethasone, an anti-inflammatory medication, is the first drug proven to save lives of coronavirus patients.  It was already a well-known pharmaceutical before this pandemic.  Encouragingly, it is also inexpensive.  It has now been shown to reduce the death rate of critically ill patients by 20 – 30%. 40 However, it has not been properly vetted for side effects, and is not recommended for mild cases.  Researchers are cautiously optimistic.

Hydroxychloroquine is a 1950s medicine made controversial when touted by President Trump.  It has been effective against malaria and lupus, neither one of which is caused by a virus.  It also has anti-inflammatory benefits for treating arthritis.  It showed early promise at reducing SARS-CoV-2 in petri dishes (though nobody knew why).  Clinical trials in humans have been inconsistent. 41 Hydroxychloroquine actually appears to suppress the initial immune response against SARS-CoV-2 42 , and it can be harmful to vital organs. 43 The FDA and WHO have dropped it from consideration.

4. Cocktails and computer-aided concoctions

Why choose just one?  The strongest remedies could turn out to be hybrids or pharmaceutical “cocktails”, as for AIDS.  Roche and Gilead are conducting a trial to combine remdesivir with an anti-inflammatory; expect Phase 3 results this summer. 44 Carprofen and Celecoxib are anti-inflammatories that also appear to slightly inhibit replication of SARS-CoV-2. 45

The latter two drugs were identified by computerized analysis of pharmaceutical databanks.  A crowdsourcing project is underway to identify, synthesize, and test more super-candidates like these.  The world’s top chemists are submitting their ideas, and new supercomputer lab PostEra is running simulations to see if and how they can be made.  PostEra has pledged to release any winning chemical formulas into the public domain.  When I first read about this, I called it a “global brainstorm.”  PostEra has a better name for it: “COVID Moonshot”. 46

🦠🌒

Continue to Coronavirus Primer Part 3: Epidemiology

III. Citations

  1. U.S. Air Force photo by Tech. Sgt. Anthony Nelson Jr., in the public domain as the creative work of a US federal agency. https://www.kunsan.af.mil/News/Article/2134889/sky-warriors-covid-19-response/, Photo 1
  2. Alexandar E. Gorbalenya, “The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2”, Nature Microbiology 5, 536-544 (3/02/2020), https://www.nature.com/articles/s41564-020-0695-z (accessed and saved 7/23/20).
  3. Kristian G. Andersen et al., “The proximal origin of SARS-CoV-2”, Nature Medicine 26, 450-452 (3/17/2020), https://www.nature.com/articles/s41591-020-0820-9 (accessed and saved 7/03/20).
  4. Kangpeng Xiao et al., “Isolation of SARS-CoV-2-related coronavirus from Malayan pangolins”, Nature (5/07/2020), https://www.nature.com/articles/s41586-020-2313-x (accessed and saved 7/03/20).
  5. Josephine Ma, “Coronavirus: China’s first confirmed Covid-19 case traced back to November 17”, South China Morning Post (3/13/2020), https://www.scmp.com/news/china/society/article/3074991/coronavirus-chinas-first-confirmed-covid-19-case-traced-back (accessed and saved 7/03/20).
  6. Kate Kelland, “Italy sewage study suggests COVID-19 was there in December 2019”, Reuters (6/19/2020), https://www.reuters.com/article/us-health-coronavirus-italy-sewage/italy-sewage-study-suggests-covid-19-was-there-in-december-2019-idUSKBN23Q1J9 (accessed 7/03/20).
  7. “Coronaviruses as early as December?  Diagnosis of French patient shakes up pandemic chronology,”  KHN Morning Briefing (5/06/2020), https://khn.org/morning-breakout/coronavirus-cases-as-early-as-december-diagnosis-of-french-patient-shakes-up-pandemic-chronology/ (accessed 7/03/20).
  8. Xiaonan Zhang et al., “Viral and host factors related to the clinical outcome of COVID-19”, Nature (5/20/2020), https://www.nature.com/articles/s41586-020-2355-0 (accessed and saved 7/03/20).
  9. From a sample of animal tissues at the market by the Chinese CDC and / or Wuhan Institute of Virology.  I have not yet seen the original report, but it was published shortly before 5/26, when the Wall Street Journal reported on it. The Chinese report was vetted by American scientist Colin Carlson, who finds its results credible.  Carlson communicated the report to LiveScience.  See excellent summary at Rafi Letzter, “The coronavirus didn’t really start at that Wuhan ‘wet market’”, LiveScience (5/28/2020), https://www.livescience.com/covid-19-did-not-start-at-wuhan-wet-market.html (accessed 7/03/20).
  10. Lizhou Zhang et al., “The D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases infectivity”, Scripps Research Institute (June, 2020; not sure if it’s peer-reviewed yet), https://www.scripps.edu/news-and-events/press-room/2020/20200611-choe-farzan-sars-cov-2-spike-protein.html (accessed and saved 7/03/20).
  11. WHO-China Joint Mission on Coronavirus Disease 2019 (COVID-19), Report (2/24/2020), p. 12, https://www.who.int/docs/default-source/coronaviruse/who-china-joint-mission-on-covid-19-final-report.pdf (accessed and saved 7/14/20).
  12. Paul Sax, “What We Know – And What We Don’t – About ‘Asymptomatic COVID-19’”, WBUR (6/26/2020), https://www.wbur.org/commonhealth/2020/06/26/asymptomatic-covid-faq-what-we-know (accessed, saved, and archived 7/19/20).
  13. Tamar Lapin, “Coronavirus may Damage your Kidneys, Heart and Liver”, New York Post (4/15/2020), https://nypost.com/2020/04/15/coronavirus-reportedly-damages-patients-kidneys-heart-liver/ (accessed 7/04/20).
  14. Krishna Sriram, Paul Insel, and Rohit Loomba, “What is the ACE2 receptor, how is it connected to the coronavirus and why might it be key to treating COVID-19?  The experts explain”, The Conversation (5/14/2020), https://theconversation.com/what-is-the-ace2-receptor-how-is-it-connected-to-coronavirus-and-why-might-it-be-key-to-treating-covid-19-the-experts-explain-136928 (accessed and saved 6/26/20).
  15. Heng Meng et al., “CT imaging and clinical course of asymptomatic cases with COVID-19 pneumonia at admission in Wuhan, China”, J. Infect. 81(1):e33-39 (4/12/2020), https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7152865/ (accessed and saved 7/04/20).
  16. Waradon Sungnak et al., “SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes”, Nature Medicine 26, 681-687 (4/23/2020), https://www.nature.com/articles/s41591-020-0868-6#Fig1 (accessed and saved 7/14/20).
  17. Staff writer, “Severe Acute Respiratory Syndrome (SARS)”, American Lung Association, https://www.lung.org/lung-health-diseases/lung-disease-lookup/severe-acute-respiratory-syndrome-sars (accessed and saved 7/04/20).
  18. Staff writer, “People with Certain Medical Conditions”, CDC (7/17/2020), https://www.cdc.gov/coronavirus/2019-ncov/need-extra-precautions/people-with-medical-conditions.html (accessed, saved, and archived 7/22/20).
  19. Staff writer, “SARS-CoV-2 Antibodies”, Sino Biological (apparently continuously updated), https://www.sinobiological.com/research/virus/sars-cov-2-antibody (accessed, saved, and archived 7/19/20).
  20. Li-Ping Wu et al., “Duration of Antibody Responses after Severe Acute Respiratory Syndrome”, Emerging Infectious Diseases 13(10):1562-4 (Oct., 2007), https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2851497/ (accessed and saved 7/19/20).
  21. Quan-Xin Long et al., “Clinical and immunological assessment of asymptomatic SARS-CoV-2 infections”, Nature Medicine (6/18/2020), https://www.nature.com/articles/s41591-020-0965-6 (accessed and saved 7/21/20).
  22. Lydia Bourouiba, Eline Dehandschoewercker, and John W. M. Bush, “Violent expiratory events: on coughing and sneezing”, Journal of Fluid Mechanics 745:537-563 (4/25/2014), https://www.cambridge.org/core/journals/journal-of-fluid-mechanics/article/violent-expiratory-events-on-coughing-and-sneezing/475FCFCBD32C7DB6C1E49476DB7A7446 (accessed and saved 7/19/20).
  23. The facts about incubation and contagion are taken from Xi He et al., “Temporal dynamics in viral shedding and transmissibility of COVID-19”, Nature Medicine (4/15/2020), https://www.nature.com/articles/s41591-020-0869-5 (accessed and saved 7/19/20).  See esp. fig. 1c.
  24. Sax, op. cit.
  25. Matthew E. Staymates, “My Stay-at-Home Lab Shows How Face Coverings Can Slow the Spread of Disease”, NIST (6/11/2020), https://www.nist.gov/blogs/taking-measure/my-stay-home-lab-shows-how-face-coverings-can-slow-spread-disease (accessed, saved, and archived 7/19/20).
  26. Rich van Wyk, “Do face masks really slow the spread of COVID-19?” WTHR (7/07/2020), https://www.wthr.com/article/news/investigations/13-investigates/do-face-masks-slow-the-spread-of-covid-19/531-96479b50-7041-4f95-a88c-e33e2355fa37 (accessed and archived 7/19/20).
  27. Photo by Scot Fagerland
  28. Neeltje van Doremalen et al., “Aerosol and Surface Stability of SARS-CoV-2 as Compared with SARS-CoV-1”, New England Journal of Medicine 382:1564-1567 (3/17/2020), https://www.nejm.org/doi/full/10.1056/nejmc2004973 (accessed and saved 7/14/20).
  29. Staff writer, “Food and Coronavirus Disease 2019 (COVID-19)”, Nat’l Center for Immunization and Respiratory Diseases, Div. of Viral Diseases, US CDC (6/25/2020), https://www.cdc.gov/coronavirus/2019-ncov/daily-life-coping/food-and-COVID-19.html (accessed, saved, and archived 7/14/20).
  30. William F. Marshall III, M.D., “Can COVID-19 (coronavirus) spread through food, water, surfaces and pets?” Mayo Clinic (2020), https://www.mayoclinic.org/diseases-conditions/coronavirus/expert-answers/can-coronavirus-spread-food-water/faq-20485479 (accessed, saved, and archived 7/14/20).
  31. The full list is updated at Jeff Craven, “COVID-19 vaccine tracker”, Regulatory Focus (updated regularly since March, 2020), https://www.raps.org/news-and-articles/news-articles/2020/3/covid-19-vaccine-tracker (accessed 7/19/20).  
  32. Lisa A. Jackson et al., “An mRNA Vaccine against SARS-CoV-2 – Preliminary Report”, New England Journal of Medicine (7/14/2020), https://www.nejm.org/doi/full/10.1056/NEJMoa2022483 (accessed and saved 7/20/20).
  33. Pedro M. Folegatti et al., “Safety and immunogenicity of the ChAdOx1 nCoV-19 vaccine against SARS-CoV-2: a preliminary report of a phase ½, single-blind, randomized controlled trial”, The Lancet (7/20/2020), https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)31604-4/fulltext (accessed and saved 7/21/20).
  34. Amy Rose et al., “Pfizer and BioNTech Announce Early Positive Data from an Ongoing Phase ½ study of mRNA-based Vaccine Candidate Against SARS-CoV-2”, Business Wire (7/01/2020), https://www.businesswire.com/news/home/20200701005576/en/ (accessed, saved, and archived 7/20/20).
  35. Ciaran Lawlor et al., “The Timelines and Expectations for COVID-19 Vaccines”, BCG (5/14/2020), https://www.bcg.com/en-us/publications/2020/covid-vaccines-timelines-implications (accessed 7/20/20).
  36. Staff writer, “NIH Clinical Trial Shows Remdesivir Accelerates Recovery from Advanced COVID-19”, NIH-NIAID (4/29/2020), https://www.niaid.nih.gov/news-events/nih-clinical-trial-shows-remdesivir-accelerates-recovery-advanced-covid-19 (accessed, saved, and archived 7/21/20).
  37. Staff writer, “Coronavirus (COVID-19) Update:  FDA Issues Emergency Use Authorization for Potential COVID-19 Treatment”, FDA (5/01/20), https://www.fda.gov/news-events/press-announcements/coronavirus-covid-19-update-fda-issues-emergency-use-authorization-potential-covid-19-treatment (accessed, saved, and archived 7/21/20).
  38. Staff writer, “Lilly Begins World’s First Study of a Potential COVID-19 Antibody Treatment in Humans”, Eli Lilly (6/01/2020), https://investor.lilly.com/news-releases/news-release-details/lilly-begins-worlds-first-study-potential-covid-19-antibody (accessed, saved, and archived 7/21/20).
  39. Ardan M. Dondorp et al., “Respiratory Support in COVID-19 Patients, with a Focus on Resource-Limited Settings”, Am. J. Tropical Medicine & Hygiene 102(6):1191-7 (6/03/2020), https://www.ajtmh.org/content/journals/10.4269/ajtmh.20-0283 (accessed and saved 7/21/20).
  40. Peter Horby et al., “Effect of Dexamethasone in Hospitalized Patients with COVID-19 – Preliminary Report”, medRxiv (6/22/2020), https://www.medrxiv.org/content/10.1101/2020.06.22.20137273v1 (accessed and saved 7/22/20).
  41. Jennifer Tran, “Can Hydroxychloroquine and Chloroquine Be Used to Treat Coronavirus (COVID-19)?” GoodRx (7/08/2020), https://www.goodrx.com/blog/coronavirus-medicine-chloroquine-hydroxychloroquine-as-covid19-treatment/ (accessed, saved, and archived 7/21/20).
  42. Nils Rother et al., “Hydroxychloroquine inhibits trained immunity – implications for COVID-19”, medRXiv (6/09/2020, peer review in progress), https://www.medrxiv.org/content/10.1101/2020.06.08.20122143v1 (accessed and saved 7/21/20).
  43. Staff writer, “FDA cautions against use of hydroxychloroquine or chloroquine for COVID-19 outside of the hospital setting or a clinical trial due to risk of heart rhythm problems”, FDA (7/01/20), https://www.fda.gov/drugs/drug-safety-and-availability/fda-cautions-against-use-hydroxychloroquine-or-chloroquine-covid-19-outside-hospital-setting-or (accessed, saved, and archived 7/21/20).
  44. Nicholas Dunant et al., “Roche initiates phase III clinical trial of Actemra/RoActemra plus remdesivir in hospitalized patients with severe COVID-19 pneumonia”, Roche (5/28/2020), https://www.roche.com/media/releases/med-cor-2020-05-28.htm (saved, accessed, and archived 7/22/20).
  45. Aleix Gimeno et al., “Prediction of Novel Inhibitors of the Main Protease (M-pro) of SARS-CoV-2 through Consensus Docking and Drug Reposition”, Int’l Journal Molecular Sciences 21(11):3793 (5/27/2020), https://www.mdpi.com/1422-0067/21/11/3793 (accessed and saved 7/22/20).
  46. Alpha Lee et al., “COVID Moonshot:  Help Us Fight Coronavirus”, PostEra, https://postera.ai/covid (accessed, saved, and archived 7/22/20).
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Coronavirus Primer, Part 1: Background

Color-enhanced but real image of viruses (green) infecting a human cell (blue) 1
 

I. About This Primer

II. Viruses

III. Coronaviruses

IV. Citations

I. About This Primer

Without a doubt, the biggest story of 2020 is the coronavirus epidemic. 2 By the middle of the year, I, like many others out there, felt overwhelmed in a muddle of fragmented news and science, misinformation, and general confusion.  I announced on Facebook that I wanted to “digest it all” and assemble the best known information into one primer.  “Any questions you’d like me to research?” I asked, and a few friends immediately chimed in with requests.  Hopefully, this will help us understand coronavirus basics from the ground up.  I will begin this primer with the big picture and then gradually zoom in from viruses to coronaviruses to this year’s unwanted pests.  There is far too much ground to cover in one article, so I’m breaking it into multiple parts.  Today’s post is Part 1:  Background.  This article discusses viruses and coronaviruses in general. 

II. Viruses

A. Square One: What is a Virus, Anyway?

B. Infection, Immunity, Inoculation

C. Human Viral Diseases

D. Measuring Epidemics

E. Treatment Options

A. Square One: What is a Virus, Anyway?

Viruses occupy one of the most intriguing positions in the whole grand scheme of things.  They are microbes right at the boundary of life and non-living chemistry.  This makes them primary subjects of interest for scientists studying the origins of life.      

You are made of about 30 trillion cells. 2 We call a cell the smallest unit of life because it performs all the functions that we expect of a living thing.  A cell grows, responds to stimuli, metabolizes, heals, sustains and defends itself, reproduces, and dies.  However, it is not a unitary blob of spittle.  A cell is a complex system with hundreds of interacting parts, with names like macromolecules and organelles.  Most of those parts specialize in just one life function, so by themselves they are not fully alive.  If I could compare a virus to anything else, I’d say it’s like a cell organelle that specializes in reproduction. 

Viruses are like living things in numerous ways.  They are made of the same basic macromolecules as us:  nucleic acids, proteins, lipids, and carbohydrates.  At the core of every virus is a bundle of DNA or RNA comprising a few genes.  Viruses reproduce and evolve / speciate.  Biologists classify them and give them Latinesque scientific names.  Viruses can be “killed” by heat, chemicals, or radiation.             

However, viruses are like lifeless chemicals in that they don’t metabolize, respond, heal, change, or grow.  Nor are they able to protect themselves from the environment.  And although viruses specialize in just one thing – reproduction – they can’t even do that by themselves.  A virus is an absolute parasite.  In order to function, it must inhabit a living cell.  The “life” cycle of a virus is to invade a cell and exploit the cell’s resources to make dozens of copies of itself, which then burst forth to invade other cells.  Viruses infect the cells of all living things, from bacteria to whales.  They kill more life forms, and more humans, than any other force of nature.

B. Infection, Immunity, Inoculation

While some viruses are harmless or even beneficial, most of them cause irreparable or fatal damage to their host cells.  Rapidly reproducing viruses consume a cell completely and then burst out like a battalion of creepy little microscopic robots.  Since they are vulnerable outside of cells, they must pass quickly from dying cell to living cell.  They can pass from one person to another through skin, body fluids, or air currents.

Viral infection involves proteins on the surfaces of viruses and cells.  Proteins have complex three-dimensional shapes like locks and keys.  If a virus has the protein “key” to a cell’s outer “lock”, it will latch on and inject its genes inside.

In a human or animal body, fragments of viruses called antigens react with our white blood cells, aka our immune system.  In lucky cases, the immune system produces a protein called an antibody, a natural defense.  An antibody latches onto the antigen that stimulated it.  Sometimes, the antibody disfigures the virus’s “key” so that the virus can no longer penetrate cells.  Other antibodies “flag” a virus so that white blood cells can easily identify and destroy it.  While a person has an antibody in his blood, he is immune to that virus.  The next time the virus comes along, his antibodies will latch onto the virus’s antigens and slow it down or stop it.  Some antibodies last a lifetime, while others disappear from the bloodstream in a few years.  A vaccine is a human-made, finely tuned dose of antigens – just enough to stimulate an immune response without a full-blown infection.  If enough people in a community become immune to the virus, whether through natural immunity or vaccine inoculation, the virus begins to die out and can even go extinct.             

It’s important to note that viruses evolve quickly.  This is especially true of RNA viruses, which most human viruses are.  When a virus evolves, its proteins can change shape.  That is a headache for us; we are forced to keep reinventing new locks to morphing viral keys.  Occasionally, a virus that infects one animal will evolve to a new form that infects another animal, including humans.  A virus that jumps ship from one species of host to another is called zoonotic.

C. Human Viral Diseases

A viral disease is not quite the same as the virus that causes it.  A disease is the physical manifestation of the virus, its effects on the person.  Sometimes a virus and its disease have different names, as HIV (Human Immunodeficiency Virus) causes AIDS (Acquired Immuno-Deficiency Syndrome).  In other cases, we use a single term, like “Ebola”, to name both the virus and its disease.  There are too many human disease-causing viruses to list here.  Examples include adenoviruses, astroviruses, encephalitis, enteroviruses, hepatitis, herpes, HPV, influenza, measles, meningitis, mumps, noroviruses, parainfluenza, polio, pox, rabies, rhinoviruses (which cause colds), roseola, rotaviruses, rubella, West Nile, Zika, … you get the picture.

D. Measuring Epidemics

Viruses are inherently public health threats.  Human viruses would quickly die out if they did not have lots and lots of people to infect. Viral infections can be quantified in numerous ways. The three most fundamental independent metrics are reproduction number, transmission time, and infection-fatality rate.

Reproduction number is commonly abbreviated as R.  It measures the average number of healthy persons who catch the virus from each infected person.  For example, if each sick person makes four other people sick, then R = 4. 

Transmission time is the average time it takes a virus to spread from one person to another.  I don’t see this factor discussed very often, but it makes a big difference whether a sick person infects others in a matter of hours (like an airborne virus in a mall) or years (like a sexually transmitted virus). 

Finally, the infection-fatality rate is the most morbid statistic of them all: the percentage of infected persons who die.  The number of serious illnesses or hospitalizations may be measured as well; they will be closely correlated to the fatality rate.

Unfortunately, the fundamental metrics above are difficult to measure.  We can’t measure them all in a lab because they are not entirely intrinsic to the virus.  They depend on human activity too.  It’s hard to know how many people are infected when not everyone is tested and / or exhibiting symptoms. We reserve the word “case” for a known infection. That is, if 100 people carry the virus but only 60 of them have been tested and confirmed, then there are 100 infections but only 60 cases. In some epidemics (especially new ones) there can be quite a gap between actual infections and known cases. 

The easiest way to measure the severity of an epidemic is with the number of deaths and / or hospitalizations.  These numbers are documented well.  There will still always be some over-reporting (deaths attributed to the virus that were really due to something else) and under-reporting (deaths due to the virus that weren’t counted).  On a societal level, sheer numbers are more important than rates.  It doesn’t really matter if there are 1,000 infections that are 10% fatal or 10,000 infections that are 1% fatal.  Both scenarios will result in 100 deaths and should be considered equally dangerous.  Of course, if you get infected, you sure will be interested in knowing if you have a 1% or 10% chance of dying!

Taken together, the reproduction number and transmission time determine the doubling time, or the amount of time it takes for the prevalence of infections to double in the population.  The pattern characterized by a constant doubling time is called exponential growth.  In real life, exponential growth never lasts long, because it runs up against limitations like immunity or finite populations.  Doubling time is the metric we hear most on the news, because it is easy to calculate by simply counting cases.  Breaking it down offers slightly more insight, if only theoretically.  When doubling time increases, it demonstrates that each sick person is infecting fewer healthy people and / or she’s doing so more slowly, which are the intended effects of social distancing.

When doubling time slows down (as it always must) the simplest model for epidemic growth is the logistic formula.  This S-shaped curve represents the all-time number of infections “flattening” as it reaches its maximum and stops growing.  The point where the number of daily infections starts to decrease is the point of inflection.  I hear some people using the term “inflection point” as if it means the point where a virus “really takes off”.  That’s the opposite of the correct meaning, and there is no well-defined point of acceleration on the curve.

Real epidemiologists use sophisticated numerical algorithms that model the interactions among Susceptible, Immune, and Recovered people.  These SIR  or compartmentalized models are run on supercomputers.

The logistic curve, unlike exponential growth, models the “flattening” or maxing out that must eventually occur.  The inflection point is where growth starts to slow down; it is shown at (5, 50) on this example. 3

E. Treatment Options

Besides vaccines, there are at least two medical options for some viral infections.

Antiviral drugs kill viruses after infection.  Antiviral pharmacology is recent technology.  It is more sophisticated than vaccinations.  To produce an antiviral medicine, researchers sequence the virus’s RNA and proteins and then engineer molecules to target the virus’s vulnerable points.  This highly advanced research developed in response to the AIDS pandemic. 

Each vaccine or antiviral medication is engineered specifically for one strain of virus.  Though the vaccines for polio and smallpox were “miracle cures” that drove their viruses to extinction, they are useless against other viruses.  Medical labs are experienced and pretty effective at making influenza vaccines.  On the other hand, centuries of effort have still yielded no rhinovirus vaccines.

Because vaccines and antivirals are not always available, hospitals must also rely on symptomatic treatments, which only mitigate the disease without managing the virus.  Some drugs treat symptoms such as inflammation (also known as cytokine storm).  In extreme cases, medical equipment like ventilators assist with breathing while the virus passes.

III. Coronaviruses

A. What Coronaviruses Are

B. The First Two Killer Coronaviruses

A. What Coronaviruses Are

Coronaviruses are classified as the family Coronaviridae in the virus family tree.  They get their name from the “spike” proteins, also known as S proteins, embedded in their fatty envelope.  The spikes look like the corona (crown) of the sun, and they are the killer proteins involved in latching onto host cell membranes. 

Coronaviruses have infected bats and birds for tens or hundreds of millions of years. 4 They are occasionally transmitted to other mammalian species that come into contact with bats.  There are now five genera of coronaviruses.  Two of them, Alphacoronavirus and Betacoronavirus, include species that infect humans.  Today’s living alpha- and beta-coronaviruses descend from a common ancestor four or five millennia ago. 5

Some animal diseases that are now recognized as coronavirus infections came to veterinary attention in the early 20th century.  The viruses themselves were only observed and named in the 1960s.  Since then, the medical community has identified seven coronaviruses that infect humans.  Four of them only cause colds.  The three most recent strains, all beta-coronaviruses that evolved in the 21st century, are much more severe.  There are no known treatments for any of them. 

B. The First Two Killer Coronaviruses

The first alarming coronavirus outbreak was the SARS epidemic of 2002 – ’04.  SARS stands for Severe Acute Respiratory Syndrome. 2 The virus that caused it was named SARS-CoV.  The SARS coronavirus originated in horseshoe bats in southern China. 6 It was then apparently transmitted to intermediary species that were sold in exotic animal markets: the palm civet (a wild cat), the raccoon dog (a wild dog), and / or the ferret badger.  All of these species carried SARS-CoV-like viruses.  The exact pathway from bat to carrier to human has not yet been solved.   

SARS had a high infection-fatality rate, about 10%.  It was easy to detect infected people, though, because almost everybody who caught it broke out into fever and coughs within 2 – 3 days.  The sick were quickly quarantined and questioned about their most recent contacts, who were also isolated.  Local governments also ordered a mass killing of palm civets. 7 Even without a vaccine or anti-viral remedy, the anti-SARS campaign was a complete success.  Only 8,000 people ever caught this disease.  Canada was the only non-Asian country with more than one death.  Curiously, just like COVID-19, SARS barely touched Africa.  The peak of the outbreak lasted just a few months, February – July 2003.  The onset of summer weather slowed it down.  By 2004, SARS-CoV was extinct. 

Living in a world city, Los Angeles, I have long noticed Chinese nationals wearing face masks all the time, and I always wondered why.  It’s the SARS outbreak that got them in the habit, and many have worn masks routinely ever since 2003.  It doesn’t seem so unusual anymore!

The next major coronavirus outbreak was called MERS (Middle East Respiratory Syndrome) because it was concentrated in Saudi Arabia and neighboring countries.  The MERS virus passed from bats to camels in the 1990s and then to people who made close contact with camels in 2012.  This virus had a distinct profile.  MERS had an even higher infection-fatality ratio.  30 – 35% of the patients who caught it died!  Fortunately, it did not easily pass from one person to another.  The MERS virus still exists, but it has only killed 900 people, just a few each year now. 

In 2017, the scientists who traced SARS-CoV to a bat cave in Yunnan Province observed that the viruses were recombining (intermixing) to form myriad new combinations.  Their discussion included this prophetic warning:

“We have also revealed that various SARSr-CoVs … are still circulating among bats in this region.  Thus, the risk of spillover into people and emergence of a disease similar to SARS is possible.” 8

Ben Hu (2017)

Continue to Coronavirus Primer Part 2: SARS-CoV-2, COVID-19, and the Individual

IV. Citations

  1. Photo Credit: C. GoldsmithContent Providers: CDC/ C. Goldsmith, P. Feorino, E. L. Palmer, W. R. McManus / Public domain.  https://commons.wikimedia.org/wiki/File:HIV-budding-Color.jpg (accessed and saved 6/23/20).
  2. Ron Sender, Shai Fuchs, and Ron Milo, “Revised Estimates for the Number of Human and Bacteria Cells in the Body”, PLOS Biology (8/19/2016), https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002533 (accessed 7/06/20).
  3. Logistic curve by Yapparina / CC0, https://commons.wikimedia.org/wiki/File:Logistic_curve,_r%3D1,_K%3D100,_N0%3D1.png (accessed 7/07/20).
  4. Joel O. Wertheim et al., “A Case for the Ancient Origin of Coronaviruses”, Journal of Virology 87(12):7039-45 (June, 2013), https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3676139/ (accessed and saved 6/25/20).
  5. Patrick C.Y. Woo et al., “Discovery of Seven Novel Mammalian and Avian Coronaviruses in the Genus Deltacoronavirus Supports Bat Coronaviruses as the Gene Source of Alphacoronavirus and Betacoronavirus and Avian Coronaviruses as the Gene Source of Gammacoronavirus and Deltacoronavirus”, Journal of Virology 86(7):3995-4008 (Apr., 2012), https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3302495/ (accessed and saved 6/25/20).
  6. Ben Hu et al., “Discovery of a rich gene pool of bat SARS-related coronaviruses provides new insight into the origin of SARS coronavirus”, PLOS Pathogens 13(11):e1006698 (11/30/2017), https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1006698 (accessed and saved 6/25/20).
  7. Jane Parry, “WHO queries culling of civet cats”, BMJ 328(7432):128 (1/17/2004), https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1150312/ (accessed and saved 7/03/20).
  8. Hu (2017), op. cit., “Discussion”, last paragraph.
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“A” is for Agnostic / Atheist

AWESOME

I am an atheist.  I am an agnostic.  I’m an agnostic atheist.  Most people understand these words poorly and like them even less.  I don’t proclaim my irreligious identity very often, but increasingly I feel that I should.  I know that there is nothing wrong with atheism, although public opinion is not on my side.  Perhaps it’s time to stand up and explain why I believe atheism is probably true, why agnosticism is certainly right-minded, and how these twin tenets can even be good for the world.

I. What Are Agnosticism And Atheism?
II. Why Agnosticism?
III. Why Atheism?
IV. But Isn’t It “Bad” To Be Atheist Or Agnostic?
V. Upshot

I. What Are Agnosticism And Atheism?

The words atheism and agnosticism both begin with a-, the Greek prefix meaning “without”.  Each word means “not religious” in its own sense.  When we say that someone is religious, we could be referring to what he believes (God, the supernatural, the afterlife, miracles, etc.) or how he holds that belief (a subjective sense of absolute certainty that is not objectively demonstrable to outsiders, based on faith, emotion, authority, personal conviction, etc.)

A·theism = “A” (Without) + “Theism” (Belief in God / gods).

An atheist does not believe in God or the other supernatural elements that religious people do.  The Evolution of Human Chapter 5 3 will discuss the neurological basis of our inborn belief in gods, spirits, and a supernatural world – probably a side effect of humans’ very strong theory of mind and the power of abstract thought.  Theism is a human instinct, so atheism has always been a minority point of view.  Nevertheless, some strands of atheism can be traced to the dawn of the philosophical age in the -1st millennium.  Modern atheism is an outgrowth of the 18th century European Enlightenment.  This history is traced in TEOH chapters 2 – 4.

A·gnosticism = “A” (Without) + “Gnosticism” (Mystical knowledge).

Thomas Henry Huxley in 1876, around the time he coined the word “agnostic”

Agnosticism refutes the religious way of holding beliefs, whatever those beliefs are.  An agnostic recognizes that belief goes beyond the bounds of knowledge: there are many things I can believe that I can’t really know or prove to others.  Unlike atheism, agnosticism is a relatively new term, a realization of the scientific age.  The word agnostic was coined by Thomas Henry Huxley, a 19th century English scientist and philosopher.  2  He defined it in opposition to religious people who “were quite sure that they had attained a certain ‘gnosis’ – had … successfully solved the problem of existence; while I … had a pretty strong conviction that the problem was insoluble. 1 In his essay Agnosticism, Huxley keenly advised, “Do not pretend that conclusions are certain which are not demonstrated or demonstrable.” 2

Agnosticism might sound obvious in the abstract.  I think we all understand the difference between “I believe it will rain tomorrow” and “I know it will rain tomorrow”.  Many times, our “knowledge” about the rain is proven incorrect and we are forced to recognize that we had a false belief.  But when that concept is applied toward religion, most people find it impossible to apply the same standard.  Religious people are absolutely convinced that their beliefs are true.  In fact, religious / supernatural beliefs are the classic example of unfalsifiable ideas.  Nobody can disprove them!  It’s like always believing that it will rain gold coins – not tomorrow, but “someday”.  Even if it hasn’t rained gold coins for the last 10,000 days, you can always hold on to the belief that it will eventually.  Soon you’ll probably feel emboldened to say you “know” it will rain gold coins someday, because in the end either you’ll be proven right or at least you won’t be proven wrong.

Religious thought predates the age of reason by hundreds of millennia.  It is instinctual, and as such it involves many logical fallacies:

• “If it could be true, then it must be true.” (Aristotle’s classic “confirming the consequent”)
• “If I believe it, then it must be true.” (Gnosticism)
• “If my family or community teaches it, then it must be true.” (Peer pressure)
• “If it is comforting or pleasant to believe, then it must be true.” (Denial)

The agnostic is the party pooper who finally says, “But you don’t really know, do you?”

II. Why Agnosticism?

Maybe there was once a time when a person could spend his entire life in a religious bubble, knowing only one creed for his entire life. That is certainly not possible anymore. I grew up as a Christian, but I was fully aware that my Christian community taught different scriptures from Judaism, Islam, Buddhism, Hindu, and numerous other religions. I had friends and neighbors from different faiths. I couldn’t help but ask, “Which of us is right?”

I ran a thought experiment. What if Earth were visited by an alien who had never seen or heard of any of the world religions? If each religion were to present the alien with its supporting evidence, which one would make him say, “Yes, you’re right – this one is the truth!”? Some of the natural / historic excerpts from scripture could be corroborated (for example, there really was a walled city of Jericho) but the supernatural stories could not. I think the alien would have to call it a stalemate. No religion is convincingly true to people who were not raised within its culture. 3 Religion is a belief, not a truth.

In devising the space alien, of course what I was doing was taking a neutral perspective to remove my biases from the decision-making process. If there is a true religion, it shouldn’t matter what I believe. That is the essence of agnosticism – evaluating evidence objectively at face value, divorced from your own preconceived notions. Changing your mind really doesn’t hurt – don’t be afraid of it!

III. Why Atheism?

“Okay,” a religious person might agree, “My religion is a belief that I can’t prove to you. But I still believe it. You can’t prove my beliefs false either.” In fact, for a few years as a teenager I was an agnostic Christian. Why would someone go further down the path toward atheism and give up on religious belief altogether?

Some people come at atheism from moral or emotional grounds. My path was dispassionate and scientific. I was interested in the epistemology – “How do we know?” No, I can not prove that God doesn’t exist. I just find that (1) the natural world seems to be self-contained and (2) “belief in God” is due more to “belief” than to “God”.

A. The Natural and the Supernatural
B. The Psychology of Religion

III.A. The Natural and the Supernatural

People see themselves reflected in the world around them. When modern humans had the wherewithal to ask where they had come from, the first model they had was themselves. Humans can direct their willpower into making things – tools, clothing, meals, even children. By that reasoning, they probably concluded that we must be here because someone directed his willpower into making us too. When the world works in mysterious ways, we personify it as magic willpower. For most people in most times and places, that “explanation” seemed perfectly adequate.

It’s an incredibly strong instinct, because only in the last few centuries have some people realized that this explanation doesn’t clarify anything at all. A religious person once tried to convince me that we and our world couldn’t have come from a big bang, because “0 + 0 ≠ 1.” “You can’t get something out of nothing,” he said. His conclusion was that we must have been designed by God. He seemed unaware of the paradox that he was trying to resolve one hard question with an even harder one: where did God come from? If it is hard to explain mortals and the material world, it would be even harder to explain super beings in an invisible realm who can make mortals by magic willpower. It’s like saying that 0 + 0 = ∞. So why does God satisfy people as a convincing explanation?

Pre-scientific people only understood a few principles of nature. Beyond that, speculation was useless. Invoking gods was a way of punting the explanation: “We don’t understand how the world works, but there’s someone who does.” People envisioned a dualistic universe: There was the “natural” world that presented itself to our senses, but behind it all were the unknowable spirits of the “supernatural” realm. Renaissance philosophers like Descartes were interested in delineating the boundary between these realms. The popular “Flammarion engraving”, whatever its original intent may have been, is a nice visual metaphor of this perspective.

The essence of the scientific revolution was to show that some “inexplicable” phenomena had natural explanations.  The moon goes around the world because it is falling like a cannonball – it just happens to be too far away to strike Earth.  Fire burns because chemical reactions release heat and light.  Animals reproduce with DNA molecules, which obey chemical laws like other forms of matter.  Every small discovery expanded the natural world just a little more, at the expense of the supernatural.  After centuries of this, there wasn’t much left for the supernatural world to “explain” anymore, and those explanations were feeling like increasingly far-fetched punts.  It started to seem more likely that the entire idea of a “supernatural” realm was a figment of the human imagination.

III.B. The Psychology of Religion

A big part of atheism, then, is the psychology of belief.  We can’t discuss religion without addressing the natural human bias to be religious.  Without intense educational training, people acquire beliefs by becoming emotionally attached to them.  We usually hold a belief either because we want it to be true or because we socially identify ourselves with followers of a particular creed.  Almost without exception, people die with the religion that they were born into.

When pressed for evidence, religious believers justify their faith with three recurring themes:  scripture or tradition (discussed above), emotional conviction, and the perceived witnessing of miracles or answered prayers.  I have asked a few religious people how they “know” that there is a God.  None of them claimed to have seen or heard God, but they commonly described a special experience where, “I got a warm feeling inside.”  Unfortunately, such a subjective feeling inside one person cannot convince another.  We atheists believe that it is strictly in the mind.

Religious persons often speak of prayers that came true or a loved one who survived against the odds.  This is a classic example of filtering evidence.  Many good things happen without prayer, and many horrible things happen despite it.  If we are going to decide if prayer works or miracles are real, we can’t just pick and choose our favorite experiences.  One thing that is easy to test scientifically is the power of prayer, and the collective evidence for it is essentially zero. 3

IV. But Isn’t it “Bad” to be Atheist or Agnostic?

Surveys show that religious people distrust atheists, 4 do not feel “warmly” toward them, 5 and do not vote them into office. 6 Why such virulent anti-atheism?!

Religion has served some extremely important social functions in the last 10,000 years.  It has bound communities, provided the unimpeachable source for kings’ authority, and deterred immoral behavior by fear of punishment.  Organized religion and public morality are easily conflated, having emerged together when people started to live in large settlements.  To confuse matters further, Christianity and Islam became aggressively anti-heretical in the Middle Ages.  The idea persists that “turning away from God” is a terrible offense.

Religious people may distrust atheists because they believe that we are morally unrestrained. 7 If there is no God to punish us, then what’s to stop us from lying, cheating, and stealing, right?  That is a ridiculous stereotype.  Atheists are still subject to state law, and we are all judged by the same reputation networks, which are a whole new force to be reckoned with in the internet age.  More importantly, though, atheists understand that you shouldn’t have to rely on the fires of Hell to justify good behavior.  Morality has its own inherent value.  It came from people’s desire to live together in peace, and it should always be at the core of our legal systems.  You and I both believe in Good.  Maybe we just spell it with a different number of o’s.

Today’s world is pluralistic.  Followers of different religions cannot use doctrine to persuade one another of righteous behavior.  We have to rely on our common humanity to be humane.  This is increasingly urgent, because today’s “cultural divides” are largely religious divides.  Division is the very antithesis of religion’s original function.

Religious and irreligious people alike will be sharing the world for a long time.  It is important for us to understand and respect each other and not try to force each other out.  However, in closing, I am going to make a brutally honest plea to today’s and tomorrow’s youth.

V. Upshot

Yes, religion played an indispensable role in history – but that era has passed.  God was a crucial metaphor, a cosmic parent to fledgling civilizations.  Now it is our turn to grow up and leave home to strike out on our own.  Today’s human activity affects billions of people on a global scale.  When we make public policy decisions about economics, war, education, and health, we can no longer afford to leave things “in the hands of God” or to base our actions on ancient mythology and prophecies.  If we are going to be stewards of the Earth, then we should do so based on an understanding of how the world really works.

So … how will your descendants remember the third millennium?  Will we waste our time fighting about what happens in the next world, or will we unite with the common purpose of making this world the best it can be?

Scot Fagerland
2017 – ‘18

 

  1. Thomas Henry Huxley, “Agnosticism”, Collected Essays, Vol. 5: Science and Christian Tradition (1889), p. 238.  Public domain; available free online e.g. at https://mathcs.clarku.edu/huxley/CE5/Agn.html
  2. T.H. Huxley, “Agnosticism”, ibid p. 246.
  3. “Studies of intercessory prayer”, Wikipedia, https://en.wikipedia.org/wiki/Studies_on_intercessory_prayer (accessed 5/30/2018).
  4. W.M Gervais et al, “Do you believe in atheists?  Distrust is central to anti-atheist prejudice”, J Pers Soc Psychol 2011 Dec; 101(6):1189-206.  https://www.ncbi.nlm.nih.gov/pubmed/22059841 (accessed 5/05/2018).
  5. Michael Lipka, “U.S. evangelical Christians are chilly toward atheists – and the feeling is mutual”, Pew Research Center (7/16/14), www.pewresearch.org/fact-tank/2014/07/16/u-s-evangelical-christians-are-chilly-toward-atheists-and-the-feeling-is-mutual/ (accessed and saved 5/05/2018).
  6. USA Today / Gallup poll, February 9 – 11, 2007.  http://news.gallup.com/poll/26611/some-americans-reluctant-vote-mormon-72yearold-presidential-candidates.aspx (accessed and saved 5/05/2018).
  7. This was the central conclusion of the Gervais study.
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Logic Problems involving others’ minds

black_white_hats

Sometimes to solve a puzzle you must think about what other people are thinking. In fact, the very skill of logic could have served the evolutionary function of outsmarting others.

Many scientists believe that the evolutionary purpose of logical thinking is to outsmart other people.  This Christmas vacation, my family was mulling over a logic puzzle that requires thinking about what other people do or do not know, and what they can or can not figure out based on their knowledge.  I realize that this problem has two forms, easier and harder, but they both involve the same backstory, something like the plot to the opera Turandot:

Prince Peter travels to a nearby kingdom to ask the king for the princess’s hand in marriage.  Unfortunately, two other princes are also there to make the very same request.  The king takes advantage of the competition to marry his daughter off to the smartest prince; he pits them against each other in a battle of wits.  The king seats the princes at a round table and blindfolds them.  “I have five hats,” he tells them.  “Three of them are white, and two are black.  I am placing one hat on each of your heads, and I will hide the other two.”  As he does so, he tells the princes that he will shortly remove their blindfolds.  “The princess will go to the first prince to correctly identify the color of his own hat,” he explains.  “If you guess incorrectly, I will kill you.  If you cheat by looking at your hat directly or in a mirror, I will kill you.  Don’t answer until you have correctly surmised the color of your own hat!”  He then has his assistants remove the blindfolds simultaneously.  The princes look at each other’s hats.  None of them offers an answer for several minutes.  Finally, Prince Peter laughs with delight.  “Of course!” he cheers.  “My hat is _______________ !!”  He and the princess live happily ever after.

The hard version of the question leaves off here, and simply asks, “What color was Peter’s hat, and what colors were the other princes wearing?”  You can try your hand at this question first, and if you’re stumped, peek at the clue in the easier version.

To view the clue, highlight the blank area below this line:

The “easier” (but still hard) version of the question adds, “Prince Peter saw that the other two princes were both wearing white hats.  What color was Peter’s hat?”

In order to arrive at the answer to this question (which I’m not going to post today), we have to give some thought to what the other princes would know / think, and how they would react, if they saw certain colors.  We have to assume that the princes are acting rationally (because of the high price for random guessing) but that the others have either less information or less intelligence than Peter.

____________________________________________________

This problem reminds me of a moment when I was listening to the radio at about age 12.  The DJ announced that he would award a cash prize to the 10th caller.  My first thought was, “If I wait enough time for nine people to call, then I can call and be the tenth.”  But then I realized, “Wait a minute.  Everyone else will be playing by the same strategy!  They are all going to wait and try to be the 10th caller.  Since nobody will even start to call for ten minutes, I’ll wait for 20.”  This turned into an infinite regress: “But wait.  Everybody will think the same thing again, so they will all wait 10 minutes longer, so I should delay longer … on and on to eternity!”  I wondered how this game could possibly be won.  I was flabbergasted when the song ended four minutes later and there was already a winner!  People had rushed to call!  That wouldn’t make any sense unless they hadn’t thought it through — or unless they knew that at least nine other players wouldn’t think it through.  I learned that sometimes to win a game, you have to be irrational or to assume that you are playing against unintelligent or irrational competitors.

__________________________________________________________

Finally, we come to the hardest logic problem I have ever heard.  In this problem, the rules are that each player is infinitely intelligent (but not clairvoyant).  The judge selects two different natural numbers, m and n.  (The natural numbers are the counting numbers:  1, 2, 3, 4, 5, …).  The judge reveals the numbers’ sum (m + n) to Player 1, and he gives their product (mn) to player 2.

“I do not know what the two numbers are,” says Player 1.

“Neither do I,” says Player 2.

“Oh, then I do know what the two numbers are!” says Player 1.

“Then so do I!” says Player 2.

What are the two numbers?

In an ideal world, I won’t have to reveal the answers to these puzzles because someone else will in the comments below.  Is that a rational assumption?  😛

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Why do we have Leap Year?

Why is Leap Year necessary?

Leap Year is necessary because our clocks (based on Earth’s rotation on its own axis) and our calendars (based on Earth’s revolution around the sun) are incommensurate, based on unrelated cycles.  We need to fudge one system or the other every now and then to keep them synchronized.  Leap Year is just the system we have historically adopted.  Actually, even the Leap Year needs tweaks of its own.  This video discusses the first, second, and third order corrections to make clocks and calendars agree as precisely as possible!

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AWESOMEness

When I was thinking about pitching TEOH to publishers, I wrote a book proposal to summarize the book and its target audience.  I brainstormed some of the adjectives I would use to describe the book’s point of view.  The first three that came to mind were “Scientific, Agnostic, and Moderate.”  That gave the acronym SAM.  Pretty bland!  In an early draft of my proposal, I wrote,

The book champions a scientific, agnostic, existential, objective, moderate outlook.

Now I was up to the acronym SAEOM, which was unwieldy and didn’t make any sense.  With a little thought, I realized that I was anagramatically close to AWESOME.  I just needed a W word and another E word.  Then it clicked …

Agnostic + Worldly + Existential +  Scientific + Objective + Moderate + Educated =

awesome

In our world of hype, the AWESOME voice easily gets lost.  Religion is considered to be righteous, and the irreligious are still lumped in with communists and fringe extremists.  News programs love to interview guests at the far left and far right to get opposing strong opinions.  Political parties force politicians into dramatically polarized teams.  Conspiracy theorists, religious fundamentalists, and bitter cynics dominate every online forum.  Nationalism is still a matter of pride, and globalism is viewed with suspicion despite all its clear benefits.

Beliefs, biases, opinions, allegiances, and emotions all have their place.  Yet if your goal is to truly understand the world we live in, you must try to rise above these distractions.  You can’t take sides or get married to preconceived notions.  You have to be agnostic, worldly, existential, scientific, objective, moderate, and educated.

In a series of follow-up posts, I will delve into each of these words and further define what it means to be AWESOME! The plan is for each essay to be about 2,000 words. Altogether, they will form my AWESOME manifesto.

Apply to join the AWESOME Thought Facebook group

A is for Atheist / Agnostic : Posted 6/05/18

W is for Worldly : Posted 4/22/20 (Earth Day)

E is for Existential: Coming next

S is for Scientific / Statistical

O is for Objective

M is for Moderate

E is for Educated

As far as I can tell, the image credit belongs to Yoyo Games.  If you own rights to the image and wish to correct this attribution or remove it from this page, please let me know! 

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