Viruses–an Orientation

One of my readers asked if I would provide a basic orientation to the science of virology, a way of making viruses a little less mysterious than the “unseen enemy” featured on TV and in newspapers. I try to start at the beginning. I see viruses through the lens of the history of science. Seen that way, viruses are a part of story of how we see ourselves in the universe. That sounds ambitious, but bear with me.

The basic unit of life is the cell. People studying nature have seen, described, and studied cells since the mid-1600s, the early days of the light microscope (the optical instrument present in every junior high school science lab). Single-cell creatures, wee-beasties visible with the light microscope, i.e. bacteria, fungi, and protozoa, are nearly everywhere, once one looks. Bacteria, for example, are present on our skin, in our intestinal tracts, in pond water. In the 1600s the light microscope opened up a whole new world of inquiry and insight, much like early telescopes helped open up a new understanding of our place in the cosmos, and the study of fossils and atomic chemistry changed our understanding of time (for most of us). But I digress…

We tend to focus our attention on the wee-beasties that cause diseases in humans (and in our stock animals and crop plants). The single-celled organisms that cause anthrax, cholera, syphilis, malaria, tuberculosis, gonorrhea, leprosy, and african sleeping sickness (among others) were intensely studied in the 19th and early 20th century by researchers like Louis Pasteur, Robert Koch, Theobald Smith, and Walter Reed. All these people strove to find treatments or vaccines to rid humanity of these scourges. The stories of these scientists made news at the time, but today most of us barely recognize their names. Many physicians in “developed” countries like ours have never seen a patient suffering from leprosy, tuberculosis, malaria, or any of the diseases these researchers fought, diseases that had been part of life and literature for much of human history, 

Every disease mentioned above is caused by a single-cell creature that can be seen with the light microscope, but the light microscope, because of the physics of light itself, allows us to see organisms only as small as about 1 micrometer (µm). Contemplate that. Think of a millimeter (mm), the distance between two of the thinnest lines on the metric side of a modern ruler. Within that millimeter there are a thousand micrometers (µm) (aka “microns”). The world messured in micrometers (µm) is the domain of cellular life. For example, one phase of the malarial parasite, the “trophozoite phase”, is 1-2 micrometers (µm) in diameter. On the other end of the micrometer range are some free-living single-cell organisms like certain paramecia and amoebae whose size is between 250 and 750 micrometers (µm), one quarter to three quarters of a millimeter, a size visible to a young, healthy, naked human eye.

Cellular organisms, tiny as they are as members of the micrometer world, are still structurally complex. There is huge variation, but even the simplest bacteria contain genetic material (DNA, deoxyribonucleic acid), lipids (molecules of the material we generally call “fat”), and a variety of proteins. All of these organic molecules are organized in structures that provide cells the means to use chemical energy, energy to function and reproduce themselves, energy almost always ultimately traceable to the sun.

But what of the agents that cause smallpox, chickenpox, measles, mumps, polio or rabies? Scientists knew these disease organisms were smaller than known bacteria by running what now look like fairly simple experiments, but which, at the time, were revolutionary. By the early 1700s the word “virus” (originally “potent juice” in Latin) was applied broadly to any fluid from a diseased person that could infect another person. (At the time such fluid might have contained both viruses and bacteria.) In 1892 a Russian biologist, Dmitri Ivanovsky, used a filter developed by French scientists to filter out all the cells and bacteria from a fluid that could pass mosaic disease between tobacco plants. He went on to demonstrate that the remaining fluid was still infective. The filter removed everything which could be seen with the light microscope, the only tool then available at the time. 

A few researchers used the term “virus” to designate only the infective agent that passed through the filter, but through the first half of the 20th century the word was in common circulation to mean any infective fluid. (See P.S. below)

A new tool was needed before we could understand what the infective agent in this filtered fluid looked like. The first images of viral particles were made using early versions of the electron microscope in the 1930s. They were images of tobacco mosaic virus (TMV), the infective agent causing the mosaic disease mentioned above. A whole new sub-light-microscopic world opened up, a world measured in units of nanometers (nm), thousandths of a micrometer (µm). (Remember that micrometers, thousandths of millimeters, are used to measure the world of single cells, including bacteria.) Images of TMV particles obtained with the electron microscope show cylinders 300 nm in length and only 18 nm in diameter. Viruses are no longer “unseen.” SARS-CoV-2 particles are spheres measuring between 50 and 200 nanometers, i.e. a twentieth to a fifth of a micrometer. (The mammalian cells they infect and destroy range between 10 and 100 micrometers, 50-200 times the diameter of the virus.) 

In contrast to bacteria, which contain their own metabolic machinery, a virus is basically a protein and (sometimes) a lipid-encased blueprint for its own replication. (Coronavirus blueprints are encased in a lipid bilayer, think “fat”, hence their sensitivity to soap and alcohol.) Viral blueprints can be either RNA (ribonucleic acid) or DNA (deoxyribonucleic acid). (Coronaviruses are “RNA viruses.”) The details of the viral proteins that accompany the viral blueprint in a viral particle are essential for gaining access to the cells the viruses infect. Once inside the cell membrane or cell wall of the victim cell, the viral RNA (or viral DNA) hijacks the machinery of the cell to make countless copies of itself, weakening or destroying the infected cell in the process. (Netflix has a great verbal and visual explanation of this process, Coronavirus, Explained, you might find worth watching.)

I hope you find this as interesting to read as I have found it to review. For me, knowing some of the history of the scientific endeavor helps me understand how we know what we think we know (epistemology). It takes away some of the mystery with which some people seem to view science in general. Science is firmly rooted in observation and experimentation in the natural world. It consists of ideas that are testable and accretive. Understanding the basics upon which modern science rests is proof against those who see fit to make dangerous pronouncements based in deplorable ignorance as in a recent infamous example.

I give credit for this presentation to my parents and a long line of teachers, professors, and authors and to the volunteer editors of Wikipedia, front which much of what I present here was gleaned and suitably checked and cross-checked through its references.

Keep to the high ground,

P.S. What a word means changes over time. In doing the research for this article I wondered if the use of the word virus is different now from what it was when Paul de Kruif wrote the original Microbe Hunters in 1926, the book that engaged my mind with medical science as a youth. Sure enough. The original text of the book is available here. Searching the text for “virus” using CMD-F yields forty-three instances of the use of the word “virus” in de Kruif’s book. The very first use of the term–for the contagious material that causes cholera (a bacterium)–means that de Kruif used the word virus in the broad sense, i.e. any infective material, not just the nanometer-sized particles we label viruses today. No wonder I was confused in my youth. (Contemplate for a moment what this means for the interpretation of ancient texts that have gone through multiple translations…)

P.P.S. Among the many millions of viruses that co-inhabit our planet are a whole class of viruses called bacteriophages that infect bacteria. Think of that. Some bacteria that make us ill have their own viruses that infect them.

P.P.P.S. Note on Viruses and Atoms: The next “zone” smaller than nanometers (nm) are picometers (pm), one thousandth of a nanometer. This is the realm of atoms and parts of atoms. A typical atom is in the range of 100 picometers = one tenth of a nanometer. Think of the 18 nm diameter of the tobacco mosaic virus. Strung out along that 18 nm diameter line you might put roughly 180 atoms. In a 100 pm cross-sectional layer of that 18 nm diameter cylinder you might sandwich in 8085 atoms. (Think area of circle = π times r squared.It follows that in the entire 300 nm long cylinder of the tobacco mosaic virus you might fit around 8085 atoms/layer X 3000 .1nm thick layers = about 97 million atoms. Check my work. My math skills are rusty 🙂

Covid-19 Stories from the Front

I come to writing this today from an peculiar place. I am profoundly angry at our nominal “leader” and profoundly ashamed of the stain he puts on our country. Our “leader” is a man who finds it appropriate to claim that his rambling delivery of “disinfectant” and “strong light” Corvid-19 treatment options was merely sarcasm. I imagine his intent was to bait the press, sarcasm cynically delivered with a straight face to a suffering country. We are left to choose between crippling ignorance and mean-spirited inhumanity. I encourage you to read Heather Cox Richardson as she dissects this event.

From that angry place I read a series of medical articles that appeared over the last few days. I offer them to you sequentially. They all come from places where the pandemic is in full rage. I hope we avoid these scenes, but if we do not, understanding them a little better will serve us well. This in not the flu.

The first is an opinion piece entitled “The Infection That’s Silently Killing Coronavirus Patients; This is what I learned during 10 days of treating Covid pneumonia at Bellevue Hospital.” that appeared in the New York Times. The title does not do the contents proper justice.

This was my take-away: Covid pneumonia somehow selectively impairs the lung’s ability to transfer oxygen to the blood while, relatively speaking, it does not so much impair the ability of the lung to blow off carbon dioxide. Key concept: at the altitudes at which most of us live what drives us to take a breath is the build up of CO2, not lack of oxygen. What Dr. Levitan is suggesting is that many Covid-19 patients don’t know they are getting short of oxygen (decrease in “O2 saturation”) until they are really in trouble, until their brains start to malfunction and they are about to lose consciousness. (For more, see the P.S. below) It may be good insurance to order a pulse oximeter, a device to measure the oxygen saturation of the blood in your nail beds in the event of illness.

The second article, entitled Why Some People Get Sicker Than Others appeared in The Atlantic. It discusses the interaction of our immune systems with this new threat. After all, the outcome of the sometimes mortal battle with this viral intruder depends on how our immune systems react. I do not think this article offers an action item. Rather, it offers some insight into what some of us might face. 

Finally, 32 Days on a Ventilator: One Covid Patient’s Fight to Breathe Again that appeared in the Sunday NYTimes, left me in tears. I know this hospital. I trained next door. I am familiar with each of the treatments described. Some of the devices used in this cases are not widely available, nor is the expertise with which to reasonably apply them. I know the lengths to which the physicians and staff who practice at this hospital may go in pursuit of a cure. I’ve been there. I have watched. This story hit home with me.

And, finally, the very thought that some callous supporters of the current President might label me a “snowflake” for shedding tears as read this account, that thought brings me back to the anger with which I started this piece.

Keep to the high ground,

P.S. The physiology recounted in the first article reminds me of stories I’ve heard of swimmers who drown (or nearly drown) competing to swim the furthest under water. Typically, one intentionally hyperventilates before diving in. That hyperventilation blows off more CO2 from the system than what the CO2 level is asking for. That removes the drive to breathe, the sense of air hunger, that would otherwise (as a secondary effect) keep one from using up the oxygen stored in the blood and lungs. In this hypocarbic, hyperventilated state swimming under water the first sign that you’re in trouble may be that you black out for lack of oxygen—and drown. My mother, probably not understanding the why of this phenomenon, warned me about hyperventilation. Her story very much impressed me, but I didn’t understand the physiology until many years later.]

Covid-19–It Gets Real

We humans are story-tellers and story-learners. It is one thing to read about numbers of Covid-19 cases and deaths; it is something different to hear the story of a fellow Spokanite. A friend of a friend of mine had been feeling crummy for a couple of weeks. She obtained one of original tests for Covid-19. A week and a half later It came back negative –certainly not a “rapid” test–or very useful one from the standpoint of case management. The crummies persisted, spurring a second test–and that second test came back positive. She is still convalescing. Another contact, a funeral director in his fifties described his test positive case of Covid-19 as feeling the worst he has ever felt for seventeen days straight, constantly wondering if he would die. A few weeks later he reports being back to “about 85%” of normal. This is not the flu, no matter what they say on Fox. 

We hear a lot about the need for testing. Early on, tests for Covid-19 took more than a week to come back. Such a tests may help for gathering statistics, but it is nearly useless for identifying people who need to be quarantined because they’re shedding virus. 

Abbott Laboratories announced FDA approval of its new ID NOW COVID-19 testing device March 27. The device tests one sample at a time. It requires about five minutes to detect the virus and offers a negative result in fifteen minutes. The devices shipped to laboratories, but only with very limited available test kits (in spite of the unrealistic Presidential hype). Last Wednesday, April 22, a hitch appeared. Testing by the Cleveland Clinic revealed that ID NOW COVID-19 accurately reports negative results if the nasal swab goes directly from the nose into the machine, but if the sample is placed in a “viral transport medium” (the typical method of getting a sample to a lab, even a lab just down the street), the test produces about 15% false negatives, offering false reassurance safety. 

Of course, at one critical place there is no lack of test kits–and swabs go directly from the nose into the machine. Visitors to the White House have been screened with that Abbott Laboratories’ rapid test since early April. With this level of testing Mr. Trump can safely declare that “wearing a mask is optional” and the he won’t wear one. When you function in a protected bubble it costs you nothing to recommend that others expose themselves.

Speaking from his bubble, Mr. Trump feels free to exhort his followers to go out and make a display of their patriotic bravery (irony alert), threatening Democratic governors and grabbing media attention with demands for the “liberty” to gather and ignore public health recommendations. 

Closer to home, Stacey Cowles, in an Editorial in the Spokesman on April 19, argued for the urgency of re-opening of Spokane’s economy. He, somewhat breezily, cited a Spokesman article to indicate “good progress” in testing availability. 

Let’s examine that. According to the article, rapid testing would be available in Spokane through Providence Express Care starting last Friday, April 16. That was great news, but the fine print told a more nuanced story: a “pilot program will target health care workers, first responders and high-risk patients who can access rapid testing by referral and appointment only.”

There is a disconnect between these scenarios.

In Trump’s virus-free bubble, everyone who sees him, asymptomatic or not, has been proven minutes earlier to be free of viral shedding. Presumably, if the same person visits again in a week, that person will again be tested before coming into his presence. 

In Spokane, where Mr. Cowles is arguing to start opening up for business, there is zero chance (as an asymptomatic person-on-the-street) of my obtaining a rapid test for SARS-CoV-2 before I go out to a re-opened factory, restaurant, or shop. It offers me no reassurance that the guy next to me at the gym isn’t spewing virus after protesting with Heather Scott last weekend or attending a church gathering. 

No matter how much Mr. Trump, the talking heads on Fox News, and Mr. Cowles want the economy to re-open, the reality is that we still lack anything close to the testing (and contact-tracing ability) to make it safe to do so. Letting up on social distancing now in anything but a very careful and measured way will guarantee a body count that will make the flu look tame.

Keep to the high ground,

Liberty v. Virus, Liberty for Me, Virus for You

Their credo: My liberty is more valuable than the lives of others.

The title in the April 16 Spokesman read: “Idaho Rep. Heather Scott calls governor ‘Little Hitler,’ compares nonessential workers to Holocaust victims.” The previous day eastern Washington’s very own legislative pariah, Rep. Matt Shea (LD4, Spokane Valley north to Mt. Spokane), was the lead subject of another article: “Far-right politicians denounce government’s COVID-19 response in Washington, Idaho” (Both articles are free to read on the internet as part of the Spokesman’s Covid-19 coverage.)

In times of national crisis we have a history of pulling together for the common good. When the threat is clear, people pitch in and help. During the time of threat they may grumble about personal hardship and perceived injustices, but intelligent people understand the threat, unite, and deal with it. Ask your parents or grandparents (or if you’re over 80, just think back) about the federally mandated rationing of gasoline and many food items during World War II

We cut our leaders some slack in dealing with an immediate threat (at least insofar as their leadership is reasonable and skillful). Not allowed to go fishing? Hmmm. I can comply with that for a while as things get adjusted. I don’t like it and I don’t quite see the logic to it, but I won’t squawk for now. It is patriotic and humane to have some patience.

Times such as these show the baseline stuff of which people are made, especially people in public office, and for some of them, like Shea and Scott, their stuff does not show well.

We must pay attention. These are their true colors. Elections are coming. 

Matt Shea and Heather Scott value their “liberty” to do as they wish, they value it over the lives of others.  Here’s where they’re coming from: “Government regulation of where I go and what I do is UNCONSTITUTIONAL under all circumstances! You say gatherings where one asymptomatic person might spread virus to a hundred others? No problem! On April 25 in Franklin Park (across from the Northtown Mall in Spokane) at 1:30PM we’ll hold a Liberty or Death Rally for our candidate for Washington State governor, Loren Culp(current Police Chief of Republic, WA)! We’ll carry our AR-15s and demonstrate our claim to the liberty to threaten your life by aiding the spread of virus!” (If you have the stomach for it, I recommend a visit to these folks’ common website, Redoubt News, to sample the crazy trash they put on display.)

So where does liberty stop and the common good start in a lethal pandemic? When does it become immoral, plainly disgusting?  A friend put it this way: “This is like the careless pickup driver whose boards fly out of the back of his truck killing you as they fly through your windshield. But HE ignorantly drives on with no idea that his carelessness has caused multiple causalities in the multi-car pileup behind him.”

Elections are coming. We need to pay close attention and get ready to remove people like Shea and Scott from elected office. We’ll have closer looks at upcoming races in later emails.

And what is our cretinous divider-in-chief doing by way of crisis management? Instead of leading and uniting, organizing and managing the response to the threat, Donald Trump is tweeting out encouragement to these crazies, “LIBERATE VIRGINIA, and save your great 2nd Amendment. It is under siege!” “LIBERATE MINNESOTA” and “LIBERATE MICHIGAN” soon followed, all states with Democratic Governors that might be in play in the November election. Take note Mr. Trump did NOT tweet out support for protesters in Idaho or Washington, with similarly restrictive policies and Republican and Democratic governors, respectively. Tellingly, neither Idaho nor Washington is likely to be a swing state in November.

Governor Jay Inslee’s (WA) said Trump’s LIBERATE tweets were “unhinged.”  Inslee’s response to upcoming protests in Olympia could not have been better put (understand as you read Inslee’s words that the population of Washington State is about 7,000,000):

Inslee said they [the protesters] were “welcome to express their First Amendment rights to say what they want to say.

“I do encourage them to socially distance when they do that, try to maintain 6 feet apart. … We care about your safety as well,” he said. “But I will say, if a thousand people show up this weekend, that would mean there would be 6,999,000 Washingtonians that care enough about their families to pitch in a little bit to try to prevent our loved ones from dying.”

Keep to the high ground,

P.S. Doug Muder in his “The Weekly Sift” this week was particularly eloquent about: 

1) The Liberate protestors and identity politics:  Off the Table and 

2) Trump’s transparent gambit to take no responsibility for a bad outcome while position to take credit for any improvement: Trump’s Guidelines Aren’t What He Says They Are

Look Over There! (Not Here)

The conspiracy theorists and blame shifters are hard at work at the highest levels of our government, and the rest of the Republican Party is falling into line. On Friday, April 17, the Spokesman shared an Associated Press article entitled, “Trump, aides float outlier theory on origins of coronavirus.” This quote stood out:

“More and more, we’re hearing the story,” Trump says. Secretary of State Mike Pompeo adds, “The mere fact that we don’t know the answers – that China hasn’t shared the answers – I think is very, very telling.”

“More and more we’re hearing the story.” No surprise there. Over the last few weeks especially, the cesspools of conspiracy theory on Fox News, The Epoch Times, and a host of less widely known sources on the net have churned out stories suggesting the Chinese are systematically hiding important facts about coronavirus. The common theme is distrust.

It has been interesting–and unsettling–to watch the right wing media build-up to Trump “hearing the story.” About two weeks ago a Limbaugh-devotee of my acquaintance emailed me an article that accused the Chinese of vastly under-reporting their number of dead from COVID-19. The evidence? Rapidly spreading hearsay around photographs and reports of large numbers of funerary urns shipped to the Wuhan region and rumbling accusations that the Chinese Communist Party was hiding from their own people the truth about of the numbers of dead from Corvid-19. Googling “Wuhan crematorium” yields a huge news bubble led by one article posted in “Radio Free Asia” published March 27. Note that Radio Free Asia is a U.S. government funded non-profit, “anti-communist” outlet. This RFA article planted the initial seed of distrust. 

Is all this hearsay backed up by fact? Burning thousands of bodies might produce measurable changes in air pollution, for example, an increase in sulphur dioxide emissions. Showing a spike in SO2 would a key fact. In a brilliant demonstration of the adage that a lie can make it halfway around the world before the truth gets it shoes on, such a confirmation first appeared as a satellite photo on Twitter on February 9. It was re-tweeted more than 12,000 times and was covered by uncritical media the world over, thoroughly embedding distrust in the minds of millions of readers. The trouble is that the striking satellite photo displayed showed no such thing. NASA, the National Aeronautics and Space Administration, to which the SO2 data was attributed, denies that it even makes such fine-grained measurements. The whole sad story of this mis-information can be reviewed here at AFP Fact Check

That the Chinese cannot be trusted is a powerful message for the news consumer, especially with a leading nationalist and xenophobe at the helm of government. The story, it’s origin and veracity unquestioned, was amplified in social media and (mostly) right wing conventional media outlets like Fox.

Then someone noticed the Wuhan Institute of Virology is located in, well–Wuhan–and that researchers there are studying (among other things) coronaviruses in wild animals, including bats (a prominent reservoir of coronaviruses, for reasons of bat physiology). The conspiracy theorists keep it in the news. For a detailed analysis read “Inside the Viral Spread of a Coronavirus Origin Theory” 

Clearly, something was up when my media feed produced this headline from Fox on April 16: “Sources believe coronavirus outbreak originated in Wuhan lab as part of China’s efforts to compete with US.” The same day a Fox banner floated through my media feed reading something like, “Attorney General William Barr demands China ‘come clean’ on coronavirus” and Trump said he would defund the World Health Organization (WHO)–in the midst of a worldwide pandemic.

“More and more we’re hearing the story,” Trump says. Our conspiracy theorist-in-chief, a man unable to understand the threat of exponential spread of Covid-19 for weeks, but an avid listener to listener to the wisdom of Fox, is “hearing the story.”

“Look over there, get excited about my defunding WHO, but, whatever you do, take your eyes off my ignorance and incompetence in the face of this pandemic. I will dominate the news!”

Then there are Cathy McMorris Rodgers (WA-CD5) and Sen. Jim Rich (ID) climbing on board last Thursday in agreement with Trump that WHO must be investigated. They must be “More and more hearing the story,” too. 

Keep to the high ground,

P.S. For me, this quote of the last two paragraphs of the extensive Vanity Fair article on this conspiracy theory points up the clearest reasoning on the original of SARS-CoV-2 I’ve found:

Bill Hanage, associate professor at the Harvard T.H. Chan School of Public Health’s Center for Communicable Disease Dynamics, doesn’t buy it at all. Given the highly elusive nature of SARS-CoV-2, and how we are learning that it causes a lot of minimally symptomatic infections alongside the serious ones that crash health care systems, he said, it strains credulity to imagine that anybody would have extracted it from a bat and actually been able to realize what they were dealing with to the point that it would warrant serious study in a lab for dangerous diseases. It’s also hard for Hanage to believe that any researchers who might have been studying the virus would have understood what it was capable of—in other words, he said, it’s more logical to believe that the new coronavirus was never in a lab in the first place.

“If the first case of this had been anywhere at all in the world, somebody would have found something suspicious nearby,” he said. “If it were in Boston, it would be the National Emerging Infectious Diseases Laboratories. If there is evidence to really support this theory beyond the coincidence of the location of the lab, then I haven’t seen it, and I don’t make decisions on the basis of coincidence.” Hanage’s scientific opinion? “I would probably leave it in the conspiracy theory area.”

Trump and his Science Problem

On Friday, January 31, Mr. Trump announced a policy of restricted entry for travelers coming from China, mistakenly satisfied that Covid-19 could be bottled up there.  From early January a growing chorus of advisors tried to get his attention without success. That story is told in an exhaustive analysis of White House bungling: “He Could Have Seen What Was Coming: Behind Trump’s Failure on the Virus.” I recommend it. It will be a must read for later historians. 

The email below is from Dr. Robert Kadlec, a member of the White House coronavirus task force and an expert in biodefense, to a research scientist asking about the truth of an article in the Journal of the American Medical Association published on February 21. Dr. Kadlec accurately recognizes that if the article is true, then “we have a huge whole [sic] on our screening and quarantine effort.” She replied ““People are carrying the virus everywhere.” It would be three more weeks before Mr. Trump absorbed the message and announced “social distancing”–for fifteen days–starting on March 16.

Now Trump wants to rewrite the history of his own actions. He wants vindication based on his January 31st travel restriction. He deserves no such credit. His travel restriction fit his simplistic belief in walls as solutions–and completely denies what his advisors knew and were trying desperately to make him hear. By January 31st, the date of his travel restrictions, Covid-19 had already jumped the barriers, with more than 100 cases in twenty countries. 

Trump’s denial of scientific consensus is, of course, widely known from his declaration that climate science is a “Chinese hoax.” Self-characterized as a “stable genius” with “absolute power,” his ignorant denial of the best available science is costing lives. 

So how effective were Trump’s travel restrictions in the face of a virus known to spread from asymptomatic carriers? Researchers in the field of genetics have an answer: Most of the virus that sickened and killed thousands in New York arrived in New York in the month of February from Europe. SARS-CoV-2, easily masquerading as the flu, was quietly spreading, likely killing the occasional patient as it masqueraded as seasonal influenza. After all, Mr. Trump reassured us it was “under control,” while Fox talking heads (see P.S.) reassured Trump and the country that Covid-19 was “just the flu.” Meanwhile, community doctors were flying blind in flu season with inadequate access to timely testing that could have helped them recognize the early stages of the pandemic.

Scientists have well-understood technology available to rapidly “sequence” genetic material, whether DNA (as in mammals) or RNA (as in SARS-CoV-2 and many other viruses). The same technology is fundamental to “23 and Me” and “” and to all the “cold” murder and rape cases recently solved by DNA detectives using genetic sequencing and databases.

SARS-CoV-2’s genetic material is a single strand of RNA (ribonucleic acid) consisting of a string of about 30,000 “bases,” the organic molecules guanineuraciladenine, and cytosine (denoted by the letters G, U, A, and C).  That string of bases (the order of appearance of them being the “sequence”) is the blueprint the virus uses to direct the cellular machinery of the host’s cells to make millions of copies of itself. Like all RNA and DNA, random mutations occur in the viral genetic material at some background rate, i.e. a G, U, A, or C molecule is replaced by the wrong base–or is dropped out–or a base is incorrectly inserted as the genetic material is copied. Important to note: only rarely do these mutations cause any change in how the virus works. However, each mutation is passed on to all the subsequent viral copies in the endless chain of viral multiplication and transmission to new victims. Each mutation serves as a marker of lineage of the virus as it infects the next host.

This is standard modern day biological and evolutionary science. The exact sequence of the G, U, A, and C molecules in the RNA strand of the original SARS-CoV-2 was worked out with stunning speed. On January 10, 2020 the sequence of five genomes of SARS-CoV-2 samples was already published by Chinese and Australian collaborators. The results were posted on line. Researchers the world over went to work on more sequencing and related research. The study of virus samples from New York City linked below built on this worldwide collaboration to construct a genetic lineage of SARS-CoV-2 for NYC. 

The results are stunning. The majority of the 84 viral genomes the researchers sequenced came from multiple introductions of virus through Europe, introduced virus that had been circulating undetected in the New York area since mid-February. While Trump was denying the threat of Covid-19, congratulating himself over how his restrictions on travel from China were keeping the virus “under control,” SARS-CoV-2 was already smoldering in his home town, having come in through the back door with travelers carrying the virus from Europe.

Now Mr. Trump and his Fox surrogates are trying to re-write history. He is flailing about, casting blame on the Chinese and the World Health Organization for his own failure listen to his own advisors, learn, and act. He wants us to believe his early leadership was perfect, that he fully understood the problem from the beginning and that he took the appropriate and proper action early on. The record tells the opposite. 

On the bright side: While Trump was keeping to his xenophobic, science-denialist mindset, scientists around the world were (and are) engaged in a spectacular example of information sharing and cooperation that should, by simple example, put Trump to the shame he deserves.

You can read the NYTimes Science article here: 

or the raw pre-publication science article on which the NYTimes article was based, “Introductions and early spread of SARS-CoV-2 in the New York City area,” here:

Keep to the high ground,

P.S. If you have not yet watched “Heroes of the Pandumbic” click and watch it now. It is a great antidote to Mr. Trump’s and Fox’s efforts to re-write history. (Sadly, if your youtube ads are like mine you will also be forced to watch at least of few seconds of an irritating and ubiquitous ad for  “The Epoch Times” with details of mis-information it contains, all sponsored by a lavish ad budget from the Falun Gong in support of Donald Trump.]

Science, Exercise, and Covid-19

The main purpose of science is to predict the future, based on what is already known. In the context of the Corvid-19 pandemic, the predictions requested of scientists may be narrow or broad. “Will I catch Covid-19 from someone I’m running or biking with in the open air?” is an example of a narrow question. “How many will die of Covid-19 if we do ______?” is a very broad question. 

The answer to the narrow question of the risk of contracting Covid-19 while exercising is remarkably tricky–and tricky is frustrating for humans. By our very nature, humans want answers that are certain. It is this quest for certainty and simplicity that gives rise to reasonable, simple recommendations like the  specified six foot spacing of “social distancing.” 

The best answers scientists can provide are subject to modification based on new data. In the early stages of the Corvid-19 pandemic in the United States, wearing a mask was not thought necessary as long as six foot spacing was maintained. That prediction, based, I believe, on ideas about droplet spread in normal conversation, was dashed by the unintentional and unfortunate experiment conducted by the Skagit Valley Chorale in March [See Airborne Spread], where 45 of 60 participants fell ill with Corvid-19 and two died in the weeks following a 2.5 hour choir practice, a choir practice in which members someone nervously complied with hand-washing and social distancing recommendations then in effect. In no small part due to this new data, the recommendation changed from no mask necessary to, “Wear a mask!” [even as our  White House resident declared, like a rebellious child, that he wouldn’t wear a mask and that compliance was “voluntary”–never mind that the White House now uses a rapid test that screens all visitors for Covid-19, a test unavailable to the general public]. 

The CDC recommendations around masks changed in response to new evidence. That’s how science should work. 

So can I catch Covid-19 when exercising without a face mask with proper distancing, especially if I’m outside? The answer, as is usual in science, is, “Maybe.” There are some reasonable ways to be more careful.

First, understand that we have no documented evidence of Covid-19 spread from one exerciser to another. That would be hard to detect and document, after all. One hopes there is no Skagit Chorale-like experiment unwittingly performed among runners and bikers. However, without such an awful experiment (the infamous Tuskegee Airmen experiment comes to mind), quite a lot is known about the basic physics of droplets and aerosols, coughing, sneezing, and breathing that can be hypothetically applied to the question of disease spread. 

I’ll give you the punchline first, but if you want to understand the scientific basis for the recommendation read on.


On the basis of these results the scientist advises that for walking the distance of people moving in the same direction in 1 line should be at least 4–5 meter, for running and slow biking it should be 10 meters and for hard biking at least 20 meters.

The quote is from an article that appeared in (a very good, but not always, reliable source–read their disclaimer) “Belgian-Dutch Study: Why in times of COVID-19 you should not walk/run/bike close to each other.” Please check it out. The illustrations are impressive and memorable. The other impressive thing about the article is the science upon which it was based,
Towards aerodynamically equivalent COVID19 1.5 m social distancing for walking and running.” If you want a window on the kind of understanding of physics upon which this recommendation is based, click and have a look. 

So are these recommendations hard and fast, fully “ready for primetime”? Of course not, like all science, the hypothesis that one could catch Corvid-19 from biking too close behind an infected but asymptomatic biker is subject to further investigation. Even so the hypothesis, the prediction, is reasonably presented and bolstered by the underlying knowledge base. 

As with all scientific hypotheses many questions remain. Is the dosage of virus particles suggests might be delivered sufficient to transmit disease? What is the actual risk number? Has anyone actually caught the virus in this way under real world circumstances? Answers to these questions may never be known, but in the meantime, I’m going to be a little more careful when I’m exercising in the open air.

Keep to the high ground,

P.S. The CDC “Recent Studies” section under the new face mask recommendations all concern disease spread from asymptomatic carriers documented in peer-reviewed medical literature. They do not list a reference to the Skagit Chorale cluster. As far as I know a formal epidemiological study of that incident has not been done or published, except for fairly detailed and compelling coverage in the mainstream media.