Viral buttknuckles

Slapping Rand Paul around would probably be a satisfying but useless endeavor.  You can’t beat stupid out of someone like him because I think he’s doing it on purpose.  Even if I were given the opportunity to try to calmly and patiently explain the biology behind the inane assertion that Chinese researchers created the COVID-19 coronavirus, it wouldn’t help.  Most congresspeople, regardless of party, were the kinds of college students who were willing to take a C in their required science courses just to get out of them.  Math and Science are poison to them.  Unfortunately for us, math = logic and biological sciences are based on the application of tested principles. There are several majors in college that are the refugia for the illogical and unprincipled, and very often they go into politics. Rand Paul should know better; he’s supposedly a doctor.

The COVID virus was not made by researchers or even modified by them.  This can be easily argued based solely on principles of evolutionary biology. I’ll start with an analogy.

Let’s take the national anthem of Russia.  I’m going to insert a couple of random words into it and step back and say, “There!  I improved it!”  No, let’s be real. I’m going to take the anthem, in Russian, which I do not speak or read.  Then, I’ll take the Cyrillic alphabet, which has some parallels with the English alphabet, and I’m going to add some letters to the anthem.  THEN, I’m going to step back and say, “There!  I improved it!”  Response? Not a chance in hell.  Random changes to an anthem, or a Shakespearean sonnet, or a great work of art does not improve it. Ever.

But viruses aren’t great works of art, you say?  You are so wrong. Nature does not produce perfection because perfection is an illusion. Nature does, however, produce complexity beyond human understanding. As researchers understand and describe genetic and biochemical processes more and more, it’s like listening to someone describe art. That such complexity and efficiency could arise by natural processes is difficult to comprehend.  And viruses are the simplest of productions because they aren’t even alive. And we still don’t understand them.

We’ve been studying the HIV genome for 38 years.  It has 9 genes that we understand pretty well. We’ve studied Influenza A extensively and we know a bit about coronaviruses. But in general, what we know about viral genetics is only from those we’ve studied, and in total it’s pretty bare.  So, we’re still figuring out how they infect, how they integrate into the host genome, how prions are assembled, and so on.  We’re stumbling along.  We know it’s basically mechanical, but absurdly complicated at the same time.

Along comes COVID-19. Nature has produced some 600 known coronaviruses and this is just one and almost certainly from a bat. The idea that we collected this virus and then subjected it to a modification scheme in the lab, even by those devilishly clever Chinese researchers, is absurd.  We barely speak the language.  We are linear thinkers.  We are in a plug-and-play mode in the lab.  But for some reason, buttknuckles like Rand Paul want to argue that we are capable of adding selected letters or words to Shakespeare and improving his sonnets. (Or that we paid the Chinese to beat us to it.)

But it could have been an accident, you say?  That’s even worse!  Adding not selected words, but random words to Shakespeare?  Viola!  A masterpiece made better! DaVinci look out!

And then what? China inoculated bats and sent them out to spread the virus? China allowed researchers to leave the lab and wander through the marketplace with their work clothes on?  The researchers were asymptomatic carriers who then spread the virus when they stopped to grab some produce at the market?  If the virus did escape the lab, it was by infected researchers, not because some clever humans have unlocked the secret code of virulence.

Oh, and if we added selected to words to Shakespeare, what words? As viral geneticists, we only know the meaning of a few words.  If we used those words to modify COVID-19, our fingerprints would be all over the resulting virus.  We would have used genes from other viruses because we have no clue, zero, zip, zilch, how to write a gene for improved viral function.  We would have to borrow one from a different virus and it would be immediately obvious. It would be analogous to my undergraduate students plagiarizing some scientific text, but changing a few words in hopes that I wouldn’t notice. They don’t know the difference between affect and effect, but they think I won’t notice when they use the phrase “transgenerational phenotypic plasticity” correctly and in context.

How can conspiracy theorists think scientists are the most brilliant (and evil) people on the planet, yet also believe that everything they say is just unproven “opinion?”  How do you argue with such a deep-seated lack of appreciation of what science is and the rules it operates by? How do you convince someone who is incapable of forming rational mental constructs that their argument on a subject they know nothing about is shit?  I’m open to suggestions. 


COVID was not a failure of the system; it was an inevitability.

The COVID pandemic was way overdue.  It’s amazing it took this long. That isn’t a reference to COVID specifically, but that COVID and other pandemics are expected and have been expected for many years. And then we got one.  Yay for accurate predictions!

            The COVID pandemic is analogous to wildfires in California (and now the rest of the western states).  The current situation was predicted by Harold Biswell in the 1950s and 60s, and the fire patterns in California were described by Richard Minnich in 1983.  That is, if we put out all of the small fires as they occur, we create the conditions for large fires that we can’t control.  Biswell predicted that dry, windy conditions with high fuel loads would create a situation that was beyond our capacity to control. He died shortly after the first fire to demonstrate his predictions: the Oakland Fire (or Tunnel Fire) of 1991.

            In modern medicine, we have worked assiduously to put out each and every viral and bacterial fire that comes along. We developed numerous vaccines since about 1900 and that stopped a great many diseases and saved countless lives, mostly among children.  We have deployed huge quantities of  many antibiotics since 1945 and ushered in the medical era wherein we can stop almost any pathogen we encounter.

            However, we keep coming across worrying signs that we still don’t really have control and, worse, we really don’t understand viruses and how they interact with a world populated with nearly 8 billion people.  Perhaps the biggest red flag was HIV in 1980.  One of the great outcomes of HIV is that we are now a thousand times more knowledgeable about white blood cells than before HIV.  We understand how the body is reacting to the virus and how the virus is using our own cells against us. We have learned a huge number of amazing things about ourselves. We also haven’t solved HIV or developed a vaccine after 40 years.

            SARS (2002-2003) was another wake-up call. Like HIV, the spread of these new viruses can seem almost instantaneous because an infected individual can travel from one side of the globe to another in a day, can interact with hundreds of people on the way, and may be asymptomatic the entire time.  In contrast to HIV, SARS was highly communicable and we stopped its spread because of remarkably fast actions.  SARS has an Ro of ~1 (capable of producing an epidemic), but COVID-19 may be as high as 6. 

            However, what exactly have we learned from these earlier experiences?  As a culture, I would say next to nothing.  This pandemic has clearly demonstrated that most of us are in disease denial and governments are almost helpless to do anything about that. And a virus with Ro of >1 is very hard to stop and one with asymptomatic spread is essentially impossible to stop.

            Today we have almost 8 billion people living in crowded cities. In America, the urban population is more than 250 million (75%). In China, that number is 900 million; in both India and Europe, it’s 500 million. The WHO estimates almost 4 billion people live in urban and suburban areas.  Why are we surprised at disease outbreaks?

            There are about 90 cities in the world with 5 million or more inhabitants.  All of the factors that govern epidemic spread are met and exceeded in these places.  Large cities have many places for mass gatherings including sports, culture, recreation, marketplaces, and seasonal events. And the cities all have airports that connect them within hours of the entire world.  The potential for superspreader events exists daily.

            International travel is available to almost the entire population of the planet.  We do not screen for disease. We do not have a strict health declaration policy.  We did not require ppe in airports or on planes until COVID. We do not have the capacity for filtering air around individuals on planes.  We do not have the capacity for enforcing personal distance under normal conditions.  We live in a world that pretends disease is the exception, not the rule, and as a consequence have created the perfect conditions for epidemic spread.  And yet, although we know this, we seem to be surprised.

            Individually, prior to COVID, few people sneezed into their elbow, wore face masks, stayed home for a slight fever, paid much attention to a cough.  We worked and played even when we knew we might be fighting off some minor disease.  We were “troopers” and “warriors” and we were complemented for being tough and stoic.  It showed “leadership” and a “can-do attitude.”  And most of us can’t wait to get back to a situation where all of that is true again. 

            The fact that we have not had devastating pandemics within the lifetime of anyone currently living is a testament to medical technology and the watchfulness of government and private entities, such as WHO and the CDC.  Their failure in the case of the COVID pandemic is not a failure of the system, it is an inevitable result of population growth and concentration.  It reflects the human effect on the environment, it reflects how our food is produced, and it is an outcome of the unrelenting pressure we have put on the resource base that supports us.

            And unfortunately, it is also a demonstration of the predictions made by Garrett Hardin in 1968 (The Tragedy of the Commons) about what happens to commonly owned spaces and resources when we fail to enact protections against human selfishness.  Unfortunately, western societies are about to find out the hard way that social restrictions are either going to be a way of life for us going forward… or else, we can continue to ignore natural laws and fall prey to natural selection for stupidity.  The latter choice is the path chosen by anti-vaxxers who live by the highly respected tenet that one should die in defense of one’s philosophy. Even if it’s the philosophy of ignorance.

The Microbiome Owner’s Manual – the last chapter from my new book

34. Epilogue: A World View Based on Quality

French winemakers understand the microbial world. They understand inherent complexity, particularly in the interactions between the grape vines and the land on which they grow. The results of those interactions are the grapes.  French winemakers have given us a word for how the environment shapes the qualities of the grapes: terrior (pronounced ter-war).

Terrior is the influence of the thousands of different elements in the local environment on the organisms growing in that environment. The grapes are the vine’s expression of its genotype living in that environment and the winemaker’s job is to make wines that express the potential of the grapes.

The quality of the wine cannot be manufactured. Winemaking is a slow process of coaxing the terrior out of the grapes and that terrior is expressed in the flavors and aromas of the countryside that became part of the grapes themselves. The grapevines live in that environment; they collaborate with and tolerate all of the plants and animals, they experience the seasons, they cycle with the soils, and the grapes produced each year reflect that life and that journey. With the environment, the grape is the expression of potential; without the environment, the grape is just a fruit.

Our health is also a product of our ecosystem and in much the same way. In a very real sense, our complex omnivore digestive system is our superpower. Because we are omnivores, we can sample nearly everything in the environment. In some ways, nothing is really off limits because the microbiome we carry with us provides the capacity for testing almost every plant for its potential as food. But we at risk of losing that superpower and we must work consciously and assiduously to maintain it. We must collaborate with our microbiome such that we allow it to express its potential relative to our human physiology. This mutualistic relationship is a slow dance, one that must be practiced and studied, and it does not happen overnight.

Terrior carries with it additional nuances. In vineyards, the terrior is derived from the soil type, the microbes in the soil, the slope and exposure of the hillside, and the seasonal changes affecting those factors. The plants, animals, and microbes interact with the soil and produce what ecologists call “legacy effects”. That is, lasting effects of the presence of those organisms even after they are gone. Thus, a soil that is damaged and depleted of microbes cannot provide the same complexity to the grapes as a stable, healthy, diverse soil. In other words, the quality of the grapes produced in a region depends on the health of the other organisms in that region and the vines are not at their best unless the surrounding environment is intact and healthy.

And so it is with the expression of human potential, our “tomato-ness”. Each of us relates to the environment in different ways. Each of us has our own particular microbiome, whether on the skin, in the mouth, or in the colon. Each of us has our personal history and that determines how we react to stress. As a consequence, each of us will react differently as we each experience the same environmental stress. This is important.

The ability to react and the intensity of the reaction is modified by our prior experience. Our makeup, our capacity, is a function of the quality of the environment we have been living in. The more diverse and challenging the environment we have lived in previously, the more capable we are of handling new stressors now. Our external environment has given us that capacity by eliciting it from us. Every challenge we faced and overcame in the past has helped to condition and develop our ability to handle future challenges.

If our environment is impoverished, we will be impoverished. We will be handicapped in our ability to respond or to resist or to bounce back. We will be like greenhouse tomatoes lacking the qualities and characteristics that are inherent in our genetic makeup or in the makeup of our healthy microbiome. We will be like germ-free mice lacking a defense system that is absolutely a natural condition in a healthy being. And it is important to recognize that we depend on the internal ecosystem for our daily health, but also on the external ecosystem for the stimuli that bring out our best and for the flow of information that maintains our internal ecosystem. Our microbiome is nested within us and we are nested within the ecosystem that surrounds us.

We know next to nothing about the details of the interactions between the human body and the microbiome and the infinite number of cascading effects those interactions likely influence. But claiming a lack of knowledge is not an excuse for a lack of action. Nobody has complete knowledge and in the case of the microbiome, nobody has much of anything (despite what they might advertise to the contrary). We don’t understand prebiotics, we don’t understand probiotics, we don’t understand how our chemical world is affecting us internally. And that won’t change much in the near future (despite what you might see in advertisements.). Our ignorance of the specifics matters, but it also doesn’t matter.

If we understand that 30 trillion bacteria with 5 million genes in our internal ecosystem are working on our behalf by helping to maintain a healthy host, and that we can help them by modifying our eating habits and by avoiding unnecessary anti-microbial dangers, then we have some degree of control over our own health.

If we recognize what a healthy external environment looks like, we have some measure of control over our own health. And we can take steps to improve one to improve the other.

Ultimately, given the road we are on with 8 billion people, mass-produced food, and life in megacities, we have little choice unless we are resigning ourselves to a shortened life of poor health. To me, the choice is easy and the changes we can make in our lives are pretty easy too. And it is no more of a chore than shopping with my eyes open and paying attention.

Buy organic, buy natural, buy from local growers, shop the farmer’s market, make food connections, create food co-ops, encourage local restaurants, read the labels, use your money to make change, and use your voice to find other voices. Those who claim that high-quality foods are niche, or too expensive to make, or can’t possibly feed the world, or aren’t better for you are actually the Pollyannas of the world. They truly believe that life is great and all is well. Food is cheap, food is flavorful, and food is good for you. Technology has and will continue to provide the answers. This is not about saying they’re wrong. It’s about recognizing that we are not alone and we have been ignoring our partners.

(This summarizes a number of the main topics from the book which is really about how to understand personal health by understanding the basis of that health: the microbiome and the food we eat that supports it. Please check it out.)