Mad Science, Sane Science

Alas, I smart from wounds that my own darts have made.
—Ovid

Ancient science was attractively harmless: It saw human beings as inseparable from nature, and tried to describe the web within which we dwell. Nature was looked up to with the respect one accords the divine. Nature—as the ancients understood it—was seen as a whole, likened to a vast living organism, meaning something alive and organized. Nature had a purpose. Nature, they believed, could be understood—was intelligible—because it was seen as a kosmos, meaning “order,” or “good order,” or “an orderly arrangement” and, for the Greeks, anything orderly was seen, as in some way, partaking of intelligence.

This kind of intelligence, called nous, was not merely the highest human faculty, but also a transcendent principle manifest throughout the cosmos. It was because the human microcosm mirrored that macrocosm that we had the capacity to understand, and resonate with intelligible nature in awe and amazement. This was knowledge for its own sake, a dignified form of contemplation of a cosmic order that inspired the questing feeling that, according to Socrates, underlies the fundamental philosophic attitude: Wonder.

But modern science sees knowledge as power—and science as a means to other, greater, more useful and more practical ends. Since its origins, modern science has emphasized that “nature” is harsh, and often rallies against us, and so, following Francis Bacon (1561-1626), has come to see itself as a method of mastering nature, “for the relief of man’s estate.” Henceforth, “utility” was science’s purpose, not wisdom, and nature was there not to be contemplated, but conquered. To become our servant, like a dumb animal, to be “harnessed”—a Baconian term we still use. Nature’s purpose—if there ever was one—no longer mattered; what mattered was our needs, and what we needed first and foremost was to dominate nature.

Thus, Bacon weaponized the wonder that drove ancient philosophy, and spoke of using the new science to extend “the empire of humanity” over “the universe.” He was to science what Machiavelli —to whom he explicitly said he was beholden—was to politics: He discarded the ancient approach to nature, which took as the primary question of study, how we might understand it better, to live, “the good life,” in accord with nature, and replaced it with the study of the science as a means to acquire power, to master nature. In a philosophical dialogue Bacon had an advocate say, “I am come in very truth leading you to Nature with all her children, to bind her to your service and make her your slave.”

Even if they had aspired to conquer nature, the ancients had, to use Bacon’s term, too few “instruments” (to measure and make things) and thus produced few “works” to bring it off. We, followers of Bacon, now blur “instruments” and “works” together in our word technology. Bacon argued that to succeed, science and technology must henceforth always go hand in hand, and would need to replace the individual investigator, with new institutions, filled with armies of scientists. It was he who first articulated the STEM mindset.

If conquering and enslaving nature sounds like the saber-rattling ravings of a mad man, consider that Bacon actually did so change the West’s mental set, that we actually have, through science, acquired, and become able to unleash, awesome powers. What did he understand that the ancients did not, which allowed this to happen?

For starters, Bacon pointed out, correctly, that while many of nature’s patterns and activities—such as the paths of the stars across the sky, or the habits of animals—were, as the ancients claimed, evident to us though unaided observation, there were also hidden chains of causes and laws that were not. Nature had “secrets,” and to take charge of nature we needed to first understand these secrets. To do so, we needed tools, to “penetrate” (his word) nature. This would be done, as he famously proposed, through something quite new, the scientific experiment. The experiment, he said, would “find a way at length into her inner chambers.” Aristotle, he reminded us, had left “nature herself untouched and inviolate.” The new experimental techniques, or arts, that Bacon envisaged would not, like older sciences, “merely exert a gentle guidance over nature’s course, they have the power to conquer and subdue her, to shake her to her foundations.” These experimental “trials” (his term, still in use today), would be like “inquisitions,” to extract the truth from nature, as an inquisitor would confessions and admissions from an unforthcoming witness at a trial, who had something to hide. Bacon had worked in the Star Chamber; and he was a lawyer, and courtroom metaphors abounded.

It is not trivial that even the sexual metaphors he employed were of using power to violate, and depicted a very rough kind of sex, indeed, akin to rape. Bacon apprehended that to bring about his project, he needed to break a taboo, and aimed to redirect human instincts, and actually encourage a lust to defile nature, because our reverence for it, going back to the Greeks, and the view of it as God’s creation in the Torah, and traditional societies’ depiction of Mother Nature as deserving the adoration accorded a mother, were serious impediments that subverted his goal: to take charge of it, and conquer it.

Bacon’s books may have had scholarly titles, like The Advancement of Learning (1605), but their goal was anything but disinterested scholarship, and his military metaphor, and science reconceived as the conquest of nature, took hold, and is so with us today, that we don’t give it a second thought and often take it literally.

One cannot underestimate the extent to which modern medicine took up Bacon’s military metaphor of conquest and applied it to itself. This involved rejecting the ancient Hippocratic idea of healing, which—being part of that Greek worldview that saw us as of nature, and not against it—saw the physician as trying to work in alliance with nature, the patient (mind and body and spirit) and the patient’s family. But by the mid-1600s Thomas Sydenham, who became known as the “English Hippocrates,” saw medicine in a new way: “I attack the enemy within by means of cathartics and refrigerants, and by means of a diet”; he wrote, “a murderous array of disease has to be fought against, and the battle is not a battle for the sluggard …” Little has changed since. We see ourselves as engaged in endless wars: “The war against the virus,” “the war against cancer,” or against AIDS, “the war on drugs,” the “battle against heart disease,” we “combat” Alzheimer’s, and so on. As modern physicians came to see themselves as warriors and disease as “the enemy,” treatments became “weapons,” and drugs went from being healing potions to “magic bullets” and vaccines became “shots.” We combat the enemy with “doctor’s orders,” from the medical “armamentarium,” or “arsenal” as we physicians call our bag of therapeutic tricks.

This military metaphor in medicine gives rise to a mentality that esteems invasive high-tech treatments as somehow more serious than less invasive ones—any collateral damage be damned. Of course, there is a time for a martial attitude in medicine, as, say, in emergencies: If a blood vessel in the brain bursts, the patient needs invasive surgery and a neurosurgeon with nerves of steel, to operate. But there are times when it sets us back. Today, rather than work with the patient as a key ally, we physicians often barely have time to listen to him or her speak. In this metaphor, the patient’s body is less an ally than the battlefield, and the patient is rendered passive, a helpless bystander, as he watches the confrontation that will determine his fate between the two great antagonists, the doctor (plus the scientific research establishment) and the disease (or pathogen). And of course, in the “war against the virus,” it is total “eradication” of such an enemy that is the goal. That, it would seem to us, Bacon’s offspring, as the only sensible approach.

As it turns out, so much of what ails us today are products of modern science and technology gone wild: lethal antibiotic-resistant organisms that our “total eradication of disease mentality” produced because we vastly overused the antibiotics we had (which, by the way, were originally natural products of nature, not the lab); pollution (of every element), chemicals in our baby food, toys, floors, and mattresses causing skyrocketing childhood illnesses; bioterrorism; loss of biodiversity affecting the food chain; fabulous totalitarian surveillance tools called cellphones, global networks that allow our enemies thousands of miles away to reach into the controls of our electrical grids, water systems, food delivery systems, banks, nuclear systems, computers, and control them, turning them on and off with a keystroke; 3D printers to make assault weapons in the basement, nuclear weapons to empower lunatics, industrialized death camps with cyanide showers, and, not to mention man-made environmental disruptions causing ecological catastrophes.

On this list of course, is also a pandemic that spread so rapidly because of air travel, and the “efficient” design of our urban centers which maximize overcrowding—and a microbe that may have originated in a lab known to be unsafe, and experimenting with bat viruses. “Just last year,” an article in Newsweek reported, “the National Institute for Allergy and Infectious Diseases, the organization led by Dr. Fauci, funded scientists at the Wuhan Institute of Virology and other institutions for work on gain-of-function research on bat coronaviruses.”

“Gain-of-function research” in this case means augmenting the virus’s contagiousness, and even lethality for the purpose of getting a head start on developing therapeutics or vaccines should it mutate in that direction. Such research is also the meat and potatoes germ-warfare research.

In 2011, two researcher groups announced they were working on the avian flu virus, which has a 60% mortality rate but which is not, thankfully, very transmissible because it can’t be passed on through the air. They decided to see if they could change that—and ultimately did.

Many esteemed scientists argued this “transmission enhancement” of a lethal virus could trigger a pandemic, and so in 2014 the research was put under a moratorium by the United States. After all, SARS-CoV-1 had leaked several times from Chinese labs, and there have been hundreds of dangerous leakages from American labs too, including anthrax in 2014.

In 2017, that moratorium on GOF research was reviewed, in secret, and then quietly lifted by the NIH, in part because Drs. Fauci, and Frances Collins, head of the NIH, did not want the funding to end. It’s not that modern science doesn’t produce some scientists who urge caution. It’s just that it also creates an appetite, and a climate of opinion, in which those who counsel restraint and moderation (another ancient, but not a modern virtue), just about always lose eventually.

Newsweek reported that in 2015 the Wuhan lab GOF research with SARS-CoV-1: “They took a piece of the original SARS virus and inserted a snippet from a SARS-like bat corona virus, resulting in a virus that is capable of infecting human cells.” By 2016, they were working with a virus that was 96.2% similar to SARS-CoV-2. More and more scientists are now speaking out, arguing that a variety of reasons make the assertion the current SARS-CoV-2 virus may have been a product of GOF modification at that Wuhan lab a credible one. Whether or not Wuhan’s gain-of-function work involved creating an artificially enhanced coronavirus has been made almost impossible for outsiders to ascertain, because that lab’s government conveniently insisted it destroy its virus samples and records before an outside investigation could be done.

Gain-of-function research is just one example of the tendency of modern science to relish taking bold action before understanding the complex systems in which those actions are undertaken. It’s one of many such tamperings: putting human genes into monkeys to make their brains bigger; releasing genetically modified mosquitoes into the Florida wild which, when they mate with the females of the species (which carry Dengue fever), cause all the females to die. Or putting the growth genes of other species into salmon so they will grow faster and bigger, and bring more profits, or modifying pig genes, so pigs don’t get a particular disease. Sometimes, nothing happens, that we yet know of; sometimes, as when farmers began feeding cows the brains of dead cows (not their natural feed), a new malady, mad cow disease arises, then jumps to humans—giving us the deadly Alzheimer’s-like brain disorder (which, incidentally, killed a relative of mine). The “conquest of nature” approach argues if science causes problems, they’re nothing that a little more science won’t fix. It’s an attitude not far from Mark Zuckerberg’s “move fast and break things” ideology—an attitude which doesn’t so much show a lack of wisdom (which involves cultivating foresight), but is rather, opposed to the very idea of wisdom and foresight, because they slow conquest.

We are so reliably surprised and caught off guard by the unforeseen consequences of our technologies, and there are now so many serious cases of “science going wrong,” that it might be argued that, in practice, modern science (and the tech it produces) seems to be a machine designed to generate and maximize unintended consequences. And is hence, along with being powerful, also, quite often, ridiculous.

But we persist. Why? Nature—especially as we have reconceived it—can be so terrifying to us that we are willing to overlook the Chernobyls and other horrific byproducts of this struggle if what we get in return is control. The conquest of nature is a big idea. Arguably mankind’s most ambitious and reassuring idea—the idea that “Science,” or “Man” or “Humanity,” in the abstract, might have the power to control this monster. But, as scholar-physician Leon Kass pointed out, if we look at the actual individual human beings who wield this power, and how little they are, we are quickly brought to our senses.

At one point Bacon argued we would need an elite of the most educated minds—philosophical scientists—to make sure that science was used for good, and not ill. For all Bacon’s genius and depth, this is rather shallow, and embarrassingly un-Machiavellian, like the kind of solution our university administrators might come up with: First we teach our students to split the atom, then we give them a multiple-choice test in ethics. Indeed, Bacon never showed how his scientific “elite” would outwit the despotic types or regimes that would seize their work to amplify their power. He even wrote there was good reason to believe that scientists might very easily become quite mercenary, as nothing about science bound them to any particular regime. He proceeded as though developing a science that would unleash massive power was the hard problem, and that reigning in those who might abuse it, was a separate, lesser problem, the might be solved later.

But it never has been. The first we conquer nature, then we conquer human nature approach isn’t working out, and it is not just despots getting hold of that power that is the problem. It is what this utopian fantasy does to our own judgment. Science starts by giving us good things, and we extrapolate wildly from this, to the belief we can conquer nature—which itself whets the appetite of our grandiosity. Instead of reining in desire, intellectual hubris, impulsivity, greed, and our denial of death—as wisdom might—it inflames them. And that is the profound theme of almost every science fiction “fantasy” novel ever written—how modern scientific utopias, always go too far, all end up, by necessity, as dystopias. Science fiction of this sort is not escapist fantasy, but the opposite: A cautionary tale, a resurgence of ancient wisdom that sees in modern science itself something dangerously escapist, out of touch with human reality, incapable of moderating itself, and drunk on power. There is something inherently rash in science as conquest.

All of this is relevant to the current pandemic. In a way, there are three grand “strategies” to deal with a pandemic. But only one of them indulges the more lunatic strains of military metaphor in medicine.

• The first strategy is never let it in.
• The second, the approach most widely used at present, is to go to rather blunt lockdowns, while we develop therapeutics and vaccines to eradicate the virus.
• The third is to resist lockdowns whenever possible, and instead focus on more differentiated measures than total societal closures, again while we develop therapeutics and vaccines to eradicate the virus.

If the virus doesn’t get in, people are not dying, there isn’t talk of eradication and the military metaphor isn’t used. That strategy has worked so far in Nauru, an island speck, in the paradise of Oceania, a country that is isolated, and small enough to walk across and around in one day, and which, along with Oceania’s Tuvalu, is tied for the record as being the least visited country in the world.

Even the relatively isolated, double-island paradise of New Zealand, was still too connected with the rest of the world to keep the virus out. When it did arrive there, New Zealand tried the second strategy, to eradicate it with a blunt lockdown.

The military metaphors began. Prime Minister Jacinda Ardern set the goal of “complete elimination of the virus.” France’s President Emmanuel Macron said, “We are at war … The enemy is there—invisible, elusive—and it is advancing.” Donald Trump described himself as “a wartime president.” War requires emergency measures, which require emergency powers, which demand the immediate suspension of civil liberties—with executives not bothering to go to legislatures because the enemy is coming at us “in waves,” and “surges,” is “killing us in droves.” We “hunker in our bunkers”—in total lockdown. Home’s the only place that’s safe. We must “mobilize” all society in immobility. Punish those who disobey orders. We do it, too, for the health care workers, the heroes on “the frontline,” who risked their lives. But these undeniable similarities do not mean that medicine is war, any more that war is healing.

Perhaps the biggest problem with the military metaphor, is how it causes us to narrow our focus almost exclusively on “eradicating the virus,” and “cases of the infected.” This causes us to miss other important ways of dealing with it, that might help us survive it. Public health officials in the “the eradication mode” almost never mention how we can boost our immune systems with vitamins D and C, and zinc, exercise and weight loss. Not their focus. And the narrow focus on eradicating the virus is now causing serious “collateral” harm and death.

As everyone knows, lockdowns were sold as being required for several weeks originally—to flatten the curve, so that hospitals would not be overloaded. But by April, it was clear governments were now insisting they should be extended indefinitely. “People in countries with stay-at-home orders are understandably frustrated with being confined to their homes for weeks on end,” Tedros Adhanom, the director general of the World Health Organization said. “But the world will not and cannot go back to the way things were. There must be a ‘new normal.’” 

The short-term lockdown that was promised had turned into an ongoing, or recurring one, and multiple examples (especially throughout Europe, a huge contiguous land mass) show that countries that had extreme lockdowns have continued to have some of the worst outbreaks. Indeed, as the Oxford epidemiologist, Dr. Tom Jefferson, and professor Carl Heneghan, the director of Oxford’s Centre for Evidence Based Medicine, write: Lockdowns don’t eliminate the virus, they “kick the can down the road.”

Past a few weeks or months, lockdowns are useful if the time is used to reorganize hospital and health care resources to keep up with admissions, restore bearable conditions to frontline workers, and they can be used to teach, and persuade people how to behave, and use mitigating measures once the lockdown lifts. But at this, public health officials have too often done very poorly for a variety of reasons: in part because these involve privations people resist, in part because the officials so frequently get caught disobeying the rules they proposed often on the very day they proposed them (a psychiatric study in itself), and in part because the skill required to teach and persuade a population to change behavior in complex ways is not one sloganeering politicians and public health officials necessarily have. The latter group is also hampered by the fact so many followed WHO guidance, which early on actually facilitated the virus spreading out of China, admonishing nations not to close off air flights from Wuhan, implying it was xenophobic to do so, at the very moment that the Communist Party of China itself had prohibited flights from Wuhan to other parts of China, knowing the rest of the world would suffer greatly. Many competent, devoted public health officials, and the nations that listened to them, were played for suckers.

But it was not maliciousness but rather the virus eradication mindset that has caused much of the harm. That mindset has led many politicians, and also public health officials, to become oblivious to the death, illness, and devastation that have resulted from the lockdowns. Tedros’ own language speaks this obliviousness, when he says he knows people are “understandably frustrated with being confined to their homes” as though “frustration” is the extent of the problem. What is actually happening is that people’s worlds are collapsing. Fauci early on called the lockdown measure “inconvenient.”

Tedros and other lockdown supporters are almost all themselves employed, and working comfortably, many from home. They are part of a class that has government, bureaucratic, educational, media, and corporate salaries, or are in Big Tech, which thrives in lockdown. With an often staggering indifference, they gloss over that fact that the measures they recommend “for all of us” are devastating to those working-class people, the poor, and small-business owners who are losing or have already lost their life savings, health insurance, health, and who are at risk of, or who have already been evicted from their apartments. By September we knew that nearly 60% of (mostly small) businesses that had been forced to close in lockdown were destroyed so their workers would have no jobs to return to. Many more have gone under since. They were closed by often illegal edicts, that left their large corporate competitors like Costco and Walmart open. Thus, instead of going to small widely separated community stores, that admitted a few at a time, people crowded into a few stores without social distancing—the complete reverse of a sensible, scientifically based policy. How did public health officials get away with destroying small business? This is war! Ignore that a meta-analysis of 10 countries and their regions, shows that during last spring, stringent stay and home and business closures did no better in slowing the virus than those that rely on voluntary measures (such as hand washing, social distancing, discouraging travel and large gatherings, successful case tracking, and testing). Gov. Andrew Cuomo’s own latest scientific statistics confirm that 74% of all New York COVID-19 transmission comes from indoor gatherings in private homes, and only 1.4% from in-restaurant dining (all set up for COVID now). The commander in chief says no to indoor restaurant dining in December. Now, even the WHO, which supported lockdowns, is claiming that closed Western economies are devastating poorer countries that are trading partners, and its special envoy for COVID-19, Dr. David Nabarro, has said the WHO anticipates a doubling of world poverty and a doubling of childhood malnutrition because of lockdowns.

Meanwhile, epidemiologists and others are documenting the massive health consequences of destroying small businesses and the jobs they create, in terms of skyrocketing suicidality, depression (especially in the young: One out of four American teenagers reported being suicidal in June). In some California locations, the number of young people who completed suicide during this lockdown doubled or tripled compared to before the pandemic; opioid and other drug overdoses far exceed COVID deaths, in San Francisco, for instance. Hospitals in a number of countries closed down non-COVID wards, even though they were not close to being overrun—only a bizarrely narrow-minded mindset that restricts itself to “taking aim at the virus” and aims to eradicate it “at all costs,” could possibly explain such lunacy. Stroke evaluations went down 40%, so treatable strokes were missed, heart attacks went undetected and untreated, there were missed cancer diagnoses, 50% of chemotherapy sessions were missed, and there were missed cancer surgeries. Then there is the trauma that extended school closure allows for in terms of ongoing undetected childhood physical and sexual abuse (often picked up by the schools), and also malnutrition, not to mention the loss of a productive year of learning and social growth.

The officials, blinded by the eradication at all costs mentality, discarded the practical wisdom required to respond to such a crisis, and endorsed an intervention that defies the standard public health practice of taking a holistic approach and always taking into account a measure’s total effects, and not just its immediate effects on the pathogen labeled as “the invisible enemy.” “COVID denial” is real. So is “COVID-management-induced-devastation denial.”

The term, in medicine, for the inadvertent harms caused by a medical treatment is “iatrogenic” harm. Because public health exists on a massive scale (compared to individual doctoring), when public health officials make iatrogenic errors, millions suffer. Iatrogenic errors are underestimated for long periods because they are often made with the best of intentions (which is part of the reason they are missed, and repeated), until there is a sudden reckoning. A good rule of thumb is that the more the practitioners are certain of their good intentions (as they define them), the more vigilant we must be about the iatrogenic possibilities. And people in public health are brimming with good intentions.

What does a scientific approach that takes the best of our modern instruments that Bacon helped to facilitate the development of, but which does not get us tangled up in the military metaphor, or make delusional attempts to artificially cut us off from the rest of nature look like?

That would be the approach of Janelle Ayres, Ph.D., a brilliantly original and constructive molecular and systems physiologist, and expert in both immunology and evolution, who heads two labs affiliated with the Salk Institute. Ayres’ work opens up a radically different approach to infectious disease—radical in the original sense of the word, meaning having to do with the root, i.e., the broader biological foundations of infectious disease and health in the “biome,” the sphere of living organisms in which we dwell, and which dwell within us. Thus, to my mind, her work has echoes with some of the ancient insights and intuitions about biological interconnectedness, though I’ve not seen her make this claim.

Ayres’ work is helping us reconceive our relationship to microbial organisms, including pathogens, and showing how they can, for instance, influence our evolution, and we theirs, and it gives us a much more detailed picture of how we actually survive serious infections. She happens to have written one of the best articles ever on COVID-19, that shows a breadth and depth of biological comprehension that is extremely rare among modern scientists who are often specialists in very circumscribed areas, who analyze things into ever smaller parts, and know an incredible amount about incredibly little. Ayres is both a first-rank specialist, and a big-think generalist.

Ayres came from the small, two-highway-exit town of Livermore, California. Both her parents learned English as a second language, and she was the first in her family to attend university, which she did while working full-time to support herself, commuting two and a half hours a day to school, hoping to become a biologist. Already, in her Ph.D. work, she was working on the theme that would become her life’s work, studying not only how organisms develop standard immunological “resistance” to infections, by learning to recognize pathogens, and then attack and kill them, but also, methods of “tolerance of infections,” meaning modes in which an attacked host can adapt to the organism, and thus survive in its presence (of which more below).

She describes her father as the biggest supporter of her intellectual development. In January 2015, he got terribly ill, and needed to have his gall bladder removed—a common, and generally low-risk operation. It went well, but 12 hours after his discharge, he was suddenly unable to walk, and was rushed to hospital, ending up paralyzed in the ICU. He had developed sepsis, a life-threatening condition, in which the body’s response to an infection is so powerful, that it begins damaging many of its own organs. Something along these lines occurs in the most serious cases of COVID-19. Sepsis carries an 80% mortality rate.

When Janelle arrived at the hospital, her father was still alive, and the doctors confirmed that his gall bladder had been infected so long that the bacteria had spread to his bloodstream, infected his vertebrae, and caused his paralysis. His body’s response to his infected blood led to the sepsis. The only potential treatment was to give broad-spectrum antibiotics, “and hope for the best.” A week passed, but his blood pressure and breathing rate remained dangerously low and, as Janelle soon realized, her father had an antibiotic-resistant infection. After nine days, he died.

Antibiotic-resistant strains of bacteria have increased because we have overused these fabulous drugs, for various reasons. One is simple greed. We crowd animals together too closely, they get infections and pressure sores, so we preemptively treat them with medicines. They also cause animals to gain more weight. You can try to avoid eating such animals, but the antibiotics are excreted in their urine and feces, and ultimately spread into the environment.

Antibiotic overuse has also occurred, I would argue, because of the military metaphor in medicine, and the eradication mentality. Pathogens are the enemy, and we have a weapon, so we must use it, to eradicate them. Initially we used these drugs for serious illnesses, and then eventually for more and more trivial ones, and often preemptively, as in a dentist’s office. Their overuse is dangerous for many reasons, not least of which is that we are filled with many different kinds of organisms, some of which are very good for us, and which even support our immune and other systems, and while antibiotics can indeed kill off “the enemy pathogens,” they also kill off these good bacteria. The problem is also that “the bad bacteria” can develop mutations, and evolve, and the more they are needlessly exposed to antibiotics, the more opportunity they have to develop a means of resisting the antibiotics we have. There are now a number of deadly illnesses that we could once treat, that we no longer can. This is a crisis that did not have to occur—a classic case, of the irresistible immoderation generated by the conquest of nature delusion.

Ayres gave a talk, shortly after her father died, acutely aware that his death was the product of this mindset. In a video of the presentation, she can be seen trembling, as she recounts:

It is because of the global spread of antibiotic resistance and our current strategies for treating infectious diseases, that my dad died, and that we are further away than ever from closing the book on infectious diseases. But why? If we really had such great success with the early generation antibiotics, how is it possible that we screwed things up so badly, that we are now in far worse condition, than we were fifty years ago? And the main issue is our perspective on how we should be dealing with problems. When we’re faced with a challenge, we think that in order to solve that challenge, we have to annihilate the source of the problem ... All of our current strategies to fight infectious diseases are based on the question, “How do we fight infections?” And as a result we have declared a war against infectious diseases and we have put all of our efforts into developing weapons in the form of antibiotics and antivirals in order to win this war.

But bacteria and viruses are incredibly slippery targets, and they can evolve so quickly, resistance to our weapons, making them obsolete. So what do we do? Well, our solution has been to just make more weapons, make more antibiotics, make more antivirals, and it’s not surprising that the microbes have evolved resistance to our new weapons. So our perspective is fueling an ever escalating arms race between us and infectious diseases, and the scary fact is that it’s an arms race we can never win.

She returns to the question of sepsis, the “collateral” damage, caused by our own immune systems, and bodies, once infected. It is often this that kills patients, and yet we have almost no medications to limit this pathology. Once the bacteria, or virus, or fungus, enter the bloodstream, the immune system mounts its killing response, and the liver, the kidneys, the intestines, lungs, cardiovascular system, can all get damaged. “For my dad, even if his infection was sensitive to the antibiotics, the likelihood of him just surviving was very low, because he had suffered so much physiological damage from the infection. What he needed were therapies that would fix that physiological damage. But he wasn’t given any drugs that do that because those drugs don’t exist.”

She says, “The way we have been thinking about treating infectious diseases is that we have to annihilate the pathogens through vaccines and antimicrobials.” She completely reframes the problem, and challenges our thinking: “Instead of asking how do we fight infections, we should be asking ‘how do we survive infections?’”

Changing that single word—“fight” to “survive”—transforms everything. Consider, for example, that new organisms, and strains are evolving all the time. A new coronavirus strain identified in December is said to be 70% more transmissible. Some new strains may be resistant to our existing vaccines and antivirals. Developing different antibiotics or vaccines to eradicate each of them, is not always possible, and when it is, generally takes a long time, and costs a fortune. But if, as is often the case, death is caused by our bodies’ own reactions to the infection, reactions which are very similar, regardless of the pathogen that caused them, learning to block the body from going into overdrive should help people survive multiple infections. As well, there is no reason to believe this approach will cause antibiotic-resistant, antiviral-resistant, or vaccine-resistant strains, because it is not targeting the pathogen per se.

The project of developing these new kinds of therapies (which is well underway in Ayres’ lab) requires having a better understanding of the “tolerance defense system,” alluded to above. Not every infection kills us, in part because an innate tolerance system has already evolved to help our bodies coexist in the sea of microbes in which we live, and which dwells within us (the microbiome). It is the product of a cooperative two-way evolutionary process.

To understand this cooperative co-evolution, it’s best to first look at its “opposite,” the traditionally studied antagonistic co-evolution. An organism gets inside us, we evolve ways to kill it, then it evolves ways to resist that, and perhaps we, the host, evolve more aggressive means of attack, but that also leaves us with an overactive immune system, which perhaps then also predisposes us to causing collateral damage to ourselves. This basically describes the traditional immune resistance system, and the collateral “autoimmune” damage it causes. This is not good for us, but, if a pathogen’s host dies it is not necessarily helpful to it either. After all, once the pathogen gets inside us, we are its environment, so, if it kills us (a Baconian specialty) it’s created a disaster for itself (as it were).

Offense is not always the best defense. In a more cooperative co-evolution, as Ayres calls it, both host and pathogen acquire traits that are not mutually destructive. Ayres hypothesized this must exist, and then began demonstrating it did. In cooperative host microbe evolution, cycles occur, in which the host influences the microbe and the microbe influences the host, such that they co-evolve, together, and cause each other to select for traits that maximize their mutual ability to both survive, and replicate. From the point of view of the microbe, for instance, it does well to develop traits that let it acquire nutrients from our bodies to meet its metabolic demands, and to replicate, and get passed on to another host, whom we can meet at a party, because the microbe hasn’t killed us. This is not a kumbaya moment, it is an alternative survival strategy. In this situation, there is an evolutionary pressure on the organism to develop mutations that are less lethal (which happens sometimes) and Ayres and her lab have shown that the host can, in certain cases, trigger these anti-virulence traits in the pathogens, so that while they are present in a host, they don’t trigger a disease. (We would be most fortunate if the virus we are dealing with now, mutated in this direction.) It is staggering, and humbling, to consider what is going on microscopically within us—much of which is positive.

In cooperative co-evolution, there is an incentive for us (or any infested animal) to develop methods to both prevent collateral damage to ourselves, as well as fix it when it occurs. That is the essence of the tolerance system. What Ayres and her colleagues are doing is describing these mechanisms—in minute molecular detail—in the body, and learning to read how organisms that are co-evolving with their hosts are communicating with them—sending signals back and forth. Ideally, the lab would ultimately learn how to use this information to enhance co-evolution in some way, to treat disease.

One of the ways that the lab is doing this is by studying microscopic reactions to the many beneficial microbes in host bodies, which are essential to health and survival. (We all have about three pounds of microbes on and within us.)

Consider the microbe, E. coli. Many people know of this bacterium because one of its many strains, if it contaminates meat, can make us sick. But many, and perhaps most strains actually are essential to our health. In one of the lab’s groundbreaking accomplishments, they identified one of these healthy versions, which lives in mouse intestines, and which can be easily accessed with a stool sample (i.e., it lives in excrement) then used to cure a number of infectious diseases. They found, if it was given to a mouse infected with Salmonella typherium (a mouse equivalent of typhoid fever), it cured the animal of that infection, and prevented muscle wasting that goes with the disease. The same E. coli, given to mice infected with pneumonia cured them.

Ayres’ approach to COVID is not to minimize other approaches but point out that “if we can step beyond our focus on the virus,” there is much more we can learn. For instance, it was assumed early in the pandemic, that severe cases were caused by high viral load, and now we know it is the secondary collateral damage caused by our bodies that is the real killer.

Consider how she reframes the well-known COVID-19 risk factor for death, Type 2 diabetes. Physicians assumed that patients with this disorder (and the often related “metabolic syndrome” which includes obesity) are more at risk of dying from COVID-19 because diabetes lowers immunity. But Ayres points out Type 2 diabetes is a chronic inflammatory condition (something long emphasized by “functional medicine” and certain more complimentary approaches to the illness), and this heightened inflammation may well be what renders these people more susceptible to the collateral damage from their own bodies. To protect these people, we need to focus on dealing with their preexisting inflammation. (Sugar, by the way, is inflammatory.) Then, if they get the illness, they, it is hoped, will “survive it.”

Ayres has “opened a new dimension to understanding host-microbial interactions,” Dr. Ruslan Medzhitov, professor of immunology at Yale University, has said, “and that created a whole new discipline within immunology, and within infectious disease. What I think puts Janelle apart from most of her peers is that she finds these new perspectives that are very much grounded in a deep biological intuition. She doesn’t follow the crowd.”

Not the living crowd, anyway. But the biological intuition, of which he speaks, if not fully elaborated by the ancients, is consistent with some of their intuitions. The classical ideas have not been totally obliterated in some of our finest scientists, even if the sources of these intuitions are increasingly less familiar.

So, back to our opening question, is modern science, and the idea that we can conquer nature, mad?

Not to put too fine a point on it, but we are but a narcissistic speck of that nature. We’ve not yet figured out what the Universe is (its borders, when it began, its purpose, or if it has one—we can’t even define the word “Universe” really, because we don’t know its boundaries). We’ve not figured out what Life is, how to define it, how it began, where it begins and ends (we can’t even agree whether viruses are alive or not, and scientists have battles about this). We’ve not even solved the problem closest at hand: What is Consciousness? Every serious neuroscientist concedes “consciousness is the big problem” and we don’t quite know what it is, or how to define it, apart from spitting out a bunch of synonyms, and saying, “Well, it is ‘awareness’ or ‘subjective experience’ or ‘mental experience’” each overlapping and equally hard to define.

What is the Universe? What is Life? What is Consciousness? These are the three great questions of science, and perhaps even philosophy, and they are all unsolved; and so, yes we are a somewhat delusional, somewhat mad speck, when we claim “we can conquer nature.” We don’t even know what that statement means.

When we transfer that metaphor to medicine, and speak of conquering disease, we do harm, not because a military is necessarily a bad thing, but because, this is not its place.

So, then, what metaphor do we need for the physician, medicine, and this enterprise that seeks to pursue, or restore health?

How about no metaphor? How about we describe medicine and healing on their own terms? We could start by thinking of some of the first physicians, such as Hippocrates, and understand what was unique about the tradition they founded. We physicians could actually aspire to be physicians, rather than pretend warriors. But modern medical schools, so smitten with “relevance” have turned their back on Hippocrates, because he didn’t get everything right (as though we have!). But he did get right that it is often wisest when possible to work with nature, and the patient, when possible, rather than against them. Fewer and fewer medical schools now require the graduating physician to take the ancient Hippocratic oath, the first recorded articulation of medical ethics, that sanctified medical confidentiality and the idea that the doctor worked for his or her patient, and not a third party. How sad, how telling.

It is the same Hippocrates, who boiled all medicine down to two principles in his Epidemics Book I, “Practice two things in your dealing with disease: either help or do not harm the patient.”

And, in this light—of doing no harm, or at least far less—we might remember that we are part of nature, depend on it, it lives in us, and we have links to parts we think remote from us, that we often cannot even see. We might consider setting aside the utopian dream that always becomes a nightmare, because all too often we can’t conquer nature without conquering ourselves.