Pathogenesis: A History of the World in Eight Plagues

by Jonathan Kennedy

infectious diseases have killed so many people throughout history that they are one of the strongest forces shaping human evolution.

This suggests that humans’ struggle for existence was a fight against microbes rather than alpha males and apex predators.

This book pulls together this ground-breaking research, much of which has been published in pay-walled scientific journals and is not widely read outside of academia, and places it in the context of research from other disciplines, including archeology, history, anthropology, economics and sociology.

Neanderthals appear to have survived until between 41,000 and 39,000 years ago.[11] The expansion of Homo sapiens and disappearance of other species fundamentally transformed the planet and laid the foundations for the world we inhabit today. Why this happened is one of the biggest mysteries of human prehistory.

In Werner Herzog’s documentary film about Chauvet, Cave of Forgotten Dreams (2010), he says of the appearance of prehistoric art in what is now France and Germany: “It was not a primitive beginning or a slow evolution. It rather burst onto the scene like a sudden explosive event. It is as if the modern human soul had awakened here.”

But if Homo sapiens were already capable of symbolic behavior—and were therefore superior to all other species of humans—300,000 years ago, why did it take them a quarter of a million years to break out of Africa and spread across the world? The answer is simple. A plethora of recent discoveries point to the fact that Homo sapiens weren’t, in fact, smarter than other species of human.

the end of the nineteenth century Ernst Haeckel, a German zoologist, Social Darwinist, promoter of scientific racism, and strong influence on Nazi ideology, proposed calling Neanderthals “Homo stupidus” to distinguish them from Homo sapiens.[30]

Sooner or later, genetic mutations would have occurred that allowed Homo sapiens’ immune systems to mount an effective response to Neanderthal pathogens. Because people with these gene variants were more likely to survive, over time they spread widely through the population. But Homo sapiens took a much quicker route to immunity—by interbreeding. Reproducing with another closely related species is an unintentional kind of biohacking: it immediately endows a species with gene variants that are already adapted to the new environment.

When you think about it, however, the immune system might well be the most remarkable superpower of all.

The Dawn of Everything, David Graeber and David Wengrow,

But this doesn’t mark a point in time when everyone in the Middle East suddenly gave up hunting and gathering to instead cultivate crops and rear animals. Rather, it was the start of a long-drawn-out process. The first people to try to grow plants and breed docile animals probably weren’t motivated by the desire to produce more food: it was already available in abundance in the Fertile Crescent—hence the name—and the change in climate would have been a boon for foragers as well as farmers. Rather, farming likely began as a series of playful experiments or as a way to spend longer each year in a semi-permanent settlement rather than on the move.[11]

Humans lived in a milieu of happy abundance until we decided to take up farming.

This may have had the benefit of allowing us to produce more food, but it also led to the emergence of despotism, inequality, poverty and back-breaking, mind-numbing work. Jean-Jacques Rousseau is perhaps the most notable champion of the “Fall of Man” theory, and more recently Jared Diamond argued that the adoption of settled agriculture was the “worst mistake in the history of the human race.”[16]

almost everywhere that humans adopted settled agriculture, early farmers were less healthy than hunter-gatherers. Their skeletons were shorter and more likely to show signs of anemia due to iron deficiency and enamel defects as a result of lack of vitamins A, C and D, calcium and phosphorus.[26]

James Scott refers to Neolithic villages as “multispecies resettlement camps.”[27]

An array of DNA evidence is now vindicating one of William McNeill’s key arguments: that the adoption of settled agriculture, coupled with population growth and increased trade, created a golden age for viruses, microbes and other animals.

But in his recent book The Fate of Rome, Kyle Harper

In this belief system, the best way to save oneself from Apollo’s wrath was to try to deflect his anger by making a sacrifice or some other form of offering. In contrast, Jesus’ message that hardship brought redemption was much more reassuring in the face of the recurring devastation of plagues. It offered hope and meaning by explicitly promising a better life in the next world for those who were suffering on earth.

The arrival of plague was a hammer blow to Justinian’s revitalized empire. The Byzantine writer Procopius, who witnessed the first wave of the epidemic, describes how “the whole human race came near to being annihilated.” He claims that 10,000 people died every day in Constantinople at its height. This might well have been an exaggeration, but the message is clear: the outbreak was devastating.

Then the plague struck. And it devastated Europe. But in spite of the havoc it wrought, it did a service to the West. It guaranteed that in the generations after 1348 Europe would not simply continue the pattern of society and culture of the thirteenth century. —David Herlihy

Ingmar Bergman’s The Seventh Seal (1957)

How do we account for the decline of medieval Europe and the emergence of the modern world? The Black Death played a crucial role, triggering a series of events that—over several centuries—resulted in this transformation. It was, as one historian put it, “the great watershed in medieval history” that ensured “the Middle Ages would be the middle, not the final, phase in western development.”[3]

The Norwegian historian Ole Benedictow estimates that roughly 60 percent of the population of Europe—that is about 50 million out of 80 million people—died from the plague between 1346 and 1353.[18] Analysis of an ice core drilled in the Swiss Alps reveals that lead pollution disappeared from the air in these years.[19] No silver mining occurred during the Black Death. The economy appears to have simply ground to a halt.

Venice built the first permanent lazaretto in the early fifteenth century. There were still occasional outbreaks, as noted above, but quarantine was deemed to be an effective public health intervention and it was adopted throughout western Europe.

Parts of “Le Mur de la Peste,” a wall built during the Great Plague of Marseilles in 1720 to stop people moving between the city and the hinterland, are still visible.

The introduction of regulations such as quarantine and cordons sanitaires in late-medieval societies had significance well beyond public health, because they extended state power into areas of human life that had not previously been subject to political authority. Michel Foucault saw the shift in the focus of states from controlling territory to governing people’s bodies as a key feature of the modern world.[35] (During the Covid-19 pandemic, lockdowns and other restrictions on movement were controversial precisely because they so starkly revealed the enormous power of the modern state over our lives.)

Wycliffe criticized the Church for veering away from the word of the Bible. He argued that there was no justification in the scriptures for many of the ideas they promoted—such as attending Mass, repenting for one’s sins, praying to saints and buying indulgences. Wycliffe claimed that the clergy were not required to mediate laypeople’s relationship with God; rather, the Bible was the only reliable guide to how they should conduct themselves. People should study the Holy Book—in the vernacular if they didn’t speak Latin—and decide for themselves what God’s message was. Wycliffe played a prominent role in the first translation of the Bible from the Latin Vulgate into Middle English in 1382.

The Reformation’s greatest impact was on the way that people in western Europe thought. Luther’s ultimate message, like Wycliffe’s, was that each person should read the Bible and come to their own conclusions. This shifted the focus away from mindlessly obeying the Church’s authoritative interpretation of Christianity and instead emphasized the critical faculties of the individual. Eventually, some people began to read the scriptures and reject them altogether. Instead, they tried to explain the world using reason and observation. In this sense, existential questioning triggered by the Black Death didn’t just lead to the rise of Protestantism but also paved the way for the emergence of secularism.

Yellow fever is also common in West Africa, but the epidemiological dynamics are different. The virus tends not to be deadly in childhood, and after one infection you have lifelong immunity and can never again serve as a host to the pathogen. But yellow fever is a very serious disease for adults.

The fact that European attempts to settle in the Americas foundered without the help of infectious diseases suggests that the Portuguese would have struggled to colonize West Africa even if malaria and yellow fever hadn’t intervened to help the indigenous population. But these mosquito-borne diseases created a defensive force field that made military conquest all but impossible. Writing in the sixteenth century, João de Barros, the historian who is referred to as the “Portuguese Livy,” lucidly captured the frustrations of the would-be colonists: But it seems that for our sins, or for some inscrutable judgment of God, in all the entrances of this great Ethiopia that we navigate along, He has placed a striking angel with a flaming sword of deadly fevers, who prevents us from penetrating into the interior to the springs of this garden, whence proceed these rivers of gold that flow to the sea in so many parts of our conquest.[74] In the late eighteenth and early nineteenth centuries, when Britain was on its way to becoming the dominant colonial force in the world, malaria and yellow fever—the flaming sword of deadly fevers—still made tropical Africa all but unconquerable.

The interior of the African continent was even more deadly. Colonial explorers tended to travel inland via navigable rivers. The “rivers of gold” that appeared on medieval maps were in reality “rivers of death.”[78]

Jesuit powder didn’t slay the “angel with a flaming sword of deadly fevers” that guarded the continent. But it did weaken her.

The arrival of West African pathogens turned the Caribbean into a new white man’s grave.

Oliver Cromwell shipped several thousand political opponents, many of whom were Irish, to the Caribbean.[35] The term “barbadoesed”—to be exiled to Barbados—was in common use in the middle of the seventeenth century. With no way of making a living in this strange land, many exiles had little choice but to enter indentured servitude.

Although John McNeill is careful not to completely ignore the role of Great Men like George Washington, he drolly suggests that the female Anopheles quadrimaculatus mosquitoes should be considered one of the “founding mothers of the United States.” As he points out, malaria killed eight times more British troops than American guns.

There was a simple economic reason for the brutal treatment of enslaved Africans: they were cheap to replace—so cheap, in fact, that it was more cost-effective to buy new laborers every few years than to provide them with decent living standards and encourage them to have children.

The rebels knew from experience that newly arrived Europeans died in droves every summer during the rainy season, when mosquitoes thrived, and they planned to fully utilize the advantage that their immunity to yellow fever offered them. As Dessalines prepared to attack the French for the first time in March 1802, he reminded his troops: “The whites from France cannot hold out against us here in Saint-Domingue. They will fight well at first, but soon they will fall sick and die like flies.”[77]

Twelve thousand reinforcements arrived from France early the following year, but they suffered the same fate. According to John McNeill, a total of 65,000 French troops were sent to reconquer Saint-Domingue. Over 50,000 died, the vast majority from yellow fever. The rebels were, of course, barely affected by the disease. It was as if Makandal really did live on as a mosquito and had returned to finally fulfill his plan to poison the French.

According to one estimate, 40 percent of Union soldiers fell ill each year with the disease. The debilitating fevers were massively disruptive to the war effort and, if they didn’t kill sufferers outright, made them susceptible to other infectious diseases such as dysentery and measles. Throughout the Civil War, twice as many Northern troops died from disease as were killed in battle by Confederate guns.[87]

A greater revolution for humanity than the theories of Copernicus, Darwin, and Freud put together came with the invention of the toilet. —Goce Smilevski

the rapidly growing urban population in the late nineteenth century was experiencing what Simon Szreter terms the “4 Ds”: disruption, deprivation, disease and death.

Many people looked at all these facts—the symptoms, the sudden appearance of outsiders, the disproportionate burden on the lower classes—and surmised that cholera wasn’t a previously unknown disease at all, but a plot by the authorities to poison the urban poor.[32] This time Jews avoided the blame—even in eastern and central Europe where the feudal system persisted. Instead, popular suspicion focused on the authorities who led the public health response to the outbreak, as the power of the state had expanded enormously since the Black Death but had done little or nothing to improve most people’s lives.

While cholera vaccines are still used today, their development was far too late to explain the decline of the disease in Europe. Cholera didn’t disappear because of innovations in medical technology but because of improvements in hygiene and sanitation driven by political reform.

In 1958, the state urged the population to “exterminate the four pests,” which were rats, flies, mosquitoes and sparrows—the latter because they were accused by the Chinese Communist Party of being capitalist birds due to their penchant for “stealing” large amounts of grain and fruit from hard-working peasants.

With the threat from natural predators vastly reduced, the locust population boomed and then feasted on the harvest in a manner far more destructive than anything that sparrows could have achieved. In this way, the campaign to “exterminate the four pests” contributed to the famine that killed 45 million people during the Great Leap Forward.

The local doctors have coined the phrase “Shit Life Syndrome” to refer to the common denominator for most of the maladies they see: destitution and hopelessness.[57]

This whole thing is not about heroism. It’s about decency. It may seem a ridiculous idea, but the only way to fight the plague is with decency. —Albert Camus

Epidemics have played a critical role in, among other things, the transformation from a planet inhabited by multiple species of human to one in which Homo sapiens reigned supreme; the replacement of nomadic foraging with sedentary agriculture; the decline of the great empires of antiquity; the rise of new world religions; the transition from feudalism to capitalism; European colonialism; and the Agricultural and Industrial Revolutions. In other words, bacteria and viruses have been instrumental in the emergence of the modern world.

And while the Haitians were up against the French army, one of the best-trained, best-equipped forces the world had ever seen, they managed to devise a strategy that used yellow fever as a deadly weapon.

when Covid-19 struck, many of us began to live our work and social lives in the online realm.[3] We worked from home rather than commuting to the office, ordered our groceries online instead of going to the supermarket, got food delivered instead of eating in restaurants, and caught up with friends on Zoom rather than over a coffee in town. Schools, churches and even courts moved online. Since the pandemic died down, many people have continued to spend much more time in the virtual world than before coronavirus. This shift seems to be permanent.