Pathogenesis: A History of the World in Eight Plagues

by Jonathan Kennedy

It is therefore not the strongest or most intelligent members of our species who were most likely to survive long enough to pass on their DNA to the next generation; rather, it was humans who had the most effective immune system to cope with the onslaught of infectious diseases, or those who had mutations that made their cells unusable to microbes. Lots of these mutations not only conferred resistance to pathogens but also had a negative impact on cell function. This suggests that humans’ struggle for existence was a fight against microbes rather than alpha males and apex predators.

The evolutionary reason why bacteria produce chemicals that improve our moods may be that it makes us more likely to be gregarious and therefore provide them with opportunities to colonize other hosts.

Harari and many other scholars argue that modern humans underwent a “cognitive revolution” between 70,000 and 30,000 years ago that transformed the way they thought and behaved.

A further challenge to the notion of a cognitive revolution is recent evidence that Homo sapiens were capable of symbolic behavior a long time before modern humans spread out of Africa. Most striking is a recent study based on excavations at a dried-up lake bed in Olorgesailie, Kenya.[26] Archeologists found lumps of rock that appeared to have been processed to create pigments over 300,000 years ago: manganese ore, ground down to produce black or dark-brown coloring, and iron-rich minerals that were used to make ocher. The ocher rocks did not come from the nearest source, which suggests that they were transported from farther afield because of their particularly bright hue. So, just as Homo sapiens were emerging as a distinct species, they were going to great efforts to get their hands on pigments in order to decorate themselves or paint things.

A plethora of recent discoveries point to the fact that Homo sapiens weren’t, in fact, smarter than other species of human.

In 1856 Johann Carl Fuhlrott, a schoolteacher, discovered the bones of a hitherto unknown species of human in a cave in the Neander Valley, western Germany. Following the publication of On the Origin of Species just three years later, there was a fierce debate about where the new specimen fit into the Tree of Life. Had Homo sapiens evolved from this strange humanoid or did it belong on an altogether separate branch? Conservative paleontologists working in cahoots with the Catholic Church made a concerted effort to emphasize the differences between the two species. By portraying Neanderthals as only very distantly related to Homo sapiens, they hoped to retain our status as a separate and exceptional species. When the first complete skeleton of a Neanderthal was discovered by three Catholic priests in 1908 in La Chapelle-aux-Saints in southern France—about 300 kilometers west of Chauvet—the Church made sure it ended up in the hands of someone who shared their worldview, Marcellin Boule, director of the Laboratory of Paleontology at Muséum d’Histoire Naturelle in Paris, reconstructed the specimen so that it looked much more simian than human, with its forward-jutting head, slouching shoulders, hunched spine, bent knees and even opposable toes. Boule’s work was flawed, but it had a profound impact on scientific understanding of Neanderthals for the next half-century and it still informs the popular stereotype of the ape-like cave man.[27]

There is archeological evidence that Neanderthals manufactured stone tools requiring cognitive skill and dexterity,[31] made fire on demand,[32] sailed from mainland Europe to Crete and the Ionian Islands,[33] produced glue from the bark of the birch tree,[34] and appear to have treated maladies with medicinal plants that had anesthetic and antibiotic properties: traces of DNA from poplar trees, which contain salicylic acid—the naturally occurring inspiration for the synthetic aspirin, and Penicillium mold, the source of penicillin—have been found in the calcified plaque of Neanderthals.[35] In 1989, archeologists found a Neanderthal hyoid, the delicate U-shaped bone that anchors ligaments and muscles in the throat and is key to human speech. This indicates that they would have been able to talk, albeit in a very high-pitched tone.[36] While we don’t know anything about Neanderthal language, the fact that there wasn’t a big behavioral gap between them and Homo sapiens is a strong indication that it would have had a similar level of complexity.[37] We also know that Neanderthals buried their dead.

The remarkable artistic accomplishments that seemingly emerged from nowhere between 40,000 and 30,000 years ago in western Europe may have occurred when Neanderthals and Homo sapiens began to mix and exchange ideas after being separated for several hundred thousand years.

Beyond the immune system, introgressed Denisovan gene variants account for much of the remarkable physical diversity of modern humans, allowing them to live in a variety of extreme habitats.

When Homo sapiens gained immunity to Neanderthal diseases between 50,000 and 40,000 years ago, they were finally able to migrate northward out of Africa into areas inhabited by Neanderthals without getting horribly ill. The curse that had made the Eastern Mediterranean all but uninhabitable for tens of thousands of years was lifted. Our ancestors traveled deep into Eurasia, where they encountered Neanderthal and Denisovan communities that had never been exposed to African pathogens and hadn’t had the opportunity to build up any tolerance. Within a relatively short period of time all other human species died out and were replaced by the newly ubiquitous Homo sapiens. The world would never be the same again. It ceased to resemble Middle-earth, with its rich cast of human species, and quickly became the Homo sapiens–dominated planet that we still inhabit today. Skip

Prehistory was punctuated by massive waves of migration that resulted in a new population moving into a region and almost completely wiping out the previous inhabitants. Nearly always, the migrants were unwittingly aided by an invisible but devastating weapon of mass destruction: infectious diseases to which they were to some extent immune but to which original communities had little or no resistance.

A study based on observations of foraging communities over the last fifty years or so estimated the average lifespan of hunter-gatherers to be around seventy-two years.[10] Remarkably, this figure is only one year less than the global life expectancy today according to World Bank data.

Disease or adverse weather could wipe out the harvest. Stored surplus could be stolen by raiders, eaten by pests, or destroyed by mold. Consequently, settled agriculturalists were much more likely to starve than hunter-gatherers.

The Aedes aegypti mosquito that spreads yellow fever also benefited greatly from recent human activity because it likes to reproduce in containers full of stagnant water. This had led the American historian John McNeill to suggest that they are, in fact, a domesticated insect.[38]

Could diseases have helped a relatively small community of shepherds to replace a well-established farming society in northern Europe in the first half of the fifth millennium BCE? Although we don’t yet have a smoking gun, there is strong circumstantial evidence that indicates this might have been the case. The population in the region did not keep on growing inexorably after agriculture was adopted. In the northwest of the continent the initial period of growth occurred between around 6,000 and 5,500 years ago, but then the population crashed; by 5,000 years ago it was up to 60 percent less than it had been at its height.[65] It remained low for another half-millennium. In Britain the population continued to raise livestock, but many people seemed to have abandoned cereal cultivation and instead reverted to foraging.[66] Interestingly, it was between 5,000 and 4,500 years ago—when the population was at its lowest point—that the Neolithic European Farmers went to all the trouble of building Stonehenge. Was the construction of this great monument an ultimately futile effort to appease their gods and arrest the decline of their community?

The influx of the Steppe Herders in the third millennium BCE was the last great migration movement in Europe. Although various groups of immigrants have continued to enrich the gene pool in the intervening years, with the Steppe Herders’ arrival all the components of the modern European genome were present. People of European ancestry are a mixture of three genetically distinct population groups (plus, in some cases, trace amounts of other DNA).[79] First, Western Hunter-gatherers, such as Cheddar Man, who had dark skin and hair and light eyes.[80] Second, olive-skinned, dark-haired Neolithic European Farmers like Ötzi the Ice Man who migrated into Europe from Anatolia approximately 9,000 years ago, bringing farming with them, and arriving in Britain three millennia later. And third, the Steppe Herders: tall, fair-haired, light-skinned shepherds who migrated westward from the Eurasian Steppe about 5,000 years ago and adopted farming when they settled in Europe. The implications of this are momentous: contemporary Europeans are neither genetically “pure” nor are they the region’s indigenous people. Even white Europeans are mongrel immigrants.[81]

It is remarkable to think that the impact of the migration of a small number of shepherds out of the Western Eurasian Steppe 5,000 years ago, which was most likely made possible by a devastating plague pandemic, can literally still be seen and heard today across the world.

From plague bacteria’s perspective, humans and black rats are second-rate hosts because of their tendency to die quickly after the pathogen enters their bodies. Some other species, most notably great gerbils and marmots, both of which live in mountainous areas of Central Asia, have partial resistance to Yersinia pestis. Their bodies provide an environment where the bacteria can reproduce without killing the host. This means that while plague epidemics quickly burned out in human and rat populations, the pathogens could survive for centuries or even millennia in gerbils and marmots, before once again spilling out into the rat and then human populations when conditions allowed. William McNeill notes how nomadic people living on the Steppe “had mythic explanations to justify epidemiologically sound rules for dealing with the risk of bubonic infection from marmots.” This included taboos on trapping or touching the animals. Such measures were not always successful at stopping the spread of the plague. Ancient DNA analysis has identified a nomadic Hun who died from a strain of Yersinia pestis, similar to the one that caused the Plague of Justinian, in the Tian Shan Mountains of Central Asia in the second century BCE.[59] (This does not seem to have led to a big outbreak, presumably because the Hun’s nomadic lifestyle meant that the disease killed them before they came into contact with others.) When the climate got markedly colder in the 430s, gerbils and marmots were forced to ...

But the Arab commanders learned that when an epidemic struck it was safest to remove their troops from the city to isolated highland or desert locations until the danger had passed. Similarly, the Umayyad Caliphs would retreat to the desert palaces and live like Bedouins during plague season.[71]

The Arab armies’ expansion played an important role in forging the modern world well beyond the areas they conquered. Since the days of the pax Romana, the Mediterranean had been the main route along which people, goods, ideas and germs flowed from the much more advanced east to northwestern Europe. With the devastation of the Eastern Roman Empire, this artery was severed. The renowned Belgian historian Henri Pirenne famously argued that without Muhammad, Charlemagne would be inconceivable.[73] The political vacuum in northwestern Europe ultimately led to the emergence of a new order that was dominated by a patchwork of small kingdoms, feudal lords and thriving city-states but was at the same time unified by its Christian identity, in opposition to its Muslim neighbors to the south and east.

Another eyewitness in Florence wrote of throwing bodies into a mass grave, covering them with earth, adding more bodies and then earth, “as one makes lasagne with layers of pasta and cheese.”

As Philip Ziegler wryly notes, “it is a curious and somewhat humiliating reflection on human nature that the European, overwhelmed by what was probably the greatest natural calamity ever to strike his [sic] continent, reacted by seeking to rival the cruelty of nature in the hideousness of his own man-made atrocities.”

So many people had left property to the Church when they died that by the Middle Ages it owned about a third of all cultivated land in western Europe.

The increasing use of labor-saving devices was a direct response to the challenges created by the Black Death and subsequent outbreaks of the plague, because there were now so few workers that labor-intensive processes had become unviable.

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.

Critically, for the first time since the Neolithic Revolution, most of the population could no longer grow their own crops and had no other option but to work for someone else in order to earn money to buy food and other essentials.

As Charles Darwin succinctly put it: “Wherever the European has trod, death seems to pursue the aboriginal.”

If modern-day Americans want to be historically accurate, then their gratitude at Thanksgiving should be directed to the Old World pathogens that made the settlement of Plymouth Colony possible.

The continent “had become a place of darkness,” Marlow remarks, by which he seems to mean that European exploitation and oppression had turned it into an almost unimaginably unpleasant place.[83]

The continued threat posed by infectious diseases in tropical Africa had an enormous impact on the specific form that colonialism took. The region attracted ambitious and unscrupulous Europeans motivated by making as much money in as little time and with as small a capital expenditure as possible—and then cutting and running before they were struck down by disease. They weren’t colonial settlers. So, unlike in New England, they didn’t bring their families with them, settle down and build institutions in the image of their home country. Rather, the Europeans who colonized Africa in the last decades of the nineteenth century created “extractive institutions” that used violence and the threat of violence to coerce the population into mining natural resources and transporting them to the coast, where they were shipped to Europe. The ultimate aim of this brutal endeavor was not to build a new and better society, but to enrich a small group of Europeans by draining wealth from the region.[92]

The ten poorest countries in the world are all former colonies in sub-Saharan Africa. It is not unreasonable to conclude that these societies would have been better off if Europeans had never discovered a moderately effective treatment for malaria and the region had remained a white man’s grave.

The median household wealth of African Americans is $17,600 compared to $171,000 for whites,[2] and they are almost six times more likely to be incarcerated.[3]

As West Africa was connected to Europe and Asia by overland and now sea routes, the local population had been exposed to Old World pathogens and fared much better. Between 1550 and 1650, 650,000 Africans were trafficked to Spain and Portugal’s American colonies—more than twice the number of Europeans who crossed the Atlantic in that period.[19] The early conquistadors’ decision to use enslaved Africans on their sugar plantations had unexpected but momentous consequences: it inadvertently set the whole of the American tropics on an inescapable path toward racialized slavery because the nascent transatlantic slave trade carried not only people but also some of the mosquitoes and microbes that made West Africa a deadly place for Europeans.

The failure of New Edinburgh didn’t just kill 2,000 people; it also wiped out all the money that had been invested in—or gambled on—this doomed project. Cannily, the English promised to compensate the investors if they agreed to closer ties between the two countries. Even committed Scottish nationalists supported the 1707 Act of Union when faced with the possibility of financial ruin. “Thus,” wrote the historian John McNeill, “Great Britain was born, with the assistance of fevers from Panama.” Over 300 years later, the union is a major political issue and pro-independence parties currently hold a majority in the Scottish parliament.

Women were subject to widespread rape and sexual coercion. Perhaps the most notorious sexual predator was Thomas Thistlewood, a British plantation owner in Jamaica whose diary describes 3,852 acts of sexual intercourse with 138 enslaved women over thirty-seven years in the mid-1700s.[43] A recent study based on the DNA provided to the biotech company 23andme by 50,000 people demonstrates that he was far from the exception.[44] Almost twice as many males were transported across the Atlantic as females, and yet African women provided twice as much DNA to the modern-day population of former British colonies in the Caribbean.

The massive expansion in the transatlantic slave trade and American slavery in the seventeenth and eighteenth centuries coincided with a period of great intellectual energy in Europe, the Age of Enlightenment. One of its major preoccupations was ordering the natural world into various categories. This included humans, who were classified into different races, each with their own supposed physical, intellectual and moral characteristics. The pseudoscientific, racist taxonomy of humans had a clear hierarchy, with the white Europeans who came up with the schema placed at the top. Immanuel Kant, for example, wrote that the “race of the whites contains all talents and motives in itself.” Black Africans, in contrast, “can be educated, but only to the education of servants” or, in other words, “they can be trained.” Native Americans were, according to Kant, “uneducable” and “lazy,” which might have served to soften European guilt for colonizing their continent and literally decimating them. Curtin points out that immunity to infectious diseases was a major factor in these stereotypes. The idea that Black people are well suited to a life of hard labor was influenced by African immigrants’ apparently unique ability to survive on the plantations in tropical regions of the Americas. In contrast, Native Americans were seen as a “weak race” because they often died after their first encounters with “white people.”

In August 2019 the New York Times launched its 1619 Project, with the aim of “placing the consequences of slavery and the contributions of Black Americans at the very center of the United States’ national narrative.” The inaugural magazine issue, which has been turned into a bestselling book, contained an array of articles that emphasized the profound influence that racialized slavery has had on almost every aspect of contemporary American society, from traffic jams to health care. The project’s title and the date of the publication referred to the arrival of the first trafficked Africans in Britain’s North American colonies exactly 400 years earlier; the twenty-odd men and women had been transported across the Atlantic by Portuguese slave traders, but were then seized off the coast of Mexico by English pirates and brought to Point Comfort in Virginia. The fact that Africans have been present on the continent since 1619 is remarkable: even the Pilgrim Fathers—whose story plays such a central role in American mythology—didn’t get there until the following year.

The first record of what can be recognized as racialized slavery doesn’t appear until 1640, when three indentured laborers from Virginia—two white and one Black—ran away from their place of work. After they were captured, the colony’s highest court sentenced the two Europeans to four additional years of servitude. In contrast, the unfortunate African American—whose name was John Punch—was condemned to “serve his said master or his assigns for the time of his natural Life here or elsewhere.” Still, at the time, John Punch was very much an exception to the rule.[50]

Falciparum malaria first appeared in Virginia and South Carolina in the mid-1680s—that is, just before African American slavery began to catch on in the North American colonies.[57] The timing is not an accident. As with so many other disease outbreaks we’ve encountered in this book, it coincided with a period of climate disruption. In this case, El Niño events were much more frequent in the 1680s than in the preceding two decades, which may have aided the spread of malaria by creating the stagnant pools of water in which Anopheles mosquitoes need to breed.[58] The climate influenced the distribution of malaria in North America in another important way: as Plasmodium falciparum requires long stretches of relatively warm temperature in order to reproduce, it could survive in the southern colonies but not in the northern ones. In fact, the geographical boundary between areas where the parasite could and couldn’t reproduce falls more or less exactly on the Mason-Dixon Line that divided Maryland from Pennsylvania and Delaware.[59] In the south, agricultural workers who hadn’t developed immunity to falciparum malaria were likely to get very sick. As a result, European indentured laborers were no longer wanted, and nor did they want to settle there.[60] From an amoral economic perspective, West African labor suddenly became a much more appealing proposition for plantation owners. The Italian economist Elena Esposito estimates that the arrival of falciparum malaria in the 1680s e...

Esposito’s analysis of a database of 3,000 Africans sold in the slave markets of Louisiana between 1719 and 1820 shows that those who came from the most malaria-ridden regions of West Africa—who therefore had the highest level of immunity—commanded significantly higher prices than those who did not.[62]

Those Europeans who didn’t die developed immunity to falciparum malaria, as did their surviving children. At this point the descendants of settler colonies were capable of working on the land without getting gravely ill, but the die was already cast: there was an entire ideology in place to justify a racialized class system in which it was seen as natural that African Americans toiled on plantations while the white population raked in the profits.

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. A couple of decades later in the Caribbean, mosquitoes—in this case Aedes aegypti—once again came to the assistance of a colony that was fighting to win independence from another European Great Power.

The legacy of previous infectious disease outbreaks catalyzed the Industrial Revolution in a number of other ways too. Most of the raw cotton used to produce textiles in the factories of northern England was cultivated in the American South by malaria-resistant enslaved Africans. And sugar, which provided the growing urban working classes in the UK with a cheap source of calories in the form of jams, cakes and biscuits, was produced by enslaved Africans in the Caribbean.[3] Furthermore, a large proportion of the vast profits from colonialism and slavery were reinvested in Britain. In this way, the suffering of enslaved Africans and colonized peoples paid for the construction of vital infrastructure such as the roads, canals, docks and railways that made the Industrial Revolution possible.[4]

Jenner used this insight to develop a “vaccine”—vacca being the Latin for cow.

The continued high incidence of infectious diseases in sub-Saharan Africa constitutes a major barrier to economic growth. Sick people cannot go to school or work, often need a family member to take time off to care for them, and require medical attention that can force a family into catastrophic debt.

Recurring outbreaks of infectious disease have been a feature of human existence for millennia. 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.