Pathogenesis: A History of the World in Eight Plagues

by Jonathan Kennedy

Many of these DNA sequences don’t seem to do anything in the human body, but retrovirus infections allowed our distant ancestors to acquire the capacity to perform functions that are fundamental to human existence. One remarkable example is a gene inherited from a retrovirus infection about 400 million years ago that plays a crucial role in memory formation. The gene does this by coding for tiny protein bubbles that help to move information between neurons, in a manner similar to the way that viruses spread their genetic information from one cell to another.

The idea of the cognitive revolution is conveniently Eurocentric. It locates modern-day France and Germany as the site of the metamorphosis of human behavior and identifies the first Homo sapiens capable of symbolic thought as those who left Africa and then turned left when they reached the Levant. This isn’t surprising. The discoveries of Lascaux in 1940, Chauvet in 1994 and the Venus of Hohle Fels in 2008, as well as the reconstruction of the Löwenmensch in the 1980s, dazzled several generations of scholars who grew up believing that “white” people originating in Europe were inherently superior to “non-white” people from elsewhere.

Bearing in mind the overwhelming lack of evidence, you might be wondering why anyone still thinks that there is a significant cognitive gap between Neanderthals and Homo sapiens. The answer seems to be blind prejudice. One recent academic article argues that it is the result of a “modern human superiority complex,” while an anonymous archeologist quoted in the New York Times refers to “modern human supremacists.”[48] It is true that Neanderthals did not produce anything comparable to the striking beauty and sophistication of the Chauvet cave paintings or the Löwenmensch figurine—but neither did Homo sapiens until after the Neanderthals disappeared.

About a decade ago, researchers managed to extract DNA from Neanderthal bones and sequence the genome.[51] When they compared their findings to the Homo sapiens genome, they realized that anyone alive today whose ancestors are Europeans, Asians or Native Americans has inherited about 2 percent of their genes from Neanderthals.[52] While this might not sound like much, we don’t all have the same bits of Neanderthal DNA and when we pool all these gene variants they account for about 40 percent of the Neanderthal genome[53]—providing incontrovertible evidence that the two species not only met, but had sex and reproduced.

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.

This process has been called the “poison-antidote model” of adaptive introgression: Neanderthals gave Homo sapiens a “poison” by exposing them to a novel pathogen, but also the “antidote” in the form of introgressed gene variants that confer resistance to the pathogen.[61] As a result, many of the Neanderthal gene variants that remain in our genome relate specifically to our immune response.

Denisovan DNA comprises less than 1 percent of East and South Asians’ genomes, but between 3 and 6 percent of New Guineans’.[65] And just like the Neanderthal-Homo sapiens poison-antidote model, many introgressed Denisovan gene variants carried are involved in immune-related processes, suggesting that these genes facilitated Homo sapiens’ adaptation to pathogens that they encountered as they pushed into Eastern Eurasia.

Another gene variant that increases the size of the spleen is carried by the Sama-Bajau, nomadic people who live on flotillas of houseboats in the seas off the Philippines, Malaysia and Indonesia.[68] The spleen stores oxygen-carrying red blood cells, and when humans hold their breath it expels these cells to boost oxygen levels; this helps to explain how Sama-Bajau are able to dive to depths of over 230 feet or 70 meters with nothing more than a set of weights and a pair of wooden goggles.

The Last Glacial Period—which lasted from around 110,000 to 12,000 years ago—covered much of North Eurasia in ice and made it difficult for Neanderthals to survive. Estimates for their population size vary from 5,000 to 70,000—tiny when one considers that they were spread across a region that stretched from the Atlantic Ocean to Siberia.[71] It shouldn’t come as a surprise that there is evidence of long-term inbreeding.

Stonehenge wasn’t built by the earliest people to permanently inhabit the British Isles. It was constructed by farmers who originated in Anatolia and arrived in northwestern Europe about 6,000 years ago and almost completely replaced the genetically distinct hunter-gatherer population who had lived there since the end of the Ice Age.

Before the widespread adoption of settled agriculture, the planet probably had about 5 million inhabitants—less than one-thousandth of today’s total.[9] Such a sparsely populated world provided limited opportunities for pathogens to spread when they did emerge.

By growing calorie-rich cereals, farming societies were able to feed many more mouths on the same amount of land: Diamond suggests 100 times more.[17] A recent study demonstrated that our planet is capable of supporting no more than 10 million hunter-gatherers.[18] By 1800 CE, the world’s population had grown to about 900 million with only very basic technology, so this estimate is pretty much spot on.[19] The earth now supports nearly 8 billion people, albeit precariously.

It is inconceivable that the indigenous foragers would have allowed their land to be stolen and their way of life destroyed.

I'll grant you the latter, but the former assumes they had any conception of land "ownership" and property rights at all.

The majority of loos weren’t connected to public sewers because, before the invention of the U-bend, rats and all sorts of other creatures would have run amok in people’s houses. One apocryphal tale from the Roman author Aelian describes how a giant octopus swam from the sea into the sewer and entered the house of a wealthy merchant in the Bay of Naples through the toilet, then proceeded to eat all the pickled fish in his pantry.

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.

He noted that Osman’s successor, Sultan Orhan, who led the Ottomans from about 1323 to 1362, “was always on the move, never staying in the same place for more than a few days.”[41] This peripatetic lifestyle would have protected him and his followers from plague. Unlike people who lived in permanent villages and towns, nomads didn’t store large amounts of grain or accumulate big piles of food waste, both of which attracted rats. The nomadic Turkish would have suffered fewer plague casualties than their settled Turkish neighbors, the Byzantines and the Slavs in the Balkans.

The standard of living for most people in Europe had barely changed since the days of the Roman Empire. The American historian Robert Brenner points out that the feudal system leads to economic stagnation because it isn’t in the interests of either feudal serfs or their lords to maximize profits.

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.

In contrast to North America, where the colonial legacy was democracy and rule of law,

and also persistent structural inequality and racism?!?! wtf dude. eta: my bad, he does address this later on.

In fact, the single biggest factor behind the sudden and marked increase in enslaved African Americans between 1680 and 1750 in the southern colonies—but not the northern ones—was infectious diseases. Unlike the Caribbean, where yellow fever was the major hazard, in the North American colonies it was malaria that played a decisive role.

In the central areas of Manchester and Liverpool, you could expect to live for around twenty-five years—a shorter lifespan than at any time since the Black Death.[20] The figures are even worse when we focus just on the poor. Life expectancy for factory laborers was seventeen in Manchester and fifteen in Liverpool.

The crowded and unsanitary conditions in working-class urban districts created new habitats in which previously uncommon pathogens thrived. Infectious diseases weren’t receding here. In fact, in the middle of the nineteenth century they accounted for about 40 percent of deaths in England and Wales, with the figures much higher in urban areas.[25] In London they were responsible for 55 percent of deaths, and in parts of Liverpool and Manchester the figure was about 60 percent.

Chadwick and Senior certainly succeeded in designing a system that was very unpleasant for anyone who wanted to claim poor relief. To access support, families had to enter the workhouse. The fundamental principle of this dreaded institution was that life within it must be even worse than the worst existence one could have outside. This was an almost impossible feat in the first half of the nineteenth century, but its architects rose to the challenge.

This removed the stench of excrement from the local neighborhoods, but pumping several hundred tons of raw sewage directly into the river every day transformed it into what Benjamin Disraeli, the Tory leader in the Commons and Chancellor of the Exchequer, described as “a Stygian pool reeking with ineffable and unbearable horror.”

It was not lack of technology or money that stopped society from dealing with the deadly unsanitary conditions in working-class neighborhoods of provincial towns and cities; rather, it was the absence of political will. Providing sanitation and clean water to the masses is an enormously expensive undertaking, but one that delivers huge long-term economic and non-economic benefits. Such projects are not viable for private companies motivated by short-term returns on investment, so the problem of sanitation can’t be solved by the invisible hand of the market. Instead, it is imperative that the state steps in, at the very least to coordinate. Unfortunately, local and national governments in the mid-nineteenth century were beholden to the parochial interests of small business owners who voted for politicians promising to keep taxes low, and in spite of recurrent cholera outbreaks local leaders refused to invest in preventative health infrastructure.

lol love to see history repeat itself over and over and over again :(

In almost every country that industrialized in the nineteenth century, including most of Europe, the U.S. and Japan, the urban working classes experienced a generation-long decline in health and life expectancy.[68] Eventually, the state intervened to mitigate the deprivation and ensure that growth was converted into improved well-being and health. The one notable exception to this is Sweden, where the government passed comprehensive public health legislation in the 1870s in anticipation of the disruption that was to come. As a result, when Sweden went through its Industrial Revolution in the last decades of the nineteenth century, it largely managed to avoid the death and disease part of the four Ds.

Sachs and his collaborators argue that infectious diseases create a “poverty trap” that is almost impossible to escape.[16] Poor people are more likely to get ill, making them even poorer and even more prone to infectious disease. Low-income countries tend to be afflicted by more infectious diseases, which in turn undermines economic growth and makes it very difficult for them to prosper.

The Turkish-American economist Daron Acemoglu demonstrates how the settlement patterns of European colonialists between the seventeenth and nineteenth centuries were determined by infectious diseases.[39] Where death rates were low—in New England, for example—men brought their families, settled down and built new societies in the image of the ones they’d just left; in this endeavor they were aided by infectious diseases that decimated the indigenous population. These colonies grew into wealthy democracies that although imperfect were relatively responsive to the needs of the electorate. Where mortality from infectious diseases was high, the outcome was very different: entrepreneurial colonialists built extractive institutions that were designed to make as much money as possible, as quickly as possible, before they returned home to their families. This happened most clearly in sub-Saharan Africa, where malaria and yellow fever made the region almost uninhabitable for Europeans.

But at the same time, low-income countries, predominately in sub-Saharan Africa, have been denied the opportunity to follow a similar strategy; in effect, high-income countries “kicked away the ladder” that they had used to climb out of the poverty trap. Instead, sub-Saharan African countries were encouraged to use an untested approach to public health that stressed medicine and technology.[49] But states in low-income countries weren’t able to take full advantage of the exciting new possibilities offered by advances in medical science. How could they, after being hollowed out first by colonialism and then by structural adjustment?

Prior to the Covid-19 pandemic, the disparities in life expectancy within the UK were not explained by the differential impact of infectious diseases, as they killed far too few people to make a mark. Rather, inequalities in health outcomes were the result of disparities in premature deaths from non-communicable diseases, most notably cardiovascular disease, cancers and diabetes. While such illnesses obviously aren’t transmitted from one person to another by pathogens, their distribution is not random. Just as the urban working classes in Victorian slums were more likely to be affected by cholera or TB, these modern “plagues” disproportionately impact the poor—hence the inequalities in health outcomes between places like Kensington and Chelsea on the one hand and Blackpool on the other.

A recent study found that the poorest 10 percent of households in the UK would have to spend over 70 percent of their income in order to follow healthy eating guidelines.[55] As a result, we see higher levels of obesity in low-income areas.

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.

Health inequalities in the UK stem from policy choices made by the government. When Margaret Thatcher became prime minister in 1979 she reintroduced many ideas that had been popular in the mid-nineteenth century: not just the emphasis on free-market economics and an aversion to state intervention, but also the belief that people who are left behind by these brutal macroeconomic transformations are underserving scroungers who must be shamed into working harder. This was self-imposed, structural adjustment. Since 2010, the Conservative-led government has continued to push for limited state intervention in society.

ah, i can sense the seething hatred of Thatcher in these words. more than deserved!

Since 2015, life expectancy at the national level has been in decline. The Nobel Prize–winning economist Angus Deaton and his collaborator Anne Case point out that this is driven by an increase in suicides, alcohol abuse and drug overdoses, which kill about 190,000 people each year—three times more than in the 1990s.[63] The surge in deaths of despair is almost exclusively accounted for by white middle-aged males without a university degree; the death rate for this group has risen by a quarter in the last three decades.

Wages for workers who don’t have a university education have fallen by 15 percent in this period but have increased by a tenth for those with a bachelor’s and by a quarter for those with a higher degree. Today, the most that someone with a high-school education can realistically hope for is a precarious, poorly paid job without health insurance or a pension.

and if you get that college education and your parents can't pay for it, you're burdened by student loan debt for decades!

The system is so inefficient that if the U.S. had a national health service like the UK’s, its health outcomes would improve and it would save almost 2.5 trillion dollars every year. Deaton and Case point out that the dysfunction in the U.S. health care system is, in monetary terms, more of a handicap than the reparations that Germany had to pay following the First World War.

The Covid-19 pandemic has not only highlighted stark inequalities between countries. It has also drawn attention to deprivation within high-income countries. Richard Horton, editor of The Lancet, argues that the devastation wrought by coronavirus in the UK and the U.S. should be understood as a “syndemic” or “synergistic epidemic.” In other words, the impact of the coronavirus pandemic can only be understood if we take into account the pre-existing pandemics of poverty and obesity that were already ravaging wealthy societies.

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