Wealth, war and worse: plague’s ubiquity across millennia of human conquest
Unsupervised Learning Journal Club #1
For 2025, I’m trying out a new occasional feature for paying subscribers, the Unsupervised Learning Journal Club: I’ll offer a brisk review and consideration of an interesting paper in human population genomics.
In the spirit of a conventional journal club, at the end of each post, interested subscribers can vote on next papers to review. I’m open both to covering the latest papers/preprints and reflecting back on seminal publications from any time in these first decades of the genomic era.
If your lab has work we might like or you otherwise want to suggest a paper for me to cover, feel free to respond to this email or comment on this post.
Free subscribers can get a sense of the format from my ungated coverage of two favorite 2024 papers:
The other man: Neanderthal findings test our power of imagination
We were selected: tracing what humans were made for
Unsupervised Learning Journal Club #1
Today’s paper is Repeated plague infections across six generations of Neolithic Farmers. It comes out of Martin Sikora’s group at the GeoGenetics Centre at the University of Copenhagen and appeared in the July 10, 2024 issue of Nature. Contributing authors include Kristian Kristiansen, Eske Willerslev and Mattias Jakobsson. The first author is Frederik Valeur Seersholm.
A plague o’ [all] your houses
In the 1300’s, a high-stakes rivalry between the Most Serene Republic of Venice and the city state of Genoa was playing out in port cities from one end of the Mediterranean to the other. Genoa’s most far-flung colonies were a string of port cities and trading centers along the southern coast of the Crimean peninsula, south of the Pontic steppe. A western terminus of the Silk Road, these Genoese colonies were Europe’s gateway and entrepôt for the riches of the east. But more than wealth coursed out of the heart of Asia; armies of Turks and Mongols repeatedly brought the spectre of war to the busy mercantile Genoese posted at what for medieval Europeans was the known world’s furthest edge. And ultimately far worse than war: they brought their unseen and unanswerable pathogens.
There, in the port of Caffa, in 1347 the plague broke out, a silent stowaway with the armies of the Mongol Golden Horde then laying siege to the coastal Black Sea cities as a side project to the business of ravaging the Russian principalities. Over the next six years, the pestilence that first engulfed Caffa would seep inexorably all across Europe, killing 25-50% of European populations, and forever transforming the continent’s culture and economics. In A Farewell to Alms: A Brief Economic History of the World, economist Gregory Clark argues that the plague-driven population crash proved an indispensable condition for smashing the feudal bonds that had tied European peasants to the land, kickstarting an economic dynamo that, within centuries, would lead to the Industrial Revolution and drag the rest of the world into the modern age.
The Black Death, as it came to be known, heralded the High Middle Ages’ end, just as Europe had been stepping back to the fore among great world civilizations, producing minds like St. Thomas Aquinas and William of Ockham and organizing centuries-long projects like the great cathedrals. But the close of Europe’s medieval chapter turned the page to a more glorious interlude in the continent’s story, the Renaissance’s creative explosion and ultimately the achievements of modernity itself. The 14th-century plague was a tragic prologue to what ultimately became a triumphant story of resilience and renaissance. Glorious rebirth though is scarcely a fait accompli for civilizations assailed by plague. A century and a half after the Black Death cut down great swaths of unprotected Europeans, unprotected Aztec, Maya and Inca populations were in turn exposed to the ravages of European pestilence like smallpox, which ripped through their societies, leaving them weakened and vulnerable to rapid European conquest, erasing much of their societies’ legacy overnight and relegating them to footnotes in Western histories.
Plague shaping the history of Europe and the New World over the past millennium is a well known storyline. Disease drives macrohistories like William H. McNeill’s 1976 Plagues and Peoples, and plays a substantial role in Jared Diamond’s 1997 Guns, Germs and Steel. And now with genomic signatures of natural selection we are finding that the role of disease in history, and prehistory as well, was even more decisive than we had thought. The genetic code of our species has been rewritten over and over in response to the selection pressures disease imposes upon us. Sexual reproduction itself may be an adaptation to the bath of pathogens in which every multicellular organism is condemned to swim. Disease has shaped our lineage for millions of years, driving our evolution, as our immune systems race to remain one step ahead. Tuberculosis was famously a pervasive ailment in Victorian England, the root cause behind “consumption,” but now we know that even Neanderthals 40,000 years ago suffered from it. A plague of smallpox heralded the end of a decades-long period of peace in the Roman Empire called the Antonine Age, while another pestilence four centuries later halted the Roman revival under Emperor Justinian.