Rosa Rubicondior: Malevolent Design - A Paradox Creationists Pretend Not to See

Progress of the Black Death in Europe

By Flappiefh - Own work from:Natural Earth Cesana, D.; Benedictow O.J., Bianucci R. (2017). "The origin and early spread of the Black Death in Italy: first evidence of plague victims from 14th-century Liguria (northern Italy)". Anthropological Science 125 (1): 15–24. DOI:10.1537/ase.161011. ISSN: 0918-7960. (page 17),
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USF, FAU researchers solve 1,500-year-old mystery: The bacterium behind the first pandemic

The notion of intelligent design — the current flagship of creationism’s attempt to replace scientific realism with magical superstitions and Bible literalism dressed up as “alternative science” — contains a blatant paradox its advocates must ignore: the very same “logic” used to argue that the God of the Bible created living organisms can just as easily be used to argue that any such designer is a malevolent sadist who deliberately increases suffering in the world while ignoring countless ways to reduce it.

The theological problems this raises are never discussed in polite creationist circles, except for the lazy fallback of blaming everything on “The Fall.” But this move exposes intelligent design for what it really is — Bible-literalist religion in disguise. And that sits awkwardly against over half a century of insistence by the Discovery Institute that ID is not a religious idea, but rather a scientific one that should be taught in American public schools at taxpayer expense — a direct violation of the Establishment Clause and the U.S. Supreme Court’s ruling in Edwards v. Aguillard (1987).

The paradox lies in the fact that the very same so-called evidence — Michael J. Behe’s “irreducible complexity” and William A. Dembski’s “complex specified genetic information” — can be found in the genomes, structures, and processes of parasites and pathogens, making them devastatingly effective at exploiting and destroying their hosts. In fact, Behe himself has, probably without realising it, used precisely such examples. The bacterial flagellum he highlights enables E. coli to move efficiently through our gut, causing sometimes fatal food poisoning. And his example of resistance to anti-malarial drugs in Plasmodium parasites illustrate how evolution equips them to continue killing hundreds of thousands of children every year while condemning millions more to cycles of malarial fever.

Now, new research has highlighted another gruesome example. The bacterium Yersinia pestis — responsible for multiple waves of plague throughout the Middle Ages — has been shown to have evolved into its highly lethal form only in relatively recent human history. Beginning with the “Plague of Justinian” about 1,500 years ago, Y. pestis unleashed pandemics that killed between 30% and 50% of Europe’s population.

An interdisciplinary team at the University of South Florida (USF) and Florida Atlantic University (FAU), with collaborators in India and Australia, has now confirmed genomically that the Justinian plague was indeed caused by Y. pestis, as long assumed. Analysing DNA from plague victims buried in a mass grave at the ancient city of Jerash, Jordan — the epicentre of that pandemic — one group identified the culprit, while another team traced the bacterium’s evolutionary changes that made it one of history’s most notorious killers.

Background^ The Black Death. The Black Death was the most devastating pandemic in recorded history, caused by the bacterium Yersinia pestis. It spread rapidly along trade routes, carried by fleas on black rats and, later, through human-to-human transmission via respiratory droplets.

Origins and Spread

Asia: Most historians trace its origins to Central Asia in the early 14th century, possibly around modern-day Kyrgyzstan. It spread westward via the Silk Road and Mongol trade/military networks.
Middle East & North Africa: By the late 1340s it had reached the Middle East, Persia, and North Africa, killing vast numbers in cities such as Cairo, Alexandria, and Damascus.
Europe: The plague reached Europe in 1347, arriving at the Sicilian port of Messina on Genoese ships from the Black Sea. From there it swept across Italy, France, Spain, and England, reaching Scandinavia, Eastern Europe, and Russia within just a few years.

Mortality and Impact

Estimated 75–200 million deaths worldwide between 1347 and 1353.
Europe lost 30–50% of its population, with some areas, such as Florence and Paris, losing up to 60–70%.
Entire villages were abandoned, labour shortages upended feudal economies, and recurring outbreaks continued into the 18th century.
In the Middle East and North Africa, mortality rates were similarly catastrophic, though less well documented; Cairo may have lost 40% of its population.
In Asia, the plague depopulated parts of China and Central Asia, disrupting the Mongol Empire’s dominance and trade routes.

Long-term Consequences

Massive social, economic, and religious upheaval: labour became more valuable, feudal bonds weakened, and peasant revolts erupted across Europe.
Widespread questioning of religious institutions, which had failed to protect people, helped sow seeds of doubt that would later contribute to the Renaissance and Reformation.
The plague fundamentally reshaped demographics, economies, and societies across three continents.

This research is discussed in an article in USF Health by Cody R. Hawley, PhD, and in two open-access research papers: one in Pathogens and the other in Genes.

USF, FAU researchers solve 1,500-year-old mystery: The bacterium behind the first pandemic
Interdisciplinary team uncovers first genetic evidence of the Plague of Justinian in the Eastern Mediterranean, reshaping the history of pandemics
For the first time, researchers have uncovered direct genomic evidence of the bacterium behind the Plague of Justinian — the world’s first recorded pandemic — in the Eastern Mediterranean, where the outbreak was first described nearly 1,500 years ago.

The landmark discovery, led by an interdisciplinary team at the University of South Florida and Florida Atlantic University, with collaborators in India and Australia, identified Yersinia pestis, the microbe that causes plague, in a mass grave at the ancient city of Jerash, Jordan, near the pandemic’s epicentre. The groundbreaking find definitively links the pathogen to the Justinian Plague marking the first pandemic (AD 541–750), resolving one of history’s long-standing mysteries.

For centuries, historians have deliberated on what caused the devastating outbreak that killed tens of millions, reshaped the Byzantine Empire and altered the course of Western civilization. Despite circumstantial evidence, direct proof of the responsible microbe had remained elusive — a missing link in the story of pandemics.

Two newly published papers led by USF and FAU provide these long-sought answers, offering new insight into one of the most consequential episodes in human history. The discovery also underscores plague’s ongoing relevance today: while rare, Y. pestis continues to circulate worldwide. In July, a resident of northern Arizona died from pneumonic plague, the most lethal form of Y. pestis infection, marking the first such fatality in the U.S. since 2007, and just last week another individual in California tested positive for the disease.

This discovery provides the long-sought definitive proof of Y. pestis at the epicenter of the Plague of Justinian. For centuries, we’ve relied on written accounts describing a devastating disease, but lacked any hard biological evidence of plague’s presence. Our findings provide the missing piece of that puzzle, offering the first direct genetic window into how this pandemic unfolded at the heart of the empire.

Associate Professor Rays H. Y. Jiang, PhD, lead author (both papers)
USF Genomics, Global Health Infectious Disease Research Center (GHIDR)
Global Health
College of Public Health
University of South Florida, Tampa, FL, USA.

The Plague of Justinian first appeared in the historical record in Pelusium (present day Tell el-Farama) in Egypt before spreading throughout the Eastern Roman, or Byzantine, Empire. While traces of Y. pestis had previously been recovered thousands of miles away in small western European villages, no evidence had ever been found within the empire itself or near the heart of the pandemic.

Using targeted ancient DNA techniques, we successfully recovered and sequenced genetic material from eight human teeth excavated from burial chambers beneath the former Roman hippodrome in Jerash, a city just 200 miles from ancient Pelusium

Professor Greg O’Corry-Crowe, PhD, co-author.
Harbor Branch Oceanographic Institute
Florida Atlantic University, Fort Pierce, FL, USA.

Genomic analysis revealed that the plague victims carried nearly identical strains of Y. pestis, confirming for the first time that the bacterium was present within the Byzantine Empire between AD 550-660. That genetic uniformity suggests a rapid, devastating outbreak consistent with historical descriptions of a plague causing mass death.

The Jerash site offers a rare glimpse of how ancient societies responded to public health disaster. Jerash was one of the key cities of the Eastern Roman Empire, a documented trade hub with magnificent structures. That a venue once built for entertainment and civic pride became a mass cemetery in a time of emergency shows how urban centers were very likely overwhelmed.

Associate Professor Rays H. Y. Jiang.

Tooth from the Jerash architectural site

A companion study, also led by USF and FAU, places the Jerash discovery into a wider evolutionary context. By analyzing hundreds of ancient and modern Y. pestis genomes — including those newly recovered from Jerash — the researchers showed that the bacteria had been circulating among human populations for millennia before the Justinian outbreak.

The team also found that later plague pandemics, from the Black Death of the 14th century to cases still appearing today, did not descend from a single ancestral strain. Instead, they arose independently and repeatedly from longstanding animal reservoirs, erupting in multiple waves across different regions and eras. This repeated pattern stands in stark contrast to the SARS-CoV-2 pandemic (COVID-19), which originated from a single spillover event and evolved primarily through human-to-human transmission.

Together, the landmark findings reshape the understanding of how pandemics emerge, recur and spread, and why they remain a persistent feature of human civilization. The research underscores that pandemics are not singular historical catastrophes, but repeating biological events driven by human congregation, mobility and environmental change — themes that remain relevant today.

This research was both scientifically compelling and personally resonant. It offered an extraordinary opportunity to delve into the study of human history through the lens of ancient DNA at a time when we ourselves were living through a global pandemic. Equally profound was the experience of working with ancient human remains — individuals who lived, suffered, and died centuries ago — and using modern science to help recover and share their stories. It’s a humbling reminder of our shared humanity across time and a moving testament to the power of science to give voice to those long silent.

Professor Greg O’Corry-Crowe.

While very different from COVID-19, both diseases highlight the enduring link between connectivity and pandemic risk, as well as the reality that some pathogens can never be fully eradicated.

We've been wrestling with plague for a few thousand years and people still die from it today. Like COVID, it continues to evolve, and containment measures evidently can’t get rid of it. We have to be careful, but the threat will never go away.

Associate Professor Rays H. Y. Jiang.

CODA: From Justinian to the Black Death

Building on the Jerash breakthrough, the team is now expanding its research to Venice, Italy and the Lazaretto Vecchio, a dedicated quarantine island and one the world’s most significant plague burial sites. More than 1,200 samples from this Black Death-era mass grave are now housed at USF, offering an unprecedented opportunity to study how early public health measures intersected with pathogen evolution, urban vulnerability and cultural memory.

USF and FAU researchers contributing to the studies:

Rays H. Y. Jiang, PhD, lead author and PI, associate professor, Department of Global Health, College of Public Health, University of South Florida
Swamy R. Adapa, research and development scientist, Department of Global Health, College of Public Health, University of South Florida
Andrea Vianello, PhD, visiting research fellow, Department of Anthropology, College of Arts and Sciences, University of South Florida.
Gregory O’Corry-Crowe, PhD, research professor, Harbor Branch Oceanographic Institute, Florida Atlantic University.
Jorge Monroy, molecular genetics technician, Harbor Branch Oceanographic Institute, Florida Atlantic University.
Tatiana Ferrer, coordinator of research programs, Harbor Branch Oceanographic Institute, Florida Atlantic University.
Elizabeth Remily‑Wood, proteomics core director, Department of Molecular Medicine, Morsani College of Medicine, University of South Florida.
Gloria C. Ferreira, PhD, professor, Department of Molecular Medicine, Morsani College of Medicine and College of Arts and Sciences, University of South Florida.
Michael Decker, PhD, Maroulis Professor of Byzantine History and Orthodox Religion, Department of History, College of Arts and Sciences, University of South Florida.
Robert H. Tykot, PhD, professor, Department of Anthropology, College of Arts and Sciences, University of South Florida.

Publications:

Dutta, S.; Upadhyay, A.; Adapa, S.R.; O’Corry-Crowe, G.; Tripathy, S.; Jiang, R.H.Y.
Ancient Origins and Global Diversity of Plague: Genomic Evidence for Deep Eurasian Reservoirs and Recurrent Emergence.
Pathogens 2025, 14, 797. https://doi.org/10.3390/pathogens14080797
Adapa, S.R.; Hendrix, K.; Upadhyay, A.; Dutta, S.; Vianello, A.; O’Corry-Crowe, G.; Monroy, J.; Ferrer, T.; Remily-Wood, E.; Ferreira, G.C.; et al.
Genetic Evidence of Yersinia pestis from the First Pandemic.
Genes 2025, 16, 926. https://doi.org/10.3390/genes16080926

Paper 1. Ancient Origins and Global Diversity of Plague: Genomic Evidence for Deep Eurasian Reservoirs and Recurrent Emergence:

Abstract
Yersinia pestis, the causative agent of plague, has triggered multiple pandemics throughout human history, yet its long-term evolutionary patterns and reservoir dynamics remain poorly understood. Here, we present a global phylogenomic analysis of ancient and modern Y. pestis strains spanning from the Neolithic and Bronze Age to the present day. We show that pandemic-causing lineages did not arise from a single ancestral strain but instead emerged independently along deep branches of the Y. pestis phylogeny. Pandemic-associated Y. pestis strains were recovered exclusively from human remains and display clear local temporal divergence, indicating evolution driven by human transmission during outbreaks. These findings support the hypothesis that plague emergence is driven by complex, regionally rooted reservoirs, with recurrent spillovers into human populations across millennia. Our work highlights the need to view plague not as a series of isolated outbreaks but as a long-standing zoonotic threat shaped by deep evolutionary history, host ecology, and human societal structures.

1. Introduction
Yersinia pestis, the bacterial pathogen responsible for plague, has caused some of the most devastating pandemics in human history, including the First Pandemic (541–750 CE) [1,2], the Second Pandemic (14th–18th centuries, including the Black Death) [3,4,5,6], and the Third Pandemic (19th–20th centuries) [4]. Despite over a century of microbiological study and two decades of ancient DNA (aDNA) analysis, major questions remain regarding the evolutionary origin, reservoir ecology, and transmission dynamics that underpin plague’s recurrent emergence across vast geographic and temporal scales.

Recent advances in paleogenomics have enabled the reconstruction of ancient Y. pestis genomes from human remains, revealing that the pathogen was already widespread in Eurasia long before the historical pandemics began [7,8,9,10,11]. Notably, strains dating back to the Neolithic and Bronze Age have been recovered from multiple sites [9,10,12], suggesting that Y. pestis had a deep-rooted and complex history as both a zoonotic and human-associated pathogen [13,14,15]. However, many of these studies have focused on isolated outbreaks or specific time periods, leaving the global evolutionary landscape of Y. pestis incompletely understood.

The First Pandemic represents a critical transition in human history—from sporadic regional outbreaks to the first recorded global pandemic within the known world [16,17,18]. While previously recovered Y. pestis genomes from Western Europe mark the geographic and epidemiological fringes of this pandemic, the Jerash site in present-day Jordan [19,20,21,22,23] offers the first direct genetic evidence of plague near the eastern Mediterranean, long recognized as the historical epicenter [24]. The genomes recovered in western Europe came from small numbers of individuals, often single burials within established cemeteries; whereas the Jerash genomes were obtained from multiple individuals interred together in a hastily constructed mass grave. Together, these findings bridge a crucial geographic and temporal gap, providing new insight into the initiation and early spread of the First Pandemic and its movement across interconnected regions of the late antique world.

Here, we present a comprehensive phylogenomic analysis of Y. pestis strains ranging from prehistoric times to the modern era, incorporating both previously published genomes and newly reconstructed sequences [25] from a culturally and geopolitically significant Eastern Mediterranean city that hosted a mass grave during the First Pandemic.

By integrating phylogenetic reconstruction, spatiotemporal mapping, and host-range analysis, we address three major questions:

How did major Y. pestis lineages diverge and persist across millennia?
What evolutionary patterns differentiate ancient pandemic strains from modern environmental lineages?
What do the geographic origins and host associations of these strains reveal about the nature of plague reservoirs and outbreak dynamics?

Our findings demonstrate that plague pandemics did not stem from a single evolutionary lineage or event but emerged independently from diverse, regionally entrenched reservoirs. The persistence of deeply divergent lineages, combined with the absence of a unified molecular clock, challenges traditional models of linear pathogen evolution and highlights the ecological complexity underlying plague’s long-term history. This work reframes plague not merely as a historical phenomenon but as an ongoing zoonosis shaped by deep time, environmental entrenchment, and human mobility.

Figure 1. Geographic and temporal distribution of Yersinia pestis genomes across Eurasia from prehistory to historical pandemics. (A) Locations of ancient Y. pestis DNA identified to date are shown, with sites from the Neolithic and Bronze Age marked in pink and those from the First Pandemic period (~541–750 CE) in dark blue. The Jerash site (star) represents the earliest archaeogenetic evidence of plague near the historically documented epicenter of the First Pandemic in the Eastern Mediterranean. Yellow dots within dark blue regions indicate published First Pandemic genomes from Western European cemeteries. A single genome from the Tian Shan region (yellow dot) represents a potential precursor strain circulating in Central or Western Asia prior to the Justinianic Plague. (B) Geographic distribution of modern plague lineages suggests a Central/West Asian origin. Modern lineages have also been identified in other regions, including North America and Madagascar (not shown). Areas with more ancestral modern lineages (e.g., Pestoides [PE]) are shaded in purple, while those dominated by more recent lineages (e.g., Antiqua [ANT], Medievalis [MED], and Orientalis [ORI]) are shaded in yellow, reflecting historical patterns of dispersal and diversification.

Figure 2. Global phylogenetic analysis of Y. pestis from prehistory to the present. Maximum Likelihood phylogenetic reconstruction of Y. pestis genomes, with tree topology supported by 1000 bootstrap replicates. The phylogeny reveals deep-rooted patterns, highlighting the ancient origins of modern global plague lineages and indicating that many prevalent lineages began diverging early in plague evolutionary history. A Central Asian strain is clustered with First Pandemic genomes recovered from the eastern Mediterranean to Western Europe, forming a highly supported clade. Notably, most major modern lineages predate the Black Death, and several—such as the Pestoides (PE) lineage—even precede the First Pandemic. All modern lineages refer to genomes from current Y. pestis collections.

Dutta, S.; Upadhyay, A.; Adapa, S.R.; O’Corry-Crowe, G.; Tripathy, S.; Jiang, R.H.Y.
Ancient Origins and Global Diversity of Plague: Genomic Evidence for Deep Eurasian Reservoirs and Recurrent Emergence.
Pathogens 2025, 14, 797. https://doi.org/10.3390/pathogens14080797

Copyright: © 2025 The authors.
Published by MDPI (Basel, Switzerland). Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

Paper 2. Genetic Evidence of Yersinia pestis from the First Pandemic:

Abstract

Background/Objectives:
The Plague of Justinian marked the beginning of the First Pandemic (541–750 CE), yet no genomic evidence of Yersinia pestis has previously been recovered from the Eastern Mediterranean, where the outbreak was first recorded. This study aimed to determine whether Y. pestis was present in a mid-6th to early 7th century mass grave in Jerash, Jordan, and to characterize its genome within the broader context of First Pandemic strains.

Methods:
We analyzed samples from multiple individuals recovered from the Jerash mass grave. Initial screening for potential pathogen presence was conducted using proteomics. Select samples were subjected to ancient DNA extraction and whole genome sequencing. Comparative genomic and phylogenetic analyses were conducted to assess strain identity and evolutionary placement.

Results:
Genomic sequencing recovered Y. pestis DNA from five individuals, revealing highly similar genomes. All strains clustered tightly with other First Pandemic lineages but were notably recovered from a region geographically close to the pandemic’s historical epicenter for the first time. The near-identical genomes across diverse individuals suggest an outbreak of a single circulating lineage at the time of this outbreak. Conclusions: This study provides the first genomic evidence of Y. pestis in the Eastern Mediterranean during the First Pandemic, linking archaeological findings with pathogen genomics near the origin point of the Plague of Justinian. Summary Sentence: Genomic evidence links Y. pestis to the First Pandemic in an ancient city.

1. Introduction
Three plague pandemics have been recorded in history over Western Eurasia and portions of Africa. The First Pandemic, the so-called Plague of Justinian began, according to historical sources [1.1,2.1], in 541 CE and lasted until ca. 750 CE. The disease first appeared in the historical record at Pelusium (present day Tell el-Farama) in Northern Egypt, then part of the Eastern Roman (Byzantine) empire, and was believed by contemporaries to have begun in East Africa or South Arabia, whence it rapidly spread throughout the Mediterranean and Middle East [3.1] (Figure 1A). The Second Pandemic, starting with the Black Death from 1346–1353 CE, is much better documented historically and resulted in a death rate of about 65% of the European population, or 80 million people, and at least 25 million in Asia and Africa [4.1,5.1]. The Third Pandemic, started in China, has resulted in the deaths of over 15 million people and continues today, with plague remaining endemic in numerous countries worldwide and annual outbreaks reported [5.1].

Figure 1. Jerash mass grave site in the context of the First Pandemic. (A). Regions of aDNA isolated to date prior or at the First Pandemic are marked in dark brown (around First Pandemic). The Jerash site is marked by a star. The Eastern Roman Empire (indicated in dark red) historically documented the plague spreading from North Egypt and the Near East through Mediterranean regions. Yellow dots in dark brown regions denote the current available genetic evidence of Y. pestis recovered from Western European cemeteries. The single Tian Shan Hun Strain (yellow dot) in Central/Western Asia is hypothesized to be one of the early strains present prior to the onset of the Plague of Justinian. (B). Jerash (Gerasa) hippodrome ground plan. The schematic of the ground plan was redrawn based on the illustration of Anton Ostrasz. The mass graves were uncovered in the abandoned Roman hippodrome chambers W2 and W3. (C). One of the chambers (W2) where the bodies were recovered.

The plague is caused by Y. pestis, a Gram-negative zoonotic coccobacillus. Since plague leaves no bone lesions or other distinguishing skeletal features, molecular evidence of plague is required to confirm infection in human remains and can be obtained by extraction and molecular analysis of highly vascularized tissue like dental pulp [6.1]. The application of aDNA protocols to the pulverulent dental pulp led to the first molecular identification of Y. pestis in individual skeletal remains of victims of the Second Pandemic and opened the study of the paleomicrobiology of the disease [6.1].

However, to date, no Y. pestis genetic material has been recovered in the Eastern Mediterranean in geographic and temporal proximity to the epicenter of the First Pandemic. Currently, a few sites in Central and Northwestern Europe have yielded skeletal remains and ancient DNA linked to the Plague of Justinian time period; e.g., two in Germany, one in Spain, three in France, and one in England [7.1]. These sites are far from the reported epicenter of the Plague of Justinian, with Bavaria in Germany lying 2500 km distant and Edix Hill cemetery in England more than 3500 km distant from the epicenter of Pelusium.

There is also a lack of archaeological evidence of mass graves within the Eastern Mediterranean, where the plague emerged and likely had more severe effects. While mass graves, or ‘plague pits’ as they are sometimes called, have been found in considerable number relating to the Second Pandemic of the 14th century CE, none have thus far been identified as relating to the First Pandemic.

Here, we report archaeological and genetic findings of Y. pestis in multiple individuals from a mass grave approximately 550–660 CE in Jerash in Jordan, the ancient city of Gerasa, which lies 50 km north of Amman. We therefore present the first archeological and molecular evidence of Y. pestis linked to the time of the Plague of Justinian within the confines of the Roman Empire and geographically proximate to the historically attested epicenter: Jerash is just 330 km from Pelusium. Archaeological Context—Jerash (Ancient Gerasa)

Jerash was an important city during the Greco-Roman and Byzantine periods and is considered one of the largest and most well-preserved sites of Roman architecture in the world outside Italy [8.1]. Among the many accoutrements of Roman rule was the installation of a hippodrome (chariot racetrack or Roman Circus) outside the city center. The Jerash Hippodrome was built in the mid-2nd century CE and ceased to exist as a chariot racing arena in the first quarter of the 4th century CE [9.1]. (An ideal reconstruction of the 2nd century CE Roman city of Gerasa, located in present-day Jerash, Jordan, can be viewed in JR. CASALS’ rendering work.)

After the Hippodrome ceased as a chariot racing venue, the storage chambers under the seating were part of structures in the Hippodrome to be repurposed for light industry, including ceramic workshops dating from the Late Roman period that continued into the Early Byzantine period (mid-4th century CE) [10.1]. A compact layer of misfired and unfired Late Byzantine (the second half of the 6th century CE) pottery, including fragments of ‘Jerash Bowls’, sealed these installations. The entire building was abandoned around the latter part of the 6th century CE or beginning of the 7th century CE [11.1].

The 1993 excavations of the W2 and W3 chambers (Figure 1B,C) discovered human skeletons immediately above the dumps of the misfired Byzantine pottery, which had been crushed underneath and within the tumbled seating blocks [11.1,12.1] (Figure 2A). Our samples were obtained from these interments, which held approximately 150 adults and 80 sub-adults (neonates, infants, and children) [13.1,14.1].

Figure 2. Archaeological, proteomic, and genetic evidence of an ancient epidemic in Jerash. (A). Archaeological excavation records narrow the mass grave timeframe. The abandoned Roman Hippodrome site was used as a mass grave site around the time of the Plague of Justinian. (B). Proteomics analysis identified potential peptides from Y. pestis. At least three unique pathogen peptides passing quality control in experimental and analysis protocols were required. (C). Summary of samples that yielded proteomics, stable isotopes of oxygen, and ancient DNA (aDNA) results. Y. pestis-positive proteomics samples are colored in purple. For three individuals, two independent aDNA samples were generated from two teeth of the same individual.

Since the initial examination of the mass grave, access to the collection has not been possible, and only a small collection of dentition was available for selection and analysis. From this collection, thirty-seven loose molars and two ribs were chosen for further examination based on their overall completeness, lack of caries, and other dental disease.

Adapa, S.R.; Hendrix, K.; Upadhyay, A.; Dutta, S.; Vianello, A.; O’Corry-Crowe, G.; Monroy, J.; Ferrer, T.; Remily-Wood, E.; Ferreira, G.C.; et al.
Genetic Evidence of Yersinia pestis from the First Pandemic.
Genes 2025, 16, 926. https://doi.org/10.3390/genes16080926

Copyright: © 2025 The authors.
Published by MDPI (Basel, Switzerland). Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

If intelligent design were genuinely a scientific idea, creationists would have to concede that the “designer” they imagine so eagerly is also responsible for designing cholera, malaria, smallpox, and the plague — elegant in their mechanisms, ingenious in their adaptations, but horrifying in their outcomes. The result is a paradox creationists cannot solve: intelligent design points just as strongly to malevolent design.

From the perspective of evolutionary theory, the rise of parasites and pathogens is entirely predictable. Natural selection rewards organisms that exploit available niches, and for a microbe, a warm-blooded animal is a rich, mobile ecosystem to invade. The genomes of Y. pestis, Plasmodium, and countless viruses bear the unmistakable signatures of adaptive change over time.

By contrast, intelligent design creationism can only wave away the suffering by invoking theology — a fall from grace, a hidden plan, or some inscrutable “greater good” — none of which are testable, scientific explanations, and all of which fatally undermine the Wedge Strategy of the Discovery Institute and its fellows to present Intelligent Design as an alternative science and definitely not Bible-literalist creationism in disguise.

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