Category Archives: environmental history

The Microbial Anthropocene


Over the last decade or so, geologists and ecologists have begun to talk about planet earth entering a new geologic period called the Anthropocene, defined as the period when humans became the driving force of change on planet Earth. Debates continue on when the Anthropocene begins; sometime in the late 18th century when the industrial age is underway with the first steam engines, new products appear like plastic that persist in geology, and in medicine, Jenner begins his work on vaccines in the 1790s, would make sense.  I suggest that this also marks the beginning of the microbial Anthropocene — when humans become a driving force in microbial evolution.

Microbiology of the Anthropocene (Gillings and Paulson, 2013). Note the logarithmic time scale.

The graphic above is eye-opening. The Anthropocene is apparent in every level of microbial ecology examined. It is a good reminder that human intervention in microbial evolution goes far beyond infectious disease.

Perhaps most stunning message this graphic brought to me is the logarithmic nature of change. It finally dawned on me looking at this graphic that it also reflects the periods of epidemiological transition theory (ETT). The hunter-gatherer period correlates with the Pleistocene, then the first transition to the farmer-urban period (of epidemics) correlates with the Holocene, and the second transition to the modern third epidemiological phase characterized by longer lifespans and chronic disease is the Anthropocene.  Finally, the time scale of the epidemiologic transitions makes some sense. The logarithmic scale may not bode well for the speed of future transitions.

The changes of the Anthropocene filter down through all living and non-living things. Among living things, there are winners and losers: species whose range and differentiation expands and others are driven to extinction. We can see this on a huge scale in the ocean where we have coral bleaching caused by loss of microbial symbionts, while there is an increasing incidence of toxic blooms and an enlarging dead zone in the Gulf of Mexico both caused by an overgrowth of some microbial species. With each transition, natural selection seems to go into overdrive until a new equilibrium is established (Gilling and Paulsen, 2).

Michael Gillings and Ian Paulsen identified several areas of microbial evolution and ecology impacted during the Anthropocene. The strong selective pressure antibiotics have exerted on infectious agents is the most commonly discussed risk in modern medical microbiology. Changes in the human microbiome are most closely related to diet changes (another feature of the Anthropocene), but our normal flora is also collateral damage of antimicrobial treatment. We often overlook that most antibiotics consumed by humans and livestock are washed through our bodies into the watershed where they alter the microbial ecology of entire ecosystems. Antimicrobial therapy began long before traditional modern antibiotics; mercury was used in medieval medicine to treat syphilis, leprosy and as a topical treatment for lice. Arsenic is still used to poison pests like rats. These early antimicrobials prompted the increase and spread of mercury and arsenic resistance in a wide variety of pathogens and environmental bacteria.

Industrial and agricultural practices have involved bacteria in changes to the global biogeochemistry and played a major role in climate change. The spread of industrialized agriculture has increased the methane production from (bacteria in) livestock, rice patties, and landfills. Crop rotations with legumes with their nitrogen-fixing symbionts increase the agricultural output of the land but in doing so the symbionts have altered the global nitrogen cycle. Gillings and Paulsen observed that the combined effect of burning fossil fuels, cultivating legumes, and industrial nitrogen fixation in fertilizer now accounts for about 45% of global nitrogen fixation. Agriculture on an industrial scale has impacted soil microbiology to the point where it has altered the carbon and nitrogen cycle of the entire planet. Elevated levels of methane and carbon dioxide do more than raise just the global temperature. While some have breathed a sigh of relief that the oceans have acted as a carbon sink, it has not been without cost. An acidic ocean is a price we pay for the carbon sink.  The drop in marine pH will affect all microbial communities down to the depths of the abyss. Coral bleaching due to a loss of their microbial symbionts is just one of the most obvious outcomes.

Disease emergence and dispersal has been more of a mixed bag. New diseases get a great deal of attention but with the exception of HIV, they are not worse than the “age of epidemics”  (plague, typhoid fever, yellow fever, etc.).   Vaccines have still amounted to an overall decrease in infectious disease deaths. The three worst diseases to emerge during the Anthropocene are cholera, influenza, and HIV/AIDS. The greatest concerns today are the speed of dispersal for antibiotic resistant strains of old foes and development of new vaccines. Still, though, there are possibly more infectious organisms than ever.  We have driven only two viruses to extinction — smallpox and rinderpest — while new zoonotic diseases emerge at a steady clip.

Completely synthetic microbes created in a laboratory may well eventually be the primary hallmark of the Anthropocene. We are on the verge of being there now and there are an uncountable number of engineered microbes that produce a variety of products from biofuels to drugs. It will be up to us to manage the use of a technology capable of resurrecting a long-extinct bacterial strain or virus.

Do we really think we are smart enough to manage the tsunami of change occurring the microbial world?



Gillings, M. R., & Paulsen, I. T. (2013). Microbiology of the Anthropocene. Anthropocene, 5, 1-8.

Roundtable on Campbell’s Climate, Disease, and Society in the Late Medieval World

by Michelle Ziegler

Bruce Campbell. The Great Transition: Climate, Disease, and Society in the Late Medieval World. Cambridge University Press, 2016.


When I first learned that Bruce Campbell was working on this book, I wondered if it would be the first grand synthesis of the new paradigm. Although there have been some very good regional books in the last couple of years, Campbell has indeed brought forward the first analysis of the Black Death and 14th-century crisis using global evidence. Although not entirely clear from the publisher’s description, this is an economic history that draws on interdisciplinary evidence.

I proposed this session and recruited participants without ever seeing the book (though I had seen his Ellen McArthur Lectures). I got very lucky that the panel matched up so well with the book. The five panelists who were able to attend were (from left to right below) Mongolian historian Christopher Atwood, Historian of Medicine Wendy Turner, Evolutionary Biologist Boris Schmid, Archaeologist Carenza Lewis, and Economic/Environmental Historian Philip Slavin.

roundtable 2017
Great Transition Roundtable: Christopher Atwood, Wendy Turner, Boris Schmid, Carenza Lewis, and Phillip Slavin. (Photo by Nükhet Varlik, used with permission)

Everyone agreed that Campbell’s book will become the foundation upon which the new synthesis of plague history will be built. Campbell synthesized a vast amount of data with a particular appreciation for the integration of climate and disease data. Most agreed that this was a very high-level view of the crisis, an aerial view if you will, that leaves many details to be filled in. Some missed an analysis of the relationship with cascading levels of analysis down to the level of individuals. On the other hand, Atwood remarked that this is far more detailed than would be possible in Asian studies today. Perhaps not surprisingly, this interdisciplinary panel would have liked to see more evidence from other fields such as archaeology and social history used.  As Lewis noted, archaeology, in particular, could have given more support to the economic and environmental arguments without pulling away from the flow of the book.

The global evidence is primarily limited to climate data. Several panelists remarked that it is still very Eurocentric view, and Anglo-centric on top of that. There is more data that could have been gathered particularly from the Mediterranean. War as a syndemic factor and as a result of climate or disease weakened societies was not given much space in Campbell’s analysis. One effect of such a high-level regional treatment is that causes of local mortality from war (including the environmental destruction of war) can be overlooked because it doesn’t effect a large enough piece of territory. Slavin has also pointed out that Campbell’s interpretation tends to come across as somewhat deterministic, here and there. Thus, in discussing the Great European Famine of the early 14th century, Campbell provided an engaging analysis of the environmental context of the famine as its causation, without considering various intermediate links, demographic and institutional. As a result, Slavin noted that Campbell’s interpretation of the Great Famine as an exogenous disaster stands out as unilateral; famines, across space and time, are incredibly complex phenomena.

Developing a historical paradigm based heavily on scientific data is like building a house on shifting sand. Eventually, the sand will swallow the house. The best you can hope for is to be precariously perched on the ridge of a dune.  Most biological data is out of date by the time it is printed in a book. While there were a few misunderstandings, most of the discrepancies between Campbell’s portrait of the plague and other diseases is simply out of date even though he incorporates information up to about 2015. For example, ancient DNA studies have found evidence for at least one, and probably several, (still unlocated) local reservoirs of plague in or near Europe, so the idea that plague was frequently imported from the East no longer holds (but Boris disagrees on this view).

Some other hypotheses on plague transmission, though proposed several years ago, have failed to gain much traction. While evidence continues to mount that the soil plays a role in Yersinia pestis’ survival and that human ectoparasites could be the primary vector at the pandemic level, these hypotheses are not proven yet. This doesn’t mean that they won’t eventually be accepted, just that we are not yet there.

Figure 4.05 REV 6
Stages in the plague cycle (Figure 3.27, Campbell 2016)

I am reproducing figure 3.27 here because I think this will prove to be popular with teachers. With that being said there are a few comments that need to be made about it. The role of the soil in the enzootic environment of the rodent’s burrow is poorly understood at the moment. However, teachers could just explain that level 1 simply represents the environment of the rodent burrow.  Level 5 is where the real debates are going on now among those who study transmission. Campbell does leave open which ectoparasites are involved, human fleas or lice, but there is not yet general acceptance of human ectoparasites as major vectors. It may yet come, but we aren’t there yet. While local cases of pneumonic plague will occur any time there is bubonic plague, it is unlikely to be a major driver in a pandemic. The red box that I have added to the figure is where the really critical events are happening for human epidemics and pandemics. While I do believe that humans should be considered hosts in pandemic level transition, a variety of other hosts, always including rodents, will continue to be instrumental in the amplification and must be involved for the endurance of an outbreak in a locality.

While working with scientific detail is challenging for historians, after Campbell’s book I think it will be necessary to address scientific information at least to the level where there is a consensus. As long as historians stay with information that has been confirmed by a second study or that has obviously gained scientific consensus, the risks of using scientific information really are manageable. Finding a scientist who has your trust to comment on drafts is a good practice (and the reverse for scientists writing history!).

There were some concerns. There was a feeling that correlation does not necessarily equal causation. Schmid and Slavin would have liked to see more evidence of statistical analysis to support the conclusions drawn. They had a sense that the patterns that Campbell noted in a number of his overlapping time series might prove to be coincidental, rather than significant when tested with robust statistics.

Wendy Turner addressed pedological uses of the book. She found that, at least for a history of medicine course, it could not be used alone as a textbook. It does not have enough social history to address the complete impact of the Black Death. I don’t think that was its purpose, as much as some of us hoped it would be.  “The” Black Death book has yet to be written. When it is it will have to address all the social, medical, scientific, economic, and political impacts — a tall order. It is likely that aDNA studies will have more to contribute to shore up the transmission routes of such a project. Campbell’s book could be a major text (if not the only one) for an economic or environmental history course if it is supplemented by other texts. Archaeology as done by Carenza Lewis or Per Lagerås would support Campbell’s overall argument.  Turner and others agreed that it is not written for introductory students and they wondered how even upper-level students would respond to the density of the material. It should be required reading for graduate students who focus on the 14th century or any of the infectious/famine crises.

Atwood observed that historians tend to recognize a “crisis” about every couple of centuries and wondered if these mostly European events/crises over millennia were not tied to changes that had swept across all of Eurasia. In effect, Campbell’s book lays the supportive groundwork for arguing that the Eurasian land mass should be considered as a whole rather than European only or Asian only.  I think we could make an argument that the Afro-Eurasian landmass is one historic unit. The Indian Ocean is still an underappreciated communication avenue.

The most lively discussion with the audience concerned the terminology for the 14th-century events — transformation, crisis, collapse, etc. Positions seemed to be based at least partially on training, with some rejecting the term collapse under any circumstances, while others were more open to its use in areas like “population collapse”.  For me, this is an internal matter for historians to resolve. Terminology can be a fickle thing, but data is always preeminent. And that is a good place to leave this post. Campbell has done us all a service by compiling a huge amount of data that will be the foundation of a new era of analysis of the 14th century and the Black Death. For this above all else, we must be grateful.


Medieval Historians Taking Genomics into Account

At the International Congress on Medieval Studies at Kalamazoo (Kzoo) last month, I couldn’t help feeling that we have reached a turning point. I went to four sessions that engaged in genomics, human and/or bacterial, in some way. Granted, these are a tiny proportion of the 500+ sessions offered, but I have learned that if you can string together so many sessions on any topic related to your work, it’s a really good Congress.

Before and After 1348: Prelude and Consequences of the Black Death session, Kalamazoo, 2017. Pictured: Monica Green and Robert Hymes (Photo: Nukhet Varlik, used with permission)

The tone was set in the very first session when Philip Slavin brought up human epigenetics in his discussion of 14th-century famine. This was followed the next day with three sessions on the Black Death and 14th-century crisis. The two Contagions society sessions went very well. Carenza Lewis talked about her ceramics landscape survey that showed how deep the 14th-century demographic loss actually was. Fabian Crespo introduced the audience to the human immune landscape and how it can be fruitfully approached (including by epigenetics).  I will post on the roundtable on Bruce Campbell’s The Great Transition later this summer. The third plague session, Before and After 1348,  organized by Monica Green focused on Asia and generated a vigorous discussion.   I also attended a fifth session that focused on more traditional biological anthropology, ie. mostly osteology.

This turn hasn’t come all of a sudden. Historians began paying more attention to bacterial genomics a little over a decade ago when plague aDNA first hit the news. Michael McCormick, Lester Little, and Monica Green have all been instrumental in bringing science to the attention of historians. Three edited volumes stand out for putting genomics in front of historians: Lester Little’s Plague and the End of Antiquity: The Pandemic of 541-750 (2007), Linda Clark and Carol Rawcliffe’s Society in the Age of Plague (2013), and Monica Green’s Pandemic Disease in the Medieval World: Rethinking the Black Death* (2015).

On the other hand, scientists have also edited collections of papers that should make the science more accessible to historians. Didier Raoult and Michel Drancourt have edited two volumes, Paleomicrobiology (2008) and Paleomicrobiology of Humans (2017). Ruifu Yang and Andrey Anisimov edited a more technical volume, Yersinia pestis: Retrospective and Perspective (2016) that should summarize the state of the science  (as of 2016) for more advanced readers in the humanities.

Of the monographs, the historian’s usual primary venue,  books addressing genomics or using genomics as a springboard are limited. With at least three appearing in 2016 by Nükhet Varlik, Ole Benedictow, and Bruce Campbell, this should change soon. At this point, I should mention that genomics is already becoming useful to historians of other diseases, especially leprosy and tuberculosis. Historians are also becoming reinvigorated to provide context for plague and other diseases that may be of interest to geneticists and biological anthropologists. Varlik’s edited collected Plague and Contagion in the Islamic Mediterranean  (2017) is the most recent to provide context for a variety of diseases in an understudied area.

*Green’s volume was first published as a double inaugural issue of the journal The Medieval Globe and then published as a hardback book by ARC Medieval Press.