History Meets Biology at the AHA

2013Logo(250x324)I make a habit of writing about the seminars I go to so here is what you missed from the American Historical Association annual meeting. This was my first time at the AHA so I didn’t really know what to expect. The best part was all the fascinating people I met, some of whom I’ve been exchanging emails with for quite a while. I hope I can manage to keep in touch with them.

Four of the six sessions I attended can really be summed up under the title history meets biology. All four of these sessions could be said to be grappling with the “reconceptualization of the depth of human past”, to quote James Webb. In some ways I am puzzled by their difficulty and why they have previously essentially limited themselves to the last 3000 years or less. I assume that most biologists (like myself) and anthropologists think on evolutionary time, so there are no real barriers to historical thinking. The good news in these four sessions is that there are quite a few historians trying to embrace the real longue durée and are looking to biology as a new tool.

A few thoughts on the sessions in the order that I saw them.

Session 75: Evolutionary History: How Biology Can Help Us Understand History

This session was organized by Edmund Russell who appears to be leading this movement first outlined in his book Evolutionary History: Uniting History and Biology to Understand Life on Earth. (I picked up his book and will eventually review it here.) One of the themes of the session was the human role in altering evolution of other organisms.

Feral Animals in the American South: The Science and Culture of Broken Symbiosis by Abraham Gibson

Horses and swine in the southeastern states are the feral animals in question. I have to say that I didn’t know there are as many feral horses in the eastern US as there apparently are. Gibson talked about the biological distinctiveness of the feral horse and swine in the eastern US, no longer either part of the domestic or wild populations. I would have like a little more on the biological distinctiveness but even as much has he had challenged some of the historians in the audience who didn’t think it was necessary. These feral populations were not founded or sustained by escaped animals but intentional human release going back to British colonial times. It is important to bring biology into this discussion because it can unravel some of the folklore and faulty assumptions that have built up around feral animal issues. I enjoyed his talk and its a very important issue today for both the rural economy and ecology. This is a project that shows the importance of fusing history and science.  I hope we all hear more about in the coming years.

Canine Evolution and the “Improvement” of Nature in British America, c. 1600-1800 by Joshua Kercsmar

This was a very interesting paper on attitudes in colonial America on breeds of dogs raised by both colonists and Native Americans. Dogs became a proxy for views of the “other”, so colonists saw Native American dogs as savage or semi-wild. On the other hand, Native Americans saw the various European breeds brought to America as both reflecting their owners personalities and as signs of European power over nature. He talked about the common evolutionary origins of dogs and that Native American breeds go back to the same common ancestor(s). Yet Native American dogs were always viewed as more wild and savage, more wolf-like. Can you name a Native American dog breed other than a Husky? He talked about the fates of native breeds and how humans have shaped canine evolution, differently in Europe and N. America. (And yes, artificial selection is still a type of evolution.)

A Taste of Combat: How the Coevolution of Grapes and Yeast with Bacteria, Fungi, Insects and Mammals Shaped the Traits of Wine by Edmund Russell

This paper was more of a straight up discussion of coevolution with relatively little history. My notes are not as good on this talk. He focused on some of the characteristics of wine  — alcohol, sweetness, bitterness, and aroma(?) and how they are the product of coevolution. I’m not sure that the audience knew what to do with it and I think he needed more of the human element at least for that audience.

The whole concept of evolutionary history interests me a great deal. These talks show the promise of the technique but also its difficulties. Getting the balance correct between history and biology is tough. Convincing historians (or history buffs) that the biology is necessary to tell the story is a challenge at least for a biologist. This brings up the question of audience. Who is the target audience? I do believe there is an audience. A lot of science folks like history enough to be that audience, but can the humanities be convinced of this middle ground?

Session 97: Science and the Human Past: A New Initiative at Harvard University

Obviously this session was  a showcase for some new collaborations and projects at Harvard. As someone in the audience mentioned to me, only at Harvard could these kinds of projects be put together with in-house faculty (and institutional support).

Climate Change and the Fall of the Roman Empire by Michael McCormick

He presented too much detailed information for useful notes. One of his main points was that the Roman empire existed in a brief period of optimal climate that begins to degrade in the sixth century, including multiple sources of support for 18 months of extreme cold beginning in 536. He also talked about his current project the Digital Atlas of Roman and Medieval Civilization which will eventually include climate data.

How Genetics Can Inform History by Nick Patterson

I don’t have notes on this one. He talked about genetic admixture in deep time. This was more a talk about the possibilities of historical genetics than about a specific story or study.

Daniel Snail didn’t give the paper in the program. He talked about human behavior science and once again stressing that learning deep history is possible. History doesn’t begin with written documents.

Scientific Approaches to Ancient Disease: The Case of the Columbian Contact by Noreen Tuross

Tuross questioned the role of ‘virgin soil’ epidemics and its after effects. Is the concept of ‘virgin soil’ really as significant as it has been claimed? She stressed the importance of using aDNA in pre-contact cemeteries to determine what pathogens like Helicobacter pylori were already here. I didn’t take as many notes as I should have on this one. I do think it is right to question the importance of the ‘virgin soil’ concept. All it means is a lack of herd immunity and this was probably more common than we normally think for diseases that came around once a lifetime or less. Differences in immunity are surely important and does account for some of the differential mortality rates between communities, but there may be other additional causes for the drastic mortality rates of Native Americans (like the synergy of being challenged with more than one ‘virgin soil’ pathogen at a time). I do think that its important to look for pre-contact Native American pathogens in part for what it can tell us about the age and evolution of those pathogens.

Session 143: The Power of Cartography: Remapping the Black Death in the Age of Genomics and GIS.

I participated in this session and my resource post is already up here. I have to admit that I never take notes in sessions I participate in so I’m not going to try to review it. I think these talks will appear in some written form eventually. If they all appear together, I’ll be sure to mention it here on Contagions. Here is a link to all of our abstracts. I do want to thank Monica Green for organizing this session and for helping me meet so many great people in New Orleans. Hopefully this session will be a beginning of a new synergistic period in plague studies.

Session 192: A Prospectus for a Global Health History (Roundtable)

This session collected experts on a variety of history of medicine topics to discuss how develop the field taking into account new information on the depth of human history. The participants and their primary areas were: Mariola Espinosa, Yellow Fever and Caribbean diseases; Monica Green, deep history of TB and leprosy; Angela Ki Che Leung, Beriberi in SE Asia; Nukhet Varlik, plague in the Ottoman empire; and James Webb, Global Malaria. Each gave a short talk about recent developments in their area, particularly developments that challenge the standard story. For example Nukhet Varlik talked about there being no separation between the second and third plague pandemic in the Ottoman empire. The standard story of the plague is that it dies out by the early 18th century but that is not true outside of western Europe.  I think we can all agree that plague studies have been far too Eurocentric.  Their was some discussion on their areas but also on how to teach this material. James Webb reminded the panel and audience that public health and science folks in general are often more interested in the depth and history of global health than others in the humanities. Like evolutionary history in the first session, they need to conceptualize who their audience is and how to cope or adjust if they want to widen their audience.

I found all four sessions to be very stimulating. Honestly, more stimulating that I thought the AHA would be for me when I first looked at the program (outside of the last two sessions organized by Monica Green). Maybe its the sessions I chose, but a sessions seemed to be oriented toward what can be done in the future rather than conveying information. When I got back someone asked me what was the most interesting thing I learned and I had a hard time answering. In part because these sessions were more about field development than conveying specific information. There was lots of good info. These sessions are also short, so there is only so much story that can be conveyed in a maximum of 15 minutes. Conferences are about learning what people are working on and being stimulated in your own work. On those grounds the AHA was a very pleasant surprise.

For the other two sessions I indulged by inner medieval geek. I may write about one of them on my medieval history blog (and even that session was about what new technology can bring to history).

Plague doctor Marti Gras mask

Plague doctor Mardi Gras mask

What else would I bring home to remember a plague session in New Orleans but a plague doctor Mardi Gras mask? I need to find a better way to display it. The crystals just don’t sparkle enough there.

Now back to blogging about all the new plague papers that came out in just the last couple weeks!

Toward a Molecular History of Yersinia pestis (AHA)

This post a resource for the presentation I gave at the AHA meeting in New Orleans on January 5, 2013. A color handout of the slides can be downloaded here.

This map will be continually updated as new finds are published. Some of the balloons mark sites with multiple studies. Click on the balloons for citations.

References:

Achtman, M. (2012). Insights from genomic comparisons of genetically monomorphic bacterial pathogens. Philosophical Transactions of the Royal Society B: Biological Sciences, 367(1590), 860–867. doi:10.1098/rstb.2011.0303

Bos, K. I., Schuenemann, V. J., Golding, G. B., Burbano, H. A., Waglechner, N., Coombes, B. K., et al. (2011). A draft genome of Yersinia pestis from victims of the Black Death. Nature, 1–5. doi:10.1038/nature10549

Bos, K. I., Stevens, P., Nieselt, K., Hendrik N Poinar, DeWitte, S. N., & Krause, J. (2012). Yersinia pestis: New Evidence for an Old Infection. PLoS ONE, 7(11), e49803.

Drancourt, M., & Raoult, D. (2005). Palaeomicrobiology: current issues and perspectives. Nature Reviews Microbiology, 3(1), 23–35. doi:10.1038/nrmicro1063

Drancourt, M., Houhamdi, L., & Raoult, D. (2006). Yersinia pestis as a telluric, human ectoparasite-borne organism. The Lancet Infectious Diseases, 6(4), 234–241. doi:10.1016/S1473-3099(06)70438-8

Haensch, S., Bianucci, R., Signoli, M., Rajerison, M., Schultz, M., Kacki, S., et al. (2010). Distinct Clones of Yersinia pestis Caused the Black Death. (N. J. Besansky, Ed.)PLoS Pathogens, 6(10), e1001134. doi:10.1371/journal.ppat.1001134.t001

Houhamdi, L., Lepidi, H., Drancourt, M., & Raoult, D. (2006). Experimental model to evaluate the human body louse as a vector of plague. The Journal of Infectious Diseases, 194(11), 1589–1596. doi:10.1086/508995

Little, L. K. (2011). Plague Historians in Lab Coats*. Past & Present, 213(1), 267–290. doi:10.1093/pastj/gtr014

Malou, N., Tran, T.-N.-N., Nappez, C., Signoli, M., Le Forestier, C., Castex, D., et al. (2012). Immuno-PCR – A New Tool for Paleomicrobiology: The Plague Paradigm. (S. Bereswill, Ed.)PLoS ONE, 7(2), e31744. doi:10.1371/journal.pone.0031744.g006

Morelli, G., Song, Y., Mazzoni, C. J., Eppinger, M., Roumagnac, P., Wagner, D. M., et al. (2010). Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity. Nature Genetics. doi:10.1038/ng.705

Nguyen-Hieu, T., Aboudharam, G., Signoli, M., Rigeade, C., Drancourt, M., & Raoult, D. (2010). Evidence of a Louse-Borne Outbreak Involving Typhus in Douai, 1710-1712 during the War of Spanish Succession. PLoS ONE, 5(10), e15405. doi:10.1371/journal.pone.0015405

Parkhill, J., Wren, B. W., Thomson, N. R., Titball, R. W., Holden, M. T., Prentice, M. B., et al. (2001). Genome sequence of Yersinia pestis, the causative agent of plague. Nature, 413(6855), 523–527. doi:10.1038/35097083

Pusch, C. M., Rahalison, L., Blin, N., Nicholson, G. J., & Czarnetzki, A. (2004). Yersinial F1 antigen and the cause of Black Death. The Lancet Infectious Diseases, 4(8), 484–485. doi:10.1016/S1473-3099(04)01099-0

Raoult, D., Dutour, O., Houhamdi, L., Jankauskas, R., Fournier, P.-E., Ardagna, Y., et al. (2006). Evidence for louse-transmitted diseases in soldiers of Napoleon’s Grand Army in Vilnius. The Journal of Infectious Diseases, 193(1), 112–120. doi:10.1086/498534

Schuenemann, V. J., Bos, K., Dewitte, S., Schmedes, S., Jamieson, J., Mittnik, A., et al. (2011). PNAS Plus: Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the Black Death. Proceedings of the National Academy of Sciences, 1–22. doi:10.1073/pnas.1105107108

Tran, T., Forestier, C., & Drancourt, M. (n.d.). Brief communication: Co‐detection of Bartonella quintana and Yersinia pestis in an 11th–15th burial site in Bondy, France. American Journal of ….

Tran, T.-N.-N., Signoli, M., Fozzati, L., Aboudharam, G., Raoult, D., & Drancourt, M. (2011). High throughput, multiplexed pathogen detection authenticates plague waves in medieval venice, Italy. PLoS ONE, 6(3), e16735. doi:10.1371/journal.pone.0016735

Wiechmann, I., & Grupe, G. (2004). Detection ofYersinia pestis DNA in two early medieval skeletal finds from Aschheim (Upper Bavaria, 6th century A.D.). American Journal of Physical Anthropology, 126(1), 48–55. doi:10.1002/ajpa.10276

Wiechmann, I., Harbeck, M., & Grupe, G. (2010). Yersinia pestis DNA Sequences in Late Medieval Skeletal Finds, Bavaria. Emerging Infectious Diseases, 16(11), 1806–1807.

On Giants Shoulders #54: A Sleigh Load of History

Welcome to On Giant’s Shoulders #54, the history of science blog carnival! Here, we celebrate the history of science with all its oddities, and modern science delves into the past. I can’t think of a better way to spend my third blogoversary (of regular blogging) here at Contagions. Just a few days away from the winter solstice, I managed to fill my sleigh with a load of science history links. Cuddle up with a warm mug of hot chocolate (or whatever warms you) and settle in for some good reading.

Festive Science and the Holiday Season

Since the culture war between science and religion heated up, there has been friction between science and religious holidays like Christmas. Rupert Cole of Notes & Theories reminds us that this was not always so. In Victorian England, the popularity of science and Christmas festivities peaked with the public at the same time and reveled in each other. Victorian Christmas plays and pageants were followed by science lectures to explain the featured science and technology! Public Christmas trees were decorated with scientific instruments that were given to children. Those were the days. Though some science folks still know how to mix up the traditions. In a throw back to at least the sixteenth century, Diane Mcllmoyle of Esmeralda’s Cumbrian History and Folklore writes about the holiday tradition of mummer’s plays with its requisite quack doctor.

History of Pseudoscience

Let’s kick this carnival off with a stimulating discussion on, of all things, the omnipresence and worth of (what we call today) pseudoscience. Rebekah Higgitt of The H Word addresses claims that pseudoscience is on the rise with a history lesson, and ThonyC of Renaissance Mathematicus goes one step further asserting that pseudoscience has sometimes been helpful to the development of science. Faye Flam of Lightning Rod writes on Michael Gordin’s recent research on pseudoscience. Continuing with the supernatural, Lindsey Fitzharris of The Chirurgeon’s Apprentice discusses Abraham Lincoln’s conversations with the dead.

Darwin and Evolution

As always posts on Charles Darwin must be featured in On Giant’s Shoulders. Suvrat Kher of Rapid Uplift writes about Darwin’s slow, deep-thinking methods. Michael Barton of The Dispersal of Darwin calls out more quote mining of Darwin by anti-Darwinists. James Randerson writes of the private life of Charles Darwin. The Alfred Russel Wallace Correspondence Project also launched this month to coincide with the centenary anniversary of his death in 2013. Tim Jones of Zoonomian celebrated the birthday of the other famous Darwin, the polymath Erasmus Darwin (d. 12.12.1731). He also visits Annie Darwin’s grave and reviews Dr Gully’s water cures.

Joachim D of Mousetrap posted on Herbert Spencer’s synthetic philosophy and the centrality of evolution in his thinking.

Archaeology

Kristina Killgrove of Powered by Osteons summarized Nutrition and Well-Being in the Roman World: The Evidence of Human Bones, a conference this fall in Rome. Katy Myers of Bones Don’t Lie discusses how isotope data from bones informs on the social structure of an Anglo-Saxon settlement. In another post she discusses skeletal weapon trauma in medieval Ireland confirming the violence in Irish medieval records. In her most recent post she discusses the discovery and analysis of the graves of victims of the attempted mutiny of The Batavia off the coast of Australia in 1628.

Epidemiology

Katy Meyers of Bones Don’t Lie discusses a new study examining osteological and molecular evidence of TB at three neolithic sites in Germany at the transition to farming. I have a post on the Black Death Network reviewing the molecular evidence of the Black Death. If you have any interest in the 14th century crises — plague, famine, cattle murrain etc. — check out the Black Death Network. Spirochetes Unwound discusses the latest theory on the mysterious epidemic of 1616-1619 that decimated native Americans along the New England coast. Here on Contagions, I posted on the isolation of smallpox DNA from 17th century Siberia. The History of Vaccines blog posted a sketch of smallpox vaccine production in a cow, along with a discussion of vaccine production in 1872. Bringing us up to the 20th century, Rebecca Kreston of Body Horrors brings us the story of the first case of HIV in a 1961 Norwegian teenager who brought an unusual strain of HIV (group O) to his family and seeded it across in Europe.

Genomics

Genomics can help unravel the history of peoples who have left little documentary record. History of the Ancient World Blog has a post on a new study examining Scythian genetic admixture. Katherine Harmon of Observations covers a new study showing Gypsy or Roma origins in India about 500 CE/AD. This places the movement of the Roma out of India into Central Asia during the Great Migrations period that occurred when the Western Roman Empire fell in the fifth century. Interesting to think of the Roma as the last of the 1500 year old Great Migration peoples. Also covered on Past Horizons.

Mike Drout and his team at Wheaton have been applying DNA analysis and statistics software to Old English texts to determine authorship. They call it Lexomics — check them out.

Medical Practice and Public Health

Early modern medical practice was in the spotlight this month. Mike Rendell, The Georgian Gentleman puts a spotlight on contemporary views of 18th century medical practice. Home remedies were not any more successful, as ThonyC of Renaissance Mathematicus writes about in George Boole’s death from his wife’s homeopathy. Jai Virdi of From the Hands of Quacks explores the motivations of Dr Curtis‘ founding of the Royal Dispensary for Diseases of the Ear. The Secret Histories Project brings us a biography of the unconventional Dr. James Barry, child genius, military surgeon, and annoyance of Florence Nightingale. Venessa Heggie of The H Word, writes on the 70th anniversary of the Beveridge Report, that founds the modern British welfare state, about earlier attempts to build a social safety net in Britain with Elizabethan Poor Laws and the infamous Victorian workhouses. New blogger Jennifer Evans of Early Modern Medicine writes about the rhetoric of men pushing through the pain. Lisa Smith’s of the Sloane Letter project, she looks at the problem of bed wetting in the 18th century. Lindsey Fitzharris of The Chirurgeon’s Apprentice got ready for the holiday season by picking 12 (medical) instruments of Deathmas; most are sure to make you squirm. Caro of The Quack Doctor writes about the fun and games at Illinois Pharmacological Association meetings for traveling salesmen near the turn of the 20th century. Lynsey Shaw of the History of Military Aviation Hospitals writes on The Oxford Military Hospital, 1939-45.

Efforts to figure out the brain were popular this month. Michael Finn of Asylum Science wrote about the use of ophthalmoscope to view the living brain in asylums. The Public Domain Review reprinted “The Brain of Charles Babbage” (1909), the ‘father of the computer’. Darin Hayden wrote about a phrenological examination of Andrew White (who played a role in igniting the friction between science and religion).

On chemicals we are better off without, Marieke Hendriksen of the Medicine Chest writes about how mercury was viewed by early medical practitioners. Deborah Blum of Elemental writes about how early the US FDA knew about radiation dangers in cigarette smoke.

Pharmacy and Diagnostic Texts

Christina Agapakis of the Oscillator writes about the medieval Urine Wheel to diagnose metabolic diseases.

Michelle DiMeo of the Recipe Project writes about Dr Crawford Long’s exploration of the uses of ether for insect bites. Lisa Smith at the Recipe Project writes about a treatise claiming coffee cures the plague. In the area of hard to find reagents, Chelsea Clark of The Recipe Project shines light on the wonders of unicorn horns, bezoars and bones of a stag’s heart for poisoning. Alas, black markets for animal products like Rhino’s horn (a unicorn substitute) and bear gal bladder is still very active and taking its toll on increasingly rare animals. A little easier to resource, Jonathan Cey of the Recipe Project, shows us that feces-containing remedies were common in the early modern pharmacopoeia. So patients were more right than they knew when they said their medicine tasted like crap! Pamela Dangle also of The Recipe Project writes about some really “fishy” remedies for Melancholy (that seem rather unlikely to help, to me). Thinking of odd remedy names, Tim Jones of Zoonomian writes about medical misnomers of the past.

Physics, Astronomy, and Earth Sciences

ThonyC of Renaissance Mathematicus writes about the astronomical and medical roots of the first pocket diary (calendars). I’ll never look at those moon symbols on my calendar the same way again. Sorry Dad, the phases of the moon are not on the calendar to tell you when the fish are biting. Along similar lines of finding practical solutions to scientific dilemmas, Rebekah Higgit of The H Word writes about the catching and keeping of spiders to spin eyepiece filaments for astronomical observations. On the Royal Society blog, Rupert Baker writes about Thomas Hardy’s historical fiction on early astronomers and the royal society.

Let’s get a little textual with our astronomy, starting with Jenny Weston of Medieval Fragments who writes about medieval star-gazing. Astrolabes and Stuff discusses how to construct a medieval equitorium of Mercury and also for the Moon. Katy Barret of the Longitude blog writes about use of Cook’s journals and her longitude book collection. Sarah Werner of The Collation writes about volvelles (movable wheels) on folios of science and pseudoscience books.

Harald Sack at Yovisto writes about the golden-nosed astronomer Tycho Bahre and on Werner Heisenberg and the uncertainty principle. Alberto Vanzo of Early Modern Experimental Philosophy writes about the contributions Geminiano Montanari and the Italian academy. Matt Wisnioski guest posted on American Science about the motto “Change or Die!”

David Bressan of History of Geology writes about how philosophies of the nature of the world effected the study of the history of the Earth, and early efforts to measure its age. BibliOdyssey posts some of the original sketches and paintings of the discovery of Australia and its wildlife and then on Plant atlas from 1878-1783.

Dr SkySkull of Skulls in the Stars sets the record straight on Benjamin Franklin’s kite electricity experiments, outlines Priestly’s 1767 account of Franklin’s experiments and writes of the dangers of experimental ballooning in 19th century. Moving on from riding aloft to the winds on the plains, Carol Clark of Wonders & Marvels writes about the role of wind power in settling the arid American west.

Christian Hansen of Hummus and Magnets writes about the analytical programming of Babbage’s early calculating machines.

Lisa Smith will be hosting the next On Giant’s Shoulders carnival on the Sloane Letter Project in January. So watch for Lisa’s posts on twitter (@historybeagle) for more information.

I hope you found something enlightening and entertaining for a long winter’s night. Watch out for sleighs this holiday season, reindeer get spooked with all the holiday traffic!

christmas-ads-4

Remodeling the Plague Phylogenetic Tree

Understanding the molecular history of any organism requires fitting together ancient DNA with the phylogenetic tree constructed with living exemplars. Constructing a bacterial phylogenetic tree is a snapshot of a moving target because its impossible to sample all of the strains.  A recent study by the East Smithfield group ( Bos et al, 2012 [2]) seeks to fit the recent near complete genomic sequence of Yersinia pestis from the Black Death cemetery at East Smithfield into the current phylogenetic tree.

They pooled their SNP database with those used by Morelli et al [3] for a total of 311 strains, plus the parental species Yersinia pseudotuberculosis as its foundation.  The East Smithfield group expect that the SNP comparison “could provide a qualitative indication of phylogenetic signals that were lost via our original, more conservative analytical approach based strictly on complete genomes.” [2]

New phylogeny of Yersinia pestis (Bos et al, 2012)

Their analysis confirmed that the Black Death strain settles into the base of split between branch 1 & 2. This matches what Haensch et al [4] found in 14th century sites at Hereford and Saint-Laurent-de-Cabrerisse. This indicates that the split occurred after the Black Death, probably due to microevolution in geographically distinct regions. Branch 2 is localized primarily along the Silk Road route in Central Asia, while branch 1 is far more widely distributed  and produced the third pandemic strain [3].  Bos et al further identified two living strains, designated 3.ANT, with SNP profiles that match their East Smithfield Black Death SNP profile [2]. These strains have not been completely sequenced and the plasmid profiles of these strains and the Black Death strain have not been characterized, so we can not yet say that these strains are genetically identical in sequence or genomic architecture to the Black Death strain [2]. Note that genomic architecture (placement of genes in chromosome) will mostly likely effect gene expression and therefore function of the microbe.

The East Smithfield group  observed that a small group of three strains diverged from the main descent line immediately before the Black Death, designated here as 0.ANT3, were all isolated from China [2]. They suggest that these strains may have been produced during a diversifying event that produced the main Black Death strain, possibly in Asia before it reached Europe.

They also observed 11 strains of Yersinia pestis clumped at the 0.ANT1 branch point [2]. By their calculations this split would have occurred between the 8th and 10th century (732-980 AD) overlapping with the documented period of the Plague of Justinian. They suggest that these strains represent genetic radiation that occurred during the Justinian expansion. This is a change from their observations based solely on comparisons of complete genomes [1].

The East Smithfield genomic group still have not incorporated ancient DNA data from any other group in their analysis.

References:

[1] Bos KI, Schuenemann VS, Golding GB, Burbano HA, Waglechner N, et al. (2011) A draft genome of Yersinia pestis from victims of the Black Death. Nature 478: 506.510.

[2] Bos KI, Stevens P, Nieselt K, Poinar HN, DeWitte SN, et al. (2012) Yersinia pestis: New Evidence for an Old Infection. PLoS ONE 7(11): e49803. doi:10.1371/journal.pone.0049803

[3] Morelli G, Song Y, Mazzoni CJ, Eppinger M, Roumagnac P, et al. (2010) Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity. Nat Genet 42: 1140.1143.

[4] Haensch S, Bianucci R, Signoli M, Rajerison M, Schultz M, et al. (2010) Distinct Clones of Yersinia pestis Caused the Black Death. PLoS Pathog 6(10): e1001134. doi:10.1371/journal.ppat.1001134

Siberian Mummy Yields 300-year-old Smallpox DNA

Five mummies in one grave. Benigini et al. NEJM, 2012. DOI: 10.1056/NEJMc1208124

It was the mass grave that got their attention. Four bodies crammed into one casket, with one child outside but with the casket. Multiple graves are not common in Yakutia, Siberia. Examination of the late 17th to early 18th century mummies indicates that burial came quickly after death. The casket contains one adult male over age 30, an adult female, an adult female under age 23,  a male child about 5 years old, and outside the casket a child about 4 years old.

The French and Russian team led by Philippe Biagini undertook pathological and genetic analysis of all five mummies. They were able to confirm that the older woman is the mother of  the young adult woman and the adult male. They took lung and tooth specimens from each mummy at the site (in situ). Finding iron inclusions in the lungs of the young female (mummy 2), suggested to the team that she suffered a pulmonary hemorrhage shortly before death. They don’t say how they jumped from there to screening for smallpox or what other pathogens were considered.  Oddly, they make no mention of any smallpox lesions on the mummy. (Without other bioarchaeological data, is it possible that this team only received the tooth and lung specimens, but not the remainder of the mummy?)

The DNA was divided among three labs. Three short sections of Variola  (smallpox) genome were amplified by at least two labs each. They failed to amplify long stretches of the virus, suggesting that there are no intact virons left in the mummy. Their phylogenetic analysis grouped this virus, PoxSib, with Variola but distinct from both clade 1 and clade 2. They suggest that PoxSib could be an ancestral strain to both clade 1 and clade 2 or a strain that has not been previously sampled. Biagini et al. suggest this virus may have come to Siberia with the Russian conquest in early 18th century, possibly connected with a documented outbreak in 1714. This grave comes from the same culture as previously analyzed graves that isolated the first ancient whooping cough.

Reference:

Biagini, P., Thèves, C., Balaresque, P., Géraut, A., Cannet, C., Keyser, C., Nikolaeva, D., Gérard, P., Duchesne, S., Orlando, L., Willerslev, E., Alekseev, A., de Micco, P., Ludes, B., & Crubézy, E. (2012). Variola Virus in a 300-Year-Old Siberian Mummy New England Journal of Medicine, 367 (21), 2057-2059 DOI: 10.1056/NEJMc1208124 See supplemental appendix for most of the detail.

Bubonic Plague Music Video

Whoa, educational videos have changed a little since I was in high school. This video is by a group called History for Music Lovers (@historyteacherz). Their Bubonic Plague rap is set to Gwen Stefani’s Hollaback Girl. From the comments on You-tube, its being shown in history classes,  over 700,000 hits as of Nov. 15, 2012.

h/t to Tara Smith at Aetiology.

Opening the Plague Files

Book Citation: A.P. Cook & N.D. Cook.  The Plague Files: Crisis Management in Sixteenth-Century Seville.  Louisiana State University Press, 2009. 296 pp. ISBN: 978-0-8071-4360-5.

Topic:
Public Health Crisis Management

Time and Place:
Seville, Spanish Empire, 1579-1581.

Audience: 

Those interested in history, crisis management, public health, and political science; written for a general audience.

Discussion:

The Plague Files is an intensive history of the daily challenges and crises dealt with by the royal governor and city council of Seville from 1579 to 1582.  As its title implies, this book is about crisis management and it stays true to this focus. Seville was faced with two very different pandemics, influenza and plague, within the same year compounded by food shortages, economic pressures, response funding difficulties, response fatigue, and the potential of civil unrest. If you ever wondered what it would be like for plague and an influenza pandemic to go (sequentially) head to head in the same population, Seville in 1579-1580 is your ideal test population.  The challenges and limitations of both quarantine and a cordon sanitaire are highlighted throughout the book.

I was impressed by their case investigation and surveillance system.Workers were contracted and paid based on their service, so detailed reports were filed to justify their pay from the plague commission. Using these reports, the authors were able to trace the detailed steps of case investigators as they tracked exposed people and textiles that they viewed as contagious. Dispatched surveillance officers also had to file detailed reports of their efforts and findings to draw their pay. The Count of Villar, the royal governor, handed out penalties including jail time for officials and others who were deemed negligent in their duties.

It was fascinating to see how their concepts of contagion played into their public health response. Textiles were the gravest concern for controlling plague contagion inside the city walls. The trail of dead owners of some clothing or bedding seems to justify their concern. Yet, there is no evidence of personal protective equipment/behavior or concern over grain storage. On the other hand, the city was on the verge of starvation much of the time so they couldn’t be very choosy about grain shipment or storage. Physicians were advisers to the Plague Council but not central to the decision-making process. Most were hired to work for the duration of the plague, often one per hospital or outlying village. The Plague Council was primarily concerned with controlling movements of people, and  providing and paying for the poor and destitute who they knew were kindling for an explosive outbreak. Diagnosis was the physicians most useful duty to the plague council. Plague diagnoses were complicated by concurrent outbreaks of influenza, typhus, other ‘common fevers’ (possibly malaria), and malnutrition. There is no doubt that the plague with all its classic symptoms was the primary pathogen.

One of my take home lessons from The Plague Files is how long and relentless a plague outbreak could be. Response fatigue was a critical problem for everyone. People just get tired of the restrictions and become conditioned to the steadiness of death. Unlike the short, sharp influenza mortality, plague deaths often trickled in at less than ten per week for months punctuated by spikes of death.

Historical  & Scientific Content:

This microhistory draws almost entirely  from a cache of primary source documents in Seville’s Municipal Archive. Surprisingly, quotes from these documents are very short. The focus on Seville is so intense context is often lacking.

The science is anecdotal and kept at the level of sixteenth century understanding. They don’t apply modern understanding of plague or influenza.  Medical treatment is discussed vaguely; few specific treatments are detailed. For example, the council paid for apothecaries to stock and provide plague medicines but the authors didn’t discuss what they stocked or if they had difficulty obtaining medicines. It appears that there was no standard treatment or medication used in the region. They don’t make an effort to accumulate data or do any standard epidemiological analysis. By the end of the book I was craving some data. The volume of anecdotal evidence does provide plenty of evidence that diagnosis was not very secure for many individuals complicating data classification.  Historical epidemiologists will have to cope with other concurrent diseases, significant for plague outbreaks that last months to over a year. Ironically in the case of Seville, I suspect a standard epidemiological chart of total deaths vs time would have highlighted the difference between influenza and plague.

References, Illustrations, and Usability

It has a full bibliography but minimal footnotes, mostly to primary sources. I suspect that it would be fairly difficult to look for more information based on their footnotes and access to the primary sources.  They appear to have made minimal use of the secondary sources, or at least there are very minimal footnotes to them. It does have a glossary for Spanish terms; all quotes are translated. The illustrations were okay. It could have used a few more local maps fit into the text where appropriate.

I recommend this book primarily for biosecurity and crisis managers. Its usefulness to the sciences and humanities is primarily for anecdotal information.