Category Archives: blogging

Biosecurity Failures Round-up

Like many of you, I’ve been watching and reading all the recent biosecurity lapses at our top labs with some dismay. This really isn’t something I normally would cover here on Contagions, but a comment from a reader reminded me that not everyone gets all the stories I’ve been tweeting (or retweeting) for the last few months. So here is a partial roundup in no particular order:

CIDRAP: Wholesale roster change coming for US biosecurity board

Superbug: The Leader of the Smallpox Eradication Effort Speaks About the Virus’ Rediscovery

Superbug: Virus in Found Tubes of Smallpox Is Viable

Superbug: Enhancing flu in the lab: Are accidents inevitable?

Found: Forgotten Vials of Smallpox | Science Blogs | WIRED

Exclusive: U.S. says government lab workers possibly exposed to anthrax

After Lapses,CDC Admits a Lax Culture at Labs | NYTimes

U.S. inspectors find further anthrax violations, mishandling http://www.reuters.com/article/2014/07/14/us-usa-anthrax-idUSKBN0FJ29X20140714

Transcript of CDC Press Conference on Recent Biosafety Incidents

On biosecurity at a local level: Out of the Lab & Into the Mouth These are getting to be yearly stories!

Meanwhile, elsewhere  Ebola (another category A bioterrorism agent) is raging unchecked in western Africa….

“How to Ignore a Plague” (Ebola) by Umaru Fofana

Ebola cases in West Africa reach 964, deaths top 600  http://www.cidrap.umn.edu/news-perspective/2014/07/ebola-cases-west-africa-reach-964-deaths-top-600

USAMRIID Providing Laboratory Support to Ebola Outbreak http://globalbiodefense.com/2014/07/15/usamriid-providing-laboratory-support-ebola-outbreak/#sthash.GxNfldMP.dpuf

An Unnatural History of Emerging Infections

Unnatural HistoryRon Barrett and George Armelagos. An Unnatural History of Emerging Infections. Oxford University Press, 2013 (e-book)

This is not a traditional review. In keeping with this blog’s function as my shared file cabinet, this post will be something like a précis /notes with a few of  my comments in italics.

Medical anthropologists Ron Barrett and George Aremelagos argue that there have been common factors in the disease ecology that has governed all three main epidemiological transitions in human health. They argue that there is nothing fundamentally new about the driving factors of the current ecology of emerging and re-emerging infectious diseases. In all three transitions, human factors have created the ecology for acute infectious disease to thrive.

Concept: “syndemics: interactions between multiple diseases that exacerbate the negative effects of one or more diseases” (p. 10). Examples: co-infections of HIV, and combinations of infection and chronic respiratory disease (asthma etc).

Metaphor: “seed and soil” where the microbe is the seed and the ecology is the soil. Historically used by physicians who accepted Germ theory but practiced environmental medicine (sanitarians) especially in the gap between the beginning of germ theory and the availability of antibiotics. I really like this metaphor; it still works today. 

Prehistoric baseline

  • Important as our evolutionary context, first 100,000 years of human history. (that’s about 90% of total human history). At its peak only 8 million people globally; small, nomadic groups  rarely in contact.
  • Temporary shelter and carried little with them to carry vectors (or fomites?). Hunter gatherers maintained near zero population growth. More diverse nutrition but could not support large groups. Little hierarchy within the group so few inequalities (at least not consistently detectable in the osteological record.)
  • Nutrition is closely tied to immunological competence.  Protein deficiencies reduces competence to the level of AIDS patients. Nomads can move to find better nutrition, avoiding ‘famine foods’. Diets higher in lean meats and  fiber, but low in carbohydrates.
  • Too small to support acute epidemics (ran out of hosts too soon) but at an increased risk for parasites. Heirloom parasites like pin worms and lice; souvenir parasites picked up while foraging like ticks and tapeworms. Mostly chronic infections that could remain with the nomads until they could be transmitted to new groups.  New zoonoses that can be passed human to human contracted from hunting would ‘flash out’ in a small group. Groups too small for diseases like measles, smallpox or influenza.

First epidemiological transition – Agricultural revolution

  • The first transition comes with people settle down and form villages.  Settlement and agriculture allow populations to grow large enough to support acute epidemic disease and animal domestication brings humans in prolonged contact with animals sparking some important zoonotic diseases.
  • They note that agriculture and settlement begin in multiple parts of the world independently but not at the same time. It took about 9000 years for 99.99 % of the population to shift to farming and domestic animals as their primary nutrition source. Once the shift to agriculture comes, there is no going back.  They debate which comes first, settlement or agriculture, but they note that in the end for heath it doesn’t matter. (The length of time here has important implications for the incomplete nature of the second transition.)
  • Decrease in overall health seen in all societies that shifted to agriculture. Correlations between more/better grave goods and better health; ie. social inequity was bad for health as early as the neolithic. Very high childhood mortalities bring the overall lifespan down considerably. Settlement increased densities of humans and newly domestic animals making conditions ripe for the first acute epidemics and zoonotic transfers. Most zoonotic transfers in this period come from domestic animals.
  •  Nutrition suffers with settlement. Reliance on a monoculture makes them vulnerable to bad years and nutritional deficiencies of essential nutrients not found in the monoculture.  There is a general reduction in stature, increase in signs of anemia, and increase in osteological signs of infection. Examples: Nubia and Dickson Mounds, IL, USA. Correlation of age with skeletal pathologies shows that is health declines are not due to the ‘osteological paradox’ (more pathologies in stronger people because they survive what would have killed others).

Second epidemiological transition – Industrial revolution

  • Transition marked by decreasing deaths due to infectious disease and an increase in chronic diseases. Increasing life expectancy due in large part to decreasing childhood mortality. Total human population soars.
  • Germ theory vs. Sanitation reform: Germ theory is associated with quarantine tied to power of the church and state. (??) Sanitary reform has greater success in controlling diseases like cholera and food-bourne diseases. Sanitary reformers focused on building infrastructure, improving living conditions and personal hygiene. “Germ theorists had begun a revolution in medical thinking, but in the realm of medical practice, they could do little more than agree with existing recommendations of the miasmists.” “with the exception of a few vaccines and surgical asepsis, Germ Theory offered little…until well into the 20th century”. Not surprising that germ theory didn’t make much difference until antibiotics came along. 
  • McKeown Thesis: “identifies nutrition as the primary determinant in the decline of infection-related mortality” Improved nutrition best explains increasing population growth in different countries in a short time period; improved agricultural methods and transport of food. Urban growth with industrialization increased crowding and decreasing sanitation leaving nutrition as the cause for decreasing infectious disease. Correlation between increasing height and decreasing infant mortality, increasing maternal height (indicating good nutrition) increased indicators of infant health so that improving nutrition improved health from generation to generation.
  • McKeown’s critics: error rates in bills of mortality obscure particularly respiratory infections in the elderly. They also believe that he underestimates the significance of smallpox vaccination in decreasing death rates. Greatest criticism is that McKeown places too much emphasis on nutrition over non-medicinal factors.
  • “Comparing the Agricultural Revolution with the Industrial Revolution, we find the same human determinants of infectious disease: a) subsistence, via its affects on nutritional status and immunity; b) settlement, via its effects on population densisty, living conditions, and sanitation; and c) social organization, via distributions of these resources and their differences within and between groups…. As such, the First and Second Transition could be seen as two sides of the same epidemiological coin with human actions as the basic currency.” (p. 61)
  • Second transition is incomplete in many countries. Only seven nations began the transition before 1850 and 17 more by 1900 with most transitioning after World War II. “The ‘low mortality club’ consisted of richer nations whose life expectancies converged at around 75 years old at the turn of the millennium. The ‘high mortality club’ consisted of poorer nations whose life expectancies converged at the same time around 50 years of age.” (p. 66)  The poorer nations have relied more heavily on vaccines and drugs as a buffer against living conditions to achieve the transition. Drug resistant pathogens removes this buffer for poorer nations. High childhood moralities continued in the poorer countries for the same reasons as in the first transition.
  • Chronic diseases make people susceptible to different infections. example: diabetes + TB, infectious diseases causing cancer: HPV, H. pylori, EBV (lymphoma).
  • Developed world vulnerable to “reimportation epidemics” from poorer nations with agents like smallpox (prior to eradication). Increased speed of air travel allows people to travel between high and low disease areas during the incubation period through entry ports without detection.

Third epidemiological transition (current)

  • Convergence of chronic and infectious diseases in a global human disease ecology marks the Third epidemiological transition.
  • Human health determinants remain subsistence, settlement and social organization.
  • 335 novel pathogens discovered 1940-2004, mostly after 1980, 60% of which are zoonoses and 70% of those come from wild animals. With long exposure to zoonoses from domestic animals it makes sense for most new pathogens today to come from wild animals; also due to encroachment and habitat destruction.
  • Challenges of new zoonotic pathogens: establishing animal to human  transmission, then human to human transmission, and finally human population to population. Chatter is a pathogen trying to establishing the animal to human transmission but not yet getting the human to human. Chatter is often viral but can be other microbes as well. Viral chatter is a transitional moment in evolution; purely biological for the pathogen but primarily cultural for humans (human practices that help the pathogen make the transition by our behavior).
  • Attenuation hypothesis: evolutionary interests favor microbes not killing their hosts too soon. Works for the first transition when population groups were widely scattered.
  • Virulence hypothesis: Ewald’s concluded that evolution favors virulence for pathogens with multiple hosts. (ex. plague). We can’t take either hypothesis too far as both have contradicting examples.
  • We need to shift from just looking for drugs to combat pathogens and spend more time on factors of human ecology.
  • An interesting chapter on antibiotics and evolution.

Concluding focus: To dispel three myths

  1. Emerging infections are a new phenomenon. They are not. This is why the emerging infections page on this blog begins with emergences in Antiquity / Prehistoric. 
  2. Emerging and re-emerging infections are a natural or spontaneous phenomena. We have a part to play in microbial co-evolution. Epidemiological transitions are intended to balance microbiology in understanding these infections.
  3. Determinants of disease are different today than in the past. They are not.

“The purpose of this Unnatural History is to reveal the macroscopic determinants of human infection just as the germ theorists once revealed their microscopic determinants…. our approach has been one of both seed and soil, acknowledging the importance of pathogens while stressing their evolution in response to human activities: the ways we feed ourselves, the ways we populate and live together, and the ways we relate to each other for better or worse.” (p. 111)

 

I’m not an anthropologist so I’m not really going to look at this like an anthropologist.  Demographics shifts are what they are, facts. The underlying factors / variables  - subsistence (nutrition), settlement (living conditions/infrastructure), and social inequalities –are the same under all three transitions. As these conditions vary, so do the demographics. This is very useful; a reminder of the importance of human disease ecology. The Unnatural History of the title is reference to human manipulation of the environment creating the conditions for emerging infections. Epidemics are not ‘acts of god’, or simply a natural process that we are helpless to stop. We play our part. Often drugs are the easy way out of the problem, far easier and cheaper than building infrastructure or improving living conditions. 

The paradigm of epidemiological transitions is an anthropological tool. I don’t really have a practical use for labeling ‘transitions’.  As both the second and third transitions are incomplete, they are not of much use to me as concepts. The shortness of these transitions makes me wonder if we are not really looking at just one transition since ca. 1800 that is yet incomplete. It is more important to me to look at these underlying variables and their outcomes at specific times and places. From my point of view, taking generalizations about epidemiological transitions as more than a guide for research or a teaching paradigm can be problematic.

This is a short book and yet I probably highlighted more than any other e-book that I’ve read. The focus here is more theory than details. Some of their plague information is a little out of date but it doesn’t really detract from their main points. It’s a valuable resource for thinking about microbe-human co-evolution. 

On Giant’s Shoulders #66: Contagious History!

Welcome to the 66th edition of On Giant’s Shoulders, the blog carnival for the history of science, medicine and technology! I wish I could pull a bunch of holiday posts out of Santa’s bag, but the blogosphere does not appear to be in the festive mood yet. An anniversary and commemoration mood seems to be prevailing as the end of the year approaches, so for historians this should be a gift!

One thing has become clear from looking at the sources of posts this month is that history of medicine and science has indeed become contagious, no longer limited to just typical blogs. We have traditional bloggers writing feature stories in newspapers and journals, large group blogs, the rise of library, archive and society ‘blogs’, and guest bloggers being invited to give context on blogs, some not normally about history. There are a growing number of options to blog outside of traditional one author blogs.

Marking history in our times 

Most of this issue is, of course, on medieval and early modern medicine, but I can’t let a couple of important modern history anniversaries pass unremarked. The H word celebrated 30th anniversary of PCR with two guest posts: the secret life of the laboratory by Charolette Sleigh and bringing meaning to technology by Jean-Baptiste Gouyon. This month one of the great genetics pioneers of the late 20th century, Frederick Sanger passed away. This two time Nobel prize winner made the sequencing of DNA and protein possible. Without Sanger sequencing there is no telling how long the genetic revolution would have been delayed. Originally done with radioactivity, here is a modern fluorescent Sanger for those of you unfamiliar with what sequencing looks like. Festive, isn’t it?

Modern Sanger Sequencing
Modern Sanger Sequencing

Rebecca Higgitt of The H Word writes about how legends of historic scientific heroes still shapes expectations of modern science and academia, for better or worse.

Part of all the remembrances of the JFK assassination , Circulating Now had a post on JFK’s career long support of the foundation and development of the National Library of Medicine. The New York Academy of Medicine featured a post on the WHO’s  AIDS posters  from the 1987-1995, soon after recognition of the pandemic.

Pathogens and Pandemics

fungal-christmas-tree-2-300x225Although not strictly a blog post, the Royal Society has posted podcasts of the November 2013 Ancient DNA conference, including the session by Johannes Kraus whose lab sequenced the East Smithfield plague isolates. While on the topic of plague podcasts, another series of four Ellen McArthur lectures by Bruce Campbell on “The Great Transition: Climate, Disease and Society in the 13th and 14th Centuries” came online earlier in the year but I don’t think has been part of his carnival yet. Listening to these lectures is vital for anyone interested in plague history, environmental or economic history.

Guy Halsall, The Historian on the Edge, writes about pestilence and politics in sixth century Gaul, according to Gregory of Tours. Helen King of Wonders & Marvels wrote about people dying like sheep in the Plague of Athens. A bigger writing project I’m working on motivated me to write, here on Contagions, a post suggesting renaming the third pandemic and a couple of posts (here and here) on plague historiography. Medievalist.net posted a  fighting the plague in medieval towns.

Circulating Now‘s guest blogger E. Thomas Ewing writes about the Spanish Flu of 1918 in Chicago. Earlier this year, Michael Bresalier wrote a guest post on The H Word on the 80th anniversary of the discovery of the influenza virus. While on discoveries, Yovisto featured a post on bacteriologist Robert Koch and his work on tuberculosis.

The Digitized Disease Project went online this month with a beta version of its database of digitized osteological remains open to the public for study.

Recipes, Food and Medicine

Jim Chevallier’s food history blog Les Leftovers, had several medicine related posts this month starting with the great medieval water myth , a post on a narrative of soup served to Bishop Gregory of Tours that touches on medieval taxonomy and attitudes toward getting drunk in Greogry of Tours works, and another on the plum of your eye.

The Recipe Project has been productive as ever with posts by Katherine Allen on cures for the common cold and remedies for rabies by Marieke Hendriksen.

Winston Black has a trilogy of posts on Points: the Blog of the Alcohol and Drugs History Society on the medieval pharmacy: Turning herbs into drugs in the middle ages,  The drug store in paradise and How do I drug thee? Let me count the ways. The most active medieval bloggers and reporters of Medievalists.net covered a recent lecture by Nick Everett on the modern science of medieval drugs.

Paul Middleton of Early Modern Medicine wrote about poisons, potions and the use of unicorn horns.

Caroline Petit posted at Knowledge Centre on Nigella Seeds: The Vicks Inhaler of Ancient Greece and Modern Day Marrakech

Dr Alun Withey posted on 17th century remedies and the body as an experiment.

Unusual Medical Maladies and Treatments

 Felicity Roberts of the Sloan Letters blog, writes about Mary Davis, the horned woman. Yep, real ‘horns’ growing out of her head with a portrait to prove it.

Circulating Now had a post on the use of projected snowflakes on magic lantern slides to mental patients. Some of these slides still exist in the National Library of Medicine.

Caroline Rance of The Quack Doctor has been featuring a post a day for ADvent on historic ads for medical devices and quack medications. The first ad is for a health jolting chair, you can follow the posts daily from there.

Jennifer Evans of Early Modern Medicine writes about medical opinions on ambidexterity and on early modern trepanning.

Public Health

Joseph Curran of the History of Medicine in Ireland blog wrote about the funding of hospitals in Dublin from c. 1847-1880.

Sue Davies of the Wellcome Library blog wrote about early 20th century efforts to reduce the contamination of ice cream in London.

Explore Your Archive featured the strange case of Dr James Barry, a 19th century Inspector General of military hospitals, and the secret revealed at his death.

Book Reviews

Jacob Darwin Hamblin hosted the E-Environment roundtable to review  two books, Sam White’s  The Climate of Rebellion in the Early Modern Ottoman Empire  (effects of the ‘little ice age’ on the Ottomans) and Alan Mikhail’s Nature and Empire in Ottoman Egypt. E-Environment roundtable issues are open access.

Here on Contagions, I reviewed Keith Wrightson’s Ralph Tailor’s Summer: a Scrivener, his City and the Plague.

Andreas Sommer of Forbidden Histories has an interview with Gabriel Finkelstein on his biography of Emil du Bois-Reymond: Science, Progress and Superstition.

Michael Barton’s The Dispersal of Darwin has posted several book reviews in the last month including this one on  Darwin and His Children and for children The Great Human Story

Michael Barton’s other blog Exploring Portland’s Natural Areas also has a book review of Teaching Children Science: Hands-On Nature Study in North America, 1890-1930.

From Michael Barton's The Dispersal of Darwin blog.
From Michael Barton’s The Dispersal of Darwin blog.

Childbirth and Women’s Medicine

Colleen Kennedy of the Recipe Project writes about that special feminine (almond?) touch given to hand kneaded dough that Robert Herrick loved so.

Helen King of Wonders & Marvels writes about pregnancy between East and West.

Earlier this summer Theresa Earenfight and Monica Green published a series of four posts on teaching  medieval royal mothering and women’s medicine, the first of four post is linked here.

Laurence Totelin of the Recipes Blog wrote about the ancient Greek use of garlic in fertility testing.

Medieval Medical Manuscripts

Another guest blog post by Monica Green on rediscovering medieval medical texts in a digital age.

Catherine Petit of Medicine, Ancient and Modern has a post on neglected Byzantine medical manuscripts.

Lindsey Fitzharris, the Chirurgeon’s Apprentice, writes about one of my favorite medieval diagnostic devices in piss prophets and the wheel of urine.

Anke Timmermann of The Recipe Project writes about the medieval (and later) method of cleaning manuscripts with bread. Laura Mitchell of the Recipe Project writes about the erasure of charms from a 15th century household notebook.

Biological Science

Adrienne Mayor of Wonders & Marvels wrote about scorpions in Antiquity.

Caitlin Wylie of Dissertation Reviews reviews Dinosaurs: Assembling an Icon of Science, by Lukas Benjamin Rieppel. Robertson Meyer of the Atlantic writes about dragons and beasts in the margins of maps and globes. 

Christian Jarrett of Brain Watch wrote about the first brain collectors.

John Wilkins of Evolving Thoughts wrote about the theological and philosophical origins of the species concept and the 18th and 19th century origins of ‘intelligent design’ theories.

Blogger Razib Khan wrote a feature in the Telegraph on how genetics of the Caribbean peoples is rewriting their histories.

Lisa Smith of the Sloane Letters blog wrote about Sir Hans Sloan, Abbe Bignon and Mrs. Hickie’s pigeons.

Maria Popova of Brain Pickings wrote on how Maria Sibylla Merian’s (1647–1717) illustrations laid the foundations of modern entomology. On this note, we should mark the passing of a modern pioneering female entomologist, Marjorie Guthrie within the last month.

In other science blogging: 

Seb Falk of Astrolabs and Stuff wrote up a seminar summary by Hascok Chan’s on his controversial keynote address from this summer’s International Congress of the History of Science, Technology and Medicine on “Putting Science back into History of Science”.

Melinda Baldwin of American Science wrote about the current backlash against prestigious scientific journals and how submissions by scientists has shaped scientific publishing in the past.

Jenny Bulstrode guest posted on Astrolabs and Stuff on the personal touch in making scientific instruments.

Dean Zollman wrote a guest post on Kim Rendfeld’s blog on how Isaac Newton was 300 years ahead of his time. The Newton Project Canada also have posted podcasts of its recent General Scholium Symposium.

Thony C of Renaissance Mathmaticus wrote about Lord Cromwell’s code breaker and on when and how geology became a science.

Robert Hooke’s London gave us some sound advice from the 17th century.  The Origins of Science as a Visual Art has an post on progress being made on finding Richard Waller’s library; Waller was a collaborator of Robert Hooke.

Jaun Gomez of Early Modern Experimental Philosophy on Dr. Arbuthnot’s use of gender balance birth stats to prove divine providence.

Romeo Vitelli of Providentia‘s  post on the physics of four-dimensional spiritualism and a two part post on Isaac Newton’s successor mathematician William Whiston’s predictions on the Second Coming: Part 1 and Part 2.

John Liffen of Stories from the Stores wrote about the sparky beginnings of wireless telegraphy. The yovisto blog featured a post on John Boyd Dunlap’s invention of inflatable tires.

Chad Orzel of Uncertain Principles writes about the extensive banality of Nazi evil on the careers of scientists few remember.

Matt Novak of Paleofuture wrote about the unfortunate internet canonization of Nicholas Tesla.

The January edition of On Giant’s Shoulders will be hosted by Jennifer Evans (@HistorianJen) of Early Modern Medicine on January 16, 2014. Submissions are due to Jennifer directly or to The Renaissance Mathematicus (@rmathematicus) no later than Jan. 15.

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