Thursday, January 31, 2013

Reanimated post

It seems appropriate to reanimate this blog post from the graveyard

I introduced the basic SIR model for a simple epidemic to you. This model actually has a long history and was first described by Kermack and McKendrick in 1927.

As I indicated this model has since been expanded to include virtually every disease scenario you can imagine.

In 2009 a group of Canadian mathematicians used this SIR format as the basis for an analysis of a zombie epidemic. Their paper: WHEN ZOMBIES ATTACK!: MATHEMATICAL MODELLING OF AN OUTBREAK OF ZOMBIE INFECTION ) - somehow it seemed appropriate to keep that in capitals) - describes a model that should look basically familiar to you.

Notice in their S Z R model (Z for Zombie of course) there are two extra transitions - from R back to Z (reanimation of the dead is well established in the zombie movie genre) and a movement directly from S to R (non zombie related death which can be quite high in this genre and so worth taking account of).

This is, perhaps unsurprisingly, the first mathematical analysis of an outbreak of zombie infection. While the scenarios considered are obviously not realistic, it is nevertheless instructive to develop mathematical models for an unusual outbreak. This demonstrates the flexibility of mathematical modelling and shows how modelling can respond to a wide variety of challenges in ‘biology’.

In summary, a zombie outbreak is likely to lead to the collapse of civilisation, unless it is dealt with quickly. While aggressive quarantine may contain the epidemic, or a cure may lead to coexistence of humans and zombies, the most effective way to contain the rise of the undead is to hit hard and hit often. As seen in the movies, it is imperative that zombies are dealt with quickly, or else we are all in a great deal of trouble.

Wednesday, January 30, 2013

Coming back to bite you

Would Bubonic Plague make a good weapon?

A 1970 World Health Organization assessment asserted that in a worst-case scenario a dissemination of 50 kg of Yersinia pestis in an aerosol cloud over a city of 5 million might result in 150,000 cases of pneumonic plague. Of those, 80,000 to 100,000 cases would require hospitalization, and 36,000 victims would be expected to die.

Of course there are numerous difficulties involved in getting 50kg of bacteria into an aerosol cloud. You could just breed infected fleas instead but, as the video says, they may well come back to bite you...


Tuesday, January 29, 2013

Got Plague?

In 1914, three men in New Orleans examine rats to determine if they are carrying bubonic plague.  

This article from Discovery news this week has a slightly alarmist headline but makes some good points.

Plague, in humans, doesn't pop up a lot. Generally there are between one and seventeen cases per year in the United States, and only about a thousand in total since 1900. 
Remembering, and mentioning, exposure to dead or dying animals is key. As for efforts to eliminate it completely - although they've been considered, it would take too much extensive trapping and  it would take too much extensive trapping and testing of animals to be easily accomplished while the plague is still so rare. It looks like we'll continue getting the plague for the foreseeable future.

Monday, January 28, 2013

Traditional videos

The posting of the following videos has become traditional during the Bubonic Plague section of the course. The first one isn't strictly bubonic plague related, it's just included because of the flagellants.

The Daily Show with Jon StewartMon - Thurs 11p / 10c
Bubonic Plague
Daily Show Full EpisodesPolitical Humor & Satire BlogThe Daily Show on Facebook

Sunday, January 27, 2013

Lizard loss

If lizards are so important in keeping California relatively Lyme disease free then what would happen if we were to lose the lizards from an area? This is the sort of thing that might happen with a dramatic change in habitat.

Well this has been tested experimentally and the results are a little surprising.

“Our expectation going into this study was that removing the lizards would increase the risk of Lyme disease, so we were surprised by these findings,” said study lead author Andrea Swei, who conducted the study while she was a Ph.D. student in integrative biology at UC Berkeley. “Our experiment found that the net result of lizard removal was a decrease in the density of infected ticks, and therefore decreased Lyme disease risk to humans.”

The researchers found that in plots where the lizards had been removed, ticks turned to the female woodrat as their next favorite host. On average, each female woodrat got an extra five ticks for company when the lizards disappeared.

However, the researchers found that 95 percent of the ticks that no longer had lizard blood to feast on failed to latch on to another host.

“One of the goals of our study is to tease apart the role these lizards play in Lyme disease ecology,” said Swei, who is now a post-doctoral associate at the Cary Institute of Ecosystem Studies in New York. “It was assumed that these lizards played an important role in reducing Lyme disease risk. Our study shows that it’s more complicated than that.”

Notwithstanding the results in this new study, Lane pointed out that the Western fence lizard are key to keeping infection rates down among adult ticks. “This study focused only on the risk from juvenile ticks, specifically those in the nymphal stage,” he said. “The earlier finding that adult ticks have lower infection rates because they feed predominantly on the Western fence lizard at the nymphal stage still holds.”

For more information check out this press release from UC Berkeley: Tick population plummets in absence of lizard hosts or the original article here: Impact of the experimental removal of lizards on Lyme disease risk.

Saturday, January 26, 2013

Dengue Fever

 Five years ago I'd been using up some gift cards from and had bought several items. Probably some music, but I don't remember what, and some books on disease including one on Yellow Fever. Some time later I got an e-mail highlighting items they thought I might like. I was amused to see they'd combined my viral hemorrhagic fever book with music to come up with the conclusion I'd like music by a band called Dengue Fever. The sort of stupid conclusion only a computer could reach. Except they were right.

In contrast to most bands with disease related names (eg Anthrax, Cholera, Bubonic Plague, Ebola etc etc) Dengue Fever are not only not a heavy metal band but play an impressive combination of almost everything else 'Southeast Asian pop, Vietnam-war-era lounge music, klezmer, ska, surf rock, and Ethiopian jazz'. One of the band apparently caught Dengue Fever which is where they got their name. I suspect Anthrax, Cholera, Bubonic Plague and Ebola can't say that. Dengue Fever (the band) are based in LA and so play in Santa Barbara quite frequently, usually at SoHo but next Friday (February 2nd) you can catch them right here on campus at the Multicultural Center.

If you want to know something about Dengue Fever, the disease, then read on.

Although it is the Filoviruses such as Ebola that leap to mind when people hear the phrase 'viral hemorrhagic fever' (VHF) there are actually four different families of viruses that can lead to the classic symptoms of VHF's - capilliary leak leading to high temperature, shock (loss of blood pressure) and death.

This is rather important because whilst the Ebolavirus is really very rare some of the other VHF's are far more common. We'll talk about Yellow Fever in the penultimate week but another disease in the same group is Dengue Fever. Although 50-100 million people are estimated to contract this mosquito borne disease every year only a minority get a severe hemorrhagic fever. Maybe 5%. But 5% of 50-100 million is still several million people per year! In the severe form Dengue Fever causes a very high fever (over 104) and generalized muscle and joint pain (hence the common name 'breakbone fever').

It is the most common viral disease transmitted by arthropods and it is deemed second in importance to malaria in terms of tropical diseases. The World Health Organization currently counts dengue as one of sixteen neglected tropical diseases and it is found in a wide range of tropical countries across South America, Africa and Asia.

Friday, January 25, 2013

A tale of two Romneys

You can read more about America's rioting cities of the 1960's at PBS's American Experience website for 'Eyes on the Prize - America's civil right's movement 1954-1985'.

For five days in July, Detroit, Michigan descends into chaos. An economic boom has created jobs, and urban renewal projects have built new infrastructure, but blacks have been left behind. New expressways destroy black neighborhoods, and economic opportunities are scarce for black residents. The 95% white police force, notorious for brutal and arbitrary treatment of black citizens, raids an illegal after hours club and draws an angry, frustrated crowd that quickly turns hostile.

As Sunday July 23rd dawns, the growing crowd is looting and burning the city. Twelve hours into the frenzy, Governor George Romney calls in the Michigan National Guard; unprepared troops make mistakes like shooting out the street lights. Nearly 4000 people will be arrested in the first two days, and over 7000 by the third. Most are young and black. Police and guardsmen shoot at will, with some later insisting that all of their victims were armed.

Romney asks President Lyndon Johnson for federal help and by Monday afternoon 4700 U.S. Army paratroopers have arrived, under orders not to use live ammunition. A combined 17,000 law enforcement troops suppress the riot. After five days of anarchy, more than 40 people are dead, hundreds are injured, and damage estimates hit $50 million.

Yup, this is Governor George Romney, father of Mitt, and a leading Republican contender to challenge Lyndon Johnson for the presidency the following year. Romney believed the White House had intentionally slowed its response to the riots and he accused Johnson with having "played politics" in his actions. George Romney went on to lose to Richard Nixon in the Republican primary after running a poor campaign.

"Watching George Romney run for the presidency was like watching a duck try to make love to a football." Governor Jim Rhodes of Ohio

Over four decades later and it's Mitt's turn. Over those four decades the exodus from America's cities to the suburbs has played an unknown role in the rise of Lyme disease. A new political tool that has arisen is 'micro-targeting' allowing you to target each voter with the issues that are important to them.

The Romney-Ryan campaign 2012 goes with Lyme Disease in Virginia. The front of their mailer contains the rather general Romney-Ryan. Doing more to fight the spread of Lyme disease. Improve synergy. Increase awareness. Support treatment.

But the back explains just what this means.

It almost sounds reasonable until you ask yourself why a doctor would need protection from lawsuits...

Soundtrack for this post: Motor City is Burning by the MC5

Thursday, January 24, 2013

Chronic Lyme

People will probably interpret this study in a way that fits their favorite theory but on the face of it this paper from a couple of months ago in the New England Journal of Medicine argues against persistent Lyme disease infection being the cause of chronic Lyme disease.

Differentiation of Reinfection from Relapse in Recurrent Lyme Disease
None of the 22 paired consecutive episodes of erythema migrans were associated with the same strain of B. burgdorferi on culture. Our data show that repeat episodes of erythema migrans in appropriately treated patients were due to reinfection and not relapse. 

An editorial in the same issue states the implications quite explicitly:
The issue of relapse versus reinfection has a broader context because of patient-advocacy groups that promote months or years of antibiotic therapy for “chronic Lyme disease.” Moreover, chronic Lyme disease has become a common diagnosis for medically unexplained pain or neurocognitive or fatigue symptoms, even when there is little or no evidence of previous B. burgdorferi infection. Even so, these patients are said to have persistent infection, which can be suppressed only with months or years of antibiotic therapy, and the therapy must be restarted when symptoms recur. As concluded by the Infectious Diseases Society of America, there is no evidence of persistent B. burgdorferi infection in human patients after recommended courses of antibiotic therapy. Although B. burgdorferi infection may persist for years in untreated patients, the weight of evidence is strongly against persistent infection as the explanation for persistent symptoms in antibiotic-treated patients with Lyme disease.

Here's a report on the paper from the New York Times: New Infection, Not Relapse, Brings Back Lyme Symptoms, Study Says

(A) new study finds that repeat symptoms are from new infections, not from relapses.

The results challenge the notion, strongly held by some patients and advocacy groups, that Lyme disease, a bacterial infection, has a tendency to resist the usual antibiotic treatment and turn into a chronic illness that requires months or even years of antibiotic therapy.

Wednesday, January 23, 2013

New Borrelia on the block

From the LA Times last week:
New Lyme disease-like infection is on the map in U.S.

There a new tick-transmitted spirochete in town, and this wily relative of the organism that causes Lyme disease is probably sickening more than 4,300 Americans a year with relapsing fevers and flu-like symptoms, according to a new report. The good news: A round of common antibiotics appears capable of vanquishing the newly discovered threat.

The organism, called Borrelia miyamotoi, was discovered in 1995 in Japan, but it was not until 2011 that disease hunters found and described evidence that it was making people sick in Central Russia. The organism was found in deer ticks in Connecticut in 2001 and in Northern California in 2006. So it was only a matter of time before the illness it causes was detected in American patients.

That time has come. The New England Journal of Medicine on Thursday published two reports documenting its arrival on U.S. shores. One is a case study of a confused and unsteady elderly woman stricken by Borrelia miyamotoi; the other reports on a broad sampling of blood from patients in New England, where Lyme disease is widespread, and suggests that Borrelia miyamotoi infection "may be prevalent in areas where Lyme disease is endemic in the United States."

The NEJM papers are:
Meningoencephalitis from Borrelia miyamotoi in an Immunocompromised Patient
We report a case of progressive mental deterioration in an older, immunocompromised patient, and even though Koch's postulates were not met, we posit B. miyamotoi as the cause, owing to its direct detection in cerebrospinal fluid (CSF) with the use of microscopy and a polymerase-chain-reaction (PCR) assay.
Human Borrelia miyamotoi Infection in the United States
The identification of B. miyamotoi antibody in 18 of our study patients, including seroconversion associated with symptoms in 3 patients, suggests that B. miyamotoi infection may be prevalent in areas where Lyme disease is endemic in the United States.

Tuesday, January 22, 2013

New antibiotics

A recent Op-Ed in the New York Times addressed the topic of antibiotic resistance and why drug companies aren't developing new antibiotics.
Let’s Gang Up on Killer Bugs.

What makes the rapid loss of antibiotics to drug resistance particularly alarming is that we are failing to make new ones. We are emptying our medicine chest of the most important class of medicines we ever had. 

One of the big problems is the economics of drug development today.

Historically, the drug industry thrived on antibiotics. But if an antibiotic is useful against only one type of bacterium, relatively few people need it during its patent life. And if an antibiotic is “broad spectrum,” meaning it works on many different types of bacteria, wider use shortens its commercial life because it quickens the pace at which bacteria develop resistance. Moreover, antibiotics are designed to cure an acute disease — not to palliate a chronic one — so people need them only for a limited time. Compared with drugs that are used for years to treat widespread conditions like high cholesterol or asthma, antibiotics pale as a corporate investment.

The article contains some suggestions for a better way forward from collaborative drug research to a different economic model.

There are, however, other ways for drug makers to profit beyond using monopoly to protect prices. As Thomas Pogge of Yale and Aidan Hollis of the University of Calgary have pointed out, an intergovernmental fund for drug discovery could reward drug makers for products in proportion to their impact in reducing the loss of healthy years of life. The lower the cost of a lifesaving drug, the greater the number of people who could use it; the more lives protected, then, the greater the monetary reward. An investment of $20 billion a year could encourage more open-lab collaborations to find new medicines in challenging settings like antibiotic discovery and make them accessible to all who need them.

Monday, January 21, 2013

What's in a name?

This time last year I reported on news from India  that a new, even more resistant, strain of Tuberculosis had been isolated and that the name TDR-TB (totally drug resistant TB) was being used. Even at the time the Indian Government was disputing whether the strain is totally or merely 'extensively' drug resistant.

A year later the debate rumbles on. The World Health Organisation (WHO) does not approve of the term TDR or Totally Drug Resistant tuberculosis and the term XXDR or Extra Extensively Drug Resistant Tuberculosis is being used in some places.

The WHO has a fairly extensive explanation of why they don't consider a strain of Tuberculosis that is resistant to all known antibiotics in use to be totally drug resistant. Their arguments seem very weak:

1) A strain of TB that shows itself to be totally resistant to antibiotics in lab tests may in fact be susceptible to  them in the human body.

2) New drugs are under development, and their effectiveness against these “totally drug resistant” strains has not yet been reported.

Sunday, January 20, 2013

Tuberculosis educational game

I found this game at the Nobel Prize website. It ties into many topics we have covered, or will cover in  this class.

The Tuberculosis educational game and related reading, are based on the 1905 Nobel Prize in Physiology or Medicine, which was awarded for investigations and discoveries concerning the disease tuberculosis, "TB".

Maybe I'm just not in the mood but this has to be the worst game ever. I knew exactly what I was supposed to be doing but got so bored after 10 minutes I tried hitting Wilma, the 'clever virtual maid' with the microscope. I guess there's a reason they don't let you do that. It also seemed sexist to have the scientist be a man and the 'maid' be a woman. But then you have to remember that history WAS very sexist. Just for the record I would have tried hitting Professor Koch with the microscope but he is strangely absent. Wilma is the only person present. Now I feel bad for trying to hit her. Sorry Wilma. I guess Koch probably had many assistants but I think they should have put Julius Petri in the game rather than the, presumably fictitious, Wilma.

Saturday, January 19, 2013

Sampling the antibiotic resistome

Remember the soil bacteria Streptomyces I mentioned as being the source of several of our antibiotics? You will probably not be surprised to find that this bacteria is also the source of resistance genes. A paper from the end of 2006 shocked many people though when it was discovered just how many antibioticsStreptomyces was resistant to.

In the paper, they isolated 480 different strains of the bacteria from soil samples and then exposed them to 21 different antibiotics to see if they could survive. The average strain was resistant to between seven and eight antibiotics and two particularly hardy ones were resistant to 15 drugs. The danger is that these genes will pass from harmless soil bacteria such as Streptomyces into more deadly bacteria. This is known to happen, for example the genes that allow some harmful bacteria to resist vancomycin, one of the last lines of antibiotic defense, originally came from soil-dwelling bacteria.
"The chances that these genes will end up in a disease-causing organism at some future point is high," microbiologist Abigail Salyers, University of Illinois at Urbana-Champaign.

Friday, January 18, 2013

Tuberculosis animation

An excellent animation showing how the body deals with Tuberculosis bacteria. From the website of Travis Vermilye 'BioMedical Illustrator And Animator.' This video explains how, although Tuberculosis causes many of its worst effects in the lungs, it can also become widely disseminated throughout the body.

What you are seeing is a single tuberculosis bacillus as it has come to rest in an alveolar air sack of the lung. A white blood cell senses the presence of the bacteria and ingests it although it is unable to break it down due to its thick waxy coating. The macrophage with tuberculosis bacilli inside then makes its way to a lymph vessel.

In the lymph node, the macrophage dies and releases its contents, including the tuberculosis bacteria. This stimulates other white blood cells and, as a response to the escalation, our immune system tries to contain them in a spherical object known as a granuloma. Granulomas are comprised of connective tissue and other types of white blood cells.

In the animation one white blood cell, containing tuberculosis bacteria, escapes the forming granuloma  and travels on through the blood stream to other parts of the body. This macrophage will also die eventually and release bacteria to other parts of the body where new granulomas may form.

Thursday, January 17, 2013

Selman Waksman and streptomycin

Although Mycobacterium tuberculosis has a thick layer of peptidoglycan like the Gram-positive bacteria the mycobacteria are usually considered separately because they have a thick waxy layer surrounding their cell wall. So, unusually, they are classified as Gram-positive because they lack the outer membrane of the gram-negatives but they don't actually retain the Gram stain like the other Gram-positives.

This is actually of considerable significance because they are also not susceptible to beta-lactam antibiotics like penicillin. The first antibiotic to be effective against tuberculosis, streptomycin, was discovered in 1943 by Selman Waksman a Ukrainian-American biochemist and microbiologist. A professor of biochemistry and microbiology at Rutgers University for four decades, he discovered over twenty antibiotics and, in fact, coined the word antiobiotic. He was awarded the Nobel Prize in Physiology or Medicine in in 1952.

Wednesday, January 16, 2013


Today's comic from xkcd - a webcomic of romance, sarcasm, math, and language. Which you should probably read. If you don't already.

Plus they have a very cool use policy:

Note: You are welcome to reprint occasional comics pretty much anywhere (presentations, papers, blogs with ads, etc). If you're not outright merchandizing, you're probably fine. Just be sure to attribute the comic to

Hand sanitizers are actually very interesting because there is a very active debate about whether their use leads to antibiotic resistance. They themselves are not antibiotics and have different modes of action but the vast majority contain a substance known as Triclosan. There is a pretty active debate about Triclosan. Stuart Levy's article Antibacterial household products: cause for concern is a good starting place if you are interested in this topic.

Scientists are concerned that the antibacterial agents will select bacteria resistant to them and cross-resistant to antibiotics. Moreover, if they alter a person's microflora, they may negatively affect the normal maturation of the T helper cell response of the immune system to commensal flora antigens; this change could lead to a greater chance of allergies in children. As with antibiotics, prudent use of these products is urged.

Hand sanitizers can be great if you aren't able to wash your hands but should not be used in place of hand washing. Use of compounds like Triclosan in other products is rarely warranted.

Tuesday, January 15, 2013

A Killer Quietly Gains Strength

I missed this when it came out last year but the Wall Street Journal has had a series of articles 'chronicling the world's imperfect response to the rise of drug-resistant tuberculosis, an ancient disease that modern medicine, until recently, could defeat.'

Monday, January 14, 2013

Flu trends

Well in case you hadn't read the news, or noticed all the sick people, it's a pretty bad flu season this year. It's already shaping up to be worse than 2009 in terms of total cases and the virulence is actually worse as this year's strain appears to be quite nasty.

Google's flu tracker now has data by state and by cities and is a great illustration of using our search data for public good. Google can track flu trends several weeks before healthcare data is available simply by tracking the search terms people use (see 'How does this work?')

We'll talk more about influenza, why strains vary, why you need a new vaccine every year and where pandemics come from in a later class. But for now, here's a public service announcement from the executive director of UCSB student health.

Due to the increasingly serious influenza illnesses spreading across the country, we encourage all students and staff to receive a flu shot as soon as possible. Faculty & staff are encouraged to obtain their shots from their local healthcare providers, and many retail pharmacies also offer flu shots.

Student Health will be offering special times when flu shots for students can be obtained quickly without appointments in the Student Health Classroom on Tuesdays or Fridays 1:30 - 3:30pm. 

Alternatively students may obtain flu shots at our regularly scheduled Immunization Clinics Monday - Friday 10:00 am - 12:00pm & 1:30 - 3:30 pm; check in at the designated Immunization computer in the Student Health lobby. There is no additional cost for students with UC SHIP insurance, and for other students the cost is $20 and is billed to BARC.

Symptoms of flu include fever, cough, fatigue and joint aches. Medications can be prescribed to shorten the course of the illness if treatment begins within the first 48 hours, but otherwise the treatment is rest and over-the-counter painkillers. Most cases of flu don’t need to see a doctor unless there are serious symptoms, or can come in the first 2 days of illness when prescription medications may shorten the course of illness.

Please DO NOT GO TO CLASS OR WORK when you are ill to avoid spreading illness to others! The best way prevent the spread of illness is by avoiding others when ill, covering your cough and washing your hands. You should not have intimate contact or share cups or food utensils with people who are ill. Further information can be found at and             

Sunday, January 13, 2013

Easy to introduce, hard to get rid of...

From NPR weekend edition yesterday:
After Bringing Cholera To Haiti, U.N. Plans To Get Rid Of It.

Haiti hadn't seen cholera for at least a century. Then suddenly, the first cases appeared in the central highlands near a camp for United Nations peacekeeping forces.

Since then the disease has struck 1 out of every 16 Haitians — nearly 640,000 people. It has killed 8,000.
Most scientists now think Nepalese soldiers unwittingly brought cholera to Haiti when they joined a U.N. peacekeeping force there in 2010. The outbreak started just downstream from their camp. Sewage from the camp spilled into a nearby river.

For its part, the U.N. hasn't admitted anything. But in December, Secretary-General Ban Ki-moon announced a plan to rid Haiti and the neighboring Dominican Republic of cholera.

Concannon says that's ambitious — but feasible.

"Cholera can certainly be eliminated from Haiti," he tells Shots. "It's been eliminated from the United States, from England, from many countries in South America," he says. "This is basically 19th century technology that needs to be installed in Haiti."

The Haitian government is expected to release a detailed blueprint for the first two years of the effort sometime this month. The entire project is expected to cost $2.2 billion and take at least 10 years.

But so far, the U.N. has identified only 10 percent of the money, most of it redeployed from earlier pledges. Concannon worries the rest may never be found.

Saturday, January 12, 2013

Tchaikovsky's death

One of the strangest Cholera stories concerns the Russian composer Tchaikovsky who died from cholera in 1893, nine days after the premiere of his Sixth, and probably most famous, Symphony, the Pathétique.

There are no end of theories about how and why this occurred, ranging from an accident to suicide to forced suicide. We do know that on 2 November 1893 Tchaikovsky drank a glass of unboiled water - an unusual event given that by this date the mode of transmission of cholera was well known and a cholera epidemic was underway in Saint Petersburg.

If you'd like to read more about this curious story then you have the choice of the exhaustive detail of Wikipedia: Death of Pyotr Ilyich Tchaikovsky, a newspaper article from 2007: How did Tchaikovsky die?, a research paper from 2010: The cause of P.I. Tchaikovsky's (1840-1893) death: cholera, suicide, or both?, or, my favorite, the Straight Dope: How did Tchaikovsky really die?

And then there's the question of whether the Pathétique was written as a farewell to the world.

After the last rehearsal of the symphony under its composer's baton, Grand Duke Konstantin Konstantinovich, a talented poet and fervent admirer of the composer, ran into the green room weeping and exclaiming, "What have you done, it's a requiem, a requiem!"

Friday, January 11, 2013

The Ghost Map

The story of London's great stink, it's cholera epidemics, and the work of John Snow is well described in many books about epidemiology and public health.

Steven Johnson 2006 book called 'The Ghost Map: The Story of London's Most Terrifying Epidemic--and How It Changed Science, Cities, and the Modern World' is very readable and fairly vividly evokes the era. As part of the publicity for the book they made an amusingly educational (or educationally amusing) animated video that is well worth 3 minutes of your time.

Thursday, January 10, 2013

Who discovered Cholera?

Or more precisely, who first discovered the organisms that cause Cholera? The smart money would be on Robert Koch who discovered many other disease causing organisms such as Anthrax in 1877 and Tuberculosis in 1882. However Koch only rediscovered Cholera (in 1883) because the causative agent had actually been discovered thirty years earlier by Filippo Pacini.

Pacini published a paper in 1854 entitled, "Microscopical observations and pathological deductions on cholera" in which he described the organism and its relation to the disease. Just to make his discovery perfectly clear to everyone his microscopic slides of the organism were clearly labeled with his name, the date and nature of his investigations.

But people still managed to overlook his work and Koch was usually given credit for the discovery - a mistake that was only fully rectified 1965 when the international committee on nomenclature adopted the formal name Vibrio cholerae Pacini 1854.

For more information check out 'Who first discovered Cholera' at UCLA's John Snow site.

Wednesday, January 9, 2013


I mentioned this in the first class but just as a reminder you can access hundreds (nearly a thousand) past posts from this class either by searching in the box at the top left (eg search on miasma) or by clicking on of the labels, on the right hand side, scroll down if you don't see them. 

For example you can access all the previous 42 Cholera posts by selecting the Cholera label on the right hand side. Here are a few previous posts I think you might find particularly interesting that relate to topics covered today to encourage you to delve into the archives.

Tuesday, January 8, 2013

Do Natural Disasters Breed Health Epidemics?

An interesting article in Popular Science that touches on several issues we will cover in this class.

Do Natural Disasters Breed Health Epidemics?
A deadly outbreak of cholera followed the 7.0 earthquake that struck Haiti three years ago this week. Jonathan Katz, the only American reporter stationed in Haiti at the time, explains what caused the outbreak--and why it was anything but inevitable.

Monday, January 7, 2013

Kindle edition of text

If you want the Kindle edition of the Coming Plague then use this link. The kindle edition doesn't show up if you just search for the book.

On a related note I will put a copy of the book on reserve in the library.

Thursday, January 3, 2013


Welcome to the blog for EEMB40 - the Ecology of Disease - for Winter 2013. It will also serve as a class website and you will find links to lectures etc. in a box at the top right imaginatively called 'links'. Lecture slides will be available shortly after each lecture. They are put there for your convenience (you don't need to scribble down details of a graph because you know it will be available later) but please note that they are not designed to be lecture notes. In fact in most cases my slides would make very poor notes. In order to help you take notes I have made a glossary for the class - also linked on the right. All the terminology you will be required to know is listed in the glossary.

You are all welcome, and encouraged to post here. To do that all you need to do is to send me an e-mail saying just that. I will then add your address and Google will send you an invitation to be an author. Just follow the simple instructions and away you go.

Postings to the blog should be relevant to the class but the blog is specifically designed to be a place where you don't need to worry about how relevant your post is. (I give you 'Basket full of puppies' as an example). I will be posting lots of things that I read in the news or that I take out of lecture (for time purposes) but that some of you may find interesting. By putting it here you can look at it at your leisure and you know it won't be on the exam.

I try to post every day when the class is running and, where possible, the postings are relevant to the current topics we are covering in class. You can access older postings (there are nearly 900 of them from the previous times I have taught this class) by using the 'Labels' (scroll down and they'll be on the right hand side) to pull up posts on particular topics.