Monday, March 19, 2012


 Some suggestions for reviewing the class from previous TAs.

o   Biology of disease, symptoms, pathogenesis, reproduction, etc.?
o   What kind of organism causes it?
o   How is it transmitted? (direct, waterborne, vector, what vector?)
o   Can we treat this disease, how? Is it curable? Preventable?
o   How does this disease affect humans?  What kind of host are we for it?
o   How does ecology of host affect transmission, what happens when this ecology changes?

o   Use the Glossary to review the terms covered and their definitions.
o   You are responsible for all terms in the glossary that we covered in class, (I took a quick look and the only terms I see that we didn't cover this year are Endogenous retrovirus and retrovirus, plus Hantavirus cardiopulmonary syndrome and Hantavirus 'sin nombre'.
o   Think about the context in which we learned each term: what disease were we studying? What concepts in epidemiology or ecology were we discussing? What other diseases does the term relate to?

o   Review how diseases relate to the theme of the week in which they were covered.  Do any diseases relate to themes covered in other weeks, how so?
o   Refer back to the Short Answer section of the Midterm and the quizzes to review concepts.  
o   Are there any diagrams used in lecture or reading which demonstrate and relate concepts?

o   Create a timeline to review when disease outbreaks and scientific discoveries happened, and when people were doing their work.  More than specific dates, focus on reviewing the context in which events/people were working, and when they were working relative to other’s work and other historical events.

Saturday, March 17, 2012


No essential information here but since I know people check in here before the exam here's something for you

The final will be a very similar format to the midterm. It will have:
20 Multiple choice questions worth 1 point each.
6 Presidential briefing document questions worth 2 points each (both have two words or phrases underlined that you need to provide a simple and clear definition of).
6 More general questions that the President has for you. These may not have a single correct answer.

This adds up to 44 points. I was going to give you a point for free but then realized I may as well collect some data. My first instinct was to have a question asking which President you imagined because I'm actually curious. Then I worried this would appear like I was interested in your political leanings - I'm not, I'm just curious which President the younger generation pictures when asked to imagine 'a President'. So the free question will ask:
Is there an infectious disease you would have liked to have seen covered in this class that we did not cover? 
Writing anything (even, 'no') will get you a point. I'm putting it here because you might want to think about this ahead of time. If there are a significant number of people who'd like to know about West Nile virus, Dengue Fever, Hepatitis, or Chlamydia for example I can make sure I fit them into the class in the future.

Friday, March 16, 2012

TED talk

I came across this video of Laurie Garrett, the author of the Coming Plague, speaking at a small TED event in 2007. This was before the H1N1 swine flu of 2009 and so she is mainly talking about H5N1 avian flu. I think she makes a lot of very interesting points and the talk acts as a great review, not just for the final week but also for other topics we covered.

Thursday, March 15, 2012

Procrastinate and review

If you want to review some topics from the class in a painless and social way then why not get together with some friends to watch and discuss Steven Soderbergh's movie Contagion that came out in Fall 2011? (I just checked and it isn't on Netflix on demand but it is on Amazon instant video for $1.99 for a 48 hour rental).

As a movie I think it is decent, but not great, but what is interesting is that it takes its science very seriously. So much so that at least two science outlets wrote reviews praising the movie for this. Whether it is the origin of the virus, the importance of R0, how vaccines are made (and the difference between live, attenuated and dead vaccines), or the importance of fomites the film gets it right.

Contagion doesn't skimp on science at New Scientist
Soderbergh and screenwriter Scott Burns practice what is in effect very successful science communication: they keep the viewer's attention as they explain statistics like the all-important R0 - the average number of people an infected person infects - and truths about the scientific process, such as the fact that before researchers can study a virus, they need to figure out how to grow it in cell cultures in the lab, without the virus destroying all the cells.
Contagion, the Movie: An Expert Medical Review at Medscape
The moviemakers did a very good job of illustrating how Southeast Asia can essentially serve as a "genetic reassortment laboratory" with influenza strains being created as a combination event among strains from pigs and chickens (and in this case, bats) to create a strain that the population has never seen before. They do a very good job of explaining that possibility and in showing how easy the virus can spread from one person to another. In fact, in bringing up the concept of contagiousness as "R0," they compare the R0 of influenza, polio, and smallpox. It's very interesting that they were willing to spend time explaining what contagiousness means.

Wednesday, March 14, 2012

Swine flu (and conspiracy theories)

I just watched a whole bunch of videos about swine flu to see if there was a nice simple summary I could post here. It's amazing some of the crazy stuff that is out there. Not only is there a whole Swine flu conspiracy theory but its wrapped up with chemtrails, the new world order and probably Lee Harvey Oswald if you watch further than I did. You can get all your conspiracy theories covered in one go in this video which takes a look at some of them.

The video above is a nice simple illustration of where Swine Flu came from and reviews some of the topics we covered in class. It also simply explains why we might expect more contagious strains of flu to be less dangerous - it's all down to which part of the respiratory tract they infect.

Tuesday, March 13, 2012

To publish or not?

Some of you may have read about an interesting disease related debate that is going on right now and is attracting quite a lot of media attention. It concerns the H5N1 strain of influenza that appears to have a high mortality rate in people but is currently poorly transmitted between people (if it is even transmitted at all).

In 2011 two teams of scientists created mutant strains of H5N1 influenza (ie avian or bird flu) that could be more easily passed between mammals in a laboratory setting (ferrets are the animals of choice for flu studies apparently). Scientifically this is interesting research and could address several public health issues: can this strain become more easily transmitted without losing its virulence? Which changes should we watch out for? How many mutations does such a change require?

However as the papers were reviewed the US National Science Advisory Board for Biosecurity (NSABB) recommended that the results of the two studies should only be published in a redacted form. They advised that methods and details should be left out for fear the research could fall into the wrong hands and be used to create a pandemic that might kill tens of millions of people. This unprecedented move sparked a broader debate about censorship and responsibility in potentially dangerous research.

It also provoked some sensational headlines:
Controversial 'Armageddon' super virus recipe to stay secret - for now - Sydney Morning Herald

In a meeting last month the World Health organization came to a different conclusion. A panel of 22 experts  concluded that the mutant flu studies should be published in full. They argued that redaction would likely be ineffective and that the benefits outweighed the potential risks.

Nature have put together a web special on the H5N1 controversy that compiles a variety of papers, reports and commentary (and is also the source for this fantastic chicken image).

Monday, March 12, 2012

Vaccination then and now

As I mentioned in an earlier class vaccines become victims of their own success. As the diseases they cause become rare and fade from our memory we tend to focus on the possible side effects of the vaccine - sometimes real, sometimes imagined.

However when the actual disease in in your neighborhood, crippling and paralyzing children then you queue around the block to get your child their vaccination shot.

One fact I didn't mention in lecture was that neither Jonas Salk nor Albert Sabin (who invented the oral polio vaccine) patented their vaccines - they donated the rights as gifts to humanity. In fact there's a fairly famous story about Jonas Salk, who worked at the University of Pittsburgh, being asked by a reporter “Who owns your polio vaccine?” On hearing the question, Dr. Salk looked at the reporter and said “Who owns my polio vaccine? The people! Could you patent the sun?”

Sunday, March 11, 2012

Polio at the Smithsonion

Thanks to a link from Clark I discovered that the Smithsonian National Museum of American History has a fantastic online exhibition about Polio.

I think they've done a great job with a nice combination of text, pictures and audiovisual material. In addition to the direct impact of the disease itself it is interesting to read how the large number of disabilities caused by it led to fundamental changes in the way that the disabled were treated in this country.

Before Mom found an opportunity to go down to the grade school office to register me, three members of the school board came to visit us …. ‘It has been brought to my attention that you folks have a son in a wheelchair. It is our duty to inform you he will be unable to attend school….’”
—Don Kirkendall, 1973

Saturday, March 10, 2012

India celebrates a milestone

New Delhi, Feb. 25 2012: The World Health Organisation has deleted India from its list of polio endemic countries, acknowledging the absence of any new instance of illness caused by the wild polio virus for more than a year since a child was diagnosed with the disease in Howrah in January 2011.
“This is the first time in history we’re able to put up a map like this one,” Bruce Aylward, an assistant director-general for polio in the WHO, told a conference here today. He presented a map displaying polio cases over the past year in Africa, Pakistan, Afghanistan and China but none in India.
Indian health authorities had recorded 741 patients paralysed by the wild polio virus in 2009 and 42 patients in 2010, but have detected no new patients since January 2011.
“But the big risk is to think we’ve finished,” Aylward said. India will need to remain free of any paralysis caused by the wild polio virus for three years from the last case before it can seek WHO certification for having eradicated polio — in January 2014.

Recall that because there may be 100 cases of mild, subclinical,  polio for each diagnosed case then India may have had dozens of cases of Polio last year. That's not to say that this isn't a big step in the right direction - just that surveillance and vaccination need to remain high and the presence of endemic polio in Afghanistan and Pakistan will always threaten India until those countries too can establish her immunity and eradicate this disease.

Following this vaccination success India is now looking to eradicate measles and tetanus.

Friday, March 9, 2012

Polio - a miscellany

We didn't have much time to talk about polio but if you'd like to know more here are some polio related items culled from past posts. 

Polio in comic book form

The story of Polio in comic book form. by James Weldon, a journalism student at the University of British Columbia. Learn the full story from the polio virus itself as it tells all in a group therapy session for 'diseases nearing extinction' with smallpox, guinea worm and leprosy. Lots of little jokes in here and a surprising amount of information.

Iron Lungs

When people are nostalgic for the 'simpler' times of the 1950's (after the war but before the turbulence of the sixties) they usually conveniently forget about horrors such as polio and iron lungs. These days many people probably only think of an iron lung as a Radiohead song, and even then many people miss the metaphor - something that keeps you alive but becomes very restrictive.

I am amazed by people who have lived their whole lives in them but have remained cheerful and happy. As well as the story about John Prestwich there is also the story of Martha Mason who has lived in an iron lung for over 60 years.

(A)s one of the few surviving people left who live their lives encased in an iron tank, she said she intends to continue as she always has -- making the most out of what life has offered her.
"Get as much joy from life for yourself and others as you can squeeze out of it," she said.

Polio eradication - is it worth it?

Check out this New York Times article about Polio eradication that contains some interesting comments about Bill Gates funding for the initiative in particular:

The effort has now cost $9 billion, and each year consumes another $1 billion. By contrast, the 14-year drive to wipe out smallpox cost only $500 million in today’s dollars. 

“Bill Gates’s obsession with polio is distorting priorities in other ... areas. Global health does not depend on polio eradication.” 

Bin Laden vaccination Ruse

There's a fairly factual report in the New York Times, Vaccination Ruse Used in Pursuit of Bin Laden, but they miss the serious implications of this that are discussed in this post at Wired, File Under WTF: Did the CIA Fake a Vaccination Campaign?

This is awful. It plays, so precisely that it might have been scripted, into the most paranoid conspiracy theories about vaccines: that they are pointless, poisonous, covert shields for nefarious government agendas meant to do children harm.

Thursday, March 8, 2012

Protect your children

 Disney themed DDT impregnated wallpaper sold in the US in 1947.

Because of evidence of environmental damage DDT was banned in the US in 1972 and was subsequently banned for agricultural use worldwide under the Stockholm Convention. It still has a limited use for vector control but there are some who would like to see this use greatly expanded -

WHO Backs Use of DDT Against Malaria: The World Health Organization today announced a major policy change. It's actively backing the controversial pesticide DDT as a way to control malaria. 
NPR - September 2006

It's an interesting and fairly complex issue. Here's another NPR article from 2009 that addresses the same issue but with a specific program in Uganda. It addresses both the consequences for organic farmers:

 Many farmers feared the DDT could ruin their livelihoods. A lot of farmers here grew organic cotton and sold it -- at a premium -- to the international market. After harvesting, they stored the crops in their homes -- in the very same space where the DDT was to be sprayed.

and how fear of DDT was being used for political gain by others:

Public health experts generally believe that if DDT poses potential health risks, they're far smaller than the known risks posed by malaria. But the Ugandan government didn't paint this nuanced picture of risks verses benefits.
As public concern grew, it wasn't long before politicians stepped into the fray.
"Your President wants to kill you all in broad daylight. I say this because DDT is a highly toxic chemical," said Ken Lukyamuzi.
Lukyamuzi is the charismatic leader of the conservative party -- a small but vocal opposition party in parliament. 

Wednesday, March 7, 2012

Malaria in the US

A fascinating map of malaria in the USA in 1870 from the Library of Congress digital history collection (click here for a zoomable version).

Even though malaria was never a massive problem in the US as a whole it was certainly a problem in parts of the South as this map indicates. The darkest red color indicates a malaria mortality of over 1,400 per 10,000 - ie 1 in 7 people were dying of malaria.

In the US Civil War, where much of the action took place in these malarious states, large numbers of soldiers contracted Malaria and tens of thousands were killed.

The most shocking fact is that in 1870 no-one yet realized that mosquitoes were transmitting the disease.

Here's an excerpt from a Scientific American article entitled The Civil War and Malaria.

It is difficult for us to realize the fact, but we all know that any soldier is in five times more danger of dying from malarious disease than of being killed in battle.

What malaria is nobody knows. It may consist of organisms, either animal or vegetable, too minute for even the microscope to detect or it may be some condition of the atmosphere in relation to electricity, or temperature, or moisture; or it may be a gas evolved in the decay of vegetable matter. The last is the most common hypothesis, but it is by no means proved, and it has some stubborn facts against it. There is no doubt, however, that malaria is some mysterious poison in the atmosphere, and that it is confined strictly to certain localities.

Tuesday, March 6, 2012

Global Malaria burden

Here's an article from the Guardian newspaper about some recent revisions to the number of people estimated to die from malaria each year.

Malaria deaths country by country: how many are there?
What we thought we knew about Malaria deaths is wrong: the reality is much, much worse. See what the new detailed data says.
Whilst the good news is that the current estamted total number of deaths is still down from a high of nearly 2 million people per year, the bad news is that it nearly doubles some other estimated figures. The discrepancy largely comes about from a difference in adult deaths.

Monday, March 5, 2012

Malaria proof mosquitoes

A 'malaria proof' mosquito' would be an valuable tool in the fight against malaria. It looks like scientists have created just such a mosquito - through a combination of disrupting the parasite development and reducing the mosquitoes lifesapn (as we discussed in class). Now all we need is a way to give such mosquitoes a competitive edge so that they replace the
 native mosquitoes...

It was known that the Akt enzyme is involved in the mosquito's growth rate and immune response, among other things," Riehle said. "So we went ahead with this genetic construct to see if we can ramp up Akt function and help the insects' immune system fight off the malaria parasite."
The second rationale behind this approach was to use Akt signaling to stunt the mosquitoes' growth and cut down on its lifespan.
"In the wild, a mosquito lives for an average of two weeks," Riehle explained. "Only the oldest mosquitoes are able to transmit the parasite. If we can reduce the lifespan of the mosquitoes, we can reduce the number of infections."

Sunday, March 4, 2012

Rinderpest @ number 2

The eradication of smallpox (certified by the WHO in 1979) led to a period of optimism that other diseases would be soon vanquished. I don't think anyone expected that it would be over three decades before another disease fell - Rinderpest declared extinct by the WHO in 2011.

A number of newspapers had nice articles describing both the historical importance of Rinderpest and also the eradication program.

The New York Times made the point that with the disease is relatively unknown in America because with the exception of a brief, contained outbreak in Brazil in 1920, it never reached the Americas. (Rinderpest, Scourge of Cattle, Is Vanquished.)

The Washington Post explains that three things made rinderpest eradicable. Animals that survived infection became immune for life. A vaccine developed in the 1960s by Walter Plowright, an English scientist who died last year at 86, provided equally good immunity. And even though the virus could infect wild animals, it did not have a reservoir of host animals capable of carrying it for prolonged periods without becoming ill. (Rinderpest, or ‘cattle plague,’ becomes only second disease to be eradicated.)

Saturday, March 3, 2012

Swimming in sick seas

There was a session on ocean health at last month's Annual Meeting of the American Association for the Advancement of Science (AAAS) in Vancouver, Canada.

A number of news outlets picked up on the news that pathogens of terrestrial animals are killing ocean mammals: Iconic Marine Mammals Are 'Swimming in Sick Seas' of Terrestrial Pathogens

Parasites and pathogens infecting humans, pets and farm animals are increasingly being detected in marine mammals such as sea otters, porpoises, harbour seals and killer whales along the Pacific coast of the U.S. and Canada, and better surveillance is required to monitor public health implications, according to a panel of scientific experts from Canada and the United States.

Between 1998 and 2010, nearly 5,000 marine mammal carcasses were recovered and necropsied along the British Columbia and Pacific Northwest region of the U.S., including whales, dolphins and porpoises, sea lions and otters.

"Infectious diseases accounted for up to 40 per cent of mortalities of these marine animals," says Stephen Raverty, a veterinary pathologist with the Animal Health Centre in the British Columbia Ministry of Agriculture and Lands, and an adjunct professor in UBC's Marine Mammal Research Unit.

"In many cases, the diseases found in these marine mammals have similar or genetically identical agents as those infecting pets and livestock. We don't yet know how these diseases are affecting the health of marine mammals" says Raverty.

Friday, March 2, 2012

After the Rinderpest

Bill Knight is a South African musician who has a whole album about the Rinderpest epidemic that devastated Africa.

The Scene is the Cape Colony border, late 19th century, a terrible plague, the Rinderpest (rather like Foot & Mouth), has decimated the livestock and lives of the Boers, Brits and Amaxhosa alike. The infected animals have to be piled in pits and burned. The land is covered in smoke and weeping.

You can download a free mp3 of the title song , After the Rinderpest, from the Last.FM website.

After the Rinderpest
There’s a wicked wind on the smoking ground
All out hopes and dreams, we had to burn them down.
And our poisoned wells took our first and best
Gave our childrens’ lives to the Rinderpest.
Sent our youths away to be militarized
And we couldn’t see into their empty eyes.
Would you have the strength, if they confessed
To what they saw, in the wilderness.
With a burying pit full of burning beasts
With the crimson coals of the heat beneath.
Holding out our hands to be cauterized
But the Rinderpest left us paralyzed.
And a tattooed child full of battle scars
With a heart of iron, hammered hard.
Do we act surprised, as though we never knew
What the sulphur air would have done to you.
There are bands of us that have survived
And all we have is how we live our lives.
As we struggle on, we must not forget,
Just what we learned, from the Rinderpest.

Thursday, March 1, 2012

Sperm bank shortage

One of the oddest consequences of the United Kingdom's BSE epidemic of the 1990's has been the United States ban on sperm from Scandinavia.

In September 2003 the Food and Drug Administration banned the import of donor sperm from 30 countries, where Mad Cow disease has been detected in cattle - despite the fact that most scientists believe it is virtually impossible for vCJD to be spread through sperm.

Up until this point Scandinavian sperm had, apparently, been the most popular choice for US sperm bank customers who frequently seek blond haired blue eyed babies. Although the ban was enacted in 2003 it didn't really attract much attention until 2007 and 2008 when sperm banks ran out of their stocks of Scandinavian sperm.