Tuesday, September 9, 2008

Final words

Well I told you summer was fast.
We will grade the final as quickly as possible and the results will be entered before the end of the week - probably by Thursday. As far as I know they should be available to you shortly after they are entered.
If you have questions about the final exam, the course or infectious diseases generally then e-mail is the best way to reach me. I may take a few days off before the next quarter starts but then I'll be having regular office hours on Weds and Thurs 12-1 if you want to catch me (or other times by appointment of course).

I have been musing over developing a similar course on the ecology of non-infectious disease (diabetes, heart disease, cancer etc for beginners) - although some of that is already covered by other courses here eg. MCDB23 Biology of Cancer and MCDB24 Genetics and Human Disease both taught by David Kohl. Or maybe a much more general course - How and why we die (including infectious disease, non-infectious disease and 'accidental' death, homicide and suicide). That would be fun, if a little morbid. I think I'd also need to enlist some help with that one. If anyone has any suggestions I'd really appreciate your comments.

Final exam review

Just a reminder: there's a link to a final exam review guide below. Please take a look before you come to the review session at Woodstocks, 2 pm today.

Why should you come to the review session?
1. I'll be answering questions from lecture, quizzes, and the review sheet.
2. I'll give you your total grade up to now, along with Quiz 4.
3. I'll go over some more review questions that aren't on the review sheet.
4. You can eat pizza the whole time.

Monday, September 8, 2008

Pandemic flu

Sometimes it's easy to overlook the obvious sources. The CDC maintains a very nice Pandemic flu webpage ('One stop access to US Government avian and pandemic flu infomation.')

I was just looking at this before putting a link to it on the blog when I noticed it had exactly the figure I tried to find yesterday - an up to date and clear map of the distribution of H5N1 in both birds and humans.
Relevant material previously on the blog:
Flu season (I briefly mentioned this today)
Spanish flu
Malaria control for the 21st century (the star wars mosquito defence system)
Morbidity and mortality

Sunday, September 7, 2008

Measles vaccine (again)

TV stations, Radio Stations and Newspapers are all in the business of attracting customers. Whilst they all present the news they do so in a way that they hope will grab your attention and keep you watching, listening or reading.

For many subjects this doesn't matter and for some it enhances the experience - 'Coming next: you won't believe what happened in the Red Sox game.'

But when it comes to health I think the news media has an obligation to ensure that the headlines, crawl lines or whatever they call them, do not distort the message.

This week there was news of yet another study that found no link between the measles vaccine and autism. eg. the AP news report:

New research further debunks any link between measles vaccine and autism, work that comes as the nation is experiencing a surge in measles cases fueled by children left unvaccinated.

This science story was picked up by most news outlets as an item that would be of interest to their readership. A quick google news search suggests over 300 articles in the last couple of days. But, bearing in mind that many more people scan the headline than will read the article, let's look at some of the headlines.

The good
Autism and measles vaccine: no link found -- again
Study Dispels Link Between Autism and Measles Vaccine

The Bad
As Seen on TV: MMR Vaccine and Autism
MMR and autism again

and the Ugly
Do Measles Vaccines Put Children At Risk For Autism?
Measles vaccine linked to autism?

All these articles are reporting the same story.

Saturday, September 6, 2008

Modern perils

In poor countries inadequate sanitation and garbage disposal, combined with poor resources at a local level mean there are numerous habitats for mosquitoes to breed in. From abandoned drainage ditches to discarded tires, buckets and bottles the problem is immense. In the absence of environment blanketing DDT the focus has turned to bednets - keeping mosquitoes (at least the nocturnal ones) from biting people.

In the developed world a new problem is arising - abandoned swimming pools. This problem has increased with the recent sharp rise in foreclosed and abandoned homes. In America the concern is not Malaria but West Nile virus. Fortunately such mosquito magnets can be detected remotely (although somewhat expensively) by the use of aerial surveys. Abandoned pools are generally green with algae. This is a regular tool in mosquito abatement in the Bay Area. For example, see this article today in the San Jose Mercury News:

The Santa Clara County Vector Control District will conduct an aerial search Monday for mosquito breeding sources that could potentially carry West Nile virus.

The district has made two previous aerial surveys this year, in early May and early August, which have led to more than 860 inspections and 135 treatments or fish plantings on local properties.

There's a longer article here about the problem in San Bernadino County. Remember the bottom line from this class - whenever anything changes in society there are new possibilities for disease transmission, potentially leading to outbreaks of new diseases or resurgences of old diseases.

Friday, September 5, 2008

HIV and Malaria

Coinfection, a term we introduced last week, that describes the simultaneous infection with two or more diseases is big news these days. In Africa the big coinfections are HIV and Tuberculosis, which we briefly mentioned, and HIV and Malaria.

The interaction between AIDS and Malaria is complex and only just being unraveled. One conclusion though is that coinfection has helped fuel the spread of both diseases in sub-Saharan Africa. (eg this 2006 paper and this 2007 paper).

A student, Randa, sent me this great link to a symposium on HIV and Malaria held at Caltech this year. There are videos of all the talks and the split screen with presenter and slides makes the talks very watchable. You can see:

David Baltimore, Ph.D., Nobel prize-winning discoverer of the molecule that HIV uses to copy itself into our DNA, discusses the origins of HIV, the failure to find a cure, and his own approach toward treatment.

Kimberly Shriner, M.D. , leader of the Phil Simon Clinic Tanzania project, discusses the difficulties and rewards of ministering to HIV positive patients in Africa.

Joel Breman, M.D., D.T.P.H., Senior Scientific Advisor at the Fogarty International Center of the NIH, discusses the battle against Malaria

Bruce Hay, Ph.D., Caltech Associate Professor of Biology, explains a new way to spread genetically-engineered malaria-resistance throughout the African mosquito population.

Martha Sedegah, Ph.D., Senior Scientist at the NMRC's Malaria program, discusses two promising new malaria vaccines.

Thursday, September 4, 2008


I hope that you found something in Wednesday's lecture to make you think a little. How far can we infringe on human rights if the ends justify the means? (and who decides?)

Are there species that we should deliberately drive to extinction?

Before you say no, try reading Olivia Judson's controversial article in the New York Times entitled 'A bug's Death: Should we send the malaria mosquito the way of the dodo?' . In this article she advocates the extinction, or "specicide", of thirty mosquito species through the introduction of recessive knockout genes".

Would this be the first step on a very slippery slope (a lot of people hate snakes, many people dislike spiders etc. etc.) or would the ends justify the means - eliminating the mosquitoes that vector malaria would save at least one million human lives every year?

Wednesday, September 3, 2008

Presidents Malaria Initiative

Workers trained in Indoor Residual Spraying (IRS) march on World Malaria Day in Agoro Sare, Kenya.
Source: James Kei/The Standard

"Americans are a compassionate people who care deeply about the plight of others and the future of our world, and we can all be proud of the work our Nation is doing to fight disease and despair. By standing with the people of Africa in the fight against malaria, we can help lift a burden of unnecessary suffering, provide hope and health, and forge lasting friendships."
-- President George W. Bush in a Malaria Awareness Day Proclamation on April 24, 2007 .

For more about the President's Malaria Initiative check out their webpage.

Relevant material previously on the blog:
Smallpox 2002 (Don't click on this one unless you've got 90 minutes to spare)
Gates foundation
Heroes and Villains
Polio eradication

Tuesday, September 2, 2008

Sciencedebate 2008

An organization called Science Debate 2008 has been working to restore science and innovation to America’s political dialogue. As part of this process they came up with a list of 14 science related questions for the candidates to answer. Barack Obama has submitted answers which you can see here. John McCain has said he will also answer the questions.

Of particular interest for this class is question 6:

Pandemics and Biosecurity. Some estimates suggest that if H5N1 Avian Flu becomes a pandemic it could kill more than 300 million people. In an era of constant and rapid international travel, what steps should the United States take to protect our population from global pandemics or deliberate biological attacks?

Here is Senator Obama's answer (in white) with my comments interspersed in black. This is a non-partisan blog, if Senator McCain submits answers before the class ends I'll comment on that too.

It’s time for a comprehensive effort to tackle bio-terror. We know that the successful deployment of a biological weapon—whether it is sprayed into our cities or spread through our food supply—could kill tens of thousands of Americans and deal a crushing blow to our economy.

Overseas, I will launch a Shared Security Partnership that invests $5 billion over 3 years to forge an international intelligence and law enforcement infrastructure to take down terrorist networks. I will also strengthen U.S. intelligence collection overseas to identify and interdict would-be bioterrorists before they strike and expand the U.S. government’s bioforensics program for tracking the source of any biological weapon. I will work with the international community to make any use of disease as a weapon declared a crime against humanity.

Hmm, I rather wish that they had left the last four words out of the question. I'm going to be disappointed if the answer is solely about bioterror when the intent of the question was about pandemics more generally. There's nothing here that is very interesting from a disease perspective except perhaps the mention of bioforensics. We now have the capability to trace strains of bacteria and viruses to particular source strains and often particular labs.

And to ensure our country is prepared should such an event occur, we must provide our public health system across the country with the surge capacity to confront a crisis and improve our ability to cope with infectious diseases.

This is a bit more interesting. Hospitals have been losing 'surge capacity' (aka empty beds) for years - either in search of greater efficiency or greater profits. There's no mention how this will be done, but the acknowledgment that we need it is a good sign.

I will invest in new vaccines and technology to detect attacks and to trace them to their origin, so that we can react in a timely fashion. I have pledged to invest $10 billion per year over the next 5 years in electronic health information systems to not only improve routine health care, but also ensure that these systems will give health officials the crucial information they need to deploy resources and save lives in an emergency.

This is getting more interesting. Funding for health information systems is a great idea. This will allow us to catch an epidemic in the early stages AND even when there isn't an epidemic we will still help improve people's health by tracking any long term changes in endemic diseases and making causal connections.

I will help hospitals form collaborative networks to deal with sudden surges in patients and will ensure that the U.S. has adequate supplies of medicines, vaccines, and diagnostic tests and can get these vital products into the hands of those who need them.

Ah, interesting, but what does it mean when a presidential hopeful promises to 'help hospitals form collaborative networks'? Does he mean there will be funds available or incentives or he will push for new legislation?

We also have to expand local and state programs to ensure that they have the resources to respond to these disasters. I will work to strengthen the federal government’s partnership with local and state governments on these issues by improving the mechanisms for clear communication, eliminating redundant programs, and building on the key strengths possessed by each level of government. I introduced legislation which would have provided funding for programs in order to enhance emergency care systems throughout the country.

Sounds like some obligatory politician phrasing.

I will build on America’s unparalleled talent and advantage in STEM fields and the powerful insights into biological systems that are emerging to create new drugs, vaccines, and diagnostic tests and to manufacture these vital products much more quickly and efficiently than is now possible. Unfortunately, the Bush administration has failed to take full advantage of the Bioshield initiative. Because of the unpredictability of the mode of biological attack, I will stress the need for broad-gauged vaccines and drugs and for more agile and responsive drug development and production systems. This effort will strengthen the U.S. biotech and pharmaceutical industry and create high-wage jobs.

Whilst no-one will be surprised that Senator Obama got a shot in at President Bush I would have advised him to take the high road and to praise President Bush's commitment to both malaria and HIV programs in Africa. He could have pledged to match or increase funding.

Monday, September 1, 2008

US can block mad cow testing

I almost missed this. An appeals court ruling coming out right before the holiday weekend. AP had the story but I didn't notice it on Friday.

The Bush administration can prohibit meat packers from testing their animals for mad cow disease, a federal appeals court said Friday.

A federal judge ruled last year that Creekstone must be allowed to conduct the test because the Agriculture Department can only regulate disease "treatment." Since there is no cure for mad cow disease and the test is performed on dead animals, the judge ruled, the test is not a treatment.

The U.S. Court of Appeals for the District of Columbia Circuit overturned that ruling, saying diagnosis can be considered part of treatment.

Gut-boosting molecule could fight off stubborn bugs

From this week's New Scientist magazine, a report on how to deal with a particular drug resistant bacteria:

Taking antibiotics can make us vulnerable to attack by tougher, antibiotic-resistant invaders, leading to nasty stomach bugs and the spread of dangerous infections in hospitals. Now a molecule has been found that could be mixed with antibiotics to thwart these harmful invasions.

The gut bacterium vancomycin-resistant enterococcus (VRE) has trouble taking root in a healthy intestine, but after a course of antibiotics it can multiply a thousand-fold and spread to the blood. The reason for this was thought to be that antibiotics kill not only their target bacteria but also harmless gut microbes, freeing up nutrients and niches that allow VRE to thrive.

But when Katharina Brandl of the Sloan-Kettering Institute in New York and colleagues treated mice with antibiotics, they found that levels of Reg3g, a protein made by "friendly" bacteria that kill VRE, dropped by 80 per cent. This suggests that a lack of Reg3g is partly to blame for the VRE increase that follows antibiotic treatment.

To see if boosting Reg3g levels could help, Brandl's team gave mice doses of lipopolysaccharide along with antibiotics. LPS is a molecule found on the surface of some bacteria that stimulates the gut to make Reg3g. These mice ended up with higher levels of Reg3g than mice that just took antibiotics, and they also had fewer VRE colonies - about the same number as mice that had taken no antibiotics. Brandl suggests giving LPS orally to humans taking antibiotics.