Posts tagged with mathematical.

Science tackles zombie attacks

Jennifer Gardy, August 10, 2009 at 11:07 AM

My apologies for the prolonged radio silence - it turns out the real world is a rather busy place. I have a sneaking suspicion that this may have something to do with the fact that I am working at a Centre for Disease Control IN THE MIDDLE OF A PANDEMIC, but I haven't got a control job in place so cannot reliably confirm whether my hypothesis holds true with any measure of statistical confidence.

I can, however, confirm that working in the realm of infectious disease research is tremendously interesting. Global surveillance is constantly turning up cases of the usual assortment of gnarly human ailments, from anthrax to rabies to pneumonic plague, and the animal kingdom is verily rife with exotic zoonoses. In the last two weeks, for example, I have received reports on Ecuadorian penguins with malaria, herpetic horses, a tuberculotic cow, and a bunch of vampire bats with SARS.

All the rabid humans, coughing cows and sneezing febrile bats of the world, however, cannot even come close to the most interesting bit of infectious disease research I've come across lately - the mathematical modelling of the potential outcomes for humanity should zombies attack.

I came across the paper a couple of weeks ago, when I was giving a workshop on practical conference-going skills to a group of students about to attend the Annual Meeting of the Society for Mathematical Biology. The pre-conference meeting also featured introductory lectures from many of the conference session chairs, 45-minute cheat sheets introducing the students to the different areas the conference plenary sessions would cover. I arrived early to the check out the session before mine - an introduction to mathematical modelling of infectious disease - and discovered Robert Smith?'s (yes, that is a question mark) zombie model.

Now I am certain that most readers will agree with me when I say that mathematical modelling does not sound like the most compelling of subjects. Partial differential equations, eigen decomposition and matrix diagonalization are all very important concepts that the advanced undergraduate in physics, engineering, or math ought to be familiar with, but when one is being taught the aforementioned concepts through examples that include latent semantic analysis and pharmacokinetic cumulation processes, the material can get a little, uh, dry.

When you use zombies as your example process, however, students sit up and take notice.

There is no nerd on the face of this earth who hasn't at least idly considered what they'd do in the event of a zombie attack, and there are a good many more of us who have actually thought through our specific plans and debated their various benefits and pitfalls with others (my solar-powered-chainsaw-studded fence, for example, while brutally effective in the short term, would likely soon enough result in the build-up of a ramp of zombie carcasses in front of the fence, blocking the chainsaw blades. See, it's good to think of these things now.)

Smith? and his colleagues decided to apply the basic principles of mathematical modelling to a zombie outbreak situation. They define a series of classes to which people can belong (susceptible, zombie, or removed) and a set of parameters modelling the transition between classes (the rate at which susceptible become zombies, for example). From this they can construct a basic epidemiological model that predicts how quickly zombies will take over the world. The model can be successively refined by adding new parameters, like the effect of quarantine, treatment, or what the authors politely refer to as "impulsive eradication" (nuking the $#!% of the zombies, in other words).

By explaining a highly technical scientific method using a flat-out cool pop-culture example, the authors manage to make concepts like Jacobians, unstable equilibria, and mass-action transmissions infinitely more palatable and memorable to students and researchers alike.  The approach is one more and more profs are adopting - at UBC, for example, a second-year physics course in instrument design is taught as a Robot Wars-eqsue competition, where the students build robots to carry out a specified task and then battle it out of at the end of term to see whose robot emerges triumphant. In my own work, a colleague and I recently jazzed up a textbook chapter on the computational analysis of immunology data by using an exotic and disgusting case of purulent smallpox as our example dataset.

Using a catchy example is a fantastic way to engage students with your subject matter. For proof, you need to look no further than the fact that you, dear reader, kept reading past matrix diagonalizations and mass-action transmissions to find out what happens to humanity in the event of a zombie outbreak. The bad news is that in most cases - the basic model, the latent infection model, the small-scale quarantine model - the disease-free equilibria are unstable and zombies take over the world. Treatment doesn't do a fat lot of good either, as humanity continues to exist but at much lower population numbers than before the outbreak. The good news, however, is that under the model of impulsive eradication, in which large-scale assaults on the zombie population take place as resources permit, humanity survives. So stock up on nukes, folks - the ordinary differential equations don't lie.

Tagged with mathematical, teaching, zombies, modelling | Comments (31) |

Bacon bites back: a scientist’s fascination with swine flu

Jennifer Gardy, May 4, 2009 at 4:07 PM

I can't help but feel sorry for the pig flu.

 

I'm passionate about infectious diseases and, ever since "Swine '09: Bacon Bites Back" burst onto the scene amidst a storm of headlines, press briefings and concerned Tweets, I've been consuming news of all things pandemic with insatiable interest, watching with great curiosity as scientists uncover new knowledge about this novel virus on a near daily basis. I wake up every morning and check the case count, cheer when a new batch of genome sequences is released, and chase down all the interviews and press briefings from CDC officials that I can. To use a timely Canadian analogy, I'm pretty much flying the pig flu playoff flag from my car window.

 

I can appreciate, however, that not everyone shares my rabid interest in swine flu. After all, I am the girl who opted to study microbiology after seeing Dustin Hoffman in Outbreak. I'd secretly hoped that one day my job would take me to Africa, where I'd sport a blue biohazard suit and run nimbly through the jungle, trapping haemorrhagic monkeys with a big butterfly net and, after a flash of brilliant insight, saving civilization from perishing due to systemic visceral organ necrosis.  

 

Most people just want to grow up and have a nice house and fast car, not a biolibrary of primate nasal swabs and fecal samples.

 

But now we're a week and a half into l'affaire du cochon and I'm realizing that my cuddly-wuddly loveable pig flu - one of the most interesting diseases to register on the scientific radar in recent years - is getting a bad rap. The media focus, with few exceptions, has been on the spread of the disease and its potential impact, and much of what makes swine flu and the pandemic so fascinating has been largely ignored.

 

Thus, in an effort to improve public perception of influenza A/H1N1, I'd like to present Three Fascinating and Scientific Things You Probably Didn't Know About the Pig Flu.

 

1. The movement of money is helping to predict the spread of pig flu. For many years, mathematical modeling has been used to simulate and predict the spread of disease in a population. In order to develop a model, however, researchers need data on how humans move at the local and national level. Models based on things like highway systems and population centres are often used, but a group at Northwestern University has modeled H1N1's spread using data gathered from tracking currency. By using data from the wheresgeorge.com bill tracker, they developed a description of human traffic (Lévy flights, superdiffusive random walks, and bi-fractional diffusion equations, oh my!) and have used that in their pig flu projections. Or porkjections.

 

Their disease models, which are based on the worst-case scenario of no public health intervention, are available at http://rocs.northwestern.edu/projects/swine_flu/. You will doubtless be happy to know that even if we sat back and did nothing, by month's end the U.S. would still only have registered about 2,000 cases of H1N1, about the same number of cases of Beaver Fever they expect to see.

 

2. This is the first "open-source" outbreak. In early 2003 when SARS broke out, there was a three-week gap between when the virus responsible for it was identified and when its genome was sequenced and made available to researchers. Since then, genome sequencing technology has improved to the point where only three days after the first WHO report of H1N1, 40 viral genome sequences had been completed and released. As of today, over 180 complete H1N1 genome sequences from the current outbreak have been made available. With all of this data, many types of evolutionary analyses are now possible. Keen researchers are exploring these genome sequences and are sharing the results with the community through collaborative wikis and blogs. Other scientists are further blogging and Twittering these sites in a spirit of data sharing and openness that is heartening to see.

 

A team comprising researchers from Edinburgh, Oxford, and Hong Kong, for example, is publishing its analyses at http://tree.bio.ed.ac.uk/groups/influenza/, where they've reported all sorts of fascinating findings. By using the open-source genome sequence data, they've estimated that the pig flu virus first appeared in September, 2008, and have been able to calculate a statistic that indicates that at the moment, H1N1 isn't spreading very efficiently - only enough to keep itself going at current infection levels.

 

3. Why the flu is more fatal in Mexico is un gran misterio. To date, there have been 26 confirmed cases where people have succumbed to swine flu, 25 of whom were in Mexico and one of whom was a Mexican who had crossed the border into the U.S. Why haven't any of the other cases been fatal? That remains one of the most fascinating aspects of the outbreak.

 

The explanation that jumps to the forefront of most peoples' minds is that the Mexican strains must be more virulent than those seen globally. While this is, of course, a possibility, the open-source evolutionary analyses indicate the available Mexican strains aren't too far removed genetically from isolates found in Auckland, New York and Ohio.

 

Some researchers suspect that pre-existing health factors in the Mexican population might have influenced the disease's outcome, while one leading theory suggests that the increased mortality has to do with the Mexican patients' delays in seeing a physician.

 

While no one can predict for certain what will happen with pig flu, all indications so far suggest that there's no need for panic. It is, nevertheless, an important reminder that pandemic influenza is a very real threat, with new viruses appearing on a regular basis.

 

For now, though, just relax, cover your mouth when you cough, and keep washing your hands. And cook yourself up a nice B.L.T. - pigs need all the good press they can right now.

Tagged with genome, sequencing, h1n1, fatal, mexico, mathematical, flu, source, swine, modeling, open | Comments (13) |