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Archive for April, 2009|Monthly archive page

Google on H1N1 swine flu

In Biology, Delights on April 30, 2009 at 3:38 am

For your datahead enjoyment, a user has added a layer to Google Maps that lets you track cases of swine flu as they are reported.  We are still very much at the point of discovering preexisting cases of swine flu, so this will be a lagging indicator, but it’s still fun (and a little unsettling) to see how many cases of the disease have been spotted in the vicinity of Princeton.


A more utilitarian Google widget is Flu Trends, which tracks common search terms that, according to a Nature paper published by the company correlate well with actual disease levels.  (These terms include searches for symptoms that are related to flu; as Google points out, you get more allergy searches during allergy season and more sunburn searches during the summer.)  This can actually predict disease loads two weeks before health authorities announce new outbreaks.

Considering the hubbub about H1N1, it may surprise you that Flu Trends shows that influenza levels in the US are low and steady.  In the media blitz as new cases are discovered, it’s important to keep in mind that the normal seasonal flu causes 36,000 deaths a year.  While swine flu is newsworthy because of its potential to mushroom into a full-blown pandemic, in absolute numbers it is still a minor player in the disease world.

While the disease cannot be acquired by eating pork, pig farmers are naturally concerned that calling H1N1 “swine flu” will hurt sales.  However, the disease did originate in pigs, recombining with avian and human flu viruses, so it is unlikely that the industry’s calls for it to be redubbed will be heeded.  (“Mexican flu” was one suggestion, and I can think of at least one group that would be riled up over the name.)

Update: A remarkable new website allows you to tell whether or not you are suffering from swine flu.  This represents a significant step forward for online diagnostics.  Get yourself checked out here!

Flu intervention: then and now

In Biology, Policy on April 27, 2009 at 8:18 pm
Policemen in masks, San Francisco, 1918
Policemen in masks, San Francisco, 1918

In our earlier swine-flu related post, we mentioned that early intervention may well make the difference between an isolated outbreak and a deadly repeat of the 1918 Spanish flu.  Just how important is starting countermeasures early, and what kind of interventions work?  The tragedy of the Spanish flu provides a natural laboratory for public health measures, as cities throughout the US differed both in scale and timing of their interventions.

Medical science in 1918 was still getting on its feet.  The majority of older physicians of the time were not educated under the scientific regimen of the Flexnerian revolution.  The leading bacteriologists of the day mistakenly believed that influenza was a bacterial disease, and it was not until 1943 when it was recognized that a virus was responsible. As a result, medical intervention in the pandemic was of questionable value, not least because most of the best doctors had been drafted to serve in the military for WWI.

However, nonmedical interventions were also employed.  These included quarantines, isolation of the sick in makeshift wards, closure of public gathering places such as churches and schools.  A recent study examined the effects of timing and duration of these measures, with the major findings summarized in two graphs:

C: Mortality vs. time to intervention.  D: Mortality vs. length of intervention

C: Mortality vs. time to intervention. D: Mortality vs. length of intervention

The study examined the experience of 23 cities in implementing various public health measures, and measured the impact of response time and duration of intervention.  They found that quick action (as measured by when flu cases rose to double the baseline number of cases) had a strong correlation with reduced mortality, and that maintaining the measures was important to keep the disease from spreading.

St. Louis, for example, closed schools and canceled public gatherings early, and maintained quarantines for over ten weeks, leading to a significantly lower mortality rate.  However, not all cities were as proactive; the median duration of these interventions was only four weeks, insufficient to protect the population.  Some cities were even counterproductive: Philadelphia hosted a military parade to promote war bonds, over the objections of numerous doctors and public health officials.  Soon afterwards, it became one of the hardest-hit cities in the US.  (Here is more, from the New York Times.)

In a sense, we are both better and worse off than those who experienced the Spanish flu.  On one hand, our medical science is more advanced; we can now produce vaccines against new influenza strains, albeit at a delay of several months.  (Because the flu virus mutates rapidly, older vaccines, including the one prescribed this past winter, are ineffective against emergent strains such as this one.)  We have also learned the importance of quick and sustained public health measures: witness the recent warning against traveling to Mexico as a result of the disease.

However, modern transportation makes it easier for civilians to pass the flu from country to country, making it harder to isolate the disease to a single region.  In 1918 the flow of soldiers throughout the US and between the US and Europe are credited with helping to spreada disease that originated in the Midwest to every corner of the globe.  This time it may be passenger jets, not steamships, that spread this emerging pandemic.

New swine flu outbreak

In Biology, Policy on April 26, 2009 at 7:42 pm

For years we’ve been worried about a bird influenza strain (H5N1) mutating to infect humans and permit human-to-human transmission.  Now it appears that a pig flu (H1N1) has in fact adapted to humans, infecting almost a thousand in Mexico and several in the US, and causing nearly 100 deaths.

The United States government declared a public health emergency Sunday as the number of identified cases of swine flu in the nation rose to 20.

The declaration is part of a “standard operating procedure” that will make available additional government resources to combat the virus, Homeland Security Secretary Janet Napolitano said at the White House.

Additional cases of swine flu are expected to be reported in the coming days, added Dr. Richard Besser, acting director of the Centers for Disease Control and Prevention.

Past flu pandemics have caused up to a million casualties, and the epic 1918 “Spanish” flu pandemic is estimated to have killed up 10% of young adults worldwide.  However, there have been false alarms as well; a few cases in 1976 prompted massive immunizations in the US for an epidemic that never materialied, and the vaccine caused a number of adverse reactions.

Unlike earlier epidemics, however, it appears that public health services are being more proactive, both in monitoring the disease and in responding, in Mexico, with closure of gathering places such as schools.  It’s thus very possible that we will avoid repeating the mistakes of past pandemics that led to mass casualties.  However, this is a story to keep an eye on.

Here’s a presentation that two classmates and I did for an infectious disease class.  It talks about the experience of the 1918 flu pandemic, the biology of the influenza virus, and the precautions necessary to prevent a new pandemic (bird flu in this case, but relevant to today).

Masks in Mexico City subway

Masks in Mexico City subway

Learning: so easy a slime mold can do it!

In Uncategorized on April 19, 2009 at 7:44 pm

This is pretty amazing.  Single-celled slime molds have been shown to learn to anticipate events after repeated stimuli.  In this case:

As the cells crawled across an agar plate, the researchers subjected them to cold, dry conditions for the first 10 minutes of every hour. During these cool spells, the cells slowed down their motion. After three cold snaps the scientists stopped changing the temperature and humidity and watched to see whether the amoebas had learned the pattern. Sure enough, many of the cells throttled back right on the hour in anticipation of another bout of cold weather.

This sort of learning has been demonstrated before, in organisms as simple as earthworms and planarians.  But even then, these animals have at least a rudimentary “brain” consisting of specialized neurons.  Slime molds, on the other hand, are independent single-celled organisms.  They do, however, have the ability to aggregate to form complex systems, migrating as a single unit and forming a stalk to sporulate.  This new finding suggests that these emergent properties can also produce intelligent behavior, without the need for a nervous system.

For a bonus: detailed and colorful pictures of slime molds, with a focus on their fruiting bodies.

Smarter than most lower eukaryotes, including Congressmen.

Computer discovers the laws of physics

In Uncategorized on April 7, 2009 at 2:42 pm

In just over a day, a computer program at Cornell has extrapolated Newton’s laws of motions from a pendulum’s swings. The program starts with random combinations of addition, subtraction, multiplication, division and a few algebraic operators. Then, via a genetic algorithm, the program refines the formulae to pick out ones that fit the data better. It came up with the law of conservation of momentum and Newton’s second law of motion.

This raises some serious questions about the nature of science. It took physicists centuries to develop laws of nature to fit observed data; it took Hod Lipson’s program a day. We could worry about machines replacing human ingenuity. Or — a view I find more compelling — we see these algorithms as an aid to deriving the laws that explain other agglomerations of data, such as the genome or proteome. We don’t know the “laws of biology” in the way we know the laws of physics; and still less do we know the “laws of social science.” Maybe artificial intelligence is the best way to make progress on that.

Here’s Lipson giving a TED talk on robotics.