Want to stave off swine flu? Catch a cold

Paul Raven @ 13-11-2009

sneezeOK, before anyone says it, the headline is not to be taken as medical advice (I am not a doctor, nor do I play one on television, etc, etc). But research into surprisingly low incidences of swine flu in France in recent months suggests that the common cold may be suppressing the ability of the H1N1 virus to get a toe-hold in our immune systems. [image by trumanlo]

… the percentage of throat swabs from French respiratory illnesses that tested positive for swine flu fell in September, while at the same time rhinovirus, which causes colds, rose […] in late October, rhinovirus fell – at the same time as flu rose. He suspects rhinovirus may have blocked the spread of swine flu via a process called viral interference.

This is thought to occur when one virus blocks another. “We think that when you get one infection, it turns on your antiviral defences, and excludes the other viruses,” says Ab Osterhaus at the University of Rotterdam in the Netherlands.

How important such interference is in viral epidemics is unclear, however: there are also cases in which there is no interference, and people catch two viruses at the same time. Normally, we don’t get a chance to see how rhinovirus affects flu, as flu epidemics usually strike in winter, whereas rhinovirus hits when schools start (late summer in the northern hemisphere).

In other words, the effect isn’t fully understood, or even well enough understood to provide some sort of solution. But it might provide a starting point…

So why hasn’t the US, for example, seen a dip in pandemic cases during a back-to-school rhinovirus outbreak? Mackay speculates that interference from rhinovirus may not be enough to fend off flu if someone is exposed repeatedly. There were far more cases of swine flu in the US in September than in Europe.

The effects of rhinovirus, often dismissed as “only” a cold, are too poorly understood, say all the researchers. Its seeming ability to block swine flu may already have saved lives in France by buying the nation time before the vaccine arrived. It may even lead to a drug that induces the antiviral state, but without the sniffles.

Fight fire with fire, as the old saying goes.


Swine flu compared to computer viruses

Paul Raven @ 03-09-2009

influenza virusHere’s an interesting link, coming to us via the one and only Bruce Schneier. Haker/maker type person Bunnie draws a fascinating analogy between influenza viruses (like our topical and quite possibly overhyped amigo, swine flu) and the computer viruses with which he is more familiar. The result? A computer geek’s guide to molecular biology…

For those not familiar with molecular biology, DNA is information-equivalent to RNA on a 1 to 1 mapping; DNA is like a program stored on disk, and RNA is like a program loaded into RAM. Upon loading DNA, a transcription occurs where “T” bases are replaced with “U” bases. Remember, each base pair specifies one of four possible symbols (A [T/U] G C), so a single base pair corresponds to 2 bits of information.

[…]

If you thought of organisms as computers with IP addresses, each functional group of cells in the organism would be listening to the environment through its own active port. So, as port 25 maps specifically to SMTP services on a computer, port H1 maps specifically to the windpipe region on a human. Interestingly, the same port H1 maps to the intestinal tract on a bird. Thus, the same H1N1 virus will attack the respiratory system of a human, and the gut of a bird. In contrast, H5 — the variety found in H5N1, or the deadly “avian flu” — specifies the port for your inner lungs. As a result, H5N1 is much more deadly because it attacks your inner lung tissue, causing severe pneumonia. H1N1 is not as deadly because it is attacking a much more benign port that just causes you to blow your nose a lot and cough up loogies, instead of ceasing to breathe.

Researchers are still discovering more about the H5 port; the Nature article indicates that perhaps certain human mutants have lungs that do not listen on the H5 port. So, those of us with the mutation that causes lungs to ignore the H5 port would have a better chance of surviving an Avian flu infection, whereas as those of us that open port H5 on the lungs have no chance to survive make your time / all your base pairs are belong to H5N1.

So how many bits are in this instance of H1N1? The raw number of bits, by my count, is 26,022; the actual number of coding bits approximately 25,054 — I say approximately because the virus does the equivalent of self-modifying code to create two proteins out of a single gene in some places (pretty interesting stuff actually), so it’s hard to say what counts as code and what counts as incidental non-executing NOP sleds that are required for self-modifying code.

So it takes about 25 kilobits — 3.2 kbytes — of data to code for a virus that has a non-trivial chance of killing a human. This is more efficient than a computer virus, such as MyDoom, which rings in at around 22 kbytes.

It’s humbling that I could be killed by 3.2kbytes of genetic data. Then again, with 850 Mbytes of data in my genome, there’s bound to be an exploit or two.

[image by kat m research]


Swine flu – panic, precautions and practicalities

Paul Raven @ 27-04-2009

flying pigWelcome to the 21st Century, wherein you will be informed of potential disasters more quickly than ever before… and, quite possibly, in indirect proportion to their actual threat. Unless you’ve been ignoring digital media completely for the last two days, you’ll already be aware of the swine flu outbreak in Mexico – but how much do you really know, and how much of that is actually useful? [image by aturkus]

New Scientist is a good place to start for a factual overview of the swine flu situation:

Should I worry about this flu?

That depends on two things: how severe the flu is, and how far it spreads. Its severity is still unknown. Those who died in Mexico were young adults who don’t often die of flu, so we know this virus can be serious. But it isn’t always bad: the cases picked up in the US were mild. Outbreak investigators are now trying to find out how many people have had the virus, and how many of those were seriously ill, to get an idea of how bad it is.

In other words, panic is not only unproductive but as yet unwarranted, despite being amplified by Twitter, whose rapidity and limited bandwidth is spreading fear faster than facts. Of course, there’s always some humour to be found in the darkest of situations.

That said, this is a serious situation and there is the possibility of a global pandemic, though without access to hard data it’s impossible for anyone to really assess the likelihood in anything more than hypothetical terms… which is doubtless why the conspiracy theorists are having such a frenzied field day.

But it’s grist for the mills of thinkers with a less alarmist bent, as well:

Swine flu, we could say, is a spatial problem – an epiphenomenon of landscape.

I’m reminded here of a point made recently by geographer Javier Arbona. Referring to the increasingly popular and somewhat utopian idea that, in the sustainable cities of tomorrow, agriculture will have returned to its rightful place in the city center, Arbona asks: “Did everyone think that so much lushness and farming envisioned in the city aren’t going to open up new Pandora’s boxes of infectious diseases and sanitation problems as we come into contact with more manure, more bacteria, and more wild animals that we urbanites are not at all ‘naturalized’ to?”

Thought experiments aside, the sensible thing to do is ignore anything repeated in hysterical terms by media outlets with a reputation reputation for sensationalist reportage, while making sensible and proportional preparations for the worst. Although at time of posting it is currently missing (in what is presumably a Wired CMS brainfart – ZOMFG kover-up kkkonspiracy!!!1), Bruce Sterling has an uncharacteristically level-headed and sensible analysis of the true global extent of the threat (in short: compared to the ongoing AIDS pandemic, swine flu at its worst will be a picnic); in the meantime, Charlie Stross links to some genuinely useful practical advice:

Oh, and if you want to know how to ride out a flu pandemic, Jim MacDonald explains how to tell flu from a cold, what you should have in your home in case you catch the flu, and how to wash your hands. Pay attention at the back: I don’t want to be needlessly alarmist but knowing how to wash your hands properly might just save your life.

The panic and hype around swine flu is certain to get louder before it gets quieter, especially once the daily tabloids take up the slack after the weekend, so let’s all try to keep a level head. Life can get messy, but it’s not a Michael Crichton novel.