Some thoughts on Swine Flu

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Jeremy
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Post by Jeremy »

This weeks New Scientist editorial is pretty good;

http://www.newscientist.com/article/mg2 ... oject.html
We need a flu Manhattan project

WELL, it's happened. A pandemic is looming though it comes not from bird flu in Asia, as we thought it might, but swine flu in Mexico (see "Scientists have warned about swine flu for last decade"). It may yet fizzle out - viruses like this have done before - but no researcher we have spoken to is hopeful.

So what now? Things look bad, but rather than panicking we should use the best science we have to assess the situation. And then we should scream and scream again at the people in charge - caution-merchants and commercial interests for the most part - until someone does something.

Because right now, we are not really in a position to defend ourselves, though it's true we're better off than we were. Since the wake-up call of the narrowly averted SARS catastrophe in 2003, and concerns about H5N1 bird flu since 2004, there has been a vast amount of research on vaccines, treatments and pandemic response.

Here is what we know. Measures such as washing a lot and cancelling public events can slow the spread of the virus, but they won't stop it. There are a few antiviral drugs, which can be effective if taken early enough. But stocks are limited, and without quick and accurate diagnosis they could be wasted on the worried well at the height of a panic, or controlled too carefully and therefore administered too late. There's also the spectre of virus resistance.

The best bet, as always, is vaccines. But there are problems. The extent of global vaccine R&D and manufacturing capacity has been largely dictated by companies' commercial interests. No more or less can be expected of companies, of course, but with few exceptions we've left everything to them. The best that they can do now is to divert all resources to tackling this virus instead of ordinary flu. Commercially, that means a huge leap of faith: if the pandemic doesn't materialise, firms will be left with no ordinary vaccine and useless swine flu shots. They may only do it if governments pick up the tab.

But if they do, and if this swine flu is no harder to make a vaccine against than H5N1, which has been the focus of most research, then according to one recent study, we could have 340 million doses of vaccine in four months. If it turns out to be easier to make, we could have a billion. But let's not forget there are nearly 7 billion people in the world.

Four months could be critical. Pandemics vary enormously, so history is a poor guide, but the last time this family of flu viruses went pandemic, in 1918, there was a four-month gap between the first, mild wave of illness and the big attack. The usual toll cited is 50 million.

What if we can't make enough vaccine? The final edition in 1918 of the Journal of the American Medical Association carried a poignant message. Though the year saw the end of "the most cruel war in the annals of the human race" the journal concluded that science "must turn with its whole might to combating the greatest enemy of all - infectious disease".

That message still resonates. The 1918 pandemic death rate translates into 170 million victims today. A pandemic now could take fewer lives, but it could also take more. A policy of "it may not happen" will not do when a pandemic could cost the lives of millions and derail what's left of the global economy. So we must make vaccine. But who's "we"? As New Scientist has warned for years, only a few countries have vaccine plants, mainly in Europe. They may be unwilling to export their product.

Distributing limited stocks of vaccine between countries bids fair to be a mess, never mind between people. Some countries have thought about who should get drugs and vaccines first, but plans could come unstuck if a pandemic tears the fabric of society.

The Manhattan Project is an overworked metaphor, but throwing your resources into one activity sometimes makes sense. We could also launch a crash programme of testing and developing new drugs and vaccines that are now only at the experimental stage. These include vaccines that focus on parts of the virus that do not mutate, meaning they will still work if the virus evolves; new DNA and protein vaccines; antibody therapies based on the serum of survivors; and anti-inflammatory treatments (see "How to survive pandemic flu").

We've had five years to prepare for a pandemic. We aren't ready. Either we use every tool at our disposal to shore up our defences or we keep telling people to wash their hands a lot, and watch the death toll rise.
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Jeremy
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Post by Jeremy »

There was also a good blog post on the issue here;

http://scienceblogs.com/effectmeasure/2 ... =nytwidget
Swine flu: the overreaction overreaction
Category: Infectious disease • Influenza treatment • Infrastructure • Pandemic preparedness • Progressive public health • Public health preparedness • Swine flu
Posted on: May 2, 2009 10:38 AM, by revere

Laurie Garrett of the Council on Foreign Relations and a well-known authority on emerging infectious diseases was on PBS's Newshour last night and she made a very important but little appreciated point. Mexico has made a major national sacrifice for global public health by shutting down its country and interrupting transmission of disease. The cost to Mexico has already been enormous it will continue to pay in other ways. The reputation of the government has suffered because of the way it handled this -- the lack of transparency, the initial slow footedness (which of course it denies), its lack of credibility in the eyes of its citizens. There will continue to be a halo of risk and danger for an indeterminate time. And there will be the inevitable backlash against the government's actions, which went from cold to scalding hot in a week. We are starting to see this in the US as well: the "overreaction" backlash. So it's important to sort all of this out. What is the Big Picture at this point?

It's now been a little over a week since swine flu (rebranded H1N1/2009) popped its head above water in southern California. From two cases discovered in mid-April in San Diego, the virus is now confirmed to have spread, mostly from Mexico, to 15 countries in North America, Europe and Asia. Confirming a case takes time so there are significant differences between reports of suspected, probable and confirmed cases, but as of this moment WHO acknowledges 17 deaths (16 in Mexico, 1 in the US) and confirmed 615 cases. The confirmed cases are new, not previously existing but unrecognized cases and there is clear and convincing evidence of person to person transmission. It appears the age distribution continues to be shifted toward younger age groups as compared to endemic seasonal influenza, probably a reflection of the fact that most people are immunologically naive to this flu virus. There remains an open question as to whether people who were born before 1957, the date that H2N2 replaced a previous H1N1 as the predominant subtype, may have some cross-reactivity to the current H1N1 strain. In any event, a novel influenza virus has spread quickly worldwide and is transmitting efficiently, pretty much the dictionary definition of a pandemic.

The extent and speed of spread is one factor of concern. The other is the clinical severity of the disease. The good news is that so far, clinically this influenza virus looks much like a mild seasonal influenza. "Mild" is a relative term. Any influenza infection is a potentially serious disease, and while we have no hard figures, good estimates of the excess mortality caused by influenza yearly in the US is around 35,000 to 40,000. These deaths and the significant but non-fatal illnesses that require hospitalization each flu season are the upper tails, the tip of the iceberg, of flu infections. Most people have milder cases. Some of these "milder" cases are still miserable affairs, with severe headache, joint and muscle aches and hacking coughs that can to on for weeks and malaise and tiredness lasting much longer. Some people are infected and have no symptoms at all. But the more people infected the more people who are in the upper tail of the distribution. You don't have to shift the distribution much to double or triple the number of people in the tip of the iceberg (think of the tip as a pyramid, and as you raise the iceberg up slightly the new people are in its base, which is much wider). These are the people that will stress our already over stressed medical care system. US emergency departments are already overcapacity. They would break during a bad flu season.

So that's where we are at this moment. There is some evidence from 1918 that cities that acted immediately to interrupt transmission by reducing opportunities for contact ("social distancing") did better than those that didn't. We would of course expect this on common sense grounds as well. That's what Mexico has done -- and I echo Laurie Garrett's point, they have done so at great cost to everyone's benefit. That is what is behind CDC's recommendations that a school be closed as soon as a case is confirmed. There is a cost to that, too. Proms are canceled, to the deep disappointment of the prom go-ers and the economic loss of the venues and ancillary businesses. Exams are delayed. Child care needs for younger students produce a ripple effect throughout the community. And as in Mexico, these costs can produce a backlash if the public doesn't understand why they have been incurred.

The irony is that the overreaction backlash will be more severe the more successful the public health measures are. If, for example, the virus peters out this spring because transmission was interrupted long enough for environmental conditions (whatever they are) to tip the balance against viral spread, CDC and local health officials will be accused of over reacting. It's another example of the adage, "When public health works, nothing happens." On the other hand, if local officials do nothing and things get worse, they will be accused of being slow.

It's not just the current reputation of local officials that concern me, however. If this virus does wane with the summer months (something we expect to happen), it's current mildness and its disappearance may lead citizens and decision makers back into the kind of reckless disregard of public health facts that has produced our current weak and brittle health infrastructure. But flu season will come again next fall, and it would be no scientific surprise if this strain is part of flu's repertoire. Most of the world would still be unprotected unless we spend the interim preparing for the possibility it will reappear in a more serious clinical form (flu viruses are notorious for that kind of change). When I say prepare, I am not just talking about a vaccine, although that will be an important, but difficult< part. We will also need to invest urgently in a health care, public health and social infrastructure to absorb the consequences of potentially large scale absenteeism. We will also need to work out policies that will allow social distancing measures to work (child care, sick leave policy and other issues).

It's an urgent task that must be started immediately. If there is an overreaction to perceived overreaction, the job of rationally preparing for a plausible near future event will be made much more difficult.
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Post by Blue_turnip »

BainbridgeShred wrote: The fact is, the number of deaths is pretty meaningless. What we need to find out is the denominator, the number of infections, divided by the number of deaths. The bad part is it's nearly impossible to figure out how many people have caught this thing and thus to determine how fatal it is.
Determining the ratio of cases/deaths still won't do much good, because it ignores how easy it is to catch the flu. Getting hit on your head by a coconut has an extremely low case/death ratio, but nobody gives a fuck about coconuts because its fairly difficult to have one fall on your head.
BainbridgeShred wrote: The reason y2k wasn't worse was a direct result of the founding generation of computer programmers tireless work to correct the system. Unfortuneatly, this generation is retired now, and most computer science majors are dumbfuck java cookiecutter idiots.
Who are the founding generation of computer programmers? I don't know what group you're even referring to.

What the hell is a "java cookiecutter idiot"? I don't know where you got the idea that most computer science majors are idiots of any kind. And I don't know how java and cookie parsers have anything to do with it.
BainbridgeShred wrote:Anyways, we are overdue for a big pandemic. Usually there's about 2 every century.
Okay.

1. Go here: http://en.wikipedia.org/wiki/Geometric_distribution
2. Scroll down to "other properties"
3. Read the second dot point.
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Post by BainbridgeShred »

Determining the ratio of cases/deaths still won't do much good, because it ignores how easy it is to catch the flu. Getting hit on your head by a coconut has an extremely low case/death ratio, but nobody gives a fuck about coconuts because its fairly difficult to have one fall on your head.
.....People catch the flu all the time, every year. It only matters if people are dying from it..... How virulent it is doesn't matter until you know the denominator aka number of deaths/per number of cases. lawl

What the hell is a "java cookiecutter idiot"? I don't know where you got the idea that most computer science majors are idiots of any kind. And I don't know how java and cookie parsers have anything to do with it.
If you have to ask, then you probably should've just kept quiet to begin with. It isn't only that computer science courses have been dumbed down, it's IT internationally. As far as what Java has to do with it, it is by far the most commonly taught programming language in any college in the world. Why it's a problem is that Java is retardedly easy to master, so there's no real weeding going on in schools where you could tell the great programmers from the medicore ones. The other problem is that for atleast that last 20 years mathematics requirements have been shrinking in compsci programmes.

It isn't that compsci students don't understand the basics (Flow of control, assignments, subroutines) or that they don't get that a variable can be floating or a string, it's that when something unexpected happens they don't know what to do because they never had to learn how using Java. Try telling anyone used to using Java that the value on a variable isn't an interger but a pointer to one, and you'll for sure blow their minds. How this can create a problem, in idiot terms, is in sitations like memory management (Thrashing, fragmentation, too much memory w/e) where poor integration has created problems that no one knows how to go back and fix.

Not that unqualified students are the only problem with IT today. They are, however, being taught a skill set that is becoming very easy to replace with outsourcing.
Who are the founding generation of computer programmers? I don't know what group you're even referring to.
Well real computer programming hasn't been around for very long... Use a bit of deduction and figure it out yourself.

1. Go here: http://en.wikipedia.org/wiki/Geometric_distribution
2. Scroll down to "other properties"
3. Read the second dot point.
Wow, a virus doesn't have a working knowledge of the fact that other virus' came before it? What a revelation. That was exactly what I was referring to.
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Post by Jeremy »

A couple of corrections;

1. Contagious illness creates significant economic losses, even if it doesn't kill anybody and even if nobody takes a day off work. Any illness that lowers people's performance at work is going to have a negative effect on the economy. A WHO assessment on the costs of a serious infectious epidemic found that panic was the number one cause of economic stress.

2. We are not "due" for a pandemic and there are not 2 every century. This is rubbish. There have been numerous serious infectious diseases that have been effectively wiped out in the last century and the conditions today are incomparable with conditions 100 years ago. If we look at the last flu pandemics to kill over 1 million people, all happened within 70 years of each other but the last one was 40 years ago and 3 out of the 4 "only" killed 1 million, while the other killed around 40 million.
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Post by Tsiangkun »

Cuba joined the countries with the flu.
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Post by Blue_turnip »

BainbridgeShred wrote: .....People catch the flu all the time, every year. It only matters if people are dying from it..... How virulent it is doesn't matter until you know the denominator aka number of deaths/per number of cases. lawl
As I was saying when I talked about coconuts and as Jeremy pointed out, assuming it only matters if people are dying from it is just a wrong assumption to make.

Anyway, not arguing that knowing the deaths/cases isn't important, I'm saying it won't do much good unless we know how virulent this flu is. From what I've heard and read on wikipedia "not much is known about the risk of airborne transmission of this particular virus". That matters a shitload and I'd argue that knowing the deaths/cases doesn't matter until you know how contagious it is.
Bainbridgeshred wrote: If you have to ask, then you probably should've just kept quiet to begin with. It isn't only that computer science courses have been dumbed down, it's IT internationally. As far as what Java has to do with it, it is by far the most commonly taught programming language in any college in the world. Why it's a problem is that Java is retardedly easy to master, so there's no real weeding going on in schools where you could tell the great programmers from the medicore ones. The other problem is that for atleast that last 20 years mathematics requirements have been shrinking in compsci programmes.

It isn't that compsci students don't understand the basics (Flow of control, assignments, subroutines) or that they don't get that a variable can be floating or a string, it's that when something unexpected happens they don't know what to do because they never had to learn how using Java. Try telling anyone used to using Java that the value on a variable isn't an interger but a pointer to one, and you'll for sure blow their minds. How this can create a problem, in idiot terms, is in sitations like memory management (Thrashing, fragmentation, too much memory w/e) where poor integration has created problems that no one knows how to go back and fix.

Not that unqualified students are the only problem with IT today. They are, however, being taught a skill set that is becoming very easy to replace with outsourcing.
Obviously, I can't reliably speak for people studying computer science at other unis. But I find it hard to believe that any reputable computer science course does not cover C programming in detail, let alone not at all - In which case pretty much all of the above problems are solved. But hey I don't doubt that there are places retarded enough not to teach C and some form of assembler language (even for like MIPS, lol).

While I don't know exactly in what way you're talking about it, I totally agree on your point about maths (do you mean maths requirements to do the CS course or the maths you have to do in the CS course), however I have to acknowledge that the changes regarding the maths you do in the course have more or less reflected the shift in the role of computer scientists and software engineers since 20 years ago.
Bainbridgeshred wrote:
Who are the founding generation of computer programmers? I don't know what group you're even referring to.
Well real computer programming hasn't been around for very long... Use a bit of deduction and figure it out yourself.
Well I don't think that the same people programming in the 60's (who I suppose I see as the 'founding generation') were the same dudes fixing the bug in like 1999.

And had the problem for some wierd reason been the year 2030 bug, I don't think it would have made any difference even though the people fixing it would be the people getting their comp science degrees from here onwards.
Bainbridgeshred wrote:
1. Go here: http://en.wikipedia.org/wiki/Geometric_distribution
2. Scroll down to "other properties"
3. Read the second dot point.
Wow, a virus doesn't have a working knowledge of the fact that other virus' came before it? What a revelation. That was exactly what I was referring to.
Sigh, you said we were 'overdue for a big pandemic'. I was merely trying to make the point that we were not.
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Post by BainbridgeShred »

As I was saying when I talked about coconuts and as Jeremy pointed out, assuming it only matters if people are dying from it is just a wrong assumption to make.
Well for the sake of this thread, it does only matter if people are dying. Yeah yeah if you wanna talk about the economic consequences of a flu (Even if not often fatal) then go ahead but that shit's boring. Might as well talk about how India has too many religious holiday's where they get off work, or how the French get a bunch of vacation days. Who gives a fuck. Might as well talk about the economic effects of particuliarly nasty bout of mono going around. C'mon, this is swine flu bitches, if people aren't keeling over then I'm relinqushed to not giving a fuck.

And it seems moot anyways because even the virulency of this flu doesn't seem especially high abnormal.
Obviously, I can't reliably speak for people studying computer science at other unis. But I find it hard to believe that any reputable computer science course does not cover C programming in detail, let alone not at all - In which case pretty much all of the above problems are solved. But hey I don't doubt that there are places retarded enough not to teach C and some form of assembler language (even for like MIPS, lol).
Java basically is C/C++ except made even a bit more simpler. How knowing C would fix any of the above problems is beyond me though. Knowing C++ doesn't teach someone about pointers and data structures.
While I don't know exactly in what way you're talking about it, I totally agree on your point about maths (do you mean maths requirements to do the CS course or the maths you have to do in the CS course), however I have to acknowledge that the changes regarding the maths you do in the course have more or less reflected the shift in the role of computer scientists and software engineers since 20 years ago.
I meant math you have to do as a part of the CS course. Anything done up until that point that point is probably a little too low-level to even really apply except in theory.
Well I don't think that the same people programming in the 60's (who I suppose I see as the 'founding generation') were the same dudes fixing the bug in like 1999.
They were. What makes you think they wouldn't be is beyond me. They were the ones who began the process of this faulty coding to beging with.
And had the problem for some wierd reason been the year 2030 bug, I don't think it would have made any difference even though the people fixing it would be the people getting their comp science degrees from here onwards.
Well, you're simply not taking into account the broader life experiences of the "people programming in the 60's" that would've made them partculiarly apt at solving a problems inherent in trillions upon trillions of of lines of computer code across the world. The fact that Y2k went over so smoothly is one of the greatest accomplishments of our time. Our Pyramids. Sadly, the fact that it went over so smoothly led the masses to think it was overblown to begin with, and now whenever anyone mentions Y2k it's always wth contempt. Everyone knows what Y2k was, but no one knows why we transistioned so smoothly into the 21st century.
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Post by Blue_turnip »

BainbridgeShred wrote:How knowing C would fix any of the above problems is beyond me though. Knowing C++ doesn't teach someone about pointers and data structures.
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