An engineering student’s Blog

” …All of this. All of this was for nothing – unless we go to the stars.” – Infection, Babylon 5, J. Michael Straczynski

A question of severity & evidence of evolution

At risk of stating the obvious the flu appears to spread quickly.  DOH!  Its rate of transmissibility is high.  But its severity or virulence maybe indirectly related to its transmissibility.  People don’t have to be oozing with the virus and litterally falling apart for this thing to spread.  As a result the new H1N1’s initial fatality rate maybe low.  Quite low.  The danger however, still exsist that it can better adapt to human physiology, it could borrow the right code in a reassortment somewhere and come out with the right protiens to be much more lethal.  But for now its missing crital protiens needed for it to be much of a threat.  More information here at the Wall Street Journal by Peter Palese and Here at the Virology Blog

The most likely result in the short-term is the continued spread of a new, mild-flu which no one has any immunity to resulting in a larger number of hospitalizations as the virus spreads over a larger fraction of the population,  taxing our healthcare system.  In fall this will become a problem as it could come back as a slightly more virulent form during the usual flu season – or it just reach an even larger fraction of the population, sending a fraction of the population to the hospital for treatment.  

A healthcare crisis is possible in even a moderate flu epidemic.  At least it doesnt have the capability of the 1918 Spanish flu.  If we take this as an oppurtunity now would be the time to lobby and push for improvements to a healthcare system with some serious wholes in it.  Now before a more deadly organism emerges.

USEFUL LINKS ::,-And-When-Do-They-Open


About evolution – I’ve always thought of it as a useful theory in simplifying complex problems in the lifesciences.  A philosophical construct, a tool.

I’ve never accepted that there are solid arguements and real articles of evidence, in mutations occurring allowing a new genetic branch or new organism to thrive better than previous itterations which could eventually replace previous ones – evolution.  A few weeks ago I was thinking about this again and thought about insects and thought ants are ants, bugs remain the same for millions of years.  And I thought what about bacteria, something with a faster life cycle, something where a new generation appears on a more compressed time scale you maybe able to notice changes in genetics and potential improvements.  But I left it at that.

It would appear the evidence I was looking for smacked the world in its face recently.  A new virus – a random reassortment of genetic code gave us this new influenza A, which was of benifit to the organism experiencing the mutation allowing it access to more resources (humans) thru its new found quicker rate of transmissibility. So I will be investigating and entertaining the idea that evolution is more than just a philosophical construct or a useful way of aproaching lifescience problems.  

Although I will not quickly give up what I believe – it would be wrong to ignore the possibility that I was wrong.  The bible says, “make sure of all things.”  Essentially – it commands us to question, inquire and seek the truth.  Well evolution appears more to be a working theory with physical, real relevance and supporting evidence that needs to be explained.  As a human being with a head on and a heart pumping life thru it I have an obligation to do nothing less.


Filed under: Health, Science

Current WHO phase of pandemic alert is 5

UPDATE :: Make that 5 – that is, The world health organization has confirmed a pandemic is imminent.


The current world health organizations phase of pandemic alert is still at 4 but I wouldnt be surprised if they raise this to level 5 before the end of the week – Level 5 means theres evidence of human-to-human spread in two different countries, like the US and Mexico, for example.

Phase 4 is characterized by verified human-to-human transmission of an animal or human-animal influenza reassortant virus able to cause “community-level outbreaks.” The ability to cause sustained disease outbreaks in a community marks a significant upwards shift in the risk for a pandemic. Any country that suspects or has verified such an event should urgently consult with WHO so that the situation can be jointly assessed and a decision made by the affected country if implementation of a rapid pandemic containment operation is warranted. Phase 4 indicates a significant increase in risk of a pandemic but does not necessarily mean that a pandemic is a forgone conclusion.

Phase 5 is characterized by human-to-human spread of the virus into at least two countries in one WHO region. While most countries will not be affected at this stage, the declaration of Phase 5 is a strong signal that a pandemic is imminent and that the time to finalize the organization, communication, and implementation of the planned mitigation measures is short.

Phase 6, the pandemic phase, is characterized by community level outbreaks in at least one other country in a different WHO region in addition to the criteria defined in Phase 5. Designation of this phase will indicate that a global pandemic is under way.

Filed under: Health, Science

1 fatality out of 66 cases in the US

My wife said she’d die if she were the mom – I can’t imagine the horror and tragedy this family just experienced.

UPDATE :: The CDCs 11 oclock update is up.

Which makes my attempt at a CFR look hasty indeed.

UPDATE :: Our first death was a patient originally infected in Mexico and brought to the US for treatment, not originally infected here in the US and maynot be statistically appropriate include if youre trying to estimate an effective CFR for the US.  I need to read m0r3.

A CFR is an extremely difficult value to get
See this post at “Effect Measure” for more information 


A rough, very rough, CFR (case fatality ratio) of 1/66, about 1.51%, or 15 fatalities for every 1000 infections is possible.  In statistics one of the most important things you learn is how to look at the sample number and data of the statistic to analyze its usefulness, a sample number of 66 out of a potential population of 305 million may not be a good idea.  The actual CFR for this strain of H1N1 maybe end up being way off this initial value.  I should try to construct an error estimate.  But I wont.  Im not a statician, Im not a medical expert, I just felt like writing down what worries me about this new flu.

A gross approximation of the potential of such a virus can now be done, if you allow a number of assumptions, in the absence of much more valuable, real data.  

If the spanish flu infected 25% of the population and killed 2.5% of those effected, and this virus seems milder but its ability to be transmitted between humans is still unknown even if we know its happening.  Lets assume this aspect of the virus will also be milder.  Say 10% of the population infected 30.5 million out of which 462000 could be serious, fatalities could be reduced in this group if promtp and appropriate action is taken, and antiviral medications like tamiflu and relenza remain effective against it, reduced by about 2/3rds to about 154000 fatalities in the US.  Of course this gross estimate ignores a lot of factors like not being in flu season and if this will reduce the potency of the virus and how much and how fast it spreads, if it does effect it.  We still dont know why there even is a flu season.  And more importantly we don’t know much at all about this very new virus to expect an estimate like this from anybody who knows anything about disease and epidemiology.

Maybe this number isn’t useful – maybe I took a number and ran too far with it.  Kinda like forest gump catching the football and running off the field, down the street, …and what.  You didnt see the movie?!  Its a blog not a news source, you want safe and reliable analysis?  Wait a few years for the CDC to cruch the data.  But this is my number and I hope im wrong I hope its another flu we just deal with every year – makes us miserable for a week and we shrug it off then get the regular flu – and shrug it off.  But Im worried that we’ll be lucky to see only 154000 fatalities at the end of this.

Remember if you’ve seen one flu pandemic – you’ve seen, one flu pandemic.

Filed under: Health, Science

If you’ve seen one flu pandemic – You’ve seen one flu pandemic.

UPDATE 04.29.2009 :: At least 66 cases in the US with our first fatality – a 23 month old baby in Texas. 

Germany Confirmed its first 3 cases.

UPDATE 04.28.2009 :: Statement issued Tuesday by the state health department:

INDIANAPOLIS – State health officials report test results from the Centers for Disease Control and Prevention have confirmed a case of North American Human Influenza A (H1N1) in northern Indiana.

This case does not appear to be included in the latest CDC update meaning there are at least 65 confirmed cases in the US now.


Snipped from Effect Measure at


Posted on: April 28, 2009 11:07 AM, by revere

It would be nice to think that the 28 cases at the NY Prep School are it for the city and that the virus has been contained there. But that was always more a wish than a plausible reality:

CBS 2 HD has learned of a confirmed case of swine flu at the Ernst & Young headquarters in Times Square.One of the staffers became ill over the weekend after coming into contact with a family member who had been exposed to the virus.

The staffer is said to be resting at home and the company believes, due to the virus’ 24-hour incubation period, that no one else at Ernst & Young was exposed. The company released a statement on Monday night:

“An employee in our offices at 5 Times Square was diagnosed on Sunday with swine flu, which she contracted from a family member. The individual had not been in offices since last Thursday. According to the Center for Disease Control, the disease has a 24-hour incubation period. Given the timeframe, we believe that it is unlikely that any other of our people have been infected.

“The health of our people is our foremost priority. Since learning of the diagnosis, we have followed the procedures outlined by the Center for Disease Control, including closing the offices on the floor where she worked and retaining a skilled sanitation service to clean the area. We have alerted our people and have told them to feel free to work from home if they would be more comfortable doing so. We have also notified the appropriate authorities.” (CBS2, NY)


As we keep looking, we will find cases, so the total will rise, probably on a daily basis. Like poll numbers, it is probably wise not to pay attention to daily fluctuations but look at the big picture. Right now the big picture isn’t visible, but with the passage of days or a week, it should become clearer. The current spate of cases could burn itself out as warmer weather ensues. Flu is a highly seasonal disease, for reasons we don’t understand. That wouldn’t mean we were home free, however. Wherever flu hides in the “off season” (flu does find work in the southern hemisphere’s winter), it can come back the following year. Those familiar with 1918 know there seems to have been a milder “herald wave” the previous spring which came back like a freight train in August. CDC is well aware of this possibility and should this outbreak wane will clearly urge and engage in continued preparation in the event this evolves in the same way.

If it evolves the same way. Influenza is a virus full of mystery and surprises. The more we study it the more complicated it becomes. Remember the adage: “If you’ve seen one flu pandemic, you’ve seen one flu pandemic.”

Filed under: Health, Science

a new influenza A/H1N1 virus has emerged in our modern world

Update :: CNN’s Sanjay Gupta in Mexico City says the rate of deaths from this outbreak seems to be decreasing.

Update :: 50 confirmed cases in the US – 82 world wide, and the world health organization upgraded this situation to a phase 4, that is confirming sustained human-to-human spread.

Update :: Mexicos Health Minister just announced there have been 149 fatalities out of 1995 cases of severse flu, which they are investigating weather it is in fact Swine Flu.  776 patients remain hospitalized.

I just saw on CNN that the number of confirmed cases has just doubled from 20 to 40, although these were already suspect days ago and only confirmed now.  It was intriguing to follow this developing story over the weekend where on Saturday I learned there was a family in Texas and a half dozen cases in southern California with the same virus that shut down schools and public events in Mexico.  Thru to this morning where there are confirmed cases in New York, Kansas and Ohio – as well as New Zealand, Nova Scotia, Scottland, Spain and France.  This morning in Mexico the numbers a saw were 103 dead out of 1614 cases, although these have not all been confirmed to be the new strain, and there may have been more than the reported 1600 cases.  Saturday the number of fatalities in Mexico was 68, the day after 81.  Something I want to see over the next few days is weather the number starts to top off or if the rate continues to grow.

The fatality rate is extremely disturbing if the vast majority of those cases and fatalities can be confirmed to be the new virus, especially since the pattern of infected indicated the young and middle aged rather than the typical elderly and children who are more affected by this new strain of influenza.  This is a hallmark of previous pandemics like the spanish flu of 1918 – which was also an H1N1 virus, but now extinct – where it is believed most fatalities came quickly due to a sort of over reaction of a healthy immune system, a positive feedback loop they call a cytokline storm, or hypercytokinemia.  Although realiable, solid information and analysis is slow to emerge – and the flu and epidemics are difficult to predict.  What we know for sure if that there is a human-to-human transmitted new influenze A virus out there.  We know that the confirmed cases in the US have so far been mild to date – and pending the nature of the rest of the cases just reported in the US by the world health organization.

Its something of a paradox that our modern age of quick and easy transportation can spread a virus like this to distant and diverse populations, but other advances in medicine and our knowledge of these diseases can save us from a catastrophy similar to 1918s influenza, or hopefully mitigate its effect, hopefully not repeat a grim chapter in history.

There is a lot of noise out there and some exageration of the threat as we can scientifically confirm it to date, but one site Ive found helpful in clearifying some things is a blog at Effect Measure –

another useful link is the CDC site on the topic

Filed under: Health



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