Family Guy, S07E02 ‘I Dream of Jesus’:

Peter: Brian, can I see that paper for a sec?

(Brian gives Peter the paper. Peter peruses the paper.)

Peter: Huh… that’s odd… I thought that would big news.

Brian: You thought what would be big news?

Peter: Well there seems to be an absence of a certain ornithological piece: a headline regarding mass awareness of a certain avian variety.

Brian: What are you talking about?

Peter: Oh have you not heard? It was my understanding that everyone had heard…

Brian: Heard what?

Stewie: Brian Don’t!


Last week the infamous OMFG KILLER FLU WARBLEGARBLE research was finally published.  Science put out a special issue almost all about ‘killer bird flu’, editorials, commentary, and the actual research– and ALL of the articles are freely available to everyone!

The research comes in two parts–

1– What does a Bird Flu need to change to turn into a People Flu?

 Airborne Transmission of Influenza A/H5N1 Virus Between Ferrets

As Ive said before, very simplistically, Bird Flu and People Flu are that way because they like Bird Sugar and People Sugar on Bird and People Proteins.  But occasionally Bird Flu can infect people, and it stops there.  Bird Flu cant infect people, and then turn into a People Flu.  People are a dead-end host for Bird Flu.

But what if it wasnt?

Evolution will find a way…

So, why dont we get one step ahead of evolution?  Evolve it in the lab first?

Thats exactly what these folks did.  Evolved a Bird Flu that could transmit between mammals, in this case, between the small animal model for influenza, ferrets.

They found that regular ol Bird Flu regularly found the exact same ‘answer’ to the ‘problem’ of mammalian transmission.  Five amino acid mutations– four in hemagglutinin (think influenzas Env) and one in basic polymerase 2 (think influenzas Pol).  Thats not really all that much, especially for an RNA virus.

Now, just because this happened in the lab doesnt mean it will happen in nature, or, that it will happen this way in nature.  But having an answer to how Bird Flu could turn into a pandemic, a virus to study that could turn into a pandemic– it will help us be prepared.

We can study a virus that doesnt even exist yet.

We can study antivirals/develop antivirals for a virus that doesnt even exist yet.

We might have a vaccine to a virus that doesnt even exist yet.


A further benefit is that knowing at least an evolutionary pathway Bird Flu can take means labs working with Bird Flu can keep an eye on their cultures to make sure this guy isnt accidentally evolving under their noses (‘noses’, heh).


2– What are the odds of this actually happening?

The Potential for Respiratory Droplet–Transmissible A/H5N1 Influenza Virus to Evolve in a Mammalian Host

In this paper, they data-mined a ton of Bird Flu sequences from all around the world and calculated what needed to happen where for a human transmissible virus to evolve (again, just to stress this point, they looked for one answer that was found in the laboratory– evolution could find another answer in nature).

They considered several factors that could increase the odds:

  • “Random mutation” – Viruses mutate.  Things happen. Explore sequence space, and youre going to find something.
  • “Positive selection” – Things happen.  But what if the intermediate steps have a benefit on viral fitness?
  • “Long infection” – Virus can get comfy in its new environment.
  • “Functionally equivalent substitutions” – Some amino acids kinda look/act alike. Wink is the same as a blink to a blind man.
  • “Avian-to-mammal transmission of partially adapted mutants” – We are assuming bird-to-human. What if the bird flu already has three of the necessary mutations on its own, just by chance?
  • “Mammal-to-mammal transmission of partially adapted viruses” – These five mutations might be the ‘best’ (well, good enough, evolutionarily), but what if two mutations can be transmitted between mammals, but less optimally?

And several factors that could decrease the odds:

  • “An effective immune response” – If we can readily neutralize these guys (cross-reactivity of antibodies) then it dont much matter, does it?
  • “Deleterious intermediate substitutions” – Edge of evolution! LOL!  No, for real, sometimes you cant get from A to , evolutionarily.
  • “Order dependence in the acquisition of substitutions” – Making 5 mutations is one thing.  Making 5 mutations in a precise order is something else.

Of course the risks were different for every simulation they ran.  So they came to a few conclusions on how we can better protect ourselves (this paper was a series of lists. I didnt necessarily mind that, but it actually make me lol):

  • “Additional surveillance in higher-risk regions” – We know what to look for.  From previous sequence data, we know which regions are more likely to produce mammal transmissible Bird Flu.
  • “Deep sequencing of avian and other nonhuman virus samples” – The more sequences we have, the more accurate our predictions will be.
  • “Which substitutions, besides the already identified receptor-binding substitutions […] are capable of producing respiratory droplet–transmissible A/H5N1 viruses” – Again, we have an answer to mammal-to-mammal transmission.  How many different ways are there to fly?  How many different ways are there to see?  How many different ways can this virus evolve to be mammal transmissible?
  • “Within-host fitness and between-host transmissibility” – We need to study this virus more in the lab.

So thats it.  Thats what the big hubub was about.  Really cool research with really cool implications.  I have no friggen clue why the US government freaked out.  And Im not saying that sarcastically.



  1. #1 spence
    July 7, 2012

    Ah, medical peer review days of posting removed like the Pope, so the meeting concluded that selective editing was too diffiicult, let’s go for total removal, it’s only PR afterall and no one is really looking.

  2. #2 spence
    July 7, 2012

    Meanwhile kids are being paralysed in India, right now because the vaccine campaign is failing. More evidence to follow later.

    “You are wrong because you have asserted spontaneous generation of germs” Uh and where was this stated, germs don’t just appear thats Orac’s assertion and apparently the only solution is antibiotics?


    In 1988, the World Health Assembly passed resolution WHA 41.28, which committed the World Health Organization (WHO) to the global eradication of poliomyelitis by the year 2000. In spite of the combined efforts by UNICEF, National Polio Surveillance Project (NPSP), Indian Academy of Pediatrics (IAP) and Rotary International, Polio Free India is still a distant dream.

    Though oral polio vaccine has succeeded in polio eradication from many countries but there is high incidence of vaccine failure in India. Oral polio vaccine (OPV) has failed to provide full protection to many children who have developed paralytic polio even after taking 10 or more doses of OPV. In some children, OPV has caused paralysis-vaccine associated paralytic polio (VAPP). Number of children developing polio due to vaccine is high and on increase. Reasons for this could be that even immunocompromised children are being administered OPV because IPV is not available. Vaccine failure has exaggerated the problem of VAPP. No efforts have been made to find the causes for high incidence of vaccine failure and VAPP.

    Paralytic poliomyelitis;
    Vaccine failure;
    Vaccine associated paralytic poliomyelitis

    Corresponding author contact information
    Corresponding author. Tel.: +91 141 2

  3. #3 wow
    July 7, 2012

    Hmm. Moron hasn’t figured out the designs next to the post andwhat they do.

  4. #4 wow
    July 8, 2012

    Septic sucker hasn’t realised that he is avoiding the subject. Well it’s only PR

  5. #5 spence
    July 8, 2012

    Blimey, Doctors kill more people than terrorists!

  6. #6 orac
    July 8, 2012

    I have just realised that no one is listening.

  7. #7 sharon
    July 8, 2012

    So if doctors can rename polio, like they are doing in India to hide the fact that the Polio campaign has not only failed it has changed the disease into one twice as deadly, don’t you think we have a duty to write about this instead of pretending all vaccines work?

  8. #8 wow
    July 8, 2012

    The subject is how much a moron you are.

    When huntingdon sciences ask for a law to be passed that makes disroption of medical research illegal even to plan, they can take your posts as proof the anti-research group are dangerous psychopaths.

    You’re ensuring that independent review is forbidden, because you will be used to demonstrate that psychos against ANY medical research exist.

    Well done, you idiot.

  9. #9 Optimus Primate
    July 8, 2012

    buckthetrend, how about you cut out the sock puppetry? You amuse me, and I’d hate to see you get banned for such stupidity.

  10. #10 Orac
    July 8, 2012

    This has been avert interesting discussion and has finally thread some light onto this complex very polarised argument. I know realise that everything I previously stood for is wrong. After promoting the vaccines that crippled and killed 47500 Indian children last year alone and caused autism in countless other susceptible children by overloading their imature immune systems with toxic waste. The whole vaccination issue really should be reinvestigated from the ground up and not based on the assumption that it works. I have been such a complete tosser.

  11. #11 spence
    July 8, 2012

    Well done buckthetrend, you must be very proud of yourself.

    And you continue to do more to destroy the credibility of anti-vaxxers on your own more than any of us could manage engaging in rational debate with you.

  12. #12 wow
    July 9, 2012

    Bucker may just be trying to get ERV in trouble with NationalGeographic and using a cariacature rabid antivaxxer to kill two birds with one stone.

  13. #13 duh
    July 11, 2012

    The time warp of medicak peer review continues, how can ERV get into trouble with the NG, they believe in vacciine woo!

  14. #14 bouquet
    July 11, 2012

    I have no idea what the pro or anti vaxx position is, you look at the evidence and you see corrupt figures, renaming of vaccinated diseases that are the same, dishonest claims, conclusions in published studies that are 180 degrees from the raw data, there is no efficacy data, the idea of there being a pro or anti stance is a straw man, Poe, apple to authority, banana republic Blair discussion.

    At some point you will stop discussing whether rain came before seas or eggs and chickens and realise that the idea you can ‘stimulate’ an immune system into making better choices than nature is vindaloo science, we can but pray for that day. Medical science may wake up and join the rest of science and realise that natural selection is pants ahead of GM, GMO or vaccination.

  15. #15 bouquet
    July 11, 2012

    How about an ‘antiseptic’ vaccine, that would be worth investing in.

  16. #16 Niche Geek
    July 12, 2012

    “Vindaloo Science”?

    Does that mean it’s hot and appealing?

  17. #17 Optimus Primate
    July 13, 2012

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