So could we kill off all the 'typical' flu viruses allowing the evolution of something more aggressive?
Probably not inconceivable; but there are a couple of points to consider: TFA mentions targeting structures that are 'highly conserved' between different virus subtypes. Typically(and I am not a molecular biologist, so feel free to cringe and/or correct me) the fact that a structure is 'highly conserved' between genetically distinct populations means that it is extremely important for some reason. Mutations happen(and very, very fast in influenza), so regions that aren't life-critical can diverge significantly over time. Life-critical regions, on the other hand, do experience mutations; but most of the mutants die. The degree of conservation across genetic lineages that diverged at a known period in the past can tell you a lot about how important that area is, even if you don't yet know exactly what it does.
Second, while this also doesn't preclude a really nasty bug, it is important to remember that diseases aren't little agents playing Pandemic 2 and trying for a high score. Killing your host can be a viable strategy, if you gain enough from doing so; but (in the very weak sense that mindless evolving virues can even have 'goals') the 'goal' isn't body count, it's survival and reproduction. Very high mortality is frequently counterproductive, because hosts die faster than the disease can spread to new ones. In broad strokes, high mortality tends to occur when a novel pathogen shows up for the first time; but ends up being selected against over time(see the classic attempt to use Myxoma virus against feral rabbits in Australia).
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