On Wed, 2005-12-14 at 11:37 +0000, Julian Bradley wrote:
> At 11:28 14/12/2005, you wrote:
> >On Wed, 2005-12-14 at 11:08 +0000, Julian Bradley wrote:
> >
> > > Whether a vaccine will be available early or late turns out to be
> > > affected by how a readily human transmissible variant arises.
> > >
> > > Gradual mutation would probably give us time to develop a vaccine.
> >
> >Gradual?
> >
> >I don't think it can do it gradually.
> >
> >I suppose if we got a new transaminase as well as the H5 then it would
I meant Neuraminidase of course.  Ooops.

> >be worse than H5N1, but the determining factor AFAICS is the degree of
> >difference in the recombinant virus from what we have seen before.  I
> >don't think it arises gradually, and indeed if if it did carry on
> >changing, our new vaccine might be for a previous version by the time
> >the virus cauhgt up with us.
> 
> I'm no virologist but see 
> http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/I/Influenza.html
> for a discussion of antigenic drift vs antigenic shift.

A lamentable piece in the paragraph 
Epidemics and Antigenic Drift

One knows what they _mean_ (probably) but it is an anthropomorphic
argument, even worse than assuming intelligent design. 

> The chance of drift outpacing vaccine development exists every year 
> for normal flu, but seems modest.

I think we differ on the interpretation of gradual - mutations either
occur, or do not, what is variable about them is the degree of
difference in the expressed protein and the orgnaism's properties they
produce.

So if there is  a (sudden) mutation of small effect we are OK (drift)
and if there is a (sudden) recombination of large effect, we may be less
OK (shift).  I'd use mutation relative to a single gene, and regard
recombination not as mutation, but as re-assorting a gene that
presumably mutated to its present form some time ago and in a different
strain or species.

Drift I take to be mutations occurring in the gene without it jumping
strains/species, althugh I suppose there is no rule against a large
mutation occurring in place.


-- 
Dr Adrian Midgley
www.defoam.net