Read other letters about this article
Ivins' papers indicate that he was interested in creating a better "recombinant" vaccine. That is one where proteins that confer immunity are cultured in a host organism, negating the need to culture the actual anthrax. The current ( BioPort AVA ) vaccine is produced by a relatively ancient techique. It is the supernatent from the culture of actual anthrax, containing the protein domain "protective antigen". Thus PA refers to the active ingredient, and you may notice the abbreviation PA in some of the technical clips Glenn has posted.
The BioPort product has some problems, to put it very mildly. It has been known to cause a rare blood disease called "aplastic anemia".
A case study reference to the relationship between AA and AVA is here.
http://tinyurl.com/aplastic-cases
I have seen at least one reference indicating that Ivins himself believed he was suffering from AA. That's quite some motivation, and in fact he was a victim multiple times over.
VaxGen, now defunct, was the company working on the modern recombinant vaccine. But what fun would a recombinant vaccine be? Our anthrax national monument, BioPort, wouldn't be able to play with their anthrax anymore. Obviously, the FBI had to shutdown Ft. Dietrich and VaxGen at any cost. They are truly an efficient organization.