I'm no chemist, but this guy is: http://homebrewandchemistry.blogspot.com/2007/02/hop-chemistry.html
He has a diagram of a possible way in which the alpha acids are isomerized. I have no idea if he's right or wrong.
On Deck: Jamil's Vanilla Robust Porter
Fermenting: Orange Blossom Mead
Kegs: Element 56 Pale Ale, Ron's Belgian Blonde, Summer'n Saison, Furloughktoberfest '09, Grateful Pale Ale, Sam Adams Cream Stout Clone, EdWort's Apfelwein