"Ever since Pope John Calvin had moved the seat of the Papacy to Geneva"
John Calvin
Public DomainJohn Calvin

John Calvin (1509-1564) was one of the leaders (along with Martin Luther) of the Protestant Reformation, the movement that established Protestantism as a constituent branch of Christianity, in opposition to the doctrine and rituals of Catholicism.

In Lyra's universe John Calvin is Pope, suggesting that Calvinism has combined with, or even replaced, Catholicism to create the Magisterium. 

Geneva was the unofficial capital of the Protestant Revolution.  Calvin left his native France after a backlash against Protestants, fleeing to Basel in Switzerland.  He eventually settled in Geneva, where he led the church and took control of the city council.