Doctor Faustus at Goodreads
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Most interesting about Marlowe's Faustus is not that an open atheist can write a work that at a glance matches the overt morals of The Summoning of Everyman and other medieval morality plays, but that critics can wonder why an atheist would write such a piece. Though on a surface level the play appears to be retelling the Faust legend with the purpose to scare Christians (and non) from practicing sin (and magic), it is the struggle and inner turmoil the play is most concerned with, and not on damnation. Granted the focus does shift, as Marlowe weaves base comedy into the work. That inclusion, however, assuming he did write or commission those particular scenes, is a reflection of stylistic conventions of the period, such as the use of a chorus narrator, rather than an attempt to illustrate the play's main ideas.
The story of a brilliant intellectual with few worthy lifelong prospects sells his soul for a handful of years of pretty much anything he wants cannot ignore either the concept of Christian salvation/damnation nor the idea of an individual's terrible sacrifice for seemingly so little. In light of this the attempt of scholars to figure out exactly who wrote which parts of the play seems to add little value to understanding the work, though it has other significance. The central ideas concern the desire for higher knowledge, so that the inclusion of works on magic are not an attempt to link the supernatural with the almighty, or to denounce medieval notions of magic, but rather part of a man's search for knowledge beyond that of the corporeal world. This idea is highlighted by Faustus's questioning Mephistophilis on astronomy, and later his continued attempts to seek truth from a science that takes us beyond the world that encases us physically.
Important to the play is understanding the controversies of astronomy at that time. For many centuries to openly theorize about new ideas of the solar system and beyond was challenging to the point that the theorist was risking his life. How humans viewed the solar system and the Earth's place within could easily contradict the doctrine set forth by the Vatican. Was Marlowe using astronomy to illustrate that his protagonist was seeking ideas beyond the realm of the known physical world, or subtly commenting on the different views, Catholic or otherwise, of man's place in the greater universe?
Faustus's greatest sin from a Catholic perspective is perhaps denying that God will forgive him his sins if he were to repent and embrace the Lord. If he were clear on Catholic teachings, and at the time any literate scholar such as he would undoubtedly be clear on all the major Catholic points, just as Marlowe himself was certainly aware. Questioning the idea is therefore an important point in the play, particularly since he seems to be rejecting not God but the earthly teachings related to God. Moreover, assuming he is aware of Catholic doctrine, he nonetheless believes his own sins are beyond the power of God's forgiveness, which is perhaps, in a Christian world, the vilest form of hubris possible.
At this time I would argue that Marlowe is presenting the idea that man is moving away not from God, necessarily, but from the church. His exploration of astronomy and questioning of one set of contemporary beliefs, along with his act of incredible hubris, takes Faustus and his struggle away from the church.