Although the furor over Pope Benedict’s University of Regensburg lecture has centered on a perceived insult to the prophet Mohammed, I believe that the remarks were directed at a more recent figure, Sayyid Qutb, an Egyptian writer active in the Muslim Brotherhood in the mid-20th century whose writings are widely read in the Islamic world today. Qutb’s works have been a major influence on the modern philosophy of Islamic radicalism, including that of Ayatollah Ruhollah Khomeini of Iran. After Qutb was executed by the Egyptian government in 1966, his brother fled to Saudi Arabia, where he became a teacher of Osama Bin Laden.
It is doubtful that it is mere coincidence that both Pope Benedict’s supposedly provocative lecture and many of Sayyid Qutb’s writings concern the split between faith and reason embodied in Western philosophy. According to Luke Loboda’s invaluable essay on Qutb’s work, Qutb believed that Christianity, under the influence of Greek philosophy and Roman tradition, had created a separation between faith and reason that was unnatural, unspiritual, and ungodly. In the Christianized West, maintaining social order became a purely rational process separated from religious faith. The separation left individuals in a state of disharmony with God’s creation, forced to deny the truth that faith and reason were inextricably linked.
In Qutb’s view, God had provided man with a system for uniting faith and reason in his day-to-day life — the system of Islamic law. Reason was acceptable when used for interpreting or implementing Islamic law, but not useful for discovering truths outside of its structure. Social orders claiming a rational basis and without relation to Islamic law and were especially unacceptable; Qutb viewed them as restrictions on and distractions from the precise instructions provided by God on how to exist harmoniously within the universe.
At the end of his Regensburg lecture, I believe that the Pope offers an olive branch to those sympathetic to Qutb’s idea that reason and faith cannot be healthily separated from one another. The Pope asserts directly that the West has gone too far in separating faith and reason…

In the Western world, it is widely held that only positivistic reason and the forms of philosophy based on it are universally valid. Yet the world’s profoundly religious cultures see this exclusion of the divine from the universality of reason as an attack on their most profound convictions….The West has long been endangered by this aversion to the questions which underlie its rationality, and can only suffer great harm thereby. The courage to engage the whole breadth of reason, and not the denial of its grandeur — this is the program with which a theology grounded in Biblical faith enters into the debates of our time.

But then the Pope makes his challenge, taking the position that harmonizing faith and reason does not imply the subordination of reason…

“Not to act reasonably (with logos) is contrary to the nature of God”, said Manuel II, according to his Christian understanding of God. It is to this great logos, to this breadth of reason, that we invite our partners in the dialogue of cultures. To rediscover it constantly is the great task of the university.

In other words, since God’s nature is ultimately loving and reasonable, achieving harmony with God’s creation requires humans to be loving and reasonable. Doing unto others as you would have them do unto you is equally as or more important than following any particular system of rules.
Qutb and the modern Islamists under his influence reject this view. They believe relations between individuals should be regulated first through Islamic law. Then they go further. Qutb advocates the destruction of any worldly institutions not based on Islamic law because the very existence of non-Islamic institutions places barriers between men and God. This is the basis of the modern Islamist conception of jihad. Qutb advocates waging offensive wars to destroy non-Islamic institutions until nothing but a social order based on Islamic law remains on the Earth. Quoting directly from Qutb’s Jihad in the Cause of God…

Islam is not a “defensive movement” in the narrow sense which today is technically called “defensive war”. This narrow meaning is ascribed to it by those who are under the pressure of circumstances and are defeated by the wily attacks of the orientalists who distort the concept of Islamic Jihaad. It was a movement to wipe out tyranny and to introduce true freedom to mankind, using resources according to the human situation, and it had definite stages, for each of which it utilized new methods.

Qutb’s definition of jihad is the basis upon which Islamists rest their claim that their violent acts are consistent with the Koranic sura that “there is no compulsion in religion”. Technically speaking, they do not seek to force anyone to convert to Islam. They seek “only” to obliterate completely all non-Islamic institutions everywhere, thus creating a world where it is easier for people to choose Islam on their own (because there is nothing else to choose).
In the end, Pope Benedict never argues that Islam is inherently flawed or that radical Islam is an inevitable and natural outgrowth of “authentic” Islam. The Pope argues that anyone — be they Islamic, Christian, Jewish, Hindu or whatever — who subordinates their reason to comply with a set of rules or the decree of an individual leader risks acting contrary to God’s nature. No matter what the letter of the law says, human beings should strive to embody God’s loving and reasonable spirit in every action that they take. Though radical Islamists — the Muslims who get most of the press these days — find this position unworthy of consideration, Pope Benedict is inviting moderate Muslims to a dialogue on this subject.