Muslims are experiencing problems due to a misunderstanding of Islam. The misunderstanding of revelation resulted from the repression of reason by Muslim tradition. Reason is gift from Allah. To reject the blessing of reason betrays ungratefulness, which is among the meanings of kufr. Reason is disparaged by persons that feel threatened by it. The fear of reason precipitated the extermination of 5,000 rationalists by Musa al-Hadi during the mihna or Inquisition of 786. The killing of the philosophers confirms that "orthodoxy" was established by force rather than arguments. The persons that perpetrated this atrocity were not well versed in argumentation. Thus, they resorted to violence to force their perceptions on the umma through coercion, prohibited by revelation. The misunderstanding of revelation encouraged extremists to follow their passions. The misunderstanding was the result of traditional exegesis, which requires understanding revelation through the prism of tradition. Traditional exegesis treats traditions as a furqan of revelation. This is reflected in the perceptions that tradition "judges" revelation, and that revelation requires tradition more than tradition requires revelation. By treating tradition rather than revelation as the furqan, traditional exegesis defied tauhid. Treating tradition as a "judge" of revelation is tantamount to scriptural shirk. The traditional approach entails the repression of reason. But the refusal to use reasoning to understand revelation made it harder to understand revelation. It rendered traditional exegesis unreasonable and unreliable. The assumptions that render the traditional exegesis unreliable comprise the perception that reason is the enemy of revelation, that reason is subordinate to tradition, and that tradition may "judge," "abrogate," and "replace" parts of revelation. The repression of reason enabled the emergence of perceptions that defy revelation, the perceptions that revelation is "unclear," "incomplete," and "incoherent." Problematic assumptions encompass the perception that tradition is "equal" to revelation and that tradition is a root of the sharia. These perceptions generated unwelcome effects. The allegation that tradition is equal to revelation embedded scriptural shirk in exegesis. The perception that tradition may "abrogate" and replace the rulings of revelation by rulings from tradition embedded juristic shirk in traditional jurisprudence.
The embedding of scriptural and juristic shirk into the fabric of the religious knowledge corrupted knowledge and a warped the penal code. The death penalties for blasphemy, apostasy and adultery, were incorporated into Islamic law without endorsement in revelation. These punishments embedded extremism into the law. The punishments were drawn from tradition rather than revelation. They result in injustice and impart to Islam a reputation for cruelty. The shirk at the foundation of the exegesis of revelation renders the knowledge brought by traditional exegesis and jurisprudence unreliable. Thus, requires reconstruction and rehabilitation. The reconstruction of religious knowledge requires a return to reason and the affirmation of the preeminence of revelation in relation to all tradition. Reconstruction also requires the affirmation of revelation as the foundation of all legislation in religion. It requires a return to a rational methodology of understanding revelation.