islamic civilization’s care for freedom of thinking
islam has enshrined the freedom of thought and cared for it. the islamic civilization stands as witness for this. this was clear as islam has called for thinking and making as functional the powers of reason in thinking about the whole universe with its skies and earth. islam urged all the people to do this and god almighty said: “say: "i do admonish you on one point: that ye do stand up before allah,- (it may be) in pairs, or (it may be) singly,- and reflect."[saba: 46] and also: “do they not travel through the land, so that their hearts (and minds) may thus learn wisdom and their ears may thus learn to hear? truly it is not their eyes that are blind, but their hearts which are in their breasts.” [pilgrimage: 46]
islam urges use of mental faculties, proofs
islam has blamed those who block their sensual and mental faculties from functioning and put them in a rank lower than beasts. god almighty says: “they have hearts wherewith they understand not, eyes wherewith they see not, and ears wherewith they hear not. they are like cattle,- nay more misguided: for they are heedless (of warning).”[the heights: 179]
islam has also launched a strong campaign against those who follow conjectures and illusions. god almighty says:“they follow nothing but conjecture; and conjecture avails nothing against truth.”[the star: 28]. islam has also blamed those who imitate their ancestors or chiefs without looking out whether they are right or wrong. god almighty says belittling their value: “and they would say: "our lord! we obeyed our chiefs and our great ones, and they misled us as to the (right) path.”[the clans: 67]
islam has also depended in proving the islamic creed on mental evidence and that is why muslim scholars said that akl (reason) is basis of naql. the cause of allah’s existence has proven reason and cause of muhammad’s prophecy was also proven through reason first and latter by miracles that proved the credibility of his prophecy. and that shows how islam respects reason and thought.
value of thinking in islam
thinking in islam is a religious duty that a muslim should not abandon in all cases. islam has left the door wide open for the practice of thinking in religious affairs to search for legitimate solutions for everything new in our life. and that what muslim scholars call “ijtihad” i.e. the process of making a legal decision by independent interpretation of the legal sources, the qur'anand the sunnah. 
the principle of ijtihad, which embodies the freedom of thought in islam, had a great influence in enriching jurisprudential studies with quick solutions to affairs that had no peers during the first stage of islam. the famous mazahibs (schools of thinking) of islamic jurisprudence, which the muslim world still follows their teachings until nowadays, were based on ijtihad. ijtihad is the first pillar for well-established role of mind in islam and this attitude was considered the foundation on which muslims built their prosperous civilization throughout the history of islam.
1. look: mahmud hamdi zaqzuq: islamic facts in face of campaigns to cast doubts (on islam) p. 53
2. mahmud hamdi zaqzuq: man caliphate of allah- thinking is duty, article published in al-ahram newspaper, edition 1 ramadan 1423 hijri, november 2005