Freedom of Thought
Islam's principle concerning freedom of thought does not differ from its principle concerning political freedom. Islam grants every human being the right to express his or her opinion in the manner that he or she chooses. Islam considers that one of the most important characteristics of a Muslim is his conviction that he should declare what he believes and not fear censure or opposition.
The Prophet Muhammad, blessings and peace be upon him, and the Four Rightly Guided Caliphs who succeeded him, adhered to this principle, and freedom of thought was guaranteed and sanctified. During this Golden Age of Islam in which its principles were the true representation of the Faith, there is no record of any attempt by those in authority to prohibit or restrain any expression of free thought.
The principle of the freedom of thought was also guaranteed during the Ommayad Dynasty and at the beginning of the Abbassid Dynasty. The Caliphs of these two dynasties only opposed the opinions that incurred the danger of the security of the state or spread sedition among the people of the nation.
During the reign of `Omar ben Abdel Aziz and Al Ma'moun, son of Haroun Al Rashid, people were granted the right to discuss, in the Caliph's presence, matters that concerned the Caliph's right to rule over them, without fearing any retribution from those in authority.
Freedom of thought includes the freedom of scientific and academic thought which means that every person has the right to declare what he believes concerning the phenomena of nature, astronomy, animal life, plant life and mankind, according to the theories by which he is convinced. Islam grants Muslims this freedom in common with the other branches of freedom and never attempts to dictate any particular theory or precept concening cosmic, human, animal or plant phenomena. Islam does not even indirectly suggest any theory concerning the aforementioned matters, but urges people to meditate upon the phenomena of the universe in order to understand the general laws that govern it. Freedom of thought accordingly encourages one to contemplate and to attempt to discover more about the manifestations of the universe that had not previously attracted one's attention, and to ponder upon the order, arrangement and recurrence of these phenomena. It also leads to the realization that such matters are worthy of meditation, examination and merit scientific and academic research.
Matters that we take for granted are in fact wonders that are created by God Almighty such as night and day, the sun and the moon, the sequence of the seasons of the year, the reproduction of animals and the propagation of plants, in addition to the floating of certain bodies on water and other scientific phenomena.
The following Quranic verses are evidence of the aforementioned phenomena
"Do they not look at the camels, how they are made? And at the sky, how it is raised high? And at the mountains, how they are fixed firm ? And at the Earth, how it is spread out".
"And among His Signs are the ships, smooth-running through the ocean (tall) as mountains. If it be His Will, He can still the Wind then would they become motionless on the back of the (ocean). Verily in this are Signs for everyone Who patiently perseveres and is grateful". 90
"Do they see nothing in the government of the heavens and the earth and all that God hath created ?" 91
"A Sign for them is the earth that is dead : We do give it life, and produce grain therefrom, of which ye do eat. And We produce therein orchards with date-palms and vines, and We cause springs to gush forth therein" 92
"Glory be to God, Who created in pairs all things that the earth produces, as well as their own (human) kind and (other) things of which they have no knowledge. And a Sign for them is the Night : We withdraw therefrom the Day, and behold they are plunged into darkness : and the Sun runs his course for a period determined for him : that is the decree of (Him). The Exalted in Might, The All-Knowing, And the Moon, We have measured for her mansions (to traverse) till she returns like the old (and withered) lower part of a date-stalk. It is not permitted to the Sun to catch up the Moon, nor can the Night outstrip the Day Each (just) swims along in (its own) orbit (according to Law). And a Sign for them is that We bore their race (through the Flood) in the loaded Ark ; and We have created for them similar (vessels) on which they ride" 93
"See they not that it is We Who have created for them - among the things which Our hands have fashioned - cattle, which are under their dominion ?" 
"Seest thou not that God sends down rain from the sky, and leads it through springs in the earth ? Then He causes to grow, therewith, produce of various colours " 
"Seest thou not that God makes the clouds move gently, then joins them together, then makes them into a heap ? - then wilt thou see rain issue forth from their midst. And He sends down from the sky mountain masses (of clouds) wherein is hail : He strikes therewith whom He pleases and He turns it away from whom He pleases. The vivid flash of His lightning well-nigh blinds the sight. It is God Who alternates the Night and the Day verily in these things is an instructive example for those who have vision "
"And among His Signs is the creation of the heavens and the earth, and the variations in your languages and your colours verily in that are Signs for those who know. And among His Signs is the sleep that ye take by night and by day, and the quest that ye (make for livelihood) out of His Bounty : verily in that are Signs for those who hearken. And among His Signs, He shows you the lightning, by way both of fear and of hope, and He sends down rain from the sky and with it gives life to the earth after it is dead verily in that are Signs for those who are wise".
It is clear from the aforementioned verses that there is no suggestion of imposing any specific scientific theory or precept on the Muslims. These Quranic verses urge human minds to meditate and ponder upon the phenomena of the Universe in order to discover the laws that govern these phenomena. Every human being is then perfectly free to adhere to the theories that he believes to be true.
Freedom of opinion, freedom of speech, freedom of the press and freedom of scientific thought which the modern democracies claim to have introduced, have all been established by the Faith of Islam more than twelve centuries before these modern democracies existed.
 Surah LXXXVIII, verses 17-20.
 Surah XXXVI, verse 71.
 Surah XXXIX, verse 21.
 Surah XXIV, verses 43-44.
 Surah XXX, verse 22-24.