Does Islam permits critical thinking about religion??

I remeber the days when I was in university doing my engineering. I had many friends to whome I used to discuss different ideas, conspirancies, technicalities and so on. We used to talk on everything from a pin to plane, from religion to history etc. We dint care about our limits. We wanted to conquer each and everything. Sometimes our discussions gone so lengthy that we had to take rest.
One day one of my friend starts discussion about different things in Islam. He was taking each and everything in Islam in a materialistic sence. I was trying to convince him that we can't understand all the things in Quran. But he was so sure that no..we can understand. Soon we started critical discussion. He came up with different Ayats from Quran and tried to prove them wrong. For example in one of the ayat it is mentioned that man is made from dust (matti). He disagreed with it claiming that it is proved now a days that no dust is used in the composition of man. In the same way he came up with other Ayats which seems to be unclear. I advised him to consult a good tafseer or an alim for clarification. Finally after considering different tafasser we came to the conclusion.
Now the question is does Islam permits such type of critical thinking about Quran and other fundamental theories of the religion. Is it wrong to do that?? I think its permissible. But the direction should be correct. Otherwise such thinking may led us to somewhere else. I would rather say that Islam encourages critical thinking instead of just permitting it. At scores of places in the Holy Qur'an, the Almighty has exhorted man to think about the signs that are spread around him and that testify to the greatness of Allah. The Holy Qur'an reads:

None will grasp the message but men of intellect? (2:269)

Most certainly the worst of animals in Allah's sight are the deaf, the dumb who do not use their brains. (8:22)

Behold in the creation of the heavens and the alteration of night and day, there are indeed signs for men of intellect. (3:190)

We are not supposed to close our eyes and live this life being obsessed with worldly pleasures as animals who only know how to strive for their bodily desires. We are rather supposed to ponder, deliberate and choose a proper course of action for whatever undertaking we venture. Thus, critical thinking is not confined to thinking about the stars and the moon. It is rather moving ahead in every field of science and arts. The discoveries that we succeed to make in these fields will evidently guide us how to appreciate the Original Creator of everything, who always partake in our lives like a concerned and active Mentor.