I doubt the integrity of pseudo scientists who have actually studied fine arts who pretend to be knowledgable about biology and evolution.
Anyway, the first major doubt that i had has already been mentioned - the concept of predestination.
In about 2005, it started to puzzle me and I bought a book from the Islamic Propagation Centre (an accurate name for the business), and I read the book and it still puzzled me and didn't make much sense. I asked someone about these ayat:
2:6-7 As for the Disbelievers, Whether thou warn them or thou warn them not it is all one for them; they believe not. Allah hath sealed their hearing and their hearts, and on their eyes there is a covering. Theirs will be an awful doom.
Some Atheists also accuse religious people of being stubborn. There is whole thread here on the subject. They claim that no matter how much scientific evidence is presented to some religious fanatics, they are so brainwashed that they will never leave their delusions.
Its a fair criticism. And it is a true observation. Some religious nutters are totally closed off.
That criticism is exactly what the verse is making about some Atheists: That no matter how good the reason, or, even if they were shown a divine miracle, they would dismiss it as a trick, and reject all reasonable arguments.
After a certain number of chances given to them to use or abuse their God given-intellect, God says that as a punishment He has sealed their mind. They will now burn in Hell.
I also do not accept predestination. But you have to ask is that what is being presented in the verses?
Honest thinkers would never have double standards in evaluating things.
Any serious researcher should use their intellect to its best capacity and not follow what suits their wishes and desires.
If a person is not truly objective then he willl only hear whatever he LIKES to hear.
Truth never fits the biased.