Short answer
On atheism, there is no good reason to trust our reasoning. The mind would have come only from a blind, unguided process that kept whatever helped our ancestors survive. But surviving and being right are not the same thing. Yet the atheist must use that same mind to conclude that there is no God. That view gives no reason to trust the tool used to reach it. Charles Darwin himself, in 1881, doubted whether the convictions of a mind that grew out of animal minds could be trusted at all. That doubt reaches every conviction, including atheism. The believer has no such problem. The Qur'an says God (﷾) gave people hearing, sight and understanding, and it calls on them to use them. A mind given by the One who made the world it studies is a mind worth trusting.
Full explanation
Surviving is not the same as being right
Natural selection keeps what helps a creature survive and have young. A belief can help with that whether or not it is true. True beliefs about food and danger often help. But selection rewards the behaviour, not the truth behind it. A false belief that leads to the same behaviour serves just as well. Selection gives even less reason to trust beliefs far from survival. Examples are beliefs about mathematics, the origin of the universe, or God (﷾). So if unguided evolution is the whole story of the mind, we have no firm reason to think our deepest beliefs are true. That includes the belief that there is no God. Alvin Plantinga, an American philosopher, set this out in full. On naturalism (the view that nature is all there is), the reliability of our thinking is unlikely or unknowable. So naturalism undercuts itself: it removes the ground it stands on.
Argues that if naturalism (no God) and unguided evolution are both true, the chance that human thinking is reliable is low or cannot be known, so the naturalist has a reason to doubt all his beliefs, naturalism included. The conflict, he concludes, is not between science and belief in God but between science and naturalism.
Darwin's own doubt
Charles Darwin was the 19th-century naturalist who set out the theory of evolution by natural selection. He raised the same doubt in a letter written in the last year of his life. He was writing about his own inner conviction that the universe is not the result of chance. Then he asked a question. Can the convictions of a mind that developed from the lower animals be trusted at all? Darwin aimed the doubt at his own sense that the world was designed. But it applies to every conviction such a mind holds. That includes the conviction that there is no God.
“But then with me the horrid doubt always arises whether the convictions of man's mind, which has been developed from the mind of the lower animals, are of any value or at all trustworthy. Would any one trust in the convictions of a monkey's mind, if there are any convictions in such a mind?”
An atheist philosopher's verdict
Thomas Nagel is an American philosopher who does not believe in God (﷾). Yet he concluded that the purely materialist, Darwinian account of nature is almost certainly false. Materialism is the view that everything is only matter. His reason is that it cannot explain how minds came to grasp truth by reason.
Nagel, an atheist philosopher, argues that the materialist neo-Darwinian picture of nature is almost certainly false, because it cannot account for consciousness, reason and value. He does not accept belief in God, but holds that reason's grasp of truth cannot be explained as a by-product of natural selection.
A mind given by the Maker of the order
The Qur'an says God (﷾) brought every person out of the womb knowing nothing. Then He gave them hearing, sight and understanding. People will be asked how they used them. They are told not to follow what they have no knowledge of. A mind given for knowing the truth, by the One who made the world it studies, is a mind a person has reason to trust.
“It is He Who brought you forth from the wombs of your mothers when ye knew nothing; and He gave you hearing and sight and intelligence and affections: that ye may give thanks (to Allah).”
“And pursue not that of which thou hast no knowledge; for every act of hearing, or of seeing or of (feeling in) the heart will be enquired into (on the Day of Reckoning).”
Reason points back to its Maker
The Qur'an asks people to reflect in their own minds and to look at the heavens and the earth. It asks whether they were created from nothing, or whether they created themselves. Reason, used honestly, leads to the Creator who gave it.
“Do they not reflect in their own minds? Not but for just ends and for a term appointed, did Allah create the heavens and the earth, and all between them: yet are there truly many among men who deny the meeting with their Lord (at the Resurrection)!”
“Behold! in the creation of the heavens and the earth, and the alternation of night and day,- there are indeed Signs for men of understanding,- Men who celebrate the praises of Allah, standing, sitting, and lying down on their sides, and contemplate the (wonders of) creation in the heavens and the earth, (With the thought): "Our Lord! not for naught Hast Thou created (all) this! Glory to Thee! Give us salvation from the penalty of the Fire.”
“Were they created of nothing, or were they themselves the creators? Or did they create the heavens and the earth? Nay, they have no firm belief.”
The usual reply
Where the Conflict Really Lies (2011)
Argues that if naturalism (no God) and unguided evolution are both true, the chance that human thinking is reliable is low or cannot be known, so the naturalist has a reason to doubt all his beliefs, naturalism included. The conflict, he concludes, is not between science and belief in God but between science and naturalism.
Cited for
True beliefs help survival, so evolution gives us reliable minds, and the success of science proves it.
The response
Survival needs useful behaviour about food and danger, not true beliefs about mathematics, physics or the origin of the universe. Yet a creature from one small planet can write the laws of the universe in mathematics. Eugene Wigner, a physicist of the 20th century, called this the unreasonable effectiveness of mathematics. That is what one expects if one Mind made both the order and the mind that studies it. Survival alone does not explain it. And using science's success to prove that reason is reliable assumes the very reason being tested. The believer uses the same mind, but his view gives him reason to expect it to work. The atheist's view gives him reason to doubt it.
Where it lands — Survival explains useful instincts, not a mind fitted to the mathematics of the universe.
Perspectives
An atheist philosopher who agrees on the problem
Thomas Nagel rejects belief in God. Yet he accepts that a purely materialist account of the mind cannot explain why reason reaches truth.
Thomas Nagel, an atheist, judges the materialist neo-Darwinian picture almost certainly false because it cannot account for reason.
Rebuttal
Nagel is right that the purely material story cannot explain reason. He rejects God (﷾), but rejecting God (﷾) does not fill the gap he found. The Qur'an fills it: God (﷾) gave people hearing, sight and understanding.
The Islamic perspective
The human mind is a gift from the Creator, made to know the truth about His creation. That is why reason can be trusted, and why reason leads back to Him.
Evolution with no one guiding it selects what helps survival, not what is true. So if nature is all there is, nothing backs the claim that reason can be trusted.
Selection rewards useful behaviour, not true belief. So it backs beliefs far from survival even less, such as beliefs about the origin of the universe, or about God (﷾).
An atheist who uses reason to deny God (﷾) relies on reason. Yet his own view gives him no grounds to trust it.
Darwin himself doubted whether the convictions of a mind developed from the lower animals could be trusted.
The Qur'an says that God (﷾) gave people hearing, sight and understanding. And it holds them answerable for how they use them.
A mind made by the Creator of the world it studies is expected to understand that world.