"My question is this, do you believe your cognitive faculties are providing you with true beliefs? According to the materialistic paradigm, our bodies, including our brain, is a product of time, matter, energy, and chance. Again, according to this worldview, there was no Intelligent Being who formed us, but rather we are the result of non-personal, materialistic causes... If our brains are just products of blind chance, why should we trust anything they tell us? I would argue that the atheist, has no reason to trust his own brain, and that atheism is then completely irrational. On the other hand, the theist believes that his mind was created by an Intelligent Being, and thus there is a reasoning power behind it."
He quoted Charles Darwin as saying in a letter:
"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?"
The answer to this question comes in two parts. First, our scientific understanding of the evolution of consciousness; and second the philosophical question of the nature of knowledge.
Darwin was always prepared to admit doubt in his thinking - that's part of what made him one of the greatest scientists of the nineteenth century. Our understanding has increased greatly since then. The leading authority on the Evolution of consciousness was the now-retired Harvard University psychologist Dr Jerome Kagan. His "Evolutionary Psychology" provides a basis for answering part of your question... Kagan argues that we have evolved a capacity for abstract thought not shared by other animals. So, he says, monkeys do not have the same consciousness as humans.
But, how do we know what is real and what is not? The question is one of epistemology - the theory of knowledge.
René Descartes (1596-1650) argued that the existence of God gives certainty. This was the basis for his famous declaration: "cogito, ergo sum".
His thinking, however, was ridiculed by the great Prussian thinker Immanuel Kant (1724-1804). Since, he argued, metaphysical propositions such as the existence of God seek a truth beyond experience, they cannot be established within the bounds of reason. In other words, thinking that God exists does not make him exist. Unless we have prior knowledge that God actually does exist, Descartes' argument is worthless.
Kant attributed the "reasoning power" attributed to the theist mind is a self-delusion. He wrote:
"The wish to talk to God is absurd. We cannot talk to one we cannot comprehend - and we cannot comprehend God; we can only believe in Him."
Moreover, this was a delusion in which Kant himself was prepared to share:
"I have therefore found it necessary to deny knowledge, in order to make room for faith."
"Here is Kant perpetrating the same fraud on humanity as every other form of religious morality. He does little more than give new words to the same sad argument that has been passed down through the ages: Sacrifice your happiness in this life and this world, the witch doctor promises, and you will be rewarded with happiness in the next one..."
Science tells us that there is no such thing as indisputable, unquestionable reality. We can't be absolutely certain of anything in a formal sense. To that end, the atheist and agnostic world-view entirely reflects reality.
"Apart from moral conduct, all that man thinks himself able to do in order to become acceptable to God is mere superstition and religious folly."
"Reason can never prove the existence of God."
"He who has made great moral progress ceases to pray."
"Human reason has this peculiar fate that in one species of its knowledge it is burdened by questions which, as prescribed by the very nature of reason itself, it is not able to ignore, but which, as transcending all its powers, it is also not able to answer."
