What the series does explain is that those who perform human transmutation are pulled through The Gate to be shown infinite knowledge of the universe at the physical cost of the users body.  A growth in faith through this process is the main protagonist Edward Elric. At the beginning of the series, Ed’s beliefs are rooted in science, that anything can be explained through science. Being an alchemist as well also exacerbates this point of view. Whenever challenged by ideas of a higher being, whether it was Rose, Scar or the homunculi, Ed refutes the possibility due to his personal experiences. Ed believed that when he entered The Gate after performing human transmutation as a child, he did not recognize why he was being shown infinite knowledge nor why he and his brother Alphonse lost physical body parts. He believed that it was due to a failure in his alchemy, not that it went against the laws of the universe.  When Edward enters The Gate again, he realizes it is something alchemists refer to as The Truth. This dimension is a higher plane of existence where all knowledge and matter converge at once. It is suggested that the source of life, and more specifically the human soul, can be found within this place. Even so, it is still very much beyond human understanding. As the series concludes, Edward learns that his simply part of a much bigger whole, and his use of alchemy is but one way of taking part in a much grander design. Thus he relinquishes his alchemy, his pursuit of knowledge, to be a simple human, in order to save his brother’s trapped body. Thus Ed accepts that we are not meant to have all the answers but a compromise can be found through faith in a higher being.