If all I have is my sense perception, I would be caught in quite a pickle. Should I believe my senses when they tell me water is in a place or should I believe them when they tell me there is no water here? It is here I use something different than my senses to break the tie: I use reason. I can reason that while I've associated wavy ripples with water, there may be other things that cause the effect of wavy ripples that I saw. I can also reason that my senses have misled me in the past; I've seen optical illusions that are not real, though they appeared to be. I can therefore draw a conclusion that there is no water and the wavy ripples may have in fact been an optical illusion just like others I've experienced.
In all of this, reasoning has an objective quality that stands above sense experience. To reason is to shoot at an objective criterion: the truth. The truth lies outside the individual and can stand in contrast to things like sense experience. Your sense experience may tell you that the sun circles the earth, but by reason and knowledge you are able to understand that it is the earth that is circling the sun.1 This fact is as true in ancient times, when it wasn't believed, as it is today when nearly everyone believes it. The truth is, then, something that stands apart from the organism while sense experience is something subject to the organism.
Philosopher Thomas Nagel draws this distinction as well. He states:
"Thought and reasoning are correct or incorrect in virtue of something independent of the thinker's beliefs, and even independent of the community of thinkers to which he belongs. We take ourselves to form true beliefs about the world around us, about timeless domains of logic and mathematics, and about the right thing to do. We don't take these capacities to be infallible, but we think they are often reliable in an objective sense, and that they can give us knowledge. The natural internal stance of human life assumes that there is a real world, that many questions, both factual and practical, have correct answers, and that there are norms of thought which, if we follow them, will tend to lead us toward the correct answers to those questions. It assumes that to follow those norms is to respond correctly to values or reasons that we apprehend. Mathematics, science, and ethics are built on such norms."2In in his recent book Mind and Cosmos: Why the Materialist Neo-Darwinian Conception of Nature is Almost Certainly Wrong, he looks at the problem of deriving reason from a materialist position. He first dismisses the attempts to reduce reason to some property held within the elementary particles that make up the organism. He writes that rationality "cannot be conceived of, even speculatively, as composed of countless atoms of miniature rationality."3 He then underscores the point that reasoning is something different than just cause and effect relations. Cause and effect relations are what computers do. If you feed the computer an input, it will, by the nature of its programming, produce an output. There is no understanding that happens.
In rejecting these options, Nagel says any explanation of reason that reduces it to merely matter, chemistry, and physics is increasingly unlikely. He writes, "This would mean that reason is an irreducible faculty of the kind of fully formed conscious mind that exists in higher animals, and that it cannot be analyzed into the mind's protomental parts, in the way that sensation perhaps can be."4 Thus Nagel, an atheist himself, rejects the materialistic explanations for reason and says that some new explanation is needed.
References1. Copernicus used reason and geometry to show the earth rotated around the sun. It wasn't until Galileo that there was new observational data to confirm Copernicus' model. See J. L. E. Dreyer History of the planetary systems from Thales to Kepler. 312-316. Available online at http://archive.org/details/historyofplaneta00dreyuoft
2. Nagel, Thomas. Mind and Cosmos: Why the Materialist Neo-Darwinian Conception of Nature is Almost Certainly Wrong. Oxford: Oxford University Press, 2012.71.
3. Nagel. 87.
4. Nagel. 87-88.