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Naturalism makes some assumptions 1. that we have free will to think and reason as we please. (some naturalists) 2. that the soul does not exist.(The soul which is something invisible something you cannot see, like the mystical beast in the sky is something you cannot physically see, because it is not physical, but spiritual). Now how do we get 1 without 2? You see physical entities do not possess conscience, a cell does not act on will, but on a process much like a computer. It follows a set of predetermined systems that cause it to move and act. Now one could state that evolution has created a system within the brain to allow conscience to run freely, but this is only possible if there is conscience to be had to begin with, we know that you cannot give what you do not have. For instance it doesn't matter how complicated my irrigation system is if there is no water to irrigate the fields. So if you are to hold onto the notion that Naturalism is true than you most also hold that man has no freewill, no conscience, in order to sustain rational thought, everything that he would think would merely be a coincidence of the events that were bound to occur. In other words, naturalism's only end is one against rational thought rather than for it.

I would also like to add that there are evidences against naturalism, one of which being our ability to decide, an impossibility of the purely natural world, as proven above. Surely, we all do have this ability, for when we find ourselves with two instincts fighting against the other we are able to decide between those two instincts whether or not the one instinct was stronger than the other, which is often found in bravery or good will, this is an evidence of conscience thought. Another would be our ability to imagine images and conceive words within our minds. These are actions which cannot be seen nor measured through any scientific means, all science is able to do is prove that these actions are occurring but cannot prove that such images exist, they seem to exist outside of the physical(natural) world. No matter how hard science tries if I were to imagine the color green, they could not see that color in my head, or if I were to think the words "Pink elephant" they could not hear them.