I recently found this response to an "atheist" man I was having a discussion with long ago. It is unedited, and therefore may not make sense in some places. Hopefully it will be useful to you in some way none the less.
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It is interesting that you credit your newfound interest and understanding of philosophy to your "conversion" to atheism. I suppose the opposite sort of thing has occurred in my experience. That is, before I started living my life with a real acknowledgement of Jesus Christ as my Savior and Lord, I cared little for matters of truth and philosophy. My conversion has resulted in a hunger for the Word of God, and stemming from this an interest in all things academic. I never knew before how very important education is to God. I returned to school at my old community college and brought my GPA from a 1.49 to a 3.6 by the grace of God, and recently transferred to a private liberal arts school to begin double majoring in Philosophy and Religion.
We are not capable of being objective so far as we would most likely normally suppose. Take your atheism for example. Atheism, and even more evidently your assumption that all things are natural, do not allow for any sort of "objective" investigation of either the Word of God or His world. At the back of all of your reasoning is the presupposition that you are an autonomous human being, meaning in this context that you possess an ability to set yourself over against the Christian God as the final authority in matters of truth and reasoning. Now, all of us have to use our reasoning of course, and there is nothing wrong with this. In fact, contrary to what many fundamentalist and evangelical Christians tell us by their words and behavior, God encourages the use of reason that He has given to us (having been created in His image). We can, must, and should use our reason; this is not what I mean by autonomy. It is when we assume that we are able to use our reasoning independently of God that we commit sin, and are incapable of rendering things intelligible upon our own presupposition of human autonomy in reason. The claim to objectivity and/or neutrality regarding the subject of the existence of God assumes from the outset that God does not exist. God tells us in His Word that Scripture is His Word, that everyone believes in Him, that it is futile and foolish to do otherwise, and that there is abundant and plain evidence for His existence. When atheists set themselves up as a final authority to deliberate between the options of acceptance and rejection of these claims of God, they set themselves in the place of God and so sin against Him. This does not put a non-Christian on very good terms with God. From the outset then you are turned against Him, unable to have objectivity regarding the subject. Now it is important to note that I do not pretend to posses any sort of neutrality or objectivity regarding the subject either. I interpret evidence based upon my presuppositions just as you do. It does not follow from this that we cannot communicate about the subject. We should be able to do so by looking at who adheres to those presuppositions which alone can account for things such as logic, morality, induction and redemption and who adheres to those presuppositions which yield contradictions, incoherency, detachment from objective reality and a need to borrow from another worldview in order to render anything intelligible.
You state that everything that exists does so within nature. You adhere to an atheistic, naturalistic worldview. Everything is material. If it is not material, it does not exist. As has been explained already, this is a presupposition. You say that you are justified in holding this position because everything understood in science demonstrates that everything that exists does so within nature. The trouble is that if we assume that science deals with those things natural and nothing else (which is not necessarily true, but that is not important right now) then obviously anything supernatural is outside of the scope of science and science so narrowly defined will deal with only natural explanations. It is like me favoring the use of my eyes for sensory data and then assuming that anything I cannot see does not exist. You assume that science must deal with only material things, see that science only tells us about material things, and then conclude from this that only material things exist. It would be a silly thing for me to say that only what my eyes can see exists, would you not agree? Science is a wonderful way of obtaining knowledge about the natural world, but it quite possibly has nothing to say about the supernatural world and further it is without a doubt not the only means by which we may obtain knowledge. I agree that just because there are some things we cannot currently explain through science it does not mean that there will not be some explanation forthcoming. However, we should be very careful about relying upon blind faith in science by saying that maybe sometime in the future there will be a scientific answer to problem x. I realize that you will say it is not blind faith since we have seen science answer questions before, but this just blindly assumes again that the current problem x has some sort of scientific explanation, and there is no way to know that. Perhaps it is wise for us to deal with information that we do know, rather than looking to some future explanation that may never come. It is also advantageous to remember that there are many things we know we cannot explain through science. For example, how do we know that science is the only way or the best way to knowledge? It is impossible to scientifically justify science. Its validity rests upon a great many assumptions that are outside of the field of science.
This helps us when we come to your problems with belief in God. For example, you may say that you base what you believe upon what is rationally verifiable, but by this you must mean what is verifiable through scientific means. If this is not what you mean then I apologize, I do not want to make a caricature of your position, but I do not see what else you might be referring to. You say that you do not believe that there is a God because you see no rational reason to believe in anything not bound by the laws of nature, but this appeals to your naturalistic presuppositions which are, again, unjustified as far as I can tell. Certainly if we take "rational reason" to mean "those reasons which can be obtained through naturalistic science" then God might not be the end result. This is to commit a category fallacy though. If I want to listen to Mozart I do not use my eyes. We do not come to the knowledge of God through studying the composition of a rock (although there is a sense in which we do, which I might explain later). We cannot answer all questions in the same way, by the same methods, etc. You are correct that an immaterial, non-corporeal, etc. God cannot be verified through naturalistic science. This presents no problem for my worldview. Naturalistic science is not the only way to obtain knowledge.
I am not sure why your study of the Bible and how it was compiled renders you incapable of believing in God except for that you interpret evidence based upon your presupposition of human autonomy. My study of the Bible and how it was compiled only builds my faith up. Reading and hearing the Word of God and seeing how God in His sovereignty has delivered His Word down through history to us both supports my presupposition of the God of Christian Scripture and excites me. Obviously the so called Abrahamic faiths have a similar origin, Islam and Judaism being Christian heresies. For whatever reason most people do not recognize this though.
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