I highly encourage you to read the wiki on qualia, it is quite excellent in presenting definitions and arguments for and against the non-physical world. What I'll explain here is very brief.
The definition of qualia is a little complicated. However, essentially the only qualia ever discussed is color, so when I saw qualia, just think of color. In long discussions with an atheist friend of mine in college, he seemed to say that color is an illusion, something that our brain conjures up in order for us to think about what we see - it's a filtration or a language. Here is the thought that inspired this post: when he describes our brain communicating color to us, why is he separating us from our brains? He is, in effect, creating two characters. For a language is only created in the context of at least two independent entities. By describing it this way, he is saying that we are not our brains, we are something deeper. What is this? I have no idea what to call it. Labeling it 'soul' might be a little odd, 'will' seems a little off topic. Anyway, I hope you get the idea.
If we did not have this soul, we would not have the perception of thought, of color, or of anything for that matter. We would simply be an incredibly complicated chemical machine that has no consciousness of its own.
You think of yourself, atheist, to be your body. Yet you yourself are one, distinct perceptual entity, and your body is simply a continuous array of matter, only distinct from the matter around it by an illusion in our brains. What part of that matter makes you who you are? How much of your body could we cut away and still have you? If we switched your brain with someone else's, would you wake up in their body or in your own? If we somehow hooked up a second brain to your nervous system, would you have two thoughts going on at once, would you be in mental conversation with that poor other fellow, or just be a whole lot smarter? What if we took only your left brain and switched it? Your right? Your spinal column with basic motor functions? Your other singular brain parts such as the hypothalamus?
Who ARE you? or perhaps as you might say, WHAT are you?
The color we see, the sensation of fabric you're wearing, the feeling of gravity underneath your feet, sound, taste, even thought itself, all testifies to a deeper you, and to the one who created you.
Romans 1:20 "For since the creation of the world God's invisible qualities - his eternal power and divine nature - have been clearly seen, being understood from what has been made, so that people are without excuse."
Psalm 19:1-4, Psalm 97:6 "The heavens declare the glory of God; the skies proclaim the work of his hands. Day after day they pour forth speech; night and night they display knowledge. There is no speech or language where their voice is no heard. Their voice goes out into all the earth, their words to the ends of the earth."
P.S. you may say that animals see color, so do we claim they have souls? No, think as you would explain it. All of their physical functions may work without having a consciousness. I don't know if they have one...I'm not going to even make a guess.
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