I don't think that there is any good reason for the spirit to be terribly conflicted with reality.
Thank you for making my point.
You're just cold, Bubba...
While it does come in useful at times (business, troubleshooting, survival in complicated circumstances), it's not how a lot of other folks are going to be centered. It was once explained to me that there are "visual people" and "audio people." "Visual people" need to see something in order to comprehend and remember it best while the primary sense for "audio people" is obviously through sound, so they work better hearing something. I have found that I get it far better by reading it or seeing it. Take a hypothetical situation where an audio person is trying to communicate something to a visual person with words and it's just not working. Frustration starts building up and first thing you know there's an argument.
By the same token, there are people who process logically and others who process emotionally. For some logical people, the group labels could be changed to "smart" and "stupid" and they'd think it more accurate, albeit pedestrian.
Since your original question (the subject of the thread) appears to ask whether our consciousness is the result of the individual particle vectors from the Big Bang (and therefore have all the meaning of the structure of a DvD that just happens to have a movie recorded on it) or if there's something... more, then it seems to me that your science has failed to give you an answer that some side of you is thirsting for.
Don't suppose you ever saw STAR TREK: THE MOTION PICTURE, didja'? The underlying theme is the same question. Crap, this enigma has been asked a thousand thousand thousand times (and then some) and for a loooooooonnngg way back. While "Cogito Ergo Sum" seems a pronouncement of conviction, if a person REALLY has to SAY it, then you GOTTA' wonder if that person had his doubts and NEEDED the mantra to get through the day.
How many countless times has a male engineer or architect done his day's work, pounding on the calculator keys, designing wonderful creations of steel and stone only to come home to his wife, cower to her scolding him to take out the garbage and pick up his &@#% socks, and then later to find the true meaning of life in her bed? And a few months later to marvel at the wonderful creation of the child she bears, something that all of our science is unable to explain. It wasn't the thought process that did that, it was emotions and spirit lashing through flesh and blood.
Now, if you seriously want to go looking for the essence of
that, you have quite simply got to factor in the idea that spirit IS reality because if you demean that side of this question, you will likely go to your grave without an answer.