Yesterday I attended the wedding of a dear friend. The conversation with the person sitting next to me turned on the spiritual, I will paraphrase his point:
The first time I noticed the startling difference in the spiritual perspective was when my mother died. My sister, whose worldview is scientific, had a very difficult time dealing with the loss. As her death was sudden, she couldn't say goodbye. She left with many things unsaid. She would never see her again. My mother was torn away from my sister as an unfair act of an uncaring universe.
On the other hand, I dealt with the loss much better. In my understanding of things she is in a better place, I cannot speak with her directly, but in my wordless dialogue with God I ask Him to reflect the love that I feel for her, and I found peace in the fact that her spirit needed to be reclaimed suddenly without us being prepared for it. I won't say it wasn't hard, but the difference in our spiritual understanding made a world of difference in our grieving process.
His example brought memories of a conundrum very difficult to transcend in the transition from the scientific to the spiritual worldview. The transition does not represent an abandonment of scientific values, that would be regressing into a magical worldview. It threads both worldviews into a single stream in which both perspectives are valid.
The integration is not meant to be understood intellectually. In Plato's writing one encounters the word reason to refer to this concept, but it is not the discursive rational reason we refer to nowadays. The ancient greek concept is logos spermatikos (seminal reason), which is found in silence and not in discursive thought.
But--with reason--the rational person finds it impossible to compromise truth for emotional convenience. You may think "I am incredibly lonely and isolated. I wish I could have a friend and confidant like some people find in Jesus, but I won't believe in Jesus just because he makes a convenient imaginary friend". But, if pain pushes you a bit further, you may experiment:
"If I create a sandbox where Christ is real, and I have conversations with him, at least I can sense from experience how this feels", and so you may meditate for an hour or so, having a conversation with an all-loving, all-compassionate being who would love you despite all your flaws. "Ah, the things that this 'imaginary person' says to me is way more truthful than the horrible things which I say to myself. How is that?".
And so if a truth is recognized, the sandbox would grow a little bit each time you'd do this exercise. Soon you'll find vast expanses of sand and undefined borders in your sandbox. It may be that the ratio becomes inverted: you are mostly a spiritual person with moments of rational skepticism. The wise thing is become aware when each kind of cognition is necessary.