It's important to note that talking about the world in terms of atoms and quarks is just using a particular language. The principle of Turing equivalence is relevant. (One weird idea is to talk about how many equivalent-of-bits it takes to specify the equivalent of Turing equivalence for the equivalent of a Turing language. "Analogy" is a cluster of confusing concepts!) Talking about souls isn't taboo, and in fact I find it useful sometimes. The important part is having an accurate model of the world such that you can make correct testable predictions, and in fact that's only important insofar as it helps you make correct decisions. Unfortunately, figuring out what "correct" means is an incredibly hard problem, and the language of moral absolutes is only so helpful. The important heuristic for using languages is to avoid the mind projection fallacy and instead remember that all maps can be inaccurate, including maps of maps.
Background
I was raised in the Churches of Christ and my family is all very serious about Christianity. About 3 years ago, I started to ask some hard questions, and the answers from other Christians were very unsatisfying. I used to believe that the Bible was, you know, inspired by a loving God, but its endorsement of genocide, the abuse of slaves, and the mistreatment of women and children really started to bother me.
I set out to study these issues as much as I could. I stayed up past midnight for weeks reading what Christians have to say, and this process triggered a real crisis of faith. What started out as a search for answers on Biblical genocide led me to places like commonsenseatheism.com. I learned that the Bible has serious credibility problems on lots of issues that no one ever told me about. Wow.
My Question
Now I'm pretty sure that the God of the Bible is man-made and Jesus of Nazareth was probably a failed prophet, but I don't have good reasons to reject the supernatural all together. I'm working through the sequences, but this process is slow. I will probably struggle with this question for months, maybe longer.
Excluding the Supernatural was interesting, but it left me wanting a more thorough explanation. Where do you think I should go from here? Should I just continue reading the sequences, and re-read them until the ideas gel? I'm coming from 30 years of Sunday School level thinking. It's not like I grew up with words like "epistemology" and "epiphenomenalism". If there is no supernatural, and I can be confident about that, I will need to re-evaluate a lot of things. My worldview is up for grabs.