Interesting topic! 3 comments...
1. Nature of Emergence
I like to start simple with the analogy of waves of water.
A wave is composed of water molecules, but takes on an emergent existence of its own described by wave equations that don't involve the underlying water molecules.
It's possible that the wave transmits energy and information, described by wave equations independent of the physical system it's waving in, and you can even see the shape of the wave traveling as some entity on its own (think tsunami wave), but each individual water molecule itself only oscillates in a local area and is not an individual sub-wave(let).
What is the nature of the wave? Is it an entity in itself? Why is it that the smallest unit of a wave is not a tiny wave, but an entirely different thing altogether: a water molecule? Same goes for waves can in molasses, plasma, liquid nitrogen, and other liquids.
Similarly, a computer program takes on an existence above it's lower level, think of a word processing program written in C, Python, Java, etc. A piece of music that's not comprised of its individual notes or specific instrument.
Following on these ideas, could the soul or consciousness be emergent like a wave or a program and takes on a different nature of its constituents?
2. Physics is Incomplete
Just what exactly is Dark Matter already is enough of a mystery that may upend the foundations of physics. We still don't know what it is and it could very well force us to revise most of our physics.
3. Physics and Metaphysics
It's very exciting to think metaphysics beyond what exists in physics, so long as we are explicit and clearly demarcate what exactly is physics, a empirical science that depends on measurable data ...and what is not.
Sometimes it's hard to tell what is science and not, such as the Everettian quantum multiverse. This classification of Science vs. not can be full-time philosophy of Science even for definition.
It's also important to acknolwedge that there are question and ideas that are beyond physics, even in principle, such as the issue of where physical laws came from in the first place, and this properly belongs in metaphysics and philosophy, just like issues of what constitutes human value, meaning, freedom, and other abstract ideas that can't be addressed by Science.