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I'm an atheist through and through, but the one thing I'm unsure about is consciousness.
We basically made zero progress in figuring out what it physically is, how to test for it or how it is created, despite every single one of us experiencing it first-hand every day of our lives. That might be a sign that our physical understanding of reality is just not equipped to deal with this question.
On the other hand, if it has physical consequences then it must measurably interact with the physical world, and maybe it emerges from the complex interactions in the brain somehow. I personally just cannot imagine how the thing I'm subjectively experiencing as myself could ever arise from "dead" atoms and molecules.
The main reason I think consciousness is just advanced firing of synapses in the brain is because drugs can impact it, surgeries can impact it, flaws in the system can impact it.
If it was anything more than physical, these things wouldn't affect consciousness so easily.
Take those who have had their Corpus Callosum split. It's widely viewed that patients with this procedure end up with two distinct consciousnesses communicating with each other (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7305066/) which suggests to me that consciousness must be nothing more than the effects of complex physical systems in our brains.
If it was anything more than physical, these things wouldn’t affect consciousness so easily.
We know that it changes perception and behavior, because those are the things we can measure. We have no idea if it affects consciousness, because we don't even know what that is.
[...] which suggests to me that consciousness must be nothing more than the effects of complex physical systems in our brains.
The problem I have with these studies is that they all test the functions of the brain and its hemispheres, and then argue what the produced consciousness(es) could look like based on some preconceived notion of what a consciousness can an cannot do. But who says that one consciousness cannot make two different choices simultaneously for example? Ofc it's the best we have right now and imo very interesting and important work, but it's still nothing like actually "detecting" consciousness and analyzing its properties. The sad truth is that we still have no f*cking clue.
I know that this all sounds very ominous, but that's kind of the point. Consciousness as I'd define it is not just the mechanical function of the brain, but the experience of being "present".