My rejection of the soul came from the study of science, and relates to the question of life
The first shock came with the study of bacteria, when I learned about
lyophilization. Take a bacterial culture, add 10% glycerol, freeze it in liquid nitrogen, and then sublime the water. You're left with a dry powder that you can store at room temperature indefinitely. It doesn't metabolize, reproduce, move. It just sits there, for all intents and purposes dead. Add water, and it becomes living bacteria again, just like before you froze it.
Then there are viruses. The simplest are little pieces of DNA or RNA in a protein coat. No machinery to reproduce, respire, move. Bind them to a receptor in a cell, they get internalized, take over the cell's machinery, and start cranking out copies. Are they live? are they dead? If they aren't dead, how do we "kill" viruses to make vaccines?
Then I learned about all the stuff in between. The obligate intracellular parasites, that look like cells but lack the ability to grow on their own: sort of like a half-cell, half virus. Or the defective viruses like Hepatitis D. It's not even a complete virus: it can only reproduce if coinfected with hepatitis B. Or transposable elements, which act sort of like viruses inside a cell, and can "jump" from one site on the DNA to another, but couldn't independently transfer between cells. Or plasmids, little mini-chromosomes, some of which can code for their own transfer and some of which just hitch along with the cell's machinery. Just about any way there was for a piece of genetic material to reproduce and disseminate itself, it existed somewhere in nature. Life and death, it seems, was not a black and white thing.
So what does that have to do with the soul? Well, the second shock to my beliefs came when I started to think about embryology, in particular IVF and the quintessential question in the abortion debate: when does human life begin?
Take an fertilized cell. grow it up to the 64 cell stage. Is it alive? certainly. Now split it into 4 embryos. Each can now grow into a complete organism. Or remove a few cells. You could grow them into a new embryo, or destroy them for genetic testing. You probably see where this is going: does the first embryo have a soul? if so, did I create new souls when I split it, and destroy one when I did the genetic testing?
We can go one step further. After the embryos have split, we can fuse 2 back together. They will grow up into a single organism, a mosaic of the two original embryos. Did I destroy one of the souls? Did I create a hybrid soul, half of each?
And just to bring everything full circle (almost). I can now take those embryos, mix them with glycerol, and freeze them in liquid nitrogen. I can't suck out the water and bring them back to life like I can with bacteria, but I can keep them suspended, frozen, inert, not metabolizing, not dividing, for years. For all intents and purposes dead. And then thaw them out and bring them back to life.
One final set of experiments. We certainly have the technology to synthesize a virus. We could synthesize a piece of DNA in the laboratory, synthesize the protein capsule in the laboratory, mix them together in the right conditions, and I have no doubt that the virus we created would be just as functional as the "natural" virus that we copied. Clearly, doing the same with the much more complex bacterial cell would be a technically much more difficult task, but I have little doubt that if we could get the DNA, protein, lipids, ATP, etc. all assembled correctly that our cell would be just a viable as any bacteria. I don't think we need any good fairy to wave a wand to bring it to life. And although a human cell would be another order of magnitude or two more difficult than a bacteria, I have no doubt that if we could get all the molecules in the right places we could create a living human cell as well.
So where is the soul supposed to live? If humans are supposed to have them from the time that the cell is fertilized, as the pro-life advocates would like us to believe, then don't I have to believe that dog embryos have souls as well, and then why not bacteria? What is special about a set of chemical reactions that it spontaneously creates a metaphysical soul, especially one that lives on after the chemical processes that created it have ceased?
I couldn't think of a good answer, and was thus forced to discard the concept entirely.
Sorry, that's the best I can do at 2 AM. I hope it makes sense in the morning.