I started wondering where does the soul begin (physically and temporally), and when does it end? I've found this topic to be very interesting to me. And it's something that's always been in the back of my mind as I've studied biology and religion. And after years of pondering, I think I have my answer.
One of my favorite passages from the Bible describes God molding us in the womb, like a potter with a clay masterpiece. And it says before we were formed, God knew us. It's such a beautiful message, and it leaves me with no doubt that the soul is created before we were physically made, and put into our human form at the moment of conception.
We don't have any memories as a baby, and I'd say that babies can't think rationally. Any actions are probably out of instinct, like crying when they need something. Does that mean that the soul inside us is worthless as a baby? I'd say no. Humans consist of two properties: the flesh and the spirit. Our soul is timeless and makes up our spirit. Our mind (and being able to think) is part of the flesh along with the body.
Here's how I define the difference between our mind and soul. The mind is part of the flesh and not the spirit because some are born with genetic deficiencies, and others have debilitating injuries. For example injuries to specific parts of the brain will cripple some specific aspect of rational ability such as long term memory, being able to recognize faces, being able to understand sounds as words, being able to understand written characters as words, etc. It's painfully clear to me that our ability to think is confined to the here (physical) and now (temporal). Some people want to believe that their memories and rationality are eternal; that their mind is more than their body. I used to want to believe that too, but I can't deny what I've learned in neuroscience. For example... sometimes you smell something and you get a random memory. It may not be a flashback, but you get a feeling of an emotion from some time in your life. Sometimes when I use Clearasil, the scent gives me emotions and excitement of being a teenager again. The reason this happens is because the area of your brain that processes smell is related to the amygdala, the part of your brain that is in charge of emotion and memory. Speaking of which... do you wonder why women have better memory of fights and "keeping points" than men in a relationship? They are more emotional, which hyperactivates this part of the brain. Almost anything we think or feel can be explained by neuroscience. Our minds are always changing, it can't be the eternal soul. Tomorrow you will be a different person physically and mentally than you are today. It's only the soul that is the same. Therefore I believe the soul, being eternal, is separate from our ability to reason.
I would define the soul as the part of us that chooses whether to sin or not. This leaves no excuses for our behavior. You can't say you aren't liable for beating up someone due to roid rage or PMS, you still have a choice. The mind allows us to weigh the factors on a decision, and the soul is the final decider. When we sin, we know it, and in that moment we would rather do the sin rather than follow God's rules. The idea of a "conscience" is the part of our soul that tells our mind whether something is right or wrong. Our soul gets judged by God at the end of our lives. God may be tough, but he is fair. God judges us on what we know, what we choose, and every little factor.
As an example to show the difference between mind and soul, what happens to a person that gets severely damaged in the head and loses most of their intelligence? Of course the "mind" takes a nosedive, but the soul is still there and still the same. Their ability to do great things in life is gone, but so is the ability to commit horrible evils. Their range of behavior is greatly restricted, but they can still choose to do good or bad within those restrictions.
This goes back to my earlier point that a soul is judged based on what a person knows and the conditions they are in. In math terms, it's not the absolute value but the relative value. Of course an adult can do more absolute good in the world than a child, but who loves God more? A child can glorify God by loving their parents and laughing. They are without sin. Their relative rate loving God is 100% and it can't go any higher. Whereas an adult could be a good Catholic but still only love God at 25% of what they are capable of. Who is greater? The child is. I think that's what Jesus meant when he said we must be like children to enter God's kingdom. The relative rate is what matters, the mental capability does not matter. For example, Saint Ignatius (founder of the Jesuits) was more intellectual than Saint John Vianney (who struggled through seminary). But they are both saints because they gave 100% in their own ways.
Some people say life isn't fair. I'd agree, but I would phrase it as life is random. We don't get to pick our physical bodies. But that doesn't mean you can't work out to be in as best shape as you can. In the same way, we aren't given equal intelligence and reasoning, but that doesn't mean we can't try our best to glorify God with our lives.
Our soul is the part of us that reaches out for God. It doesn't matter the state of our mind or reasoning, what we do with what we can do is all that matters. For example, Pope John Paul II spent the last years of his life mentally wasting away due to Alzheimer's Disease (and also Cha Nghiem). As their mental capabilities eroded, do you think they loved God any less? Of course not, if anything their love increased.
Another difference is that we can only attain faith through the soul, not the mind. Faith comes to the soul through the Holy Spirit as a grace. There's no way to find God through reason (aka science). In my opinion, years of philosophy and theology will never give the same happiness and inspired purpose as a simple sight at the beauty of nature. I will never argue with an atheist that God is in nature. I'm just saying that these are the little tidbits that God graces us with. It's these little things our souls tell us that God exists. And then we have the free will to follow God or not.
So when does our soul depart our body (and mind)? Some probably think when our mind is gone. But I think the soul stays there, even with mental degradation. It only leaves when we're dead, mentally and bodily. So even if someone transforms into a vegetable, their soul does not lose value. And since our souls are connected to bodies while we're alive, the value of a life is infinite no matter how bad it gets. We need to leave it to God to decide when a life starts and ends.
I'm not really trying to prove a point, I wrote this just because it was something of an "Ah hah!" moment for me, and I wanted to share my thoughts. But if you're looking for something to satisfy you after reading this long post, I would say I just made my case against abortion and euthanasia. But for someone who doesn't believe in God or souls, this argument wouldn't matter.
Here's something else that I'm curious about. If I have Alzheimer's and die and go to heaven, what state of mind will I have? Will I be at my most intelligent? Or will I be simple? To answer this, I bring up another common question that has a good answer. If a good man remarries after his first wife dies, who will he be with as his wife in heaven? The answer is neither. He will be see both of him, but heaven is about happiness due to being with God. Earthly things don't matter. All three will be infinitely happy, but not because of each other. Similarly I think when we die, we will be blessed with not only God's love but God's wisdom. We will understand everything. And so we'd probably be more knowledgeable and wiser than we ever were on earth.