I guess from the Pope's point of view, from what I understand, the reasoning was that if god made humans with a soul, and god also made animals, so they have a soul too purely because god made them.
That would be a faulty point of view though, considering God made humans in His image. That in itself should set us apart from the animal kingdom.
I wonder if the belief in everything having an energy does come from the science of energy not dying?
My understanding of everything having an energy (note:frequency) comes from the Bible, not science. When Cain killed Abel, God said that his blood 'calls out' to him. In Psalms David says that the heavens 'declare' the Lord's glory, and somewhere else in the Bible somebody says that even if believers were stilled, the rocks would still 'cry out' praise. Everything has an energy to it.
The way humans are made of all sorts of minerals that have lasted for millions...billions of years before they were formed into humans, and when humans die, those parts are reabsorbed and become a part of another lifeform. That kind of thing? Almost like a Lion King's 'Circle of life' moment