Awhile ago I read a book by Charles Stross called Accelerando. It was a crazy Sci Fi story about the future of the human race as technology and innovation approached the point of infinity. It included uploading conciousnesses, intelligent AI personalities, space travel, you name it. Like most of Stross' work I find the ideas incredibly interesting and the characters and plot sadly lacking. Apparently a lot of people have contacted Stross under the assumption that he actually believes in all the stuff that appeared in the book and he wrote a really interesting piece about his thoughts on the matter. He is a firm atheist and part of his assumption about the idea of uploading human minds into computers is that it would be a worldwide disaster - both for religions and for those who would be caught up in the conflicts fought over the controversy. I can certainly see that religions would have a lot of tricky issues when it came to explaining immortal souls for human minds that can be infinitely replicated inside a computer but his scenario of religious cataclysm rings false.
Christianity has managed to decide that slavery is immoral, despite the fact that the Bible explicitly endorses it and the fact that it supported slavery enthusiastically for centuries. Christianity has managed to deal with the fact that the Earth goes around the Sun, heaven is not actually a physical location in the sky and weather is scientifically explicable rather than the product of a whimsical God. The church used to have a big say in who was king, when wars would start, what the common people would eat at every meal and who got to learn to read. All those things are long gone and the everyday man sitting in the church pew doesn't even notice that most of his life and knowledge directly contravenes church policy or theory from centuries past. The fact is that the vast majority of churchgoers have a thousand theoretical reasons to think that religious doctrine is bogus but the great majority of them completely ignore those reasons and continue on with their day. If you tell a person that they must forswear their religion they will often fight you to the death but if you offer them a convenient new product that clearly demonstrates that their beliefs are false they will happily buy it and ignore the theological consequences.
I don't think that the 'just upload your brain' day is ever going to arrive. Rather it will be a very gradual thing as we all slowly outsource more and more of our thinking and memory to machines. Gradually we will adopt biological enhancements that will feed us information from the internet, allow us to shop any time, make constant, instant communication omnipresent and help us remember everything we ever knew. At first the machines will be handheld but eventually they will end up being part of us and somewhere far down the road there will be so little human left that we will be able to say that a new species has been created but where exactly that happened will not be so clearcut. Presumably people of my generation will shake their fists at the young people and their newfangled implants and their moral decay in the same way every generation has been suspicious of the newest things and young people of the next generation. There are plenty of practical problems with uploading minds into machines that will take a tremendous amount of time and innovation to surmount but this is one issue where religion isn't going to have any significant say. The Pope will probably make a speech about how uploading your mind is immoral and everybody will continue to do whatever the hell they want anyway.
John Scalzi wrote about this too, and he has one line in particular that I like.
So, no, I don’t think uploading implicitly refutes the soul. It just means that if the soul does truly exist, it will have to live with you longer.
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