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I think this is likely implementation issues. Transplanting a different persons hand to your body that doesn't look like your hand probably would be quite jarring. If we could recreate an exact replica of someones hand then I doubt the same issues would occur. Ergo it is likely a technological problem that could be solved. Granted, it will likely take a long time to get to that state.

It's not necessarily about looks. People have had similar issues with heart transplants and other organ transplants, when they've felt afterwards like they weren't themselves anymore, or that there was something foreign about their body (which technically there was).

The uploaded consciousness or gradual brain replacement are pretty different from this case, though, it's true. So maybe these issues wouldn't exist or not exist in the same way, but philosophical issues of identity would remain.

When organs are transplanted today they were formed from DNA that was not your own, so it would not surprise me if there is some physiological reason that might explain why people feel that way. When I mention recreating a replica I don't just mean the appearance. An ideal exact replica would be an exact cellular recreation of the original organ or appendage. If we did achieve such technical abilities I'm not sure how anyone would be able to discern any difference. The only possible explanation I can see would be the simple knowledge that something had been replaced. (Kind of coming back to this being a perception that people hold in their head) Absent such knowledge, I doubt anyone would be able to discern that they are in fact not themselves.

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