Hi,
I know this is quite a common objection to healings, but I don't ask it as an angry atheist, because I am genuinely wanting a good answer.
I don't want to be too presumptuous about a 'good' answer, but I have an answer that satisfies me.
I've noticed that effectively what God heals is disease or malformation (like congenital blindness). He heals what is already there. Let's say a person was blind because of a lack of a cornea. It's arguable that he wouldn't heal such a person.
In the meantime, the body may be seen by God as an integrated whole. So if a part is removed and permitted to die off: that's the end of that. God has promised to give us new bodies at the resurrection, but if we lose it or parts of it in this life, we'll just have to wait. What I'm suggesting here is that there is some underlying reality of the human spiritualised body ('integrated whole') that means that it doesn't make sense for God to regenerate limbs. What that is, I don't know.
Now, for an atheist, I imagine that my side-stepping answer is not satisfying. But note that at least there is a distinction between diseased and lost parts. That means that it's qualititively not the same kind of 'healing'. That opens this issue to 'stuff that god hasn't told us about'. And there's a lot of that and it's on that basis that God gives us opportunities to trust in him, which is a fundamental work of worship. So it's not correct of 'Why Won't God heal Amputees' website to claim that God is being capricious.
(Of course, such an answer may be enough for a Christian for another reason which is that after all, if we have real faith then we personally know God, so we know there is an answer even if we have to wait until death for it. We know that God must have a decent reason for not doing it. When I say 'real faith' I don't mean the atheist redefinition of faith "Belief without evidence" which is practically the opposite of what we mean by faith.)
So there is one outstanding question: if Jesus says that God will do anything for us if we ask in Jesus's name, then where are the healed amputees? Well, it's worth pointing out that while Jesus often doesn't qualify his statements in one place, he does in another. But even putting aside that, whatever we ask must make sense. We can't ask of him a nonsense, to put it more obviously. If it doesn't make sense then God isn't going to do it because logically we aren't really asking for anything. Did Jesus say that? No, but in talking to the apostles and the common folk he wasn't attempting a fully qualified and consequently long-winded philosophical discourse suited to a doctrate dissertation. He rather depended on their good sense to realise the obvious. And he's also left his representatives guided by the Holy Spirit to work out the details for future generations if they really need them.
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