Obvious question (not related to the opener so let's keep it brief) everyone apparently failed to ask :
are you Satoshi Nakamoto? Why did you pick this name if you aren't?
Actually, this kinds of reminds me of Stanovich's Dysrationalia and also of Eliezer's "Outside the laboratory", if only more uncompromising and extreme than those two. Then again, I tend to have a charitable interpretation of what people write.
While they aren't separated, sometimes you have to make a choice of simplified models with certain boundaries because of limited computational power. See also the sequence about reductionism for more on that.
People also did this historically because some categories intuitively seemed more concrete than others. We're moving away from that because those categories have been explored thoroughly enough that we can see the links between them, and which new hybrid categories this points to.
But, yes, you're right, the frontier is moving, and cool stuff awaits beyond.
I think this is the best piece of advice overall. You are likely not going to convince your father, whose opinions probably even predate your birth. The real thing at stake here isn't scientific truth, and trying to convince him is to fight the wrong battle.
People have a lot of beliefs they don't feel the need to constantly justify to others, and I think it's an accepted social convention to seek shelter in that principle. Being evasive and using relativism can help : admitting you can't be sure about science and evolution is an acceptable compromise if you can trade it for the opposite fact that your father and people like him can't be sure about God either.
Once swamped in such a position on both sides, you can also simply chose not to pursue the argument further, and believe your stuff "just because I feel this is the truth", the same way they do for their own stuff, at which point it would be hypocritical for them to still try to convince you they're right. This may not seem like a "truth seeker" thing to do, but you're playing by his rules already anyway, and in his world, truth may not have the same meaning as it does in ours.
Also, trying to justify atheism like this feels like you're playing a game where you've both already agreed tacitly that atheism is the side of the argument that has the burden of proof, which it hasn't. Once again, don't fight on your father's ground with weapons adapted to your own. Either use other tools adapted to this battle ground (where truth is relative and backhanded arguments will be used), or move to another battle ground adapted to your tools.
We see the world, not the way it is, but the way we are.
Talmud
edited