It seems you first need to show that spirit exists before proposing it in science as an answer to anything.
I'd say that it was enough to propose that spirit exists if one has an observation not explainable without the idea. Here's the sine qua non of calling something real or actual: It has to be detectable in space and time as some sort or interaction in some place at some time with other real things, even if only a ping on a Geiger counter. Real things can do that. Things that cannot be detected at any time at any place by any means should not be called real, or existing.
if people want to claim things about Gen 2 I don't know how I can rebut them.
If you know where and how they are incorrect, it's because you can demonstrate that, but if they are correct, you cannot successfully rebut them. That's the power of rebuttal (debate, dialectic) and the reason for the impotence of all other forms of dissent and why it doesn't persuade those who require sound argument before believing. This has been an extremely difficult concept to share with the faithful not experienced in critical thought. I don't expect such people to master that over night or even ever, but it would be nice to see somebody that would even consider that possibility, or be able to repeat what is being claimed. But perhaps that's an unreasonable expectation. If so, I can't say why. I can't say why I never see it.
I was referring to God in timelessness. God's knowing probably replaced a need to think and work things out over time.
God knowing replaced a need to think? Is this god considered conscious? Does its mental content evolve like occurs in conscious minds as they observe and assess the parade of conscious content? If it does either of things, it exists in time. Why is that anathema to an Abrahamic theist? Is it because you'd like to say that God created time? If so, that's as incoherent as claiming that God created consciousness. Creation occurs over time, and nothing could be the intelligent designer of consciousness. Think about that for a moment. Intelligence implies consciousness already in existence.
they are abstract things that do not take up space.
Ideas exist in conscious brains and presumably are distributed through and/or around them.
It was Christianity that promoted learning over the centuries and which started the first universities.
Christian scripture had nothing to do with the advent of science or universities or their liberal arts curricula. Christians and the church are capable of adopting humanist methods and doing the same work, but the neither the work nor the inspiration for it come from biblical doctrine. Newton was a Christian, but his lasting contribution to mathematics and physics has nothing to do with his Christianity.
Principia could have been written by an equally gifted atheist up until the part where Newton actually does inject a Christian idea into his celestial mechanics. Newton's math predicted that larger planets would toss planets like earth into the sun or out of the solar system, and so, he added his god ad hoc right where he ran out of knowledge, who was needed to nudge the planets back into position. That's where Newton jumped the shark and began adding useless faith-based ideas. That was the Christian part. Then, a century later, Laplace supplied the mathematics Newton lacked, restoring the solar system to a clockwork needing no intelligent supervision.
It was Christianity from which the more profound implication came (and to which you refer) and possible without which, the study of and testing of nature might not have begun nearly as early.
So you have already claimed. Where's your evidence. Where in the Christian Bible does that idea appear. Did Moses make that claim? Abraham? David? Jesus? Paul? None did or advocated anything like rationalism. Christians began experimenting with it in the Middle Ages (scholasticism) after reacquiring classical learning from the Arabs, who had saved Thales, Pythagoras, Plato, Aristotle, and Euclid. But what did they add but a bunch fallacious "Proof of God" and a head count for angels dancing on pins?
Observation was added by Christians, notably I hear of Francis Bacon who is seen to be the father of empiricism.
It isn't a Christian innovation just because a Christian thinks of it as we just saw with Newton. And empiricism is the enemy of wrong ideas.
Are you saying that deism and atheism were not tenable before science?
Yes. They wouldn't have been for me. The first wave of scientists showed us the clockwork universe, where heavenly bodies move without gods or angels pushing them, gases equilibrate without any intelligent oversight, and electrons move through circuits unaided. This ushered in the age of deism, where the ruler deity was no longer needed. But how did this all get here? The builder god was still needed, but not thereafter. Then the second wave of scientists showed us how the cosmos and the tree of life assembled themselves without intelligent oversight, making the builder god no longer necessary, and making atheism tenable. It became very reasonable to believe that no god was involved in any of it.
But a naturalistic mechanism for things that were previously seen as things that God did, does not push God aside or the need for God.
It squeezes him into a narrower gap. And there is no need for a god in any scientific theory. What would it be required for? What would its job be if building and moving the world can occur without one? If one has already decided that such a god exists and was involved in creating our universe, he'll want to find a job for it - one only an intelligent designer could do. There is nothing like that. None of the unanswered questions in science require positing a god. Agreed, that doesn't rule gods out, but that's not reason enough to add them to science. Mere possibility isn't enough.
You talk science as if belief in God is and should be a matter of science.
For a critical thinker, all belief should be empirically justified.
He was saying that if you aren't going to believe in God because of nature, then God will not do a miracle especially to convince you.
His words were, "God never wrought miracle, to convince atheism, because his ordinary works convince it." He was saying that no miracle is needed to believe in God, that sufficient evidence exists in observing nature.
So I am automatically wrong even if I am right?
You are not believed until you demonstrate that you are correct according to the rules of those you are trying to convince. Motivated reasoning violates them. It's what anybody trying to be convincing who doesn't respect humanist values does. We see it in Putin in his explanations for why he had to attack Ukraine in defense (does anybody believe that apart form somebody biased in favor of Putin or Russia?). We see it from Trump in his litany of excuses following the exposure of the Stormy Daniels hush money payments and stolen classified documents. If you are correct, you don't need to resort to specious argumentation.
I think you show a case of "motivated reasoning".
Show me where any of my reasoning is biased in any direction apart from a bias for sound argument, which is a rational bias and therefore desirable, such as a bias against drunk driving. If you are correct, you can do that. If you are incorrect, you cannot.
You're a Christian apologist. You are biased in favor of your god existing and scripture being from it, which belief is not rational but rather faith-based, and your agenda is to promote that belief.