Some disagreements can be settled by science. What is the chemical composition of this cookie? Ask science. Some questions cannot be settled by science. To give one simple example, math questions are answered by scientific investigation.
So far, so obvious.
Science herself cannot choose between big ideas regarding the makeup of the cosmos. Take idealism and materialism/physicalism. Either big picture of reality could be true and everything science finds also true. For example, science could proceed just as it does now if everything was (fundamentally) an idea in the Mind of God or if everything were matter and energy.
We might think one (say idealism) has less of a problem with a phenomenon like consciousness. Ideas in a mind are fundamental in some forms of idealism, so there is no mind/body problem and consciousness is just what it seems to be. On the other hand, physicalism fits another intuition: matter is “stuff” and not “just” an appearance. That might suggest dualism: both ideas/mind and matter exist. Dualism is attractive, but has the problem of how the immaterial mind and the material bodies interact (in people and the cosmos).
The metaphysical assumptions we will make will be informed by how we think science works, what we think science shows, but nothing science finds is likely to give us a final reason to pick between the three.
How can we choose?
We use metaphysics to examine our personal experiences. For example, if we have an experience of God, then we might explain that experience without needing a God as a materialist or we might provisionally accept it as an idealist or dualist*. One way to determine if our experience of God is rational or as it seems would be to look to philosophical arguments of all sorts.
If we have a powerful experience of God and find arguments for God’s existence sound, then we could then ask questions about how we think God relates to the cosmos and humankind. If we began with a religious experience, deism is unlikely to be true, so we might proceed to see if one of the world’s religions best explains the God of philosophy and of our experience.
I think philosophical arguments point us to monotheism and so the great monotheist traditions merit attention. There are many arguments, experiences, and possibilities here, but if one is to become a Christian the central figure is Jesus: his life, teachings, and divinity. If one combines an experience of Jesus and reasons to believe, then a person can proceed to other issues and choices.
Naturally, this is not an argument for any of these moves, just that the adoption of a big idea has implications for many smaller ones. If there is no God, Jesus is not God. Of course, it could be that the evidence that Jesus is Divine is so compelling that the argument works both ways: If Jesus is, then God is.That happens sometimes.
However, this is not always true. Sometimes a phenomenon can be interpreted differently depending on our starting point. Miracles are well documented. However, if one is a naturalist, then we can invoke either naturalistic explanations and will prefer them, however, convoluted or simply invoke a naturalism to fill gaps in naturalist knowledge. “We don’t know how this happened, but we know it is not miracle!”
A miracle can happen, prayers can be answered, and these event only be compelling within a theistic framework! They may not compel a major change of belief in a physicalist. Why? Any given set of miracles is generally too small to overturn whatever metaphysical reasons that caused a person to choose materialism. This is predictable even if miracles happen, since God set up a universe that is law-like with exceptions to patterns that must be fairly rare!
Of course, if everything (mind, consciousness, all miracles) had compelling material cause or explanation, then no rational person could be a theist. Mathematical objects prove this is not true. Many atheist mathematicians find the arguments of the immaterial existence of math objects persuasive and so are not materialists!
In any case, there are many phenomena that by nature might be tentatively accepted by a theist (exorcism), based on many other beliefs that are much stronger. The validity of exorcism or the evidence for demons is, however, not useful in proving the bigger ideas. These beliefs are secondary.
In short, some phenomenon may exist and be subject to different explanations. The “facts” themselves will not determine which is best, but the assumptions one brings to the investigation.
An idea (X) might suggest an explanation (Y) for a phenomenon that is plausible if X is true, but not at all attractive if X is not true. The plausibility of Y depends on X and Y does little to make X more likely.
Some Christians (and more than a few Internet atheists) miss this relationship. I have met Christians who think every claim in the Bible (understood woodenly in modern terms as translated in English!) must be true or as likely independent of any other.
Instead our beliefs are like a spider web (pardon me WV Quine!) with some beliefs connecting us tightly to external reality (metaphysical and physical) and other beliefs keeping our web coherent and whole. Some strands are merely off shoots of the greater strands and do little work in either direction . . . They are provisional indeed!
A kind of fragile thinker looks for “killer arguments” that will force those people to join our team. Thank God that God allows us liberty to think, examine, consent. My best take on my experience of Jesus, the arguments, and supporting evidence is that Christianity is true.
God is there, God is not silent, but God is hidden enough so that we are not overwhelmed. We can choose. Thank God. My job is to keep thinking, tell you my experience (Jesus is wonderful, even if I am not!), learn from you, and leave the rest to God.
*Neither an idealist or a dualist must be theists.