The most important reason anyone is an atheist

[Neo-Scholastic]

And exactly what evidence do you have that physical reduction is true, especially since it is so strongly counterintuitive?

Strongly counterintuitive? You do realize that is saying that there must be more to my mind because my mind tells me so? Given the flaws of the human brain and its desire to perceive things in a manner that keep it at ease, saying physical reduction is counterintuitive is a bold statement that you can't possible defend properly.

Perhaps I was not sufficiently clear. By themselves intuitions cannot confirm that your understanding is correct. For example, the idea that space and time are absolute seems intuitive, but you know that in actuality they are relative (not only in Einstein's theories, but in Thomist philosophy as well). Objects appear to be solid, but at the atomic scale they are mostly empty space. And so on... In cases like these, what we commonly assume to be true is out-weighted by the results of many other inquiries.

At the same time you shouldn't ignore them. Intuitions can serve as a useful guide you in your acquisition of knowledge. For example, imagine you have two equally plausible paradigms. Which best describes reality? You can base your decision on many factors. Is the paradigm internally consistent? Does it explain more phenomena than others? What is the purpose of the paradigm? Etc. But also, does the paradigm go against our common everyday experiences? Based on your experience it makes sense to believe that other people have conscious minds, that the world exists independent of our own, etc.

That said, take a look at physical reduction. I call it strongly counter-intuitive because it goes against the way we commonly think and feel every day. Its determinism goes against you feeling and acting as-if you have the liberty to choose between alternatives. You recognize the identity of objects as they change over time, whereas in physical reduction everything is an undifferentiated continuum. You can attribute meaning to symbols and processes, whereas in physical reduction no physical process can have significance. You can watch animals engage in goal directed behavior, whereas physical reduction makes all actions inherently undirected, including your own.

In each of these examples, the difference between what you strongly intuit and what physical reduction demands is the presence of a knowing subject. You live as-if you are a You. That does not mean physical reduction is false. All I am saying is that materialism comes at a very high price because it undermines our humanity. As such it should be very well supported before living your life as-if it were the case. As a point of fact, I do not know anyone that actually lives their life as if they were an undirected and meaningless physical process. And if you don’t aren’t you kinda living a lie as bad as appealing to a non-existent god.