Why Sacrifice the Bad Metaphysics, When You can Sacrifice Reason?

Can you recognize the following scheme?

1.Have a bad metaphysics
2.Interpret the scientific results through the prism of this metaphysics
3.Deny that you have metaphysics, but think of the interpretation as the result of the science itself.
4.When the resulting metaphysical picture doesn’t make sense, blame the reason itself!

By bad metaphysics I think here of the metaphysics where what is taken as ground of all phenomena is little self-subsistent particles, with their self-subsistent properties existing in the self-subsisting space-time container, and where some self-subsistent physical laws (which are seen as more or less arbitrary, so that it is just matter of some incident that they are such as they are) control what happens with the former.
The combination of this metaphysics with the empirical results has given us all kind of strange results in Relativity and Quantum Mechanics, which are said to be “unintuitive”.

And instead of being critical of this “invisible” metaphysics, what is done?

It is said that evolution tends to select useful traits. Our faculty of reason is nothing more than such a trait. It is selected for reasons which are connected to our staying alive and reproducing in particular environments, so we are not to expect that it is infallible and if something doesn’t make sense to us (even under our ideal reasoning), doesn’t mean that it is impossible in reality. We are not to wonder why we get weird results “from science”.

So, instead blaming bad thinking, we are to blame the thinking in general!

I’ve quoted Hegel on this once, by I think it is worth repeating:

At present, students of nature who are anxious to avoid metaphysics turn a favorable ear to Atomism. But it is not possible to escape metaphysics and cease to trace nature back to terms of thought, by throwing ourselves into the arms of Atomism. The atom, in fact, is itself a thought; and hence the theory which holds matter to consist of atoms is a metaphysical theory.[…] The real question is not whether we shall apply metaphysics, but whether our metaphysics are of the right kind.