"Abstracting" means extracting the commnon parts of multiple instances, and making everything else a parameter. The difficulty for software is that developers often start by writing the abstraction, rather than having multiple existing instances and then writing code that collects the common parts of those multiple instances into a single abstraction. I guess that is what "refactoring" is about.

In sciences and humanities abstraction is applied the proper way, studying the instances first then describing multitude of existing phenomena by giving names to their common repeating descriptions.

This matches my "ideal" way of writing software, which is something close to "reverse waterfall". Start with the non-negotiable truths at the lowest level, then work your way up towards the goal, which is sufficiently defined. As you go, the patterns became apparent, collapsing into nice abstractions.

The code always ends up nice and clean and modular. And, since I'm working towards the idea, I can say "here are the modular pieces I have to work with, dictated the fundamentals beneath, how do I use them to accomplish the task?". When working from the idea, I think it's easier to want to write something to achieve the immediate task, in a "not see the forest for the trees" kind of way (abstractions are about the goal, rather than the reality under). Of course, both directions are required, but I get the best "separation of concerns" going in reverse.

I call that lasagna code! From what I've seen, developers start with spaghetti, overcompensate with lasagna, then end up with some organization more optimized for the human, that minimizes cognitive load while reading.

To me, abstraction is an encapsulation of some concept. I can't understand how they're practically different, unless you encapsulate true nonsense, without purpose or resulting meaning, which I can't think of an example of, since humans tend to categorize/name everything. I'm dumb.