I don't get the second brain thing. I don't keep a second brain, I just read and think a lot. I once did a physics masters and, when asked how to make steady progress, one of the professors (who had published with Paul Dirac no less) made the comment "well, my secret is that I think about physics all the time"
I started practicing this for the stuff I'm interested in ... and the result is that I generate a lot of ideas. 99% of them are garbage.
Before AI, a conversation with colleagues would help me weed out the garbage, and possibly give me a new perspective ("here's something surprising about what you just said!")
Now, AI plays a helpful role in helping me weed out the garbage for the subset of ideas that I can test empirically -- and sometimes it does give me a new perspective, but with significantly more noise than my colleagues, who would take me right to the point that would be useful for me to see.
I've never felt like I needed a second brain ... because if I had such a thing, I think I would be keeping the 99% garbage around -- instead I just let biology GC it.
A key part of maintaining a second brain is revisiting and pruning it. Much like a todo list, without that practice it absolutely just accumulates bunk.
So I operate more in line with how you do, but having tried some organizational systems I think I understand the "second brain" people.
One, it forces you to do a crude approximation of critical thinking. It allows you to examine and organize your thoughts, either physically or digitally. It isn't the same as being able to sit and break something down in your mind, but for those who struggle with that, a "second brain" allows them to reap some of those benefits.
Two, it allows you to turnover things quickly in your head. By training yourself to immediately dump out an idea into an organizational system, you don't have to hold so many things in your head. Furthermore, words are immutable and the thoughts in your head aren't.
But for me, the good thoughts usually rise to the top. And there are a lot of things I'm thinking about that are so vague, it's just a feeling. And trying to write those down robs those thoughts of the long term, "on the backburner" mental processing they need to become actual ideas. They're thoughts that are still in the embryonic phase. I can't write down the qualia of them, and when I try to I move them into a "second brain" I lose it.
I think organizational systems are work dependent. Running a business lends itself well to an organizational system. Where it's good to try a lot of shallow things. But something like physics, for example, requires playing with ideas in your mind over a long period of time until they become solid enough to chase more seriously.
I think programming probably straddles that line and it depends on what you're doing at any given time.
Hey, love the hivemind comment to mine. Maybe we do have kind of a second brain...? /s
How do you take notes, generally speaking ?
I don't think I do the second brain thing well but keeping some detailed notes (using a daily note at a scratch pad for one off queries, small scripts etc) and occasionally branching them off into dedicated markdown files like "Database debugging" or "MongoDB" has saved me a lot of time on aggregate.