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🌲 Obsidian is my Thinking Environment not my Second Brain

Obsidian is modeled on integrated development environments like Visual Studio Code, not neuroscience, and I prefer it that way.

Eleanor Konik
Written by Eleanor Konik

I write stories & articles inspired by all eras of history & science... so I wind up putting notetaking software like Obsidian & Readwise thru their paces.

5 min read.
🌲 Obsidian is my Thinking Environment not my Second Brain

Obsidian's tagline is "A second brain, for you, forever," but being honest, I don't really like the metaphor of my notes app as a "second brain." My gut? Sure, I understand why Gershon would call my gut a second brain, he's writing about nervous disorders of the stomach. But honestly, I don't even like to think of my computer as a "second brain," and arguably computers bear a stronger resemblance to a brain than a single app — isn't that the whole goal of artificial intelligence research?

I don't mean to be pedantic, but as much as I love Obsidian...

Obsidian doesn't do my thinking for me.

Obsidian doesn't make connections for me. More importantly, it doesn't do all the really important stuff brains do — it doesn't breathe for me, it doesn't regulate my temperature, it doesn't interpret things I see, it doesn't feel. Calling a notetaking app a "second brain" abstracts away all the essential parts of being human that don't count as "objective" "thought."

Maybe I'm bringing a little too much of my philosophy background into what is essentially a marketing phrase, but I'm always nervous around the hyper rationalist parts of the Western philosophical tradition that lean hard into the mind-body distinction and privilege the mind and the soul — preferably divorced from emotion and environmental stimulus — over our bodies and our hearts.

Besides, the metaphor lets us forget that...

our brains do more than record, reshuffle and regurgitate information.

I don't mean to be down on notetaking apps. I mean, I obviously love Obsidian. I've written before about how it's changed my life by encouraging a daily writing habit and helping me become the prolific author I've always dreamed of being.

But I really prefer the language of an integrated thinking environment to the metaphor of the "second brain," even though the latter is probably superior from a marketing perspective. Ryan's terminology riffs off  integrated development environments like Visual Studio Code, which appeal to an even smaller, more technical niche than backlink-based notetaking apps; software developers could make the connection between an IDE and an ITE to get the reference, but I certainly wouldn't have two years ago, before I'd been exposed to the Obsidian community.

I don't really love the term "Tools for Thought," either, since it's so broad. Offloading mental work onto external tools is something that humans have been doing for many thousands of years. If my notetaking app is a tool for thought or an auxiliary brain, then so is an abacus, and so is a Mesopotamian stele containing tax codes that people might otherwise struggle to retain.

And really, why would the notetaking app be the "auxiliary unit" instead of, say, the computer itself — which is exponentially more powerful, and more closely mirrors the capabilities of my "actual" brain, given that it interprets visual and audio inputs and even "sleeps."

But our brains are not storage devices. They are not neural networks. They are not separate from our bodies. Computers have a long way to go before they can mimic thought, much less all the other stuff brains do — and even the people most afraid of what AI could do to our world aren't claiming that brains are like computers or vice versa.


If a computer isn't a second brain, nothing is.

I guess I just have a different approach than other people. I believe that some people really do use their notes for passive synthesis — but my vault is more like a "digital assistant." I "communicate" with it when I tell it things like, "today, my throat was a little sore." I use it for reminders — I tell it, "hey, the next time I glance at this file, remind me that I need to take the trash out." I tell it "this quote could inspire a story, don't lose this" and "the next time you're in the mood to think about domestication, don't forget about this new discovery about donkey hybrids." It's awesome, and it's made me not just more productive — it's made me happier and more at peace with myself.

I have a good capture process for notes, I'm very organized, and I share my own original thoughts regularly. Tools like ResearchRabbit, Refind, Readwise, Obsidian and Ghost help with that. I have a digital slipbox where I write down claims and insights and ideas and link them to references and products to make it easier to trace idea chains. I have file after file of essays and articles in various stages of completion, extensively marked up and connected and organized for easy retrieval as-needed.

As much as I automate things, though,

none of my thinking is done by a tool.

Even with plugins like Graph Analysis, I never feel like I'm being presented with emergent connections — tho this is what the plugin is intended for, and I believe it works for other people. For myself, though, I usually just feel like I'm able to actually forge a connection between concepts, instead of having the same thought over and over again with no good way to record it for future rediscovery.

Sometimes I wonder if I'm doing it "wrong," since I've only been doing this for a year or so. I've been writing every day, though. I've exponentially increased my writing output, write short fiction and nonfiction every week, have over 600 notes just in the "slipbox" part of my vault, over 2,000 files, and 950,000 words worth of content. Quality matters more than quantity, of course, but there's something to be said for the idea that you can't get good at something until you actually do it. I've definitely done the "using Obsidian seriously for long enough to understand how it all works" thing, albeit not using any particular method or orthodoxy.

I've always believed that you shouldn't claim to really understand something unless you can explain it, and I can't explain how to use a graph view to discover connections (although I think the graph view is really useful). I don't really understand what it looks like to have a conversation with your notes.

Maybe for people who do those things, Obsidian feels closer to a "brain."

There's certainly something seductive about seeing our files-as-nodes as representations of neurons, the connections between them serving as synapses. And yeah, sure, it's marketing copy, it's a metaphor. But I guess what I'm saying here is that

my perfect auxiliary brain would not be a notetaking app

I know that a lot of people use tools like Obsidian to help them manage things like ADHD or age-associated mental decline. Obsidian can function like a prosthesis, but it can also be more than that.

If I were going to set out to design a second brain, it would probably resemble a fully integrated computer prosthesis, like the ones hooked up to Helva in The Ship Who Sang by Anne McCaffrey. Even then, I'd probably want something closer to Tony Stark's JARVIS, or the implants from Tanya Huff's excellent Confederation series.

Obsidian is great. It lets me puts all of my notes in one place, except that "place" is "every device I own." It is my source of truth, my repository of knowledge, my whiteboard, my workbench, my blank page. It's so flexible that I can almost always find a way to accomplish what I need — but compared to my actual brain?

It might as well be an abacus.

Note: There are a couple of affiliate links & codes scattered around, but these always come from links I was already recommending and usually I share them because they benefit you too (i.e. getting you extra time on trials).

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