One of my favorite uses of Devonthink was during some continuing education courses for theology. At the end of 6 weeks I would dump my reading notes, essays, lectures, etc. into devonthink and use it to write my final paper. It made it so much nicer to surface those connections. Then I could leave it in there or move it out.
I think that was nice because it was a project, and I could move stuff in and out as needed. Sometimes these research apps seem amazing, but also overwhelming. It’s kind of like when you learn to program and they say you’ll do much better if you already have a project, same with something like guitar.
I enjoyed this talk (full disclosure: I am an academic especially interested in research apps), so many thanks for this!
And since @MacSparky talked about the emergence of the “Zettelkasten” approach, let me add a few facts and links (David, I hope you’ll find that interesting!).
The “Zettelkasten” is named after the enormous slip box (which is the literal translation) that Niklas Luhmann, a professor of sociology at the University of Bielefeld in Germany (not Austria!), built up over three decades of academic work. It encompassed some 90.000 (!) slips which were hand-written or typed up. Each has a designator (akin to a unique digital key), and there was a complex system of linking between slips.
Luhmann claimed that his slip box was able to communicate with him. Since he defined “communicating” as “being able to surprise”, this was certainly true – similar to David in MPU 559 talking about “organizing serendipity”.
Luhmann died in 1998, and the University of Bielefeld has tried to preserve the Zettelkasten. A long-running research project has recently managed to digitize it, and there are some webpages that those interested in “Zettelkasten” may find fascinating (only some of it is in English, but the pictures of the “Zettels” may still be interesting):
I would disagree a bit on the Obsidian fitting into Gardener mindset primarily. I think it’s also got a lot of Librarian features with the ability to store lots of data and get to it easily. Although the structure does tend to grow more organically than in DEVONThink, unless you’re like me and sunscribe to the Usenet method of developing a filing system.
For years I’ve used (* comment *) in all my text writings (Showing my Pascal foundation) It’s also a rarely used sequence of characters so easy to search for and repalce with something else later.
I tend to agree with you. But I am finding that I am slowly gettign used to it with my Obsidian use case.
Finder is great when you know exactly what you are looking for but IMO falls flat on its face when trying to create links across structures or need to find small things you kinda remember but yoru memory is faults. Indexed folders in DEVONThink tends to solve most of those problems.
I’m finding the Kettelkasten method very helpful in documenting and tracking the use of SNPs vs Microsattelites vs mitochondrial DNA as a way to determin genetic variability in domestic farm animals. Very much a STEM research project and I’m making more progress since implementing even basic Zettelkasten methods in the stuff I’ve collected and where I want to take the research.
Good question @JakeBernsteinWA. Historically, they both grew out of early hyptertext theory. The implementation diverged.
It’s certainly possible to create a Tinderbox document that mimics the linkages between atomic notes which are possible with TheBrain. With TheBrain a link is a parent, or a child, or a “jump” relationship between two nodes. Tinderbox has a different notion of links.
TheBrain is more of a “permanent” database that can easily be cultivated and expanded. With Tinderbox links are not required. But when links are used, everything is always built-up bottom-up in a very manual process. Whereas TheBrain, IMO, makes the linking process simpler.
Another difference is metadata. A “note” in Tinderbox can have a potentially limitless set of standard and custom metadata (“attributes”) associated with it, thus augmenting the meaning of the note in a very plastic manner. TheBrain’s notes (“thoughts”) have only a small handful of metadata elements associate with them – and does not support custom metadata at all.
I use both, of course, and pickup Tinderbox when I want to focus on a project, and when I’m done I forget about that particular document. OTOH, I turn to TheBrain when I want to build up and maintain over the long term a base of related notes. My databases in TheBrain have been cultivated over a long horizon.
That’s why I said “only a small handful” and “does not support custom metadata”
Tags and Types in TheBrain are actually a special category of “thoughts” (nodes) – adding a tag, e.g., makes the selected “thought” a child of the tag “thought”. Is that metadata? Perhaps if liberally defined it is.
I downloaded and tried The Brain. While the Mac app had some good features, the iOS app was a deal killer for me. Hope they continue to develop the platform.
So…would you view TheBrain more as competition with Roam/Obsidian and other “Zettelkasten” apps (The Archive, Zettlr, etc.)?
It’s interesting to me that both TheBrain and Tinderbox are quite old apps (if I’m not mistaken, over a decade for each, easily?) but have taken such different approaches. It’s clear to me that TBX is still meant to be a document-based app, though I know there are people who just have one TBX file to rule them all.
I’d be curious to read more about the differences between TheBrain and Obsidian/Roam, particularly as I’m one of those people that remains skeptical of the value of “the graph” when it comes to text notes. It looks cool, sure, but to what end? I’ll have to fiddle around with TheBrain a little more to see if the Pro cost is worth it to me.
Given that none of Obsidian, Tinderbox, or Roam really have iOS apps at all (though Roam is at least a web app usable in Safari…sort of), this isn’t a huge deal for me at the moment.
I have difficulty making judgments about pairwise comparisons of applications. It all depends on the feature set and what the end user is capable of and wants to accomplish.
I don’t like zettlekasten wannabes, never liked The Archive, haven’t tried Zettlr, and wouldn’t get involved in that school of note taking. It’s a fad and will disappear in time.
(Though I am fascinated by the psycho-cultural implications of zettlekasten’s popularity. Something I intend to study a bit more in depth. When I read the Obsidian forums I feel I’m in the middle of the geek apocalypse.)
TheBrain was first published around 1998-2000, IIRC, and Tinderbox about 2002. Their intellectual roots go back to post-war research on textual systems and technology. The technology available to commercialize the theoretical framework often lagged the theory, as it did 20 years ago. I think this has changed over the past few years, and favored the publication of Roam and other offerings.
I can give you a concrete use right now. I have a curated collection roughly 1000 research papers gathered over the last 30+ years. I have moved nearly all of them into PDFs. I annotate those PDFs with both highlighted passages and personal notes. I’m still moving the various annotations out into separate files and linking but the general average is that I have around 30 items per PDF that are either a quote or a note. The quoted pieces and the notes have a lot more value to me when I can link them together. So I save them out as markdown and am using Obsidian to show those links.
A visual overview of what is linked and how many individual items are linked in any given area is critical to understanding the overall collection. It is also pointing me to areas where I need to do more literature review to understand the concepts. I can zoom in on specific nodes to see the links more effectively. I also see linkages that I miss as I am adding in links for terms and that helps me broaden the places I look when seking specific information. The graphical representation of the data is the primary beneft to me of using Obsidian.
I tend to think hierarchically and so I have used a relatively flat hierarchical system for a long time but the system falls down when trying to find the things you kinda remember but not quite. If you have done a decent amount of linking you can find it faster.
Both a folder/hierarchical view and a graphical linkage view are valuable. They each help in different ways and I really like using both of them depending on my specific need at the time.
I agree that @OogieM’s case is a good argument for graphical information browsers. The thing that Obsidian provides, however, is a silly toy compared to what she’s looking for. (Same for Roam.).
Too bad there isn’t a robust, reasonably-priced, commercial NLP tool that will ingest a corpus such as @OogieM’s and do to the graph that I think she’s describing.
That said, a user can manually craft a similar result with TheBrain – takes a heck of a lot of time and curation to get good results.
It’s also worth differentiating between the visual graph as a feature and the graph-structure underlying these apps.
It’s possible to create a graph between pretty much anything on a computer these days, thanks to URL schemes, deep linking, and apps like Hook. Still, apps like TheBrain/Obsidian/Tinderbox/Roam/etc. make it even easier, and surface features that help take advantage of these links in previously-unreachable ways.
I never look at the graph in Obsidian, save when I want a screensaver or something. But the ability to quickly and easily link seemingly-disparate pieces of content (and navigate through those links) grants me an agility that was hard to achieve before these apps.
For a trivial example, I use Obsidian as a task manager. I can quickly and easily link separate projects, tasks, and materials related to those tasks. In my experience, this has reduced cognitive overload and increased time-to-action in ways nearly impossible via OmniFocus, Todoist, and so on.
Not really, it is working much better as I get more of the historical data into it and I can see that the linkages I am making are in fact useful. I’m still working on the exact workflow for newly identified sources but that’s also coming along. I’ve already used Obsidian to make some interesting comparisons that I missed the first several times looking at the entire set of stuff.
I do agree that any sort of cross linking of data does require curation and thought. And that that takes time. But the benefits are pretty obvious if you actually try it on an already well defined set of materials.
For example: My research papers broadly fall in these main categories, genetics and breeding with an emphasis on breeds of domestic livestock, historical and prehistorical fiber and textiles, farming tools and methods from between about 1825 to WW II. There are minor categories about various DNA analysis tools and some on more general archeology topics, some on fodder cropping systems and some on population census data on livestock and livestock breeds. What is interesting is the cross linking of what on the surface seems like very different pieces of information.
Take M.L. Ryder’s papers on the evolution of sheep breeds, cross link with the fiber analysis of garments found in digs in London, Greenland, various bogs and at Viking sites, mix in some nanopore sequencing data from living examples of the breed types Ryder mentions as well as wild sheep and from neolithic bone pits and toss in a dash of fiber tools from Scandinavia and breeding systems from Monrovia and you get some very interesting information abut the movement of domestic animals and types and how the clothing changed the animals and then when you add the later farming data you see how the animals changed the landscape and how politics and economics impacted the environment. (Spain’s restriction of the Merino sheep breed and the Wool Churches in England and the before Mendel and Bakewell livestock evaluation and breeding schemes from Monrovia that got Mendel his idea of looking at basic genetics and similar papers.) For fun the Viking data sends you off into the whole ship and sail building area which then sends you into dissemination of woodworking tools which affects the architecture of the building of the time. Or look at how the warp weighted loom that came from the north met the ground warp loom of Egypt and what happened to that. Or look at the Jaccquard looms and draw or dobby looms controled by cards leading to Hollerith and computer punch cards and computer paper tape.
See I’ve been collecting what on the surface seem like totally unrealted bits of cool info and research and then by evaluating and making linkages I can see patterns that were not readily observable before. Plus it’s a whole lot of fun and then even more useful to apply that to current issues.
I can see a place for a geographic tag of where the research came from or the archeological sites on a map and over time as also being very interesting but haven’t figured out a way to enter in the tags/links now in such a way that I can parse that sort of picture out eventually. But software like Obsidian and roam are heading down that path and I think will get there eventually.
Hi all. Some fascinating reading and ideas here. It may not be worth much. But I wanted to share a video I did about 8 years ago of how I use TheBrain as my PKM system. Forgive the poor quality sound
