Think first

An open door, yes: always a good idea, to think first. And yes, thinking is what philosophers do. Or they think about what others have thought. Or both. But that is not the kind of thinking that I mean.

I am in search of a documentation and retrieval system for my thoughts and notes and everything that goes into future publications, phd, whatever. I suppose having spent most of my working life in information science, I have a penchant for organising (although this does not extend to my very large, ever messy desk).
The problem is, Philosophia must have the largest number of digital illiterates of any discipline. The modus operandi does not seem to have changed in thousands of years: reading books and holding forth. Ok, so the reading may be on a computer and the holding forth via zoom – but that is as far as innovation has touched philosophy. In fact, philosophers seem to think that because their thinking led to the Computer (see Aristotle introducing it below), they are under no obligation to do anything with it. That is for the people. Somewhat like how the policy makers in the Hague look upon us civil servants to do the actual work (sorry, the day job crept in again).


During the ReMa journey, I tried various systems of organising what I learned. Some of these I have documented here, and I introduced the idea of using tools here.


I started off making mind maps. This is something I really like doing, and I found it worked well with short essays of the type that we were set during year-long skills seminar. One of my professors once saw one of my maps and professed total admiration – how had I done that? I did not have the heart to tell him that children get taught this at school nowadays, and that there are many many people who are much better at creative mind mapping than I am. Which I love coz I love infographics – see here. But the problem with mind maps is that they become incomprehensible when they get larger. So much so, that I would find a really nice mind map of some complicated problem on my hard drive, and think: “now where did I get this from” ? Only to remember a while after that I had made it myself – some weeks before. Ok, so not a good memory aid, that much is clear.

Zotero and Calibre

I had a look at my citation manager, Zotero. Which is a nifty program, and getting better all the time. It can do a lot (see here) but beyond storing articles in different collection, it cannot help me much. This is because all of its features, like tagging and grouping and linking are the level of the individual paper, whereas I want to organise the text content. Calibre is not an option either – it is wonderful for organising ebooks, but it cannot even handle papers properly.


Next I started to create my very own Wikipedia. The software that created Wikipedia is called mediawiki, and I managed to install in a subdomain to this blog. I then spent an inordinate amount of time tweaking the installation and teaching myself how to use it, how to create boxes, use colours, deploy pre-programmed templates and generally make my DIY wiki look pretty and interesting. Then I went to fill it. I spent a long time thinking about the categories (Mediawiki-speak) I would organise my information, and eventually came up with this: Philosophers – Positions – Arguments – Topics – Definitions. These two features of mediawiki really helped: hotlinking to another page and relating any page to one or more categories. I started pouring stuff into my wiki, but gradually slowed down. The problem was that wiki-pages are great to make – once you have finished with the material you want organise and you know exactly how. By the time I have worked out all of that, it is time to move to the next paper. I concluded I needed something that would help me create an organising system on the fly.


Next my love affair with Atlas.TI. I got the idea from architectural modelling in my day job. I even used archimate once to model autopoietic enactivism. Atlas.Ti is much more flexible than archimate, it is really quite wonderful. I got it for next to nothing in the student webshop, and later found out that the university distributes it for free. I also bought a competing program, MAXQDA plus. Both programs help you to annotate texts and then organise the labels into a scheme for easy retrieval and analysis. The philosophy behind them is different – there is a good article here, explaining how MAXQDA is based on qualitive content analysis, whereas Atlas.TI works allows you to find patterns in a text, using your own codingin system – more akin to grounded theory. Atlas.TI seemed to fulfill all my needs – for a while. I was so happy with it, I even bought an upgrade to the version 9 because I could not wait for the university to supply one for free (which of course by now they have done). Below you can see how it works. You annotate a paper through codes. Codes can be reused across a project – this project contains 135 papers.

You can then use the codes to create network diagrams, like so:

I have done some really nice analyses with this tool – for a presentation in my ReMa course in Amsterdam on advanced language and logic I worked out how my professor’s articles are related to various concepts he has investigated, and also for the last Philosophy of Mind seminar, when I investigated how various philosophers used different words for common ground. I also used the Atlas.TI network diagrams in my research logbook, which really looked wonderful. The only problem was that after a few months, I could not longer read the complicated diagrams I had made myself – well, not without rereading the entire paper, which sort of defeats the point. The other problem was that Atlas.Ti is not really geared toward the kind of use I make of it, nor do they plan to. The autocoding feature (which allows for automatic coding throughout a large set of documents) does not work in reverse. That means that your coding system has to be ready from before you start reading the papers. Ough. Same problem as with mediawiki. The other problem is that it cannot handle more than say 50 documents or books in any one project at one time, and you cannot interrelated projects or their codings systems. So alas. I wrote to Atlas.Ti. a couple of times, hoping to hear that they would build in the features I need, but they won’t – text annotation is not their core business. Pity.


Yet another search for philosopher’s tooling yielded a surprising result: one philosopher actually created his own tooling to dealing with philosophical research: organising and retrieving philosophical statements, knowledge, insight. Quite impressive, a philosopher-cum-programmer. The software impressed me as well. Until I tried to use it. I watched all of the instruction videos several times (there is no manual), but was not able to distill a workflow that was right for me, and the look-and-feel of the program felt awkward. Also, I did not like the manual zotero integration much. But my main worry was with becoming dependent on the author. Yes yes, the database is all readable XML, but I am not a modern programmer – I just manage procedural language programming (only in my sleep as it is a long time ago that I actually did any programming), and I positively loathe the object-oriented stuff. So what would I do with bunch of XML files? Too many worries. I needed something else.

Obsidian, my second brain

I had seen references to Obsidian before, but ignored them. Mainly because I did not know what markdown is, so I could not image why anyone would be interested in organising a bunch of markdown files, however prettily. But as it turns out, markdown is just plain text plus. Since its inception, many different versions have appeared, but they are all html-convertable and will be readable als txt files forever. Obsidian gives me all of the advantages of mediawiki without the disadvantages. It is fast and flexible. It integrates with zotero. I can link and tag notes and files. I can edit files on my PC and on my mobile devices, using icloud. The only thing that is missing is being able to publish to website (other than the paid version). But that will come, I am sure.

I started out with a work problem – a huge text that needed cutting up, the ISO27002 guidelines. This I needed to do anyway, so it seemed a good place to start. And yes, I was able to deconstruct the document and then put it back together again, although the learning curve was a bit steep – as it always is with these things. I will write up a post on the configuration(s) I arrived at and publish it on the thinking tools page, at some point. See below a snapshot of my folder structure, and a graph based on the word enacted.

Obsidian has a great online support community and extensive documentation. There are many plugins. It also integrates with Zotero. Cannot wait for the new Zotero release! Anyway, I think Obsidian may be it for me. The hierarchical tagging system is particularly helpful, because of another problem which I will describe next.

Towards a metamodel or a taxonomy of philosophy

Actually, there are not that many who tried. There are a few lone papers. This one is the best I came across: Grenon, P., Smith, B. Foundations of an ontology of philosophy. Synthese 182, 185–204 (2011). It did not receive much attention. But I thought I’d try and model the ontology component they recommended in UML (nice reason to update my visio license), as a data model.

The problem is in the centre part. Grenon and Smith assume two things:

a) concept, proposition, argument, theory and method are disjunct

b) the philosopher’s workflow is like so: think a concept, propose whether it is true or not, supply argumentation, and then develop a theory using a method.

Unfortunately, philosophers are agreed on neither. They are not even agreed on the meaning of terms like concept or theory.And there is the addition problem of nesting – ad infinitum. I was a miserable when I saw this. And then I thought: who cares that philosophers don’t agree on their definitions or way of working. This is about my work, and I can define terms and workflows in whatever way I want. And I do want, because I need to store and retrieve.

So I decided to organise philosophers into single authors, groups and main fields (branches). I also have terms, topics, theories and approaches. See the image below. For my folders, I use the Johnny.decimal numbering system (which I have also started using at home and at the office). Folders and some notes are displayed on the left. I use aliases for my notes (at the top, with the metadata) so I can refer to them in different ways (with or without capitals, etc). I use a hierarchical tagging system, shown on the right.

I have already harvested my best essays in this system and am now in the progress of harvesting whatever may be useful from my diy wikipedia before I close it down forever. Let’s hope Obsidian will support me through the next few years, but I am hopeful. I also enjoy watching the videos Tall guy Jenks makes. He is a self-proclaimed ADHD sufferer, and he says the only way he can live and work is by outsourcing his information management as much as possible. Wow. I suppose the same is true of me, but with me coz of a not-so-young-anymore memory and too many things to do in a day.

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