How Stephen Wolfram Takes Notes

It seems I never tire of reading about tools that others use to pursue their creative endeavors. This very long, very detailed dive into Stephen Wolfram’s workflow is fascinating to me.

Seeking the Productive Life: Some Details of My Personal Infrastructure—Stephen Wolfram Writings

Wolfram is just a couple of years younger than me, so we share the journey from starting out in the early days of computing (time sharing main frames, terminals, the early PC era through today’s ubiquitous computing environment). It’s interesting that he is just as set on filing and knowing where things are as I am. He also defaults back to paper and pen for ubiquitous capture. Saves all of his emails, filed away. He thinks in terms of projects and stores by project, knowing that he’ll return to previous work by exploring an old project.

Of course, Wolfram uses his own company’s system, the Wolfram Notebook which they’ve been continuously developing for decades now. I wish I had been a bit more consistent about staying with plain text over the years. I’ve got work filed away in multiple formats including Word, but also stuck in database programs like WordPress, Ulysses, and. Tinderbox. I can and have transferred work in and out, but those are the places I can’t quickly assess through a file system search or indexing with a tool like DEVONthink.

I like my current Markdown text workflow since it’s so tool agnostic. I’ve been playing a bit with EMacs over the last few weeks as a way to get even more text focused but with some of the organizational power I’ve enjoyed with tools like Tinderbox, but admittedly it’s hard to get it to play as nicely with the iPad and iPhone mobile environments the way the modern crop of markdown focused text editors like Drafts, IA Writer or 1Writer are optimized for.

In fact, as I’ve looked into Emacs, it’s clear to me that many of the features of these tools have been around for a long time in Emacs, just restricted in use to that traditional text based computing environment. As I’ve mentioned before, this exploration of tools and workflow is part of the tinkering. Always gets out of the way as work needs to get done.

These Hobbies of Mine

I’m back from my first international travel in two years. A short trip to Lisbon. I had a few hours free each day I was there, so well over a hundred image captures came back with me.

I don’t take lots of images on these city walks. The camera provides way of looking more closely at how the light falls on the urban landscape. I look for little assemblages of objects that strike me as a still life or miniature landscape put together randomly from the usual components of the city scene. Usually it’s one capture, a quick look at the image for composition, exposure and focus and I move on. It’s a sketch, not a painting.

I’ve been working toward this style of casual photography for a few years now. It’s an expensive hobby, but its gratifying as self expression. My images are my own for myself and anyone who happens to see them here or on social media.

Oh, so many hobbies. This site, the workflows, cycling and fitness, philosophy and neuroscience. As I’ve become more busy with work, these outlets get squeezed for time, but gain in importance as an outlet. Writing takes a lot of energy, so I often find myself tinkering on other projects not so intellectually demanding.

The hobbies bring me into rich communities, again providing quick trips into bigger worlds. Networks of blog posts and discussions on Twitter and Reddit. Lately I’ve been tuning into the big world of Linux, window managers and Emacs which is a world full of tinkerers. Since it’s all just hobby for me, a nice place to relax. After all, there’s just one Wordle puzzle a day.


Winter View

While I’ve been posting and archiving notes here, the photography side of things has taken a back seat. I’ve realized during the pandemic that my photographic practice is very much tied to travel. I’ll bring a camera on a trip and if I capture some good images, the enthusiasm to capture more stays with me, particularly if another trip is on the horizon. I just don’t leave my house for interesting areas as a matter of course these days, so if I’m going to capture images, it’s going to take a conscious effort on my part to bring a camera with me and get some images.

The Leica M10 Monochrom continues to be my tool of choice. The APO 35mm f2.0 Summicron has been my lens of choice, particularly with the accessory Visoflex electronic viewfinder mounted so that I can take advantage of the remarkable macro capabilities built into the lens, a first for an M lens, but made practicial for use by Live View or the EVF.

The next interation of the M, the M11 has been announced by Leica. At this point, I’m not motivated to upgrade to get a 50% bump in megapixel count or the bigger battery. I find the resolution of the M10 fine for now, even when I crop and I rarely run into battery issues when out shooting for most of a day when traveling. I do like the 20% lighter body of the black M11, but overall this may be an iteration that I skip.

I’m optimistic that into the spring I can get back into some shooting discipline and add more images here.

Recent Reads and Watches

I’m with Dave. I enjoyed both Don’t Look Up and The Matrix Resurrections

It took me a little while to get the time to what them, but enjoyed both. Don’t Look Up was some of the best social satire I’ve seen in a long while. In 20 years, if someone wanted to know what living through the last few years has been like in America, I think this movie will be a nice culture artifact capturing the impact of social media, post-truth media and the divide between real life and public fantasy. Plus, a nice depiction of religious belief with real sympathy. So rare in our media of public fantasy yet so pervasive in real life. It’s funny to me that the focus was so much on the climate change/comet metaphor. Maybe those who believe they influence are upset seeing how little power they actually have in the face of self-serving delusion.

As for the Matrix, I’ve been a fan and re-watched the trilogy before getting around to Resurrections. I’m glad I did because the movie did play to the fans and those knowledgeable of the cannon. I always thought the movies were about the concept of “Savior” with Neo being a Christ-like figure somehow born to be the savior and giving his life for humanity, or at least what was left of it. The new movie is the logical second coming of the savior. I’ve read other metaphorical readings of the movies, but on rewatching I was struck once more with my previous interpretation.

I finished William Gibson’s Agency this afternoon. Unfortunately, in this case I didn’t go back and read The Peripheral, so there was the usual lost context that I gradually pieced back together from the first book of some years ago. A lesson I’ve learned and apparently forgotten- don’t start trilogies until they’re completed or at least nearly so. Hopefully when I get around to the final Expanse book, Leviathan Falls I’ll still remember enough since the last book came out almost 3 years ago. When the 3rd book in Gibson’s series comes out, maybe I’ll reread the first two as warmup.

Gibson has created a unique approach in Science Fiction where he places stories in the present but, in these last two books, simultaneously portrays a future. Since these are branching timelines, to get around time travel paradoxes of course, it’s really like present and future as fantasy. But, maybe like Don’t Look Up it provides a more direct way to reflect on our times and where we may be going. Within the first pages of the book, we meet an AI arising from an interesting technology, much closer to the way I would see AI agency coming about than the spontaneous awakening stories or the mind upload yarns, none of which I find remotely plausible.

Working in the Background on Zettelblogging

While I’ve got the workflow down to do my capture through drafts and database my collections through DEVONthink, I’m a bit stuck on the step of publishing the results.

On the one hand, the simplest way forward is to just craft posts and publish them right here on the WordPress site. Using MarsEdit I have a full list of blog posts going back as far as I want. With tags I can create collections of related posts for editing and linking with a trivial way of reposting my changes. The truth that I already know is that this is the preferred path.

This fits well into my realization that publishing and note taking have two different audiences. Publishing is for you, my imaginary, ideal reader. Smart, curious, generally knowledgable but not an MD, PhD with decades of neuroscience, neurology and philosophy work filling your head. The notes are for me, that guy who just needs to be reminded what I thinking at the time.

But then I’m known to be over-ambitious. And I really want to create some friction free ways of this republishing after pulling together ideas in the Zettelblogging repository. So there’s an output of summary and index notes that is a well reasoned, more complete version of the notes. More like lecture notes or a paragraph in a book or review. My last couple of posts on Grainger Causality and Emergence in the Brain were those kinds of posts.

Basically what it means is that I want to take the linked notes in Tinderbox and turn them into a set of interlinked web pages. This fits in well with ideas of moving to static pages and simple website construction.

For example: This Page is Designed to Last: A Manifesto for Preserving Content on the Web

Return to vanilla HTML/CSS – I think we’ve reached the point where html/css is more powerful, and nicer to use than ever before. Instead of starting with a giant template filled with .js includes, it’s now okay to just write plain HTML from scratch again. CSS Flexbox and Grid, canvas, Selectors, box-shadow, the video element, filter, etc. eliminate a lot of the need for JavaScript libraries. We can avoid jquery and bootstrap when they’re not needed. The more libraries incorporated into the website, the more fragile it becomes. Skip the polyfills and CSS prefixes, and stick with the CSS attributes that work across all browsers. And frequently validate your HTML; it could save you a headache in the future when you encounter a bug.

And Craig Mod is an advocate for simple, static web side construction:

Running a Successful Membership / Subscription Program — by Craig Mod

I still generate my own website using the Hugo static-site tool. It has gotten a bit too complex over the years, though, and were I starting again today, I’d consider 11ty. My sites are hosted on a Digital Ocean vps (if you sign up with that link you get $100 in free credit (and I get a sweet $25, too)). After 15+ years, I stopped using Google Analytics and switched to Plausible for more privacy-friendly webstats. Fathom is also a good option with spectacular, heartwarming support.

For tools? I’ve been leaning very heavily on Drafts over the last few months. My web clippings land here from my iPhone, iPad and Mac. So a simple idea would be to just push notes from Tinderbox back out to Drafts and publish as usual.

On the other hand, the static sites want a folder based set of content, which isn’t how Drafts is designed to work. I can keep the writing in Tinderbox with export as text or even HTML. Maybe move back to text editors after export? BBEdit.

Obviously this whole Tools For Thought goes back a ways. Maybe go old school?

How to Learn Emacs: A Hand-drawn One-pager for Beginners / A visual tutorial :: Sacha Chua

I thought I’d draw a one-page guide for some of the things that people often ask me about or that would help people learn Emacs (and enjoy it). You can click on the image for a larger version that you can scroll through or download

Org-mode for Writing: Structure & Focus | The Aware Writer

Org-mode is a structured editor that combines the best features of a powerful outliner and a powerful editor in one package. I’ve been fooling with org-mode a lot lately, digging into capabilities, solving issues and fine tuning, always asking the question — is org-mode the best environment for my writing? The answer is an unqualified yes.

I see our friend Jack Baty, now using Tinderbox, is a long time Emacs user:

Weaning Myself From Emacs and Org-mode – Jack Baty’s Weblog Archive (2000-2020)

Whenever I try moving out of Emacs I have to find replacements for all sorts of tools and processes. Things like task management, journaling, email, project notes, text editing, and general note taking are all things that I’ve been doing in Emacs for a while now and if I’m ever going to move away from it I’ll need to find replacements.

If Emacs is so powerful, maybe it’s my solution? Then again, I’m suspicious of “Theory of Everything” apps.

Monday Musings: MaxThink, The Only Idea Processor | The Aware Writer

first glance, MaxThink is a powerful outliner, but the real power is under the hood. MaxThink came with a fat, printed manual that by some miracle, I still have. Neil’s book is more than a user manual for MaxThink. It’s a well written tutorial on ways of thinking: Evaluative thinking with the Prioritize command, synthesis thinking using Binsort and Randomize to combine information in new ways, curiosity or experimental thinking with the Lock command, systematic thinking using Get, Put and Gather, creative uses of the Sort command, and one of my favorites, segmented lists.

So for now, expect more of this working in public mode.

Granger Causality and Emergence in the Brain

(Note: Another publication out of my Zettelblogging Tinderbox File. This comes from notes on reading a paper in the scientific literature. I’m seeing that my notes need to be cleaned up a bit for publication even when they are written to be understood by future me, since current you may need a bit more help understanding terms and logic. Plus I have links in Tinderbox to  files like PDFs in other apps. Those links need to be taken out or redirected to web sources. Publishing notes takes a few extra steps)

See: Granger Causality

This is a summary of a nice review of Granger Causality: “Wiener-Granger causality: a well established methodology by Bressler and Seth, 2011

Even though Granger Causality is quite limited in its utility, it’s a good starting point for understanding how to view cause and effect in complex systems. As a method, it only works with linear models- where any input causes a proportional effect. We’ve know that most of the world isn’t linear and exponential, non-linear effects are the rule in the real world rather than the exception.

Granger Causality also requires the time series to be stationary, that is not changing over time. Now over shorter intervals, some complex systems may be stable, but again, the nature of complex systems is to change and be unpredictable over time. It’s what makes prediction hard, so it’s not surprising that assigning causal effect would also be hard.

And finally, this kind of analysis can’t account for hidden variables. We might measure Y and see whether it predicts future states of X, but it’s entirely possible that Z is the real driving factor, loosely connected to X, so we mistakenly say the Y causes X because we were entirely ignorant of the real significance of Z.

The more general approach is called “Transfer Entropy” based on time-asymmetric information flow. This is nonparametric and based on Shannon entropy based on the amount of information measured between two processes. Can be used when the Granger assumptions (linearity, stability) don’t hold as it is a generalization of the Granger autocorrelation method.

But if you have time series and want a description of effective connectivity, then Granger Causality may be a good method.

There are lots of time series in neuroscience like EEG, neural spike trains, and fMRI. We can look at causal interaction between brain areas or between different types of data. For example, we might want to predict behavior from spike train recordings of individual neurons. If the data contains predictive information in addition to past events plus everything else, then is causal in this G-causality sense.

If a neural activity precedes and predicts an event, like reporting of conscious perception, it shows “Granger Causality”. This is a bottom up, weak emergence where we can say that the neural activity caused the behavior even though we know that the pure physical causal change was at a lower level, but with a courser grained analysis brain activity causes behavior, subjective experience.

This is a first step in linking causality to emergence.

Granger Causality

(Note: What follows is an example of a topic note in my Zettelblogging Tinderbox file). I was able to drop it into the revision of the ODB manuscript pretty much as is. I’m posting it here as an example, pending building out a way to more directly publish these notes on a dedicated Zettelblogging site).

Clive Granger won 2003 Nobel prize in Economics for the idea we know as Granger Causality. Causality seems intuitively obvious when a system can be explicitly understood. But in complex systems or systems that appear to us as a black box (like the brain) how do you define cause and effect?

In the early 1960’s, Granger was looking at how two time de processes could seem to be related over time. Did one cause the other? Norbert Wiener had suggested had suggested that a causal relationship could be defined simply by seeing whether series Y together with series X predicts the future series X’ better than X alone, then Y causes X.

Granger Caausality

This is causality defined purely on the basis of predictive information, with the predictor a possible explanatory variable coming before it in time. Granger expanded it to say that:

If you have Xt, Yt and Wt and try to forecast Xt+1 from Xt and Wt, if Xt, Wt and Yt proves a better prediction than Xt and Wt alone, then we can say that Yt provides some predictive information. Think of W as what you know about the world in general, (which should be really large to reflect everything you know) then if you add Yt to be really specific and it is better that X plus W alone, then Yt is passing a stringent test of containing information that we can call “causal”

Granger had created analysis methods for time series analysis using earlier events to predict later events. He had created a systems definition of causality based on information. It’s a weak causality, as it is not understood mechanistically, so we like to refer to it specifically as Granger Causality, sometimes G-Causality.