Reading Jaynes on Plausible Reasoning and Exploring the Logic of Scheme

I was so fired up to bring my manuscript to conclusion that I started the editing process. I had been in the midst of the chapter on probability which is the end of the first, philosophical section of the manuscript. Since next up was the brain and neuroscience section, I started ramping up some background work there, taking notes on The Idea of the Brain and The Entangled Brain.

Now that I finished note taking on both of those, I returned to the probability section. It’s got a solid grounding, but I realized that it was short and superficial. So I’ve gone back to sources and am taking notes on the first few chapters of E.T. Jaynes’ Probability Theory: The Logic of Science, which I had been reviewing last fall but without good note taking.

So that puts me way behind sharing my work here in public. Yet slowing down for me is fine as I have not deadline or even any compelling reason to actually finish the manuscript itself. As a tool in the process of exploring these subjects, it’s been valuable. It’s also been a project that has provided some focus on my tools like my Linux computer, the Kindle Scribe and Devonthink.

Over and over again I learn the same lesson that the first step is to define the problem and desired outcomes well. Start with the end in mind and Covey phrased it. Only then is it possible to choose a set of tools for the task, with reassessment of workflow from time to time improving efficiency and keeping the work enjoyable.

Yet projects keep presenting themselves. Since Twitter is pretty dead to me at this point, Reddit has emerged as a random feed to satisfy my endless curiosity. Of course the subject matter is a bit different and I miss Philosophy Twitter and Neuroscience Twitter. There’s lots more computer talk presented to me on Reddit, so I’ve gotten engaged in programming languages, specifically this functional programming paradigm that I learned through doing statistics in R. So I’ve spent a bit of time playing with Scheme variants now and reading some discussions on computation. May take some time away from general reading, but it’s all good when it comes to ensuring one lives in a rich, mentally healthy intellectual environment.

ODB Manuscript

My recent reading in the creative space has inspired me to get the manuscript for the Deciding Better book to the next level. Both Rick Rubin and Haruki Murakami both see the artist as the primary audience for their work, with audience developing as a result of putting work out in the world.

I’ve long been convinced that I have something to say about how we should approach decision making in our lives based on my wide ranging explorations of Decision Theory and the underlying brain mechanisms we use to make decisions. In the end, I’ve come to realize that the seemingly naive view of deciding as an intuitive process is the appropriate one. But it’s rare to find a real justification for the idea that decisions simply come from the heart. And that care of that heart is the core of better decisions.

To finally cut through the rationalist, Cartesian fallacy of rationalism and materialism, I had to understand that rational view of decision making. Since those systems do not turn out to be very useful, I turned to an exploration of how we actually do make decisions, using my own training in Neuroscience. Oddly, I arrived back where I started a very long time ago, with an ecological, systems level approach.

It was my own Hero’s Journey:

and I think it’s worthwhile telling.

The hero’s journey is a classic story structure that has been used for centuries. This timeless storytelling technique encompasses the three core aspects of a protagonist’s journey. Using it in fiction often seems like common sense, but the secret is to use it in nonfiction as well.

Of course all of this reading and notetaking get in the way, but as those who have traveled this road before know, it’s about pushing through to the end once the journey has begun.

I Too Contain a Large Language Model

Stephen Wolfram is the kind of thinker that sees things as simply as possible. His work on emergent phenomenon, physics and metamathematics reveal how what we see as mysterious can be built up from simple parts. I’ve written about how he takes notes, a process that is more about capturing that thought process than cataloging facts.

He’s written a clear and very simple explanation of ChatGPT ,/a> that provided a fundamental understanding of the technology for me.

The first thing to explain is that what ChatGPT is always fundamentally trying to do is to produce a “reasonable continuation” of whatever text it’s got so far, where by “reasonable” we mean “what one might expect someone to write after seeing what people have written on billions of webpages, etc.”

It had an unfortunate side effect for me last week. I was about to get up and give a lecture a faculty member for the NINDS sponsored course, Training in Neurotherapeutics Discovery for Academic Scientists, when I suddenly realized that I myself am a Large Language Model, knowing that I would soon stand up and for an hour allow my left temporal and frontal lobe language areas to chose words sequentially to go along with the planned talk and accompanying slides. I would be aware of listening to what I was saying and providing oversight, but those language areas would just be generating word strings autonomously.

Of course once I said good morning, all I could think about was what I was saying, so all good in the end.

Reading: Novelist as Vocation by Haruki Murakami

I really never intended this site to turn into a book blog, but once I started tracking my reading here, it only makes sense to at least briefly write about the books. It seems best to do this to capture first impressions of my first read of the book. If I go back to collect notes and write a summary, then hopefully those notes would lead to a bit more in depth exploration of these themes.

I’ve read most of Haruki Murakami’s books. This collection of essays on the process of writing, Novelist as Vocation, speaks so clearly with the voice that one gets to know through reading the stories and novels. Murakami has written like this before, in What I Talk About When I Talk About Running, which is also a memoir centered around a personal activity that reveals as much about the man as it does the activity.

Like his book on running, this book on writing serves as a memoir that reflects Murakami’s attitude towards the act of creation. Which is pretty simple- sit down and trust the process to produce work. It seems Murakami’s process is very inwardly directed, so the production is not forced or overly planned. It’s intuitive at the start.

But then the craft of editing begins, polishing the output until it seems like a finished product.You can see how Murakami reflects on the work in progress both to improve the work but also to develop his skills as a writer. He found an audience early on, but as he has developed, his audience has grown. While he has high regard for his readers, he sees them a coming along with him on his personal journey. Clearly he’s thought about how to get his work out in front of that audience, but he writes for himself, knowing there are those willing to buy books to see what he’s been up to.

There’s plenty of overlap with Rick Rubin’s The Creative Act, probably because of these creators focus on craft and production without much pretension. Both emphasize creation for the sake of self, not for audience. I’d recommend both books to those who find personal satisfaction from the act of creation. I think both provide good advice from accomplished master craftsmen on how to work on craft.

Reading: Picture This: How Pictures Work by Molly Bang

This was one of those email on sale alert impulse purchases I make for Kindle Books from time to time. It looked like it would fit into my current theme of reading on creativity and craft. It turned out to be a great intuition.

This a 25th anniversary editon of what is called in the blurbs “a classic book”. Picture This is very simply a short, illustrated deconstruction of how some identifiable elements of an image (color, position in the frame, shape, distance from other objects) are interpreted by us emotionally. Since it’s a classic book and I readily agreed with almost all the observations, these truly appear to be universal, wired in aspects of brain function in interpreting the visual world. Often Bang takes exactly the kind of ecological approach I’d use, talking about why something would feel a certain way based on relationship or common experience without resort to theory or some evolutionary design concept. Quite simply, we can’t be sure how we got here, but here we all are. In fact, it would be interesting to know to what extent these observations hold true across cultures.

Right after I finished the book, I pulled up my public gallery in Flickr. It’s been a while since I actively used the app, but it’s a quick way to get an overview of my photographic work.

Looking at my work through the eyes of Bang’s book, it’s amazing how almost all of my images are restful, balanced and lacking tension. I chose this image from a few years ago as a good example. There are two objects in frame, the white paint square to the left and the remnant window sill on the right. There are the background gray and white color blocks. The main characters here are off center vertically, but balanced. They seem friendly as if they might be chatting with each other. Even though nothing is centered vertically, the greater weight of the dark object rests comfortably away from the picture edge and the the white square takes up the other side, getting close to the dark bar in its space.

Will my images change? Actually, I doubt it, given that this is how I see the world. Maybe more a reflection on me than on the art. Or both.

Reading: Slough House by Nick Herron

Number seven in the series, Slough House by Mick Herron is another great addition to this spy thriller series. Of course, if you’ve read any of the series or watched the AppleTV+ show, it’s character drama and commentary on post-cold war bureaucracy and politics. This book focuses particularly on the domestic politics of England.

I’ve realized through reading the series that by focusing on this outcast group in the spy world and their often inept efforts that are always successful ultimately, the books have a way of looking upwards into the corridors of power- both political and organizational. Like much good fiction, we get a pointed reflection of our times. This is what life was like.

Macrofactor: How to Lose Weight in 2023 as an Endurance Athlete

Let me tell you how to reach and maintain your target weight as an endurance athlete.

Weight loss is a difficult subject for endurance atheletes. Eating disorders, obsession with intake and crash diets are big problems in athletes historically. While the idea of fitness for all body types is a great inclusivity goal, it’s true that for most endurance sports, body weight and composition are among the most important factors in performance.

I’ve been training seriously as a cyclist for 4 years now. By nature, I’m an endomorph, meaning that I tend toward body roundness. After graduating from high school, I was never able to wear 31 inch waist shrink to fit Levi 501’s and remember one dieting episode while in medical school when my weight was as low as 137 pounds. As someone who is 5 foot 5 inches tall, my usual weights in the 150 lb range are in the overweight range on the standard BMI chart.

I did make some progress with simple food logging using Lose It which provides a comprehensive food database. Regardless of calorie target, honest food logging reveals where exess calories are coming from and provides feedback for better eating and nutrition.

Even riding thousands of miles a year on the bicycle, my weight has been remarkably stable. For endurance athletes, the challenge is fueling the efforts that need hundreds of calories for energy yet create a minor deficit that creates a negative caloric balance. THe problem with simple food logging is handling the daily expendature variations for big effort days, regular training and rest days. Without good control, the body adjusts intake for stable weight at its setpoint. Which for me as a cyclist has long been unnessesarily high. There’s no real reason why I need to walk around with 25% of my body weight as fat that needs to be accelerated and dragged up hills on my super light carbon fiber bicycle.

The solution I’ve found is an iPhone app called MacroFactor. I discovered Macrofactor from this post at Lifehacker The Best Paid Diet App. That title is not really accurate because MacroFactor is really a weight management system, not a diet app.

The new approach taken by the system is to control caloric intake based on weight trajectory. So if one wants to maintain a weight, the app will find the daily calorie intake that produces a flat weight curve without gain or loss. If the goal is weight gain, it will increase calorie target until the desired positive weight slope is achieved. And the same for weight loss. Since expenditure is varying day to day, week to week and month to month, the process is dynamic, adapting to the rate of change. The algorithm used isn’t explicit, but after using it for a few months, I can see that it is primarily looking at slope over time to predict current expenditure.

Here’s a screen capture of the last 3 months of my weight data:

You can see that the dark blue trend line doesn’t run through the center of the data like a moving average or a smoothing technique like a loess curve. Instead, it looks like the line is showing the slope in the underlying data, often sitting above the line as it trends down. And yes, I’ve been able to get back down toward that goal weight in just a few months. A few flat sections as well- when I had recovered from COVID and the last week or so.

Now here’s what the. expenditure curve looks like over the same period.

The initial suggested daily burn was way too high and as my weight was not trending down at the targeted rate, the algorithm reduced it day by day until the desired rate of decline was in view. Actually, it overshot a bit and then, when my weight leveled off, it brought the expenditure down to a pretty low level of 1800 kcals/day. This oscillation is one of the problems anticipated with a simple feedback loop where the output is controlled by a lagging input. Like a simple thermostat, temperature oscillates above an below the target temperature as the thermostat cycles the furnace on and off. But the oscillation is around the correct value, providing a homeostatic control over time. We’re talking about one or two hundred calories a day- a 10 or 15 percent error range.

The app tracks macronutrients in a nice display as well with targets for protein, fat and carbs. So as it shifts the calorie allowance based on weight change, it pushes me to keep protien intake up. So I base all of my meals around protien often supplemented with a protein shake, fueling the exercise sessions with all the allowed carbs. I’ve shifted body composition without being underfueled and without being too hungry between meals.

For me, one of my favorite aspects of the program is how non-judgemental it is. If I go over the day’s caloric intake target to fuel a big workout, the app doesn’t care. In fact, the whole approach not only discourages cheating, it encourages complete entry of all dietary intake. After all, the more I say I eat, the more it allocates as calorie expenditure, since all it knows is what I say I eat and what I weigh. Expenditure is based only on the relationship between calories in and weight.

The monthly subscription is $11.99 a month, but has certainly been worth it for me. I believe that even once I’m at a goal weight and stable I’ll be happy to support the developers and see how training and life influence my metabolism over the longer term..

Reading program update

Today I finished summarizing my notes on The Idea of the Brain: The Past and Future of Neuroscience by Matthew Cobb. Looking back, I don’t think I’ve written about it here, so I’ll need to remedy that with a note on the book.

I learned two things in taking reading notes on the Cobb book. Last fall I started a more formal practice of Bullet Journaling. Along with it came my reading note taking method of reading straight through the book and then going back and taking notes in the Bullet Journal. With this book, it got unwieldy as there ended up being 16 pages of notes scattered across 6 writing sessions. It seems to me that while putting the notes in the BuJo is convenient, it becomes hard to find and review the notes. So for the next book I’ll be taking notes on, I’ll use a dedicated reading notes notebook.

My second discovery was that the Cornell format of notes works well for reading notes. The most viewed page on this site has long been How Bill Gates Takes Notes, which is really about the value of using the Cornell system for meetings. I realized that by laying the reading note page similarly, I could clearly see the topics discussed at the left margin and at the bottom, my own thoughts and followup items occuring to me during the note taking session.

I’ve finished my read through of Luiz Pessoa’s The Entangled Brain. It’s a really nice book serving both as an introduction to modern neuroscience and the view that I’ve long held that only systems theory approaches will help us understand how brain activity underlies behavior and awareness.

I’ve been not only been writing brief notes as I finish books, but I’ve been keeping the Reading 2023 page updated as I finish books and move on to the next. So far, it’s 6 fiction and 4 non-fiction books read. Keeping the page updated and committing to writing at least brief notes on the books has turned into a nice discipline to keep me writing regularly here.

Reading: Klara and the Sun by Kazuo Ishiguro

It seems to me that the themes of science fiction have been moving into works that would be considered literary fiction and outside the genre of SciFi. While some SciFi, like the work of Ursula Le Guin, had literary aspiration but was seen as part of the Genre, I think the separation now is mostly one drawn by publishers and bookstores as to where to shelve or categorize certain books.

Certainly, if Klara and the Sun hadn’t been written by the winner of the Nobel Prize for Literature, Kazuo Ishiguro, it would very comfortably find its place on the SciFi shelf. I’ve never read any of his books before, so can’t comment on how it fits stylistically with previous work. My only point of reference in Japanese fiction is Murakami, who’ve I read for many years. There’s certainly some similarity in having a relatively simple narrative line with a single character point of view and a straightforward story that moves directly from inception to conclusion.

I’m reminded once again of the idea that the power of fiction is to relate ideas that can’t be simply put into words. Instead, the story evokes themes where characters and situations provoke questions as we witness the unfolding story. Here, the book is narrated by Klara, an Artificial Friend who is a self aware and independently acting android, manufactured to be a child’s companion. Having been manufactured and gifted with an interior life, Klara has aspirations. Her attempts at fulfillment provide a view into the dreams and disappointments of the family that acquires her. It’s a touching story, made poignant by the nature of the limitations of it’s narrator.

Reading: The Creative Act: A Way of Being

The Creative Act: A Way of Being by music producer Rick Rubin seems to be one of those books that brings out strong reactions in readers, good and bad. I’m on the very positive side of the argument and it was a great read for me. If you have a fear of books that seem on the surface like obvious, trivial recitations of cliche, it either may not be for you or just require some patience to get below the surface into the substance of the book.

I think that it’s fitting that a book providing advice to those who seek to create is itself a creative act. In Novelist as Vocation, the novelist Haruki Murakami asserts that to be a novelist you can’t be too smart. Or at least you can’t have crisp, well defined ideas to express. Because if you knew what you wanted to say, you’d write it in an essay as I’m doing right now. The novelist has to bring the reader on a journey of discovery, a journey the novelist travelled in the creation of the fiction. So too Rubin has an idea of what constitutes the right way of being to foster creation, but doesn’t have it down to just a few rules. So the book comes at the ideas obliquely over and over.

Rubin’s findings align with my own experience. Creation is a process and the audience is just the creator. It’s nice when others can also experience the work and take the journey, but the creative act belongs to the artist. It’s what keeps me creating here- photography, philosophy, book reviews, what have you. It’s the result of my process of discovery.

Rubin rightly starts out by asserting we are all creators in one way or another. Making this a worthwhile read for those who create at work, in their family or dabble in the arts.

The book probably doesn’t lend itself to a second reading and note taking. I think it will be more valuable to dip into it from time to time, seeking relevance in its own time.