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I’m interested in building up a personal store of knowledge – good ideas, data, memories, and notes – and saving it in a way that I can quickly and easily make use of this information. Without some external way of saving things, I tend to forget them. The dream is that these ideas and pieces of information don’t have to be re-thought up or re-found each time but can be explored to rapidly generate more ideas. Ideally this would help me solve problems and help generate new knowledge for the wider society.

In reality this has turned out to be much harder than I expected. In my experience, it is easy to save information but hard to find it and make use of it later. The vast majority of my files have never been used after I saved them. When I do happen to remember a piece of information that I want to look up, I tend to have trouble finding it. This unfortunate situation surprised me. I had bought into the idea that there is essentially no cost to saving things digitally so I should save everything, and second that digital tools should make it easy to find things. I was wrong on both counts.

The difficulty of storing information became a real problem for me in grad school when I was doing research for my PhD in physics. I had to deal with countless journal articles, presentations, calculations, brainstorming sketches, experimental data, notes from talks/classes, and different versions of code (I wasn’t using version control, aaahhh!). At first, I thought my problems were just caused by the wrong organizational system. So I tried different systems, but despite having advantages and disadvantages they didn’t solve the underlying problem for me.

Thanks to my misadventures, I’m learning that forgetting is a feature not a bug. When I try to remember all my ideas and information, the default organizational systems struggle and while specialized tools can help they also tend to silo information. It turns out, there is a need to limit the inflow of information and the amount of work in progress. I need the information and ideas that are relevant to me, and everything else is unlikely to be needed, and should be let go. In a way my organization system for saving ideas and information is an extension of my brain. My brain is quite good at forgetting things (sometimes too good!). So while it is important to have good tools and organization, shouldn’t my system also forget things?

The default ways of organizing tend to be digital analogues to the way we store papers: papers on the desk, in notebooks, and in folders. These systems fail in similar ways to paper based systems. The simplest approach is to just put everything you need on the desktop, but this quickly fails if you have more than around ten files. The next simplest is to create notebooks; essentially storing the files in chronological order (for example by starting the filename with the date). This helps because you can quickly find a file if you remember when you worked on it, which tends to happen for things you recently worked on. However this approach makes it hard to see connections between ideas from different times1. You can’t re-arrange the ideas as you learn more; they are fixed in chronological order.

The next strategy that I’ve tried is putting files in a folder structure according to topic. This seems like a reasonable idea, but quickly becomes quicksand for ideas. Inevitably, I need to change the folder structure as I learn to better reflect the association between my files. The changes make it hard to remember where things are and breaks any references to file paths. As I create more folders, I find it difficult to remember the context underlying the relationships between folders. This can lead to folders with mashed up collections of files and sub-folders that don’t make sense.

Based on these struggles, I have turned to more specialized tools as a way to solve my organizational challenges. They can make a huge difference, but can create silos of information. For example, I started using Zotero in grad school, to keep track of all my research articles. This was a huge improvement over putting papers in topic based folders and trying to cram paper keywords into the filenames. Zotero has useful tools that allowed me to generate bibliographies automatically and to save papers directly from the browser. But now I had a separate store of papers that wasn’t tightly integrated with my research data and information; it was in a separate silo. This turned into a problem when I needed to reinstall my operating system. All my other files were restored but I had trouble recovering my Zotero papers. Eventually I was able to recover them, but it highlights that separate silos increase the complexity of securing my data.

Ultimately tools won’t help if the information is not useful. Marie Kondo says throw away all papers (except what you really need)2, and I think the same could be said for digital information too. She says this because according to her core principle, your things should “spark joy” and she finds papers rarely spark joy. Do my digital files and information spark joy? The majority probably don’t. I’m not totally sure because most are in these old folders that I never look at.

Information tends to bring me more joy when it is connected to something bigger, and this is where tools can help. For example, the “Untitled” file in an old folder called “New” is probably not useful. The context is lost; it is just a fragment. In contrast, a note in an Evernote notebook is part of something bigger. Evernote allows the notes to be displayed in different ways which can help the context to be recovered, and it is easy to search. It’s also easier to make connections between different notes with tags or with links.

Based on these experiences, I have begun to seriously fight the accumulation of unnecessary fragments and now try to only keep things that are part of a “whole”. One practice that has helped a lot is to channel the inflow of information. By default, there many different places that new files are saved, which is bad because it’s hard to evaluate what should be kept. To make things more manageable, I create a single “Inbox” folder where any new file is saved temporarily until it can be saved in an appropriate place (I got the idea from this blog post3). This little change gave visibility to the problem, because I could easily see files building up. Now that the files were in one place, it was more straightforward to decide what to keep and what to delete (although I still put it off sometimes!). This is a small step toward protecting my digital space and being intentional about what I allow in.

Limiting the amount of work in progress is also critical. Work in progress can be many things: unfinished projects, ideas that need to be pursued, or emails that need to be responded to. Too much work in progress is bad for multiple reasons (Agile frameworks like Kanban4 and Scrum5 are dedicated to limiting work in progress), but in regard to storing information, the unfinished work means that there are lots of associated files and information that don’t bring joy. Instead of being sources of useful information, these incomplete files require additional work and are difficult to understand because of missing context. One tactic that helps limit the work in progress is to create a single “Current Projects” folder for things that are being actively worked on (this is another good idea from this blog post3). With all the active work in one place it is easier to see when things are getting overwhelming. When that happens, I need to let go of things that I am never going to do and work to finish the projects that are important.

Organization requires deep change in behavior. I am part of the knowledge organization system, so if the system is going to succeed then I need to be working too. This means being more intentional with what I keep and with how I keep the things that are important. The hard part is letting go. Sometimes that means deleting now and sometimes it means letting something be buried in the bottom of a list of notes. Either way this reserves the prime spots for the most useful information. As part of my system, I also need to focus on what is most important. This is a huge challenge because it requires saying “No” to some demands, and risking the disapproval of others. When those demands come from bosses, significant others, or children it’s difficult to say no. But by setting limits, I will be able to make the most of my limited resources and give the most back to those in my life.

The effort is worth it for me. As I have been implementing these changes, I have found that I spend less time searching for files, notes or projects from a few months ago. It still happens sometimes, but usually when I didn’t follow my own rules! My store of information is not some magically useful thing that I will use in the future, but a limited resource that I rely on and enjoy now. It has room to grow, with plenty of unneeded information that can be pruned and lots more that can be added in an integrated way. This practice is helping me to think more clearly. Letting go of information, forgetting, is helping me to make connections between the important ideas that are left.

  1. David B. Clear, “Zettelkasten — How One German Scholar Was So Freakishly Productive”, https://writingcooperative.com/zettelkasten-how-one-german-scholar-was-so-freakishly-productive-997e4e0ca125.
  2. Kondo, Marie. the life-changing magic of tidying up. 2014 p 96.
  3. Mark Virtue, “Zen and the Art of File and Folder Organization”, https://www.howtogeek.com/howto/15677/zen-and-the-art-of-file-and-folder-organization/.
  4. David J. Anderson, Kanban: Successful Evolutionary Change for your Technology Business.
  5. Kenneth S. Rubin, Essential Scrum: A Practical Guide to the Most Popular Agile Process.

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Image of restored specimen of a squat quadruped with knobby back
An ankylosaurus: by Emily Willoughby (e.deinonychus@gmail.com, http://emilywilloughby.com) – Own work, CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=30925563

Like many kids, I was into dinosaurs. I had fun reading about the different types of dinosaurs, and trying to figure out which was the biggest, strongest, or most powerful. Over the years, I got interested in other things so dinosaurs have not been in the front of my mind. Recently my son has helped me to reconnect with the amazing world of dinosaurs. My son (two and half years old) loves dinosaurs and has been starting to learn some of their names (like ankylosaurus) so I have naturally been learning with him. To my surprise I’ve found that dinosaur research, and paleontology as a whole, has made tremendous progress since I was a kid.

Here are some specific examples:

  • Spinosaurus is the largest carnivorous dinosaur ever and had a crazy looking spine on its back. The finding of new Spinosaurus fossils as spurred a lot of research trying to understand whether it was aquatic, what the spine was for, and what it ate. The evidence is suggesting that it may have been one of the only swimming dinosaurs!
  • Tyranosaurus Rex was huge, but how fast was it? There has been a lot of back and forth but according to this 2017 paper, they probably weren’t that fast and mostly walked. Very disappointing! I still am hopeful that they could run as fast as a Jeep, but it did get me interested in the general relationship between animal size and speed (see this interesting blog post going into the details about animal speed)
  • Dinosaurs had efficient respiration with air sacs like birds (living dinosaurs!). In addition their bones were often pneumatic meaning that the air passages went through the bone. This made the bones light and strong which may have been one of the traits that allowed dinosaurs to get so big.
  • There is a wealth of evidence and theories about how different dinosaurs and other animals evolved. I really enjoyed this Eons show exploring how pterosaurs evolved the ability to fly.

Dinosaurs remind me that the world has not always been like it is now; it has changed and most likely will continue to change. The dinosaurs showed that huge land animals are possible. Could they evolve again? Could genetic engineering help? Jurassic park made it seem like a bad idea, but I would be for it. On a darker note, the asteroid impact that wiped out the dinosaurs (except the birds!) in particular is a reminder that millions of years worth of effort can be erased in a day. But perhaps the survival of our ancestors and the ancestors of other current species is an inspiration that life could survive the next big catastrophe. I like to remember we are part of the same story that includes the dinosaurs, and it is not over yet!

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When developing software, I want to build applications quickly. In my sometimes painful experience, low quality work gets in the way of this goal. There are a lot of problems with poor code quality, but I want to focus today on how code quality is directly tied to the amount of work in progress. Low quality code leads to large work in progress which in turn causes slow and uncertain delivery time of new features.

I tend to think of low quality code as any code that leads to defects that require rework, i.e. bugs. There is an inherent challenge in this definition because it’s hard to know what will cause a bug until the bug shows up. But from experience, I know there tend to be more bugs when I write the code quickly, working alone, and without writing or running tests. There are a lot of different ways to write bad code, but those are some of the common ways I do it : ).

The low quality code really starts to be a problem when I “finish” some features and move on to developing new features. The poorly written code is not really done. Most likely it still needs some rework to really function the way it is intended. So in reality, I have more work on my plate than I can handle efficiently. Major bugs crop up more frequently interrupting me and causing the time to finish any feature to increase.

It turns out that there is no way to get around the fact that more work in progress leads to longer delivery time; it’s Little’s Law. If you have a system with items coming in that have to wait in a queue before they can exit the system, then the number of items in the queue is directly proportional to how long, on average, that it takes to process a single item. This makes sense. Long lines mean long wait times. But when it comes to planning work, it is easy to think that I can get everything done at once.

To achieve a quicker cycle time, I need to insist on high quality work to avoid the pile of work in progress from unexpected bugs. A faster feedback cycle is super beneficial. With complex products each bit of work that we complete gives us new insight into the system, and ideally we would like to incorporate those learnings into deciding what to do next. The only way we can do that effectively is to have short delivery time of features.

This is my understanding of the connection between work in progress and delivery time related to my experience, but I learned about this connection first in Kanban: Successful Evolutionary Change for your Technology Business by David J Anderson and more recently in Essential Scrum: A Practical Guide to the Most Popular Agile Process by Kenneth S. Rubin.

I hope to write upcoming posts about specific things that I have found helpful in my efforts to improve the quality of my code.

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I was at the the beach this past week, and one of the days we got a chance to do some star gazing. It was a new moon, and the sky was full of stars (and some satellites). I wanted to take a picture to capture the majesty. In the past, I’ve tried to take pictures of the stars and have failed, but recently I’ve been getting better at manual mode on my Galaxy S9, so I tried again. This time it worked! Here was the result:

The night sky at the Jersey Shore.

There were a couple of settings that made the picture possible. With manual mode, I set the focus to infinity so the stars would be resolved. I fully opened the aperture to let in more light, and I set the phone down on a box so that it did not move. When it was taking the picture, the phone automatically determined the exposure time which ended up being around 10 seconds. I also raised the ISO level, but that may not have been the best idea because it can introduce noise. If you’re interested in learning more, there are many guides available, I came across this one today and found it to be informative.

Good luck with your astrophotography! Here’s a picture of the big dipper to close:

The big dipper.

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I recently finished reading A Tale of Doings by Phil Quense. I really enjoyed it. As I read it, I felt immersed in the world of the story and the lives of the characters. It is a dystopian future, with the world owned by a few large corporations, that felt relatable really a natural progression from the way things are now. I enjoyed how the complexities of the world unfold through unexpected revelations throughout the story.

But the characters really make the story. There are several who play major roles in the story, and I felt like I got to know them. Sometimes I would get frustrated at a character for making a terrible decision, but they all have good hearts (except perhaps a few of the villains). I would root for them and get excited as they got swept up in the adventure.

Sometimes life can be numbing. We go to school, so we can get a good job, so that we can retire, so that we can . . . die. The default life in our society seems to be selfish and narrow. This story raises the hope that life can be rich and meaningful although perhaps more dangerous and exciting than we could imagine.

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I keep on going back to the same sites for updates about coronavirus. Here are the ones that I like:

Update 5/5/2020

Also I like reviewing the IMHE predictions.

Update 5/26/2020

Update 7/29/2020

Nice dashboard of covid reproduction rates https://rt.live/

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From what I understand (non-expert), meat does not have any fiber. I know that some parts of plants are not digestible by humans such as soluble and insoluble fiber. Even though we can not use these molecules directly, they are eaten by gut bacteria and thus are important for a healthy gut microbiome. Having a vibrant gut microbiome has a variety of positive health effects from regular poops to less inflammation.

I am curious if the gut bacteria obtain nutrients from other molecules in food especially from meat. I know that meat doesn’t have fiber, but does it have other types of molecules that can not be digested by humans but that can be broken down and used by gut bacteria?

Part of the reason why I think this may be possible is that human breast milk contains oligosaccharides, which are not digestible but that are important for the gut health of new born babies. Does meat contain any molecules such as these that are not digestible by humans? What are these molecules?

I think there must be some molecules in meat that are not digestible because animals on a purely carnivore diets still have gut bacteria (see this paper for example). These bacteria have to eat something.

I also posted a version of this question on Biology Stack Exchange.

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I was super excited to go skiing for the first time as an 11 year old. My older brother and I had signed up for a ski trip run by our town, and we were on a bus with a bunch of people I didn’t know. Going skiing was something I had dreamed of doing ever since watching Olympic alpine skiing as a very small child. Every winter I would sled fanatically any time it snowed, but I longed to go skiing. This was my chance!

I ended up learning how to ski quickly and loving it. My first day, my brother and I stayed on the beginner hill, but by the end we were flying down that little hill. Since then I have gone on to ski black-diamond slopes.

Why did I learn skiing quickly, while other people struggle greatly? Since then I have failed multiple times trying to “teach” friends how to ski. But then I have another friend, Keith, who learned how to ski even faster than me and was on black diamond slopes on his very first day!

How people learn is a whole field of study that fascinates me. Today, let me share a few of my thoughts about how learning works based on my own experience and from what I have picked up from reading about learning.

I think that there are many, many mini skills that are needed to accomplish any physical skill like skiing, swimming, or even walking. Having a toddler in the house makes that very clear. My son will try all sorts of variations on manipulating objects and repeat again and again. I believe that these games help him to build up a suite of mini skills that can eventually be drawn upon to learn skills like shooting a basket or doing stand up paddle boarding.

Perhaps getting stuck when attempting to learn a new skill is just a sign that one needs to learn some more of those mini skills. I had that experience with snowboarding which I tried for the first time with my friend Keith who was trying skiing. I had hoped that my experience with skiing would help me to pick up snowboarding. No luck! I kept on falling, and just felt very unstable on the board. I couldn’t turn or stop, so I had to fall. Sometimes the falls were awkward half-falls, and other times I would do a face plant into the icy snow. In the end, I gave up and switched my snowboard rental for a ski rental. Then Keith and I had a blast for the rest of the day racing down the advanced hills.

I didn’t try snowboarding again for over a decade, but when I did try snowboarding I picked it up right away and I loved it! I’m not sure how this happened, but I attribute it to learning how to do the RipStik (see the image below). A RipStick is like a skateboard but has only a single wheel at each end attached with swivel casters. To move you have to swivel you legs back and forth which somehow generates motion. It was definitely a challenge to learn but I learned it during a summer living with a group of my friends while going to Rutgers.

RipStik_Classic_BL_Product
The Razor RipStik

Somehow when I returned to snowboarding I felt like I was able to transfer some of the skills I had picked up from the RipStik. I felt much more comfortable balancing on the board. I could swing my legs and hips to enter in to turns and I could control how the edge slid through the snow.

When I tried snowboarding as a teenager, I wasn’t good at it, but when I tried it again over a decade later I was a ‘natural’. This experience and others like it, make me question the idea that some people are inherently good or bad at certain skills or sports. Yes, some people will learn skills much faster than others. But do not write off the slow learners! Once they master the necessary mini-skills they can catch up pretty quickly and perhaps they can experience the joy of flying down a mountain on a snowboard!

Do you have the experience of failing to learn something the first time and then picking it up years later? I’d be curious to hear about it. I’m also interested in learning more about what the scientific research says about how people learn.

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I have decided that it is time for me to leave Facebook. It has a negative influence on me, my friends, and our larger society. This decision has not been easy since Facebook provides many useful services and most importantly lets me connect with so many of you. I want to explain some of the top reasons, and to share with you where I am going.

Facebook has lost my trust by:

  • Encouraging addictive behavior (infinite scrolls among other things).
  • Sharing our private information with whoever will buy it.
  • Not playing nicely with other applications. Instead of including the contents of a post in an email notification, Facebook forces you to pull up Facebook (and risk getting sucked into the news feed time sink).
  • Contributing to the fragmentation of our society by selecting posts full of outrage and provocation for our news feeds.

Facebook is “free”, but we pay in so many ways. I’m not buying it anymore. And I’m taking my data with me.

Before I go, I want to thank you, Facebook, for helping me to remember people’s names, for providing a way to share my thoughts and pictures, for giving me a sense of who got married or had a baby or took a cool vacation. 

My new home on the internet will be my website davidbruffner.com. Feel free to visit and say hi. I write little posts from time to time about what I am interested in. I’m still sorting out whether to spend time on other social networks. My favorite ways to connect are talking on the phone and meeting in person.

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The first weekend of December, I took part in the 2019 Omega Center conference titled Love at the Heart of the Cosmos. The Omega Center is an organization dedicated to building a new understanding of religion and science. The conference explored the idea that God’s love permeates the physical world and that the physical world matters to God. I attend online, but despite the distance, was still able to feel the excitement of the speakers and the attendees. I felt a sense of finding my “home”, other people like me who care deeply about religion, but are searching to find an understanding of religion they can wholeheartedly believe in.

To give a sense of the conference, here are a few examples:

  • Matthew Fox talked about the importance of holding on to a sense of wonder. He argued that God is not static, so we should be open to updating our beliefs and doctrines. I found it particularly encouraging how he has worked on new forms of liturgy.
  • Kathleen Duffy , a Catholic sister and physicist, described the struggle of Jesuit priest and paleontologist Pierre Teilhard de Chardin as he navigated writing about evolution and how it impacts his Catholic faith while facing censure from the Church. It is helpful to learn from Teilhard’s struggle, because we still face obstacles today. There is real resistance towards fully embracing evolution which necessarily causes dramatic changes to our understanding of God.
  • Ilia Delio, Catholic sister and theologian leading the Omega Center, spoke about the need for inner work, including contemplation, to contribute toward the future that God is calling us to. She described how technology is changing our very definition of what it means to be human, and the role of religion in this time of change.

Throughout the talks, the questions, and other events, there was a sense that we are on the edge of a big change in religion and society. In some way the current world religions will need to change to make sense of our changing world. There is a hope that a new religion or religions could emerge and help humanity face existential challenges.

I am just one person, and can not do much on my own, but I am part of something bigger. Maybe I can and we can, in some small way, contribute toward this epic story.