Reframing and simplifying the idea of how to keep a Zettelkasten

Given many of the misconceptions I see online of how to keep a zettelkasten, particularly given the focus on the arcane addressing system used by Niklas Luhmann, perhaps it may be helpful to dramatically reframe the question of how to keep a zettelkasten? One page blog posts from people who’ve only recently seen the idea and are synopsizing it without a year or more practice themselves are highly confusing at best. Can I write something we don’t see enough of in spaces relating to zettelkasten? Perhaps we should briefly consider the intellectual predecessor of the slip box?

(Editor’s note: I’m using content within my own “slip box” to write this.)

Start out by forgetting zettelkasten exist. Instead read about what a commonplace book is and how that (simpler) form of note taking works. This short article outlined as a class assignment is a fascinating way to start and has some illustrative examples: https://www.academia.edu/35101285/Creating_a_Commonplace_Book_CPB_. If you’re a writer, researcher, or journalist, perhaps Steven Johnson’s perspective may be interesting to you instead: https://stevenberlinjohnson.com/the-glass-box-and-the-commonplace-book-639b16c4f3bb

The general idea is to collect interesting passages, quotes, and ideas as you read. Keep them in a notebook and call it your commonplace book. If you like call these your “fleeting notes” as some do.

As you do this, start building an index of subject headings for your ideas, perhaps using John Locke’s method (see this for some history and a synopsis: https://publicdomainreview.org/collection/john-lockes-method-for-common-place-books-1685).

Once you’ve got this, you’ve really mastered the majority of what a zettelkasten is and have a powerful tool at your disposal. If you feel it’s useful to you, you can add a few more tools and variations to your set up.

Next instead of keeping the ideas in a notebook, put them on index cards so that they’re easier to sort through, move around, and re-arrange. This particularly useful if you want to use them to create an outline of your ideas for writing something with them. Once you’ve got index cards (slips) with ideas on them in a box, you now literally meet the minimum requirements of a zettelkasten (German for “slip box”, though in practice many will have their ideas in a metaphorical slip box using a digital note taking tool.

Next, maybe keep some index cards that have the references and bibliographies from which your excerpting and note taking comes from. Link these bibliographical cards to the cards with your content.

As you go through your notes, ideas, and excerpts, maybe you want to further refine them? Write them out in your own words. Improve their clarity, so that when you go to re-use them, you can simply “excerpt” material you’ve already written for yourself and you’re not plagiarizing others. You can call these improved notes, as some do either “permanent notes” or “evergreen notes”.

Perhaps you’re looking for more creativity, serendipity, and organic surprise in your system? Next you can link individual notes together. In a paper system you can do this by following one note with another or writing addresses on each card and using that addressing system to link them, but in a digital environment you can link one note to many multiple others that are related. If you’re not sure where to start here, look back to your subject headings and pull out cards related to broad categories. Some things will obviously fit more closely than others, so be more selective and only link ideas that are more intimately connected than just the subject heading you’ve used.

Now when you want to write or create something new on a particular topic, ask your slip box a question and attempt to answer it by consulting your index. Find cards related to the topic, pull out those and place them in a useful order to create an outline perhaps using the cross links that already exist. (You’ve done that linking work as you went, so why not use it to make things easier now?) Copy the contents into a document and begin editing.

Beyond the first few steps, you’re really just creating additional complexity to a system to increase the combinatorial complexity of juxtaposed ideas that you could potentially pull back out of your system for writing more interesting text and generating new ideas. Some people may neither want nor need this sort of complexity in their working lives. If you don’t need it, then just keep a simple commonplace book (or commonplace card file) to remind you of the interesting ideas and inspirations you’ve seen and could potentially reuse throughout your life.

The benefit of this method is that beyond creating your index, you’ll always have something useful even if you abandon things later on and quit refining it. If you do go all the way, concentrate on writing out just two short solid ideas every day (Luhmann averaged about 6 per day and Roland Barthes averaged 1 and change). Do it until you have between 500 and 1000 cards (based on some surveys and anecdotal evidence), and you should begin seeing some serendipitous and intriguing results as you use your system for your writing.

We should acknowledge that that (visual) artists and musicians might also keep commonplaces and zettelkasten. As an example, Eminem keeps a zettelkasten, though he calls his “stacking ammo”, but it is so minimal that it is literally just a box and slips of paper with no apparent organization beyond this. If this fits your style and you don’t get any value out of having cards with locators like 3a4b/65m1, then don’t do that (for you) useless make-work. Make sure your system is working for you and you’re not working for your system.

Sadly, it’s generally difficult to find a single blog post that can accurately define what a zettelkasten is, how it’s structured, how it works, and why one would want one much less what one should expect from it. Sönke Ahrens does a reasonably good job, but his explanation is an entire book. Hopefully this distillation will get you moving in a positive direction for having a useful daily practice, but without an excessive amount of work and perhaps a bit less cognitive dissonance. Once you’ve been at it a while, then start looking at Ahrens and others to refine things for your personal preferences and creative needs.

Differentiating online variations of the Commonplace Book: Digital Gardens, Wikis, Zettlekasten, Waste Books, Florilegia, and Second Brains

A fluorescence of note taking tools

Over the past three or so years there has been a fluorescence of digital note taking tools and platforms.

Some of these include:

Open source projects like Org Mode, Logseq, Foam, Jupyter, Trilium, Databyss, Athens, Dendron, Anagora, and Hypothes.is.

Closed sourced projects like: Roam Research, Notion, Knovigator, Amplenote, RemNote, Memex, Nototo, nvUltra, and Are.na.

Some are based on earlier incarnations of note taking and writing tools like OneNote, Evernote, Simple Note, TiddlyWiki, DEVONthink, Scrivener, etc.

This brief list doesn’t take into account a sea of other mobile apps and platforms in addition to a broad array of social media platforms that people use for similar note taking or annotations.

My particular interest in some of this note taking field comes in the growing number of people who are working in public and sharing their notes in online settings with others. This has been happening organically since the rise of the internet and has happened on blogs within the blogosphere and on personal and communal wikis.

As was highlighted (pun intended) at the recent I Annotate 2021 conference, the note taking space seems to have been coming to a new boil. With the expansion of the ideas of keeping a zettelkasten or a digital garden, these versions of notebooks seem to be a significant part of this new note taking craze.

One thing I have noticed, however, is a dramatic lack of continuity in the history of note taking within the longue durée of Western civilization. (Other cultures including oral cultures have similar traditions, but for our purposes here, I won’t go into them except to say that they’re highly valuable, spectacularly rich, and something of which we should all be aware.)

Many of these products are selling themselves based on ideas or philosophies which sound and even feel solid, but they’re completely ignoring their predecessors to the tune of feeling like they’re trying to reinvent the wheel. As a result, some of the pitches for these products sound like they’re selling snake oil rather than tried and true methods that go back over 2,000 years of intellectual history. I can only presume that modern education is failing us all dramatically. People are “taught” (maybe told is the better verb) to take notes in school, but they’re never told why, what to do with them, or how to leverage them for maximum efficiency. Perhaps the idea has been so heavily imbued into our culture we’ve honestly forgotten the basic parts and reasoning behind it?

Even Vannevar Bush’s dream of the Memex as stated in his article As We May Think (The Atlantic, 1945), which many of these note taking applications might point to as an inspiration, ignores this same tradition and background, so perhaps these app creators and users aren’t all to blame?

Delineating Online Forms

I’ve been doing some serious reading and research into these traditions to help uncover our missing shared history. I’ll write something longer and more specific about them at a later date.

In the meanwhile, I want to outline just a bit about the various flavors as they relate to some of the more public online versions that I see in the related internet spaces. I hope to help better delineate what they have in common, how they differ, and what they may still add to the mix to get us to a more robust version of Bush’s dream.

Other’s thoughts and comments about these various incarnations and their forms and functions are both encouraged and appreciated.

Commonplace books

Historically commonplace books are one of the oldest and most influential structures in the note taking, writing, and thinking space. They have generally been physical books written by hand that contain notes which are categorized by headings (or in a modern context categories or tags. Often they’re created with an index to help their creators find and organize their notes.

They originated in ancient Greece and Rome out of the thought of Aristotle and Cicero as a tool for thinking and writing and have generally enjoyed a solid place in history since. A huge variety of commonplaces have been either copied by hand or published in print book form over the centuries.

Most significant thinkers, writers, and creators throughout history have kept something resembling a commonplace book. While many may want to attribute the output of historical figures like Erasmus, Newton, Darwin, Leibnitz, Locke, or Emerson to sheer genius (and many often do), I might suggest that their works were the result of sustained work of creating personal commonplace books—somewhat like a portable Google search engine for their day, but honed to their particular interests. (One naturally can’t ignore their other many privileges like wealth, education, and time to do this work, which were also certainly a significant factor in their success.)

Many people over the past quarter of a century have used a variety of digital forms to keep digital commonplace books including public versions on blogs, wikis, and other software for either public or private consumption.

Florilegium

Florilegia are a subcategory of commonplace book starting around 900 CE but flourishing in the 12th and 13th centuries and primarily kept by theologians and preachers. The first were a series of short excerpted passages often arranged in order of their appearance in a single text, but eventually were arranged systematically under discrete headings. Medieval florilegia where overwhelmingly, and often exclusively, concerned with religious topics from the works of scriptures, the moral dicta of the Doctors of the Church, and—less frequently—the teachings of approved, classical moral philosophers. The idea and form of florilegium generally merged back into the idea of the commonplace book which had renewed interest and wide popularity during the Renaissance.

These didn’t add any new or innovative features over what had come before. Perhaps, if anything, they were a regression because they so heavily focused only on religion as a topic.

Few (if any) examples of florilegia can be found in modern digital contexts. Though I have seen some people talk about using digital note taking tools for religious study, I have yet to see public versions online.

Zettelkästen

Born out of the commonplace tradition with modifications by Conrad Gessner (1516-1565) and descriptions by Johann Jacob Moser (1701–1785), the Zettelkasten, a German word translated as “slip box”, is generally a collection of highly curated atomic notes collected on slips of paper or index cards. Zettelkasten were made simpler to create and maintain with the introduction of the mass manufacture of index cards (and card boxes and furniture) in the early 20th century. Slips of paper which were moveable within books or files and later on index cards were a significant innovation in terms of storing and organizing a commonplace book.

Generally zettels (or cards) are organized by topics and often contain dates and other taxonomies or serialized numbers as a means of linking them to other cards within the system. The cross linking of these cards (and thus ideas) were certainly a historical physical precursor of the internet we have today, simply in digital form.

Almost all the current references I’ve seen online to Zettelkasten mention Niklas Luhmann as their inspiration, but none of them reference any other well-known historical examples despite the fact the idea has been around and evolving for several centuries now.

This productivity system and sets of digital tools around it came to greater attention in Germany in 2013 with the exhibition “Zettelkästen: Machines of Fantasy” at the Museum of Modern Literature, Marbach am Neckar and in 2014 with the launch of the zettelkasten.de website. A subsequent boost in the English speaking world occurred following the publication of Sönke Ahrens’s book How to Take Smart Notes – One Simple Technique to Boost Writing, Learning and Thinking – for Students, Academics and Nonfiction Book Writers in February 2017. The recent ability to use platforms like Roam Research, Obsidian, Notion, et al. has helped to fan the flames of their popularization.

More often than not, most of these digital tools (like their card-based predecessors) are geared toward private personal use rather than an open public model. Roam Research and Obsidian Publish have features which allow public publishing. TiddlyWiki is also an excellent tool for this as its so-called Tiddlers have a card-based appearance and can be placed in custom orders as well as transcluded, but again not many are available to the online public.

Waste books/Sudelbücher

This sub-genre of notebooks comes out of the tradition of double-entry book keeping where accountants often kept a daily diary of all transactions in chronological order. These temporary notes were then later moved into a more permanent accounting ledger and the remaining book was considered “waste”.

In the commonplace book tradition, these books for temporary notes or (fleeting notes in a Zettelkasten framing), might eventually be copied over, expanded, and indexed into one’s permanent commonplace collection.

In modern digital settings, one might consider some of the ephemeral social media stream platforms like Twitter to be a digital version of a waste book, though to my knowledge I may be the first person to suggest this connection. (To be clear, others have certainly mentioned Twitter as being a waste and even a wasteland.)

Wikis

Inspired, in part, by Apple’s HyperCard, Ward Cunningham created the first public wiki on his website on March 25, 1995. Apple had designed a system allowing users to create virtual “card stacks” supporting links among the various cards (sound familiar?). HyperCard was designed as a single user system.

Wikis allowed multiple users to author and edit pages on the web with a basic web browser. They were also able to create meaningful links and associations between pages, whether they existed or not using [[WikiLinks]]. They were meant to allow the average visitor to participate in an ongoing process of creation and collaboration.

Here there is some innovative user interface as well as the ability to collaborate with others in keeping a commonplace book. Transclusion of one page into another is a useful feature here.

Personal wikis have been used (as have many blogs) for information aggregation and dissemination over the years in a manner similar to their historical predecessors.

Second brain

Second brain is a marketing term which stands in for the idea of the original commonplace book. It popped up in the note taking context in early 2017 for promoting the use of commonplace books techniques using Tiago Forte’s expensive online course Building a Second Brain which focused on capturing, organizing, and sharing your knowledge using (digital) notes. It is a platform agnostic method for improving productivity wholly using the commonplace underpinning.

Google searches for this term will be heavily mixed in with results about the gastrointestinal system being the body’s “second brain”, the enteric nervous system, second brain tumors, a debunked theory that dinosaurs had two brains, and other general health-related topics.

Some websites, personal wikis and other online versions will use the phrase second brain, but they generally have no innovative features that are missing from prior efforts. Again, I view the phrase simply as marketing with no additional substance.

Digital Gardens

Informed heavily by their cultural predecessors in commonplace books, zettelkasten, and wikis, digital gardens are digital first note collections which are primarily public by default and encourage the idea of working in public.

Digital Gardens arose more formally in 2019 and 2020 out of the work and influence of Mark Bernstein’s 1998 essay Hypertext Gardens: Delightful Vistas, Ward Cunningham’s Smallest Federated Wiki (which just celebrated it’s 10th anniversary), Mike Caulfield’s essays including The Garden and the Stream: A Technopastoral as well as some influence from the broader IndieWeb Community and their focus on design and user interface.

Digital garden design can often use the gardening metaphor to focus attention on an active tending and care of one’s personal knowledge base and building toward new knowledge or creations. The idea of planting a knowledge “seed” (a note), tending it gradually over time with regular watering and feeding in a progression of 🌱 Seedlings → 🌿 Budding → 🌳 Evergreen is a common feature.

There are a growing number of people with personal digital gardens in public. Many are built on pre-existing wiki software like WikiMedia, the Smallest Federated Wiki, or TiddlyWiki, static site generators like Jekyll, note taking platforms like Obsidian Publish and Roam Research, or even out of common blogging software like WordPress. A growing common feature of these platforms is that they not only link out to resources on the open web, but contain bidirectional links within themselves using either custom code (in a wiki-like manner) or using the W3C Webmention specification.

The Future?

With luck, application and platform designers and users will come to know more about the traditions, uses, and workflows of our rich cultural note taking history. Beyond this there are a few innovations, particularly in the public-facing arena which could be useful, but which aren’t broadly seen or available yet.

Still missing from the overall personal knowledge and note taking space is a more tightly integrated version of both a garden and a stream (in Mike Caulfield’s excellent framing) that easily allows interaction between the two arenas. Some of the more blog-based sites with notes, bookmarks, articles and IndieWeb friendly building blocks like Webmention, feeds (RSS, JSON Feed, h-feed), Micropub, and Microsub integrations may come the closest to this ideal.

One of the most fascinating recent entrants on the scene is Flancian’s Anagora which he uses as a personal commonplace book in a wiki-esque style. Over other incarnations it also has the ability to pull in and aggregate the notes of other digital commonplace books to create a larger marketplace of ideas. It also includes collaborative note taking space using Etherpad, which I’ve seen as a standalone tool, but never integrated into a digital commonplace book.

Ultimately, my dream—similar to that of Bush’s—is for individual commonplace books to be able to communicate not only with their users in the Luhmann-esqe sense, but also communicate with each other.

Niklas Luhmann apparently said:

Ohne zu schreiben, kann man nicht denken; jedenfalls nicht in anspruchsvoller, anschlussfähiger Weise.

(Translation) You cannot think without writing; at least not in a sophisticated, connectable way.

I think his conceptualization of “connectable” was much more limited and limiting than he might have guessed. Vannevar Bush, as the academic advisor of Claude Shannon, the godfather of the modern digital age, was more prepared to envision it.

(Luhmann’s “you” in his quote is obviously only a Western cultural referent which erases the existence of oral based cultures which have other ways to do their sophisticated thinking. His ignorant framing on the topic shouldn’t be a shared one.)

This post has grown out of my own personal commonplace book, portions of which are on housed on my blog, in a wiki, and in a private repository of which I hope to make more public soon. Further thoughts, ideas and expansions of it are more than welcome.

I’ve slowly been updating pieces of the history along with examples on shared commonplaces in both the IndieWeb Wiki and Wikipedia under the appropriate headings. Feel free to browse those or contribute to them as you would, at least until our digital commonplace books can communicate with each other.

I’d also invite those who are interested in this topic and who have or want online spaces to do this sort of thing to join us at the proposed upcoming Gardens and Streams II IndieWebCamp Pop up session which is being planned for later this Summer or early Fall. Comment below, stop by the page or chat to indicate your interest in attending.

Congratulations to Christoph Adami (@ChristophAdami) on release day for The Evolution of Biological Information: How Evolution Creates Complexity, from Viruses to Brains! I’m awaiting the post for my own hardcover copy. 

Bookmarked Tibor Gánti (1933- 2009): Towards the Principles of Life and Systems Chemistry (Journal of Theoretical Biology | sciencedirect.com)
Edited by Eörs Szathmáry
Volume 381, Pages 1-60 (21 September 2015)
ᔥ Michael Marshall in He may have found the key to the origins of life. So why have so few heard of him? ()

D

Bookmarked Vocabulary of Definitions of Life Suggests a Definition by Edward N. Trifonov (Journal of Biomolecular Structure and Dynamics Volume 29, 2011 - Issue 2)
Analysis of the vocabulary of 123 tabulated definitions of life reveals nine groups of defining terms (definientia) of which the groups (self-)reproduction and evolution (variation) appear as the minimal set for a concise and inclusive definition: Life is self-reproduction with variations.
https://doi.org/10.1080/073911011010524992

ᔥ Michael Marshall in He may have found the key to the origins of life. So why have so few heard of him? ()

Bookmarked Cellular Homeostasis, Epigenesis and Replication in Randomly Aggregated Macromolecular Systems by Stuart A. Kauffman (Journal of Cybernetics Volume 1, 1971 - Issue 1)
Pages 71-96 | Published online: 15 Apr 2008
https://doi.org/10.1080/01969727108545830
Proto-organisms probably were randomly aggregated nets of chemical reactions. The hypothesis that contemporary organisms are also randomly constructed molecular automata is examined by modeling the gene as a binary (on-off) device and studying the behavior of large, randomly constructed nets of these binary “genes.” The results suggest that, if each “gene” is directly affected by two or three other “genes,” then such random nets: behave with great order and stability; undergo behavior cycles whose length predicts cell replication time as a function of the number of genes per cell; possess different modes of behavior whose number per net predicts roughly the number of cell types in an organism as a function of its number of genes; and under the stimulus of noise are capable of differentiating directly from any mode of behavior to at most a few other modes of behavior. Cellular differentiation is modeled as a Markov chain among the modes of behavior of a genetic net. The possibility of a general theory of metabolic behavior is suggested. Analytic approaches to the behavior of switching nets are discussed in Appendix 1, and some implications of the results for the origin of self replicating macromolecular systems is discussed in Appendix 6.

ᔥ Michael Marshall in He may have found the key to the origins of life. So why have so few heard of him? ()

Bookmarked Budding and Division of Giant Vesicles Linked to Phospholipid Production by Juan M. Castro, Hironori Sugiyama, Taro Toyota (Scientific Reports volume 9, Article number: 165 (2019))
The self-reproduction of supramolecular assemblies based on the synthesis and self-assembly of building blocks is a critical step towards the construction of chemical systems with autonomous, adaptive, and propagation properties. In this report, we demonstrate that giant vesicles can grow and produce daughter vesicles by synthesizing and incorporating phospholipids in situ from ad-hoc precursors. Our model involves acyl chain elongation via copper(I)-catalyzed azide-alkyne [3 + 2] cycloaddition reaction and the ensuing production of synthetic phospholipids to induce budding and division. In addition, the growth and budding of giant vesicles were compatible with the encapsulation and transfer of macromolecules as large as lambda phage DNA to the buds. This chemical system provides a useful model towards the implementation of cell-like compartments capable of propagation and transport of biological materials.

ᔥ Michael Marshall in He may have found the key to the origins of life. So why have so few heard of him? ()

Bookmarked Nonenzymatic Template-Directed RNA Synthesis Inside Model Protocells by Katarzyna Adamala (science.sciencemag.org)
The potential for self-replication makes RNA an attractive candidate as a primordial catalysis in the origin of life. Catalysis may have occurred in some kind of compartment, possibly a fatty acid vesicle. However, RNA catalysis generally requires high levels of magnesium, which are incompatible with fatty acid vesicle integrity. Adamala and Szostak (p. [1098][1]) screened magnesium chelators and found that several—including citrate, isocitrate, and oxalate—could maintain the membrane stability of fatty acid vesicles in the presence of Mg2+. Citrate also allowed Mg2+-dependent RNA synthesis within protocell-like vesicles, while at the same time protecting RNA from Mg2+-catalyzed degradation. Efforts to recreate a prebiotically plausible protocell, in which RNA replication occurs within a fatty acid vesicle, have been stalled by the destabilizing effect of Mg2+ on fatty acid membranes. Here we report that the presence of citrate protects fatty acid membranes from the disruptive effects of high Mg2+ ion concentrations while allowing RNA copying to proceed, while also protecting single-stranded RNA from Mg2+-catalyzed degradation. This combination of properties has allowed us to demonstrate the chemical copying of RNA templates inside fatty acid vesicles, which in turn allows for an increase in copying efficiency by bathing the vesicles in a continuously refreshed solution of activated nucleotides. [1]: /lookup/doi/10.1126/science.1241888

ᔥ Michael Marshall in He may have found the key to the origins of life. So why have so few heard of him? ()

Read He may have found the key to the origins of life. So why have so few heard of him? by Michael MarshallMichael Marshall (Science)
Hungarian biologist Tibor Gánti is an obscure figure. Now, more than a decade after his death, his ideas about how life began are finally coming to fruition.
Good to see Tibor Gánti finally getting some credit. This is a great little article with a nice overview of the Origin of Life problem (and references). The author Michael Marshall has a new book out on the topic.

ᔥ Peter Molnar in IndieWeb Chat ()

Read What Is an Individual? Biology Seeks Clues in Information Theory. (Quanta Magazine)
To recognize strange extraterrestrial life and solve biological mysteries on this planet, scientists are searching for an objective definition for life’s basic units.
I’ve been following a bit of David’s work, but obviously there’s some newer material I need to catch up on. I like the general philosophical thrust of their direction here. I can see some useful abstractions to higher math here, maybe an analogy to a “calculus of biology” which doesn’t look at single points, but rates of change of that point(s).
Read The Wuhan Virus: How to Stay Safe by Laurie Garrett (Foreign Policy)
As China’s epidemic continues to spread, things may seem scary. Here are 10 simple precautions that can protect you from contracting the coronavirus.

Some simple and easy to carry out precautions for the coming months.

ᔥ On the Media Black Swans ()

👓 What can Schrödinger’s cat say about 3D printers on Mars? | Aeon | Aeon Essays

Read What can Schrödinger’s cat say about 3D printers on Mars? by Michael Lachmann and Sara Walker (Aeon | Aeon Essays)
A cat is alive, a sofa is not: that much we know. But a sofa is also part of life. Information theory tells us why
A nice little essay in my area, but I’m not sure there’s anything new in it for me. It is nice that they’re trying to break some of the problem down into smaller components before building it back up into something else. Reframing things can always be helpful. Here, in particular, they’re reframing the definitions of life and alive.

🔖 Origins Of Life | Complexity Explorer

Bookmarked Origins Of Life (complexityexplorer.org)

About the Course:

This course aims to push the field of Origins of Life research forward by bringing new and synthetic thinking to the question of how life emerged from an abiotic world.

This course begins by examining the chemical, geological, physical, and biological principles that give us insight into origins of life research. We look at the chemical and geological environment of early Earth from the perspective of likely environments for life to originate.

Taking a look at modern life we ask what it can tell us about the origin of life by winding the clock backwards. We explore what elements of modern life are absolutely essential for life, and ask what is arbitrary? We ponder how life arose from the huge chemical space and what this early 'living chemistry'may have looked like.

We examine phenomena, that may seem particularly life like, but are in fact likely to arise given physical dynamics alone. We analyze what physical concepts and laws bound the possibilities for life and its formation.

Insights gained from modern evolutionary theory will be applied to proto-life. Once life emerges, we consider how living systems impact the geosphere and evolve complexity. 

The study of Origins of Life is highly interdisciplinary - touching on concepts and principles from earth science, biology, chemistry, and physics.  With this we hope that the course can bring students interested in a broad range of fields to explore how life originated. 

The course will make use of basic algebra, chemistry, and biology but potentially difficult topics will be reviewed, and help is available in the course discussion forum and instructor email. There will be pointers to additional resources for those who want to dig deeper.

This course is Complexity Explorer's first Frontiers Course.  A Frontiers Course gives students a tour of an active interdisciplinary research area. The goals of a Frontiers Course are to share the excitement and uncertainty of a scientific area, inspire curiosity, and possibly draw new people into the research community who can help this research area take shape!

I’m totally in for this!

Hat tip for the reminder to:

Listened to Steven Johnson on the Importance of Play and the Decisions We Make by Alan Alda from Clear+Vivid with Alan Alda

How do we come up with ideas? How do we make decisions? And how can we do both better? Steven Johnson has explored this question and written a dozen books about it. In this playful, thoughtful episode, Steven has some fascinating stories, like how Darwin made the decision to get married — or how a defecating duck helped lead to the invention of the computer. Through their own stories, Steven and Alan Alda share their thoughts about the transformative nature of ideas and what sort of environments best give rise to creativity.

I love the idea of the slow hunch discussed here. It’s part of the reason I keep a commonplace book. Johnson also discusses his own personal commonplace book, though he doesn’t give it that particular name here.

The commercial about Alda Communication Training makes me wonder if they recommend scientists and communicators have their own websites? In particular, I’m even more curious because of Johnson’s mention of his commonplace book and how he uses it in this episode. I suspect that scientists having a variety of interconnecting commonplaces (via Webmention) using basic IndieWeb or A Domain of One’s Own principles could better create slow hunches, create more links, increase creativity and diversity, and foster greater innovation. I’ll have to follow up on this idea. While some may do something slightly like this within other parts of social media, I don’t get the impression that it’s as useful a tool in those places (isn’t as searchable or permanent feeling, and is likely rarely reviewed over). Being able to own your digital commonplace as a regular tool certainly has more value as Johnson describes. Functionality like On This Day dramatically increases its value.

But there’s another point that we should make more often, I think, which is that one of the most robust findings in the social sciences and psychology over the last 20 years is that diverse groups are just collectively smarter and more original in the way that they think in, in both their way of dreaming up new ideas, but also in making complicated decisions, that they avoid all the problems of group think and homogeneity that you get when you have a group of like minded people together who are just amplifying each other’s beliefs.—Steven Johnson [00:09:59]

Think about a big decision in your life. Think about the age span of the people you’re talking to about that choice. Are they all your peers within three or four years? Are you talking somebody who’s a generation older and a generation younger?—Steven Johnson [00:13:24]

I was talking to Ramzi Hajj yesterday about having mentors (with a clear emphasis on that mentor being specifically older) and this quote is the same sentiment, just with a slightly different emphasis.

One of the things that is most predictive of a species, including most famously, humans, of their capacity for innovation and problem solving as an adult is how much they play as a newborn or as a child.—Steven Johnson [00:28:10]

Play is important for problem solving.

I think you boil this all down into the idea that if you want to know what the next big thing is, look for where people are having fun.—Alan Alda [00:31:35]

This is interesting because I notice that one of the  binding (and even physically stated) principles of the IndieWeb is to have fun. Unconsciously, it’s one of the reasons I’ve always thought that what the group is doing is so important.

Ha! Alda has also been watching Shtisel recently [00:50:04].

📑 Solomon Golomb (1932–2016) | Stephen Wolfram Blog

Annotated Solomon Golomb (1932–2016) by Stephen Wolfram (blog.stephenwolfram.com)

As it happens, he’d already done some work on coding theory—in the area of biology. The digital nature of DNA had been discovered by Jim Watson and Francis Crick in 1953, but it wasn’t yet clear just how sequences of the four possible base pairs encoded the 20 amino acids. In 1956, Max Delbrück—Jim Watson’s former postdoc advisor at Caltech—asked around at JPL if anyone could figure it out. Sol and two colleagues analyzed an idea of Francis Crick’s and came up with “comma-free codes” in which overlapping triples of base pairs could encode amino acids. The analysis showed that exactly 20 amino acids could be encoded this way. It seemed like an amazing explanation of what was seen—but unfortunately it isn’t how biology actually works (biology uses a more straightforward encoding, where some of the 64 possible triples just don’t represent anything).  ❧

I recall talking to Sol about this very thing when I sat in on a course he taught at USC on combinatorics. He gave me his paper on it and a few related issues as I was very interested at the time about the applications of information theory and biology.

I’m glad I managed to sit in on the class and still have the audio recordings and notes. While I can’t say that Newton taught me calculus, I can say I learned combinatorics from Golomb.

Bookmarked From bit to it: How a complex metabolic network transforms information into living matter by Andreas Wagner (BMC Systems Biology)

Background

Organisms live and die by the amount of information they acquire about their environment. The systems analysis of complex metabolic networks allows us to ask how such information translates into fitness. A metabolic network transforms nutrients into biomass. The better it uses information on available nutrient availability, the faster it will allow a cell to divide.

Results

I here use metabolic flux balance analysis to show that the accuracy I (in bits) with which a yeast cell can sense a limiting nutrient's availability relates logarithmically to fitness as indicated by biomass yield and cell division rate. For microbes like yeast, natural selection can resolve fitness differences of genetic variants smaller than 10-6, meaning that cells would need to estimate nutrient concentrations to very high accuracy (greater than 22 bits) to ensure optimal growth. I argue that such accuracies are not achievable in practice. Natural selection may thus face fundamental limitations in maximizing the information processing capacity of cells.

Conclusion

The analysis of metabolic networks opens a door to understanding cellular biology from a quantitative, information-theoretic perspective.

https://doi.org/10.1186/1752-0509-1-33

Received: 01 March 2007 Accepted: 30 July 2007 Published: 30 July 2007

Hat tip to Paul Davies in The Demon in the Machine