Category Archives: Self-organization

The Garden

The Garden of Earthly Delights by Hieronymus Bosch

“The Garden is the optimal juxtaposition of nature and culture” – Jordan Peterson (on the Ben Shapiro Show)

A Garden is a wonderful exemplar, not only metaphor, of how humans ought to (must!) relate to the world if we hope to live in harmony with natural processes. 

Humans are unique in their ability and willingness to transform the environment around them. 

The problems begin when we overestimate what we can build, understand, govern and control without pathological side effects.

Gardening is ‘engineering’ in which what we build is the context in which we hope living organisms will flourish that in turn create a favorable environment for us to flourish within. We don’t, and can’t, build the organisms — they must build themselves. 

The attempt to industrialize the nurturing of living organism for human benefit, as in industrial agriculture and animal farming, has led to ecosystem damage, unethical treatment of animals, and in its most acute form, massive systemic risk that is deeply under-appreciated.

These negative aspects are not incidental, but flow directly from the framing and assumption set. The mistake is to treat these systems as a complicated machines, rather than organic and complex.

In order to direct complex living systems towards human ends, without pulling out the rug from underneath ourselves as a result of unintended consequences, we must recognize that our ability to build must be applied in a way that generates environments within which self-organizing, living systems can generate themselves. 

You don’t build a sunflower. You don’t build a tree. You can’t. 

The best you can do is create the conditions in which the sunflower will thrive as it builds itself. 

The Garden is the exemplar for achieving harmony between man’s imposition onto the world, and the world’s essential self-generating nature. 

What Life Is and Crafting Exposure

Or when life gives you X make f(X)

A central question in the biological sciences is “what is life?”. What are the properties that make some system qualify as living and others as non-living?

The hardest scientific challenges are often the ones that seem intuitively easy. We don’t know what makes a system a living one, but we know it when we see it. 

What is clear is that life is complex. Living systems are without exception composed of many interacting parts that are interdependent and mutually-constitutive. This is essentially a formulation of one theory of life put forward by biologists Humberto Maturana and Francisco Varela and expanded upon by Evan Thompson termed ‘autopoiesis’. For them, a living system is one organized as a closed network of ‘enabling dependencies’. (They also claim this organizational property is prior to features such as self-replication and heredity in defining life. I’ll avoid that debate for now, but it is worth consideration.)

The leaves and the roots of the plants enable one another’s continued existence. They are also enabled by the sun, but nothing in the plant enables the sun, so it is outside this closed enabling-network and therefore not part of the autopoietic (living) system. However, the sun and the rain are crucial for the plant. All far-from-equilibrium systems need flows of matter and energy to maintain their structure. And life is nothing if not far-from-equilibrium.

The problem I see with autopoiesis as a definition of life is that phenomena we would intuitively identify is non-living seem to fit the bill. Hurricanes have their form maintained over time by virtue of their internal organization (the ‘spiral’ dynamic of the relevant atmosphere is self-reinforcing) coupled with the enabling flow of matter and energy from the warm, wet ocean. This sounds a lot like the plant.*

But a hurricane is not alive. There is a missing ingredient.

In Nassim Taleb’s book Antifragile he drives home the essential distinction between a random variable X and an agent’s exposure to a random variable f(). If we can properly craft f(), we can do a lot less work in trying to predict or control X, and let our payoffs come from f(X) — not the naked X. Taleb goes into great specificity on the form(s) f() might take, and what that means for the system’s gains and losses in the face of uncertainty, but we won’t delve into that here. 

For purposes of thinking about the question “what is life?”, we can think of the environment at large as a random (high-dimensional) variable that a system is exposed to and interfaces with.

And here is the key difference: the hurricane is exposed, nakedly, to X. If the water warms => persistence. If a cold front moves into the area => disintegration. The internal structure of the hurricane does not in any way adjust itself to a more favorable exposure for increasing persistence. 

But life does. The plant doesn’t merely receive sunlight, it reaches for it. The internally generated behaviors of the plant actively craft their exposure: increasing exposure to enabling dependencies, and decreasing exposure to sources of harm. 

This is a non-trivial difference. We summarize with the following speculation:

Living systems are those which are both autopoietic and whose internally generated structures, dynamics, behaviors, and forces are involved in crafting its exposure f(X) to increase its persistence. 

*[Note added after initial publication: In correspondence, Evan Thompson has disputed that a hurricane is autopoietic. I am not convinced by his arguments here, as I read them to depend on particular substantial properties rather than organizational properties. Nonetheless, Evan admits of autopoietic systems that are indeed not living, so the dispute over whether hurricanes are autopoietic or not is immaterial to the main thrust of this post.]

Complex Systems Science: An Informal Overview — Part III: Synthesis of purposeful systems

 This is Part 3 of a multipart series, see Part 1 and Part 2 for additional context.

Purposeful System Synthesis

When we look around the world, we notice that many systems seem to work. That is, they accomplish some task that is useful, they fulfill a purpose or serve a function. The heart beats in order to pump oxygen through the distributed tissues of the body, and inner ear bones play a role in transducing air pressure waves into neural patterns that can inform behavior.

These terms — use, purpose, function — are extremely familiar to us. We live with them as concrete realities. I use the car to get to the store, to get food, to cook a meal, to eat with the family.

Reductionism has no place for these realities. It has no room function or purpose. In a reductionistic universe, nothing happens in order that something else can happen; it just happens. Period. End of story.

Anything that appears otherwise is an epiphenomenon, essentially an illusion.

In biology this deficiency has been most acute. Reductionistic biologists are forced into continuous doublespeak in which they discuss how living systems function — with the implicit understanding that the things they discuss don’t really exist and don’t really have any functions.

This is not mere semantics. This philosophical-blockage has delayed many important conversations in science, and in connecting science to a mature ability to synthesize purposeful systems.

Of course we can salvage a scientific understanding of function as soon as we admit emergent phenomena into our discourse. Functions emerge out of relations. The function of the heart is not something to be found by looking at the heart, but at looking at its network(s) of relationships. For a highly-recommended deep dive into this topic, see Life Itself by Robert Rosen.

Not all emergent properties are functional, but all function is emergent.


For manmade systems, the typical answer to “how did that system get organized so that works?” is “someone put it that way”. That is, the organization is imposed by an external agent who understand how the parts work together to make something useful happen.

This is also how creationists explain where we, as biological creatures, came from, and why we are organized the way we are: an agent arranged us that way. “Intelligent design”.

Of course as a scientific answer to the question of our existence this is no good. But it still sounds pretty good for cars.


How do things get organized when there is no one to organize them? Simply, they organize themselves!

In self-organized systems, all the parts that compose the system just “do their thing”. No part needs to know about the system it’s a part of, its organization, or even that it exists. Each part interacts locally with its neighbors (in physical or abstract space), and often its behaviors are characterized by a simple set of rules. Order that persists is a consequence of there being something globally stable about an arrangement that these parts discover by chance — by wiggling around randomly, essentially. 

A tangible example is the formation so-called micelles. Micelles are physical systems that are similar in many ways to cellular membranes found in living organisms. They are organized in a roughly spherical pattern, embodying a boundary between an ‘internal’ and ‘external’ environment.


This arrangement is entirely a consequence of the properties of the molecules and their relations with each other and their local environment. The relevant properties are as follows: some lipid molecules happen to be structured with a head and a tail. Further, the heads of the lipids are attracted to water, whereas the tails are repelled. This polarity doesn’t mean much for a single lipid molecule, but when a bunch of them get near each other, something special happens: the tails, being repelled by the water they are in, find refuge in huddling together, so to speak. The more that bunch together, the less water there is locally, and the less repulsive that environment becomes to the tails. The heads, being attached to the tails, can’t go far. But they don’t mind being wet, so they point out away from the huddled tails. And voila, a membranous sphere.

That’s it. No designer, no constructor, no external agent, but an organized system. Organization for free. (Well, sort of.)

Micelles are not in any direct sense “functional”. But cell membranes are. Every cell relies on the self-organization of its membrane in order that it persists by constraining critical operations within a semi-controlled environment.


Not all such arrangements persist, of course. Things break. Cells die. The volatility of the environment tests the fragility of everything, weeding out those patterns that do not withstand the variability.

This is, simply, Natural Selection. With enough time, and therefore enough volatility, the patterns that persist are those which are able to respond to volatility by adjusting their internal patterning and/or modifying their exposure. In other words, things become alive.

These are the two sisters of evolution: creation and destruction. Self-organization provides a rich variety of ordered patterns, environmental stress tests these structures for ability to persist.


Engineering is the practice of synthesizing systems to solve human problems. Many of the problems we face today are of enormous complexity. The systems we synthesize in an attempt to address these problems necessarily involve many interacting parts including individuals, organizations, and technologies.

Traditional engineering practices are reductionistic, and assume that a plan of roughly the following form will successfully solve any given problem:

    1. Break problem into pieces
    2. Construct a component that solves each problem-piece
    3. Put pieces together into working whole

The realities that throw a wrench in this process when it comes to large-scale complex systems are myriad, but the regularity of costly failures that result from its application is reason enough to look for a more sufficient way of thinking and doing. 

A figure-ground reversal is needed in the engineering practices in order to facilitate the synthesis of purposeful systems whose complexity is outside the cognitive scope of any individual: a shift in emphasis from the specific structure of a complete solution, to the evolutionary environment in which problem-solving systems can evolve.

Without further argument about the potential for evolution to generate complex adaptive systems with the ability to solve a huge variety of problems, I offer several practical principles informed by evolutionary synthesis for systems engineers and systemic designers to consider in the face of complex real world challenges.

Practical principles:

    • Foster (non-toxic) variety

Evolution happens over ensembles, not individuals. Without variety there is no potential for evolution. Consider how variety is generated in the system, and foster it even when ‘reasonable’ solutions are already discovered. Never put all your eggs in one basket.

    • When resources are abundant, foster the non-obviously-useful

Unlike explicitly designed systems, what is not obviously useful, sometimes is, or can be.  Our inner ear bones that we use to hear evolved from the jawbone of our fishlike ancestors. The reductionistic engineer would have optimized away our ability to hear long ago.

    • Allow for heredity

Systems that show signs of success should be able to pass on their form to subsequent generations. The nature and mechanism of this process will vary from domain to domain.

    • Detect and fail fast, and local, the toxic

Again, harmful varieties should be rooted out as early and as locally as possible, before becoming systemic.

    • Coevolve components

Things work well together when evolved together. The corollary is: don’t expect components that did not coevolve to work well together.

    • Expose to the ecological early

Exposure to the real problem environment the system is supposed to operate in during development/evolution of varieties will buffer against over-designing, and provide an opportunity for the maturation of systems that can handle the true complexity of their task.

    • But not too early

Sometimes it may benefit a system to have some simulated experiences or otherwise explore its range of behaviors with buffered consequences before deployment. This can be seen in the biological world for example in the propensity for play in the most complex organisms. Balancing the potential benefits of playtime with the need to get a big boy job is an art, not a science.

    • Figure-ground reversal: attend more to the selective and generative aspects of the evolutionary environment, less to a specific imagined solution

This does not imply imagined solutions should play no role, but that they should be part of an ensemble of potential solutions. Again: eggs, baskets.

    • Resist the temptation to scale quickly a promising solution

Solutions should prove themselves in time. Often, success can be incidental but look causal; we are fooled by randomness. Moreover some malignancies develop slowly and quietly. We will be thankful when they show up that we moved slowly.

Complex Systems Science: An Informal Overview — Part II: Organization and Scale

This is part 2 of a series informally introducing and discussing ideas in complex systems science, and their relevance to how we build our world. Here is part 1. 

Complex Systems Science and the Special Sciences

We are familiar with science being broken down into different categories depending on what is being studied: particle physics (e.g. electrons), chemistry (molecules), biology (organisms), psychology (minds), sociology (groups of humans), etc. Call these the special sciences as their role is to look into a certain kind of stuff.

Complex systems science is not defined by what the stuff under study is, but rather how one asks and attempts to answer questions about whatever stuff is of interest. Recall that in complex systems, the properties we are interested in might emerge from interactions among components, i.e. emergent properties. For this reason, in complex systems science we pay special attention to the interactions and relationships among the parts, and how they give rise to (emergent) patterns of behavior.

We can do this in physical systems, biological systems, social systems, or any other system of interest. The answers we get will often look remarkably different than those from the special sciences.

Organization and Interdependence

When we attend to the interactions and relationships in a system, the organization of the stuff becomes more central to our understanding than the stuff itself. To illustrate this point, imagine a mad scientist takes each cell of your body one by one and relocates it to a random location — would you feel much like yourself? I think not. When the organization is disrupted, so are the interactions, and the nature of the system changes.

This also means when you change one part of the system, you may affect a larger portion of, or even the whole, system. This is because the behavior of the parts are interdependent. What part A is doing affects what part B & C are doing (and perhaps vice verse) — what my heart is doing affects what my lungs and muscles are doing. Interdependent behavior presents all kinds of challenges to standard statistical approaches which assume the independence of parts of a system.

Whether or not the change in one part of a system has affects on other parts of the system depend on its organization. If you had to choose between losing a kidney or a heart, which would you choose? Would a tree do better off losing ten-thousand leaves or one trunk?

These are hints to be cautious of centralization, and to use redundancy for robustness when possible. When we build systems we should ask ourselves, “what would happen if X failed?” — even if we are pretty sure X won’t fail.

More is Different

‘More is different’ is another way of saying ‘emergence happens’. It is no easy task to predict what the emergent effects will be when we scale a system (i.e. increase its size/number of components), especially when operating under reductionistic assumptions (emergent effects will always surprise the reductionist).

When engineering systems, emergent effects are often detrimental, or even catastrophic, to the integrity of the system, and therefore the purpose it was intended to fulfill. This is because, at the smaller scale, what appear as irrelevant side-effects (which may not have been noticed or attended to at all) are able to be absorbed or dissipated into the system’s environment in some way or another. When we grow the system, these ‘side-effects’ can coalesce and become relevant to the behavior of the system.

This is why we don’t see land animals much bigger than elephants throughout Earth’s history: the mechanical forces that are mere side-effects for smaller critters become causes of failure. Darwin puts a harsh limit on the scale of a design motif.

There are countless engineering failures that are of enormous cost to society (e.g. F-35, USS Zumwalt, the global financial system). Overgrown elephants.

The holy grail of systems engineering is to leverage emergence rather than fighting against it. Nature manages to do this via evolutionary tinkering. Perhaps we can take a cue from her.

Thoughts on Brexit and Persistent Complex Systems

All complex biological systems have boundaries. Cells have membranes, and some have walls. Multicellular organisms are bounded in skin, and there are many internal barriers that limit access to select agents (e.g. the blood-brain barrier). Swarms, flocks, and herds limit their exposure to predators by aggregating spatially, forming a boundary between in- and out-herd. Human societies live more peacefully with their neighbors when their boundaries are clearly established, often by physical features like mountains and rivers.

This is not a coincidence. For all of these systems, what is most essential to their persistence is their internal organization and selective interfaces with the environment. This organization is not a given, it has been achieved over the chronicle of evolutionary history. For all of these systems, to ‘open them up’ means a breakdown of that organization. Consider what happens to a cell when you ‘open up’ its membrane and allow any agents in the environment to flow freely through it. The organization is lost — the cell is lost.

The United Kingdom has made history by voting for their independence, and taking a step in reaffirming their functional boundaries. We will see more of this in the coming weeks, months, and years. Despite those who cite fragile economic predictions as reasons to ‘remain’ subject to centralized bureaucratic actors, there are much more basic reasons to ‘leave’, and the economists don’t have them in their equations.

In biological systems, boundaries are permeable, but not arbitrarily — they are semi-permeable. Systems which depend on their internal organization for persistence in the face of uncertainty must be free to manage their own semi-permeable boundaries, else they will make a Darwinian exit, making room for those organizations that are more able and willing to do so.

Self-organizing Patterns: Local Activation, Long-range Inhibition

These automata follow a simple rule: Try to be the same color as those near me, and the opposite color of those a little further away. Slight biases vary background/foreground relations, and initial conditions determine other aspects of the transient and stable patterns (e.g. the random initial condition in Video 3 vs the approximately symmetrical ring set as the initial condition in Video 4).


Video 1


Video 2


Video 3


Video 4