ECCO Working paper 2015-01

Chemical Organization Theory as a universal modelingframework for self-organization, autopoiesis andresilience
Francis Heylighen1,3, Shima Beigi1,2 and Tomas Veloz3,4,5Abstract: Chemical Organization Theory (COT) is a recently developed formalism inspiredby chemical reactions. Because of its simplicity, generality and power, COT seems able totackle a wide variety of problems in the analysis of complex, self-organizing systems acrossmultiple disciplines. The elements of the formalism are resources and reactions, where areaction (which has the form a + b + … → c + d +…) maps a combination of resources onto a
new combination. The resources on the input side are “consumed” by the reaction, which“produces” the resources on the output side. Thus, a reaction represents an elementary
process that transforms resources into new resources. Reaction networks tend to self-organize
into invariant subnetworks, called “organizations”, which are attractors of their dynamics.
These are characterized by closure (no new resources are added) and self-maintenance (noexisting resources are lost). Thus, they provide a simple model of autopoiesis: theorganization persistently recreates its own components. Organizations can be more or lessresilient in the face of perturbations, depending on properties such as the size of their basin of
attraction or the redundancy of their reaction pathways. Concrete applications oforganizations can be found in autocatalytic cycles, metabolic or genetic regulatory networks,
ecosystems, sustainable development, and social systems.

Introduction
Complex adaptive systems are systems consisting of many interacting agents that exhibit somedegree of self-organization (Holland, 2012): coherent patterns or forms of organization
spontaneously emerge out of the network of interactions. Most of the phenomena we are confronted
with in real life are such complex adaptive systems: people, organisms, societies, ecosystems,
markets, communities, cultures… Great progress has been made in understanding the dynamics ofsuch systems by means of multi-agent computer simulations (Miller & Page, 2007). However, on the

1

Global Brain Institute, Vrije Universiteit Brussel

2

Department of Civil Engineering, University of Bristol

3

CLEA, Vrije Universiteit Brussel

4

Instituto de Filosofía y Ciencias de la Complejidad - IFICC, Santiago, Chile.

5

Mathematics department, University of British Columbia - Okanagan

2more general theoretical level, our understanding of self-organization and adaptation remains rather
superficial and fragmented.
Part of the reason is that the conceptual and mathematical building blocks of our theories arepoorly fitted to describe emergence and interaction. Scientific models start by analyzing a system
into its static components together with the properties in which these components can vary. The
values of these different variables then define the state of the system. The different possible states
determine a predefined state space. Only after introducing all these static elements can we start todescribe the evolution of that system as a trajectory in state space. This approach makes it very
difficult to understand the kind of fundamental changes that lead to the emergence of newcomponents, properties or systems.
An alternative approach is to start from a process metaphysics (Rescher, 1996; Whitehead,1978) or action ontology (Heylighen, 2011; V. F. Turchin, 1993). Such a philosophy assumes thatreality is not constituted out of static “things”, but out of dynamic processes or actions. The problem
until now was to represent such processes in a way that is simple, precise and concrete. As noted,
traditional scientific formalisms model processes as transitions between states. In addition to an apriori specification of the state space, this requires a system of equations, laws or dynamics thatspecify why and how a particular state is mapped onto a particular other state.
This paper wishes to introduce an alternative formalization of processes, namely the reaction
networks used in what has been called Chemical Organization Theory (COT) (Dittrich & Fenizio,
2007; Dittrich & Winter, 2008; Peter, Veloz, & Dittrich, 2011). In COT, the relation between statesand dynamics is turned upside down. The processes are primary, in the form of the “reactions”,
which are the most fundamental elements of a reaction system. States only appear in a second stage,as the changing concentrations of the “molecules” that the reactions are processing into othermolecules. The molecules therefore are not static objects, but merely raw materials that are
constantly being produced, consumed, and recreated by the reactions. In that sense, COT seems to be
the first formalization of a process ontology that is both practical and fundamental.
The fundamental character means that COT can describe systems and processes in any
discipline—from elementary particle reactions via systems biology and cognitive science to thepolitical organization of society. Its particular strength is that it provides an elegant mathematicalmethod to define and construct organizations, i.e. self-sustaining networks of interactions within alarger network of potential interactions. As such, it is eminently suited to describe self-organization,
autopoiesis, sustainability, resilience, and the emergence of complex, adaptive systems out of simpler
components.
Next to its deep philosophical foundation, COT derives its power from its concreteness andsimplicity: basically, you can represent any process in the real world as a combination of reactions
between suitably chosen “molecules”, and then start analyzing the resulting reaction system for selfmaintenance, closure, and other observable properties. Moreover, COT models are eminently
modular: it is trivial to add or to remove molecules or reactions from an existing model, and(somewhat less trivial) see what effect that has on the emerging organizations and other properties.
This makes it possible to model systems of great complexity, where you start with a simple model in3order to get an intuitive grasp of what is going on, and then gradually add more detail andsophistication in order to achieve a more realistic representation.
Finally, COT focuses on what are the truly most important questions about a complex
adaptive system: in how far is it sustainable and resilient, i.e. able to maintain itself bothautonomously and in the face of external perturbations? In how far does it grow, remain the same, or
perhaps diminish and decay? If it is perturbed to such a degree that it cannot maintain its present
organization, which new type of organization is it likely to evolve into? How do its components andprocesses co-evolve, mutually adapt, and become coordinated into a synergetic whole? In summary,
how does it self-organize into a robust, coherent whole?
The latter is perhaps the most important question in the whole of science and philosophy, andtheir applications to society. Practically all the phenomena we are confronted with—including
matter, organisms, ecosystems, societies, and minds—are the result of self-organization producing
complex wholes out of simpler components. Any general theory that would help us to understand,model and control that process is likely to revolutionize our worldview, while opening up an endlessvariety of concrete applications.
The present paper wishes to make the case that COT, together with its future extensions,provides an extremely promising foundation for such a general theory. It will do that first by pointing
out how the COT formalisms avoids the pitfalls of earlier approaches, then by offering a preliminary
survey of existing and potential applications of COT in a wide variety of domains. It will do this in a
simple, non-technical way, emphasizing the basic formalism and the core new insights, while
avoiding some of the (relatively) more complex mathematical techniques required for a full
implementation of COT.

Reaction networks
As its name implies, the COT formalism (Dittrich & Fenizio, 2007) is inspired by chemistry, and theway it describes how chemical reactions recombine molecules into new molecules. Therefore, it has
inherited much of its terminology from chemistry. In order to widen its appeal and to convince otherscientists of its potential for transdisciplinary unification, it may be wiser to replace somespecifically chemical terms by more broadly applicable ones. The present paper will therefore
replace some COT terms by new terms—however, while clearly pointing out the changes.
The basis of a COT model is a reaction network. It consists of two types of entities, which wewill call resources (“molecules”, “molecular species”, or “species” in the traditional COT
formulation) and reactions. A resource is an abstract representation of a specific kind of substance,
entity, or, most generally, distinguishable phenomenon. Examples of resources are particular types ofmolecules, elementary particles, biological species, products, objects, tools, messages, words, ideas,or statements. All the resources in the model are assumed to be available in some shared container orworkspace, which in COT is called the “reaction vessel”, but which we will simply call the medium.
This joint presence allows them to interact or react with each other. Reactions denote elementary
processes that create or destroy resources. They typically produce combinations of new resources out

4of combinations of existing resources. However, the simplest reactions just create or destroy a single
resource.
Formally, a reaction network is defined by the 2-tuple <M, R>, where M = {a, b, c, …} is theset of resources, and R ⊆ P(M) × P(M) is the set of reactions, where P(M) denotes the power set (i.e.
the set of all subsets) of M. Each reaction r transforms a particular subset X of M into another subset
Y of M:
r: X → Y: {x1, x2, …| xi ∈ M} → {y1, y2, …| yj ∈ M}
We will call X the input set and Y the output set of r, and denote them respectively In(r) and Out(r).
We will call the elements of In(r) the reactants of r, and the elements of Out(r) its products.
Borrowing the chemical notation for reactions, a reaction is conventionally written as:
r: x1 + x2 + … → y1 + y2 + …
The “+” symbol here represents a conjunction of the resources: x1 and x2 and … all need to be
simultaneously present in In(r) for the reaction to take place, while the reaction simultaneously
produces y1 and y2 and ….
Note that in traditional COT it is assumed that In(r) and Out(r) are multisets. This means thatthe same element xi can occur more than once (say ni times) in In(r). This is necessary to describe
reactions of the form:
2a + b → 3c + d,
or more generally:
n1x1 + n2x2 + … → m1y1 + m2y2 + … with ni, mj ∈ N
For simplicity, we will here work only with ordinary sets, i.e. resources that only occur once in areaction. If necessary, reactions with more than one copy of a resource can be represented as asequence of substages, each adding just one instance of a resource. E.g. 2a + b → e could be
rewritten as a + b → x, x + a → e.

5

a
b

d
r

c

e

Fig. a depiction of the reaction r: a + b + c → d + e

Reaction Networks vs. Traditional Networks
The combined system <M, R> forms a network because the resources in M are linked to each otherby the reactions in R that transform the ones into the others. But this is not a traditional network (i.e.
a directed graph), in which a link connects a single element (“node”, “vertex”) x to a single element
y. A reaction connects a set X of elements to a set Y of elements. In mathematics, a network with thisproperty is called a directed hypergraph (Gallo, Longo, Pallottino, & Nguyen, 1993). This appears tobe the essential generalization that gives reaction networks their power with respect to traditional
network models. Let us try to explain how that happens.
A traditional network consists of nodes N and links L, with L ⊆ N × N. Thus, <L, N> is areaction network, but where the reactions r ∈ L are limited to one input and one output:
r: x → y, with x, y ∈ N
A general reaction network provides much more richness and flexibility because it allows
combinations of inputs to produce combinations of outputs, opening up an exponentially wider range
of interacting processes. In a traditional network, the only way processes can “interact” is by sharing
input or output nodes, e.g.
r1 : x → y
r2 : x → z
r3 : u → yHere an initial state x can lead to y and/or to z via respectively r1 and r2. This immediately creates anambiguity: are r1 and r2 both taking place, producing y and z simultaneously? Or does the process
make a choice between r1 and r2, ending up in either y or z? Similarly, y can be produced via r1
and/or r3 from x and/or u. Do we need both x and u, or is one of them sufficient to produce y? The

6

problem is that in traditional networks there is no way to distinguish between conjunction (“AND”)
and disjunction (“OR”) of nodes and links. Next to juxtaposition of links/reactions, there simply is
no operator to express a different type of combination.
In reaction networks, we have an additional operator, denoted by “+”, that plays the role ofthe conjunction. The juxtaposition of reactions plays the role of the disjunction. Consider thefollowing reactions:r4: x + u → y
r5: w → yThis expresses unambiguously that in order to produce y we need either (x AND u), OR w. Now,
different processes can interact in many ways to produce complex organizations, as we will see infurther sections.
Reaction networks and propositional logic
Interpretation of COT operators in terms of conjunction and disjunction points us towards formal,
Boolean logic, where propositions can be combined in terms of these operators, together with theoperators of implication and negation. Implication is naturally expressed by the “→” operator. This
directly suggests the logical formalism of Horn clauses (Chandra & Harel, 1985). These have thefollowing form:
a&b&…→xThis is to be read as “if a and b and … are true, then x is true”, or “x can be derived from theconjunction of a, b, …”. The translation in terms of reaction networks requires a qualification,
though, which is that if you derive the new proposition x from the conjunction of propositions on the
input side of the inference, then the propositions on that side remain actual (they are not destroyed by
the process). They therefore should properly be listed on the output side as well. This gives us thestraightforward COT translation of a Horn clause:
a+b+…→x+a+b+…
Note that in this interpretation, logical inference is a special type of reaction, namely one in which no“resources” ever get consumed: inferences can only add true propositions to our knowledge, theycannot remove any. This is why logic is inherently static: nothing really changes by making logicalinferences; at most we become aware of additional statements that were already true implicitly, but
had not been proven yet. That is the fundamental reason why all attempts to derive process, actions,dynamics or time from logic are bound to fail, in spite of a plethora of formalization attempts such as“dialectical logics”, “process logics” or “dynamic logics” (see e.g. (Harel, Kozen, & Parikh, 1982;
Ilyenkov, 2008; Van Benthem, 2007). Insofar that these logics describe genuine changes in the state

7of the world, they have left the domain of logic proper and entered the domain of dynamics, which ismore properly described by a formalism such as reaction networks.
The last fundamental operator of logic, negation, does not seem to have any equivalent in the
COT framework. However, we can introduce it by applying the same convention that you use whenmoving variables from one side of an equation to the other side: the variable changes sign, frompositive (“+”) to negative (“–“). For example:
r6: a + b → c + d
could be rewritten as :a→c+d–b
The interpretation is that r6 consumes b, and therefore it produces the absence (“negation”) of b,which we write as “–b”. In logic we have the similar principle of contraposition, which states that
propositions turn into their negations when moved to the other side of an implication:a → b ⇔ –b → –a
To express the negation of a single resource, we may note that reactions can have the empty set (∅)
as their input or output. The production of a out of nothing (“affirmation”) can then be written as:∅ → a, or more simply: → a
The pure consumption or elimination (“negation”) of a is then written as:a→
According to the rule of changing signs when moving to the other side of the arrow, this becomes:→ –aThis is in turn equivalent to the affirmation of –a (“not a”).
Yet another way to grasp the meaning of the negation operator is to start from the “trivial”
reaction, which merely asserts that if a then a:a→aMoving a to the other side then produces the following two reactions:a + (–a) = a – a →

8

→a–a
An intuitive interpretation in terms of processes is that a and –a are like a particle and its antiparticle:
they annihilate each other when they are brought together, or they can be produced together out of
nothing (a “quantum fluctuation of the vacuum”). The interpretation in terms of logic is the law ofcontradiction: a and its negation cannot both be true.

Competition and cooperation
A practical use of negative resources in reaction networks is that they offer us a simple way toexpress contradiction, inhibition or conflict, where the presence of a resource a suppresses thepresence of another resource b: a → – b, which is equivalent to: a + b → ∅ (a and b annihilate eachother). This means that the more a is produced, the more b is consumed, and therefore the lower theconcentration of b becomes. The causal relation between a and b is then negative: increase in a
implies decrease in b, decrease in a implies increase in b. More generally the relation “a inhibits b”
holds when:∃ r such that a, b ∈ In(r), b ∉ Out(r)This means that a is necessary to run a reaction r that consumes, but does not produce, b. The
opposite relation, “a promotes b” applies when a is necessary for a reaction that produces, but does
not consume, b. The relations of inhibition and promotion can be (but need not be) symmetric, inwhich case a and b inhibit or promote each other. In this case, we might say that a and b arecompetitors, respectively cooperators.
Inhibition is a negative causal influence, promotion is a positive one. If you connect anuneven number of negative influences in a cycle, you get a negative feedback loop: the resources
will indirectly suppress themselves. If you connect only positive influences, or include an evennumber of negative influences, the cycle becomes a positive feedback loop: the resources in the cycle
will indirectly promote their own growth. A negative feedback loop leads to either an oscillation or astabilization of the concentrations of the resources around an equilibrium level. Positive feedback
produces an exponential growth of the resources. Systems dynamics (Sterman, 2000) is a very usefulformalism for modeling networks of positive and negative causal influences, and the positive andnegative feedback loops they form. Compared to COT, however, it lacks the ability to combine
different resources in one reaction.
Inhibition seems useful for modeling cognitive processes—both those expressed by formal
logic, and those modelled by neural networks with inhibitory connections. A concrete application
may be the modeling of competitive social communications in which one type of message (say x)
denies, contradicts or suppresses another type (y).
Thus, reaction networks provide an elegant model of competitive or conflictual relations. Theinteractions between reactions take place through their shared resources (“nodes” or “vertices” in9traditional network terminology): the same resource can appear in input and output sets of different
reactions. Because these resources are either consumed or produced by the reactions, different
reactions can either facilitate each other (e.g. when the one produces a resource needed by the other)or hinder each other (when the one consumes a resource needed by the other). This creates acomplex, non-linear dynamic of cooperation (mutual amplification or synergy) and competition(mutual inhibition, conflict, or friction), which is the hallmark of self-organization.
Since the type and quantity of available resources will change under the effect of thereactions that are processing them in the medium they share, reactions too will be initiated,
amplified, suppressed or shut down while the overall process is running. The general logic of selforganization, co-evolution and natural selection (Heylighen, 1992, 1999, 2008) will ensure that thisprocess moves towards a self-sustaining regime, as resources and reactions that do not fit in with the
emerging system are eventually eliminated, while those that efficiently exploit the more abundantresources grow and take over. This is the origin of the “organizations” that we will define further.
Organizations
The most important new concept introduced by COT is an organization. This denotes a reaction
system that is fundamentally self-sustaining: the resources it consumes are also the resources it
produces, and vice-versa. This means that although the system is intrinsically dynamic or processbased, constantly creating or destroying its own components, the complete set of its components(resources) remains invariant, because what disappears in one reaction is recreated by another one,while no qualitatively new components are added.
This property is an essential part of what is called autopoiesis or self-production, a conceptthat Maturana and Varela introduced to characterize living organisms (Maturana & Varela, 1980;
Varela, 1979). Organizations are simpler than living systems, though, because they do not produce aspatial boundary separating them from their environment—the second defining characteristic ofautopoietic systems. As such, they were introduced as simple models for the origin of life out ofcycles of chemical reactions, before the emergence of the first cells that would enclose suchautocatalytic cycles in a membrane, thus separating them from the environment.
Consider a subnetwork <M’, R> of a larger reaction network <M, R>, i.e. M’ ⊆ M. The
formal definition of an organization is derived from three characteristics that such a reaction network<M’, R> can have:• closure: this means that nothing new is generated: the only resources produced by thereactions are those that were already in the starting set M’: ∀ r ∈ R such that In(r) ⊆ M’, therequirement holds that Out(r) ⊆ M’.
• semi-self-maintenance: this is the complementary condition that nothing existing isremoved; each resource consumed by some reaction is produced again by some other reaction
working on the same starting set: ∀ x ∈ M for which ∃ r ∈ R such that x ∈ In(r), ∃ r’ ∈ Rsuch that I(r’) ⊆ M, and x ∈ O(r’).

10•self-maintenance: this is a stronger form of the semi-self-maintenance condition, whichstates that each consumed resource x ∈ M’ is not only produced by some other reaction in<M’, R>, but that the amount produced is at least as large as the amount consumed.

The determination of self-maintenance is more complex than the other two conditions, because it
requires the introduction of a quantitative dynamics in the reaction network, which specifies the rate
at which resources are consumed and produced by the different reactions. This is necessary toestablish the long-term maintenance of the resource set M, because the reactions producing x may beslower than the ones consuming it, so that the concentration of x eventually goes to zero. The rate ofproduction for each of the reactions defines the “flux vector”. Note that the rate of a reaction isnormally proportional to the concentration of its reactants: it increases whenever one of its input
resources increases, and decreases whenever one of its input resources decreases. The flux vector
then needs to be multiplied with the “stoichiometric matrix”, specifying which reactions consume
and which produce a particular resource, in order to calculate the net balance ofconsumption/production (Dittrich & Fenizio, 2007). A resource being produced by a reaction islisted as a positive number in the matrix; a resource being consumed is listed as a negative number.
The product of flux vector and stoichiometric matrix then determines the net rate of production(production minus consumption) for each of the resources.
The requirement for self-maintenance is that this rate is non-negative for all resources, i.e. all
resources either increase or are conserved. The reactive network fulfils this condition if there exists aflux vector (i.e. list of reaction rates) for which this requirement holds. Note that if such a selfmaintaining flux vector exists, then the reaction network will tend to automatically converge to it,
because resources that are consumed more than they are produced will decrease in concentration up
to the point that the reactions consuming them slow down enough so that production (which is notaffected by the concentration of the products, only by the concentration of the resources consumed)compensates for consumption. For simplicity, we will not further discuss this quantitative aspect in
the present qualitative description. Therefore, we will ignore the flux vector and the calculations thatneed to be performed on it in order to determine whether self-maintenance is possible for the given
set of reactions and resources, and just note that this requirement is easy to check computationally.
We are now able to define the crucial concept of organization: a subset of resources andreactions <M’, R> is an organization when it is closed and self-maintaining. This basically meansthat while the reactions in R are processing the resources in M’, they leave the set M’ invariant: noresources are added (closure) and no resources are removed (self-maintenance).
This may seem a rather uninteresting property: nothing really changes. Most theories, models
and formalisms are based on invariant elements, sets and structures, so what is novel here? The
fundamental contrast with classical modeling frameworks is that we started by assuming thateverything changes: all resources are in a constant flux, being consumed by some reactions,produced by others, but by default processed into something different. The concept of organization
establishes that stability can arise even within this turbulent network of changes.
An organization is an emergent, self-producing system, which sustains itself only by
reprocessing its components, and thus constantly rebuilding itself. This is the peculiar property of

11living systems that Maturana and Varela have tried to capture with their concept of autopoiesis.
What COT adds is that the same kind of emergent organization can arise in a wide variety of otherdomains outside of biology, on the sole condition that we have a sufficiently rich network ofreactions and resources. Moreover, COT reformulates the rather difficult and confusing notion of
autopoiesis as a simple mathematical property characterizing even simpler sets of resources andreactions.
Some examples
The simplest organization would consist of the single resource a, and the single reaction: a → a. This
would be the description of a resource that just maintains itself, without interacting with anythingelse. The organization becomes slightly more interesting when we add the reaction → a. Here a is
not just maintained, it is also created out of nothing. We can make it more interesting by adding: a →. This means that a is not only produced or added, it is also removed from the medium (the “reaction
vessel”). This would describe a situation where some resource fluctuates in and out of existence.
For the simplest non-trivial organization, we need two resources {a, b} that interact. They
define an organization when the reactions form a cycle: a → b, b → a. This can be extended with anunlimited number of intermediate stages:
a → b, b → c, c → d, …, z → a.
This is still too simple to be very useful, but we can make it more complex by considering reactions
with more than one input or output, e.g.
a + b → c,
c→d+e+fe → a,
d + f → b.
Here an a and a b together are transformed into a c, which is then converted to d, e and f, which again
produce a and b, so that the cycle can start again. Let us make it more concrete by considering
recognizable resources and reactions, in this case describing the organization of the Earth’s
ecosystem at an abstract level.
→ sunlightplants + sunlight + carbon dioxide + minerals → plants + oxygen
plants + animals + oxygen → animals + carbon dioxide + detritus
detritus + bacteria → bacteria + carbon dioxide + minerals
This describes the recycling of oxygen, carbon dioxide and minerals by plants, animals and bacteria,
fueled by the energy of the sun (which enters the system from the outside, which is why the reaction

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producing it has no input within the system). This is subtler than a simple cycle, because reactions
require several inputs while producing several outputs that are all needed to sustain the organization.
But the system is properly autopoietic, as it produces all its essential components: nothing that isneeded to sustain the organization gets lost; nothing new is added.
Note that some resources (such as bacteria in the last reaction) appear in both the input andoutput of a given reaction. That means that they are neither removed nor added by that reaction. Yet,they are necessary for the reaction to happen. In chemistry, such resources are called catalysts: they
enable or facilitate a reaction, but are not themselves affected by it. In our more generalinterpretation, we may call them agents (Heylighen, 2011): they act on the other resources in thereactions, processing them into something else. For example, the bacteria are the agents that turn
detritus into the carbon dioxide and minerals that are needed by the plants. The plants are the agentsthat transform these resources, with the help of sunlight, into oxygen (and more plants). The animals
act on the plants and oxygen, converting them to detritus and carbon dioxide, which then again
function as “food” for respectively the bacteria and the plants.
Extending the modelThis model of global recycling is of course much too simplified. To start with, it does not specify the
relative proportions of the different resources produced and consumed. For example, plants do not
produce just oxygen, they grow, thus producing more plants. In the multiset version of COT, theadditional amount could be specified e.g. by writing “2 plants + oxygen” on the output side of thereaction. While this may clarify the relative proportions, the actual rate of production would need thefull, quantitative version of COT, which includes the rates of the different reactions as expressed by
the flux vector. We will ignore these complications in the present introductory survey, and continue
focusing on the power of COT for qualitative modeling.
Qualitatively, the simple model could be extended by noting some additional processes, suchas: plants → detritus (plants die, thus producing matter to feed bacteria), and: animals → detritus(animals similarly die). We may also want to specify that it is not only bacteria that break downorganic matter, but fungi as well, thus adding: fungi + detritus → fungi + carbon dioxide + minerals.
But fungi are sometimes eaten by animals: fungi + animals → animals + carbon dioxide + detritus.
A different kind of extension may occur by making the general resource categories more
specific. For example, we could note that not all animals eat plants or fungi, but that some arecarnivores. This leads us to split up the category “animals” into the categories “carnivores”,“omnivores” and “herbivores”, each characterized by its own specific reactions. In this way, we cango on adding reactions and the concomitant resources until we feel the model is detailed enough toinclude everything that seems relevant for a realist description.
But the crucial question remains: is the resulting network an organization? By adding aparticular reaction, we may create a “source” or a “sink” for a particular resource, either injecting it
into a system in which it was previously absent (thus interrupting closure), or removing it from thesystem (thus interrupting self-maintenance). Let us then try to better understand how organizations
emerge.

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Self-organization
An arbitrary subset of a reaction network will in general not be an organization: its reactions working
on its resources will produce additional resources (non-closure). These additional resources may
react with some already present resources producing even further new resources. Thus, every
addition may activate reactions that produce further additions. However, this process of growth of
the resource base must come to an end when there are no further resources that can be produced byreactions working on the already present reactions. At that stage, all produced resources are alreadyin the present set, and closure is reached. Thus, closure can be seen as an attractor of the dynamics
defined by resource addition: it is the end point of the evolution, where further evolution stops.
Let us now apply the same reasoning for self-maintenance, starting from the previously
reached closed set. Some of the resources present in that set will be consumed by the reactions, but
not produced, or at least not produced in sufficient amounts to replace the amounts consumed. These
resources will therefore disappear from the closed set. Note that this does not affect the closure,because loss of resources cannot add new resources. Without these resources, some of the reactions
producing other resources will no longer be able to run. Therefore, the resources they otherwise
produce will no longer be replaced if they are consumed by some other reaction. If no other reactions
continue producing these resources, they too will disappear from the resource set, possibly triggering
the disappearance of even further resources that depend on them for their production. Thus resources
disappear one-by-one from the set. However, this process too must come to an end, when theremaining resources do not depend for their production on resources that have been removed, but
only on resources that are still being produced in sufficient amounts. Thus, self-maintenance too canbe seen as an attractor of the dynamics defined by resource removal.
The combination of resource addition ending in closure followed by resource removal ending
in self-maintenance produces an invariant set of resources and reactions. This unchanging reaction
network is by definition an organization.
This scenario for the spontaneous emergence of an organization illustrates the generalprinciple of self-organization (Ashby, 1962; Heylighen, 2001, 2008): any dynamic system will
eventually end up in an attractor (originally called “equilibrium” by Ashby), i.e. a stationary regimeof activity that the system can enter but not leave. In the present, qualitative formulation of COT,
such an attractor is defined as a particular subset of resources that is self-sustaining and therefore
invariant.
To investigate the quantitative dynamics of the amount or concentration of resources present
at a particular moment, we must specify a concrete dynamical law governing the rate with which
resources are produced and consumed. In COT it has been proven that every fixed point (thesimplest, 0-dimensional type of attractor) of such dynamics corresponds to an organization (Peter &Dittrich, 2011). However, the opposite is not true. In particular, certain organizations cannot berealized as fixed points within a dynamical regime (Peter & Dittrich, 2011). Instead, we may
encounter more complex attractors, exhibiting oscillatory regimes, limit cycles, and even chaotic
behavior (Strogatz, 2000). In (Peter & Dittrich, 2011) it has been shown that these dynamically14stable regimes correspond in most cases to organizations. This means that while the set of resourcesin an organization is invariant, the concentration of the individual resources can vary.
In the attractor regime, the different components of the system have mutually adapted, in thesense that the one no longer threatens to extinguish the other: they have co-evolved to a “symbiotic”
state, where they either peacefully live next to each other, or actively help one another to be
produced, thus sustaining their overall interaction.
This is the default state of an evolved ecosystem—such as a forest or a coral reef—in which
all the different species of plants and animals have adapted to the network of dependencies they all
together constitute. While some of these species are predators of other species, they will normallynot consume more of their prey than what is produced from other resources in the ecosystem. Their
predation may actually control the population numbers of their prey to such a degree that the preycannot increase in population so much that they exhaust other species on which they depend, thus
indirectly threatening their own survival. A classic example are the wolves that were reintroduced as
top predators to the Yellowstone natural reserve: their presence reduced the number of deer, thus
allowing vegetation that the deer were consuming to recover, which in turn helped other species
dependent on that vegetation to increase in number (Ripple & Beschta, 2012).
Note that the quantity of resources in the system is likely to fluctuate over time—e.g.
following the classic predator-prey dynamics that leads to periodic increases and decreases, orfollowing a more chaotic dynamics. But on the qualitative level, each of the resources should be able
to be produced at a rate sufficient for it not to disappear altogether, because this would entail apotentially radical reorganization of the ecosystem.
The relations between the different resources and reactions in an organization form a similar
web of predation, competition and cooperation—or, more generally, mutual dependencies—that has
stabilized into a self-sustaining network. Depending on the number and type of reactions, thisnetwork can be very complex. However, its defining features of closure and self-maintenance areeasy to formulate mathematically, and to verify computationally—by running the reactions andchecking whether each resource is produced at least as much as it is consumed, while no new
resources are created.
Let us illustrate the process of self-organization on an example of a reaction system (Table 1).

r1:
r2:
r3:
r4:
r5:
r6:
r7:
r8:
r9:
r10:

f
j+a
e+i+g
a+g
i+h
a
d
e+c
e
e

→
→
→
→
→
→
→
→
→
→

f+g
h
e
a+g+b
c+a
e+g+i
a+d
e+a
f+d
i+a

15

Table 1: a reaction network with 10 reactions R = {r1, r2, …, r10} working with 10 resources M = {a,b, ..., j}
The process starts from an initial state, which is an arbitrary subset of the resource set M, forexample {d, h}. The only reaction applicable in this state is r7, which adds the resource a to the set,
producing {a, d, h}. This new state enables r6, which adds e, g and i, and thus produces the next state{a, d, e, g, h, i}. The presence of a and g activates reaction r4, which adds b to the set of resources:{a, b, d, e, g, h, i}. The presence of e activates r9 which additionally produces f, resulting in {a, b, d,e, f, g, h, i}. The other enabled reactions (e.g. r10 or r3) merely add resources that are already there.
The set has now become closed: no further resources can be added by applying any of the reactions.
From this set all the elements are produced by some reaction working on other resources inthe set, except h. This resource can only be produced by r2, which requires the resource j that is notin the set. On the other hand, h is being consumed by r5. Therefore, h will eventually be eliminatedfrom the set, leaving us with {a, b, d, e, f, g, i}. This 7-element set is closed and self-maintaining andtherefore an organization. It is the attractor reached by the reaction dynamics starting from the initialstate {d, h}.
Let us now start from the state {f}. Only one reaction is applicable, r1, producing the new set{f, g}. This set is closed, because no further reactions can be applied to it, and self-maintaining,
because r1 continuously reproduces it. Therefore it is an organization, and an attractor of the
dynamics.

Sustainability and resilience
An organization is by definition a self-sustaining, and therefore sustainable, system. That means thatit can maintain perpetually, without ever running out of the resources that it needs to function—either because all resources are recycled through the inherent reactions, or because there is adependable input from outside the system. Many organizations do not just maintain: they grow,because they produce more of certain resources than they consume (e.g. through a positive feedback
cycle). Such resources are said in COT to be “overproduced” (Veloz, Reynaert, Rojas, & Dittrich,2011). (An example in the first organization derived from Table 1 is the resource b, which is
produced by reaction r4, but not consumed by any other reaction). Such organizations fulfill the idealof sustainable development: growth that can be sustained indefinitely.
Ecosystems are normally sustainable with an approximately constant level of resources.
Economic systems, however, although they grow, are often unsustainable: they consume more ofcertain resources than they produce. Therefore, they are likely to collapse when the resource reserveis eventually exhausted. For example, our present economy is largely relying for its energy on oil andother fossil fuels that are in limited supply and cannot be renewed. Creating a sustainable economy
means shifting to energy sources that are renewable, either through a dependable external input (e.g.
wind energy) or through reprocessing within the network (e.g. biofuel derived from plants grown andharvested by the system).

16

In this example, the cause of unsustainability is easy to identify as it resides in a single typeof resource (fossil fuel), and therefore the solution is obvious (replacing this resource by other,renewable resources). In general, sustainability emerges from the reactions between all the resources
used, where a shortfall in one resource may be compensated by an increased production of anotherresource playing a similar function. It is here that we need the more sophisticated mathematicalformalism of COT in order to establish in how far this reaction network is self-maintaining.
Related to the notion of sustainability is the one of resilience. Sustainability denotes theability of the system to maintain and grow on its own, without outside interference. Resilience(Beigi, 2014; Holling, 1973; Walker, Holling, Carpenter, & Kinzig, 2004) broadens this notion to theability to maintain the essential organization even in the face of serious outside disturbances. A
resilient organization is one that will survive and recover from shocks induced by the environment.
In contrast, a vulnerable, fragile or brittle organization is one that is likely to disintegrate as soon as it
encounters a serious disturbance.
In COT, a disturbance can be represented as the introduction of a new resource that reacts
with some of the existing resources, thus interfering with the network of reactions that defines theorganization, or as the removal of a resource that the organization relies upon. In practice, both typesof disturbances may reduce the availability of certain resources that are part of the organization,either by removing them at the input stage, or by inhibiting them via internal reactions. To survive
such a disturbance, a resilient organization will need to either suppress the source of the disturbance
before it interferes with the organization’s critical “metabolism”, or to replace the lost resources
before their absence makes further self-maintenance impossible. In other words, the organization willneed to counteract or compensate the disturbance and/or its effects on the network of reactions so as
to minimize the deviation from the viable configuration. This defines the cybernetic process ofregulation or control (Heylighen & Joslyn, 2003).
The simplest method of control is buffering: maintaining a large enough reserve of resources
so that temporary reductions in availability have little effect. This can be achieved by organizations
that increase their resource base through overproduction of the most crucial resources.
The next method is negative feedback: organizing the network of reactions in such a way thatdeviations from the desired concentration of resources are automatically counteracted after eachcycle of consumption and production. For example, a reduced supply of a particular resource may
automatically trigger an increased net production of that supply. This kind of dynamics is common inmetabolic pathways and in ecosystem interactions. For example, if foxes eat more rabbits, lessrabbits will be left, and therefore some of the foxes will starve. A reduction in the number of
predators will then let the rabbit population recover. Such a dynamics follows automatically from ourearlier observation that reaction rates normally increase together with the concentration of theirreactants. This creates an implicit negative feedback because reactions consuming a resource
necessarily slow down when that resource become scarcer (e.g. predation slows down when the prey
population decreases), thus allowing other reactions producing that resource (e.g. reproduction of theprey population) to catch up.
The third basic control method is feedforward: neutralizing the disturbance before it has had
the chance to perturb the functioning of the system. This can be achieved by reactions that consume

17

the disturbing resource before it could have interfered with other, vital resources. The tricky part hereis that these neutralizing reactions can only be active when a disturbance is present for them to react
with. This means that that most of the time these reactions remain “dormant”: the organization has
the potential to react, but will only do so when the right condition is present. One way to implement
such capability is by means of a collection of resources that are either overproduced, or are notconsumed by any of the reactions in the organization, and so remain in reserve. Each of theseresources can react with a particular disturbance, either getting consumed in the process, or,preferably, functioning as a catalyst that remains in the system after the reaction. The larger thevariety of such potential “neutralizers” contained in the organization, the larger the variety of
disturbances it can survive. This implements Ashby’s law of requisite variety (Ashby, 1958;
Heylighen & Joslyn, 2003).
An example of such a collection of neutralizers are the genes of an organism that are
activated via a particular chemical pathway whenever the cell encounters a particular disturbance.
Once activated, these genes produce enzymes that neutralize the disturbance. But as long as a
specific disturbance does not occur, the genes remain non-active snippets of DNA. Other examplesof “dormant neutralizers” are antibodies, which are produced by the immune system in large
quantities only in case of infection, and the armed forces of a country, which are mobilized only if
the country is attacked.

The self-organization of resilience
We have argued that arbitrary networks of reactions will self-organize to produce sustainableorganizations, for the simple reason that an organization is an attractor of their dynamics. It is lessobvious that these organizations would also be resilient. However, evolutionary reasoning shows that
resilient outcomes are more likely in the long run than fragile ones.
First, any evolutionary process starts from some point in the state space of the system, while
eventually settling down in some attractor region within that space. Attractors are surrounded bybasins, from which all states lead into the attractor (Heylighen, 2001). The larger the basin of
attraction, the larger the probability that the starting point is in that basin. Therefore, the system is apriori more likely to end up in an attractor with a large basin than in one with a small basin. The
larger the basin, the smaller the probability that a disturbance pushing the system out of its attractor
would also push it out of the basin, and therefore the more resilient the organization corresponding to
the attractor. The size of the basin corresponds to what (Walker et al., 2004) have called the latitudeaspect of resilience. Large basins normally represent stable systems characterized by negative
feedback, since a deviation from the attractor is automatically counteracted by the descent back into
the attractor.
In the example of the reaction system of Table 1, we found two attractors, the sets A1 = {a, b,d, e, f, g, i} and A2= {f, g}. The state space of this system is the power set P(M), i.e. the set of all
possible combinations of elements from the 10-element set M. The size of that state space is 210 =1024. With a computer program that simulates the dynamics of reaction systems, we found that the

18great majority of these states, namely 927, end up in the attractor A1. That means that this attractor
has a very large basin. It is therefore very resilient: the probability that the combined removal or
addition of any number of resources would make the system end up in a different attractor is only
(1024 – 927) / 1024 = 9.4%. The probability that the removal or addition of a single resource would
destroy the organization is actually zero: any missing resource in the organization can bereconstituted by other reactions working on different resources; added resources that are not in theorganization—i.e. the set {c, h, j}—are eventually all consumed by reactions that produce resourcesin the organization. We may conclude that A1 is a highly resilient organization.
The higher a priori probability of starting from a large basin does not exclude the possibilityof ending up in an unstable attractor, characterized by a small (or empty) basin. However, these
unstable attractors will normally not survive long, as nearly any perturbation will push the system outof that attractor’s basin into the basin of a different attractor. After a number of such attractor-toattractor shifts the probability increases that the eventual attractor will have a large basin, andtherefore be stable. This very general, abstract reasoning makes it plausible that systems that are
regularly perturbed will eventually settle down in a stable, resilient organization. This is anapplication of the “order from noise” principle (Heylighen, 2001; Von Foerster, 1960), according towhich increased variation (“noise”) accelerates the self-organization of a stable configuration.
In the example of Table 1, the organization A2 has a basin containing only 2 states out of the1024 possible ones, namely the states {f} and {f, g}. Practically any resource change pushes theorganization out of its basin into a different basin, and thus eventually into a different attractor—
most likely the attractor A1. For example, adding the resource a to A2 would immediately enable
reactions r4 and r6, producing the additional resources b, e and i, which would in turn enable
reactions r9 and r10, eventually producing all the resources that make up the larger and more resilientorganization A1.
The shifting from one attractor to a similar, neighboring one can be seen as a higher processof evolution, in which the system adapts to changing conditions by changing its organization, but insuch a way as to maintain some continuity. Ideally, this means that subsequent organizations
maintain most of their resources, while changing only a few. Such a “sideward shift” of organization
normally happens as a combination of two “vertical” shifts, one “upward” that adds resources (e.g.
from A2 to A1), and one “downward” that removes resources (Matsumaru, di Fenizio, Centler, &Dittrich, 2006). The ability of the system to undergo such minimal shifts in response to great
disturbances exemplifies a higher level of resilience that may be called evolvability.
What is as yet unclear is how such organizations are precisely organized: what kinds ofarrangements of reactions make up a resilient whole? A theoretical decomposition of organizations(Veloz et al., 2011) shows that organizations often are modular, i.e. they consist of subnetworks
whose self-maintenance is independent of the self-maintenance of other subnetworks. Overproduced
molecules and catalysts function as “boundaries” that connect the subnetworks but without making
them dependent on each other. Such decomposition makes it possible to identify where in the
network a disturbance would have the strongest effect. For example, a perturbation happening in asmall subnetwork will not affect the bulk of the organization.

19

A more detailed analysis is likely to come from simulations, in which reactions systems are
randomly generated and then allowed to settle into an attractor. The corresponding organizations arethen repeatedly perturbed by generating a variety of random disturbances. We can then compare theorganizations that were easily destroyed by disturbances with those that proved to be particularly
resilient. This may allow us to formalize the aspects of resilience that (Walker et al., 2004) havecalled precariousness (nearness of the organization to the boundary of its attraction basin, i.e.
minimum number of changes needed to switch attractors) and resistance (effort needed to move theorganization out of its basin). The latter might be measured as the minimum amount of resources thatneed to be added to, or removed from, the organization in order to make it shift to a different
organization.
Another approach to the problem is the study of the metabolic networks used by realorganisms. These appear to be surprisingly resilient in the face of random mutations removing or
adding gene-regulated reactions (Matias Rodrigues & Wagner, 2009). A likely reason is theredundancy—or more precisely degeneracy (Edelman & Gally, 2001)—of pathways for producing
critical resources: there is a variety of independent mechanisms that perform partly different, partly
the same functions. Thus, the loss of a pathway through mutation is simply compensated by more
activity in different pathways that perform the same function. For example, the organization A1
depends on two critical resources, a and e, that together produce most of the other resources in theorganization (see Table 1). However, both a and e can be produced by more than one reaction, so if
one of such reactions would be disabled (e.g. r3 through the lack of the resource g), the mainprocesses can still continue (e.g. a can still be produced by reactions r4 and r7). Such degeneracy is
one of the factors that explain both the resilience and the evolvability of living systems (Aldana,
Balleza, Kauffman, & Resendiz, 2007): they can afford to undergo a lot of variation without losing
their essential ability to self-maintain. This allows them to explore an immense space of largely
overlapping organizations and thus to discover ever more resilient and adaptive ones.

Metasystem transitions and topological structures
One of the most important but as yet poorly understood processes in evolution is the metasystemtransition (Heylighen, 1995; V. Turchin, 1995) or major evolutionary transition (Maynard Smith &Szathmáry, 1997): the emergence of a higher-order organization that is constituted out of lower-orderorganizations. Examples are the origin of living cells from autocatalytic cycles of reactions, theemergence of multicellular organisms out of single cells, and the emergence of societies out ofindividuals (Heylighen & Campbell, 1995). At first sight, COT does not allow us to describe such a
process, as it recognizes only two levels of systems: individual resources and the organizations
constituted out of such resources. However, an organization S behaves in a way like a resource of thecatalyst type: it is invariant under reactions, yet it still has in general an input of resources I(S) it
consumes, and an output of resources O(S) it produces. This allows us to summarize the activity ofthe organization by the following “higher-order” reaction:

20

I(S) + S → S + O(S)Suppose that I(S) = {a, b} and O(S) = {c, d, e}, then we can write this as a more conventional
reaction:
a+b+S→S+c+d+e
The fact that S is itself constituted of a network of resources and reactions does not really make any
difference when seem from the outside. S behaves like a “black box” which processes a given input
into a specific output. If S is a resilient organization, it can maintain itself even when the inputchanges, producing a correspondingly changed output of “waste products”. This means that S
behaves like a multipurpose catalyst, or “agent”, which converts certain inputs into certain outputs.
This means that is in principle possible to describe a meta-organization, as a closed and selfmaintaining network of resources and reactions that contains several organizations like S among
their catalytic resources. In practice, the problem is to maintain a separation or distinction between
these suborganizations. Since all resources are freely shared within the medium, it is likely that anorganization S will produce or consume some of the resources used by another organization S’. Thismeans that the two organizations will interfere with each other’s reactions. This will trigger a processof mutual adaptation whose end result is likely to be a single, merged organization, including
reactions from both S and S’. But if all organizations within a meta-organization eventually merge,then there is no longer any sense in distinguishing between the organization level and the metaorganization level: everything just settles down into a single organization without distinguishable
components.
In concrete systems, such as organisms or ecosystems, this problem is avoided because of theexistence of topological boundaries: the resources within one cell or organism do not mix with theresources in another cell or organism, because they are kept apart by some kind of membrane or
spatial separation. This suggests a straightforward extension to the COT formalism: introduce a
topological structure that subdivides the medium into “cells” separated by membranes or boundaries
across which resources can be exchanged in a restricted manner between neighboring cells (Peter etal., 2011). This is a classic modeling approach used in simulations of complex adaptive systems(Holland, 2012; Miller & Page, 2007) , and in chemical computing. For simplicity, such simulations
typically situate their agents in the cells of a two-dimensional, rectangular grid rather than in a more
realistic three-dimensional, continuous space. However, this approach seems rather artificial, because
the spatial structuring of organizations is imposed externally and rigidly, instead of being the productof internal self-organization. Therefore, we will explore in how far topological structure may emerge
from the abstract network of resources and reactions that constitutes a reaction system.
There is a simple “trick” to separate resources into distinct cells: label each resource with thenumber of the cell in which it is supposed to be situated (Peter et al., 2011). For example, a1, a2 anda3 can be seen as instances of the same resource a, but localized in respectively cell 1, cell 2 and cell
3. This merely produces a partitioning of resources. To introduce a topology, we moreover need to
specify which cell is a neighbor of which other cell. For example, if the three cells are arranged on a

21line, then cell 1 neighbors cell 2, and cell 2 neighbors cell 3, but cell 1 does not neighbor cell 3. The
neighboring relation can be expressed by a reaction that describes the movement or diffusion of a
resource from one cell to its neighbor, e.g.
a1 → a2
a2 → a3This means that resource a can move from cell 1 to cell 2, and from 2 to 3, but not directly from cell
1 to cell 3. Using this method to specify neighboring relationships, we can impose a variety of
topological structures on the collection of cells, without need to remain stuck with rectangular grids.
Still, this method remains artificial in the sense that we started by defining cells, and thenlabeled resources according to this imposed topology. In a basic reaction system there are only
resources and reactions, no cells or labels. Let us therefore try to reconstruct a topology if we ignore
the labels and just consider differently labeled resources (say a1, a2, a3, …) as though they were apriori different resources (say x, y, z, …). The “neighboring” reactions would then become:x→yy→z
In a typical reaction, a single resource (x) does not spontaneously turn into a different resource (y)without any other resource being consumed or produced. Therefore, we can reinterpret such one-toone reactions as cell-to-cell transitions: only the cell changes, the intrinsic qualities of the resource(which other resources it can react with) remain the same. That leaves us with all the many-to-one,
one-to-many, and many-to-many reactions. Let us call the set of these remaining reactions Rmany.
Resources participating in a reaction from Rmany may be assumed to be present in the same cell: tworesources can only react with each other if they are in direct, local contact, i.e. in the same cell.
Moreover, their products can be assumed to be formed within this same cell. Therefore, two
resources that participate in the same reaction r ∈ Rmany must be present in the same cell.
This relationship of co-presence is reflexive (x co-present with x) and symmetric (if x copresent with u, then u co-present with x). Co-presence within the same cell would also imply that therelationship is transitive (if x co-present with u, and u with v, then x co-present with v), so we need toconstruct the transitive closure of the relationship defined above. This makes co-presence into an
equivalence relation that will automatically partition the set of resources into subsets corresponding
to different cells. Thus, we can induce a partition of the resources simply by examining which
resources can react with which other resources. This means that resources present in different cells
by definition cannot react with each other. Therefore, the organizations using these reactions cannot
interfere, and must remain separate. This solves the problem of having autonomous organizations
functioning within the same reactive network.
The processes of diffusion between the cells represented by the one-to-one reactions linking
different cells then induce a topological structure by specifying which cells are neighbors (and which
resources may or may not cross the “membrane” separating them). Through diffusion, the output of22

one cell can become the input of another cell. This enables the emergence of a meta-organization thatspans several interacting cells. Thus, we have formulated a foundation for a mathematical model ofthe emergence of a topological structure that both separates and connects local, cell-basedorganizations.
Note that the cells in this construction are independent of physical space. Thus, it is inprinciple possible to have two separate organizations occupying the same space, while interacting
only indirectly. An example could be a linguistic and an economic system co-existing in the same
human society. The resources of the linguistic system would be words, and those of the economic
system would be goods. Words can “react” with each other by forming sentences, while goods canreact by being used or exchanged simultaneously. Words and good interact indirectly in the sensethat words may be produced in order to initiate an exchange of goods, while the receipt of the good
may initiate the production of words. But a word and a good together do not create a new resource
because they belong to different realms, dimensions or aspects of the human society. In systems
theory, such systems that are distinct yet spatially inseparable have been called “aspect systems” (incontrast to subsystems, which are spatially separate).
This mathematical construction needs to be elaborated further, and explored by means ofcomputer simulations of the self-organization of randomly generated reaction network. However, itsuggests that it is in principle possible to introduce a topology and a mechanism of metasystemtransition within COT without imposing additional constraints. This opens the door to the modelingof the multilevel self-organization and dynamical hierarchies (Rasmussen, Baas, Mayer, Nilsson, &Olesen, 2001) that are necessary for understanding the origin and evolution of life and society.
Concrete applications
Here we wish to give a brief survey of existing and future application domains for COT.
Most obviously, COT has been used to simulate networks of chemical reactions with a focus
on the emergence of stable systems. The first examples were models of virus dynamics (Matsamaru,
2006) and the chemistry of a planetary atmosphere (Florian Centler & Dittrich, 2007). The effects ofsmall number of particles in the discrete dynamics of organizations has been investigated in(Kreissig, Wozar, Peter, Veloz, & Dittrich, 2014). The initial inspiration for the development of COT
was to model how such chemical networks could develop the degree of autonomy that we associatewith simple living creatures (Fernando & Rowe, 2008). Previously, this problem of the origin of life
had been approached by looking for autocatalytic cycles of chemical reactions (Hordijk, Hein, &Steel, 2010; Maynard Smith & Szathmáry, 1997; Vasas, Szathmáry, & Santos, 2010). These are amore limited kind of organization that are both more difficult to build by evolution, and less flexible
and resilient than more general chemical organizations.
A related application domain is the study of complex metabolic networks in existingorganisms, such as the bacterium E. Coli (Florian Centler, di Fenizio, Matsumaru, & Dittrich, 2007).
This domain has recently attracted a lot of attention under the label of “systems biology”, but stilllacks an integrated theoretic framework (Machado et al., 2011)—which COT may be able to provide(Kaleta, Centler, & Dittrich, 2006). A classic problem within this domain is the modeling of gene23

regulatory networks, in which genes activate or deactivate each other via the proteins they produce.
These networks can settle into a variety of attractors characterized by specific patterns of expressedand dormant genes. Different attractors are assumed to correspond to different cell types (such as
liver cells, bone cells or neurons), or cell fates (such as apoptosis, quiescence or proliferation)(Aldana et al., 2007). This reaching of attractors is typically modeled by means of Random Boolean
Networks, a rather abstract and artificial formalism whose main advantage is that its dynamics iseasy to simulate. But COT suggests a model that seems both simpler and more realistic, namely as
the organizations emerging from a complex network of reactions having the following form:
active gene 1 → active gene 1 + protein 1
active gene 2 + protein 1 → non-active gene 2
non-active gene 3 + protein 1 → active gene 3(protein expression of an active gene)(expressed protein deactivates gene)(expressed protein activates gene)Because the reactions defining COT are intrinsically abstract, computable processes, they canbe used as a foundation for a new method of computation, based on “artificial chemistries”(Matsumaru, Centler, di Fenizio, & Dittrich, 2005). Here, the input of a chemical program is a choiceof input species concentrations. Because the dynamics of a chemical reaction network stabilizes inchemical organizations, it is possible to build reaction networks where reactions play the role oflogical gates, and organizations are the final states of the computation. Such “chemical computation”
can for instance be used to check models (Kaleta, Richter, & Dittrich, 2009) or to program
distributed artefacts (Matsumaru, Hinze, & Dittrich, 2009), helping them to coordinate their actions.
Modelling complex systems with many variables of course cannot be done manually, but
COT lends itself readily to the development of simple, modular computer programs that can examine
a wide range of possible situations, and that are easy to extend or update. An important issue here is
how the algorithmic complexity of COT models grows as the number of resources and reactions
increases. A basic result is that verifying whether or not a set of molecules is an organization is a
Linear Programming problem, whose computational complexity is polynomial, but of degree higher
than 2. This motivated a first algorithmic study that builds the set of organizations of a given reaction
network from a bottom-top approach that adds molecules until an organization is found, and an
intricate method that combines flux vectors of previously known organizations (F. Centler, Kaleta, diFenizio, & Dittrich, 2008). These algorithms were later extended to their parallelized counterparts(Florian Centler, Christoph, Pietro, & Peter, 2010). The computational complexity of these methods
is at first sight exponential because every subset of molecules could in principle be an organization.
However, it is possible to decompose organization into subnetworks that are independently selfmaintainance is independent (Veloz et al., 2011). This technique could permit the classification oftypes of reaction networks in terms of how complex is to compute their set of organizations.
Moreover, reaction networks are structurally equivalent to a formalism studied in distributed
processing (Veloz, 2010), namely Petri Nets (Murata, 1989), about which there is extensivealgorithmic research..

24

Once we make abstraction of the molecules that originally inspired COT, the application
domain immediately extends to the social sciences, where the resources to be processed by reactions
can e.g. be economic goods (Dittrich & Winter, 2005) or political decisions (Dittrich & Winter,2008). In the latter case, the self-sustaining network of decisions producing further decision provides
a simple formal model of the notoriously difficult theory of autopoietic social systems developed by
Niklas Luhmann (Luhmann, 1986, 1995). Another application of Luhmann's social theory is aframework to study the evolution of cooperation (Veloz, Razeto-Barry, Dittrich, & Fajardo, 2014).
The evolution of cooperation is usually studied from an agent-based perspective. The reaction
network model does not include individual agents, but models agents’ decisions as resources.
Decisions interact to produce new decisions together with the payoffs generated by the agents'
interaction. This model manages to reconstruct the known conditions for the evolution of cooperation(Nowak, 2006) at the level of decisions.
We have alluded several times at the as yet unexplored potential for applying COT toproblems in ecology, sustainable development, and the resilience of social and ecological systems. A
related issue is the understanding of business ecosystems (Moore, 1996; Nachira, Nicolai, Dini, Le
Louarn, & Leon, 2007; Peltoniemi, 2006), where different companies producing and consuming
different goods and services form a symbiotic, co-evolving network, where the one provides theresources for the others. Existing models in this domain, such as food webs or systems dynamics,
tend to be limited to networks of one-to-one interactions, in which one variable (e.g. a predator
population) positively or negatively affects one other variable (e.g. a prey population). In COT, we
can examine how several resources in combination produce or consume a combination of otherresources. While at first sight this makes modelling more complicated, the mathematics of COT
shows that such multi-resource reactions makes the emergence of stable organizations easier rather
than more difficult.
A more general advantage of COT is that you can freely mix resources of very different
types, such as organisms, chemicals, economic goods, and even human decisions (Veloz, 2014). This
makes it eminently suitable for modelling the truly complex social-technological-economicalecological-physical systems that surround us, such as cities, businesses, regions, or our planetarysociety. This is the objective of the new approach of global systems science (Helbing, 2013; Helbing,
Bishop, Conte, Lukowicz, & McCarthy, 2012)
To further illustrate the generality of COT, we wish to briefly suggest some more speculative
applications. The section on resilience noted that a highly evolved organization is likely to exhibit avariety of regulatory mechanisms characteristic of a cybernetic or autopoietic system. Such a system
is in essence a goal-directed agent that tries to sustain its essential organization while suppressing
any disturbances that may push it away from this goal. That means that it exhibits not just the mostbasic features of life, but of cognition (Maturana & Varela, 1980), intelligence, and intentionality(Heylighen, 2011). Like all living systems, the implicit goal or intention of an organization is tomaintain and grow. To achieve this, it needs to produce the right actions for the right conditions (e.g.
produce the right resource to neutralize a particular disturbance, or to exploit a particular input). Thismeans that it implicitly contains a series of “condition-action rules” that play the role of theorganization’s “knowledge” on how to act in its environment. The capability of selecting the right25(sequence of) action(s) to solve a given problem constitutes the organization’s “intelligence”. To dothis, it needs to perceive what is going on in its environment, i.e. to sense particular conditions (thepresence or absence of certain resources) that are relevant to its goals. Thus, an organization can beseen as a rudimentary “intelligence” or “mind”.
Because this abstract conceptualization is independent of any concrete substrate, such as abrain, it is applicable to systems that exhibit intelligent behavior but that are otherwise very different
from the individual humans that we tend to see as the sole possessors of minds. Examples are theintelligence exhibited by insect societies, plants (Trewavas, 2005), bacterial colonies, humanorganizations, the planetary ecosystem (“Gaia”), and the Internet functioning as a “Global Brain”(Heylighen, 2007). In all these cases, intelligence is distributed (Heylighen, 2014): it is not localized
in some central decision-making component, but it emerges from the coordinated interactions
between many components working in parallel. Providing simple models of such distributed,
dynamic organization is precisely the strength of COT.
Even the human brain is a complex, distributed network, where all the important features
such as intelligence, intentionality and consciousness are emergent rather than localized in somespecific neuron or assembly of neurons. Recently, great progress has been made in the understandingof consciousness as a pattern of activity that takes over the “global neuronal workspace” in the brain(Dehaene, 2014; Dehaene, Kerszberg, & Changeux, 1998). For conscious processing of thoughts weneed to maintain a pattern of activity long enough in our working memory so that it can be examinedand processed by different brain modules. This is intrinsically difficult because neural activation
cannot stay in the same place: a neuron that is excited by an electrical signal (“action potential”)
cannot retain that electrical charge but must pass it on to one or more neighboring neurons via its
outgoing axon ending in synapses. If a sufficient number of incoming synapses pass on a signal, thenewly reached neurons will become activated as well, passing on this activation via their outgoing
synapses to further neurons. This transmission of activation can be described as a reaction of theform: a + b + … → e + f + …, where a and b are the initially activated neurons whose combined
activation is necessary to activate the subsequent neurons e, f, etc. We may say that the activation ofa and b is “consumed” by the reaction in order to “produce” the activation of e and f.
What the neuronal workspace theory proposes is that conscious patterns of activation, in
contrast to subconscious or subliminal processes, are to some degree self-sustaining: activation thatleaves a neuron comes back to it at a later stage after having propagated through some complex,
closed network. This creates coherent assemblies of neurons that are firing in a synchronized,
coordinated manner, so as to keep the idea “alive” long enough for it to be monitored and processedin a controlled, goal-directed manner—the hallmark of consciousness. Mathematical models of thisprocess have been built (Dehaene et al., 1998), but they are quite complicated, making many ad hocassumptions about specific neurophysiological properties and structures, while being able to simulate
only the most basic dynamics of a neuronal assembly reaching “ignition” (self-sustaining activation).
By interpreting coherent neuronal activation patterns as organizations, we may be able to reach asimpler, broader and more qualitative understanding of the different conscious patterns that the brain
can produce, and how such patterns can shift into different patterns as new stimuli make them26

deviate from their initial organization, thus producing a “train of thought” or “stream of
consciousness”.
Conclusion
Chemical Organization Theory (COT) proposes a very promising new formalism for the modeling ofcomplex, self-organizing systems. Its power results from several highly beneficial properties:• the components of the formalism—resources and the reactions that map combinations ofresources onto new combinations—are extremely simple and intuitive. This makes it easy
even for people without mathematical background to start expressing their understanding of asystem in the form of a COT model• COT models are intrinsically modular: it is easy to add (or remove) components, and thus todevelop an increasingly realistic model of a complex system• these components are so general that they can be used to represent a wide variety of realworld objects and variables, including particles, molecules, biological species, economic
goods, technological infrastructures, human or animal agents, ideas and decisions. This
makes it possible to apply COT to problems in about all scientific and social disciplines, andin particular to multidisciplinary issues, such as interactions between ecological,
economical, social and technological systems• COT models are easy to analyze computationally: entering a set of reactions into an
appropriate computer program will allow you to quickly discover all the possible outcomes
together with the conditions under which they can arise• the COT formalism is intrinsically dynamic, starting from reactions rather than from static
objects or properties. This makes it particularly suitable for describing systems characterized
by an on-going creation, process, or flow of resources. Such systems, which include
organisms, ecosystems, societies, and brains, are intrinsically difficult to fit in a traditional,
Newtonian framework.
• COT shows how such dynamic networks of production and consumption tend to
spontaneously settle into invariant “organizations”, thus providing a simple model of thehitherto difficult to understand phenomena of self-organization and autopoiesis that produce
self-sustaining systems• these organizations can be easily analyzed for further properties, and in particular for thecharacteristics that make them more or less resilient in the face of perturbations:
overproduction of resources, latitude of the basin of attraction, precariousness, feedback,degeneracy of pathways, evolvability…
• as such, COT is a very promising approach to a range of notoriously difficult problems,
including the origin of life, the modeling of metabolic and genetic regulatory networks insystems biology, the resilience of ecosystems, the formalization of sustainable
development, the self-organization of socio-economic systems, and even the dynamics ofconsciousness.

27

One of the reasons why COT manages to achieve so much with so few assumptions is that theformalism consists of two levels: the very simple qualitative level listing the resources andreactions active in a particular network or organization, and the more advanced quantitative level(which we have largely ignored in this introductory survey) examining the rates of the reactions
and the changing concentrations of the resources. Precise modeling at the quantitative level will
obviously be more difficult, both analytically and numerically, but that does not prevent us fromderiving clear, unambiguous results by just examining the qualitative level. While the qualitativemodel can be seen as a mere “abstraction” of the full quantitative dynamics (Peter & Dittrich,2011), its algebraic properties are so strong that many non-trivial properties can be established at
this level without need to determine quantitative dependencies or concentrations. These
properties can be used to simplify the model to such a degree that it not only becomes intuitively
easier to grasp, but easier to turn into a computable quantitative model without need for
unrealistic simplifications. Moreover, in many cases we do not need to know the full quantitative
dynamics, but just need to establish which combinations of reactions and resources (such as
species in an ecosystem, or active genes in a genetic regulatory network) are self-sustaining andresilient.
The COT formalism is hardly a decade old and as yet has only been actively investigated by ahandful of scientists. Thus, there is of course still a lot of work that needs to be done, both infurther clarifying its mathematical and conceptual foundations, and in applying it to concrete
problems. In collaboration with other COT researchers, we intend to further develop thesedifferent aspects in a series of subsequent papers. We hope that after reading this paper, others
may become as enthusiastic as we are in joining this enterprise, and thus potentiallyrevolutionizing our conception of complex, self-organizing systems.
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