Emergence and Growth of Knowledge and Diversity in Hierarchically Complex Living Systems

W.P.
HALL KNOWLEDGE AND DIVERSITY IN COMPLEX SYSTEMS 30/09/2010
Emergence and Growth of Knowledge and Diversity in

Hierarchically Complex Living Systems
William P. Hall
Tenix Defence,
Williamstown, Vic. Australia
bill.hall@tenix.com
Evolutionary Biology of Species and Organizations

http://www.orgs-evolution-knowledge.net/
Australian Centre for Science, Innovation and Society

History and Philosophy of Science
University of Melbourne, Vic., Australia
University of Technology, Sydney, NSW, Australia
DRAFT © 2006 William P. Hall Page i

W.P. HALL KNOWLEDGE AND DIVERSITY IN COMPLEX SYSTEMS 30/09/2010
CONTENTS
Summary...............................................................................................................................................1
Introduction..........................................................................................................................................1
The Physical Framework......................................................................................................................2
Thermodynamics and Self Organization..........................................................................................2
Properties of dissipative systems......................................................................................................3
Complex Systems Terminology........................................................................................................4
Hierarchies of Complex Systems......................................................................................................4
Emergence of new levels of complexity in a hierarchically complex dynamic environment..........6
What is life?..........................................................................................................................................8
Autopoiesis.......................................................................................................................................8
Evaluating explanations of the origin of autopoiesis......................................................................11
Evolutionary Epistemology................................................................................................................11
Observers........................................................................................................................................11
Physics and semiotics.....................................................................................................................12
Karl Popper's Epistemology............................................................................................................14
What is Knowledge?..................................................................................................................14
Ontological domains where knowledge can be found...............................................................16
Forms of evolutionary knowledge..................................................................................................17
Origins of embodied knowledge in W2.....................................................................................17
Codification to preserve knowledge in W3................................................................................20
Two worlds of organismic knowledge or "code duality"...........................................................22
The origin and evolution of genetic systems to manage cellular knowledge.....................................24
Orders of Autopoiesis.........................................................................................................................27
Is There More Than One Order of Autopoiesis?............................................................................27
Second Order Autopoiesis: Multicellular Organisms.....................................................................28
Third Order Autopoiesis: Colonies, Societies and Organizations..................................................29
Colonial organisms.....................................................................................................................29
Social organisms - the evolution of 'social homeostasis'...........................................................30
Human economic organizations.................................................................................................32
Conclusions........................................................................................................................................33
ACKNOWLEDGEMENTS...............................................................................................................35
BIBLIOGRAPHY..............................................................................................................................35
DRAFT © 2006 William P. Hall Page i

Emergence and Growth of Knowledge and Diversity in

Hierarchically Complex Living Systems - A Sketch
William P. Hall
Summary
An environment conducting a flux of energy and materials between temporally or spatially separated sources and
sinks may become more complexly structured due to the emergence of cyclical, dissipative transport systems.
Selection favors transport systems able to stabilize themselves against environmental perturbations through feedback.
Continuing selection for self-stabilization over long periods of time may eventuate in the emergence of an autopoietic
assembly of subsystems (i.e., an autocatalytic set). The stabilizing 'control information' inherent in the instantaneous
structure of the autopoietic system represents a form of knowledge that enables the stabilized system to continue an
existence as a living and evolving entity. Such self-referential knowledge (defined by Karl Popper as "solutions to
problems of life") is integral to the differential survival of nascent autopoietic systems. Maturana and Varela
developed the concept of autopoiesis for the autopoietic cybernetics of self-maintenance and self-production. They
also equated the cybernetics of autopoiesis with cognition. Concepts of "meaning", "memory", "learning" and
"heredity" can also be derived from this framework of Popperian autopoiesis. Hall has argued that autopoiesis has
emerged at cellular, (multicellular) organismic, and economic organizational levels. Given an acceptance that
different orders of autopoiesis exist, it follows that forms of regulatory knowledge (i.e., solutions to problems of life)
exist at each organizational level where autopoiesis occurs. Knowledge may be "tacit", "implicit" or "explicit".
Keywords: autopoiesis, emergence of complexity, origin of life, structural and codified knowledge, evolutionary
theory of knowledge, scalar hierarchy theory
Introduction
The philosopher Karl Popper (1972) and the biophysicist Howard Pattee (1995a) independently
argued that knowledge or information (knowledge in the broad sense) are evolutionary products of
living systems. Throughout this work, I follow Popper in using the term 'knowledge' in a broad,
collective sense as an entity's solutions for solving problems of its life (Popper 1972, 1999). The
neurobiologists Humberto Maturana and Francisco Varela developed the concept of autopoiesis as a
statement of the minimal properties a complex system must have to be considered living (1974,
1980, 1987). Combining the two bodies of work, I argue that knowledge and life are inseparable
phenomena - that knowledge cannot exist without life, and that even the most basic kinds of living
things cannot exist without forms of knowledge that enable their survival. I explore the basic
properties of this conjunction between life and knowledge and discuss why such a conjunction is a
necessary consequence of physics. I am not concerned to present a specific physicochemical theory
about how life arose on Earth, but rather to explore the more general case of what may be involved
in the emergence of complex, self-organizing, self-regulating and self-producing physical systems.
However, if the arguments presented here are correct, the framework presented must encompass life
on Earth as a particular case, and the general ideas have applications to the origins and evolution of
living things over several orders of complexity on the Earth and elsewhere in the Universe.
This paper crosses and amalgamates many disciplines based on my background over four decades,
including evolutionary biology, genetics, speciation and the origin of life; a two-year post-doctoral
diversion into the epistemology of science (Hall 1983); plus my current professional involvement in
DRAFT © 2006 William P. Hall Page 1

managing organizational knowledge in a large defense company (Hall 2003a). My thinking has also
been greatly influenced by several years of correspondence with Hugo Urrestarazu, a physicist and
scientific translator who worked with Humberto Maturana and Franscisco Varela in the formative
years when the concept of autopoiesis as a phenomenological definition of life was first developed
(Varela et al 1974; Maturana and Varela 1980). From this diversity of ideas, I attempt to reconstruct
the primordial origins of knowing entities and the main evolutionary phenomena affecting the
growth of knowledge in living things.
The Physical Framework

Thermodynamics and Self Organization
As Prigogine (1955, 1981, 1999, 2000; Prigogine & Antoniou 2000) demonstrated, the convective
transport of energy through a fluid medium forces the state of the transport medium away from
thermodynamic equilibrium. When looked at spatially, random molecular motion becomes
organized into cyclical flows as material carriers physically receive activating quanta of energy
from a source and carry them to a sink where they are released. This, of course forces a return flow
of the transport medium to the source to pick up more quanta.
Such transport mechanisms may also work over time, to connect a source of activation energy and a
temporally separated sink for degraded energy. For example, high-energy photons from the sun
activate carrier molecules to a high potential during daylight hours, which may then relax over time
through polymerization reactions and radiation of low energy photons to the cold night sky.
Morowitz (1968) described in chemical terms how chemical systems can be entropically forced to
become more complex - essentially to evolve an increasingly complex 'metabolism' driven by the
dissipative transport of photonic energy from the sun to the cold night sky for an overall increase in
entropy of the world.
James Kay (1984, 2000) uses the concept of exergy (synonymous with available energy) to clarify
discussion of these phenomena. It is recognized that various forms of energy vary in their capacity
or quality to do useful work. Some of the quality or capacity of the energy driving that work to
perform additional work is irretrievably lost to entropy during any spontaneous physical or
chemical process. As stated by Kay (2000) "exergy is a measure of the maximum capacity of the
energy content of a system to perform useful work as [the system] proceeds to equilibrium with its
surroundings and reflects all the free energies associated with the system".
Kay goes on to define the second law of thermodynamics in these same terms, "during any
macroscopic thermodynamic process, the quality or capacity of energy to perform work is
irretrievably lost. Energy loses exergy during any real process." A system conducting energy from a
source to a sink will be forced away from equilibrium. The system will tend to relax towards the
attractor basin represented by thermodynamic equilibrium, and thus will tend to organize itself in
ways that maximize the dissipation of extropy along the steepest gradients to approach
thermodynamic equilibrium. It should be noted that where the transport medium is complex,
dissipation processes will be stochastic rather than deterministic and local contingencies may affect
their temporal evolution. Kay argues that the further the system is forced away from equilibrium,
the more organizational opportunities it has for dissipating exergy.
As noted above, Prigogine and others showed that random instabilities and fluctuations could lead
to bifurcations and new steady-states of the system as defined by attractor basins (Kauffman 1993,
etc.) that can be represented by coupled processes stabilized by feedback, such as convection cells,
cyclones, cyclical chemical reactions, autocatalytic systems and even living things. Feedback is an

essential feature for sustained stability that merits a deeper treatment. Complex dynamic systems
exhibit two kinds of causal feedback circuits: positive and negative. Negative feedback tends to
stabilize some variables within a range of limiting values (oscillatory homeostasis). Positive
feedback can either fatally disrupt system organization or lead to chaotic excursions in a phase
space that may converge towards strange attractors representing new steady states. Thus, a transient
wandering on the edge of chaos caused by turbulence may provide an opportunity to move away
from a near equilibrium situation where even small external perturbations could become
catastrophic for the continued integrity of the system. The robustness of a system’s resistance to
catastrophic perturbations depends strongly on the density of positive feedback circuits affecting
each node of its causation network (Thomas & Kaufman 2001, 2003). .
Where such stabilized cyclical systems exhibit coherent self-regulatory behavior, it may be possible
to discriminate the systems from their environment as discrete entities. Organization in such
dissipative systems normally resides in a zone of the continuum between an area close to
thermodynamic equilibrium where energy transport can be achieved by simple radiation and
conduction—where nothing interesting happens, and states of very high flux—where ordered
feedback is disrupted into chaotic turbulence.
Properties of dissipative systems
Table 1 (from Kay 2000) summarizes the properties of dissipative systems:
Table 1: Properties of Dissipative Systems (after Kay 2000)
• Open – exchange material and energy with environment.

• Nonequilibrium – persist in dynamic steady states away from thermodynamic equilibrium
• Energy gradients (exergy) between system boundaries maintain nonequilibrium.
• Exergy is irreversibly degraded in forming and maintaining organized gradients.

Entropy exported to other hierarchical levels
• Material or energy cycling - physical transport or chemical cycles are formed to
transport material or energy along gradients maintained within systems.
• Chaotic and catastrophic behavior - systems may change discontinuously and
unpredictably in response to small environmental perturbations
• Organized - As dissipative systems are forced away from equilibrium their organization
may increase:
- to dissipate more exergy
- to become more structured
- to exhibit non-linear change as new attractors become accessible
- to increasingly resist moving still farther away from equilibrium
Extending ideas of Morowitz (1968), Kay & Schneider (Kay 1984, 2000, 2001; Schneider & Kay
1994, 1994a, 1995) explored how exergy dissipation drives hierarchically complex systems to
evolve. They view the Earth as an open thermodynamic system where a large gradient exists
between incoming solar radiation and the radiation of heat to outer space. Systems transporting
fluxes along parts of that gradient are driven by the second law of thermodynamics to reduce the
fluxes by all available physical and chemical processes. Where there are intermediate fluxes of
energy, above those that can be dealt with by radiation and conduction and below those that drive
the system into chaos (i.e., a 'short circuit'), hyper-cyclic self-organizing processes may evolve to
facilitate that dissipation. The selective survival of more effective dissipation paths leads to
increasing complexity.

Complex Systems Terminology
The following definitions derived from Kay (1984) provide a vocabulary for discussing the
emergence of complex autopoietic systems.
Complex systems, by definition, are comprised of dynamically interacting components, where

different components have different functions relating to the overall system. "Complexity" implies
something more than just complicated. In terms of what is physically possible to compute, the
detailed dynamics of complex systems are practically incalculable or indeterminate from the
detailed properties and positions of their components (Schrodinger 1944; Polanyi 1968; Davies
2004) which is not to say that they are formally uncomputable.
Flux. This refers to the entropically driven transport or flow of energy and matter through an
identifiable system. As noted above, the emergence of dynamic complexity is a possible outcome of
the dissipation of exergy as energy flows from sources to sinks. Other useful terms include:
− Component: a subunit/subsystem carrying out a particular dynamical process within

the system. Components are dynamically interconnected by the flow of mass and energy.
− Function: The function of a component in a dynamic system is defined by the mass-

energy transformation process it performs.
− Structure: The structure of a dynamic system is determined by the functions of the

interconnected components.
− Control structure: Some of the energy flux may be involved in regulatory feedback
stabilizing the system around a steady-state away from thermodynamic equilibrium. The
interconnections of the components involved in this regulatory feedback forms what Kay
defined as the control structure.
− Redundancy of function: In some cases, components involved in connections can be

removed from the system without seriously affecting the overall dynamics of the system. The
component may be able to continue functioning as an entity in its own right only if it is not
highly dependant on the system for its microenvironment.
− Environment: A system's environment is the set of elements that are not part of the
system but may affect it. The environment provides the thermodynamic source of high exergy
materials and a sink for degraded materials and heat as exergy dissipates.
− Resource/Source: Resources are those elements of material and energy the system
requires to transport or incorporate from the environment (i.e., the source) for the system to
maintain its dynamic state.
− Sink: For an energy flux to exist, allowing the dissipation of exergy to maintain system
dynamics, the system must also connect to sinks that are at a higher entropy than the sources.
Hierarchies of Complex Systems
Biological systems are dynamically complex systems, and the problem with complex systems is
that complexity may occur at many levels of size. For example, some living systems are themselves
part of a larger living system (e.g., cells within a multicellular organism).

Kay and Schneider adopt Koestler's (1978) concept of Holarchy as an expression of how
complexity can be manifested. As discussed in the present work, the holarchy of natural systems
comprises the complete hierarchy of complexity–of physical systems and their cybernetic processes
(see also Simon 1962; Salthe 1985, 1993; Gould 2002; Lemke 2000, 2000a, 2000b; Lane 2006).
The holarchy consists of distinguishable Holons (i.e., systems), such that each holon is always a
component of a larger holon (the super system), and is in turn composed of smaller holons
(subsystems). This accounts for Koestler's reference to Janus, the two-faced god. One face of the
holon always looks inward (downward in scale) to its constituent components that establish
possibilities as determined by their capabilities, while the other face always looks outward (upward
in scale) to its environment that determines what is allowed by the circumstances at any particular
time. Scales (axes) of complexity may be determined along axes of size, time (speed of dynamic
interactions), mass, total energy content, etc. (Lemke 2000).
I use the term Entity here in Kolasa & Pickett's (1989) sense as a "primitive term" that cannot be
defined within the axiomatic system, where entities may have internal structures consisting of
smaller scale entities. The structure of an entity may be comprised of the internal complex of other
entities and their static and dynamic interconnections with one another. Following Kay (1984), the
observer/analyst determines a level of interest in the hierarchy, and it may be difficult to determine
which entities are parts of the system and which parts of the environment.
A related issue is to distinguish between different entities (systems) at the same hierarchical level—
the System identification problem. Kay, following Webster (1979), discusses concepts of vertical
and horizontal separation in the holarchy. Vertical separation refers to the separation between
different scalar levels. "'If we focus on a single level in the hierarchy, higher level behavior occurs
so slowly that it is perceived as a constant. Lower level behavior occurs so rapidly that all we
observe is a sampled statistical behavior.'" Horizontal separation refers to the separation of
presumed systems (entities) at the one scalar level. This "'depends on the isolation of the system
making up any level and upon their segregation into groups which form the systems of the next
higher level ... some things are more connected than others ... The integrity of a system exists by its
high degree of internal interaction.' The stronger the interactions between two systems at one level
in the hierarchy, the smaller their horizontal separation."
To determine the boundary of a given system, an observer must select the focal level (Figure 1) for
observing the system; then the respective levels containing the environmental super system on one
hand, and the level containing the system's components and subsystems on the other hand (Kay
1984; Salthe 1985, 1993; Gould 2002; Lemke 2000, 2000a, 2000b; Lane 2006). The next step is to
identify the focal system's Environment at its own level of focus by first eliminating those
elements or systems which do not interact dynamically with the focal system. Those that are left
form the immediate dynamic environment. The Microenvironment is the environment analyzed at
the level of the components and the Macroenvironment is the environment of the supersystem
containing the holon.
Kay (1984) considers the utility of reductionist vs holistic approaches for understanding the
behaviors of hierarchically complex systems. Reductionism assumes that the behavior of a higher
level entity can be fully explained in terms of the behaviors of its subsystems. Polanyi (1968) and
Davies (2004) demonstrated the physical incalculability of the higher-level properties of even fairly
simple systems, an argument also supported by Ulanowicz (2000, 2002). Kay (1984) argues:

Figure 1. Establishing a level of focus on a system in a hierarchically complex world. (Hall et al. 2005)
The reason we cannot is that we cannot have sufficient information to predict how the components will interact, a
priori.... Most of the information we lack is about the past stresses on the system and its components. These stresses
have caused the components to EVOLVE certain interactions, which cannot be apparent from simply examining the
components at the current moment in time. In short, living systems have "memory" about [or history of] past events
and this is reflected in their structure and function. As well the interaction of living system can be probabilistic in
nature. However we can explain, a posteriori, the higher level behaviors in terms of the lower level behavior.
Salthe (1985, 1993) and Chaisson (2001) explored in considerable depth the origins and structures
of hierarchically complex systems. The behavior of a holon is basically generated by the activities
of its components as governed by physical laws, while its trajectory is regulated and constrained by
local environmental possibilities provided by its macroenvironment.
Emergence of new levels of complexity in a hierarchically complex dynamic environment.
Salthe (2004) focuses specifically conditions for the emergence of organized systems. Given that
today’s world is already complex, new layers of organization will emerge at intermediate levels of
complexity in the scalar hierarchy. Between the most fundamental particles and the universe as a
whole, entities at all scalar levels are bounded by higher and lower levels. An entity at any level is
regulated by conditions provided by the higher scalar levels, while its possible behaviors are
generated by capabilities inherent in lower level components. This produces what Salthe (2004:336-
337) calls the basic triadic system of scale hierarchies. "The lowermost level of the triad proposes
(materially causes), while the uppermost level disposes (mediates what happens at the focal
level)..."
One could visualize an endless bubbling up of possibilities as fluctuations from what might come to be the lowest
level in a future triad of them after a focal level has emerged with the cohesion of some of those possibilities. Only
those possibilities supported by boundary conditions from what would come to be the highest level of the triad could
become stabilized for the duration of those boundary conditions -- or even beyond if they become supported by other
forms of information (such as genes in cells) as well. In this way, focal level cohesion might evolve from being
supported by continued proximate dynamical maintenance by boundary conditions to one involving internal
information as well.
Salthe suggests that a new level of complexity (i.e., system) can emerge in an exergy gradient
when:

1. The emergence increases the overall production of entropy of the local supersystem. This is
possible only when:
2. The emerging dynamic processes can separate themselves from the existing dynamics of other
levels - increasing the rate at which exergy in the flux is dissipated. This happens only if there is
a suitable match of
a. boundary conditions and,

b. initiating conditions.
The initiating conditions of course must include a large enough local gradient of exergy to fuel
emergence of the new system.
Assuming that dynamic processes at different scales proceed at different rates, and assuming that
the universe starts in a state of disequilibrium, large-scale processes would take much longer to
reach equilibrium from a given starting point, which implies in turn, that systems at different scales
would in general exist at different distances from thermodynamic equilibrium.
[U]sing the classical equilibrium approach, it can be seen that there would be no thermodynamic opposition to the
formation of new levels generally because a new one would in principle be further from local thermodynamic
equilibrium than the lower level which gave rise to it, but closer to its local equilibrium than the upper level that
regulated its emergence. Therefore the interpolation of new levels would not change the total entropy of the global
system. [Salthe 2004:338]
In the realm of nonequilibrium thermodynamics, the emergence of a new level can be seen as the
"cleaning up" or streamlining of energy fluxes to dissipate gradients to heat energy as rapidly as
possible (but in most cases a 'short circuit' will not occur because the necessary catalytic conditions
for complete dissipation do not exist). However, competition exists between different paths such
that those that can consume exergy the fastest will consume the most, creating new, lower quality
gradients in the process and possibly "starving" the competing pathways (i.e., systems).
The production of new levels in a scalar hierarchy is here viewed as the way a material system can streamline or
linearize its overall energy gradient dissipation rates, this being mandated by the Second Law of thermodynamics
which, because of the radical thermodynamic disequilibrium of the Universe, calls for the degradation of energy
gradients and the production of physical entropy at the fastest rates possible. The very fastest rates conceivable are
not materially possible because of the necessary embodiment of the energy consumers, which requires some portion
of the dissipated gradients to be put to work creating and maintaining them. Presumably, without these, often very
specialized, consumers, some energy gradients in the Universe would not get dissipated at all. Evolution, then, is the
Universe’s devious route to its own negation. [Salthe 2004:339]
However, instabilities in the flux dissipation systems can lead to chaotic flows that substantially
reduce flux rates and destabilize the conducting system - leading to its disintegration. The example
is the electrical short-circuit that blows the fuse, and thus totally blocks the current flow.
The conclusion here, as amplified in a number of other works, is that for certain spatial and
temporal distributions of fluxes between sources and sinks, the second law of thermodynamics may
basically cause the world to become more complex through time. The basic properties of matter and
energy provide circumstances where complex dynamic systems can emerge spontaneously at a
variety of levels of organization within the hierarchy of a complex system. Processes of selection
based on maximum entropy production favor systems that can dissipate fluxes faster and more
effectively while retaining the necessary structural organization to provide the conduit between
sources and sinks. Cyclones and tornados are examples of systems that provide rapid rates of
dissipation but are eventually disrupted and disintegrate as the result of minor climatic or
geographic perturbations that either reduce the availability of exergy needed to fuel their dynamic
structure or exceed their self-regulatory capacity. This is the outcome of a weak mutual interactive

connectivity between system components within a causation network with little in the way of
reciprocal or circular causation loops.
Dynamic systems possessing causation patters based on an interaction network topology with a high
number of feedback circuits affecting all components tend to be resistant to disruptive perturbations.
When self-regulation conditions are exceeded by perturbations, a high density of negative and
positive feedback loops allows the system either to stabilize around oscillatory trajectories between
some localized sources and sinks (homeostasis) or to explore quasi-chaotic regions and find more
suitable source-sink configurations that absorb that kind of perturbation and thereby avoid
disintegration. When this happens, the system is not only self-regulatory (under certain external
conditions) but also self-organizing (under changes of those external conditions) (See Thomas and
Kaufman, 2001).
What is life?
Autopoiesis
A foundation problem in biology is that there is still no universally accepted definition of what it
actually means to be alive, or for how living things can be unambiguously differentiated from the
non-living. Many biologists either avoid the question entirely or accept some set of ad hoc
descriptors that seem to fit most cases that most people would consider to be living.
To answer questions raised in biology courses they taught, in the late 1960s and 1970s the Chilean
neurobiologists Humberto Maturana and Franscisco Varela put together a framework to provide a
set of criteria that could be used to diagnose whether a system was living or not (Maturana, 1970,
2002; Varela et al. 1974; Maturana and Varela 1980, 1987). They called this conceptual framework
Autopoiesis (literally self + production).
Although Maturana and Varela did their work more or less in isolation from both systems theory
and genetically based evolutionary biology, they published their definition, and it has subsequently
survived considerable criticism and analysis across a number of disciplines allied to biology,
including artificial life and the social sciences. On the other hand, mainstream biologists have
largely ignored the works on autopoiesis (Luisi 2003), possibly because Maturana and Varela
expressed their concepts in a highly paradigmatic and iteratively defined language 1 (Lyon 2004; see
Whitaker 2001 for an invaluable guide to this vocabulary). Many biologists working in a scientific
realist paradigm would also consider Maturana and Varela's work suspect because of its
associations with social theories emerging from the radical constructivist2 and post-modernist
philosophies (e.g., Reigler 2001; Salthe 1993). However, as will be shown, Maturana and Varela's
ideas can play a central role in understanding biological systems.
1
There is a mapping between a physical-cybernetic definition of autopoietic systems and Maturana and Varela’s
explanations based on apparently “recursively” defined distinctions. According to Urrestarazu (pers. comm.) their language
(and especially Maturana’s) is not recursive but systematically concerned with the “ontology of observing”, in which
attention is focused on what is being said by an observer in contrast with what observers can gather from their experiences in
their own domain of existence (“external reality”). This effort to avoid confusion of domains produces an extremely
redundant sort of discourse where the basic ontological considerations are being recalled at all levels of analysis, over and
over again. It is an iterative language, but not recursive. However, this results in a mode of writing that requires substantial
effort to comprehend. Here, I reformulate some of these ideas using Karl Popper's (1972) ontology of three worlds.
2
Though, this is more an effect of hastily conclusions because there are some fundamental differences between
constructivism and Maturana’s epistemological stands (Maturana, 1988) with respect to the notion of “external independent
reality”, so that he cannot be considered as a genuine constructivist author (Tomm, 1989, Jutoran 1994, 2005). Maturana and
Varela do not deny the observers of a cognitive system the capacity to distinguish a “reality” external to what the observed
cognitive system itself is capable of “bringing forth as a world” according to the nature of its sensory-motor apparatus. In
this, Maturana and Varela's 'constructivism' is very similar to Popper's (1972) stance that all knowledge is internally
constructed, but subject to testing and improvement through interactions with the external independent reality.

Varela et al. (1974) listed six criteria (Hall et al. 2005 summary form), which taken together are
necessary for a system or complex entity to be considered as autopoietic or living. Whether they are
also sufficient is an issue that has provoked debate among specialists in recent years.3 In abbreviated
and paraphrased form, autopoietic entities are:
1) Self-identifiably bounded (demarcated from the environment by membranes, or the entity's

components are tagged for self-identification)
2) Individually identifiable components within the boundary (complex)
3) Mechanistic (i.e., a system driven by cybernetically regulated exergy fluxes or metabolic
processes)
4) System boundaries internally determined (self referential)
5) System intrinsically produces own components (self production)
6) Self-produced components are necessary and sufficient to produce the system (autonomy).
In a physical sense, an autopoietic system (i.e., a “living” entity) is an autonomously self-regulating

and self-producing complex system of dynamic cyclical processes. These cycles are driven and
maintained far from thermodynamic equilibrium by the spontaneous transport of fluxes of matter
and energy from sources of high exergy through the system to sinks of lower exergy. Such systems
are self-organizing and emergent (Salthe 1985, 1993; Schneider & Kay 1994, 1995; Jorgensen
1999; Giampietro et al. 1999; McKelvey 2004). Kauffman (1993) reviewed and summarized a wide
variety of mathematical, chemical and biological models demonstrating the emergence of organized
(i.e., ordered) structure at the "molecular" level from initially more chaotic or random states.
Bourgine and Stewart (2004) proposed a remarkable mathematical model of a 3D tesselation
automaton, considered as a minimal example of computer simulated molecular autopoiesis.
Maturana (1970, 2002; Maturana & Varela 1980) stressed in their works that autopoietic systems
had to be "circularly closed". According to Whitaker (2001), Circular organization is
[a]n early (and generic) label describing the essentially recursive, cyclical nature of living systems (Cf. circularity).
According to Maturana, the notion of this "circular organization" was the conceptual seed for what would later be
formally termed autopoiesis (Cf. Maturana, in Maturana & Varela, 1980, p. xvii). The following passage indicates
that what was originally termed "circular organization" in essence became the formal term organization :
"Living systems as they exist on earth today are characterized by exergonic metabolism, growth and internal
molecular replication, all organized in a closed causal circular process that allows for evolutionary change
in the way the circularity is maintained, but not for the loss of the circularity itself. ... This circular
organization constitutes a homeostatic system whose function is to produce and maintain this very same
circular organization by determining that the components that specify it are those whose synthesis or
maintenance it secures. ...Furthermore, this circular organization defines a living system as a unit of
interactions and is essential for its maintenance as a unit ..." [my emphasis] (Maturana, 1970b: reprinted in
Maturana & Varela, 1980, p. 9)
This concept of closure has been misunderstood by some critics. According to Whitaker 2001:
3
Cameron (2001), Luisi (2003) and Bitbol & Luisi (2004) suggest that the properties of autopoiesis are only necessary
in the definition of life. As will be seen in this paper, I assume provisionally that they are also sufficient – as all the present
complexity of living things as we know them can emerge naturally from the coming into existence of a minimally autopoietic
entity. The entailments of these criteria in terms of the kind of components and the kind of interaction networks that may give
raise to the emergence of a cognitive autopoietic system have not been fully analyzed yet. Enactivist authors Bourgine and
Stewart (2004) think that these criteria are not sufficient, as they consider that “a system can be autopoietic without being
cognitive, and cognitive without being autopoietic” and propose the following thesis: “A system that is both autopoietic and
cognitive is a living system.” Urrestarazu considers that there is yet more to say about the way in which the fifth and sixth
criteria of Varela et al (1974) should be worded in order to ascertain the autopoietic nature of a system. Maturana and Varela
implicitly assume that from the topological configuration of interacting components follows a spatial connectivity giving
raise to material interaction structures (forms of compact molecular concatenations occupying a volume in space) that
become the physical support for the emergence of cyclical regulatory mechanisms. In a more general (non molecular)
autopoietic system, this topological (physical) constraint should be explicitly specified.

Critics of Maturana and Varela have interpreted the defining closure of autonomous / autopoietic systems to indicate
these are "closed systems" in the traditional sense. This is quite simply not the case, and results from (a) a
misinterpretation of Maturana and Varela's terminology and (b) inattention to the manner in which the explanatory
constructs underlying a traditional ascription of system "openness" (e.g., feedback) are addressed in autopoietic
theory.
"Please note that when we speak of organizational closure, by no means do we imply interactional closure,
i.e., the system in total isolation. We do assume that every system will maintain endless interactions with the
environment which will impinge and perturb it. If this were not so, we could not even distinguish it." (Varela
& Goguen, 1978, p. 294, [emphasis in the original])
Maturana and Varela (1980; 1987) provide more extensive discussions of the concept. Hall (2005)
observes that these criteria do not consider time as a factor, and argues that for the concept of
autopoiesis to be meaningful in real-world contexts, an autopoietic entity must be able to self-
maintain its state of autopoiesis over a period of time. They did not extend their definition to
include reproduction because they made just the minimal necessary distinctions to describe living
entities while they are alive, regardless of the entities' “participation” in the maintenance of trans-
generational self-organization, self-production and self-regulation within a species. Their examples
of living things that did not and could not reproduce included differentiated nerve cells and bees. As
will be shown below, considering what happens to systems meeting the minimal criteria to be
considered autopoietic over historical time leads to some interesting conclusions.4
Maturana and Varela also equate the self-regulatory and self-productive aspects of autopoiesis with
cognition. Lyon (2004) provides a masterful exposition of this point of view. Van Duijn et al (2005)
take a somewhat different view, but still accept that a minimal form of cognition can take place
without codified or linguistically expressed knowledge, and give a good example of situational
cognition. Borgine and Stewart (2004) distinguish cases of autopoiesis without cognition and of
cognition without autopoiesis. Luisi (2003) discusses the difficulties arising from
anthropomorphizing the concept of cognition. Bitbol & Luisi (2004) do not accept that cognition
can exist without autopoiesis, but do argue that autopoiesis can exist without cognition. However,
these variant views depend on how one defines cognition - which is not the purpose of the present
paper. As will be discussed below, I follow Maturana and Varela in defining cognition as the sum
of the self-regulatory (i.e., homeostatic) processes required to maintain the state of autopoiesis in a
fluctuating environment.
Thus, defined in one sentence, autopoiesis in nature (as distinguished from computational models)
is the emergent condition achieved by a system of bounded (i.e., self-identifying), self-regulating
set of entropically driven (i.e., exergy dissipating) dynamic processes able to produce and maintain
the system’s autonomous existence in the face of environmental perturbations; i.e., that which
qualifies a complex dynamic entity as "living".
What, then, is required to turn a newly emergent system passively driven by an energy flux at an
intermediate level of organization into an actively self-identifying, self-maintaining and self-
producing autopoietic system? The first part of the answer comes from physics, the second from
philosophy.
However, the physics and the philosophy are entangled because both the question and the answer
involve us as observers. A realist physicist would argue that if autopoiesis is to be considered as an
objective phenomenon occurring in nature, it pre-existed before any kind of philosophy, since
(human) philosophers are just a particular kind of living organism evolved from amongst
uncountable other species without philosophizing capabilities. That “What” cannot be avoided as a
4
In fact, if we take evolution as an outcome of the “successful transmission” of autopoietic capabilities, generation
after generation, we are talking of a higher order complex phenomenon: self-maintenance of autopoiesis through time. As
will be seen in the following discussion, interesting things happen as autopoietic entities survives and change through
historical time.

scientific question and thermodynamic considerations are not sufficient in themselves to provide the
solution. As any physicist would expect, the second law of thermodynamics should apply to any
material system, autopoietic systems included. But the material conditions leading to the
establishment of autopoietic behavior are special and cannot be derived from a statistical theory that
accounts only for global states—even if the analysis is refined to localized levels like attractor
basins of entropy stabilization. There is something peculiar to molecular dynamics that allows the
emergence of cyclically maintained interaction mechanisms capable of generating new emerging
levels of self-sustained complexity. What these peculiarities are will be elaborated in the following
sections. The emergence of compensating mechanisms relies on these peculiar characteristics of
macromolecular interactivity that facilitated the origin of the first autopoietic systems on Earth. All
other kinds of systems I consider here to be autopoietic 5 emerged in the subsequent evolutionary
history of the growing complexity of macromolecular systems.
Evaluating explanations of the origin of autopoiesis
In this paper I seek to present an argument for the physicochemical origin of life itself, under
circumstances that existed billions of years ago that cannot be reconstructed to any degree of
determinable accuracy. My thesis can only be evaluated on the basis of the plausibility of the
claimed processes and the ability to survive logical analysis and testing of arguments about general
or universal phenomena as required in the claimed processes. Rizzotti (1994), following Deamer
and Fleishacker (1994), discussed some of the factors that should be considered in determining the
plausibility of a thesis regarding an evolutionary process. These are (1) the explanation does not
require any major discontinuity in process (i.e., it occurs gradually), (2) that the process can take
place without a need for "isolated special cases", and (3) that the expected outcome of the process is
more "robust" than others. Robustness means, (a) the overall yield of the expected products should
be reasonably high, (b) the process should be simple, "in the sense that every chemical system must
be compatible with the resumed primordial situation...", such that the proposed processes do not
depend on sophisticated media or reagents available only in the lab; and (c) that can occur in a
"random" way, i.e., where there are a variety of thermodynamically equivalent paths for steps that
does not require kinetic biases due to requirements for a specific catalyst.
I believe that the argument presented in the remainder of this paper meets these criteria.
Evolutionary Epistemology
Observers
Maturana and Varela’s definition of autopoiesis hinges on the concept of an autopoietically

cognitive entity or "Observer" able to discriminate entities and boundaries (minimally its own
identity and boundaries) in its environment. This is one of Maturana and Varela's paradigmatically
more difficult terms to define in neutral language (see Whittaker 2001 -
http://www.enolagaia.com/EA.html#observer). At least in the intersubjective case, an observer is a
cognitive subject or entity able to discriminate things and respond to or codify those observations in
a way that is meaningful to itself or other subjects. This definition will be filled out more in
discussions below. The central argument of Maturana is that the observer, while attempting to
explain cognition (or autopoiesis), cannot avoid considering the fact that he or she is also structured
as a molecular cognitive autopoietic system and thereby both subject and object in the act of
explaining the very phenomenon to be explained.
5
In the world we know first-hand, special aspects of carbon-based macromolecular dynamics favored the emergence of
autopoiesis. However, in other regimes of temperature, pressure, etc. it may be possible that very different kinds of
autopoiesis could emerge - still driven by the conduction of energy fluxes from sources to sinks.

Physics and semiotics
The key to understanding the origins of autopoiesis is to understand where and how the complex
system comes to discriminate 'self' from non-self and acquires the capacity to control the self.
Howard Pattee in a series of works beginning in 1969 has explored these fundamental questions
from a viewpoint beginning in biophysics (Pattee 1995, 1995a, 1996, 1997, 2000, 2001, 2001a). His
student, Luis Rocha has continued the work (Rocha 1997, 1998, 2001; Rocha & Bollen 2001;
Rocha & Hordijk 2005).
Pattee (1996) introduces the concept of Epistemic Operations, which include biological functions
like Observation, Detection, Recognition, Measurement and Control, that he considers
differentiate living things from non-life. Defining this set of terms at this point presupposes that we
already have a clear understanding of how these concepts follow from physical processes in the
autopoietic framework. For this reason, we will accept them for now as 'primitive', and allow their
physical definitions to emerge from the development of the paper.
Pattee also uses three important epistemological concepts in developing his concept of epistemic
operations may be relatively unfamiliar. Like Maturana and Varela's writing, Pattee's writing tends
towards circularity in its definitions. Following are my interpretations of these terms. All assume
the involvement of an observer and that which is observed.
Epistemic cut refers to the strict ontological separation (in physical and philosophical senses)
between
knowledge of reality from reality itself, e.g., description from construction, simulation from realization, mind from
brain [or cognition from physical system]. Selective evolution began with a description-construction cut.... The highly
evolved cognitive epistemology of physics requires an epistemic cut between reversible dynamic laws and the
irreversible process of measuring initial conditions. This is also known as the measurement problem." (Pattee 1995a).
Semiotic control (Pattee 1997) refers to the situation where symbolically encoded information is
used to control a physical process. In other words there is an epistemic cut between the control
information and that which is controlled that is the reciprocal to the kinds of cuts cited immediately
above (see also Corning 2001, 2002). By contrast to physical laws that are global and inexorable,
controls are local and conditional. According to Pattee (2000):
Physical laws and semiotic controls require disjoint, complementary modes of conceptualization and description.
Laws are global and inexorable. Controls are local and conditional. Life originated with semiotic controls. Semiotic
controls require measurement, memory, and selection, none of which are functionally describable by physical laws
that, unlike semiotic systems, are based on energy, time, and rates of change. However, they are structurally
describable in the language of physics in terms of nonintegrable constraints, energy degenerate states, temporal
incoherence, and irreversible dissipative events.
Local and conditional control is determined by the historically developed instantaneous structure of
the physical ensemble including both what is controlled and what is providing the controlling
constraints. Control is an effect of the instantaneous dynamics of the structure of local situation as
this constrains the possibilities allowed by universal law.
Still following Pattee (2000), at its core, physical theory does not include a capability to control.
Universal physical laws specifically relate to situations where there is no control where the
relationship between cause and effect "is invariant with respect to different observers, and
consequently those relationships between events over which the observer has no control." For
control to exist, the 'controller' [which may be no more than the instantaneous local ensemble itself]
must be able to provide some form of local circumstances or local structural constraint (which may
be positive or negative) in addition to what is dictated/expected by universal physical law.

Semantic closure provides a connection between the semantic/cognitive processes of recognition,

measurement and decision and the application of constraints (controls) to the physical world.
Semantic closure
[i]s an extension of von Neumann's logic of description and construction for open-ended evolution. Semantic closure
is both physical and logical, and it is an apparently irreducible closure, which is why the origin of life is such a
difficult problem. [Pattee (2000)]
Semantic closure is presumably what Maturana and Varela were trying to express in their concept
of "circular" closure. However, Pattee (2000) did not see a clear path by which semantic closure
could evolve from an unthinking world of purely physical processes.
Semantic closure refers to the situation where there is a cyclic process of self-reference between the
material and symbolic aspects of the organism relating (1) to the physical processes of observation
and detection, (2) the semantic processes of recognition, measurement and decision, (3) the physical
application of semiotic controls, and (4) observation of the results of that application to begin a new
cycle. An example of this is Boyd's OODA loop process (Boyd, 1976; Hall, 2003, 2005; Hall et al.
2005) - Figure 2. Maturana and Varela (1980, etc) use the concept of Cognition for the
semantically closed cybernetics of autopoietic self-regulation and self-maintenance/production.
Figure 2. John Boyd's OODA Loop concept (from Hall 2003, after Boyd 1976 - see http://www.belisarius.com)
A Symbol is some form of abstracted code that has a semantic significance by providing some kind
of control information in a particular environment. Pattee (2001a) notes that symbols are energy-
degenerate and rate-independent codes separated by an epistemic cut from the rate dependent
dynamics of the physical structures that they are used to control. Although Pattee's construction
provides a good starting point, it is incomplete. As discussed in the next section, Karl Popper's
OBSE
epistemology distinguishes two ontologically significant epistemic cuts between the pure physical
dynamics and encoded control information.
The Meaning of the symbols is determined by the effect of that control information.
It should be noted that Biosemiotics is the study of the physics and philosophy of symbolic
codification systems. Where biophysical applications are concerned, Pattee was probably the
intellectual founder of the discipline. It has been substantially extended by Søren Breier (1995,

1996, 1998, 1999, 2001, 2003, 2003a), Klaus Emmeche (1997, 1997a, 1998, 2000, 2002, 2004;
Emmeche & Hoffmeyer 1991; Emmeche et al. 1997, 2000) and Jesper Hoffmeyer (1997, 2001,
2001a, 2002, 2002a; Hoffmeyer & Emmeche 1991). However, it is beyond the scope of the present
work to go very far down this path.
Karl Popper's Epistemology
What is Knowledge?
Recognition, decision and measurement assume the existence of something to measure against and
decide in relation to, which here is termed "Knowledge". Pattee argues that knowledge is a codified
product of life. The concept of codification implies too much, and as used by Pattee, leaves a large
gap of understanding between the lifeless systems of uncontrolled physics and living systems that
are complicated enough to symbolically store an evolved knowledge in a nucleic acid-based genetic
system that enables them to control aspects of their internal organization and the external world.
Karl Popper (1934, 1963, 1966, 1968, 1972, 1974, 1974a, 1978, 1982, 1994; Popper and Eccles
1977) and Donald T. Campbell (1960, 1990, 1990a, etc - as reviewed by McKelvey 1999 and
McKelvey & Baum 1999) have developed a biologically based epistemology that supports an
exploration of the earliest stages in the emergence of control information (knowledge). Here, I
follow Popper, whose expression of the concepts is the most clear.
Many scientists and philosophers are familiar with Popper's early works, The Logic of Scientific
Discovery (1934/1959) and Conjectures and Refutations (1963). In these, he argued that it was
impossible to deductively prove that mental claims about reality were true. Following Tarski,
Popper defined Truth as "correspondence with reality". In this early work Popper argued that a
single falsification of a deductive inference from a theory/claim was sufficient to falsify the claim.
He further argued that because truth could not be proved but falsity could be, the best way we could
improve the quality of our knowledge was to make bold hypotheses to include the maximum
number of connections with the world and work strenuously to criticize or refute the connections.
Those hypotheses that survived refutation were more adequate representations of the world than
those that were refuted. (Hall 1983).
Popper, in his later works (1968, 1972, 1974, 1974a, 1978, 1982, 1994, 1999; Popper and Eccles
1977), responding to critics of the earlier works, also accepted that falsification could not
deductively prove the falsity of a hypothesis. Any hypothesis can be "immunized" against
falsification by an infinite regress of auxiliary hypotheses introduced to defend the original
hypothesis against particular falsifications. However, Popper (1972 et seq.) argues that it is possible
to approach a correspondence with reality through cycles of hypothesis construction and criticism -
an approach adopted by the critical rationalist school of philosophy.
In the 1972 book, Objective Knowledge, published in his 70th year, Popper related his approach to
natural selection and evolution, and formalized it as his "general theory of evolution".

TS1
TS2
Pn • EE Pn+1
•
•
•
•
TSm
Figure 3. Popper's "general theory of evolution" (after Popper 1972: pp. 243). I add the inferred iteration loop
to the drawing. Pn is a problem situation the living entity faces in the world, TSm represent a range of
tentative solutions the entity may attempt or propose in order to solve the problem. EE represents a process
of criticism and error elimination that selectively removes those solutions that don't work in practice. Pn+1
represents the now changed problem situation remaining after the first one is solved. As the entity iterates
the process, it will construct an increasingly accurate representation of external reality.
Elsewhere Popper abbreviates this evolutionary theory of knowledge to the "tetradic schema", P1 →
TT → EE → P2, where TT is rendered as "tentative theories" rather than TS, "tentative solutions".
This latter construction is appropriate for discussing criticism of linguistically expressed theories
rather than embodied solutions. Based on this biological point of view, Popper then defines
knowledge as "solutions to problems", and notes that "all life is problem solving" (Popper 1999).
Campbell (1960, 1990, 1990a) developed a similar approach, which he expresses in shorthand as
"blind variation and selective retention."
Thus, the philosophical stance that Popper and Campbell take is an interesting mix between realism
and radical constructivism. Maturana (1988) took a similar stance to Popper and Campbell in his
ontology of observing as expressed by the notion of "objectivity between parentheses", and
explicitly rejected all epistemological stands that lead to solipsism. Popper, Campbell, Maturana
and Varela all accept the existence of a real, physical world but argue that cognitively constructed
claims or theories about that world can never be proven to be true or false. This places them in the
radical constructivist camp. However, they also accept the existence of an external reality as an
epistemic control over claims to know. Riegler (2001) and von Glaserfeld (1984, 1993, 1997, 2001)
describe the radical constructivist stance; Niiniluoto (1999) compares his own and Popper's critical
scientific realism against a wide range of other epistemologies. McKelvey (1999) reviews Cambell's
and Popper's versions of scientific realism.
Here, it should be noted that Pattee reaches a similar understanding of knowledge from his
biophysical approach:
Knowledge is potentially useful information about something. Information is commonly represented by symbols.
Symbols stand for or are about what is represented. Knowledge may be about what we call reality, or it may be about
other knowledge. It is the implementation of "standing for" and "about" - the process of executing the epistemic cut -
that [we need] to explore. Heritable, communicable, or objective knowledge requires an epistemic cut to distinguish
the knowledge from what the knowledge is about. By useful information or knowledge I mean information in the
evolutionary sense of information for construction and control, measured or selected information, or information
ultimately necessary for survival. [Pattee 1995a - my emphasis, his italics].
Although Pattee emphasizes the existence and importance of the epistemic cut between reality and
the necessity of knowledge for survival, he did not account for the emergence of the cut. Popper
provides the key insight to identify what Pattee missed.

Ontological domains where knowledge can be found
To facilitate discussion of the emergence and evolutionary growth of knowledge, in Epistemology

without a knowing subject (1968 - as republished in his 1972 book), Popper first introduced a
metaphysical ontology of three domains or "worlds" within which various forms of knowledge
could be categorized (Figure 4).
World 1 (abbreviated here as "W1") is the world of physics and chemistry, encompassing
everything that exists, i.e., this is physical reality including the uninterpreted dynamics of complex
systems.
World 2 ("W2") is the world of cybernetics and cognition that includes the embodiment of
cognition and action and what Popper (1972) terms dispositional or subjective knowledge (i.e.,
knowledge embodied in the subject). In a physical sense, knowledge in W2 ("W2 knowledge")
represents the situational propensities or "dispositions" embodied in the structure of a complex
system that constrains the system to behave in certain ways in particular circumstances. In its
simplest form, the cybernetic control structure of a system exhibiting feedback control is the basis
for W2 knowledge. More complex forms of W2 knowledge may be represented in the structural
associations and cyclical dynamics of macromolecules in a cell, or the strengthened
interconnections of neurons in a brain that know the skills we have learned for better interacting
with the world. Polanyi's (1958, 1966) 'tacit' or 'personal' knowledge is more-or-less synonymous
with Popper's W2 knowledge.
Figure 4. Karl Popper's three worlds ontology (after Hall 2003).

World 3 ("W3") is the world of the objective products of cognition, or of continued autopoietic
self-maintenance in a changing environment, i.e., what Popper calls symbolically encoded or
linguistically expressed knowledge.6 I disagree with Niiniluoto (1999: p. 23) who states that W3 is
limited to the "products of human social action". I read Popper to say that W3 comprises the
products of all kinds of cognition. Popper clearly defined W3 to include knowledge in the objective
sense, which includes "the world of the logical contents of books, libraries, computer memories,
and suchlike" (1972: p. 74) and "our theories, conjectures, guesses (and, if we like, the logical
content of our genetic code)" (1972: p. 73), while the physical structure of the codified content
remains always in W1.7 Pattee 1995a states:
The requirement for heritable or objective knowledge is the [epistemic] separation of the subject from the object, the
description from the construction, the knower from the known. Hereditary information originated with life with the
separation of description and construction.... Von Neumann ... states this epistemology of physical theory clearly: " . .
. we must always divide the world into two parts, the one being the observed system, the other the observer. The
boundary between the two is arbitrary to a very large extent . . . but this does not change the fact that the boundary
must be put somewhere, if the method is not to proceed vacuously . . ." In physical theory, the observer is formally
related to the observed system only by the results of measurements of the observables defined by the theory, but the
formulation of the theory, the choice of observables, the construction of measuring devices, and the measurement
process itself cannot be formalized.
...
The epistemology of physics would be relatively simple if this were all there were to it, but laws and initial conditions
alone are not enough to make a complete physical theory that must include measurement. Measurement and control
require a third category of knowledge called boundary conditions or constraints. These are initial conditions that can
be compressed locally but that are neither invariant nor universal like laws. When such a constraint is viewed
abstractly it is often called a rule; when it is viewed concretely it is often called a machine or hardware.
Both experience and logic teach us that initial conditions cannot be measured, nor boundary conditions constructed,
with the deterministic precision of the formal dynamical laws. Consequently, this third category of knowledge
requires statistical laws. Statistical laws introduce one of the great unresolved fundamental problems of epistemology.
The dynamical laws of physics are all symmetric in time and therefore reversible, while statistical laws are
irreversible. ...
Forms of evolutionary knowledge
Origins of embodied knowledge in W2
Prigogine, Kay, Schneider, Maturana, Varela, Pattee and Popper provide the phenomenological and
epistemological framework for considering the emergence of knowledge-based complex systems. It
now remains to explore specific conditions for the emergence of the necessary capabilities for self-
control required for the existence of autonomous autopoietic systems.
From the prior discussion it should be clear that the key issue is to account for the origin and nature
of the self-regulatory control information an autopoietic entity uses to maintain homeostasis of the
system containing the control information. Given the extreme complexity and specificity of the
apparatus required to replicate and assort hereditary information encoded in DNA molecules, and
given that the phenomenon of autopoiesis must reasonably be assumed to have emerged from the
6
Urrestarazu (pers. comm.) would prefer to express this somewhat differently, to say that the term “objective” refers
to the resulting structure of a material “product of cognition”. This structure may cause the enaction further cognition
(problem solving ability) within a wider system if and only if it enters into a dynamical process that reproduces the kind of
“continued autopoiesis self-maintenance in a changing environment” (i.e. knowledge reproduction) for the system in which it
participates, independently of any observer. The “decoding” process is embodied by the overall structure of particular
systems and may be completely inaccessible to an independent observer.
7
It should be noted that Maxwell (2002) in his otherwise quite favourable biography of Popper, disputes the
ontological validity of Popper's three worlds. As is argued by Hoffmeyer and Emmeche (1991; Emmeche & Hoffmeyer 1991;
Hoffmeyer 2002a), and as will be shown below, the biological evidence for the existence of three ontologically distinct
domains as Popper has defined them is quite strong.

near equilibrium of an unorganized chaos, following Rizzotti (1994) the first plausible autopoietic
systems would have been very much less sophisticated.
To us the key feature not considered by Maturana and Varela for identifying an autopoietic system
is that the system must maintain some its 'self' with some degree of functional integrity through a
passage of time in the face of external perturbations. Survival through time implies that the
homeostatic system must have some properties of its structural organization that provide negative
feedback control to counteract perturbations that would otherwise lead to disintegration. The
primordial autopoietic system would have coalesced close to equilibrium through a spontaneous
emergence of simple structural mechanisms to transport and dissipate fluxes of exergy. However, to
survive changing circumstances a nascent system must be so structured that at least some exergy is
fed back into the system to maintain its integrity in the face of destabilizing perturbations and
fluctuations in the medium or as environmental equilibria move away from those supporting the
system's initial coalescence.
Assuming that the structure of the nascent system and its medium provide the possibilities, even
though there is no mechanism to objectively codify and store control information, natural selection
will begin to build survival 'knowledge' whenever/wherever systems persist long enough to begin
accumulating a connected history. In the framework of Popper's 'general theory of evolution', it is a
truism that those systems that disintegrate and return their components to the blind chaos of W1 do
not build knowledge. However, where systems have by chance ("blind variation") coalesced into a
structure that includes some homeostatic capacity that allows them to maintain their historical
integrity in the face of perturbations, this structure embodies some W2 survival knowledge. Note
that the concept of Embodiment of knowledge in an entity implies that it is diffusely present in the
overall structural organization of the entity and not present as 'control information' in a discretely
codified or even codifiable form. The control information is embodied int the instantaneous
dynamic structure.
Even if partially autocatalytic systems later disintegrate to return their components to the
environment, systems that successfully produce more of the same kinds of components that are
involved in their structure will make it easier for other autocatalytic systems using those
components to emerge from that environment. This might be considered a form of environmental
knowledge (where knowledge is defined as ‘solutions to the problems of life’). The stage between
Turbulence and Coalescence in Error: Reference source not found illustrates this stage.
Thus, even the survival over limited time of homeostatic systems having some autocatalytic
capability to produce suitable components may work to prepare the environmental medium to more
readily form such systems. It is reasonable to believe that in this epoch, the W1 environment will
itself develop in ways that shift the equilibrium between integration and dis-integration of
components so that the integrated systems do not so readily fall apart. It follows that coalescent
entities with favorable structures will 'live' for increasingly long stretches of time, until lineages are
formed that do not dis-integrate. These establish continuous historical heritages. Survival
'knowledge' accumulated in an autopoietic entity is lost if it dis-integrates. Survival knowledge
continues to accumulate in a lineage as long as the lineage survives in an organized state with an
unbroken history (i.e., heritage). In Error: Reference source not found, this is ‘stabilized
autopoiesis’.
To this point, the discussion has not considered reproduction. Although the first of the barely
stabilized autopoietic systems might survive for a while, given the range of perturbations that can
arise in a chaotic environment, they probably don't embody enough organizational knowledge to
survive for long.

Evolutionary Stage
Turbulence
Dis-integration Integration
Coalescence / Emergence
Tentative solutions
†
Stabilised autopoiesis
Stable solutions
†
Dispositional autopoiesis
Selected solutions
†
Semiotic autopoiesis
†
Criticised Shared
solutions solutions
Knowledge sharing
Figure 5. Stages in the evolution of autopoietic knowledge.
However, with historical continuity, 'reproduction' begins to play a role. In its simplest form (i.e.,
requiring the least knowledge beyond chaos), reproduction would probably have involved nothing
more than growing larger by incorporating additional components in favorable ratios and structural
locations until the assemblage becomes physically unstable and fragments into pieces. If at least
some of the fragments retained enough of the favorable structural organization to maintain an
autopoietic existence, those histories would be preserved and added to. Even this nearly chaotic
form of replication would serve to multiply the history of solutions that worked. It becomes quite
appropriate then to talk about the currently surviving entities as 'spearheads' (Popper 1972:243)
inheriting dispositional knowledge embodying in their structures solutions to the problems of life
(i.e., 'survival knowledge' or control information) replicated from their linear ancestors.
Van Duijn et al. (2005) present the case of the bacterium E. coli, where the structural organization
provides a minimal form of cognition to actively seek 'food' and avoid danger (see also Lyon 2004).
The existing structural organization of the bacterium includes receptor molecules in the cell
membrane called MCPs that respond to the concentrations of a wide range of environmental
chemicals, a phosphotransferase pathway, bistable motors that can rotate in either direction (i.e.,
counter clockwise - 'CCW', or clockwise - 'CW') to drive flagella, plus a 'switch' protein associated
with the motor that increases the probability that the motor will switch to CW mode. In CCW mode
the flagella rotate in synchrony to propel the bacterium in a linear fashion. In CW mode, rotation is
asynchronous and causes the cell to tumble randomly. A second pathway adapts to long-term
changes in concentration so that short-term changes in the concentration of attractive or repellant
chemicals can be detected and responded to. The net effect is that a short-term rise in the
concentration of repellants or decrease in attractors causes the bacterium to tumble and reorient in a
random direction. On the other hand, if environmental attractors rise and repellants fall,
unidirectional movement will continue for some time. Thus, the net directional movement will be
up the gradient of attractors and down the gradient of repellants. The 'knowledge' that attractors

equate to metabolically useful 'food' chemicals and repellants equate to 'danger', has been built into
the structure of the bacterium by selection. In E. coli, that structure is specified to a large degree by
a genetic code existing in the DNA chromosome of the cell, such that particular kinds of proteins
are synthesized that work this way.
Obviously with no genetic system to retain and reproduce control information in any objective
form, the propagation of survival knowledge would be subject to chaotic variation and it is likely
that fragmentation would perturb many incipient lineages to the extent that they dis-integrate and
lose their accumulated history. However, as long as some lineages survive, simply by surviving,
those that do will continue to accumulate more and more survival knowledge (Popper’s general
theory of natural selection and Campbell's blind variation and selective retention).
In the early days of this process when autopoietic systems do not survive for long, disintegrating
systems will return their once functional components to the medium, thus maintaining favorable
conditions for the coalescence, emergence and growth of other autopoietic systems. However, when
systems with longer and more successful histories and reproductive abilities begin to accumulate in
the environment, the more successful survivors will compete for and sequester suitable functional
components and consume exergy resources to fuel their continued growth and multiplication to
eventually destroy the close to equilibrium situation that made the initial emergence of autopoiesis
possible. This creates selection to use available resources of components and exergy more
efficiently, and to synthesize required components from simpler/lower value starting materials.
Eventually, environmental conditions will no longer favor the coalescence of new lineages and the
survivors will thus move farther away from equilibrium. In Error: Reference source not found, this
represents the stage of dispositional autopoiesis – referring to Popper’s (1972) concept of W2
knowledge embodied in the structural "disposition" of organisms. Bentolila (2005) calls this "live
memory".
Codification to preserve knowledge in W3
To this point, I have discussed the origins of autopoiesis only in the most general terms. However,
laboratory work suggests that complex organic polymers will form in the prebiotic chemistry of an
aqueous reducing environment containing compounds based on C, H, O, N, P, S, etc. that subjected
to almost any kind of excitation energy sufficient to activate simple carbon based molecules to the
point that they can relax by bonding with other molecules, or heat flux situations that favor
polymerization through dehydration reactions. Amino acids polymerize into protenoids that can
hydrophylicaly form micelles when rehydrated. Some randomly formed protenoids have shown at
least mild catalytic activity and excitibility (Fox 1980, 1991, Fox et al. 1994; Andras & Andras
2005). Lipids can group together form bilayered vesicles, where hydrophilic radicals face either the
interior space of the vesicle or the environment (Cavalier-Smith 2002; Del Guidice & Preparata
1995; Rizzotti 1994; Segré & Lancet 2005). Nucleotides with energy rich phosphate groups can
transfer activation energy held in the phosphate group to other molecules in ways that may activate
them to polymerize; or, through loss of active phosphate groups or even simple physical
dehydration (e.g., Smith et al. 1967, Kazakov et al. 2006), they can polymerize themselves to form
long nucleic acid polymers (Woese 1967; Crick 1968; Orgle 1968; Hughes et al. 2004; Muller
2006). None of these chemicals do much on their own, but a mixture of the various polymers,
monomers and substrate materials, when subjected to the organizing forces of a flux from source to
sink, may coalesce where conditions are particularly favorable to form incipiently autopoietic
organizations.
Undoubtedly, one of the problems on life in lineages whose only form of historical knowledge is
embodied in the three dimensional dynamics of their structure, is to retain through time their
successful solutions with some degree of fidelity, especially through the process of reproductive

fragmentation (Bentolila 2005). Clearly any system capabilities that serve to protect aspects of
proven solutions by codification and packaging would have selective value by comparison to the
chaotic reproduction of diffuse structural knowledge through passive fragmentation. Based on
evidence for heterocatalytic (i.e., enzymatic) as well as autocatalytic properties of nucleic acid
polymers, it is reasonable to suppose these macromolecules may have played cybernetic control
functions in early autopoietic systems. This would facilitate the evolution of a system to codify
control information by establishing an epistemic cut. By taking advantage of the self replicating
capabilities of the nucleic acid polymers, an autopoietic system replicating these molecules, would
also be replicating the structural or enzymatic functions of those molecules performed in the
autopoietic system (Hughes et al. 2004). In today's systems DNA appears to have no direct roles in
active functions. RNAs still serve both as code carriers (in transfer RNA) and structural/catalytic
roles (in protein synthesis).
Once any structural knowledge or control information relating to the autopoietic system as a whole
is able to be represented in the structures of macromolecules that are themselves autocatalytic, the
obvious value of the self-preservative capacity of autocatalysis can be shaped and improved through
further stabilization of lineages carrying such macromolecules. This represents the first population
of Popper's W3 with persistent and shareable survival knowledge. The value of protecting the tested
knowledge in such stable and self-replicating molecules sets the stage for evolution of the kinds of
DNA and RNA-based epistemic systems we now know as Genetic systems. Pattee has discussed at
length stages in the refinement of replication, transcription and translation systems for the semiotic
preservation and application of knowledge.
In this discussion it should be noted that this supposed evolutionary path offers no means to
translate embodied experience of life back into the DNA code. There is no evidence that such a
system exists even today. As discussed by Kauffman (1993), knowledge of life has been built into
DNA codes solely through the process of blind variation and death of lineages carrying code
variants that disrupted or reduced survival of those lineages. As Popper argued quite effectively,
what is left will in general encode a broader, deeper and overall more effective response to the
problems of persisting in the real world.
Early life must have still been quite fragile by comparison to the kinds of robustly self-maintaining
cellular organisms we know today. Dis-integration would have been a common phenomenon,
scattering tested components into the environment - including usefully coded nucleic acid
sequences that would then be available for incorporation into other living entities. Even today many
bacteria retain the capacity to share and incorporate exogenous DNA into their functional genomes
by processes of transduction and transformation (Avery et al. 1944). Thus, I would argue that at
least in the early stages of the evolution of life after the emergence of a codification system, all
living things shared a common pool of hereditary knowledge, more or less in every possible
combination. In Error: Reference source not found, this represents the stage of semiotic autopoiesis.
Through this point in the evolution of life, it is very likely that survival knowledge is shared
promiscuously via fissions and fusions and disintegration and coalescence of autopoietic patches in
the overall dissipative media.
However, it is likely that some combinations of genes would work better together to stabilize and
grow in some autopoietic patches than would other combinations in other patches. There would be
advantages to lineages possessing such combinations if the different genes were physically linked
together in self-reproducing packages (i.e., Chromosomes encoding compatible bits of control
information in its genes).

Two worlds of organismic knowledge or "code duality"
Hoffmeyer and Emmeche (1991; Emmeche & Hoffmeyer 1991; Hoffmeyer 2002a) have also
considered the evolutionary origins of the self-referential capability to apply control information as
required for autopoiesis and life, and end up with an evolutionary epistemology they call Code
duality that is similar to Popper's. I quote these sources at length, because they cover the same
ground with a somewhat different viewpoint from ours. Beginning with Hoffmeyer and Emmeche
(1991):
[W]hat is the basis of this self-reference, and thus the basis of life? We shall suggest here that the central feature of
living systems allowing for self-reference, and thus the ability to select and respond to differences in their
surroundings, is code-duality, i.e. the ability of a system to represent itself in two different codes, one digital and one
analog (Hoffmeyer 1987)....
In this discussion, I equate Hoffmeyer and Emmeche's "analog" code to situational knowledge in
Popper's W2 for reasons argued below.
Self-reference clearly depends on some kind of redescription. The system must be able to construct a description of
itself (Pattee 1972, 1977) [in Popper's W3]. This description furthermore must stay inactive in - or at least protected
from - the life-process of the system, or else the description will change - and ultimately die with the system. In other
words, the function of this description is to assure the identity of the system through time: The memory of the system.
In all known living systems this description is made in the digital code of DNA (or RNA) and is eventually
contributed to the germ cells.
.......
[The] need for the participation of cellular structure shows us that a sort of 'tacit knowledge' is [also] present in the...
cell (Polanyi 1958, Pattee 1977) [in Popper's W2]. And the existence of this tacit knowledge hidden in the cellular
organization must be presupposed in the DNA-description. Thus, the digital redescription is far from a total
description.
The realization in space and time of the structural relations specified in the [nucleic acid] digital code defines what
kind of differences in the surroundings the system will actually select and respond to. Through this realization a new
phase is initiated, the phase of active life. One might say that in this phase, the 'analog phase', the message of the
memory is expressed.
Hoffmeyer 2001a states:

... I have suggested the term Code-Duality to describe the semiotic dynamics of life: Organismic and cellular function
is very much dependent on surface properties, shapes and topological ordering of macromolecules in relation to the
subcellular architecture of membranes which extend throughout the cellular body. Subcellular architecture is itself
molded by evolutionary processes and thus represents successful responses to cellular, bodily, or environmental
challenges of the past which are most often also challenges of the present and very probably of the future. [i.e.,
corresponding to Popper's (1972) "solutions to problems".]
But these representations are not sequential or digital. Rather they are analog codes for particular events and
situations. The stereochemistry of a receptor molecule on the surface of a cell may for instance be constrained so that
the receptor will recognize and bind only a certain kind of hormone molecule, say adrenaline, and no other. Thus the
receptor is an analog code for adrenaline - in this case created very early in evolution and fine-tuned in its fit through
hundreds of millions of generations.
....
Suppose that eventually a living system arose from the primordial soup—or wherever it was. Then we will have to
ask: Who was the subject to whom the differences worked on by such a system should make a difference? If one
admits at all, that living systems are information processing entities, then the only possible answer to this question is:
the system itself is the subject. Therefore a living system must 'exist' for itself, and in this sense it is more than an
imaginary invention of ours: For a system to be living, it must create itself, i.e. it must contain the distinctions
necessary for its own identification as a system. Self-reference is the fundament on which life evolves, the most basal
requirement. (This does not pertain to non-living systems: There is no reason for the hydrological cycle to know
itself. Thus, rivers run downstream due to gravity, water evaporates due to the solar heat, nowhere does the system
depend on self-recognition)....

Hoffmeyer 2002a
A... major precursor for the idea of code-duality was the American biophysicist Howard Pattee's distinction between
a ‘linguistic’ and a ‘dynamic’ mode of complex systems (Pattee, 1977). Pattee explicitly refers as a source for this
idea to Niels Bohr's discussion of the complementarity principle as pertaining to the phenomenon of life and also to
the work of John von Neumann. In a recent paper Pattee quotes von Neumann saying:
We must always divide the world into two parts, the one being the observed system, the other the
observer . . . . That this boundary can be pushed arbitrarily deeply into the interior of the body of the actual
observer is the content of the principle of the psycho-physical parallelism—but this does not change the fact
that in each method of description the boundary must be put somewhere, if the method is not to proceed
vacuously. (von Neumann (1955), quoted in Pattee, 1997). [Compare this to Maturana's (1970) concept of the
observer.]
Pattee now explains von Neumann’s point in the following way:
... [T]he function of measurement cannot be achieved by a fundamental dynamical description of the
measuring device, even though such a law-based description may be completely detailed and entirely correct.
In other words, we can say correctly that a measuring device exists as nothing but a physical system, but to
function as a measuring device it requires an observer's simplified description that is not derivable from the
physical description. The observer must in effect choose what aspects of the physical system to ignore and
invent those aspects that must be heeded. This selection process is a decision of the observer or organism and
cannot be derived from the laws (Pattee, 1997).
Since not only human beings but living systems at large are fundamentally engaged in observations or measuring
processes it follows that: "we must define an epistemic cut separating the world from the organism or observer. In
other words, wherever it is applied, the concept of semantic information requires the separation of the knower and the
known. Semantic information, by definition, is about something" (ibid). And thus according to Pattee in all living
systems we must have one part of the system operating in a linguistic and time-independent mode (i.e. the DNA [in
W3]) and one part operating in a dynamic and time dependent mode (i.e. the protein system) [i.e., in W2].
Pattee underlines that he is not suggesting a Cartesian dualism here but only a ‘descriptive dualism,’ for although a
measuring process depends on choices which cannot be derived from laws, such choices are seen by Pattee as
functions coded in DNA and ultimately generated by natural selection.
But this appeal to natural selection as the mechanism for bridging the Cartesian dichotomy between knower and
known is not convincing. How could a purely mechanical process like natural selection possibly push non-knowing
dynamical systems across the logical gap separating such systems from the realm of measurement and knowledge?
Many people apparently entertain this illusion of natural selection as a mysterious bridge across the Cartesian Divide.
But natural selection is either a selection in the true sense of this term in which case a selector (and thus
measurement) must be presupposed for its working so that some kind of preference (the essence of selection) can be
executed, or it is not a true selective process: in which case it cannot possibly explain how preferences can possibly
arise in the midst of the physical world.
Like Bohr and later von Neumann, Pattee has taken a long and courageous step in facing that borderline paradox
which necessarily must appear, whenever you subscribe to an ontology of natural law. By this expression I try to
characterize the conception of the world, which Pattee formulates quite unambiguously..., where he says that ‘these
[physical] laws describe all possible behaviors.’ The transfer of Bohr's thinking about complementarity to the realm
of life processes doesn't seem to help much here. For if complementarity is thought of in ontological terms we are
immediately brought back to the dualism Pattee explicitly rejected, but if complementarity is thought of in
epistemological terms the claim for complementarity is reduced to the assertion that even though we cannot describe
the semiotic dimension of the world in the same language we use to describe the dynamic aspects of the world, this is
due to a deficiency of language or thought. The semiotic dimension of life is like glimmerings which we cannot reach
behind, because we are totally enveloped by them.
...
Code-duality transgresses the Neumann-Pattee thesis by claiming that the linguistic or symbolic mode and the
dynamic mode are both fundamentally semiotic modes. The distinction does not separate a semiotic mode from a
non-semiotic or dynamic mode but rather posits two different kinds of semiotic coding. Thus semiotic processes
characteristic of the ‘linguistic mode’ are based on digitally coded symbols, while the semiotic processes
characterizing the dynamic mode are indexical or iconic and analogically coded. The analogically coded signs thus
correspond to the myriads of topologically organized indexical and iconic semiotic processes in cells and organisms
which incessantly coordinate body parts and their relation to environment and in so doing an analogically coded sign
also is responsible for the interpretation and execution of the genomic instructions.

To me, the application of Popper's evolutionary epistemology and three worlds ontology accounts
for the two kinds of epistemic cuts involved in the origins and evolution of knowledge. The
evolutionary assembly of a cybernetic system as a consequence of blind variation and selective
elimination/retention builds structures and dynamic connections that work in ways that tend to self-
maintain the dynamic state of the system. This is a state of being organized in W1 in such a way
that the structural components are able to maintain a certain degree of self-regulated control over
the flux of energy through the portion of the environmental medium where they exist, and not in
any of the countless other ways the same structural components could be distributed that would be
at the passive mercy of their environments.
I would not call this an analog code, but rather an organizational assembly of components that
creates a kind of attractor basin keeping their mutual interactions within some kinds of bounds.
However, it can still be argued that there is some kind of epistemic cut between the otherwise
random collection of components versus the structural or dispositional knowledge represented in
the fact that the structure has a particular dynamic state of autopoiesis that has as its 'purpose' the
continuation of that state. The control information required for regulation exists in (and only in) the
direct physical relationships and dynamics of the interacting components. In Popper's epistemology
this is selected knowledge belonging to W2, but to call this kind of analog information a code
confuses the issue.
The concept of a code is that it can abstractly describe the state of a system in a more compact way
than a complete specification of the system itself. Where structural knowledge is concerned, the
knowledge is in the conformation of the structure itself. Only when the source of the control
information is physically separated from active components of the system in a compressed,
abstracted and energetically degenerate and inactive structure, such as the sequence of nucleotides
in a DNA chromosome (i.e., as described by Pattee), does the information/knowledge become
codified and begin to form Popper's W3. There is then a second cut between the codified control
information (control codes) and the control structure, while the first cut, between the physical
control structure and the dynamic activities being controlled still exists.
The origin and evolution of genetic systems to manage cellular knowledge

In today's epoch, all living entities maintain their codified (i.e., W3 - as differentiated from
structural or W2) survival knowledge in the sequences of nucleotide monomers in nucleic acid
polymers called chromosomes. As Kauffman (1993) discusses at some length, although the blind
introduction of new control information can stabilize, change or even add new attractor basins for
the organized system, new information probably more often tips the organizational dynamics of the
system out of an attractor basin onto a trajectory that leads to chaos and disintegration. There will
be obvious advantages to lineages possessing means to isolate code sequences tested through
survival in the lineage from exogenous codes by maintaining these codes behind barriers that keep
out foreign DNA and/or to evolve systems that degrade DNA strands taken up from the
environment before any information they carry is translated or recombined with inherited
chromosomes. Both strategies are well known in living organisms today.
Once barriers evolve to cut off the existing survivors of an embodied lineage from the promiscuous
exchange of codified control information, different kinds of trophic specialization can begin to
evolve as distinct Clonal species. Hall (1966) discusses some likely circumstances and selection
pressures leading to the differentiation prokaryotic and eukaryotic organisms as distinct types of
trophic specialization emerge from the era when life was physically or genetically promiscuous8.
8
Note there are important differences between Hall's approach and Margulies's (Sagan 1967; Margulies 1968, 1970).

However, there is a downside to genetic isolation. Isolated individuals of a clone no longer have
access to share in a wide range of experientially tested knowledge from other, related individuals,
and evolution of the isolated lineage is limited to the slow pace of change in single lineages. Thus, I
would expect the evolution of a number of strategies to allow the continued exchange of genetic
information between closely related lineages (i.e., those sharing many genes in common due to a
comparatively recent common ancestry, and thus unlikely to be disrupted by exogenous control
information).
One strategy for identifying whether an exogenous piece of naked chromosome taken up from the
environment might be useful is to test whether it has a sequence of code matching that in the host
cell (i.e., because it came originally from a related individual. In this case, some or all of the
exogenous DNA may be spliced into the cell's chromosome, replacing the existing - more or less
matching segment. This is known as Transformation, and was used by Avery, McLeod and
McCarthy (1944) to prove that DNA rather than protein was the carrier of hereditary information.
A second, more sophisticated strategy, would be to package or wrap chromosomal control

information in the same kind of material that members of the clone use to bound their autopoietic
spaces from the external environment. Presumably this genetic package would then be recognized
as belonging to a self sharing a common ancestry, and thus be safe to assimilate. More sophisticated
transfer mechanisms might encode specific molecules to recognize and bind to clonal members.
Today's viruses depend on both of these strategies to inject codified nucleic acids into 'host' cells.
Although in many cases the transfer mechanism has been subverted simply to make more virus
(often killing the host cell in the process), viral transfer, known as Transduction, discovered by
Zinder and Lederberg (1952), is still an important mechanism for the lateral transfer of tested
information between related lineages - although, in many cases infecting virus cause the cells they
invade to disintegrate.
A third, still more sophisticated form of genetic exchange between bacteria, involving direct
physical contact between cells, known as Conjugation, discovered by Lederberg & Tatum (1946).
In the known cases, the entire process seems to be driven by the donor cell, which carries a
specialized chromosome known as a plasmid that control its own transfer. Plasmids may also
include genes from the donor cell's primary chromosome. One can speculate that this might be a
more evolved case of what was originally a viral transduction process.
It should be noted (1) that all of these bacterial processes involve established subsystems in the cell
lines for splicing and recombining sequences of DNA between different chromosomes, and (2) that
none of these mechanisms are directly involved in cellular reproduction. However, such
recombination mechanisms known in the bacteria are evolutionarily highly important (as shown by
the speed with which drug resistance genes can be passed between different strains of bacteria) in
sharing and recombining tested solutions to the problems of life across lineages that otherwise
reproduce clonally.
Hall ([1966]) discusseed circumstances likely to be involved in the origin and early evolution of
eukaryotic cells. To date there is no new evidence to invalidate the schema presented there. Hall
argued that two major adaptive responses were open to organisms to compensate for the increasing
degradation of resources in the environmental once the existing supplies of components and energy
fluxes were fully exploited and genetic isolation was evolved. These would constrain the evolution
of the genetic systems to manage the control information in quite different directions.
1. The evolution of increasingly complex metabolic pathways able to exploit chemical and solar
exergy directly together with secondary metabolic and biosynthetic capabilities able to assemble
necessary substrates and monomers from simpler starting materials - i.e., the autotrophic

Producers in the complexifying ecosystem. The complexity of the necessary electron transfer
and other 'molecular handshaking' activities would seem to establish a requirement for a
comparatively rigid boundary and membrane system able to maintain the stereochemical
structure of the necessary molecular machinery. On the other hand this would seem to impose
few constraints on the genetic system beyond the collection of genes into a single linkage group
to ensure that daughter cells both receive a full copy of the codified knowledge (this ignores the
interesting biology associated with plasmid chromosomes). This seems to involve no more than
attaching the chromosome to a point on the cell membrane, such that when the chromosome is
replicated as the membrane also grows, the attachment points and the copied chromosomes each
end up in the separate daughter cells. This pathway led to the evolution of today's Prokaryotes.
2. The evolution of motility mechanisms to enable the organism to move around on surfaces in the
environment to sop up widely distributed patches of primordial 'food' or even whole organisms
that had captured energy and synthesized food - i.e., the heterotrophic Consumers.. In terms of
the evolutionary requirements for new information, I believe that the motility option is
substantially the simpler, in that it only requires the development of cytoplasmic motility based
a few molecules able to change their shapes in response to imposed chemical or physical
gradients such as represented in today's amoebas (i.e., a simple kind of 'measurement' system in
Pattee's terminology). However, this lifestyle would place significant constraints on the
evolution of the genetic system, where mechanisms that favored protection of chromosomes
from cytoplasmic shearing forces. Solutions to minimize damage from cytoplasmic shearing
include partitioning the genetic code into several shorter chromosomes - each with a different
part of the code, coiling and binding the naked DNA with proteins to strengthen and further
reduce the overall length of the chromosomal packages to something on the order of cellular
dimensions, and compartmentalizing the cytoplasm containing the DNA behind a second set of
cytoplasmic membranes to completely separate the hereditary apparatus from the motile
cytoplasm. This strategy led to the evolution of cells with nuclei, known as Eukaryotes.
Packaging of the coding sequences in the DNA chromosomes in a protein matrix, partitioning the
code into several chromosomes of shorter lengths, and compartmentalizing the hereditary apparatus
within a second set of (nuclear) membranes would have made it much more difficult for such cells
to share tested genetic codes with other related lineages. The advantages to retaining such sharing
capacities would powerfully constrain the further evolution of the eukaryote genetic system. Some
amoeboid types of organisms appear to have partially solved the problem by becoming
multinucleate, which would give several independent threads of heredity in the same cell. There is
also some evidence that some means for horizontal gene transfer (e.g., viral transduction) still
provides for the slow exchange of hereditary information between more distantly related lineages.
The confusion over the early evolutionary derivation of prokaryotes and eukaryotes suggests that
horizontal gene transfer must have remained fairly common even after lineages began to
differentiate (Embley & Martin 2006; Ciccarelli et al. 2006).
More effectively, the fusion (conjugation) of separate cells to form a single cytoplasm would serve
to bring two nuclei with their separate heredities together in a single cytoplasm. What remains is
some mechanism to fuse or break down the nuclei such that chromosomes from the different
sources can be brought together to exchange genetic information. In present day systems, the
mechanism of cell fusion requires a precise matching of receptors and substrates to occur to ensure
that only proper partners fuse, which is then followed by a chromosomal choreography that pairs
and recombines genetically similar codes at the level of the DNA molecule in ways that resemble
those in prokaryote recombination. Cell fusion leaves the combined cell with a double set of
hereditary information, which is followed by another complex choreography of two cell divisions
and one chromosome replication, assisted by specialized cytoplasmic motility mechanisms to sort
one complete set of the hereditary knowledge into four daughter cells. Single celled organisms
show a range of variations on this theme. This is what we know as Sexual recombination and
assortment. Except for the necessity to return the ratio of the genome to the rest of the cell to what
it was prior to the conjugation event that brought the two sets of chromosomes together, sexual
recombination does not involve reproduction. The actual reproduction of unicellular organisms is
normally asexual or clonal.
However, due to the consequence of the regular sharing of hereditary information across otherwise
clonal lineages, the lineages that are periodically mixing and sharing their genetic experience come
to share a common gene pool and can be considered to be Biological species, separated from other
biological species by Barriers to gene flow. Once separated, the different species can evolve
independently as evolutionary entities in their own rights (Gould 2002).
Orders of Autopoiesis
Is There More Than One Order of Autopoiesis?
As argued early in this paper, complex dynamics may emerge at many different levels of
organization in a dissipative system conducting energy from a source to a sink. Thus, it is
reasonable to ask whether the complex dynamics at different levels in the global system can
themselves become autopoietic. I have already shown that systems based on macromolecules can
evolve enough complexity at the 'cellular' level of organization to become autopoietic. These are
termed first order systems.
Maturana (2002), Mingers (2003), R. Kay (2001) and Urrestarazu (2004) and several others have
argued that autopoiesis as defined by Varela et al (1974) only properly applies to the cellular level
of organization. Hall (2003; 2005; Hall et al. 2005) argues that autopoietic entities may also exist at
higher levels of organization.
It remains to see if complex dynamics can emerge at higher levels of organization involving
autopoietic cells as components that would reasonably be considered to be autopoietic, and to see
what roles autopoietic cognition and knowledge would play in their subsequent evolution.
First Order Autopoiesis: Prokaryotes and endosymbiotic assemblages
Hall ([1966]) and Margulis (Sagan 1967; Margulis 1968, 1970) cited mounting evidence that
chloroplasts and mitochondria:
1. had their own DNA that was replicated and transcribed independently from cellular DNA,
2. always formed and were multiplied through division of previous organelles, and
3. respectively exhibited many structural similarities with free living blue-green algae or bacteria.
They inferred from the evidence that these organelles represented independent lines of evolution
that had subsequently formed an endosymbiotic association with eukaryotic ancestors lacking
capabilities for photosynthesis or oxidative metabolism. Supporting this argument is the fact that
the enzymes involved in the Krebs cycle for fermentive metabolism are soluble and dispersed
throughout the cytoplasm. The molecular apparatus required for photosynthesis or oxidative
metabolism is respectively tied to the internal membranes of chloroplasts and mitochondria
respectively. Hall ([1966]) also noted that similar kinds of endosymbiosis (where there are free-
living close relatives) had evolved many times in single celled organisms. In some algae (for
example), there have been cases of endosymbiosis taking place sequentially in the same lineage

(Patron et al. 2006), where cells are built like Russian dolls, with two or three layers of eukaryotic
membranes each containing an nucleus and surrounding another set of cellular components
contained within their own membrane.
Whatever the precise pathway of events, endosymbiosis represents the fusion into a single
autopoietic entity (the eukaryote cell) of separate autopoietic entities that previously held
independent existences. At least initially, the host and endosymbiont would have maintained
cognitively separate existences to achieve their own ends in the cooperative enterprise of life, as is
the case today with photosynthetic algae living in coral polyps, where either type of entity can live
on its own in favorable circumstances. In this sense the endosymbiont represents a level or order of
complexity above that of simpler free living ancestors.
However, as the symbiotic association persists through time, and the partners evolve to work more
effectively together, the association becomes obligatory and the joint entities evolve more and more
as a single biological species with different kinds of organelles, such that the activities of the
original symbiotic ancestors are no longer distinguishable as an autonomously defined level of
organization. Because obligatory endosymbionts are protected within the cytoplasm of the host cell,
they are presumably cut off from ready gene exchanges with relatives in other lineages or that may
still be free living. Based on observations of today's chloroplasts and mitochondria, and many
obligatory endoparasites, it appears that there evolutionary advantages may be gained from actually
transferring the codes for 'endobiont' genes to the nuclear genome of the host cell where they have
access to recombination and assortment using the host cells apparatus for sexual recombination.
However, the resulting compound entity, though more complex than its various free-living
ancestors taken independently, still exists as a first order (i.e., cellular) autopoietic entity.
Second Order Autopoiesis: Multicellular Organisms
Mulitecllular organisms are certainly living, but are they autopoietic and do they represent a higher
order of autopoiesis than single cells?
To briefly summarize an argument that will be developed in more detail elsewhere, I argue that
multicellular organisms represent a second order of autopoiesis.
1. Many, if not all of the cells comprising a multicellular organism are themselves autopoietic, as
can readily be proven by isolating single cells into appropriate culture media, where they will
continue living, and in many cases even continue growing and dividing.
2. When the focus of analysis is set at the level of the multicellular organism, individual cells are
the component subsystems and the environment external to the organism's integument is the
external environment or supersystem. The following complex system dynamics can be
observed, fulfilling the requirements for the system to be considered to be autopoietic:
a. Self-identifiably bounded (demarcated from the environment by membranes, or the entity's

components are identifiably tagged): In most cases there is a visible epidermis, cuticle, or
other self-produced boundary composed of or manufactured by cells working together under
the embodiment of a common developmental program.
b. Individually identifiable components within the boundary (complex). Composed of
individually discrete cells. Even for some of the minor phyla where all or part of the adult is
formed of a multinucleate cytoplasmic syncytium, the embryonic development of the
organism is based on the multiplication and differentiation of cells before the internal cell
membranes are absorbed.

c. Mechanistic (i.e., a system driven by cybernetically regulated exergy fluxes or metabolic

processes). Activities of the multicellular entity are driven by molecular metabolism as
controlled by the dissipatively dynamic activities of a cellular neuro-endocrine system
coordinating cells in the operation of musculoskeletal system, and the distribution of
metabolically essential molecules.
d. System boundaries internally determined (self referential). See part a. above. The system
boundaries are developmentally organized under direction of embryonic developmental
processes regulated by the entity's hereditary knowledge.
e. System intrinsically produces own components (self production). See previous answer.
f. Self-produced components are necessary and sufficient to produce the system
(autonomy). All cells in the organism come from the division, growth and differentiation of
preexisting cells formed within the developmental framework of the organism. The only
counter argument is that most multicellular organisms trace their existence to a single
fertilized egg cell, although in some cases there are asexual means of reproduction that
involve various kinds of fissioning or budding of multicellular offspring from the
multicellular parent.
3. 'Lower' multicellular organisms carry W3 knowledge in their DNA chromosomes that is

devoted to regulating the intercellular dynamic interactions of cells with other cells in the
organism - and is thus an evolved product of the organismic level of complexity. The fact that
each cell has its own set of chromosomal DNA is mitigated by fact that in the normal situation
all cells in the organism trace their ancestry to the fertilized egg and thus are all so to speak
working from the same codebook. The W2 knowledge embodied in the fertilized egg or other
propagule provides the necessary framework to translate the DNA code into embodied structure.
4. 'higher' multicellular organisms have well developed cognitive capacities for selective learning,
which in a very few cases is supplemented by a capacity for extrasomatic transmission of
'cultural' knowledge from parent to offspring that exists as further evidence for a level of
coordinating knowledge that is only relevant to the organizational level. Such transmission is
mediated by pheromones, imitation, and eventually language and the products of language.
Third Order Autopoiesis: Colonies, Societies and Organizations
Colonial organisms
Several classes of organisms have evolved colonial forms of structural organization. These include
lineages that alternate sexual and asexual reproduction or that have facultative or obligatory modes
of asexual reproduction. The animal cases are more easily analyzed. In most cases these are found
in lineages where the ancestral body plan is that of a polyp that reproduces by budding, where the
new polyps remain connected to form some kind of super-organism. Where all the polyps are of the
same type these are really no more than a collection of genetically identical entities that happen to
remain connected for the exchange of nutrients and perhaps warning signals via a nerve net or
chemicals circulating through the intercellular medium. However, there are also a number of cases,
such as Portuguese Men of War, sea pansies, various kinds of bryozoa (ectprocts) and tunicates (sea
squirts) where polyps become developmentally specialized to perform quit different tasks for the
overall colonial structure, e.g., defense, food capture, digestion, and reproduction. As noted by
Wilson (1975), the polyps develop sequentially from a single larva. In one sense, this might be a
similar situation to what led to the development of segmental development in a variety of different
animal groups. Again, all share in the common genome due to asexual reproduction, but boundaries
between the individual polyps may become quite indeterminate as far as the overall colonial
organism is concerned. Here, I am inclined to treat this as a developmental process of a single
organism, and thus not representing a significantly higher level of complexity.

Wilson (1975) lists the following advantages deriving from the colonial type of organization in
marine organisms:
• Resistance to physical stress for shallow water forms where organisms are subject to wave
action and sedimentation. The colonial form raises individuals away from the bottom and
enables them to create more effective feeding currents overall.
• Liberation of otherwise sessile forms for a free-swimming, pelagic existence. This has been
achieved by some kinds of polypoid coelenterates and urochordates (sea squirts).
• Superior colonizing and competitive abilities.
• Defense against predators.
However, setting the level of analysis to that of the colony does not yield a clear result. Although
the colony as a whole is clearly living and thus autopoietic, and in the complex cases clearly have
modes of life that differ from individual founding polyps, given the lack of identifiable physical or
genetic individuality of the constituent polyps, it is arguable as to whether such colonial organisms
should be considered to be a higher order of autopoiesis different from that of a common
multicellular organism.
The plant world offers similar situations to the colonial animals that simply form many polyps of
the same type. Where plant examples become more problematic is with the formation of alliances
and complex symbioses, such as the fungal rhyzosphere forming in conjunction with some trees that
allow the collective organism to survive and compete in areas where species involved in the
association could not persist on their own. However, the interesting interactions occur in the soil
where they are essentially invisible to science. Consequently, we know too little about the dynamics
of such associations to analyze them in any detail.
Social organisms - the evolution of 'social homeostasis'
The cases of social organisms such as ants, bees, termites and possibly even mole-rats are more
easily analyzed. In this case the colony in the hive, anthill or termite mound establishes the level of
focus. In the eusocial hymenoptera (ants and bees) a fertilized diploid queen carrying a lifetime
supply of sperm founds a colony, and begins laying eggs. Fertilized eggs are diploid and develop
into females; unfertilized eggs develop into haploid males. Depending on how the diploid female
larvae are fed, their sexual development is suppressed and they develop into sterile workers who
help to maintain and feed the growing population of the colony, or they develop into future queens.
In most social bees there is only one kind of worker but these will carry out a range of specialized
tasks as they age, whereas in some ant species, larvae differentiate into a variety of morphologically
different kind of workers that perform specialized jobs for the colony.
Colonial honeybees reproduces in three ways (Wilson 1971). When the colony grows to a critical
size, workers begin building special enlarged cells where the larvae will be fed in ways that cause
them to differentiate into new queens. A larger number of cells are set aside in which the queen lays
haploid eggs that develop into male drones. Before the first of these new queens eclose from the
pupal stage, the original queen is expelled from the hive by workers, and will depart with a
significant fraction of the existing workers to found a new hive. The first of the new virgin queens
will attempt to kill or drive other new queens from the hive. These departing queens will also take
swarms of workers with them. Once a single virgin queen has the hive and remaining workers to
herself she will fly out, mate with a drone, and begin adding new members to the colony. Those
virgin queens that left the hive with swarms of workers also find drones to mate with and return to
their swarms. However they were formed, the swarms along with a fertile queen will send scouts far
and wide in attempt to find a suitable hollow in which to build a new hive.

Ants have a similar genetic system to bees (i.e., diploid females, haploid males, where the presence
of an existing queen inhibits the development of fertility in other females) with some variations due
to their pedestrian lifestyle after mating. Fertile females (future queens) and males eclose with
wings and there will be mass departures and mating flights of the winged males and females. Once
fertilized, the female searches for a suitable site to begin burrowing, sheds her wings and founds a
new colony. As the first generation of workers take over food gathering and maintenance of the
burrow system different worker castes may begin to differentiate.
In the hymenoptera, all progeny of the one fertilization event will carry genetically identical male
chromosomes (because the male is haploid, all sperm carry exactly the same genes) and have 50%
of the genes inherited from their mother in common. With this degree of genetic similarity there is
no strong selection for individuality that would tend to prevent the evolution of cooperative
behavior.
Termites are complex organisms that have formed an obligatory symbiotic relationship with a
variety of phytoflagellates who provide the enzymatic machinery necessary to digest wood. They
also have a different genetic system compared to bees, where both males and females are diploid,
but they have evolved similar kinds of social organization where most reproduction is carried out by
a single fertile queen (accompanied by a single male consort who will periodically fertilize her),
there may be several castes of workers (who may be of either sex). Other differences between
termites and the social hymenoptera are that fertilization occurs only after a male and female
together find an appropriate site and together begin preparing a burrow. Hymenoptera are
holometabolous, which means that the larvae are helpless. Late instar termite larvae are able to help
out in the nest.
When examined from a level of the colony, the more developed insect societies summarised above
certainly meet all of the criteria for an autopoietic system.
a. Self-identifiably bounded (demarcated from the environment by membranes, or the entity's

components are identifiably tagged): All of the colony-building insects use pheromones to tag
and identify members of their own colony, and will often fight with and attempt to kill
individuals carrying the wrong tags.
b. Individually identifiable components within the boundary (complex). All of the members of
the colony are clearly autopoietic individuals in their own rights. However, they interact with
one another to maintain the integrity of the colony against various kinds of invaders including
conspecifics from other colonies.
c. Mechanistic (i.e., a system driven by cybernetically regulated exergy fluxes or metabolic
processes). Most of the activities of the hive or society are organized and coordinated by
various forms of communication between colony members such as pheromones, tactile
exchanges, vibration or possibly even visual cues. These serve to recruit help for defense,
repair, food gathering, escape from flooding, etc.
d. System boundaries internally determined (self referential). The establishment and
maintenance of a recognizable hive odor for the purpose of member vs non-member is
certainly a form of self-reference for the colony.
e. System intrinsically produces own components (self production). Special breeding females are
responsible for producing all of the individuals forming a single colony.
f. Self-produced components are necessary and sufficient to produce the system
(autonomy). Yes. Because all of the individuals forming a colony are the progeny of a single
individual they share many genes in common as a resource of the necessary control
information for maintaining the colony dynamics.
Wilson (1971) notes:

Social insects display marked homeostasis in the regulation of their own numbers and of their nest environment. This
class of steady-state regulation has been aptly termed social homeostasis... [p. 360]
...
The idea of social homeostasis leads easily to the visualization of the entire insect colony as a kind of super-
organism.... Wheeler [1911] saw several important qualities of the ant colony that qualified it as an organism:
1. It behaves as a unit.
2. It shows some idiosyncrasies in behavior, size and structure that are peculiar to the species and other idiosyncrasies that
distinguish it from other colonies belonging to the same species.
3. It undergoes a cycle of growth and reproduction that is clearly adaptive.
4. It is differentiated into 'germ plasm' (queens and males) and 'soma' (workers).
Interestingly, in both the termites and hymenoptera, different species represent all stages from those
that make their living as solitary individuals (i.e., with no social organization), through dominance
hierarchies to fully eusocial colonies that I do not hesitate to qualify as autopoietic. In terms of total
biomass, the extraordinarily successful autopoietic insect superorganisms (ants and termites) are the
terrestrially dominant life forms on Earth.
Human economic organizations
Hall (2003; 2005; Hall et al. 2005) presented the argument that at least some human economic
organizations are third order autopoietic entities in their own rights. The human economy is an
abstraction of real energy fluxes. Individuals as components of organizations use money to purchase
the food and fuel they need in order to maintain their lives, and thus measurements and observations
of cash flow are a reasonable abstraction of these energy flows from source to sink as high value
resources are used in the production of product and dissipated in the form of labor and distribution.
Thus, complex dynamics may evolve at a level of complexity involving the economic interactions
of humans.
Large economic organizations certainly meet requirements to be considered autopoietic:
g. Self-identifiably bounded (demarcated from the environment by membranes, or the entity's

components are identifiably tagged): Members of the organization are typically identified
with badges, and sometimes even uniforms. 'Human resource systems" in the organization
track memberships, associations, etc. to identify and track members of the organization.
h. Individually identifiable components within the boundary (complex). Individual people are
certainly autopoietic entities in their own rights, but they can work together to form and
maintain the structure of a higher level organization.
i. Mechanistic (i.e., a system driven by cybernetically regulated exergy fluxes or metabolic
processes). Cash accounting, internal processes and procedures, etc. measure and regulate the
interactions of organization members to benefit the continued survival and growth of the
organization.
j. System boundaries internally determined (self referential). Rules of association, employment
agreements, oaths of allegiance to organizational rules, etc. all work to determine who
belongs to the organization.
k. System intrinsically produces own components (self production). Processes exist to recruit,
induct and train new members.
l. Self-produced components are necessary and sufficient to produce the system
(autonomy). Well-established organizations outlive the membership of any particular
individuals in the organization.
As in the social insects, human economic human economic organizations show all stages in the
emergence of an autopoietic level of complexity ranging from single entrepreneurs, through family

groups, despotically controlled groups, through to the full panoply of large organizations. Greiner
(1998) reviews some of the structural changes organizations pass through, as they become fully
autopoietic.
Evolutionary knowledge generated by organizations is tacitly embodied in the physical and

procedural structure of the organization (Nelson & Winter 1982, 2002; Dalmaris 2006; Dalmaris et
al. in press), and explicitly in organizational documentation (Hall 2003a). Some knowledge
specifically relating to the organization is held in human memories, but the bounded rationality
(Simon 1955, 1957) of organizational members means that no one person can know everything the
organization needs to know in order to maintain itself and respond adequately to meet
organizational imperatives in a changing and competitive environment (Else 2004; Nousala et al.
2005; Nousala 2006), thus knowledge required for maintenance of the organization must be
distributed beyond the limits of any individual in the organization.
It should be noted that Niclaas Luhmann (1986, 1990, 1995) has described what he calls a form of
social autopoiesis in his studies of human social systems. This deviates substantially from the
Maturana and Varela (1980) canon in that Luhmann's 'autopoiesis' no longer focuses on the physical
interactions of material entities. Basically, it is defined on the basis of an idiosyncratic and highly
paradigmatic view of informational relationships rather than energy dynamics between physically
definable entities. It is beyond the scope of this paper to attempt to marry the energy driven
approach developed here and Luhman's work.
Conclusions
I have explored the circumstances under which organized systems can emerge in a dissipative
environment forced to transport energy from a high exergy source to a lower exergy sink and have
discussed the importance to establish a proper focal level for analyzing such systems. I have shown
that under circumstances between molecular convection and the chaos of a 'short circuit' that the
environment will spontaneously evolve towards a near steady state of dynamically cyclical
organization able to efficiently dissipate exergy. Where the environmental medium offers suitable
possibilities, such systems may evolve to a point where they can be said to have a recognizable
duration through time, such that in some of these cases the steady-state dynamical structure may
begins to homeostatically self-regulate itself. In suitable environmental circumstances, homeostatic
systems may evolve into fully autopoietic systems. Their success and survival is governed by the
accumulation of structural knowledge (in Popper's W2) that may develop further through the
evolution of mechanisms to persistently codify some of the survival knowledge (W3).
The emergence of at least three orders of autopoiesis has been documented: a first order at the
cellular level of focus comprised of macromolecular units and subsystems within a chemical
environment; a second order at a level of multicellular organismic focal level comprised of
individual cells and living within an ecosystem; and at least two different kinds of third order
systems assembled from multicellular organisms as the subunits at similar focal levels. These third
order systems include 'superorganismic colonies formed by various species of social insects within
the ecosystem on one hand, and human economic organizations formed within the economy.
Not considered due to the limited focus of this work are possible cases of autopoiesis in
multispecies assemblages of bacteria (i.e., trophic mats), obligatory symbiotic associations such as
between fungi and algae to form lichen and the rhyzospheres involving higher plants, and human
social organizations such as clubs and religions that might be seen as a different form of
organization than the economic organization. I have also not considered the possible existence of

orders of autopoietic organization above the third order: e.g., ecological communities, ecosystems,
Gaia; or nation states, industrial associations, the economy, etc.
In association with my exploration of the conditions under which autopoietic organization can arise,
I have also shown that the evolution and growth of knowledge at any order of autopoiesis is an
integral part of the process by which autopoiesis emerges. The current literature on autopoiesis
attempts to deal with this issue in highly paradigmatic 'observer centric' language. I find that
Howard Pattee's biophysical epistemology and Karl Popper's evolutionary epistemology allow the
development of an epistemology of autopoietic organization that should be much more accessible to
the main stream of science.
Basically, knowledge in the autopoietic system is the capacity for self-control. This control
knowledge exists first in the historically developed dynamic structure of the autopoietic system
itself (which exists only in a tiny fraction of the phase space represented by all possible locations
and dynamic interactions of the components contained within the physical space occupied by the
system). The knowledge is expressed in the way the structure of a particular autopoietic system
provides the instantaneous dynamics for and constrains the further trajectories of the system's
component parts. This 'knowledge' is a tangible projection of a history of the survival of an
autonomously self-maintaining autopoietic state, where the solutions to the problems of life
represented by that history populate a different ontological domain from that of the instantaneous
physical reality. This 'knowledge' resulting from the constraints of the historically determined
instantaneous present state establishes an epistemic cut between what is measured and controlled
and the capacity to measure and control.
In Popper's epistemological ontology, instantaneous physical reality and its dynamic state form
world 1, whereas the solutions to the problems of life represented in the capacity to measure and
control populate world 2. Autopoietic systems may also evolve ways to codify knowledge in
compact, energetically degenerate codes as a persistent and abstract representation of control
information. In first-order cellular life nucleic acid polymers carry the encoded control information.
Using the information requires a complex system for transcription and translation into structural
knowledge, which represents a significant epistemic cut between the codified knowledge and its
enactment into structural knowledge (world 2), where the control can be applied to world 1. This
codified knowledge forms world 3.
Every autopoietic system at any order of autopoiesis must have the world 2 structural knowledge
that embodies an instantaneous state resulting from an historical trajectory that maintains system
parameters within a part of the phase-space where the entity will continue to be self-regulating. I
argue that autopoietic systems of any order may also evolve codification systems that enable
knowledge to be accumulated in world 3. In addition to the capability to store codified knowledge
in DNA, higher multicellular organisms have evolved mechanisms in world 3 for transferring and
storing survival knowledge outside of the body, e.g., trails, pheromones and, most importantly for
humans, linguistic mechanisms.
I have argued that in the early evolution of cellular life, cellular components and codified
knowledge (DNA) would have most likely been shared promiscuously, which would have impeded
the differentiation and evolution of trophic specializations. However, as cellular organization
became fully stabilized, and increasingly larger fractions of control knowledge became codified into
DNA chromosomes, different lineages could begin to evolve their own specializations and protect
themselves from the disruptive activities of irrelevant or inharmonious control information. The
downside of encoding control information into chromosomes protected within the cell is that the
opportunities for recombination and selection of already tested knowledge in new combinations
would have been greatly reduced. Had this protection been fully effective, clonal reproduction

would have greatly slowed the evolution of favorable gene combinations. The evolution of
controlled means of sexual recombination enabled the establishment of biological species, which
enabled the proliferation of the diversity of living things we see today.
Not discussed in the present work, but of great interest for further study, are similar issues relating
to the dissemination and control of linguistically expressed knowledge at the second and third order
of autopoiesis.
The ideas presented here only scratch the surface of what is potentially a very large area for further
research.
ACKNOWLEDGEMENTS
My employer, Tenix Defence, has consistently allowed me to work on this project during business
hours. From 2002 to mid 2005, additional office and library support was provided via an honorary
fellowship arranged by Dr Frada Burstein, Faculty of Information Technology, Monash University.
During 2006 my work was facilitated by a National Fellowship in the Australian Centre for
Science, Innovation and Society, Melbourne University and by Dr Liz Sonnenberg, Department of
Information Systems, Melbourne University, who kindly arranged office space in the Department.
Without making any claim that these people agree with my conclusions, many individuals have
contributed to the intellectual content of the work and helped me sharpen my expression: Hugo
Urrestarazu, Joe Firestone, Howard Pattee, Steven Else, Susu Nousala, Peter Dalmaris, Ken Long,
Richard Vines, Tony Smith and a number of seminar participants at University of Technology
Sydney, RMIT University and University of Melbourne, plus many others I have interacted with via
various Web forums and knowledge management event.
BIBLIOGRAPHY
Note: Web links were valid on ... .
Andras, P., Andras C., 2005. The origins of life – the ‘protein interaction world’ hypothesis: protein interactions were
the first form of self-reproducing life and nucleic acids evolved later as memory molecules. Medical Hypotheses
64, 678-688.
Avery, O.T., MacLeod, C.M., McCarty, M. 1944. Studies on the chemical nature of the substance inducing
transformation of pneumonococcal types: induction of transformation by a desoxyribonucleic acid fraction
isolated from pneumococcus type III. Journal of Experimental Medicine 79, 137-158.
Bentolila, S. 2005. “Live memory” of the cell, the other hereditary memory of living systems. BioSystems 80, 251–261.
Bitbol, M., Luisi, P.L. 2004. Autopoiesis with or without cognition: defining life at its edge. Journal of the Royal
Society Interface 1, 99-107.
Bourgine P. and Stewart J., 2004. Autopoiesis and cognition. Artificial Life 10, 327–345.
Boyd, J.R. 1976–1996. Unpublished briefings under the name "A Discourse on winning and losing": Introduction
(1996), Patterns of conflict (1986), Organic design for command and control (1987), Strategic game of ? and ?
(1987), Destruction and creation (1976), and The essence of winning and Losing (1996) available via Defence
and the National Interest - http://www.d-n-i.net/second_level/boyd_military.htm
Cameron, W. 2001. Autopoiesis, agency and accident: criteria for the attribution of life. Systems Research and
Behavioral Science 18:447-459.

Campbell, D.T. 1960. Blind variation and selective retention in creative thought as in other knowledge processes.
Psychological Review 67, 380-400.
Campbell, D. T. 1990. Levels of Organization, Downward Causation, and the Selection-Theory Approach to
Evolutionary Epistemology. In: Greenberg, G. and Tobach, E. (Eds.), Theories of the Evolution of Knowing, T.
C. Schneirla Conference Series, Vol. 4, Hillsdale, NJ: Erlbaum, 1−17.
Campbell, D. T. 1990a. Epistemological Roles for Selection Theory. In: Rescher, N. (Ed.), Evolution, Cognition,
Realism, University Press of America, Lanham, MD, 1−19.
Cavalier-Smith, T. 2001. Obcells as proto-organisms: membrane heredity, lithophosphorylation, and the origins of the
genetic code, the first cells, and photosynthesis. Journal of Molecular Evolution 53, 555-595.
Chaisson, E.J. 2001. Cosmic Evolution: The Rise of Complexity in Nature. Harvard University Press, Cambridge MA.
Ciccarelli, F.D., Doerks, T., von Mering, C., Creevey, J., Snel, B., Bork, P. 2006. Toward automatic reconstruction of a
highly resolved tree of life. Science 311, 1283-1287..
Corning, P.A. 2001. "Control information": The missing element in Norbert Wiener's cybernetic paradigm? Kybernetes
30, 1272-1288. http://www.complexsystems.org/publications/pdf/control_info.pdf.
Corning, P.A. 2002. Thermoeconomics: Beyond the Second Law. Journal of Bioeconomics 4(1), 57-88.
Crick, F.H. 1968. The origin of the genetic code. Journal of Molecular Biology 38, 367-379.
Dalmaris, P. 2006. A framework for the improvement of knowledge-intense business processes. PhD Thesis, Faculty of
Information Technology, University of Technology, Sydney.
http://www.futureshock.com.au/docs/PhDDalmarisPub.pdf.
Dalmaris, P., Tsui, E., Hall, B., Smith, B. (In Press). A framework for the improvement of knowledge-intensive
business processes. Business Process Management Journal. http://www.futureshock.com.au/docs/KBPI-
BPMJ.pdf.
Davies, P. 2004. Emergent Biological Principles and the Computational Properties of the Universe Complexity 10(2), 1.
http://aca.mq.edu.au/PaulDavies/publications/papers/complexity_paper.pdf.
Deamer, D. W., and Fleischaker, G. R. 1994. Origins of life: the central concepts. Jones and Bartlett, Boston.
Del Guidice, E., Preparata, G. 1995. Coherent dynamics in water as a possible explanation of biological membranes
formation. Journal of Biological Physics 20, 105-116.
Else, S.E., 2004. Organization theory and the transformation of large, complex organizations: Donald H. Rumsfeld and
the U.S. Department of Defense, 2001-04. PhD Thesis. University of Denver Graduate School of International
Studies. http://cppe.org/SElse_Dissertation.pdf.
Embley, T.M., Martin, W. 2006. Eukaryotic evolution, changes and challenges. Nature 440, 623-630.
Emmeche, C. 1997. Aspects of Complexity in Life and Science. Philosophica vol. 59(1), 41-68 -
http://www.nbi.dk/~emmeche/cePubl/97g.complisci.html
Emmeche C. 1997a. Defining life, explaining emergence. http://www.nbi.dk/~emmeche/cePubl/97e.defLife.v3f.html
Emmeche, C. 1998, Defining Life as a Semiotic Phenomenon, Cybernetics and Human Knowing 5, 3–17.
http://www.uboeschenstein.ch/sal/awtexte/emmeche_life.html.
Emmeche, C. 2000. Closure, Function, Emergence, Semiosis and Life: The Same Idea? Reflections on the Concrete and
the Abstract in Theoretical Biology. In: Chandler, J. L. R. Chandler Van de Vijver, G. (Eds.), Closure: Emergent
Organizations and Their Dynamics. Annals of the New York Academy of Sciences 901, pp. 187-197.
http://www.nbi.dk/~emmeche/cePubl/2000a.Closure.html.

Emmeche, C. 2002. The Chicken and the Orphean Egg: On the Function of Meaning and the Meaning of Function:
SEED 2(1), 85-97. http://www.library.utoronto.ca/see/SEED/Vol2-1/Emmeche/Emmeche.pdf.
Emmeche, C. 2004. A-life, Organism and Body: the semiotics of emergent levels. In: Bedeau, M., Husbands, P.,
Hutton, T., Kumar, S., Suzuki H. (Eds.): Workshop and Tutorial Proceedings. Ninth International Conference on
the Simulation and Synthesis of Living Systems (Alife IX), Boston Massachusetts, September 12th, 2004, pp.
117-124. http://www.nbi.dk/~emmeche/cePubl/2004e.alife9_01e.pdf.
Emmeche, C. & Hoffmeyer, J. 1991. From Language to nature - The semiotic metaphor in biology. Semiotica 84, 1-24.
http://connect.nbi.dk/~emmeche/cePubl/91a.frolan.html.
Emmeche, C., Koppe, S., Stjernfelt, F. 1997. Explaining emergence - towards an ontology of levels. Journal for General
Philosophy of Science 28, 83-119. http://www.nbi.dk/~emmeche/coPubl/97e.EKS/emerg.html.
Emmeche, C. Koppe, S., Stjernfelt, F. 2000. Levels, Emergence, and Three Versions of Downward Causation. In:
Andersen, P. B., Emmeche, C., Finnemann, N. O., Christiansen, P.V. (Eds). Downward Causation. Minds,
Bodies and Matter. Århus: Aarhus University Press, pp. 13-34.
http://www.nbi.dk/~emmeche/coPubl/2000d.le3DC.v4b.html.
Giampietro, M., Mayumi, K., Pastore, G. 1999. Energy analyses as a tool for sustainability: lessons from complex
system theory. Annals of the New York Academy of Sciences 879, 344-367.
Fox S.W. 1980. Metabolic microspheres: origins and evolution. Naturwissenschaften 67(8), 378-83.
Fox, S.W. 1991. Synthesis of life in the lab? Defining a protoliving system. Quarterly Review of Biology, 66, 181-185.
Fox, S.W., Bahn, P.R., Dose, K., Arada, K., Hsu, L., Isima, Y., Jungck, J., Kendrick, K., Krampitz, G., Lacey, J.C., Jr.,
Matsuno, K., Mesius, P., Middlebrook, M., Nakashima, T., Pappelis, A., Pol, A., Rohfing, D.L., Vegotsky, A.,
Waehneldt, T.V., Wax, H., Yu, B. 1994. Experimental retracement of the origins of a protocell: it was also a
protoneuron. J. Biological Physics, 20, 17-36.
Gould, S.J. 2002. The Structure of Evolutionary Theory. Belknap Press of Harvard University Press, Cambridge, MA,
1433 pp.
Greiner, L.E. 1998. Evolution and revolution as organizations grow. Harvard Business Review, May June 1998, 55-67.
Hall, W.P. [1966]. Is the Plastid an Endosymbiont. Unpublished MS. 26 pp. http://www.orgs-evolution-
knowledge.net/Index/EvolBiolPapers/Endosymbiosis/Abstract.htm.
Hall, W.P. 1983. Modes of speciation and evolution in the sceloporine iguanid lizards. I. Epistemology of the
comparative approach and introduction to the problem. In: Rhodin, A.G.J., Miyata, K. (Eds). Advances in
Herpetology and Evolutionary Biology - Essays in Honor of Ernest E Williams. Cambridge Mass: Museum of
Comparative Zoology pp.643-679. http://www.orgs-evolution-
knowledge.net/Index/EvolBiolPapers/Content/Hall1983/Hall1983.htm
Hall, W.P. 2003 Organisational autopoiesis and knowledge management. ISD '03 Twelfth International Conference on
Information Systems Development - Methods & Tools, Theory & Practice, Melbourne, Australia, 25 - 27
August, 2003. http://www.orgs-evolution-
knowledge.net/Index/DocumentKMOrgTheoryPapers/Hall2003OrganizationalAutopoiesisKnowledgeManagem
ent.pdf.
Hall, W.P. 2003a. Managing Maintenance Knowledge in the Context of Large Engineering Projects - Theory and Case
Study. Journal of Information and Knowledge Management 2(3), 1-17. http://www.orgs-evolution-
knowledge.net/Index/DocumentKMOrgTheoryPapers/Hall2003ManagingMaintKnowledgeinLargeEngiProjects.
pdf.
Hall, W.P. 2005. Biological nature of knowledge in the learning organization.The Learning Organization 12(2), 169-
188. http://www.orgs-evolution-
knowledge.net/Index/DocumentKMOrgTheoryPapers/Hall2005BiolOrgKnowledgeLearningOrg.pdf.

Hall, W.P., Dalmaris, P., Nousala, S. 2005. A biological theory of knowledge and applications to real world
organizations. Proceedings, KMAP05 Knowledge Management in Asia Pacific Wellington, N.Z. 28-29
November 2005. http://www.orgs-evolution-
knowledge.net/Index/DocumentKMOrgTheoryPapers/HallEtAl2005BiolTheorKnowledgeApplicationsRealWorl
d.pdf.
Hoffmeyer, J. 1987. The Constraints of Nature on Free Will. In: Free Will and Determinism. Mortensen, V., Sorenson,
R.C. (Eds.). Aarhus University Press, Aarhus.
Hoffmeyer, J. 1997. Biosemiotics: Towards a new synthesis in biology. European Journal for Semiotic Studies 9, 355-
376. http://www.gypsymoth.ento.vt.edu/~sharov/biosem/hoffmeyr.html.
Hoffmeyer, J. 2001. Life and Reference. Biosystems 60, 123-130.

http://informatics.indiana.edu/rocha/pattee/hoffmeyer.html.
Hoffmeyer, J. 2001a. Origin of Species by Natural Translation. Athanor anno XII, nuova serie n. 4, pp. 240-255. -
http://www.molbio.ku.dk/MolBioPages/abk/PersonalPages/Jesper/Translation.html.
Hoffmeyer, J. 2002. The Central Dogma: A Joke that Became Real. Semiotica 138(1/4), 1-13, 2002.
http://www.molbio.ku.dk/MolBioPages/abk/PersonalPages/Jesper/CentralDogma.html.
Hoffmeyer, J. 2002a. Code Duality Revisited. S.E.E.D. Journal (Semiotics, Evolution, Energy, and Development)
2002(1), 98-117. http://www.library.utoronto.ca/see/SEED/Vol2-1/Hoffmeyer/Hoffmeyer.pdf.
Hoffmeyer, J. & Emmeche, C. 1991. Code-Duality and the Semiotics of Nature. In: Anderson, M., Merrell, F. (Eds.),
On Semiotic Modeling. Mouton de Gruyter, Berlin, pp. 117-166.
http://www.nbi.dk/~emmeche/coPubl/91.JHCE/codedual.html.
Hughes, R.A., Roberston, M.P., Ellington, A.D., Levy M. 2004. The importance of prebiotic chemistry in the RNA
world. Current Opinion in Chemical Biology, 8, 629–633.
Jorgensen, S.E. 1999. Tentative fourth law of thermodynamics, applied to description of ecosystem development.
Annals of the New York Academy of Sciences 879, 320-343.
Jutoran, S.B. 1994. El proceso de las ideas sistemico-ciberneticas. 'Sistemas familiares' Buenos Aires, Argentina 10(1).
http://www.click.vi.it/sistemieculture/Jutoran.html
Jutoran, S.B. 2005. From observed systems to observing systems. 30 pp.

http://shss.nova.edu/SusyJutoranCybernetic.pdf
Kauffman, S.A. 1993. The Origins of Order: Self-Organization and Selection in Evolution. Oxford Univ. Press, New
York.
Kay, J.J. 1984. Self-Organization in Living systems, Ph.D. Thesis, Systems Design Engineering, University of
Waterloo, Waterloo, Ontario, Canada, 458p.
http://web.archive.org/web/20030622210225/www.fes.uwaterloo.ca/u/jjkay/pubs/thesis/toc.html;
http://web.archive.org/web/20030622210225/http://www.fes.uwaterloo.ca/u/jjkay/pubs/thesis/2.html; Chapter 3;
http://web.archive.org/web/20040401070346/http://www.fes.uwaterloo.ca/u/jjkay/pubs/thesis/6.pdf; Appendix 1.
Kay, J.J. 2000. Ecosystems as self-organizing holarchic open systems: narratives and the second law of
thermodynamics. In: Jorgensen, S.E., Muller, F. (Eds), Handbook of Ecosystem Theories and Management,
CRC Press - Lewis Publishers pp 135-160.
http://web.archive.org/web/20030328023218/http://www.fes.uwaterloo.ca/u/jjkay/pubs/CRC/diss.pdf.
Kay, J.J. 2000a. Complex systems theory applied to ecosystem management. Keynote address at Modelling complex
systems conference, Montreal, 1 August, 2000.
http://web.archive.org/web/20030719022618/www.fes.uwaterloo.ca/u/jjkay/pubs/ecomod/mtl.pdf.
Kay, J, 2001. Ecosystems, Science and Sustainability, In: Ulgiati, S., Brown, M.T., Giampietro, M., Herendeen, R.,
Mayumi, K., (Eds) Proceedings of the international workshop: Advances in Energy Studies: exploring supplies,

constraints and strategies, Porto Venere, Italy, 23-27 May, 2000 pp. 319-328.
http://web.archive.org/web/20040215075314/www.fes.uwaterloo.ca/u/jjkay/pubs/pv/.
Kay, R. 2001. Are organizations autopoietic? A call for new debate. Systems Research and Behavioral Science 18(6),
461-477.
Kazakov, S.A., Balatskya, S.V., Johnston, B.H. 2006. Ligation of the hairpin ribozyme in cis induced by freezing and
dehydration. RNA 12, 446-456.
Koestler, A. 1978. Janus: A Summing Up. Random House.
Kolasa, J., Pickett, S.T.A. 1989. Ecological systems and the concept of biological organization. Proceedings of the
National Academy of Sciences USA. 86, 8837-8841.
Lane, D. 2006. Hierarchy, complexity, society. In: Hierarchy in Natural And Social Sciences, Pumain, D. (Ed). Springer
Verlag, pp. 81-40. http://www.complexityscience.org/NoE/lanehsc.pdf.
Lederberg, J, Tatum, E.L. 1946. Gene recombination in E.coli. Nature 158, 558.
Lemke J.L. 2000. Opening up closure: semiotics across scales. Annals of the New York Academy of Sciences 901, 100-
111. http://www-personal.umich.edu/~jaylemke/papers/gent.htm.
Lemke, J.L. 2000a. Multiple timescales and semiotics in complex ecosocial systems. Third International Conference on
Complex Systems (Nashua, NH; 2000). http://www-personal.umich.edu/~jaylemke/papers/NECSI-2000.htm;
http://www-personal.umich.edu/~jaylemke/papers/NECSI/necsi-1.htm; http://www-
personal.umich.edu/~jaylemke/papers/NECSI/necsi-2.htm; http://www-
personal.umich.edu/~jaylemke/papers/NECSI/references.htm.
Lemke, J.L. 2000b. Material sign processes and ecosocial organization. In: Andersen, P.B., Emmeche, C., Finnemann-
Nielsen, N.O., (Eds.), Downward Causation: Self-organization in Biology, Psychology, and Society. Aarhus
University Press, Aarhus. pp. 181-213. http://www-personal.umich.edu/~jaylemke/aarhus.htm
Luhmann, N. 1986. The autopoiesis of social systems. In: Geyer, F., van der Zouwen, J. (Eds.), Sociocybernetic
Paradoxes. Sage, London, pp. 172-192.
Luhmann, N. 1990. Essays of Self-Reference. Columbia Univ. Press, New York.
Luhmann, N. 1995. Social Systems. [Tr. J. Bednarz and D. Baecker]. Stanford University Press, Stanford [first
published as Soziale Systeme: Grundriss einer allgemeinen Theorie, Suhrkamp Verlag, Frankfurt am Main,
1984].
Luisi P.L. 2003. Autopoiesis: a review and a reappraisal. Naturwissenschaften 90(2), 49-59.
Lyon, P. 2004. Autopoiesis and knowing: reflections on Maturana's biogenic explanation of cognition. Cybernetics and
Human Knowing 11(4), 21-46.
Margulis, L. 1968. Evolutionary criteria in thallophytes: a radical alternative. Science 161, 1020-1022.
Margulis, L. 1970. Origin of Eukaryotic Cells. New Haven: Yale University Press.
Martin, J. (1996). Cybercorp: The New Business Revolution. Amacom.
Maturana, H.R. 1970. Biology of Cognition. Biological Computer Laboratory Research Report, BCL 9.0. University of
Illinois, Urbana. [as reprinted in Autopoiesis and Cognition: The realization of the Living. Reidel Publishing
Co., Dordrecht, pp 5-58]. http://www.enolagaia.com/M70-80BoC.html#I.
Maturana, H.R. 1988. Ontology of Observing: the biological foundations of self consciousness and the physical domain
of existence. Conference Workbook: Texts in Cybernetics, American Society for Cybernetics Conference,
Felton, CA. 18-23 October, 1988.

-Maturana, H. 2002. Autopoiesis, structural coupling and cognition: a history of these and other notions in the biology
of cognition. Cybernetics & Human Knowing 9(3-4), 5-34.
http://web.archive.org/web/20021218143537/http://www.inteco.cl/biology/ontology/.
Maturana H.R. and Varela F.J. 1980. Autopoiesis: the organisation of the living. In Autopoiesis and Cognition: The
Realization of the Living, Maturana H, Varela F (Eds). Reidel, Dortdrecht, pp 73-137.
Maturana H.R. and Varela F.J. 1987. The Tree of Knowledge. Shambhala, Boston.
Maxwell, N. 2002. Karl Raimund Popper. In: British Philosophers, 1800-2000. Dematteis, P., Fosl, P., McHenry, L.
(Eds.), Bruccoli Clark Layman, Columbia, pp. 176-194.
McKelvey B. 1999. Toward a Campbellian realist organization science. In: Baum J.A.C., McKelvey B. (Eds.),
Variations in Organization Science: In Honor of Donald T. Campbell. Thousand Oaks: Sage, pp. 383-411.
McKelvey B. 2004. Toward a 0th law of thermodynamics: order-creation complexity dynamics from physics and
biology to boieconomics. Journal of Bioeconomics 6, 65-96.
McKelvey B. & Baum J.A.C. 1999. Campbell's evolving influence on organization science. In: Baum J.A.C. &
McKelvey B (Eds.), Variations in Organization Science: In Honor of Donald T. Campbell. Sage, Thousand
Oaks, pp. 383-411.
Mingers, J. 2003. Can Social Systems Be Autopoietic? Bhaskar and Giddens’ Social Theories. Working Paper 44.
Canterbury Business School, University of Kent. http://www.kent.ac.uk/CBS/research-information/working-
papers/Mingers-No-44.pdf.
Morowitz, H.J. 1968. Energy Flow in Biology: Biological Organization as a Problem in Thermal Physics. New York:
Academic Press, 179 pp.
Muller, U.F. 2006. Re-creating an RNA world. Cellular and Molecular Life Sciences 63(11), 1278-1293.
Nelson, R.R., Winter, S.G. 1982. An Evolutionary Theory of Economic Change. Harvard University Press, Cambridge,
MA.
Nelson, R.R., Winter, S.G. 2002. Evolutionary theorizing in economics. Journal of Economic Perspectives 16(2), 23–
46. http://gatton.uky.edu/faculty/castaneda/GTclass/Read/Nelson and Winter 2002.pdf.
Niiniluoto, I. 1999. Critical Scientific Realism. New York: Oxford University Press, 341 pp.
http://www.oxfordscholarship.com/oso/public/content/philosophy/0199251614/toc.html.
Nousala, S. 2006. PhD Thesis, Faculty of Aerospace, Mechanical and Manufacturing Engineering. RMIT University
Nousala, S., Miles, A., Kilpatrick, B., Hall, W.P. 2005. Building knowledge sharing communities using team expertise
access maps (TEAM). Proceedings, KMAP05 Knowledge Management in Asia Pacific Wellington, N.Z. 28-29
November 2005. http://www.orgs-evolution-
knowledge.net/Index/DocumentKMOrgTheoryPapers/NousalaEtAl2005KnowledgeSharingCommunitesExpertis
eMapping.pdf.
Patron, N.J., Waller, R.F., Keeling, P.J. 2006. A tertiary plastid uses genes from two endosymbionts. Journal of
Molecular Biology 357(5), 1373-1382.
Pattee, H.H. 1961. The origin of macromolecular sequences. Biophysical Journal 1, 683-710.
Pattee, H. H., 1972, Laws, constraints, symbols, and languages. In: Towards a Theoretical Biology 4, Waddington, C.
H., (Ed.), Edinburgh Univ. Press, pp. 248-258.
Pattee, H.H. 1977. Dynamic and Linguistic Modes of Complex Systems, International. Journal of General Systems 3,
259-266.
Pattee, H.H. 1995. Evolving self-reference: matter, symbols, and semantic closure. Communication and Cognition -
Artificial Intelligence, 12(1-2), 9-27. http://www.ws.binghamton.edu/pattee/sem_clos.html.

Pattee, H. H. 1995a. Artificial life needs a real epistemology. In: Advances in Artificial Life. Moran, F., Moreno, A.,
Morelo, J. J., Chacon, P., (Eds.), Springer-Verlag, Berlin, pp. 23-38.
http://web.archive.org/web/20030730002634/http://www.ws.binghamton.edu/pattee/aepistem.html.
Pattee, H.H. 1996. The Problem of Observables in Models of Biological Organizations. In: Evolution, Order, and
Complexity, Khalil, E.L., Boulding, K.E. (Eds.), Routledge, London.
http://www.ws.binghamton.edu/pattee/boulding.html
Pattee, H.H. 1997. The Physics of Symbols and The Evolution of Semiotic Controls. In: Workshop on Control
Mechanisms for Complex Systems: Issues of Measurement and Semiotic Analysis, Las Cruces, New Mexico,
Dec. 8-12,1996. To be published as Santa Fe Institute Studies in the Sciences of Complexity, Proceedings
Volume, Addison-Wesley, Redwood City, CA, 1997.
http://web.archive.org/web/20030730005014/http://www.ws.binghamton.edu/pattee/semiotic.html.
Pattee, H.H. 2000. Causation, control, and the evolution of complexity. [1997 draft] In: Downward Causation,
Anderson, P. B., Christiansen, P. V., Emmeche, C., Finnemann, N. O. (Eds). Aarhus University Press, Århus, p.
63-77. http://www.ws.binghamton.edu/pattee/downcaus.html.
Pattee, H.H. 2001. Irreducible and complementary semiotic forms. Semiotica 134 (1-4), 341-358.
Pattee, H.H. 2001a. The physics of symbols: bridging the epistemic cut. Biosystems 60(1-3), 5-21.
Polanyi, M. 1958, Personal Knowledge: Towards a Post-Critical Philosophy, [Corrected Ed., 1962]. University of
Chicago Press, Chicago.
Polanyi, M. 1966, The Tacit Dimension, Routledge & Kegan Paul.
Polanyi, M. 1968. Life's irreducible structure. Science 160(3834), 1308-1312.
Popper, K.R. 1934, 1959. The Logic of Scientific Discovery, Sixth Impression (Revised) [First English Ed.,
Hutchinson, 1959. First published as Logik Der Forschung in Vienna: Springer, 1934]. Hutchinson & Co., Ltd.,
London, 480 pp.
Popper, K.R. 1963. Conjectures and Refutations: The Growth of Scientific Knowledge, 4th Ed. [1972] (Revised).
London, Routledge and Kegan Paul, 431 pp.
Popper, K.R. 1966. A Realist View of Logic, Physics, and History. Chapter 8, Objective Knowledge. http://evans-
experientialism.freewebspace.com/popper.htm.
Popper, K.R. 1968. Epistemology without a knowing subject. In: Proceedings of the Third International Congress for
Logic, Methodology and Philosophy of Science, 25 Aug. to 2 Sept 1967, van Rootselaar B. & Staal, J.F. (Eds.),
Amsterdam. pp. 333-373.
Popper, K.R. 1972. Objective Knowledge: An Evolutionary Approach. London, Oxford Univ. Press, 380 pp.
Popper, K.R. 1974. Autobiography. In: Schilpp, P.A. (Ed.) The Philosophy of Karl Popper. The Library of Living
Philosophers, Vol 14(1). pp. 1-181.
Popper, K.R. 1974a. Replies to my critics. In: Schilpp, P.A. (Ed.) The Philosophy of Karl Popper. The Library of
Living Philosophers, Vol 14(2). pp. 961-1197.
Popper, K.R. 1978. Three Worlds. The Tanner Lecture on Human Values. Delivered at The University of Michigan
April 7, 1978. http://www.tannerlectures.utah.edu/lectures/popper80.pdf.
Popper, K.R. 1982. Postscript to the Logic of Scientific Discovery [in three volumes]. Bartley, W.W. (Ed.), Hutchinson.
Popper, K.R. 1994. Knowledge and the Body-Mind Problem: In defence of interaction. Notturno, M.A. (Ed.),
Routledge, London. 158 pp.
Popper, K.R. 1999. All Life Is Problem Solving. Routledge. 192 pp.

Popper, K.R. and Eccles, J.C. 1977. The Self and its Brain: An Argument for Interactionism. Springer Verlag, Berlin.
Prigogine, I. 1955. Introduction to the Thermodynamics of Irreversible Processes. C.C. Thomas, Springfield, Illinois.
Prigogine, I. 1981. From Being to Becoming: Time and Complexity in the Physical Sciences, Freeman, New York 272
pp.
Prigogine, I. 1999. Laws of Nature, Probability and Time Symmetry Breaking. Physica A 263, 528-539.
Prigogine, I. 2000. The Norbert Wiener Memorial Gold Medal address: Norbert Wiener and the idea of contingence.
Kybernetes 29(7/8), 825-834.
Prigogine, I. and Antoniou, I. 2000. Science, Evolution and Complexity. In:"Genetics in Europe - Open days 2000
(GEOD 2000)", Sommet européen, Bruxelles, 16 novembre 2000, p. 21-36.
http://www.tyrrhenum..unisi.it/prigogine.doc.
Riegler, A., 2001 Towards a radical constructivist understanding of science. Foundations of Science 6, 1-30.
Rocha, L.M. 1997. Evidence Sets and Contextual Genetic Algorithms: Exploring Uncertainty, Context, and
Embodiment in Cognitive and Biological Systems. PhD Thesis State University of New York at Binghamton -
http://informatics.indiana.edu/rocha/dissert.html.
Rocha, L.M. 1998. Selected Self-Organization And the Semiotics of Evolutionary Systems. In: Evolutionary Systems:
Biological and Epistemological Perspectives on Selection and Self-Organization. Salthe, S., Van de Vijver, G.,
Delpos, M. (Eds.), Kluwer Academic Publishers, pp. 341-358. http://informatics.indiana.edu/rocha/ps/ises.pdf.
Rocha, L.M. 2001. Adaptive recommendation and open-ended semiosis. Kybernetes 30 (5-6), 821-851.
Rocha, L. M. & Bollen, J. 2001. Biologically Motivated Distributed Designs for Adaptive Knowledge Management. In:
Design Principles for the Immune System and other Distributed Autonomous Systems. Segel, L. and Cohen, I.
(Eds.), Santa Fe Institute Series in the Sciences of Complexity. Oxford University Press, pp. 305-334.
http://informatics.indiana.edu/rocha/ps/SFI99.pdf.
Rocha, L.M., Hordijk, W. 2005. Material Representations: From the Genetic Code to the Evolution of Cellular
Automata. Artificial Life 11, 189–214. http://informatics.indiana.edu/rocha/ps/caalife04.pdf.
Rizzotti, M. 1994. Lipid vesicles, are they plausible primordial aggregates. Journal of Biological Physics 20, 155-162.
Sagan, L. 1967. On the origin of mitosing cells, Journal of Theoretical Biology, 14 225–274.
Salthe, S. 1985. Evolving Hierarchical Systems: Their Structure And Representation. Columbia University Press, New
York. 343 pp.
Salthe, S. 1993. Development and Evolution: Complexity and Change in Biology. MIT Press, Cambridge, Mass. 357
pp.
Salthe, S. 2004. The spontaneous origin of new levels in a scalar hierarchy. Entropy 6, 327-343.
http://www.mdpi.org/entropy/papers/e6030327.pdf.
Schneider, E.D., Kay, J.J. 1994. Complexity and thermodynamics: towards a new ecology. Futures 24(6), 626-647.
http://web.archive.org/web/20030224033748/www.fes.uwaterloo.ca/u/jjkay/pubs/futures/tex.html.
Schneider, E.D, Kay, J.J., 1994a. Life as a Manifestation of the Second Law of Thermodynamics. Mathematical and
Computer Modelling 19(6-8), 25-48.
http://web.archive.org/web/20040215092129/http://www.fes.uwaterloo.ca/u/jjkay/pubs/Life_as/text.html.
Schneider, E.D, Kay, J.J. 1995. Order from Disorder: The Thermodynamics of Complexity in Biology. In: Murphy,
M.P., O'Neill, L.A.J. (Eds). What is Life: The Next Fifty Years. Reflections on the Future of Biology,
Cambridge University Press, pp. 161-172.
http://web.archive.org/web/20040215082932/www.fes.uwaterloo.ca/u/jjkay/pubs/sch/sch.html

Schrodinger E. 1944. What is Life? The Physical Aspect of the Living Cell. Cambridge University Press, Cambridge.
Simon, H.A. 1955. A behavioral model of rational choice. Quarterly Journal of Economics, 69, 99-118.
Simon, H.A. 1957. Models of Man. Wiley, New York.
Simon, H.A. 1962. The architecture of complex systems. Proceedings of the American Philosophical Society 106, 467-
482, [reprinted in Simon, H.A. 1981. The Sciences of the Artificial (2nd ed), MIT Press, Cambridge, MA, pp.
192-229].
Smith, A.E., Bellware, F.T., Silver, J.J. 1967. Formation of nucleic acid coacervates by dehydration and rehydration.
Nature 214, 1938-1940.
Thomas R., Kaufman M., 2001. Emergence de comportements complexes à partir de circuits simples, In: Prigogine, I.
(Ed.), L’homme devant l’incertain, Ed. Odile Jacob, Paris, pp 103-118.
Thomas, R., Kaufman, M. 2003. Emergence of complex behaviour from simple circuit structures. Comptes Rendus
Biologies 326, 205–214.
Tomm, K. 1989. The view of cognition of H. Maturana. An occasional paper and communication given at the
University of Alberta (Edmonton, Canada). January 20th, 1989
Ulanowicz R.E. 2000. Ontic closure and the hierarchy of scale. Annals of the New York Academy of Sciences 901,
266-271
Ulanowicz, R.E. 2002. Toward quantifying semiotic agencies: Habits Arising. Journal of Semiotics, Evolution, Energy
and Development. 2(1), 38-55.
Urrestarazu, H. 2004. On Boundaries of Autopoietic Systems. Journal of Autopoietic Theory. 19 May 2004.
http://autopoietic.net/boundaries.pdf.
van Duijn, M., Keijzer, F., Franken, D. 2005. Principles of minimal cognition. In: Active Agents and their
Environments as Dynamical Systems Workshop, VIIIth European Conference on Artificial Life, 5-9 September
2005, University of Kent, UK. http://www.ecal2005.org/workshopsCD/activate.d/dui.pdf.
Varela, F., Goguen, J. 1978. The arithmetic of closure. Journal of Cybernetics 8, 291-324.
Varela F, Maturana H, Uribe R. 1974. Autopoiesis: the organization of living systems, its characterisation and a model.
Biosystems 5, 187-196.
von Glaserfeld, E., 1984. An introduction to radical constructivism. In: Watzlawick P. (Ed.), The Invented Reality.
Norton, New York. [Originally published in Watzlawick, P (Ed.), Die Erfundene Wirklichkeit. Piper; Munich,
1981]. http://srri.nsm.umass.edu/vonGlasersfeld/ onlinePapers/html/082.html.
von Glaserfeld, E., 1993. An exposition on constructivism: Why some like it radical. In: Kenny, V. (Ed.), Ecology of
the Mind. http://www.oikos.org/constructivism.htm.
von Glaserfeld, E., 1997. Distinguishing the Observer: An Attempt at Interpreting Maturana. In: Kenny J.F. (Ed.)
Towards an Ecology of Mind. [Originally published as: Die Unterscheidung des Beobachters: Versuch einer
Auslegung. In: Riegas, V., Vetter, C. (Eds.) Zur Biologie der Kognition. Suhrkamp, Frankfurt, 1990, pp. 281-
295]. http://www.oikos.org/vonobserv.htm. .
von Glaserfeld, E., 2001. The radical constructivist view of science. Foundations of Science 6, 31-43.
von Neumann, J. 1955. The Mathematical Foundations of Quantum Mechanics, Princeton Univ. Press.
Webster, J.R. 1979. Hierarchical Organization of Ecosystems. In: Halfon, E.; Theoretical Systems Ecology; Academic
Press. pp.119-128.

Whitaker, R. 2001. Encyclopaedia Autopoietica: An Annotated Lexical Compendium on Autopoiesis and Enaction.
http://www.enolagaia.com/EA.html.
Woese, C. 1967. The evolution of the genetic code. The Genetic Code. Harper & Row, New York, pp. 179-195.
Wilson, E.O. 1971. The Insect Societies. Harvard University Press, Cambridge Mass.
Wilson, E.O. 1975. Sociobiology: The New Synthesis. Cambridge Mass: Harvard University Press.
Zinder, N.D., Lederberg, J. 1952. Genetic exchange in Samonella. Journal of Bacteriology. 64(5), 679-699

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HALL KNOWLEDGE AND DIVERSITY IN COMPLEX SYSTEMS 30/09/2010

Emergence and Growth of Knowledge and Diversity in

Evolutionary Biology of Species and Organizations

Australian Centre for Science, Innovation and Society

University of Technology, Sydney, NSW, Australia

DRAFT © 2006 William P. Hall Page i

DRAFT © 2006 William P. Hall Page i

Emergence and Growth of Knowledge and Diversity in

DRAFT © 2006 William P. Hall Page 1

The Physical Framework

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Properties of dissipative systems

Table 1 (from Kay 2000) summarizes the properties of dissipative systems:

Table 1: Properties of Dissipative Systems (after Kay 2000)

• Open – exchange material and energy with environment.

• Exergy is irreversibly degraded in forming and maintaining organized gradients.

DRAFT © 2006 William P. Hall Page 3

Complex Systems Terminology

Complex systems, by definition, are comprised of dynamically interacting components, where

− Component: a subunit/subsystem carrying out a particular dynamical process within

− Function: The function of a component in a dynamic system is defined by the mass-

− Structure: The structure of a dynamic system is determined by the functions of the

− Redundancy of function: In some cases, components involved in connections can be

Hierarchies of Complex Systems

DRAFT © 2006 William P. Hall Page 4

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Emergence of new levels of complexity in a hierarchically complex dynamic environment.

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a. boundary conditions and,

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1) Self-identifiably bounded (demarcated from the environment by membranes, or the entity's

In a physical sense, an autopoietic system (i.e., a “living” entity) is an autonomously self-regulating

DRAFT © 2006 William P. Hall Page 9

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Evaluating explanations of the origin of autopoiesis

Maturana and Varela’s definition of autopoiesis hinges on the concept of an autopoietically

DRAFT © 2006 William P. Hall Page 11

Physics and semiotics

DRAFT © 2006 William P. Hall Page 12

Semantic closure provides a connection between the semantic/cognitive processes of recognition,

DRAFT © 2006 William P. Hall Page 13

Karl Popper's Epistemology

DRAFT © 2006 William P. Hall Page 14

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Ontological domains where knowledge can be found

To facilitate discussion of the emergence and evolutionary growth of knowledge, in Epistemology

Figure 4. Karl Popper's three worlds ontology (after Hall 2003).

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Forms of evolutionary knowledge

Origins of embodied knowledge in W2

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Figure 5. Stages in the evolution of autopoietic knowledge.

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Codification to preserve knowledge in W3

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Two worlds of organismic knowledge or "code duality"

Hoffmeyer 2001a states:

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