EPISODE 4 - Organizations Develop Minds of their Own

Non-Equilibrium Thermodynamics and the Emergence of Complex Autopoietic Systems

In the Beginning...

when God created the heavens and the earth, the earth was a formless void and darkness covered the face of the deep, while a wind from God swept over the face of the waters [cosmos]. Then God said, "Let there be light"; and there was light. And God saw that the light was good; and God separated the light from the darkness. God called the light Day, and the darkness he called Night. And there was evening and there was morning, the first day.

And God said, "Let there be a dome in the midst of the waters, and let it separate the waters from the waters." So God made the dome and separated the waters that were under the dome from the waters that were above the dome. And it was so. God called the dome Sky. And there was evening and there was morning, the second day.

And God said, "Let the waters under the sky be gathered together into one place, and let the dry land appear." And it was so. God called the dry land Earth, and the waters that were gathered together he called Seas. And God saw that it was good. Then God said, "Let the earth put forth vegetation: plants yielding seed, and fruit trees of every kind on earth that bear fruit with the seed in it." And it was so. The earth brought forth vegetation: plants yielding seed of every kind, and trees of every kind bearing fruit with the seed in it. And God saw that it was good. And there was evening and there was morning, the third day. [The Holy Bible: New Revised Standard Version. copyright 1989, by the Division of Christian Education of the National Council of the Churches of Christ in the U.S.A. - in Bandstra (1999)]

I am not religious, I do not believe the Genesis stories are literally true, and I am certainly not prepared to fight holy wars over its interpretation. However, Genesis 1 is a good poetical description for how modern cosmology and biology think this complex thing called conscious life began, but Genesis offers little in the way of testable hypotheses about the physical causes of life or explanations of how life came to exist. In this section I will explore the physical dynamics of World 1 from which living things forming World 2 emerged as World 1 dynamics became increasingly complex. This involves consideration of the laws of thermodynamics, consideration of what actually constitutes 'life', the kinds of processes that have the capacity to give birth to life, what is known or can be guessed about the the transition from complex organic chemistry to genetically defined and evolving forms of life, and what is known or can be surmised about the actual early evolutionary history of life on the Earth.

These ideas and some of the evidence for them will be reviewed in some detail here as a background to my discussion of the origin and evolution of organizations as complex adaptive systems. 

What causes change?

Motion, change or 'evolution' in the Universe, including dynamic processes such as the metabolism and development of living things, is driven by fluxes of energy and energy-rich matter flowing from sources of high potential (i.e., the "light" of Genesis) to sinks of lower potential (Genesis's "darkness") (see Chaisson 2001228). 

The laws of thermodynamics (i.e., 'laws' are understandings expressed in World 3 of how World 1 works) describe the most fundamental rules governing all change in the Universe (Nave 2003; Farabee 2001; de Rosnay 1998). They are called the laws of thermodynamics because they were worked out in the flowering of the industrial revolution by scientists attempting to understand the limitations of steam and other external combustion or 'heat' engines in converting heat energy into work. Some understanding of the absolute physicality of the roles of these and other fundamental laws in the physical chemical existence is fundamental to understanding the origins of complexity and the evolution of cognition.

The first law of thermodynamics basically states that quantity of energy (matter is a form of energy) is conserved, but that it may change its forms (Russell 1995). 

The second law of thermodynamics basically states that energy (and energy-rich matter) will spontaneously flow (or be converted) only from high potential forms to lower potential forms.  The change in potential resulting from a particular conversion process is measured in terms of  entropy (representing degraded energy in the form of heat that cannot be used to drive reactions), whose mathematical sign is the reverse to what you would think it should be. 

The second law is often expressed in terms of entropy (or disorder), "the entropy of the universe as a whole or in a closed/isolated system (i.e., not able to exchange any form of energy with its surroundings) will spontaneously only increase with time (Russell 1995a; Klyce 2002). In other words, high potential forms of energy (with low entropy) may spontaneously transform to lower potential forms (i.e., energy conversions will only ever occur spontaneously if they increase entropy) and entropy, so it is quite reasonable to say that there is a universal tendency for ordered, organized systems to decay. Entropy has also been used to measure disorder in information theory (Shannon 1948; Gray 2001; Hillman. & Gunesch 2001). 

The concept of 'exergy' has been introduced to measure the availability or quality of a form of energy to be converted into into another form. "As energy is used in a process it loses quality, its exergy decreases."222

A major quandary for many who do not understand biological processes is to account for the evolution of increasingly complex and exergy rich living organisms that seems to run counter to the universal tendency for decay. Attempting to preserve a literal interpretation of Genesis 2 (i.e., the story of Adam and Eve), many Christian fundamentalists claim that the evolution of complex entities would be impossible under the laws of thermodynamics, and therefore the only way complex living things could come to exist is through the special actions of a creator god. For example see Wieland (1980; Evolution-vs-Creation (2002); Dalton (????) as examples of the top-ranking Google hits on the query, [thermodynamics evolution creation]. These and the links within their pages give a flavor of how "creation science" uses misunderstandings and misapplications of these laws in its attempt to discredit evolutionary argument. Several counter arguments to the creationist claims relating thermodynamics are linked via the Talk.Origins Archive (????).

The sciences are developing a coherent understanding for how the laws of thermodynamics drive physical processes in ways that account for the origin of life and biological evolution. I will show later that many of the properties of today's organizations closely parallel (at a higher level of organization) properties believed to have existed for the early protocellular organisms as they achieved self-perpetuating autocatalytic closure.

Based on research beginning with his PhD thesis in (1945), Ilya Prigogine won the Nobel Prize in chemistry (Prigogine 1977) for developing an understanding of how fluxes of energy through systems far from equilibrium lead to the formation of complex and ordered dissipative structures (see also Prigogine et al. 1972).

Although I knew some things about non-equilibrium thermodynamics from my studies in physics, Harold Morowitz's (1968) book, Energy Flow in Biology, was my first guide to provide key ideas for understanding how the fundamental processes of physics lead to the formation and evolution of increasingly complex systems such as living organisms - apparently against the trend towards increasing entropy as stated in the second law of thermodynamics. Morowitz describes the thermodynamic framework within which complex dynamic systems evolve:

The resolution of [the] apparent divergence between a biological and a physical theory is the realization that the second law of thermodynamics applies [most obviously] to systems that are approaching equilibrium, whereas the surface of the earth, the matrix of biological evolution, belongs to a different class of physical systems. Equilibrium systems require either isolation (adiabatic systems) or contact with a single fixed reservoir (isothermal systems). Most real physical systems are of another sort; there are in contact with more than one reservoir, some of which may be regarded as sources and some of which may be regarded as sinks. The description of these systems requires the consideration of the flow of either matter and/or energy from the sources through the systems of interest to the sinks. (Morowitz 1968: p 3.)

Morowitz summarises the general argument of his book as follows:

  1. The surface of the earth belongs to that class of physical systems which receives energy from a source and gives up energy to a sink. There is a constant and (on the appropriate time scale) almost steady flow of energy through the system.
  2. This flow of energy is a necessary and, we believe, sufficient condition to lead to molecular organization of the system experiencing the energy flow.
  3. This flow of energy led to the formation of living systems, and ecological process is the continued maintenance of order by the energy flow. Thus, the problem of the origin of life and the development of the global ecosystem merge into one and the same problem.
  4. The flow of energy causes cyclic flow of matter. This cyclic flow is part of the organized behavior of systems undergoing energy flux. The converse is also true; the cyclic flow of matter such as is encountered in biology requires an energy flow in order to take place. The existence of cycles implies that feedback must be operative in the system. Therefore, the general notions of control theory [cybernetics] and the general properties of servo networks must be characteristic of biological systems at the most fundamental level of operations. (Morowitz 1968: p 120.)

The concept that the origin and continuing evolution of complex living things is a direct consequence of the laws of thermodynamics as exergy is destroyed or "dissipated" in fluxes of energy as matter is cycled between high potential sources to low potential sinks (Prigogine et al. 1972). Following Prigogine and Morowitz, the role of dissipation as a driver of life and evolutionary processes has been extended substantially by a number of workers; Kay 1984; Schneider & Kay 1994, 1995; Patten et al. 1997; Straskraba et al. 1999; Jorgensen et al. 1999; Jorgensen et al. 2000; Kay 2000; Corning 2002). Kay (2000) describes the driving force of life and evolution as follows:

When moved away from their local (spatially) equilibrium state systems shift their states in a way which opposes the applied gradients and moves the system back towards its local equilibrium attractor229. The stronger the applied gradient, the greater the effect of the equilibrium attractor on the system. In simple terms, systems have the propensity to resist being moved from equilibrium and a propensity to return to the equilibrium state when moved from it. We refer to this principle as the "restated second law of thermodynamics".

[Exergy] ...measure[s] ...the maximum capacity of the energy content of a system to perform useful work as it proceeds to equilibrium with its surroundings and reflects all free energy associated with the system. ... Exergy is a measure of the quality of energy.

In terms of exergy, the classical second law of thermodynamics can be stated as: during any macroscopic thermodynamic process, the quality or capacity of energy to perform work is irretrievably lost. Energy loses exergy during any real process....

The restated second law can be formulated in terms of exergy: A system exposed to a flow of exergy from outside will be displaced from equilibrium. the response of the system will be to organize itself so as to degrade the exergy as thoroughly as circumstances permit, thus limiting the degree to which the system is moved from thermodynamic equilibrium. Furthermore, the further the system is moved from equilibrium, the larger the number of organizational (i.e., dissipative) opportunities which will become accessible to it and consequently, the more effective it will become at exergy degradation.

This has the consequence that structures and processes can spontaneously emerge which better resist the application of an external gradient, in the sense that it gets harder and harder to move the system from equilibrium because the system gets better and better at degrading the external input of exergy. ... This behavior is not sensible from a classical second law perspective, but is what is expected given the exergy degradation principle. No longer is the emergence of coherent self-organising structures a surprise, but rather it is an expected response of a system as it attempts to resist and dissipate externally applied gradients which would move the system away from equilibrium. The term dissipative structure takes on new meaning, No longer does it mean just increasing dissipation of matter and energy, but dissipation of gradients as well.

...Autocatalytic reaction systems are a form of positive feedback where the activity of the system or reaction augments itself in the form of self-reinforcing reactions. In autocatalysis, the activity of any element in the cycle engenders greater activity in all the other elements, thus stimulating the aggregate activity of the whole cycle. Such self-reinforcing catalytic activity is in itself self-organizing, is an important way of increasing the dissipative capacity of the system and can act as an active selection process between competing elements in the cycle. Cycling and or autocatalysis are fundamental aspects of dissipative systems and represent not only the building blocks of structure but is the source of complexity in nonequilibrium systems. [Kay 2000: p5-9]

Kay (2000: 9) summarises the properties of such non-equilibrium systems as driven by a continuing flux of energy from a high exergy source (e.g., sunlight) to a sink of low exergy (e.g., heat lost to the night sky). Such systems are:

Williams and Faústro da Silva (2002, 2003) take a systems approach to argue that the flow of energy from the sun through the physical/chemical system of the Earth's atmosphere, hydrosphere and geosphere have constrained the environment in which organic systems evolved to favor the development of the kinds of complex dissipative organic systems we see today.

Given the general principle that the laws of thermodynamics have the capacity to drive systems providing a pathway for the degradation of exergy to become more complex and dynamic at the expense of a net destruction exergy in the universe, apparently until they become complex enough to be considered alive. This raises the question, what does it mean to be alive?

What is Life?

It will be useful to consider just what it means to be alive. This is a question I first considered seriously in the mid 1960's when I began teaching biology courses as a graduate student224. The obvious place to start was to identify the differences between living and non-living things to see if these differences provided any heuristic power to explain some of the things living systems do for a living. In my thinking, the core property living systems had was the capacity for metabolism. I extended this to the definition that the minimal properties of life were dynamic self-maintenance, self-regulation and self-reproduction.

Maturana and Varela (Varela et al. 1974; Maturana and Varela 1980, 1987) took a similar starting point and coined the term 'autopoiesis' (self-production) to cover the list of properties they believed were necessary and minimally sufficient to define the property of life230. Maturana and Varela's starting point and their term autopoiesis has been adopted by systems and organization theorists in their discussions of the life-like properties of autonomous systems and organizations. Whitaker's (1995) hypertext discussion of autopoiesis provides necessary subsidiary definitions and explains autopoiesis in comprehensibly layered detail. The following definition, as quoted by Whitaker from Varela (1979: p 13) is the one I will follow in this work:

'An autopoietic system is organized (defined as a unity [i.e., an entity]) as a network of processes of production (transformation and destruction) of components that produces the components that:

(1) through their interactions and transformations continuously regenerate and realize the network of processes (relations) that produced them; and

(2) constitute it (the machine [i.e., the entity]) as a concrete [i.e., definable] unity in the space in which they [the components] exist by specifying the topological domain of its realization as such a network.'... [Whitaker (1995)]

In other words, 'autopoiesis' is an abstract construct known solely in relation to a system of a particular constitution which maintains its key constitutive character over time. [Whitaker 2001a]

Even more comprehensive definitions of all the necessary terms within the paradigmatic language are to be found on Whitaker's (2001...) web site, including his Encyclopaedia Autopoietica (Whitaker 2001a)224. Crucial terms in the following discussion will be hot-linked to the appropriate entry in this resource (e.g., autopoiesis).

In the definition above, the term "unity" (I prefer to use the synonymous "entity"), refers to any simple or compound object that can be distinguished or discriminated from the background by an observer ..

Maturana and Varela (1980, 1987) equate autopoiesis with the phenomenon of life as a definition that is both necessary and sufficient. Where biology is concerned, I unreservedly accept that autopoiesis defines the property "life" that differentiates living systems from the non-living. From Whitaker 2001a, "a living system is a '... homeostatic system whose homeostatic organization has its own organization as the variable that it maintains constant through the production and functioning of the components that specify it, and is defined as a unit of interactions by this very organization.' (Maturana & Varela, 1980, p. 48)".

Despite the use of reproduction in my own definition for life, Maturana and Varela note that the capacity to reproduce is not a necessary property for a system to be autopoietic or alive, and I accept this. For example, individual worker ants or bees do not have the capacity to reproduce, but no one would deny that when they are flying or running around that they are alive. Death of an autopoietic entity occurs when the capacity for dynamic self-regulation is exceeded in the face of external or internal perturbations and the entity literally 'disintegrates'.

The cybernetics225 of self-regulation are discussed at length by Stafford Beer226 (1981).

Concepts or capabilities related to autopoiesis are:

None of these capabilities on its own or together with just one of the others suffices to define autopoiesis. Autopoiesis requires all three. In other words, a system having the property of life is a dynamic self-producing, autonomous homeostat able to self-produce (i.e., maintain) these properties against some degree of perturbation. If perturbation exceeds the regulatory capacity the result is disintegration and death.

Again, following Whitaker (1995 - which see for a more detailed discussion), autopoietic or living systems form a subset of autonomous systems that Varela (1979: p 55) later defined by using the concept of 'organizational closure': 

[Organizational closure] is characterized by processes such that

  1. the processes [within/forming the entity] are related as a network, so that they recursively depend on each other in the generation and realization of the processes themselves, and

  2. they constitute the system as a unity [entity] recognizable in the space (domain) in which the processes exist.'

Kauffman (1993) uses the terms catalytic closure and autocatalytic sets in senses that correspond closely to organizational closure and autopoiesis (see below).

It follows from these definitions that the autopoietic entity has the capacity to adapt and change (or 'evolve' in the simple sense of change through time) in order to maintain its autopoietic capacity in response to stimuli (perturbations) it has the capacity to discriminate. 

According to Whitaker 2001a, Maturana and Varela use the term cognition for the collective cybernetic processes involved in achieving homeostasis and adaptation. 

[C]ognition is a consequence of (structurally-realized and structurally-determined) interactions. "A cognitive system is a system whose organization defines a domain of interactions in which it can act with relevance to the maintenance of itself, and the process of cognition is the actual (inductive) acting or behaving in this domain." (Maturana, 1970b: reprinted in Maturana & Varela, 1980, p. 13) More specifically:

"... for every living system the process of cognition consists in the creation of a field of behavior through its actual conduct in its closed domain of interactions, and not in the apprehension or the description of an independent universe. Our cognitive process (the cognitive process of the observer) differs from the cognitive processes of other organisms only in the kinds of interactions into which we can enter, ... and not in the nature of the cognitive process itself." (Maturana, 1970b: reprinted in Maturana & Varela, 1980, p. 49)

In other words, cognition is a circular, cyclic process of observation, orientation and decision leading to adaptive action driven by the environment, as discussed in earlier episodes. Cognition in this sense represents the emergence of Popper's World 2.

The spontaneous emergence of complex, autopoietic systems or "order for free"

Now that I have introduced some of the basic concepts of thermal physics that drive dynamic processes in World 1, and have reviewed what it means to be a living cognitive entity, it is time to consider pathways by which the complex cybernetics of World 2 has been able to emerge from the thermodynamically driven physical and chemical processes of World 1. As quoted and referenced earlier Prigogine, Morowitz, Kay, Patten, Corning and others have shown that the transport of fluxes of energy from a high exergy source to a lower exergy source through an intervening aqueous chemical system of carbon, hydrogen, oxygen and nitrogen under a reducing atmosphere will create a natural tendency for the system to form chemical cycles that tend to become more complex through time.

Stuart Kauffman (1993, 1995, 1996) argues that as such dissipative biochemical cycles become more complex, ordered autocatalytic systems will organize themselves, essentially "for free". For some 30 years Stuart Kauffman explored the mathematical properties of organization and chaos in cyclic and cybernetic systems to understand how ordered autocatalytic and homeostatic regulatory systems emerge naturally from initially random and chaotic assemblies of Boolean switches and wires or equivalent and more complex physical chemical constructs as these become more complex. Kauffman's (1993) 709 page abstract of lifetimes of his own and others' work, explores every step along the road from easily computable networks of Boolean switches connected by wires through a sequence of increasingly complex and life-like (i.e., catalytic) cybernetic models to explore the parameters leading to order vs chaos as the systems grew larger and more complex. In some cases his models are supported by biochemical experiments. His final chapters apply the logic and conclusions tested in his models and experiments to demonstrate that developmental and evolutionary genetics of multicellular organisms are entirely compatible with the principles demonstrated by his models. Kauffman 1996) provides an on-line summary of the logic of this progression, but no summary or abstract can do justice to immense detail of the book.

Brockman (1995) assembled Kauffman's summary of his own ideas along with responses from a number of other people working on the questions reviewed in the present section of my work.

What kinds of complex systems can evolve by accumulation of successive useful variations? Does selection by itself achieve complex systems able to adapt? Are there lawful properties characterizing such complex systems? The overall answer may be that complex systems constructed so that they're on the boundary between order and chaos are those best able to adapt by mutation and selection.

Chaos is a subset of complexity. It's an analysis of the behavior of continuous dynamical systems — like hydrodynamic systems, or the weather — or discrete systems that show recurrences of features and high sensitivity to initial conditions, such that very small changes in the initial conditions can lead a system to behave in very different ways. A good example of this is the so called butterfly effect: the idea is that a butterfly in Rio can change the weather in Chicago. An infinitesimal change in initial conditions leads to divergent pathways in the evolution of the system. Those pathways are called trajectories. The enormous puzzle is the following: in order for life to have evolved, it can't possibly be the case that trajectories are always diverging. Biological systems can't work if divergence is all that's going on. You have to ask what kinds of complex systems can accumulate useful variation.

Elert, G. (1995-2000). Chaos Hypertextbook: Mathematics in the Age of the Computer -

Corning -

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Pross, A. (2003). The Driving Force for Life’s Emergence: Kinetic and Thermodynamic Considerations. J. theor. Biol. 220: 393–406 [Science Direct] focusses on replication - not contradictory to thermodynamics

Corning, P.A. (2001). Control Information: The Missing Element in Norbert Wiener's Cybernetic Paradigm? Kybernetes 30(9/10): 1272-1288. - [Winner, U.K. Cybernetics Society 30th Anniversary Prize Competition] "Control information is not a "thing" but an attribute of the relationships between things. It is defined as: the capacity (know how) to control the acquisition, disposition and utilization of matter/energy in purposive (cybernetic) processes....

The problem first arose when physicists -- notably including Erwin Schrödinger in his legendary book, What is Life (1945) -- began to blur the distinction between thermodynamic (energetic) entropy (or its converse, which Schrödinger called "negative entropy") and physical (structural) order/disorder. The former usage refers to the availability of energy to do work, whereas the latter usage may be quite unrelated to any work potential. (More on this matter below.) Shannon was careful to differentiate between informational entropy and thermodynamic entropy, but other information theorists have not been so punctilious. Some of Shannon's followers have even suggested that there is an isomorphy, or equivalence, between statistical, energetic and physical order/disorder. However, this is not correct....

What we refer to as "statistical" and "structural" (i.e., order-related) formulations of information theory have made many important contributions to communications technology, computer science and related fields. However, these approaches cannot lead to a "unifying theory" of information for the simple reason that they are blind to the functional (teleonomic) basis of information in living (and human) systems, as Shannon acknowledged...

But more important, from a functional perspective information is not equivalent either to thermodynamic entropy or "negative entropy" (order). If it were, why confuse matters by using different terms for the same thing? In fact, this conflation of different phenomena involves a fundamental dimensional error. Information (properly defined) has no dimensions, while thermodynamic entropy has the dimensions of energy divided by temperature. It is comparable to equating voltage with length, or mass with velocity.

information (unlike energy) can be endlessly reused; there is no law of informational entropy. Nor is information "conserved"; it can be multiplied indefinitely. It has also been observed that, in some communications systems, information may flow in the opposite direction from the energy flow (for example, the old-fashioned Morse Code telegraph). Also, highly organized biological systems tend to be relatively more efficient users of energy; they use information to economize on energy consumption and, in so doing, validate the distinctions between information, energy and biological organization. A further objection is that information by itself cannot do anything; it cannot control a thermodynamic process without the presence of a "user" that can do purposeful work. In other words, information must be distinguished functionally from the process of exercising control, yet many theorists simply take this operation for granted, as F. Clerk Maxwell did with his "demon" (and as many other physicists have done since). It is this overlooked aspect -- this "free ride" -- that has allowed physical scientists to theorize about informational processes without acknowledging the necessary role of cybernetic control processes. Indeed, cybernetic processes cannot even be described by the laws of physics (see Corning and Kline 1998a).

Control information has a number of distinctive properties. First and foremost, it does not have any independent existence. It is not a concrete "thing", or a mechanism. It is defined (and specified) by the relationship between a particular cybernetic system (a "user") and its environment(s). In this paradigm, the physical environment "contains" latent or potential control information, but this potential does not differ in any way from the physical properties of the environment and, moreover, this potential is only actualized when a purposeful system makes use of it. In other words, the very existence and functional effects produced by control information are always contextdependent and user-specific.

The key point here is that "control information" causes purposeful work to be done in or by cybernetic systems. If energy, in accordance with the classical definition, is "the capacity to do work," control information is "the capacity to control the capacity to do work." Virtually everything in the universe might, potentially, have informational value (i.e., be used by cybernetic systems for some purpose), but control information is not located in the physical objects alone. It is defined by the precise relationship between a given object and a given observer/user.

First, control information is always relational and context-dependent and has no independent material existence; it cannot be identified or measured independently of a specific cybernetic process. However, it can be measured (see below). Moreover, there may or may not be a "sender", or a formal communications channel, or a "message" for that matter, but there must always be a "user" -- a living system or a human-designed system.

Second, control information does not exist until it is actually used.... Accordingly, the various mechanisms which exist in nature and human societies for coding, storing and transmitting potential information are reducible to their underlying physical processes; their informational properties arise only from the variety of ways in which these physical media may actually be utilized for informational purposes.

Accordingly, control information has no fixed structure or value. It is not equivalent to any specific quantity of energy, or order, or entropy, or the like. To illustrate, a single binary bit may (in theory) control an energy flow as small as a single electron or as vast as a the “signal” for a nuclear war; its power can vary tremendously, depending upon the context. (Another way of stating it is that all bits are not created equal.) Control information is analogous to money, whose value is not intrinsic but is defined in terms of specific transactions. 

"Potential" control information is very often "embodied" in various information storage and transmission media -- from DNA "templates" to the sound patterns in spoken language -- but the vehicle must not be confused with its driver. Control information is equally prevalent in the "state" properties of physical objects -- temperature, mass, velocity, viscosity, etc. There is no fundamental physical distinction between the two types of information; there is only a functional distinction. 

The problem, of course, is how to convert this perspective into an analytical framework. Specifically, the question is, how can you measure something that does not exist as a concrete physical entity? Our proposal, in essence, is that it can be measured in relation to what it does -- in relation to its "power" to control and utilize available energy and matter in or by a purposeful system. One can measure its "qualitative" effects, or its "meaning" in terms of the results that are produced -- the cybernetic "work" that is accomplished....

The economic aspect of our approach should also be mentioned. As noted above, our basic equation for control information is designed to measure not the total available energy involved in a particular context but the "profits", net of the entropy and the informational costs associated with the exercise of control. This approach, we maintain, brings our equation out of the realm of theory and locates it in the real-world of economic analyses, where the relationship between costs and benefits plays an important, even decisive, role in determining whether or not potential information becomes actualized. If the efficiency (benefit-cost ratio) is very low, the likelihood that a given form of information may actually be utilized to exercise control will be reduced commensurately. It is likely to remain in the realm of "latency."

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Biochemical and evolutionary aspects of anaerobically functioning mitochondria van Hellemond JJ, van der Klei A, van Weelden SWH, Tielens AGM PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY OF LONDON SERIES B-BIOLOGICAL SCIENCES 358 (1429): 205-213 JAN 29 2003 (0 citations)

Ancient horizontal gene transfer Brown JR NATURE REVIEWS GENETICS 4 (2): 121-132 FEB 2003 (0 citations)

The chemical basis of membrane bioenergetics Berry S JOURNAL OF MOLECULAR EVOLUTION 54 (5): 595-613 MAY 2002 (1 citation)

The phagotrophic origin of eukaryotes and phylogenetic classification of protozoa Cavalier-Smith T INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 52: 297-354 Part 2 MAR 2002 (16 citations)

Phylogeny of choanozoa, apusozoa, and other protozoa and early eukaryote megaevolution Cavalier-Smith T, Chao EEY JOURNAL OF MOLECULAR EVOLUTION 56 (5): 540-563 MAY 2003 (0 citations)

Mitochondrial connection to the origin of the eukaryotic cell Emelyanov VV EUROPEAN JOURNAL OF BIOCHEMISTRY 270 (8): 1599-1618 APR 2003 (0 citations)

The mesozoic radiation of eukaryotic algae: The portable plastid hypothesis Grzebyk D, Schofield O, Vetriani C, Falkowski PG JOURNAL OF PHYCOLOGY 39 (2): 259-267 APR 2003 (0 citations)

Molecular phylogeny of centrohelid heliozoa, a novel lineage of bikont eukaryotes that arose by ciliary loss Cavalier-Smith T, Chao EEY JOURNAL OF MOLECULAR EVOLUTION 56 (4): 387-396 APR 2003 (0 citations)

The phylogenetic position of red algae revealed by multiple nuclear genes from mitochondria-containing eukaryotes and an alternative hypothesis on the origin of plastids Nozaki H, Matsuzaki M, Takahara M, Misumi O, Kuroiwa H, Hasegawa M, Shin-i T, Kohara Y, Ogasawara N, Kuroiwa T JOURNAL OF MOLECULAR EVOLUTION 56 (4): 485-497 APR 2003 (0 citations)

Genomic reduction and evolution of novel genetic membranes and protein-targeting machinery in eukaryote-eukaryote chimaeras (meta-algae) Cavalier-Smith T PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY OF LONDON SERIES B-BIOLOGICAL SCIENCES 358 (1429): 109-133 JAN 29 2003 (1 citation)

The symbiotic birth and spread of plastids: How many times and whodunit? Palmer JD JOURNAL OF PHYCOLOGY 39 (1): 4-11 FEB 2003 (0 citations)

Nucleomorphs: enslaved algal nuclei Cavalier-Smith T CURRENT OPINION IN MICROBIOLOGY 5 (6): 612-619 DEC 2002 (1 citation)

Evolutionary history of "early-diverging" eukaryotes: The excavate taxon Carpediemonas is a close relative of Giardia Simpson AGB, Roger AJ, Silberman JD, Leipe DD, Edgcomb VP, Jermiin LS, Patterson DJ, Sogin ML MOLECULAR BIOLOGY AND EVOLUTION 19 (10): 1782-1791 OCT 2002 (2 citations)

Rooting the eukaryote tree by using a derived gene fusion Stechmann A, Cavalier-Smith T SCIENCE 297 (5578): 89-91 JUL 5 2002 (12 citations)

Evolved RNA secondary structure and the rooting of the universal tree of life Caetano-Anolles G JOURNAL OF MOLECULAR EVOLUTION 54 (3): 333-345 MAR 2002 (3 citations)

Obcells as proto-organisms: Membrane heredity, lithophosphorylation, and the origins of the genetic code, the first cells, and photosynthesis Cavalier-Smith T JOURNAL OF MOLECULAR EVOLUTION 53 (4-5): 555-595 OCT-NOV 2001 (13 citations)

Phylogeny of choanozoa, apusozoa, and other protozoa and early eukaryote megaevolution Cavalier-Smith T, Chao EEY JOURNAL OF MOLECULAR EVOLUTION 56 (5): 540-563 MAY 2003 (0 citations)

Evolution of the archaea Forterre P, Brochier C, Philippe H THEORETICAL POPULATION BIOLOGY 61 (4): 409-422 JUN 2002 (2 citations)

The non-universality of the genetic code: The universal ancestor was a progenote Di Giulio M JOURNAL OF THEORETICAL BIOLOGY 209 (3): 345-349 APR 7 2001 (2 citations)

The emergence of life on Earth Lahav N, Nir S, Elitzur AC PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY 75 (1-2): 75-120 2001 (3 citations)

The habitat and nature of early life Nisbet EG, Sleep NH NATURE 409 (6823): 1083-1091 FEB 22 2001 (31 citations)


PROPERTIES OF DISSIPATIVE SYSTEMS Salthe, S.N. 1993. Evolutionary Systems

Homeokinetics - the physics of complex systems -

The Emergence of Chaos and Complexity

Heylighen, F. Self-organization, Emergence and the Architecture of Complexity. -

Autocatalysis, Self-Regulation, Self-Production, Autonomy, Identity and Autopoiesis

Morowitz's generalizations:

  1. The major component of all functioning biolgical systems is water.
  2. The major atomic compoenents in the covalently bonded portions of all functioning biological systems are carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur.
  3. Most of the dry mass of functioning biological systms consists of proteins, lipids, carbohydrates, and nucleic acids.
  4. There is a ubiquitous and restricted set of small organic molecules which constitutes a very large fraction of the total mass of all cellular systems.
  5. Biological information is structural.
  6. The flow of energy in the biosphere is accompanied by the formation and hydrolysis of phosphate bonds, usually those of adenosine triphosphate.
  7. Sustained life under present-day conditions is a property of an ecological system rather than a single organism or species.
  8. Functioning biolgical systems are cellular in nature.
  9. There is a universal type of membrane structure utilized in all biological systems.
  10. All populations of replicating biological systems give rise to mutant phenotypes which reflect altered genotypes.
  11. All replicating cells have a genome made of deoxyribonucleic acid which stores the genetic information of the cells which may be read out in sequences of ribonucleotides and translated into polypeptides.
  12. All growing cells have ribosomes which are the site of protein synthesis.
  13. The translation of information from nucleotide language takes place through specific activaing enzymes and transfer RNA.

Daniel Segré & Doron Lancet (2000). Composing life. EMBO Reports 1, 3, 217–222 (2000) -

Daniel Segré , Dafna Ben-Eli, and Doron Lancet (2000). Compositional genomes: Prebiotic information transfer in mutually catalytic noncovalent assemblies. Proc. Natl. Acad. Sci. USA.  97 (8): 4112–4117 -

Daniel Segre', Barak Shenhav, Ron Kafri and Doron Lancet Journal of Theoretical Biology (2001), 213, 481-491. The molecular roots of compositional inheritance -

Segre' D., Ben-Eli D. Deamer D. and Lancet D. Origins Life Evol. Biosphere (2001) 31, 119-145. The Lipid World -

Daniel Segre', Dafna Ben-Eli, Yitzhak Pilpel, Ora Kedem and Doron Lancet In Instruments, Methods, and Missions for Astrobiology II, Richard B. Hoover, Ed., Proceedings of SPIE, Vol.3755, 144-162 (1999) GARDobes: Primordial cell nano-precursors with organic catalysis, compositional genome and capacity to evolve -

The evolution of primitive biological systems - in Corliss, J.B. (1985). The Creation of Living Systems in Archaean Submarine Hot Spring. [unublished]. see also

Buenstorf, G. (2000). Self-organization and sustainability: energetics of evolution and implications for ecological economics. Ecological Modelling 145(2-3):101-110. [Science Direct]

Toussaint, O. & Schneider, E.D. (1998). The thermodynamics and evolution of complexity in biological systems Source. Comparative Biochemistry and Physiology A - Molecular and Integrative Physiology, 120(1):3-9 [Science Direct]

A key used to recognize whether a system can properly be considered to be autopoietic (from von Krogh & Roos 1995a:46 after Varela et al., 1974)

  1. Does the system have identifiable boundaries in its interactions? If yes then,
  2. Does the system consist of elements (i.e., components) that identifiably belong to the system and can be described? If yes, then,
  3. Is the system mechanistic, in that the component elements interact and/or act to transform one another? If yes, then,
  4. Do the elements forming the system's boundaries do so as a result of their interactions with other elements that identifiably belong to the system? If yes, then, 
  5. Are the elements forming the system's boundaries produced by interactions of elements of the system, either by transformation of previously produced elements, or by transformations and/or coupling of non-component elements that enter the system through its boundaries? If yes, then,
  6. If all the elements of the system are also produced by the interactions of its elements as in 5 above, and if those elements which are not so produced participate as necessary permanent constitutive components in producing other components, the system is autopoietic within the space in which it exists.

If the answer to any of these questions is no, then the system does not have all the properties required to define it as auotpoietic.


Natural Selection and Descent With Modification

William Calvin 

"The Emergence of Intelligence", Scientific American Presents 9(4):44-51 (November 1998). See also is a 1998 revision of what appeared in Scientific American 271(4):100-107, October 1994.

William H. Calvin, "Competing for Consciousness: A Darwinian Mechanism at an Appropriate Level of Explanation." Journal of Consciousness Studies 5(4)389-404 (1998).


Calvin, W.H., 1997; The Six Essentials? Minimal Requirements for the Darwinian Bootstrapping of Quality. Journal of Memetics - Evolutionary Models of Information Transmission, 1. -

Origins and Importance of Systems of Heredity