Table of Contents
Life and persistence
Function and Metabolism
The Thought Experiment
Life as a dynamic system
What is catalysis?
What are solitons?
Solitons in biology
Scale invariance in biology
Structure, energy, unity and resonance
Application of catalysis 1
Application of catalysis 2
Life as catalysis
Ontology of consciousness
Fractal catalysis and autopoiesis 1
Fractal catalysis and autopoiesis 2
Fractal catalysis and autopoiesis - 1
The scale invariant catalytic model of living processes attempts to demonstrate that there is a common theme to all living processes -- catalysis. The consequences of the theory for how we understand living processes are far reaching. From the perspective of the scale invariant catalytic model, the evolution of mental cognition is understood to be simply a variation on the basic theme of metabolism as catalysis. Metabolism, therefore, even of the simplest prokaryotic bacterium, is also an instance of cognition.
By grounding cognition in a very basic metabolic theme, I am retracing the steps made by two theoretical biologists (Maturana and Varela) who, over twenty years ago, coined the phrase 'autopoiesis' to describe living processes. Both autopoiesis and the scale invariant catalytic model attempt to define cognition as a basic metabolic process.
'Autopoiesis' was a term created to describe the central theme of the theory -- "auto" = self, "poeisis" = creation. The idea is that living processes can be described as a network of relationships which, if taken together, can be understood as maintaining that same set of relationships as a closed unity. Thus, life is understood to have a dynamic, cyclic, and self maintaining organization. This represents a departure from our common sense view of the relationship between the organization of a process and the means by which that organization is maintained. Normally, we implicitly separate the organization of a structure or process from the mechanisms of maintenance. Thus, the product and the system of production would be expected to be essentially different aspects of the overall process. The theory of autopoiesis removes this distinction and puts forward a view of living processes where the production and maintenance of a process are understood to be identical. To formalize this idea, living systems are described as having the following elements:
Both autopoiesis and the scale invariant catalytic model of living processes argue that functionality is a redundant term and that cognition can be understood purely in terms of metabolism. The power of both autopoiesis and the scale invariant catalytic model of living processes is to demonstrate that the apparent discontinuity between functions and their supporting physical processes can be entirely eliminated because there is no distinction to be made between them. Furthermore, because both autopoiesis and the scale invariant catalytic models provide an explanation for the robustness of all living processes, questions concerning the compatibility between 'function' and robustness are also eliminated.
This similarity also introduces a subtle distinction between the two theories - i.e how the environment is understood to play a role in the living process. In the theory of autopoiesis, the organism is considered to be an essentially closed autonomous system that is loosely coupled (or structurally coupled) to the environment. The action of stimulus upon the brain is considered as a perturbation of the autopoietic state of the organism that can lead, eventually, to organizational changes. These organizational changes accommodate the effects of environmental perturbation in order to maintain the integrity of the organism as a closed autopoietic system. Therefore, cognition is an internal state of the organism which, although instigated by environmental perturbation, nevertheless, is determined primarily by the organism's overall autopoietic organization. Consequently, the phenomena of cognition are to be related primarily to the organization of the organism rather than to the organization of the stimulus.
Conversely, the scale invariant catalytic model does not delineate between the environment and the organism. The organism is understood to be a process of the environment. This point is best illustrated with an analogy. Imagine a whirlpool; a little thought reveals that, although we can seem to identify the position and limit of the whirlpool, on closer examination, there is no sense in which we can distinguish between the dynamic of the whirlpool from the environment. This point is firmly underscored by the proposition that life is a process of catalysis. If we formulate the process of catalysis in autopoietic terms, then the catalyst would correspond to the closed autopoietic system and the reagents, products and the process of catalysis itself would correspond to an environmental perturbation. By identifying the living process with the 'transition state' of a process of catalysis, the scale invariant catalytic model firmly roots the process of life in the environment. This also, has implications in terms of the claim by followers of the autopoietic theory that life is an essentially autonomous process. The concept of autonomy within the autopoietic framework can only make sense if there is, indeed, a distinction to be made between life and the environment. By abandoning this distinction, the concept of autonomy and how it might play a role in living processes (especially of the mind) cannot be decided as a consequence of the perception of life as a 'closed' system within the scale invariant catalytic theory.
The importance of the role that the environment plays can be further emphasized by examining the catalytic description of cognition. Previously we examined how the brain unites neuronal events in space and time via implicit invariance (or fixed points or symmetries) as a dynamic non-linear wave called a soliton. It was also pointed out that for a particular set of boundary conditions there were particular soliton solutions. I would conclude from this that the phenomena of cognition are to be related primarily to the relationships implicit in the stimulus rather than to the organization of the organism that is stimulated. This is not to undermine entirely the idea that our bodies contribute to 'how' the world is perceived. The claim is that, although the fact of our mind's embodiment may contribute and influence our apprehension of the world, this is to be considered a contingency that is far outweighed by the understanding that living processes are processes of catalysis that make explicit the order that is implicit in the environmental survival space.
It may be pointed out that with the use of the terms 'environmental survival space' and 'boundary conditions' that I am implying a similar duality between life as a closed system and its environment. However, I wish to stress that the reason for this is that, as yet, there is no nomenclature to describe adequately the place that life occupies within the general context of the physical processes that comprise the environment. The use of the term 'boundary' does not imply a division between the living process and the environment. The terms 'boundary conditions' and 'environmental survival space' refer to the set of environmental factors that are necessarily part of the living process. The boundary, then, is an internal boundary of the living process and defines those physical components, orders, relationships, etc., of the environment that are fixed parts of the living process in question. Of course, a cell membrane not only introduces raw materials to the complex processes of cell metabolism, but also prevents unwanted materials from entering the cell. So, if we consider the membrane of the cell to be a boundary, then it is a boundary that determines what aspects of the environment become part of the metabolic process and those that do not.
In order to elucidate other subtle differences between the two theories let us consider the question of organization at differing levels of scale as it is understood to operate within the context of autopoiesis and the fractal catalytic models. The cell is regarded to be the first level of autopoiesis. Groups of cells in the form of an organism represent a second level of autopoietic organization. So, the closed autopoietic organization of a cell is thought to be subsumed as a 'functional' component of an encompassing autopoietic organization - the organism. This can only happen if the encompassing autopoietic organization of the organism does not constitute a perturbation of the organization of the cell that is ultimately damaging to its organization - or vice versa.
The two theories share the idea that there is a common principle at the heart of living processes. However, the fractal catalytic model traces this theme all the way down to the level of the enzyme. I believe that this better explains how living systems maintain their overall integrity. Also, because the robustness of living processes is explained as a consequence of living processes acting as catalysts (mediators of transitions in the environment), rather than as a result of autopoietic organization, the role that the environment plays in the process is more directly and simply defined.
As we shall see shortly, autopoiesis also plays a major role in the fractal catalytic model. However, I suggest that autopoiesis is not sufficient to understand the robustness of living processes. By locating autopoiesis within the greater context of catalysis as the essential principle at work, we are better placed to understand the necessary relationship between autopoiesis, robustness, and the structure in the environment.