What we need is a crude first approximation to autopoietic theory so we can understand where we are heading as we develop our ontological view of autopoiesis. In that crude first approximation we will consider autopoiesis as an "existentialist biology" which is directed at the question as to whether organisms are reducible to machines or not. The answer to the question that autopoiesis gives is at first satisfying to the reductionist because it affirms that indeed organisms are machines. But then when one looks closer and realizes what kind of machine the answer becomes a bit more unsettling to the traditional theorist. In other words Autopoiesis takes sides in the traditional debate as to whether organisms are "just" machines or not. But it reinterprets the "just" in such a way that the theory itself takes on the paradoxicality of the categorizational problems associated with this dichotomy. It does this by claiming to create a different theoretical stance a lot like existentialism. Existentialism attempted to reaffirm traditional metaphysics by turning the system of metaphysics upside down. Where essence is normally affirmed by either idealists or materialists as being prior to everything else, the question has always been only what kind of essence, instead existentialism affirmed that the existence of things was more primordial than their essences. This preserves the traditional metaphysical structure but appears like a new philosophy. Autopoietic theory does something similar in that instead of affirming the primary nature of the essences of the species produced in the evolutionary process it affirmed the status of the individual organism as being prior to the species in the sense that it must exist in order for the species to evolve and develop its essence diachronically. It is odd to think that biology had lost track of the actual individual organisms in its study of plants and animals, but this is exactly what autopoietic theory charged. In fact, it said that these organisms had some strange characteristics when considered as individuals outside the panoply of the forces of evolution acting across time to define the essence of the species to which the individual belonged.
This of course brings us directly to the heart of ontology, because what is ontology if not the relation between the Being of essences and the existence of individuals? So the question becomes immediately what is the nature of the essence and existence of individuals and species. We can think of it this way. An individual organism exists first and then develops its essence as a means of participating in the species. Thus is born the distinction between structure and organization. Or we can think of it this way. A species defines the essence of individuals which then only exist to embody those constraints in individual existents. It is clear that the traditional biological viewpoint is the latter. The major subject of study has always been the species not the contribution of the individual that exists in order to make the species possible. Thus autopoiesis fines us for the liberty it allows us to take. What we desperately desire is to have organisms be ONLY machines. But what it takes in return is the fact that it imposes the existentialist view of biology that concentrates on the individual existing organism instead of the abstract species.
Now the question arises what is the relation between these two propositions? To understand this it is necessary to consider the alternative. The alternative is that Bergson is right, there is an elan vital or life energy that is different from all other energies that are normally considered by physics. The very thought of this makes biologists blanch because they like all of us desperately want to be scientific by the standard set in physics. If there is some special invisible energy in organisms then it is very difficult to gain the dream of scientific ratification of the foundations of biology by physics. But when autopoiesis gives us this gift of scientific validation of our mechanistic view of organisms it takes away something equally valuable to us. That is it takes away our view of the species being primary and the individual being secondary. It points out that without the living viable individual there would be no species. We can think of Dodos but without actual Dodos alive and kicking the species is nothing. Thus autopoiesis considers what the individual contributes beyond the species. In other words, normally our biology would just consider an individual an example of a species, and nothing else. But autopoiesis considers that the individual contributes something beyond the constraints of the essence of species. Thus you see we can only have organisms as merely machines as long as the individual existent organism contributes something beyond the species defined by the essence. Autopoietic theory is about defining just what this something more that allows the organisms to be merely a machine is. And that revolves around the traditional question concerning the relation between essence and existence.
At this point we can begin to appreciate the paradoxical nature of autopoiesis. It gives us something but also takes away something in order to be able to decide finally that organisms are just machines. Now lets consider the opposite of autopoiesis. That opposite would decide that an organism was more than a machine and then we could forget the individual and continue to think of the individual as merely an exemplar of the species. And this is exactly how biologists solved the problem in many circles for a long time. They accepted that organisms were an emergent level beyond what was merely given in physics and avoided reductionism. But as physics was more and more successful with their reductionist program this became harder and harder to sustain. So another group of biologists insisted that organisms were completely reducible to physical phenomena. But then their problem was to explain were the strange and different properties of living organisms came from. In fact, it out of this group that autopoiesis sprang. They accepted that organisms were just machines already but wanted to explain the strange properties that did not reduce to mere physics. Maturana and Verela hit upon the answer, i.e. biological existentialism. In other words, there is a residue left over from the essence imposed by the species which explains the difference between the physical properties and the emergent properties of the organism that is prior to it being any particular species. It is in fact a brilliant theoretical move with deep philosophical import.
One should notice that traditionally the Being of Essence and the Existence of the individual was confused in Greek philosophy. It was the time when the Arabs inherited the Greek tradition that the distinction was produced between the two concepts. This happened primarily because the Arabic language had no term for Being but did have a term for existence. This forced the Arab Aristotelian scholars to make the fine distinction that was translated back into Latin to become the distinction we have today. In fact until the existentialists no one thought to take philosophical advantage of the distinction. Jaspers is probably the first to realize how Existenz could open a new direction for philosophical exploration. He was also the first to realize that by intentionally leaving a key term undefined in a philosophical system it was possible to generate a surplus of meaning in that term. So in his philosophy he intentionally left Existenz undefined and its meaning was given totally by context. A similar ploy occurs in Autopoietic theory. Here instead of leaving the existence of the individual undefined we confer upon it closure to the external observer. In this way we gain the surplus necessary to explain the emergent difference while at the same time remaining congruent with a reductionist program.
Hopefully it is becoming clear that the relation between existence and essence is not easily pinned down. In fact, it is a major muddle that philosophy attempts to address. When every one poses a difference between existence and essence one is walking straight into philosophical territory whether one declares it or not. The paradoxicality of the difference between the emergent surplus of biology over physics is hidden in the paradoxicality of the relations of existence to essence. Of course, if one accused Maturana and Verela of this sophistic ploy they would deny it. But it is clear, when one considers the situation closely that there is really only this one way out of the conundrum of reduction verses emergence. Maturana and Verela were merely clever enough to think of this possibility of embracing paradoxicality. In fact, where best to place the paradoxicality but in the organism itself. Then it appears as if there is no paradoxicality anywhere, and if we do not look at the object of investigation closely enough we will never discover where all the paradoxicality of the distinction between organism and machine disappeared. However, we must pay for this reductive freedom by having our view of the field of biology turned upside down. Suddenly organisms are closed, external observers stand in uncertain relations to their subjects of study, the attributes of life and cognition become fused within the organism, the distinction between organization and structure must be scrupulously maintained. Our real interest, in species moves to the background, while enigmatic individuals take center stage.
This first approximation will allow us to keep straight what is at stake as we begin to investigate the phenomena of the fragmentation of Being and explore the relation between essence and existence. Essences have Being, but existence is somehow about the limits of Being. Existence gives us visions of life that is nasty, short and brutal. It brings to the fore the difference between necessity and suffiency. All in all we can say that Being and it's limits play a very significant role in our conception of autopoietic theory. But what is Being anyway? Well it turns out that our conception of Being has been radically transformed in this century, at least for those who do not reduce everything to word games, and thus are doomed to endlessly play word games without meaning (i.e. Analytic Philosophers).
[END TUTORIAL PART 2]