I'm perhaps best known for three different kinds of work, which seem disparate to many people but to me run as a unified theme. These are my contributions in conceiving the notion of autopoiesis self-production for cellular organization, the enactive view of the nervous system and cognition, and a revising of current ideas about the immune system.
Regarding the subject of biological identity, the main point is that there is an explicit transition from local interactions to the emergence of the "global" property that is, the virtual self of the cellular whole, in the case of autopoiesis. It's clear that molecules interact in very specific ways, giving rise to a unity that is the initiation of the self. There is also the transition from nonlife to life. The nervous system operates in a similar way. Neurons have specific interactions through a loop of sensory surfaces and motor surfaces. This dynamic network is the defining state of a cognitive perception domain. I claim that one could apply the same epistemology to thinking about cognitive phenomena and about the immune system and the body: an underlying circular process gives rise to an emergent coherence, and this emergent coherence is what constitutes the self at that level. In my epistemology, the virtual self is evident because it provides a surface for interaction, but it's not evident if you try to locate it. It's completely delocalized.
Organisms have to be understood as a mesh of virtual selves. I don't have one identity, I have a bricolage of various identities. I have a cellular identity, I have an immune identity, I have a cognitive identity, I have various identities that manifest in different modes of interaction. These are my various selves. I'm interested in gaining further insight into how to clarify this notion of transition from the local to the global, and how these various selves come together and apart in the evolutionary dance. In this sense, what I've studied, say, in color vision for the nervous system or in immune self-regulation are what Dan Dennett would call "intuition pumps," to explore the general pattern of the transition from local rules to emergent properties in life. We have at our disposal beautiful examples to play around with, both in terms of empirical results and in terms of mathematics and computer simulations. The immune system is one beautiful, very specific case. But it's not the entire picture.
My autopoiesis work was my first step into these domains: defining what is the minimal living organization, and conceiving of cellular-automata models for it. I did this in the early 1970s, way before the artificial-life wave hit the beach. This work was picked up by Lynn Margulis, in her research and writings on the origins of life, the evolution of cellular life, and, with James Lovelock, the Gaia hypothesis. Humberto Maturana and I invented the idea of autopoiesis in 1970. We worked together in Santiago, during the Socialist years. The idea was the result of suspecting that biological cognition in general was not to be understood as a representation of the world out there but rather as an ongoing bringing-forth of a world, through the very process of living itself.
Autopoiesis attempts to define the uniqueness of the emergence that produces life in its fundamental cellular form. It's specific to the cellular level. There's a circular or network process that engenders a paradox: a self-organizing network of biochemical reactions produces molecules, which do something specific and unique: they create a boundary, a membrane, which constrains the network that has produced the constituents of the membrane. This is a logical bootstrap, a loop: a network produces entities that create a boundary, which constrains the network that produced the boundary. This bootstrap is precisely what's unique about cells. A self-distinguishing entity exists when the bootstrap is completed. This entity has produced its own boundary. It doesn't require an external agent to notice it, or to say, "I'm here." It is, by itself, a self- distinction. It bootstraps itself out of a soup of chemistry and physics.
The idea arose, also at that time, that the local rules of autopoiesis might be simulated with cellular automata. At that time, few people had ever heard of cellular automata, an esoteric idea I picked up from John von Neumann one that would be made popular by the artificial-life people. Cellular automata are simple units that receive inputs from immediate neighbors and communicate their internal state to the same immediate neighbors.
In order to deal with the circular nature of the autopoiesis idea, I developed some bits of mathematics of self-reference, in an attempt to make sense out of the bootstrap the entity that produces its own boundary. The mathematics of self-reference involves creating formalisms to reflect the strange situation in which something produces A, which produces B, which produces A. That was 1974. Today, many colleagues call such ideas part of complexity theory.