PhD

L’ordine invisibile. Ripensare il vivente oltre la metafora computazionale

The Invisible Order: rethinking the living beyond the computational metaphor

University of Bergamo, 2008

English Abstract:

The aim of this thesis is to outline a systemic approach to biology which is meant to be a critical alternative to the theoretical paradigm born with molecular biology and based on the assumption of the metaphor of the genetic program. The starting point is the thought about livings systems elaborated by the theory of autopoiesis, of which I propose a rigorous analysis from the biological and epistemological points of view. The aspect which makes autopoietic theory suitable as a model of the living which stands out as an alternative to the mainstream of theoretical biology is the attention paid to the role of the unitary organization of the organism, instead of focusing on the properties of individual components (e.g. DNA etc.). According to this approach is therefore a systemic property, and not the behaviour of some component, that allows us to catch the specificity of the living with respect to other natural or artificial systems.

The primary goal of this study is to produce an analysis of the concept of systemic unity proposed by autopoietic theory, characterized by an integration of the philosophical approach with the theoretical and formal ones. In fact I considered necessary to give more biological depth to the notion of autonomy proposed by Maturana and Varela. The definitory concept they introduced – that of a particular form of organization: organizational closure – in fact, is only assumed as an explanatory principles but it has not been analysed enough in detail. Also, it lacks a suitable formal expression.

The further goals of this thesis consist in:

  • proposing a connection between the theoretical thought on the living and a suitable epistemological framework which allows us to express, at the operational level, the importance of the role of the observer in catching the definitory aspects of living systems and in elaborating the corresponding models;
  • providing a detailed comparison with the theoretical framework of the traditional molecular biology and of the contemporary Systems Biology in order to point out its theoretical inconsistencies and the most relevant and innovative aspects of the alternative approach proposed;
  • elaborating an epistemological and theoretical framework according to which to re-interpret and re-modelise the notion of emergence and to propose a solution to some of the problems related to it, like for example the apparent paradox of downward causation.

The thesis is divided into four chapters. The first one is characterized by an explicitation and an analysis of a constructivist epistemological position based on the biogenetic approach to cognition. In particular I show the mutual relationship between the view of nature (autonomy) and the view of knowledge (construction) and its differences with respect to the mechanistic/objectivistic approach. In order to elaborate this framework, I integrate the tradition of research of the studies on complexity, which in this domain has it most rigorous outcome in the theory of cognition proposed by Maturana and Varela, with the philosophical thought of Kant, Jonas, Merleau-Ponty, Sartre and Whitehead on the relationship between biology and knowledge. The results of this operation are then applied to the issue of the construction of conceptual and formal models of the living and to a critical analysis of the functional or finalistic explanation in biology.

The second chapter is dedicated to the subsequent constructive step, consisting in the characterization of the living based on the concept of autonomy. In order to do so I introduce a comparative analysis of the different modalities of identification of the fundamental invariants in the characterization and investigation of biological systems, making explicit the different definitions of “life” which derive from them. Then I provide a detailed analysis of the genealogy of the notion of biological autonomy, starting from the tradition of cybernetic and embryology, and of its most rigorous outcome: the theory of autopoietic systems. Finally I propose a modelization of the key concepts of this approach using the formal tools provided by the mathematics of Category Theory. The aim is to give more depth to the theoretical approach proposed, providing an integration between the conceptual framework derived from the tradition of studies on biological autonomy and the theoretical and formal remarks and tools elaborated by Rosen. Following this path I try to clarify from the mathematical point of view the formal model he formulated, which is almost unknown and quite obscure, and to propose a conceptual theoretical analysis of it and some possible applications to the modelization of the living phenomenology.

The third chapter is focused on the analysis of the procedure of theoretical construction of the computational metaphor in molecular biology. In this section – after making explicit the parallelism in the use of this metaphor in cognitive and biological sciences – I point out the connections between von Neumann’s work on self-reproducing automata and Jacob’s and Monod’s studies on the intracellular regulative mechanisms, and their implications for the biological modelization. The purpose is twofold and consists in (1) identifying and analysing the fundamental theoretical assumptions at the basis of the mechanistic model of the living and (2) making explicit the intrinsic limits of this theoretical framework – epistemological, logical and phenomenological ones – showing that they are shared also by the most recent re-elaborations of this mechanistic approach, which are characterized by an extension of the notion of “genome” in that of “proteome”. After this criticism of the use of the computational metaphor in biology, I delineate the opposing thesis, proposed by Rosen and others,  asserting the non-algorithmic nature of the biological processes and I put into evidence its theoretical and epistemological implication for the discipline of Artificial Life.

In the last chapter – starting from a historical review of its origins in the British Emergentism – I face the problem of emergence from an epistemological standpoint. The notion of emergence is one of the crucial factors in the process of construction of a systemic approach to biology, and a conceptual tool of paramount importance in order to characterize the specificity if this domain. In this chapter I propose an analysis of the phenomena of emergence exhibited by autonomous systems and a possible attempt to distinguish them from the processes of generation of spatial patterns, which instead can be considered as connected to the notion of structural stability. Also, I propose an epistemological solution to the paradox of downward causation derived from a re-elaboration of the constructivist framework characteristic of the biogenetic approach to cognition: according to this view, the notion of downward causation can be re-considered not as a direct or indirect influence of the whole on its parts, but as an epistemological problem which is due to the confusion between distinct observative levels.

In the second part of the final chapter I propose an application of the concept of emergence also to biological historical processes. Firstly, I outline a critical deconstruction of the notion of adaptation in biology. The idea is that in some of its aspect the computational metaphor influenced, besides the domains of investigation of cognition and life, also the elaboration of models of the interaction between organisms and their environments. In particular, the cognitive concept of representation finds in this domain its parallel in the concept of adaptation as optimization. Coherently with the constructivist epistemological framework and the model of the living characteristic of the studies on biological autonomy, I sustain here an alternative approach to biological evolution. It is a neutralist one based on the concept of autonomy and derived from the notion of “natural drift” elaborated by Maturana, Varela and Mpodozis and coherent with Eldredge’s, Gould’s and Lewontin’s thought. And I propose an emergentist interpretation of it: an idea of evolution considered as a systemic dynamics of multilevel diachronic emergences.

  • "To say that a system is complex […] is to say that we can describe the same system in a variety of distinct ways […]. Therefore a system is simple to the extent that a single description suffices to account for our interaction with the system; it is complex to the extent that it fails to be true." (Robert Rosen, 1978)
  • “Complexity is not an intrinsic property of a system nor of a system description. Rather, it arises from the number of ways in which we are able to interact with the system. Thus, complexity is a function not only of the system’s interactive capabilities, but of our own”
    (Robert Rosen, 1985)

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