The Physics and Evolution of Symbols and Codes

The work of Howard Pattee has been the chief intellectual influence in my career so far, but it was by no means a sudden realization. None of his influential ideas is received with an immediate "eureka", rather, his positions result from a thorough observation of the essential characteristics of biological systems. Unlike "headline" positions which send ripples through science by defending extremist views, Pattee seems to have always positioned himself in the middle of controversies such as dynamics versus symbols (or computation), selection versus self-organization, and the like. But his consensual approach is by no means pursued for the sake of pleasing all audiences or a lack of vision. Rather, it stems from a long, thorough, and attentive observation that complex evolving systems cannot be fully described by any one single, neat, extreme theory or another, but require instead several complementary models - a characteristic that indeed grants them the status of complex.

While such a complementary approach does not cause "revolutions" or immediate attention, it does grow on you. The more evidence one gathers, the more single models of complex systems fail, and one is catapulted back to the kinds of questions asked by Pattee. This mirrors my own development as one of his students. Initially interested in artificial intelligence and cognitive science, I never expected to study under his direction but simply to take his graduate courses. However, I found myself asking him to sit in on these same courses, semester after semester, as his ideas became increasingly more relevant and coherent in my mind. During this process I realized that the questions that bothered me about artificial intelligence, could not be treated solely from a cognitivist point of view, but demanded an inclusion of evolutionary ideas (both selectionist and developmental). Simultaneously, I became aware of the diverse community of scientists and philosophers inspired by Pattee's thought. It was with great pleasure that I saw many of these responding to the call for this special issue. I hope their contributions demonstrate the merits of Howard's complementarity approach to complex systems, and in particular his insistence on symbolic and material modes of description. Most of all, I hope this compilation leads others to miss a profound eureka, but somehow be puzzled enough to embark on a slower but deeper examination of the complex, complementary nature of living systems.

After conversations with Michael Conrad, the idea for this special issue was to mark the occasion of the retirement of Prof. Howard Pattee. The goal was to do justice to the interdisciplinary nature of Pattee's work, while maintaining a directed focus to the area that he considers his most relevant contribution to science and philosophy of science: The Physics and Evolution of Symbols and Codes. This theme encompasses theoretical and modeling aspects of biological and evolutionary systems. Indeed, at the core of biological and evolutionary systems lies the notion of codes used to construct organisms from inherited information. The study and modeling of the origin, physical constraints, evolutionary potential, and taxonomy of natural symbols and codes is extremely relevant to the disciplines of biology (particularly for the origin of life problem), complex systems research, artificial life, cognitive science, and artificial intelligence. Authors were invited to relate their work to Howard Pattee's own description of the problem area:

"The two great scientific disciplines of physics and evolution theory have traditionally been taught as disjoint subjects. Yet some billions of years ago, certain collections of physical molecules reached a level of complexity that began open-ended evolution by heritable (symbolic memory-based) variation and natural selection.

Von Neumann was the first to propose explicitly why this "threshold" of complexity requires description-based reproduction (taken for granted by biologists), but his argument was focused on the logical, not the physical requirements. He did not discuss the organizational requirements that would allow normal physical molecules to function as descriptions, nor was he clear about his logical distinction between "active" physical dynamics and "quiescent" symbolic descriptions. He did not mention the origin problem except to say it was "a miracle of the first magnitude."

Even if we still do not have a clear picture of the origin of life, the significance of this fundamental distinction between descriptions and constructions, that is, between semiotic processes (rules, codes, languages, information, control) and physical systems (laws, dynamics, energy, forces, matter) reaches to all levels of evolution. This is an essential distinction from the earliest genetic control of the synthesis of proteins, to the codes and languages of the brain, to the distinction between the mind and the brain (the knower and the known, the epistemic cut), and even to physical theory itself that requires a clear distinction between universal physical laws and the local semiotic process of measurement - an area in which there is still no consensus. This distinction between laws and semiosis, as well as how they are related, needs to be made more clearly at all levels if we are to fully understand evolution, physical laws, and the languages of the brain.

In biology, the basic physics and chemistry of elementary life processes as they exist on earth is well-developed. However, our knowledge of the semiotic controls and interactions within and between organisms and in some cases even in single cells is far from complete. In evolution theory it is still not clear that blind variation in a virtually infinite semiotic search space is adequate to explain so many successful species.

Howard H. Pattee

Eleven contributions were accepted for inclusion in this special issue, ranging from physics to philosophy of science. Howard Pattee's paper "The Physics of Symbols: Bridging the Epistemic Cut opens and grounds all subsequent contributions. It discusses his own motivations throughout his career. Pattee notes that the questions physicists and biologists ask about life are quite distinct, and have lead many to think of living systems as paradoxical. Pattee chose to work on the boundary between these two branches of science, and pursue a theoretical biophysics. From this interface position, it became clear to him that to study life and its origin one needs to study the origin of the genotype-phenotype distinction, which he observes, is an instance of the origin of symbol systems from material components. This symbol-matter or subject-object distinction occurs at all higher levels where symbols are related to a referent by an arbitrary code, and instantiates an epistemic cut, a concept he thoroughly develops here.

Michael Conrad's paper "Unit of Measurement and Motion" discusses the implications of his fluctuon model for the origin of cellular life and the development of symbolic systems, as it applies to the quantum measurement problem, so important to Pattee's theory. In particular, Conrad deals with the concept of complementarity and choice, and what this means for physics theories of life and Pattee's motivations in his origin of life lab in the 1960's.

Vahe Bedian's paper "Self-Description and the Origin of the Genetic Code" describes the model of the origin of the genetic code he developed as a student of Howard Pattee in the 1970's. This model is based on simulation and analysis of competitive code assignments with arbitrary descriptor-catalyst relationships. Bedian proposes that the efficiency of utilization of raw materials for the production of a coding family of catalysts is a selection criterion that drives such systems towards a coded state, prior to the establishment of Natural Selection.

Peter Wills' paper "Autocatalysis, Information and Coding" develops Bedian's origin of life model further. He notes that some genetic sequences possess the semiotic property of reflexivity between structural components and the functional operations they perform to synthesize themselves. His model investigates the embedding of catalytic functions in the space of polymeric structures leading to such reflexivity, which he considers essential for autocatalytic self-construction in macromolecular systems. He proposes that such reflexive sequences may serve as the basis for the evolution of coding as a result of autocatalytic self-organisation in a population of assignment catalysts.

Peter Cariani's paper "Symbols and dynamics in the brain" discusses how Pattee's work can be applied to a high-level understanding of the brain. Cariani presents an overview and history of scientific models dealing with dynamics and symbols in different domain areas, but focusing specifically in neuroscience. He also discusses Pattee's notion of epistemic cut in this context. Finally, Cariani maps the common roles that symbols might play in the self-production of organisms and in the regenerative self-production of neural signaling patterns.

Eileen Way's paper "The Role of Computation in Modeling Evolution" deals with the role of computation in artificial life models of evolution. She discusses the notion of scientific models and how they are used to explain and predict in philosophy of science. In particular, she discusses how computational models in artificial life can produce scientific discovery. Finally, she criticizes Pattee's notion of epistemic cut, particularly its quantum theory interpretations, while exploring how one could implement a cut between description and construction in artificial life models, as observed in biological systems.

Luis Rocha's paper "Evolution with Material Symbol Systems" presents a theoretical and computational study of the inter-dependencies of symbol and matter. He first uses Pattee's semantic closure principle to identify the requirements for open-ended evolution, framing this principle in biosemiotic terms and offering a definition of the concept of representation for both biological and cognitive systems. The second part of the paper describes artificial life simulations that contrast two types of evolution observed by different populations of agents: those that reproduce via genetic variation and those that reproduce via self-inspection of self-organized components. From this study, Rocha concludes that symbols are necessary to attain open-ended evolution, but only if the phenotypes of agents are the result of a material, self-organization process.

Jesper Hoffmeyer's paper "Life and Reference" proposes a broadening of Howard Pattee's distinction between dynamic and symbolic modes of description of living systems. He suggests a more general biosemiotic explanatory framework where even the dynamic aspects of living organisms possess semiotic characteristics, although indexical and analogically coded rather than symbolic and digitally coded. He further discusses and specifies the function of analog and digital codes in evolutionary systems.

Cliff Joslyn's paper "The Semiotics of Control and Modeling Relations in Complex Systems" positions Pattee's semantic closure principle in the discourse of systems theory and cybernetics. He maps different kinds of control systems, particularly those endowed with semiotic relations, as well as the constraint relations they entail. Casting Pattee's semantic closure principle in this setting, allows Joslyn to define selection as a meta-level constraint necessary for obtaining semantic relations in control systems.

Arantza Etxeberria and Alvaro Moreno's paper "From Complexity to Simplicity: Nature and Symbols" reviews Pattee's ideas from a philosophy of biology perspective. They elaborate on the concepts of constraint, record, and symbol used by Pattee in his semantic closure principle. In particular, they relate Pattee's observation of symbolic aspects of matter to the self-simplifying processes adhered to by certain hierarchical systems, such as living systems. They also discuss the notion of complementarity both as an epistemological and as an ontological principle. Finally, they discuss if biological symbols can be regarded as proper descriptions.

Finally, Jon Umerez' paper "Howard Pattee's Theoretical Biology.-A radical epistemological stance to approach life, evolution, and complexity" provides a historical overview of Pattee's contributions to and influence in science and philosophy. Umerez emphasizes in particular what he considers to be Pattee's chief contribution: the elaboration of an internal epistemic stance to better understand life, evolution and complexity. This paper offers a perfect closure to a special issue devoted to a reflection on the work of Howard Pattee.

As an appendix, this special issue includes a complete bibliography of Pattee's writings compiled by Jon Umerez. I wish to thank Jon for making this bibliography available here. Gratitude is also due to all the reviewers who committed their time to this effort. Naturally, deepest gratitude and respect is due to Howard Pattee for providing us with so many stimulating and profound ideas.

Finally, I want to especially thank Michael Conrad posthumously for his involvement and support for this issue, as well his editing guidance. He is a tremendous influence for most of the contributors in this issue, and will be deeply missed. Many thanks also to Deborah Conrad for her help and support in the last editing stages of this issue.

Special Issue of BioSystems Vol. 60, No. 1-3

The Physics and Evolution of Symbols and Codes:Reflections on the Work of Howard Pattee

Contents

Introduction

The physics and evolution of symbols and codes: reflections on the work of Howard Pattee