What makes a living system a living system? What kind of biological phenomenon is the phenomenon of cognition? These two questions have been frequently considered, but, in this volume, the authors consider them as concrete biological questions. Their analysis is bold and provocative, for the authors have constructed a systematic theoretical biology which attempts to define living systems not as objects of observation and description, nor even as interacting systems, but as self-contained unities whose only reference is to themselves. The (...) consequence of their investigations and of their living systems as self-making, self-referring autonomous unities, is that they discovered that the two questions have a common answer: living systems are cognitive systems, and living as a process is a process of cognition. The result of their investigations is a completely new perspective of biological (human) phenomena. During the investigations, it was found that a complete linguistic description pertaining to the ‘organization of the living’ was lacking and, in fact, was hampering the reporting of results. Hence, the authors have coined the word ‘autopoiesis’ to replace the expression ‘circular organization’. Autopoiesis conveys, by itself, the central feature of the organization of the living, which is autonomy. (shrink)

Tending Adam's Garden describes and explains the way in which our immune system works from a novel perspective. The book uses metaphors and examples to bring the immune system to life and explores the fundamental miracle of nature. Written in plain language for a broad audience, this book encompasses much more than just immunology, exploring more fundamental matters such as causality, information, energy, evolution, cognition and individuality, as well as the strategy of the immune system and its role in health (...) and disease. (shrink)

A fascinating exploration of the very essence of life itself sheds new light on the order and evolution in complex life systems and defines and explains autonomous agents and work within the contexts of thermodynamics and information theory, setting the stage for a dramatic technological revolution. 50,000 first printing.

Stuart Kauffman here presents a brilliant new paradigm for evolutionary biology, one that extends the basic concepts of Darwinian evolution to accommodate recent findings and perspectives from the fields of biology, physics, chemistry and mathematics. The book drives to the heart of the exciting debate on the origins of life and maintenance of order in complex biological systems. It focuses on the concept of self-organization: the spontaneous emergence of order widely observed throughout nature. Kauffman here argues that self-organization plays an (...) important role in the emergence of life itself and may play as fundamental a role in shaping life's subsequent evolution as does the Darwinian process of natural selection. Yet until now no systematic effort has been made to incorporate the concept of self-organization into evolutionary theory. The construction requirements which permit complex systems to adapt remain poorly understood, as is the extent to which selection itself can yield systems able to adapt more successfully. This book explores these themes. It shows how complex systems, contrary to expectations, can spontaneously exhibit stunning degrees of order, and how this order, in turn, is essential for understanding the emergence and development of life on Earth. Topics include the new biotechnology of applied molecular evolution, with its important implications for developing new drugs and vaccines; the balance between order and chaos observed in many naturally occurring systems; new insights concerning the predictive power of statistical mechanics in biology; and other major issues. Indeed, the approaches investigated here may prove to be the new center around which biologicalscience itself will evolve. The work is written for all those interested in the cutting edge of research in the life sciences. (shrink)

The standard assumptions that underlie many conceptual and quantitative frameworks do not hold for many complex physical, biological, and social systems. Complex systems science clarifies when and why such assumptions fail and provides alternative frameworks for understanding the properties of complex systems. This review introduces some of the basic principles of complex systems science, including complexity profiles, the tradeoff between efficiency and adaptability, the necessity of matching the complexity of systems to that of their environments, multiscale analysis, and evolutionary processes. (...) Our focus is on the general properties of systems as opposed to the modeling of specific dynamics; rather than provide a comprehensive review, we pedagogically describe a conceptual and analytic approach for understanding and interacting with the complex systems of our world. This paper assumes only a high school mathematical and scientific background so that it may be accessible to academics in all fields, decision-makers in industry, government, and philanthropy, and anyone who is interested in systems and society. (shrink)

What enables individually simple insects like ants to act with such precision and purpose as a group? How do trillions of individual neurons produce something as extraordinarily complex as consciousness? What is it that guides self-organizing structures like the immune system, the World Wide Web, the global economy, and the human genome? These are just a few of the fascinating and elusive questions that the science of complexity seeks to answer. In this remarkably accessible and companionable book, leading complex systems (...) scientist Melanie Mitchell provides an intimate, detailed tour of the sciences of complexity, a broad set of efforts that seek to explain how large-scale complex, organized, and adaptive behavior can emerge from simple interactions among myriad individuals. Comprehending such systems requires a wholly new approach, one that goes beyond traditional scientific reductionism and that re-maps long-standing disciplinary boundaries. Based on her work at the Santa Fe Institute and drawing on its interdisciplinary strategies, Mitchell brings clarity to the workings of complexity across a broad range of biological, technological, and social phenomena, seeking out the general principles or laws that apply to all of them. She explores as well the relationship between complexity and evolution, artificial intelligence, computation, genetics, information processing, and many other fields. Richly illustrated and vividly written, Complexity : A Guided Tour offers a comprehensive and eminently comprehensible overview of the ideas underlying complex systems science, the current research at the forefront of this field, and the prospects for the field's contribution to solving some of the most important scientific questions of our time. (shrink)

An innocent form of emergence—what I call "weak emergence"—is now a commonplace in a thriving interdisciplinary nexus of scientific activity—sometimes called the "sciences of complexity"—that include connectionist modelling, non-linear dynamics (popularly known as "chaos" theory), and artificial life.1 After defining it, illustrating it in two contexts, and reviewing the available evidence, I conclude that the scientific and philosophical prospects for weak emergence are bright.

NOW IN PAPERBACK"€"Starting from a collection of simple computer experiments"€"illustrated in the book by striking computer graphics"€"Stephen Wolfram shows how their unexpected results force a whole new way of looking at the operation of our universe.

What is reductionism? -- Who is reading the book of life? -- Genetics : from grammar to meaning making -- A point for thought : why are organisms irreducible? -- A point for thought : does the genetic system include a meta-language? -- Immunology : from soldiers to housewives -- A point for thought : immune specificity and Brancusi's kiss -- A point for thought : reflections on the immune self -- Meaning making in language and biology -- A point (...) for thought : meaning : bridging the gap between physics and semantics -- The rest is silence -- The polysemy of the sign : a quantum lesson -- Recursive-hierarchy : a lesson from the tardigrade -- Context and memory : a lesson from funes the memorious -- Transgradience : a lesson from Bakhtin -- The poetry of living. (shrink)

This is a presentation about joint work between Hector Zenil and Jean-Paul Delahaye. Zenil presents Experimental Algorithmic Theory as Algorithmic Information Theory and NKS, put together in a mixer. Algorithmic Complexity Theory defines the algorithmic complexity k(s) as the length of the shortest program that produces s. But since finding this short program is in general an undecidable question, the only way to approach k(s) is to use compression algorithms. He shows how to use the Compress function in Mathematica to (...) give an idea about the compressibility of various sequences. However, the idea of applying a compression algorithm breaks down for very short sequences. This is true not only for the Compress function, but also for any other compression algorithm. Zenil's approach is to construct a metric of algorithmic complexity for short sequences from scratch. He defines the algorithmic probability as the probability that an arbitrary program produces a sequence. The basic idea is to run a whole class of computational devices such as Turing Machines or Cellular Automata, and compute the distributions of the sequences they generate. Zenil presents a comparison of frequency distributions of sequences generated by 2-state 3-color Turing Machines and 2-color radius 1 Cellular Automata. He also compared these distributions to distributions found in data from the real world, and found that not only there is correlation across different systems, but also that the distributions are rather stable, and the difference between the distributions in abstract systems and real-world data can be attributed to noise. In his paper Zenil elaborates on the nature of the noise he has encountered. Zenil conjectures that the correlation distances between different systems decreases with a larger number of steps, and converge in the infinite limit case. (shrink)

This paper compares the two known logical forms of hierarchy, both of which have been used in models of natural phenomena, including the biological. I contrast their general properties, internal formal relations, modes of growth (emergence) in applications to the natural world, criteria for applying them, the complexities that they embody, their dynamical relations in applied models, and their informational relations and semiotic aspects.

We develop on the idea that everything is related, inside, and therefore determined by a context. This stance, which at first might seem obvious, has several important consequences. This paper first presents ideas on Contextuality, for then applying them to problems in philosophy of cognitive science. Because of space limitations, for the second part we will assume that the reader is familiar with the literature of philosophy of cognitive science, but if this is not the case, it would not be (...) a limitation for understanding the main ideas of this paper. We do not argue that Contextuality is a panaceic answer for explaining everything, but we do argue that everything is inside a context. And because this is always, we sometimes ignore it, but we believe that many problems are dissolved with a contextual approach, noticing things we ignore because of their obviousity. We first give a notion of context. We present the idea that errors are just incongruencies inside a context. We also present previous ideas of absolute being, relative being, and lessincompleteness. We state that all logics, and also truth judgements, are contextdependent, and we develop a “Context-dependant Logic”. We apply ideas of Contextuality to problems in semantics, the problem of “where is the mind”, and the study of consciousness. (shrink)

The mathematical theory of communication.

Why has the problematic of complexity appeared so late? And why would it be justified?

The σ profile is presented as a tool to analyze the organization of systems at different scales, and how this organization changes in time. Describing structures at different scales as goal‐oriented agents, one can define σ ∈ [0,1] (satisfaction) as the degree to which the goals of each agent at each scale have been met. σ reflects the organization degree at that scale. The σ profile of a system shows the satisfaction at different scales, with the possibility to study their (...) dependencies and evolution. It can also be used to extend game theoretic models. The description of a general tendency on the evolution of complexity and cooperation naturally follows from the σ profile. Experiments on a virtual ecosystem are used as illustration. (shrink)

1.1 - Background - page 17 1.2 - The Style of Approach - page 18 1.3 - Motivation - page 19 1.4 - Style of Presentation - page 20 1.5 - Outline of the Thesis - page 21..

This paper argues that truth is by nature context-dependent – that no truth can be applied regardless of context. I call this “strong contextualism”. Some objections to this are considered and rejected, principally: that there are universal truths given to us by physics, logic and mathematics; and that claiming “no truths are universal” is self-defeating. Two “models” of truth are suggested to indicate that strong contextualism is coherent. It is suggested that some of the utility of the “universal framework” can (...) be recovered via a more limited “third person viewpoint”. Keywords: philosophy, universality, context, truth, knowledge. (shrink)

Discusses the connections between business, science, information, disease, knowledge--just about everything--and the hubs and complex networks that create an interconnected web of life.

Complex systems are usually difficult to design and control. There are several particular methods for coping with complexity, but there is no general approach to build complex systems. In this thesis I propose a methodology to aid engineers in the design and control of complex systems. This is based on the description of systems as self-organizing. Starting from the agent metaphor, the methodology proposes a conceptual framework and a series of steps to follow to find proper mechanisms that will promote (...) elements to find solutions by actively interacting among themselves. The main premise of the methodology claims that reducing the “friction” of interactions between elements of a system will result in a higher “satisfaction” of the system, i.e. better performance. A general introduction to complex thinking is given, since designing self-organizing systems requires a non-classical thought, while practical notions of complexity and self-organization are put forward. To illustrate the methodology, I present three case studies. Self-organizing traffic light controllers are proposed and studied with multi-agent simulations, outperforming traditional methods. Methods for improving communication within self-organizing bureaucracies are advanced, introducing a simple computational model to illustrate the benefits of self-organization. In the last case study, requirements for self-organizing artifacts in an ambient intelligence scenario are discussed. Philosophical implications of the conceptual framework are also put forward. (shrink)

Reductionism has dominated science and philosophy for centuries. Complexity has recently shown that interactions—which reductionism neglects—are relevant for understanding phenomena. When interactions are considered, reductionism becomes limited in several aspects. In this paper, I argue that interactions imply nonreductionism, non-materialism, non-predictability, non-Platonism, and non-Nihilism. As alternatives to each of these, holism, informism, adaptation, contextuality, and meaningfulness are put forward, respectively. A worldview that includes interactions not only describes better our world, but can help to solve many open scientific, philosophical, and (...) social problems caused by implications of reductionism. (shrink)

This paper discusses the benefits of describing the world as information, especially in the study of the evolution of life and cognition. Traditional studies encounter problems because it is difficult to describe life and cognition in terms of matter and energy, since their laws are valid only at the physical scale. However, if matter and energy, as well as life and cognition, are described in terms of information, evolution can be described consistently as information becoming more complex. The paper presents (...) five tentative laws of information, valid at multiple scales, which are generalizations of Darwinian, cybernetic, thermodynamic, and complexity principles. These are further used to discuss the notions of life and cognition and their evolution. (shrink)

Emergence is defined as a process which cannot be described by a fixed model, consisting of invariant distinctions. Hence emergence must be described by a meta‐model, representing the transition of one model to another one by means of a distinction dynamics. The dynamics of distinctions is based on the processes of variation and selection, resulting in an invariant distinction, which constrains the variety and thus defines a new system. A classification of emergence processes is proposed, based on the following criteria: (...) amount of variety, internality/ externality of variation and selection, number of levels, and contingency of constraint. It is argued that traditional formal and computational models are incapable of representing the more general types of emergence, but that it is possible to generalize them on the basis of the dynamics of distinctions. (shrink)