Towards a first implementation of the WLIMES approach in living system studies advancing the diagnostics and therapy in augmented personalized medicine.

The goal of this paper is to advance an extensible theory of living systems using an approach to biomathematics and biocomputation that suitably addresses self-organized, self-referential and anticipatory systems with multi-temporal multi-agents. Our first step is to provide foundations for modelling of emergent and evolving dynamic multi-level organic complexes and their sustentative processes in artificial and natural life systems. Main applications are in life sciences, medicine, ecology and astrobiology, as well as robotics, industrial automation, man-machine interface and creative design. Since 2011 over 100 scientists from a number of disciplines have been exploring a substantial set of theoretical frameworks for a comprehensive theory of life known as Integral Biomathics. That effort identified the need for a robust core model of organisms as dynamic wholes, using advanced and adequately computable mathematics. The work described here for that core combines the advantages of a situation and context aware multivalent computational logic for active self-organizing networks, Wandering Logic Intelligence (WLI), and a multi-scale dynamic category theory, Memory Evolutive Systems (MES), hence WLIMES. This is presented to the modeller via a formal augmented reality language as a first step towards practical modelling and simulation of multi-level living systems. Initial work focuses on the design and implementation of this visual language and calculus (VLC) and its graphical user interface. The results will be integrated within the current methodology and practices of theoretical biology and (personalized) medicine to deepen and to enhance the holistic understanding of life.

Some resonances between Eastern thought and Integral Biomathics in the framework of the WLIMES formalism for modeling living systems.

Forty-two years ago, Capra published "The Tao of Physics" (Capra, 1975). In this book (page 17) he writes: "The exploration of the atomic and subatomic world in the twentieth century has …. necessitated a radical revision of many of our basic concepts" and that, unlike 'classical' physics, the sub-atomic and quantum "modern physics" shows resonances with Eastern thoughts and "leads us to a view of the world which is very similar to the views held by mystics of all ages and traditions." This article stresses an analogous situation in biology with respect to a new theoretical approach for studying living systems, Integral Biomathics (IB), which also exhibits some resonances with Eastern thought. Stepping on earlier research in cybernetics1 and theoretical biology,2 IB has been developed since 2011 by over 100 scientists from a number of disciplines who have been exploring a substantial set of theoretical frameworks. From that effort, the need for a robust core model utilizing advanced mathematics and computation adequate for understanding the behavior of organisms as dynamic wholes was identified. At this end, the authors of this article have proposed WLIMES (Ehresmann and Simeonov, 2012), a formal theory for modeling living systems integrating both the Memory Evolutive Systems (Ehresmann and Vanbremeersch, 2007) and the Wandering Logic Intelligence (Simeonov, 2002b). Its principles will be recalled here with respect to their resonances to Eastern thought.

Editorial.

Preparing this ambitious Special Issue has challenged everyone involved: authors, reviewers, and guest editors. The editors solicited contributions from many leading figures in a broad array of scientific and philosophical disciplines, with emphasis on phenomenological approaches to philosophy (see Section I). The motivating force was the conviction that if we could find a viable bridge for the gap between the "two cultures"(1) of science and philosophy, fundamental problems in each camp could be addressed more fruitfully than ever before and a new kind of science be born. We believe the unprecedented cross-fertilization of ideas from this initiative may furnish seeds from which that new, better integrated, and more effective approach to science may arise. This Special Issue consists of forty papers. For each one, multiple reviewers were solicited, with at least one reviewer from each "culture" (a scientist and a philosopher). In many cases, several rounds of revision were carried out. Needless to say, this required great patience and dedication of all participants. The editors gratefully acknowledge the contributions of our authors, and of our anonymous reviewers, who worked long and hard on the papers we sent them with no compensation for their efforts. We also wish to thank the Elsevier editorial and production team for the support they gave us in bringing this project to fruition. We would now like to offer a synoptic overview of the Special Issue, proceeding section by section and paper by paper. Our hope is that the reader will find this unique effort to marry science and philosophy both meaningful and enjoyable.

Yet another time about time Part I: An essay on the phenomenology of physical time.

This paper presents yet another personal reflection on one the most important concepts in both science and the humanities: time. This elusive notion has been not only bothering philosophers since Plato and Aristotle. It goes throughout human history embracing all analytical and creative (anthropocentric) disciplines. Time has been a central theme in physical and life sciences, philosophy, psychology, music, art and many more. This theme is known with a vast body of knowledge across different theories and categories. What has been explored concerns its nature (rational, irrational, arational), appearances/qualia, degrees, dimensions and scales of conceptualization (internal, external, fractal, discrete, continuous, mechanical, quantum, local, global, etc.). Of particular interest have been parameters of time such as duration ranges, resolutions, modes (present, now, past, future), varieties of tenses (e.g. present perfect, present progressive, etc.) and some intuitive, but also fancy phenomenological characteristics such as "arrow", "stream", "texture", "width", "depth", "density", even "scent". Perhaps the most distinct characteristic of this fundamental concept is the absolute time constituting the flow of consciousness according to Husserl, the reflection of pure (human) nature without having the distinction between exo and endo. This essay is a personal reflection upon time in modern physics and phenomenological philosophy.

On some recent insights in Integral Biomathics.

This paper summarizes the results in Integral Biomathics obtained to this moment and provides an outlook for future research in the field.

Integral biomathics: a post-Newtonian view into the logos of bios.

This work is an attempt for a state-of-the-art survey of natural and life sciences with the goal to define the scope and address the central questions of an original research program. It is focused on the phenomena of emergence, adaptive dynamics and evolution of self-assembling, self-organizing, self-maintaining and self-replicating biosynthetic systems viewed from a newly-arranged perspective and understanding of computation and communication in the living nature. The author regards this research as an integral part of the emerging discipline of nature-inspired or natural computation, i.e. computation inspired by or occurring in nature. Within this context, he is interested in studies which represent a significant departure from traditional theories about complex systems and self-organization, emergent phenomena and artificial biology. In particular, these include non-conventional approaches exploring the aggregation, composition, growth and development of physical forms and structures, autopoiesis along with the associated abstract information structures and processes. This paper provides a critical review of the major assumptions which guide the development of modern computer science and engineering towards emulating biological systems. For this purpose, the author explores the potential and the virtues of biology to reshape contemporary science. The goal of this survey is to discuss the present state of natural and engineering sciences in the light of a necessary paradigm change in the structure and methodology of research and deliver some insights for developing a new kind of integral science based on the principles for dynamic interdependence of the constituting disciplines and on the evolving relationships among them.