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

Individuation and the Organization in Complex Living Ecosystem: Recursive Integration and Self-assertion by Holon-Lymphocytes

Individuation and organization in complex living multi-level ecosystem occurs as dynamical processes from early ontogeny. The notion of living "holon" displaying dynamic self-assertion and integration is used here to explain the ecosystems dynamic processes. The update of the living holon state according to the continuous change of the dynamic system allows for its viability. This is interpreted as adaptation, selection and organization by the human that observes the system a posteriori from its level. Our model concerns the complex dynamics of the adaptive immune system, integrating holon-lymphocytes that collectively preserve the identity and integrity of the organism. Each lymphocyte individualizes as a dynamic holon-lymphocyte, with somatic gene individuation leading to an individual, singular antigen immunoreceptor type, promoting the self-assertion. In turn, the "Immunoception" allows for perception of the environmental antigenic context, thus integration of the holon in its environment. The self-assertion/integration of holon-lymphocyte starts from fetal stages and is influenced by mother Lamarckian acquired historicity transmissions, a requisite for the integrity of the holobiont-organism. We propose a dynamic model of the perception by holon-lymphocyte, and at the supra-clonal level of the immune system functions that sustain the identity and integrity of the holon-holobiont organism.

Time and Life in the Relational Universe: Prolegomena to an Integral Paradigm of Natural Philosophy

Relational ideas for our description of the natural world can be traced to the concept of Anaxagoras on the multiplicity of basic particles, later called “homoiomeroi” by Aristotle, that constitute the Universe and have the same nature as the whole world. Leibniz viewed the Universe as an infinite set of embodied logical essences called monads, which possess inner view, compute their own programs and perform mathematical transformations of their qualities, independently of all other monads. In this paradigm, space appears as a relational order of co-existences and time as a relational order of sequences. The relational paradigm was recognized in physics as a dependence of the spatiotemporal structure and its actualization on the observer. In the foundations of mathematics, the basic logical principles are united with the basic geometrical principles that are generic to the unfolding of internal logic. These principles appear as universal topological structures (“geometric atoms”) shaping the world. The decision-making system performs internal quantum reduction which is described by external observers via the probability function. In biology, individual systems operate as separate relational domains. The wave function superposition is restricted within a single domain and does not expand outside it, which corresponds to the statement of Leibniz that “monads have no windows”.

An extended framework for science

We may be at the cusp of a next generation framework for science which can be facilitated by understanding current limitations in the context of a divergence of 'scientific' tradition from the Axial Age (800-200 BCE) to the present. A powerful advance may come from fusing certain elements from Western and Eastern traditions, synthesizing the framework with an apt understanding of the divergence. Key traits will include the ethopoetic nature of the scientist with attention to his/her experience of self. The framework will also 'access' knowledge through a state of mind less encumbered with paradoxes, duality, incompatibility and other aporias. Case studies in biology and physics illustrate possibilities.

Biological information systems: Evolution as cognition-based information management

An alternative biological synthesis is presented that conceptualizes evolutionary biology as an epiphenomenon of integrated self-referential information management. Since all biological information has inherent ambiguity, the systematic assessment of information is required by living organisms to maintain self-identity and homeostatic equipoise in confrontation with environmental challenges. Through their self-referential attachment to information space, cells are the cornerstone of biological action. That individualized assessment of information space permits self-referential, self-organizing niche construction. That deployment of information and its subsequent selection enacted the dominant stable unicellular informational architectures whose biological expressions are the prokaryotic, archaeal, and eukaryotic unicellular forms. Multicellularity represents the collective appraisal of equivocal environmental information through a shared information space. This concerted action can be viewed as systematized information management to improve information quality for the maintenance of preferred homeostatic boundaries among the varied participants. When reiterated in successive scales, this same collaborative exchange of information yields macroscopic organisms as obligatory multicellular holobionts. Cognition-Based Evolution (CBE) upholds that assessment of information precedes biological action, and the deployment of information through integrative self-referential niche construction and natural cellular engineering antecedes selection. Therefore, evolutionary biology can be framed as a complex reciprocating interactome that consists of the assessment, communication, deployment and management of information by self-referential organisms at multiple scales in continuous confrontation with environmental stresses.

Marriages of mathematics and physics: A challenge for biology

The human attempts to access, measure and organize physical phenomena have led to a manifold construction of mathematical and physical spaces. We will survey the evolution of geometries from Euclid to the Algebraic Geometry of the 20th century. The role of Persian/Arabic Algebra in this transition and its Western symbolic development is emphasized. In this relation, we will also discuss changes in the ontological attitudes toward mathematics and its applications. Historically, the encounter of geometric and algebraic perspectives enriched the mathematical practices and their foundations. Yet, the collapse of Euclidean certitudes, of over 2300 years, and the crisis in the mathematical analysis of the 19th century, led to the exclusion of "geometric judgments" from the foundations of Mathematics. After the success and the limits of the logico-formal analysis, it is necessary to broaden our foundational tools and re-examine the interactions with natural sciences. In particular, the way the geometric and algebraic approaches organize knowledge is analyzed as a cross-disciplinary and cross-cultural issue and will be examined in Mathematical Physics and Biology. We finally discuss how the current notions of mathematical (phase) "space" should be revisited for the purposes of life sciences.

Modeling the peak of emergence in systems: Design and katachi

It is difficult to model emergence in biological systems using reductionist paradigms. A requirement for computational modeling is that individual entities can be recorded parametrically and related logically, but their transformation into whole systems cannot be captured this way. The problem stems from an inability to formally represent the implicit influences that inform emergent organization, such as context, shifts in causal agency or scale, and self-reference. This lack hampers biological systems modeling and its computational counterpart, indicating a need for new fundamental abstraction frameworks that support system-level characteristics. We develop an approach that formally captures these characteristics, focusing on the way they come together to enable transformation at the 'peak' of the emergent process. An example from virology is presented, in which two seemingly antagonistic systems - the herpes cold sore virus and its host - are capable of altering their basic biological objectives to achieve a new equilibrium. The usual barriers to modeling this process are overcome by incorporating mechanisms from practices centered on its emergent peak: design and katachi. In the Japanese science of form, katachi refers to the emergence of intrinsic structure from real situations, where an optimal balance between implicit influences is achieved. Design indicates how such optimization is guided by principles of flow. These practices leverage qualities of situated abstraction, which we understand through the intuitive method of physicist Kôdi Husimi. Early results indicate that this approach can capture the functional transformations of biological emergence, whilst being reasonably computable. Due to its geometric foundations and narrative-based extension to logic, the method will also generate speculative predictions. This research forms the foundations of a new biomedical modeling platform, which is discussed.

The resolution of ambiguity as the basis for life: A cellular bridge between Western reductionism and Eastern holism

Boundary conditions enable cellular life through negentropy, chemiosmosis, and homeostasis as identifiable First Principles of Physiology. Self-referential awareness of status arises from this organized state to sustain homeostatic imperatives. Preferred homeostatic status is dependent upon the appraisal of information and its communication. However, among living entities, sources of information and their dissemination are always imprecise. Consequently, living systems exist within an innate state of ambiguity. It is presented that cellular life and evolutionary development are a self-organizing cellular response to uncertainty in iterative conformity with its basal initiating parameters. Viewing the life circumstance in this manner permits a reasoned unification between Western rational reductionism and Eastern holism.